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  • Research Areas (15910)
    • Topic 1: Genes, Cells and Cell-Based Medicine (588)
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2024

Sensor macrophages derived from human induced pluripotent stem cells to assess pyrogenic contaminations in parenteral drugs.
Abdin, S.M. and Mansel, F. and Rafiei Hashtchin, A. and Ackermann, M. and Hansen, G. and Becker, B. and Kick, B. and Pham, N. and Dietz, H. and Schaniel, C. and Martin, U. and Spreitzer, I. and Lachmann, N.
Biofabrication 16 (3): 035017. July 2024

ADAM19 cleaves the PTH receptor and associates with brachydactyly type E.
Aydin, A. and Klenk, C. and Nemec, K. and Işbilir, Ali and Martin, L.M. and Zauber, H. and Rrustemi, T. and Toka, H.R. and Schuster, H. and Gong, M. and Stricker, S. and Bock, A. and Bähring, S. and Selbach, M. and Lohse, M.J. and Luft, F.C.
Life Science Alliance 7 (4): e202302400. April 2024

Activation of gp130 signaling in T cells drives T(H)17-mediated multi-organ autoimmunity.
Baumgartner, F. and Bamopoulos, S.A. and Faletti, L. and Hsiao, H.J. and Holz, M. and Gonzalez-Menendez, I. and Solé-Boldo, L. and Horne, A. and Gosavi, S. and Özerdem, C. and Singh, N. and Liebig, S. and Ramamoorthy, S. and Lehmann, M. and Demel, U. and Kühl, A.A. and Wartewig, T. and Ruland, J. and Wunderlich, F.T. and Schick, M. and Walther, W. and Rose-John, S. and Haas, S. and Quintanilla-Martinez, L. and Feske, S. and Ehl, S. and Glauben, R. and Keller, U.
Science Signaling 17 (824): eadc9662. 20 February 2024

Endothelial overexpression of TGF-β-induced protein impairs venous thrombus resolution.
Bochenek, M.L. and Saar, K. and Nazari-Jahantigh, M. and Gogiraju, R. and Wiedenroth, C.B. and Münzel, T. and Mayer, E. and Fink, L. and Schober, A. and Hübner, N. and Guth, S. and Konstantinides, S. and Schäfer, K.
JACC: Basic to Translational Science 9 (1): 100-116. January 2024

Elevated sortilin expression discriminates functional from non-functional neuroendocrine tumors and enables therapeutic targeting.
Bolduan, F. and Wetzel, A. and Giesecke, Y. and Eichhorn, I. and Alenina, N. and Bader, M. and Willnow, T.E. and Wiedenmann, B. and Sigal, M.
Frontiers in Endocrinology 15 : 1331231. 17 April 2024

Single-cell time series analysis reveals the dynamics of HSPC response to inflammation.
Bouman, B.J. and Demerdash, Y. and Sood, S. and Grünschläger, F. and Pilz, F. and Itani, A.R. and Kuck, A. and Marot-Lassauzaie, V. and Haas, S. and Haghverdi, L. and Essers, M.A.
Life Science Alliance 7 (3): e202302309. March 2024

Antigen presentation plays positive roles in the regenerative response to cardiac injury in zebrafish.
Cardeira-da-Silva, J. and Wang, Q. and Sagvekar, P. and Mintcheva, J. and Latting, S. and Günther, S. and Ramadass, R. and Yekelchyk, M. and Preussner, J. and Looso, M. and Junker, J.P. and Stainier, D.Y.R.
Nature Communications 15 (1): 3637. 29 April 2024

SRRM2 splicing factor modulates cell fate in early development.
Carvalho, S. and Zea-Redondo, L. and Tang, T.C.C. and Stachel-Braum, P. and Miller, D. and Caldas, P. and Kukalev, A. and Diecke, S. and Grosswendt, S. and Grosso, A.R. and Pombo, A.
Biology Open 13 (4): bio060415. April 2024

Multiscale modelling of chromatin 4D organization in SARS-CoV-2 infected cells.
Chiariello, A.M. and Abraham, Alex and Bianco, S. and Esposito, A. and Fontana, A. and Vercellone, F. and Conte, M. and Nicodemi, M.
Nature Communications 15 (1): 4014. 13 May 2024

Cancer evolution: a multifaceted affair.
Ciriello, G. and Magnani, L. and Aitken, S.J. and Akkari, L. and Behjati, S. and Hanahan, D. and Landau, D.A. and Lopez-Bigas, N. and Lupiáñez, D.G. and Marine, J.C. and Martin-Villalba, A. and Natoli, G. and Obenauf, A.C. and Oricchio, E. and Scaffidi, P. and Sottoriva, A. and Swarbrick, A. and Tonon, G. and Vanharanta, S. and Zuber, J.
Cancer Discovery 14 : 1-13. January 2024

Logical design of synthetic cis-regulatory DNA for genetic tracing of cell identities and state changes.
Company, C. and Schmitt, M.J. and Dramaretska, Y. and Serresi, M. and Kertalli, S. and Jiang, B. and Yin, J.A. and Aguzzi, A. and Barozzi, I. and Gargiulo, G.
Nature Communications 15 (1): 897. 5 February 2024

T- and L-type calcium channels maintain calcium oscillations in the murine zona glomerulosa.
Dinh, H.A. and Volkert, M. and Secener, A.K. and Scholl, U.I. and Stölting, G.
Hypertension 81 (4): 811-822. April 2024

Insulin secretion defect in children and adolescents with obesity: clinical and molecular genetic characterization.
Enders-Seidlitz, H. and Raile, K. and Gong, M. and Galler, A. and Kuehnen, P. and Wiegand, S.
Journal of Diabetes Research 2024 : 5558634. 20 March 2024

L-glyceraldehyde inhibits neuroblastoma cell growth via a multi-modal mechanism on metabolism and Signaling.
Forbes, M. and Kempa, R. and Mastrobuoni, G. and Rayman, L. and Pietzke, M. and Bayram, S. and Arlt, B. and Spruessel, A. and Deubzer, H.E. and Kempa, S.
Cancers 16 (9): 1664. May 2024

Interferon regulatory factor 4 plays a pivotal role in the development of aGVHD-associated colitis.
Frueh, J.T. and Campe, J. and Sunaga-Franze, D.Y. and Verheyden, N.A. and Ghimire, S. and Meedt, E. and Haslinger, D. and Harenkamp, S. and Staudenraus, D. and Sauer, S. and Kreft, A. and Schubert, R. and Lohoff, M. and Krueger, A. and Bonig, H. and Chiocchetti, A.G. and Zeiser, R. and Holler, E. and Ullrich, E.
OncoImmunology 13 (1): 2296712. 2024

Cell states in cancer: drivers, passengers, and trailers.
Gargiulo, G. and Serresi, M. and Marine, J.C.
Cancer Discovery 14 (4): 610-614. 4 April 2024

CoNIC Challenge: Pushing the frontiers of nuclear detection, segmentation, classification and counting.
Graham, S. and Vu, Q.D. and Jahanifar, M. and Weigert, M. and Schmidt, U. and Zhang, W. and Zhang, J. and Yang, S. and Xiang, J. and Wang, X. and Rumberger, J.L. and Baumann, E. and Hirsch, P. and Liu, L. and Hong, C. and Aviles-Rivero, A.I. and Jain, A. and Ahn, H. and Hong, Y. and Azzuni, H. and Xu, M. and Yaqub, M. and Blache, M.C. and Piégu, B. and Vernay, B. and Scherr, T. and Böhland, M. and Löffler, K. and Li, J. and Ying, W. and Wang, C. and Snead, D. and Raza, S.E.A. and Minhas, F. and Rajpoot, N.M.
Medical Image Analysis 92 : 103047. February 2024

Pangenome graph construction from genome alignments with Minigraph-Cactus.
Hickey, G. and Monlong, J. and Ebler, J. and Novak, A.M. and Eizenga, J.M. and Gao, Y. and Marschall, T. and Li, H. and Paten, B.
Nature Biotechnology 42 (4): 663-673. April 2024

Clonal dominance defines metastatic dissemination in pancreatic cancer.
Ho, I.L. and Li, C.Y. and Wang, F. and Zhao, L. and Liu, J. and Yen, E.Y. and Dyke, C.A. and Shah, R. and Liu, Z. and Çetin, A.O. and Chu, Y. and Citron, F. and Attanasio, S. and Corti, D. and Darbaniyan, F. and Del Poggetto, E. and Loponte, S. and Liu, J. and Soeung, M. and Chen, Z. and Jiang, S. and Jiang, H. and Inoue, A. and Gao, S. and Deem, A. and Feng, N. and Ying, H. and Kim, M. and Giuliani, V. and Genovese, G. and Zhang, J. and Futreal, A. and Maitra, A. and Heffernan, T. and Wang, L. and Do, K.A. and Gargiulo, G. and Draetta, G. and Carugo, A. and Lin, R. and Viale, A.
Science Advances 10 (11): eadd9342. 15 March 2024

Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma.
Hofman, D.A. and Ruiz-Orera, J. and Yannuzzi, I. and Murugesan, R. and Brown, A. and Clauser, K.R. and Condurat, A.L. and van Dinter, J.T. and Engels, S.A.G. and Goodale, A. and van der Lugt, J. and Abid, T. and Wang, L. and Zhou, K.N. and Vogelzang, J. and Ligon, K.L. and Phoenix, T.N. and Roth, J.A. and Root, D.E and Hubner, N. and Golub, T.R. and Bandopadhayay, P. and van Heesch, S. and Prensner, J.R.
Molecular Cell 84 (2): 261-276. 18 January 2024

REEV: review, evaluate and explain variants.
Hramyka, D. and Sczakiel, H.L. and Zhao, M.X. and Stolpe, O. and Nieminen, M. and Adam, R. and Danyel, M. and Einicke, L. and Hägerling, R. and Knaus, A. and Mundlos, S. and Schwartzmann, S. and Seelow, D. and Ehmke, N. and Mensah, M.A. and Boschann, F. and Beule, D. and Holtgrewe, M.
Nucleic Acids Research : gkae366. 20 May 2024 (In Press)

Complete male-to-female sex reversal in XY mice lacking the miR-17~92 cluster.
Hurtado, A. and Mota-Gómez, I. and Lao, M. and Real, F.M. and Jedamzick, J. and Burgos, M. and Lupiáñez, D.G. and Jiménez, R. and Barrionuevo, F.J.
Nature Communications 15 (1): 3809. 7 May 2024

Increased β(2)-adrenergic signaling promotes fracture healing through callus neovascularization in mice.
Jahn, D. and Knapstein, P.R. and Otto, E. and Köhli, P. and Sevecke, J. and Graef, F. and Graffmann, C. and Fuchs, M. and Jiang, S. and Rickert, M. and Erdmann, C. and Appelt, J. and Revend, L. and Küttner, Q. and Witte, J. and Rahmani, A. and Duda, G. and Xie, W. and Donat, A. and Schinke, T. and Ivanov, A. and Tchouto, M.N. and Beule, D. and Frosch, K.H. and Baranowsky, A. and Tsitsilonis, S. and Keller, J.
Science Translational Medicine 16 (743): eadk9129. 17 April 2024

Image processing and analysis of light sheet microscopy data.
Jain, A. and Ulman, V. and Krumnikl, M. and Pietzsch, T. and Preibisch, S. and Tomančák, P.
In: Light Sheet Fluorescence Microscopy. Wiley‐VCH GmbH, Weinheim, Germany, 203-229. ISBN 9783527341351 18 March 2024

Inference of differentiation trajectories by transfer learning across biological processes.
Jumde, G. and Spanjaard, B. and Junker, J.P.
Cell Systems 15 (1): 75-82.e5. 17 January 2024

SetQuence & SetOmic: deep set transformers for whole genome and exome tumour analysis.
Jurenaite, N. and León-Periñán, D. and Donath, V. and Torge, S. and Jäkel, R.
Biosystems 235 : 105095. January 2024

Peripheral priming induces plastic transcriptomic and proteomic responses in circulating neutrophils required for pathogen containment.
Kaiser, R. and Gold, C. and Joppich, M. and Loew, Q. and Akhalkatsi, A. and Mueller, T.T. and Offensperger, F. and Droste Zu Senden, A. and Popp, O. and di Fina, L. and Knottenberg, V. and Martinez-Navarro, A. and Eivers, L. and Anjum, A. and Escaig, R. and Bruns, N. and Briem, E. and Dewender, R. and Muraly, A. and Akgöl, S. and Ferraro, B. and Hoeflinger, J.K.L. and Polewka, V. and Khaled, N.B. and Allgeier, J. and Tiedt, S. and Dichgans, M. and Engelmann, B. and Enard, W. and Mertins, P. and Hubner, N. and Weckbach, L. and Zimmer, R. and Massberg, S. and Stark, K. and Nicolai, L. and Pekayvaz, K.
Science Advances 10 (12): eadl1710. 22 March 2024

SORCS2 activity in pancreatic α-cells safeguards insulin granule formation and release from glucose-stressed β-cells.
Kalnytska, O. and Qvist, P. and Kunz, S. and Conrad, T. and Willnow, T.E. and Schmidt, V.
iScience 27 (1): 108725. 19 January 2024

Bi-allelic PRRT2 variants may predispose to Self-limited Familial Infantile Epilepsy.
Koko, M. and Elseed, M.A. and Mohammed, I.N. and Hamed, A.A. and Abd Allah, A.S.I. and Yahia, A. and Siddig, R.A. and Altmüller, J. and Toliat, M.R. and Elmahdi, E.O. and Amin, M. and Ahmed, E. A. and Eltazi, I.Z.M. and Elmugadam, F.A. and Abdelgadir, W.A. and Eltaraifee, E. and Ibrahim, M.O.M. and Ali, N.M.H. and Malik, H.M. and Babai, A.M. and Bakhit, Y.H. and Nürnberg, P. and Ibrahim, M.E. and Salih, M.A. and Schubert, J. and Elsayed, L.E.O. and Lerche, H.
European Journal of Human Genetics 5 February 2024 (In Press)

Spatial single cell profiling using imaging mass cytometry: inflammatory versus penetrating Crohn's disease.
Lehmann, M. and Weixler, B. and Elezkurtaj, S. and Loddenkemper, C. and Kühl, A.A. and Siegmund, B.
Journal of Crohn's & Colitis : jjae033. 11 March 2024 (In Press)

Canonical and non-canonical integrin-based adhesions dynamically interconvert.
Lukas, F. and Matthaeus, C. and López-Hernández, T. and Lahmann, I. and Schultz, N. and Lehmann, M. and Puchkov, D. and Pielage, J. and Haucke, V. and Maritzen, T.
Nature Communications 15 (1): 2093. 7 March 2024

Metrics reloaded: recommendations for image analysis validation.
Maier-Hein, L. and Reinke, A. and Godau, P. and Tizabi, M.D. and Buettner, F. and Christodoulou, E. and Glocker, B. and Isensee, F. and Kleesiek, J. and Kozubek, M. and Reyes, M. and Riegler, M.A. and Wiesenfarth, M. and Kavur, A.E. and Sudre, C.H. and Baumgartner, M. and Eisenmann, M. and Heckmann-Nötzel, D. and Rädsch, T. and Acion, L. and Antonelli, M. and Arbel, T. and Bakas, S. and Benis, A. and Blaschko, M.B. and Cardoso, M.J. and Cheplygina, V. and Cimini, B.A. and Collins, G.S. and Farahani, K. and Ferrer, L. and Galdran, A. and van Ginneken, B. and Haase, R. and Hashimoto, D.A. and Hoffman, M.M. and Huisman, M. and Jannin, P. and Kahn, C.E. and Kainmueller, D. and Kainz, B. and Karargyris, A. and Karthikesalingam, A. and Kofler, F. and Kopp-Schneider, A. and Kreshuk, A. and Kurc, T. and Landman, B.A. and Litjens, G. and Madani, A. and Maier-Hein, K. and Martel, A.L. and Mattson, P. and Meijering, E. and Menze, B. and Moons, K.G.M. and Müller, H. and Nichyporuk, B. and Nickel, F. and Petersen, J. and Rajpoot, N. and Rieke, N. and Saez-Rodriguez, J. and Sánchez, C.I. and Shetty, S. and van Smeden, M. and Summers, R.M. and Taha, A.A. and Tiulpin, A. and Tsaftaris, S.A. and Van Calster, B. and Varoquaux, G. and Jäger, P.F.
Nature Methods 21 (2): 195-212. 12 February 2024

Single-cell multi-omics analysis identifies context-specific gene regulatory gates and mechanisms.
Malekpour, S.A. and Haghverdi, L. and Sadeghi, M.
Briefings in Bioinformatics 25 (3): bbae180. May 2024

Despite the odds: formation of the SARS-CoV-2 methylation complex.
Matsuda, A. and Plewka, J. and Rawski, M. and Mourão, A. and Zajko, W. and Siebenmorgen, T. and Kresik, L. and Lis, K. and Jones, A.N. and Pachota, M. and Karim, A. and Hartman, K. and Nirwal, S. and Sonani, R. and Chykunova, Y. and Minia, I. and Mak, P. and Landthaler, M. and Nowotny, M. and Dubin, G. and Sattler, M. and Suder, P. and Popowicz, G.M. and Pyrć, K. and Czarna, A.
Nucleic Acids Research : gkae165. 18 March 2024 (In Press)

MarShie: a clearing protocol for 3D analysis of single cells throughout the bone marrow at subcellular resolution.
Mertens, T.F. and Liebheit, A.T. and Ehl, J. and Köhler, R. and Rakhymzhan, A. and Woehler, A. and Katthän, L. and Ebel, G. and Liublin, W. and Kasapi, A. and Triantafyllopoulou, A. and Schulz, T.J. and Niesner, R.A. and Hauser, A.E.
Nature Communications 15 (1): 1764. 26 February 2024

Dissecting the spatiotemporal diversity of adult neural stem cells.
Mitic, N. and Neuschulz, A. and Spanjaard, B. and Schneider, J. and Fresmann, N. and Novoselc, K.T. and Strunk, T. and Münster, L. and Olivares-Chauvet, P. and Ninkovic, J. and Junker, J.P.
Molecular Systems Biology 20 (4): 321-337. 2 April 2024

Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets.
Müller, A. and Schmidt, D. and Albrecht, J.P. and Rieckert, L. and Otto, M. and Galicia Garcia, L.E. and Fabig, G. and Solimena, M. and Weigert, M.
Nature Protocols 19 (5): 1436-1466. May 2024

The artificial intelligence-based model ANORAK improves histopathological grading of lung adenocarcinoma.
Pan, X. and AbdulJabbar, K. and Coelho-Lima, J. and Grapa, A.I. and Zhang, H. and Cheung, A.H.K. and Baena, J. and Karasaki, T. and Wilson, C.R. and Sereno, M. and Veeriah, S. and Aitken, S.J. and Hackshaw, A. and Nicholson, A.G. and Jamal-Hanjani, M. and Swanton, C. and Yuan, Y. and Le Quesne, J. and Moore, D.A.
Nature Cancer 5 (2): 347-363. February 2024

Proteomic and transcriptomic profiling of brainstem, cerebellum and olfactory tissues in early- and late-phase COVID-19.
Radke, J. and Meinhardt, J. and Aschman, T. and Chua, R.L. and Farztdinov, V. and Lukassen, S. and Ten, F.W. and Friebel, E. and Ishaque, N. and Franz, J. and Huhle, V.H. and Mothes, R. and Peters, K. and Thomas, C. and Schneeberger, S. and Schumann, E. and Kawelke, L. and Jünger, J. and Horst, V. and Streit, S. and von Manitius, R. and Körtvélyessy, P. and Vielhaber, S. and Reinhold, D. and Hauser, A.E. and Osterloh, A. and Enghard, P. and Ihlow, J. and Elezkurtaj, S. and Horst, D. and Kurth, F. and Müller, M.A. and Gassen, N.C. and Melchert, J. and Jechow, K. and Timmermann, B. and Fernandez-Zapata, C. and Böttcher, C. and Stenzel, W. and Krüger, E. and Landthaler, M. and Wyler, E. and Corman, V. and Stadelmann, C. and Ralser, M. and Eils, R. and Heppner, F.L. and Mülleder, M. and Conrad, C. and Radbruch, H.
Nature Neuroscience 27 (3): 409-420. March 2024

Understanding metric-related pitfalls in image analysis validation.
Reinke, A. and Tizabi, M.D. and Baumgartner, M. and Eisenmann, M. and Heckmann-Nötzel, D. and Kavur, A.E. and Rädsch, T. and Sudre, C.H. and Acion, L. and Antonelli, M. and Arbel, T. and Bakas, S. and Benis, A. and Buettner, F. and Cardoso, M.J. and Cheplygina, V. and Chen, J. and Christodoulou, E. and Cimini, B.A. and Farahani, K. and Ferrer, L. and Galdran, A. and van Ginneken, B. and Glocker, B. and Godau, P. and Hashimoto, D.A. and Hoffman, M.M. and Huisman, M. and Isensee, F. and Jannin, P. and Kahn, C.E. and Kainmueller, D. and Kainz, B. and Karargyris, A. and Kleesiek, J. and Kofler, F. and Kooi, T. and Kopp-Schneider, A. and Kozubek, M. and Kreshuk, A. and Kurc, T. and Landman, B.A. and Litjens, G. and Madani, A. and Maier-Hein, K. and Martel, A.L. and Meijering, E. and Menze, B. and Moons, K.G.M. and Müller, H. and Nichyporuk, B. and Nickel, F. and Petersen, J. and Rafelski, S.M. and Rajpoot, N. and Reyes, M. and Riegler, M.A. and Rieke, N. and Saez-Rodriguez, J. and Sánchez, C.I. and Shetty, S. and Summers, R.M. and Taha, A.A. and Tiulpin, A. and Tsaftaris, S.A. and Van Calster, B. and Varoquaux, G. and Yaniv, Z.R. and Jäger, P.F. and Maier-Hein, L.
Nature Methods 21 (2): 182–194. February 2024

Pathogenic mutations of human phosphorylation sites affect protein–protein interactions.
Rrustemi, T. and Meyer, K. and Roske, Y. and Uyar, B. and Akalin, A. and Imami, K. and Ishihama, Y. and Daumke, O. and Selbach, M.
Nature Communications 15 (1): 3146. 11 April 2024

Basal delamination during mouse gastrulation primes pluripotent cells for differentiation.
Sato, N. and Rosa, V.S. and Makhlouf, A. and Kretzmer, H. and Sampath Kumar, A. and Grosswendt, S. and Mattei, A.L. and Courbot, O. and Wolf, S. and Boulanger, J. and Langevin, F. and Wiacek, M. and Karpinski, D. and Elosegui-Artola, A. and Meissner, A. and Zernicka-Goetz, M. and Shahbazi, M.N.
Developmental Cell 59 (10): 1252-1268.e13. 20 May 2024

Twisted-plywood-like tissue formation in vitro. Does curvature do the twist?
Schamberger, B. and Ehrig, S. and Dechat, T. and Spitzer, S. and Bidan, C.M. and Fratzl, P. and Dunlop, J.W.C. and Roschger, A.
PNAS Nexus 3 (4): pgae121. April 2024

Validity constraints for data analysis workflows.
Schintke, F. and Belhajjame, K. and De Mecquenem, N. and Frantz, D. and Guarino, V.E. and Hilbrich, M. and Lehmann, F. and Missier, P. and Sattler, R. and Sparka, J.A. and Speckhard, D.T. and Stolte, H. and Vu, A.D. and Leser, U.
Future Generation Computer Systems 157 : 82-97. August 2024

TLIMB - a transfer learning framework for image analysis of the brain.
Schulz, M.A. and Albrecht, J.P. and Yilmaz, A. and Koch, A. and Kainmüller, D. and Leser, U. and Ritter, K.
In: Workshops of the EDBT/ICDT 2024 Joint Conference, EDBT/ICDT-WS 2024, 25-28 March 2024, Paestum, Italy. 25 March 2024

ciRS-7 and miR-7 regulate ischemia-induced neuronal death via glutamatergic signaling.
Scoyni, F. and Sitnikova, V. and Giudice, L. and Korhonen, P. and Trevisan, D.M. and Hernandez de Sande, A. and Gomez-Budia, M. and Giniatullina, R. and Ugidos, I.F. and Dhungana, H. and Pistono, C. and Korvenlaita, N. and Välimäki, N.N. and Kangas, S.M. and Hiltunen, A.E. and Gribchenko, E. and Kaikkonen-Määttä, M.U. and Koistinaho, J. and Ylä-Herttuala, S. and Hinttala, R. and Venø, M.T. and Su, J. and Stoffel, M. and Schaefer, A. and Rajewsky, N. and Kjems, J. and LaPierre, M.P. and Piwecka, M. and Jolkkonen, J. and Giniatullin, R. and Hansen, T.B. and Malm, T.
Cell Reports 43 (3): 113862. 26 March 2024

Routing of Kv7.1 to endoplasmic reticulum plasma membrane junctions.
Serrano-Novillo, C. and Estadella, I. and Navarro-Pérez, M. and Oliveras, A. and de Benito-Bueno, A. and Socuéllamos, P.G. and Bosch, M. and Coronado, M.J. and Sastre, D. and Valenzuela, C. and Soeller, C. and Felipe, A.
Acta Physiologica 240 (3): e14106. March 2024

The challenges of research data management in cardiovascular science: a DGK and DZHK position paper-executive summary.
Steffens, S. and Schröder, K. and Krüger, M. and Maack, C. and Streckfuss-Bömeke, K. and Backs, J. and Backofen, R. and Baeßler, B. and Devaux, Y. and Gilsbach, R. and Heijman, J. and Knaus, J. and Kramann, R. and Linz, D. and Lister, A.L. and Maatz, H. and Maegdefessel, L. and Mayr, M. and Meder, B. and Nussbeck, S.Y. and Rog-Zielinska, E.A. and Schulz, M.H. and Sickmann, A. and Yigit, G. and Kohl, P.
Clinical Research in Cardiology 113 (5): 672-679. May 2024

Herpes simplex virus type 1 modifies the protein composition of extracellular vesicles to promote neurite outgrowth and neuroinfection.
Sun, G. and Kropp, K.A. and Kirchner, M. and Plückebaum, N. and Selich, A. and Serrero, M. and Dhingra, A. and Cabrera, J.R. and Ritter, B. and Bauerfeind, R. and Wyler, E. and Landthaler, M. and Schambach, A. and Sodeik, B. and Mertins, P. and Viejo-Borbolla, A.
mBio 15 (2): e0330823. 14 February 2024

EU-LIFE charter of independent life science research institutes.
Superti-Furga, G. and Agostinho, M. and Bury, J. and Cook, S. and Durinx, C. and Ender, A. and van Luenen, H. and Lund, A.H. and Medema, R.H. and Miączyńska, M. and Nickel, D. and Pelicci, P.G. and Puisieux, A. and Ripatti, S. and Sander, M. and Schubeler, D. and Serrano, L. and Sommer, T. and Sonne-Hansen, K. and Tomančák, P. and Vives, J. and Vontas, J. and Bettencourt-Dias, M.
FEBS Letters 21 March 2024

Macrocephaly and digital anomalies expand the phenotypic spectrum of PGAP2 variants in hyperphosphatasia with impaired intellectual development syndrome 3 (HPMRS3).
Susgun, S. and Ben-Mahmoud, A. and Rüschendorf, F. and Ku, B. and Hussain, S.I. and Schulz, S. and Puk, O. and Biskup, S. and Labonne, J.D.J. and Don, D.W. and Gupta, V. and Choi, T.I. and Khan, S. and Wasif, N. and Lacassie, Y. and Layman, L.C. and Ugur Iseri, S.A. and Kim, C.H. and Kim, H.G.
Human Mutation 2024 : 1-13. 5 January 2024

Protective role of the HSP90 inhibitor, STA-9090, in lungs of SARS-CoV-2-infected Syrian golden hamsters.
Teixeira Alves, L.G. and Baumgardt, M. and Langner, C. and Fischer, M. and Maria Adler, J. and Bushe, J. and Firsching, T.C. and Mastrobuoni, G. and Grobe, J. and Hoenzke, K. and Kempa, S. and Gruber, A.D. and Hocke, A.C. and Trimpert, J. and Wyler, E. and Landthaler, M.
BMJ Open Respiratory Research 11 (1) 29 February 2024

Genome-wide screening identifies Trim33 as an essential regulator of dendritic cell differentiation.
Tiniakou, I. and Hsu, P.F. and Lopez-Zepeda, L.S. and Garipler, G. and Esteva, E. and Adams, N.M. and Jang, G. and Soni, C. and Lau, C.M. and Liu, F. and Khodadadi-Jamayran, A. and Rodrick, T.C. and Jones, D. and Tsirigos, A. and Ohler, U. and Bedford, M.T. and Nimer, S.D. and Kaartinen, V. and Mazzoni, E.O. and Reizis, B.
Science Immunology 9 (94): eadi1023. 12 April 2024

Cellular landscape of adrenocortical carcinoma at single-nuclei resolution.
Tourigny, D.S. and Altieri, B. and Secener, K.A. and Sbiera, S. and Schauer, M.P. and Arampatzi, P. and Herterich, S. and Sauer, S. and Fassnacht, M. and Ronchi, C.L.
Molecular and Cellular Endocrinology 590 : 112272. 1 September 2024

AI-guided pipeline for protein-protein interaction drug discovery identifies an SARS-CoV-2 inhibitor.
Trepte, P. and Secker, C. and Olivet, J. and Blavier, J. and Kostova, S. and Maseko, S.B. and Minia, I. and Silva Ramos, E. and Cassonnet, P. and Golusik, S. and Zenkner, M. and Beetz, S. and Liebich, M.J. and Scharek, N. and Schutz, A. and Sperling, M. and Lisurek, M. and Wang, Y. and Spirohn, K. and Hao, T. and Calderwood, M.A. and Hill, D.E. and Landthaler, M. and Choi, S.G. and Twizere, J.C. and Vidal, M. and Wanker, E.E.
Molecular Systems Biology 20 (4): 428-457. 2 April 2024

Regulation of lymphoid-myeloid lineage bias through Regnase-1/3-mediated control of Nfkbiz.
Uehata, T. and Yamada, S. and Ori, D. and Vandenbon, A. and Giladi, A. and Jelinski, A. and Murakawa, Y. and Watanabe, H. and Takeuchi, K. and Toratani, K. and Mino, T. and Kiryu, H. and Standley, D.M. and Tsujimura, T. and Ikawa, T. and Kondoh, G. and Landthaler, M. and Kawamoto, H. and Rodewald, H.R. and Amit, I. and Yamamoto, R. and Miyazaki, M. and Takeuchi, O.
Blood 143 (3): 243-257. 18 January 2024

Generation and downstream analysis of single-cell and single-nuclei transcriptomes in brain organoids.
Wandres, M. and Aigner, D. and Kastelic, N. and Boltengagen, A. and Rybak-Wolf, A. and Rajewsky, N.
Journal of Visualized Experiments (205): e66225. 29 March 2024

Epigenetic regulatory layers in the 3D nucleus.
Willemin, A. and Szabo, D. and Pombo, A.
Molecular Cell 84 (3): 415-428. 1 February 2024

The cycling and aging mouse female reproductive tract at single-cell resolution.
Winkler, I. and Tolkachov, A. and Lammers, F. and Lacour, P. and Daugelaite, K. and Schneider, N. and Koch, M.L. and Panten, J. and Grünschläger, F. and Poth, T. and Ávila, B.M.d. and Schneider, A. and Haas, S. and Odom, D.T. and Gonçalves, Â.
Cell 187 (4): 981-998. 15 February 2024

Grainyhead-like 2 deficiency and kidney cyst growth in a mouse model.
Yurtdas, Z.Y. and Kilic, E. and Boor, P. and Wyler, E. and Landthaler, M. and Jung, K. and Schmidt-Ott, K.M.
Journal of the American Society of Nephrology 24 April 2024 (In Press)

DCGG: drug combination prediction using GNN and GAE.
Ziaee, S.S. and Rahmani, H. and Tabatabaei, M. and Vlot, A.H.C. and Bender, A.
Progress in Artificial Intelligence 13 : 17-30. March 2024

Smoking-associated gene expression alterations in nasal epithelium reveal immune impairment linked to lung cancer risk.
de Biase, M.S. and Massip, F. and Wei, T.T. and Giorgi, F.M. and Stark, R. and Stone, A. and Gladwell, A. and O'Reilly, M. and Schütte, D. and de Santiago, I. and Meyer, K.B. and Markowetz, F. and Ponder, B.A.J. and Rintoul, R.C. and Schwarz, R.F.
Genome Medicine 16 (1): 54. 8 April 2024

2023

Tracking early lung cancer metastatic dissemination in TRACERx using ctDNA.
Abbosh, C. and Frankell, A.M. and Harrison, T. and Kisistok, J. and Garnett, A. and Johnson, L. and Veeriah, S. and Moreau, M. and Chesh, A. and Chaunzwa, T.L. and Weiss, J. and Schroeder, M.R. and Ward, S. and Grigoriadis, K. and Shahpurwalla, A. and Litchfield, K. and Puttick, C. and Biswas, D. and Karasaki, T. and Black, J.R.M. and Martínez-Ruiz, C. and Bakir, M.A.l. and Pich, O. and Watkins, T.B.K. and Lim, E.L. and Huebner, A. and Moore, D.A. and Godin-Heymann, N. and L'Hernault, A. and Bye, H. and Odell, A. and Roberts, P. and Gomes, F. and Patel, A.J. and Manzano, E. and Hiley, C.T. and Carey, N. and Riley, J. and Cook, D.E. and Hodgson, D. and Stetson, D. and Barrett, J.C. and Kortlever, R.M. and Evan, G.I. and Hackshaw, A. and Daber, R.D. and Shaw, J.A. and Aerts, H.J.W.L. and Licon, A. and Stahl, J. and Jamal-Hanjani, M. and Birkbak, N.J. and McGranahan, N. and Swanton, C.
Nature 616 (7957): 553-562. 20 April 2023

Evolution of 3D chromatin organization at different scales.
Acemel, R.D. and Lupianez, D.G.
Current opinion in genetics & development 78 : 102019. February 2023

The interleukin-11 receptor variant p.W307R results in craniosynostosis in humans.
Ahmad, I. and Lokau, J. and Kespohl, B. and Malik, N.A. and Baig, S.M. and Hartig, R. and Behme, D. and Schwab, R. and Altmüller, J. and Jameel, M. and Mucha, S. and Thiele, H. and Tariq, M. and Nürnberg, P. and Erdmann, J. and Garbers, C.
Scientific Reports 13 (1): 13479. 18 August 2023

The evolution of non-small cell lung cancer metastases in TRACERx.
Al Bakir, M. and Huebner, A. and Martínez-Ruiz, C. and Grigoriadis, K. and Watkins, T.B.K. and Pich, O. and Moore, D.A. and Veeriah, S. and Ward, S. and Laycock, J. and Johnson, D. and Rowan, A. and Razaq, M. and Akther, M. and Naceur-Lombardelli, C. and Prymas, P. and Toncheva, A. and Hessey, S. and Dietzen, M. and Colliver, E. and Frankell, A.M. and Bunkum, A. and Lim, E.L. and Karasaki, T. and Abbosh, C. and Hiley, C.T. and Hill, M.S. and Cook, D.E. and Wilson, G.A. and Salgado, R. and Nye, E. and Stone, R.K. and Fennell, D.A. and Price, G. and Kerr, K.M. and Naidu, B. and Middleton, G. and Summers, Y. and Lindsay, C.R. and Blackhall, F.H. and Cave, J. and Blyth, K.G. and Nair, A. and Ahmed, A. and Taylor, M.N. and Procter, A.J. and Falzon, M. and Lawrence, D. and Navani, N. and Thakrar, R.M. and Janes, S.M. and Papadatos-Pastos, D. and Forster, M.D. and Lee, S.M. and Ahmad, T. and Quezada, S.A. and Peggs, K.S. and Van Loo, P. and Dive, C. and Hackshaw, A. and Birkbak, N.J. and Zaccaria, S. and Jamal-Hanjani, M. and McGranahan, N. and Swanton, C.
Nature 616 (7957): 534-542. April 2023

Body composition and lung cancer-associated cachexia in TRACERx.
Al-Sawaf, O. and Weiss, J. and Skrzypski, M. and Lam, J.M. and Karasaki, T. and Zambrana, F. and Kidd, A.C. and Frankell, A.M. and Watkins, T.B.K. and Martínez-Ruiz, C. and Puttick, C. and Black, J.R.M. and Huebner, A. and Bakir, M.A. and Sokač, M. and Collins, S. and Veeriah, S. and Magno, N. and Naceur-Lombardelli, C. and Prymas, P. and Toncheva, A. and Ward, S. and Jayanth, N. and Salgado, R. and Bridge, C.P. and Christiani, D.C. and Mak, R.H. and Bay, C. and Rosenthal, M. and Sattar, N. and Welsh, P. and Liu, Y. and Perrimon, N. and Popuri, K. and Beg, M.F. and McGranahan, N. and Hackshaw, A. and Breen, D.M. and O'Rahilly, S. and Birkbak, N.J. and Aerts, H.J.W.L. and Jamal-Hanjani, M. and Swanton, C.
Nature Medicine 29 (4): 846-858. April 2023

Sites of transcription initiation drive mRNA isoform selection.
Alfonso-Gonzalez, C. and Legnini, I. and Holec, S. and Arrigoni, L. and Ozbulut, H.C. and Mateos, F. and Koppstein, D. and Rybak-Wolf, A. and Bönisch, U. and Rajewsky, N. and Hilgers, V.
Cell 186 (11): 2438-2455. 25 May 2023

Rapid nuclear deadenylation of mammalian messenger RNA.
Alles, J. and Legnini, I. and Pacelli, M. and Rajewsky, N.
iScience 26 (1): 105878. 20 January 2023

The SPOC domain is a phosphoserine binding module that bridges transcription machinery with co- and post-transcriptional regulators.
Appel, L.M. and Franke, V. and Benedum, J. and Grishkovskaya, I. and Strobl, X. and Polyansky, A. and Ammann, G. and Platzer, S. and Neudolt, A. and Wunder, A. and Walch, L. and Kaiser, S. and Zagrovic, B. and Djinovic-Carugo, K. and Akalin, A. and Slade, D.
Nature Communications 14 (1): 166. 11 January 2023

Post-COVID exercise intolerance is associated with capillary alterations and immune dysregulations in skeletal muscles.
Aschman, T. and Wyler, E. and Baum, O. and Hentschel, A. and Rust, R. and Legler, F. and Preusse, C. and Meyer-Arndt, L. and Büttnerova, I. and Förster, A. and Cengiz, D. and Teixeira Alves, L.G. and Schneider, J. and Kedor, C. and Bellmann-Strobl, J. and Sanchin, A. and Goebel, H.H. and Landthaler, M. and Corman, V. and Roos, A. and Heppner, F.L. and Radbruch, H. and Paul, F. and Scheibenbogen, C. and Dengler, N.F. and Stenzel, W.
Acta Neuropathologica Communications 11 (1): 193. 8 December 2023

Expanding the spectrum of EEF1D neurodevelopmental disorders: biallelic variants in the guanine exchange domain.
Averdunk, L. and Al-Thihli, K. and Surowy, H. and Lüdecke, H.J. and Drechsler, M. and Yigit, G. and Smorag, L. and Hallak, B.A. and Li, Y. and Altmüller, J. and Guthoff, T. and Wallot, M. and Nürnberg, P. and Wollnik, B. and Abou Jamra, R. and Al-Maawali, A. and Wieczorek, D.
Clinical Genetics 103 (4): 484-491. April 2023

Quantifying the impact of gut microbiota on inflammation and hypertensive organ damage.
Avery, E.G. and Bartolomaeus, H. and Rauch, A. and Chen, C.Y. and N'Diaye, G. and Löber, U. and Bartolomaeus, T.U.P. and Fritsche-Guenther, R. and Rodrigues, A.F. and Yarritu, A. and Zhong, C. and Fei, L. and Tsvetkov, D. and Todiras, M. and Park, J.K. and Markó, L. and Maifeld, A. and Patzak, A. and Bader, M. and Kempa, S. and Kirwan, J.A. and Forslund, S.K. and Müller, D.N. and Wilck, N.
Cardiovascular Research 119 (6): 1441-1452. May 2023

Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C.
Beagrie, R.A. and Thieme, C.J. and Annunziatella, C. and Baugher, C. and Zhang, Y. and Schueler, M. and Kukalev, A. and Kempfer, R. and Chiariello, A.M. and Bianco, S. and Li, Y. and Davis, T. and Scialdone, A. and Welch, L.R. and Nicodemi, M. and Pombo, A.
Nature Methods 20 (7): 1037-1047. July 2023

Unwelcome guests – the role of gland-associated Helicobacter pylori infection in gastric carcinogenesis.
Beccaceci, G. and Sigal, M.
Frontiers in Oncology 13 : 1171003. 21 April 2023

The SPOC proteins DIDO3 and PHF3 co-regulate gene expression and neuronal differentiation.
Benedum, J. and Franke, V. and Appel, L.M. and Walch, L. and Bruno, M. and Schneeweiss, R. and Gruber, J. and Oberndorfer, H. and Frank, E. and Strobl, X. and Polyansky, A. and Zagrovic, B. and Akalin, A. and Slade, D.
Nature Communications 14 (1): 7912. 30 November 2023

Clonally resolved single-cell multi-omics identifies routes of cellular differentiation in acute myeloid leukemia.
Beneyto-Calabuig, S. and Merbach, A.K. and Kniffka, J.A. and Antes, M. and Szu-Tu, C. and Rohde, C. and Waclawiczek, A. and Stelmach, P. and Gräßle, S. and Pervan, P. and Janssen, M. and Landry, J.J.M. and Benes, V. and Jauch, A. and Brough, M. and Bauer, M. and Besenbeck, B. and Felden, J. and Bäumer, S. and Hundemer, M. and Sauer, T. and Pabst, C. and Wickenhauser, C. and Angenendt, L. and Schliemann, C. and Trumpp, A. and Haas, S. and Scherer, M. and Raffel, S. and Müller-Tidow, C. and Velten, L.
Cell Stem Cell 30 (5): 706-721. 4 May 2023

The C-terminus of α-synuclein regulates its dynamic cellular internalization by neurexin 1β.
Birol, M. and Douzoglou Muñoz, I.I. and Rhoades, E.
Molecular Biology of the Cell 34 (13): br21. 1 December 2023

A proteomics analysis of 5xFAD mouse brain regions reveals the lysosome-associated protein Arl8b as a candidate biomarker for Alzheimer's disease.
Boeddrich, A. and Haenig, C. and Neuendorf, N. and Blanc, E. and Ivanov, A. and Kirchner, M. and Schleumann, P. and Bayraktaroğlu, I. and Richter, M. and Molenda, C.M. and Sporbert, A. and Zenkner, M. and Schnoegl, S. and Suenkel, C. and Schneider, L.S. and Rybak-Wolf, A. and Kochnowsky, B. and Byrne, L.M. and Wild, E.J. and Nielsen, J.E. and Dittmar, G. and Peters, O. and Beule, D. and Wanker, E.E.
Genome Medicine 15 (1): 50. 20 July 2023

Spatial transcriptomics unveils ZBTB11 as a regulator of cardiomyocyte degeneration in arrhythmogenic cardiomyopathy.
Boogerd, C.J. and Lacraz, G.P.A. and Vértesy, Á. and van Kampen, S.J. and Perini, I. and de Ruiter, H. and Versteeg, D. and Brodehl, A. and van der Kraak, P. and Giacca, M. and de Jonge, N. and Junker, J.P. and van Oudenaarden, A. and Vink, A. and van Rooij, E.
Cardiovascular Research 119 (2): 477-491. February 2023

Evolution and implications of de novo genes in humans.
Broeils, L.A. and Ruiz-Orera, J. and Snel, B. and Hubner, N. and van Heesch, S.
Nature Ecology & Evolution 7 (6): 804-815. June 2023

European and multi-ancestry genome-wide association meta-analysis of atopic dermatitis highlights importance of systemic immune regulation.
Budu-Aggrey, A. and Kilanowski, A. and Sobczyk, M.K. and Shringarpure, S.S. and Mitchell, R. and Reis, K. and Reigo, A. and Mägi, R. and Nelis, M. and Tanaka, N. and Brumpton, B.M. and Thomas, L.F. and Sole-Navais, P. and Flatley, C. and Espuela-Ortiz, A. and Herrera-Luis, E. and Lominchar, J.V.T. and Bork-Jensen, J. and Marenholz, I. and Arnau-Soler, A. and Jeong, A. and Fawcett, K.A. and Baurecht, H. and Rodriguez, E. and Alves, A.C. and Kumar, A. and Sleiman, P.M. and Chang, X. and Medina-Gomez, C. and Hu, C. and Xu, C.J. and Qi, C. and El-Heis, S. and Titcombe, P. and Antoun, E. and Fadista, J. and Wang, C.A. and Thiering, E. and Wu, B. and Kress, S. and Kothalawala, D.M. and Kadalayil, L. and Duan, J. and Zhang, H. and Hadebe, S. and Hoffmann, T. and Jorgenson, E. and Choquet, H. and Risch, N. and Njølstad, P. and Andreassen, O.A. and Johansson, S. and Almqvist, C. and Gong, T. and Ullemar, V. and Karlsson, R. and Magnusson, P.K.E. and Szwajda, A. and Burchard, E.G. and Thyssen, J.P. and Hansen, T. and Kårhus, L.L. and Dantoft, T.M. and Jeanrenaud, A.C.S.N. and Ghauri, A. and Arnold, A. and Homuth, G. and Lau, S. and Nöthen, M.M. and Hübner, N. and Imboden, M. and Visconti, A. and Falchi, M. and Bataille, V. and Hysi, P. and Ballardini, N. and Boomsma, D.I. and Hottenga, J.J. and Müller-Nurasyid, M. and Ahluwalia, T.S. and Stokholm, J. and Chawes, B. and Schoos, A.M.M. and Esplugues, A. and Bustamante, M. and Raby, B. and Arshad, S. and German, C. and Esko, T. and Milani, L.A. and Metspalu, A. and Terao, C. and Abuabara, K. and Løset, M. and Hveem, K. and Jacobsson, B. and Pino-Yanes, M. and Strachan, D.P. and Grarup, N. and Linneberg, A. and Lee, Y. and Probst-Hensch, N. and Weidinger, S. and Jarvelin, M.R. and Melén, E. and Hakonarson, H. and Irvine, A.D. and Jarvis, D. and Nijsten, T. and Duijts, L. and Vonk, J.M. and Koppelmann, G.H. and Godfrey, K.M. and Barton, S.J. and Feenstra, B. and Pennell, C.E. and Sly, P.D. and Holt, P.G. and Williams, L.K. and Bisgaard, H. and Bønnelykke, K. and Curtin, J. and Simpson, A. and Murray, C. and Schikowski, T. and Bunyavanich, S. and Weiss, S.T. and Holloway, J.W. and Min, J.L. and Brown, S.J. and Standl, M. and Paternoster, L.
Nature Communications 14 (1): 6172. 4 October 2023

LZTR1 polymerization provokes cardiac pathology in recessive Noonan syndrome.
Busley, A.V. and Gutiérrez-Gutiérrez, O. and Hammer, E. and Steinegger, M. and Böhmer, L. and Schroeder, H. and Kleinsorge, M. and Altmüller, J. and Marbach, F. and Hasenfuss, G. and Zimmermann, W.H. and Wollnik, B. and Cyganek, L.
bioRxiv : 2023.01.10.523203. 10 January 2023

The matrix metalloproteinase ADAM10 supports hepatitis C virus entry and cell-to-cell spread via its sheddase activity.
Carriquí-Madroñal, B. and Sheldon, J. and Duven, M. and Stegmann, C. and Cirksena, K. and Wyler, E. and Zapatero-Belinchón, F.J. and Vondran, F.W.R. and Gerold, G.
PLoS Pathogens 19 (11): e1011759. 15 November 2023

Towards hierarchical regional transformer-based multiple instance learning.
Cersovsky, J. and Mohammadi, S. and Kainmueller, D. and Hoehne, J.
In: 2023 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW), 02-06 Oct 2023, Paris, France. 25 December 2023

Parallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells.
Chamorro González, R. and Conrad, T. and Stöber, M.C. and Xu, R. and Giurgiu, M. and Rodriguez-Fos, E. and Kasack, K. and Brückner, L. and van Leen, E. and Helmsauer, K. and Dorado Garcia, H. and Stefanova, M.E. and Hung, K.L. and Bei, Y. and Schmelz, K. and Lodrini, M. and Mundlos, S. and Chang, H.Y. and Deubzer, H.E. and Sauer, S. and Eggert, A. and Schulte, J.H. and Schwarz, R.F. and Haase, K. and Koche, R.P. and Henssen, A.G.
Nature Genetics 55 (5): 880-890. May 2023

XPF interacts with TOP2B for R-loop processing and DNA looping on actively transcribed genes.
Chatzinikolaou, G. and Stratigi, K. and Siametis, A. and Goulielmaki, E. and Akalestou-Clocher, A. and Tsamardinos, I. and Topalis, P. and Austin, C. and Bouwman, B.A.M. and Crosetto, N. and Altmüller, J. and Garinis, G.A.
Science Advances 9 (45): eadi2095. 10 November 2023

First demonstration of miRNA-dependent mRNA decay.
Chekulaeva, M.
Nature Reviews Molecular Cell Biology 24 (3): 164. March 2023

A guide to naming eukaryotic circular RNAs.
Chen, L.L. and Bindereif, A. and Bozzoni, I. and Chang, H.Y. and Matera, A.G. and Gorospe, M. and Hansen, T.B. and Kjems, J. and Ma, X.K. and Pek, J.W. and Rajewsky, N. and Salzman, J. and Wilusz, J.E. and Yang, L. and Zhao, F.
Nature Cell Biology 25 (1): 1-5. January 2023

Physics-based polymer models to probe chromosome structure in single molecules.
Conte, M. and Chiariello, A.M. and Bianco, S. and Esposito, A. and Abraham, A. and Nicodemi, M.
Methods in Molecular Biology 2655 : 57-66. 2023

Association of the human gut microbiota with vascular stiffness.
Cuadrat, R.R.C. and Goris, T. and Birukov, A. and Eichelmann, F. and Andrade, B.G.N. and Bang, C. and Franke, A. and Wittenbecher, C. and Schulze, M.B.
Scientific Reports 13 (1): 13348. 16 August 2023

Cardiovascular disease biomarkers derived from circulating cell-free DNA methylation.
Cuadrat, R.R.C. and Kratzer, A. and Arnal, H.G. and Rathgeber, A.C. and Wreczycka, K. and Blume, A. and Gündüz, I.B. and Ebenal, V. and Mauno, T. and Osberg, B. and Moobed, M. and Hartung, J. and Jakobs, K. and Seppelt, C. and Meteva, D. and Haghikia, A. and Leistner, D.M. and Landmesser, Ulf and Akalin, A.
NAR Genomics and Bioinformatics 5 (2): lqad061. June 2023

Dominance is common in mammals and is associated with trans-acting gene expression and alternative splicing.
Cui, L. and Yang, B. and Xiao, S. and Gao, J. and Baud, A. and Graham, D. and McBride, M. and Dominiczak, A. and Schafer, S. and Aumatell, R.L. and Mont, C. and Teruel, A.F. and Hübner, N. and Flint, J. and Mott, R. and Huang, L.
Genome Biology 24 (1): 215. 29 September 2023

Sodium perturbs mitochondrial respiration and induces dysfunctional Tregs.
Côrte-Real, B.F. and Hamad, I. and Arroyo Hornero, R. and Geisberger, S. and Roels, J. and Van Zeebroeck, L. and Dyczko, A. and van Gisbergen, M.W. and Kurniawan, H. and Wagner, A. and Yosef, N. and Weiss, S.N.Y. and Schmetterer, K.G. and Schröder, A. and Krampert, L. and Haase, S. and Bartolomaeus, H. and Hellings, N. and Saeys, Y. and Dubois, L.J. and Brenner, D. and Kempa, S. and Hafler, D.A. and Stegbauer, J. and Linker, R.A. and Jantsch, J. and Müller, D.N. and Kleinewietfeld, M.
Cell Metabolism 35 (2): 299-315. 7 February 2023

Global analysis of contact-dependent human-to-mouse intercellular mRNA and lncRNA transfer in cell culture.
Dasgupta, S. and Dayagi, D.Y. and Haimovich, G. and Wyler, E. and Olender, T. and Singer, R.H. and Landthaler, M. and Gerst, J.E.
eLife 12 : e83584. 30 May 2023

Systematic benchmarking of single-cell ATAC-sequencing protocols.
De Rop, F.V. and Hulselmans, G. and Flerin, C. and Soler-Vila, P. and Rafels, A. and Christiaens, V. and González-Blas, C.B. and Marchese, D. and Caratù, G. and Poovathingal, S. and Rozenblatt-Rosen, O. and Slyper, M. and Luo, W. and Muus, C. and Duarte, F. and Shrestha, R. and Bagdatli, S.T. and Corces, M.R. and Mamanova, L. and Knights, A. and Meyer, K.B. and Mulqueen, R. and Taherinasab, A. and Maschmeyer, P. and Pezoldt, J. and Lambert, C.L.G. and Iglesias, M. and Najle, S.R. and Dossani, Z.Y. and Martelotto, L.G. and Burkett, Z. and Lebofsky, R. and Martin-Subero, J.I. and Pillai, S. and Sebé-Pedrós, A. and Deplancke, B. and Teichmann, S.A. and Ludwig, L.S. and Braun, T.P. and Adey, A.C. and Greenleaf, W.J. and Buenrostro, J.D. and Regev, A. and Aerts, S. and Heyn, H.
Nature Biotechnology 3 August 2023 (In Press)

Small molecule SUMO inhibition for biomarker-informed B-cell lymphoma therapy.
Demel, U.M. and Wirth, M. and Yousefian, S. and Zhang, L. and Isaakidis, K. and Dönig, J. and Böger, M. and Singh, N. and Köse, H. and Haas, S. and Müller, S. and Schick, M. and Keller, U.
Haematologica 108 (2): 555-567. February 2023

Mucosa-associated microbiota alterations in primary sclerosing cholangitis (PSC) before and after liver transplantation—who is calling the shots?
Demir, M. and Sigal, M.
Hepatobiliary Surgery and Nutrition 12 (5): 795-797. 1 October 2023

Genome-engineering technologies for modeling and treatment of cystic fibrosis.
Dębczyński, M. and Mojsak, D. and Minarowski, Ł. and Maciejewska, M. and Lisowski, P. and Mróz, R.M.
Advances in Medical Sciences 68 (1): 111-120. March 2023

Cell fate determinant Llgl1 is required for propagation of acute myeloid leukemia.
Eifert, T. and Hsu, C.J. and Becker, A.L. and Graessle, S. and Horne, A. and Bemmann, F. and Zhang, Q. and Heuser, M. and Vasioukhin, V. and Scholl, S. and Hochhaus, A. and Siegerist, F. and Endlich, N. and Bullinger, L. and Lane, S.W. and Haas, S. and Schnoeder, T.M and Heidel, F.H.
Leukemia 37 (10): 2027-2035. October 2023

Germline C1GALT1C1 mutation causes a multisystem chaperonopathy.
Erger, F. and Aryal, R.P. and Reusch, B. and Matsumoto, Y. and Meyer, R. and Zeng, J. and Knopp, C. and Noel, M. and Muerner, L. and Wenzel, A. and Kohl, S. and Tschernoster, N. and Rappl, G. and Rouvet, I. and Schröder-Braunstein, J. and Seibert, F.S. and Thiele, H. and Häusler, M.G. and Weber, L.T. and Büttner-Herold, M. and Elbracht, M. and Cummings, S.F. and Altmüller, J. and Habbig, S. and Cummings, R.D. and Beck, B.B.
Proceedings of the National Academy of Sciences of the United States of America 120 (22): e2211087120. 30 May 2023

IL-33 expression is lower in current smokers at both transcriptomic and protein level.
Faiz, A. and Mahbub, R.M. and Boedijono, F.S. and Tomassen, M.I. and Kooistra, W. and Timens, W. and Nawijn, M. and Hansbro, P.M. and Johansen, M.D. and Pouwels, S.D. and Heijink, I.H. and Massip, F. and de Biase, M.S. and Schwarz, R.F. and Adcock, I.M. and Chung, K.F. and van der Does, A. and Hiemstra, P.S. and Goulaouic, H. and Xing, H. and Abdulai, R. and de Rinaldis, E. and Cunoosamy, D. and Harel, S. and Lederer, D. and Nivens, M.C. and Wark, P.A. and Kerstjens, H.A.M. and Hylkema, M.N. and Brandsma, C.A. and van den Berge, M.
American Journal of Respiratory and Critical Care Medicine 208 (10): 1075-1087. 15 November 2023

Machine learning-based ozone and PM2.5 forecasting: application to multiple AQS sites in the Pacific Northwest.
Fan, K. and Dhammapala, R. and Harrington, K. and Lamb, B. and Lee, Y.
Frontiers in Big Data 6 : 1124148. 24 February 2023

Single-cell profiling and zebrafish avatars reveal LGALS1 as immunomodulating target in glioblastoma.
Finotto, L. and Cole, B. and Giese, W. and Baumann, E. and Claeys, A. and Vanmechelen, M. and Decraene, B. and Derweduwe, M. and Dubroja Lakic, N. and Shankar, G. and Nagathihalli Kantharaju, M. and Albrecht, J.P. and Geudens, I. and Stanchi, F. and Ligon, K.L. and Boeckx, B. and Lambrechts, D. and Harrington, K. and Van Den Bosch, L. and De Vleeschouwer, S. and De Smet, F. and Gerhardt, H.
EMBO Molecular Medicine 15 (11): e18144. 8 November 2023

Advancements in pulsed stable isotope-resolved metabolomics.
Forbes, M. and Geisberger, S. and Pietzke, M. and Mastrobuoni, G. and Kempa, S.
Handbook of Experimental Pharmacology 277 : 165-180. 3 March 2023

A multimorphic mutation in IRF4 causes human autosomal dominant combined immunodeficiency.
Fornes, O. and Jia, A. and Kuehn, H.S. and Min, Q. and Pannicke, U. and Schleussner, N. and Thouenon, R. and Yu, Z. and de Los Angeles Astbury, M. and Biggs, C.M. and Galicchio, M. and Garcia-Campos, J.A. and Gismondi, S. and Gonzalez Villarreal, G. and Hildebrand, K.J. and Hönig, M. and Hou, J. and Moshous, D. and Pittaluga, S. and Qian, X. and Rozmus, J. and Schulz, A.S. and Staines-Boone, A.T. and Sun, B. and Sun, J. and Uwe, S. and Venegas-Montoya, E. and Wang, W. and Wang, X. and Ying, W. and Zhai, X. and Zhou, Q. and Akalin, A. and André, I. and Barth, T.F.E. and Baumann, B. and Brüstle, A. and Burgio, G. and Bustamante, J.C. and Casanova, J.L. and Casarotto, M.G. and Cavazzana, M. and Chentout, L. and Cockburn, I.A. and Costanza, M. and Cui, C. and Daumke, O. and Del Bel, K.L. and Eibel, H. and Feng, X. and Franke, V. and Gebhardt, J.C.M. and Götz, A. and Grunwald, S. and Hoareau, B. and Hughes, T.R. and Jacobsen, E.M. and Janz, M. and Jolma, A. and Lagresle-Peyrou, C. and Lai, N. and Li, Y. and Lin, S. and Lu, H.Y. and Lugo-Reyes, S.O. and Meng, X. and Möller, P. and Moreno-Corona, N. and Niemela, J.E. and Novakovsky, G. and Perez-Caraballo, J.J. and Picard, C. and Poggi, L. and Puig-Lombardi, M.E. and Randall, K.L. and Reisser, A. and Schmitt, Y. and Seneviratne, S. and Sharma, M. and Stoddard, J. and Sundararaj, S. and Sutton, H. and Tran, L.Q. and Wang, Y. and Wasserman, W.W. and Wen, Z. and Winkler, W. and Xiong, E. and Yang, A.W.H. and Yu, M. and Zhang, L. and Zhang, H. and Zhao, Q. and Zhen, X. and Enders, A. and Kracker, S. and Martinez-Barricarte, R. and Mathas, S. and Rosenzweig, S.D. and Schwarz, K. and Turvey, S.E. and Wang, J.Y.
Science Immunology 8 (79): eade7953. January 2023

The evolution of lung cancer and impact of subclonal selection in TRACERx.
Frankell, A.M. and Dietzen, M. and Al Bakir, M. and Lim, E.L. and Karasaki, T. and Ward, S. and Veeriah, S. and Colliver, E. and Huebner, A. and Bunkum, A. and Hill, M.S. and Grigoriadis, K. and Moore, D.A. and Black, J.R.M. and Liu, W.K. and Thol, K. and Pich, O. and Watkins, T.B.K. and Naceur-Lombardelli, C. and Cook, D.E. and Salgado, R. and Wilson, G.A. and Bailey, C. and Angelova, M. and Bentham, R. and Martínez-Ruiz, C. and Abbosh, C. and Nicholson, A.G. and Le Quesne, J. and Biswas, D. and Rosenthal, R. and Puttick, C. and Hessey, S. and Lee, C. and Prymas, P. and Toncheva, A. and Smith, J. and Xing, W. and Nicod, J. and Price, G. and Kerr, K.M. and Naidu, B. and Middleton, G. and Blyth, K.G. and Fennell, D.A. and Forster, M.D. and Lee, S.M. and Falzon, M. and Hewish, M. and Shackcloth, M.J. and Lim, E. and Benafif, S. and Russell, P. and Boleti, E. and Krebs, M.G. and Lester, J.F. and Papadatos-Pastos, D. and Ahmad, T. and Thakrar, R.M. and Lawrence, D. and Navani, N. and Janes, S.M. and Dive, C. and Blackhall, F.H and Summers, Y. and Cave, J. and Marafioti, T. and Herrero, J. and Quezada, S.A. and Peggs, K.S. and Schwarz, R.F. and Van Loo, P. and Miedema, D.M. and Birkbak, N.J. and Hiley, C.T. and Hackshaw, A. and Zaccaria, S. and Jamal-Hanjani, M. and McGranahan, N. and Swanton, C.
Nature 616 (7957): 525-533. 20 April 2023

Diverse but unique astrocytic phenotypes during embryonic stem cell differentiation, culturing and development.
Freitag, K. and Eede, P. and Ivanov, A. and Sterczyk, N. and Schneeberger, S. and Borodina, T. and Sauer, S. and Beule, D. and Heppner, F.L.
Communications Biology 6 (1): 40. 13 January 2023

C. elegans gene regulatory alleles and reporter bashing studies.
Froehlich, J.J. and Rajewsky, N.
microPublication Biology 2023 20 January 2023

Defining the landscape of circular RNAs in neuroblastoma unveils a global suppressive function of MYCN.
Fuchs, S. and Danßmann, C. and Klironomos, F. and Winkler, A. and Fallmann, J. and Kruetzfeldt, L.M. and Szymansky, A. and Naderi, J. and Bernhart, S.H. and Grunewald, L. and Helmsauer, K. and Rodriguez-Fos, E. and Kirchner, M. and Mertins, P. and Astrahantseff, K. and Suenkel, C. and Toedling, J. and Meggetto, F. and Remke, M. and Stadler, P.F. and Hundsdoerfer, P. and Deubzer, H.E. and Künkele, A. and Lang, P. and Fuchs, J. and Henssen, A.G. and Eggert, A. and Rajewsky, N. and Hertwig, F. and Schulte, J.H.
Nature Communications 14 (1): 3936. 4 July 2023

Aged intestinal stem cells propagate cell-intrinsic sources of inflammaging in mice.
Funk, M.C. and Gleixner, J.G. and Heigwer, F. and Vonficht, D. and Valentini, E. and Aydin, Z. and Tonin, E. and Del Prete, S. and Mahara, S. and Throm, Y. and Hetzer, J. and Heide, D. and Stegle, O. and Odom, D.T. and Feldmann, A. and Haas, S. and Heikenwalder, M. and Boutros, M.
Developmental Cell 58 (24): 2914-2929. 18 December 2023

HNF1B alters an evolutionarily conserved nephrogenic program of target genes.
Grand, K. and Stoltz, M. and Rizzo, L. and Röck, R. and Kaminski, M.M. and Salinas, G. and Getwan, M. and Naert, T. and Pichler, R. and Lienkamp, S.S.
Journal of the American Society of Nephrology 34 (3): 412-432. March 2023

Recombination between heterologous human acrocentric chromosomes.
Guarracino, A. and Buonaiuto, S. and de Lima, L.G. and Potapova, T. and Rhie, A. and Koren, S. and Rubinstein, B. and Fischer, C. and Gerton, J.L. and Phillippy, A.M. and Colonna, V. and Garrison, E.
Nature 617 (7960): 335-343. 11 May 2023

Transcription factor induction of vascular blood stem cell niches in vivo.
Hagedorn, E.J. and Perlin, J.R. and Freeman, R.J. and Wattrus, S.J. and Han, T. and Mao, C. and Kim, J.W. and Fernández-Maestre, I. and Daily, M.L. and D'Amato, C. and Fairchild, M.J. and Riquelme, R. and Li, B. and Ragoonanan, D.A.V.E. and Enkhbayar, K. and Henault, E.L. and Wang, H.G. and Redfield, S.E. and Collins, S.H. and Lichtig, A. and Yang, S. and Zhou, Y. and Kunar, B. and Gomez-Salinero, J.M. and Dinh, T.T. and Pan, J. and Holler, K. and Feldman, H.A. and Butcher, E.C. and van Oudenaarden, A. and Rafii, S. and Junker, J.P. and Zon, L.I.
Developmental Cell 58 (12): 1037-1051. 19 June 2023

Single-cell multi-omics and lineage tracing to dissect cell fate decision-making.
Haghverdi, L. and Ludwig, L.S.
Stem Cell Reports 18 (1): 13-25. 10 January 2023

Short-term mucosal disruption enables colibactin-producing E. coli to cause long-term perturbation of colonic homeostasis.
Harnack, C. and Berger, H. and Liu, L. and Mollenkopf, H.J. and Strowig, T. and Sigal, M.
Gut Microbes 15 (1): 2233689. 10 July 2023

Lung adenocarcinoma promotion by air pollutants.
Hill, W. and Lim, E.L. and Weeden, C.E. and Lee, C. and Augustine, M. and Chen, K. and Kuan, F.C. and Marongiu, F. and Evans, E.J. and Moore, D.A. and Rodrigues, F.S. and Pich, O. and Bakker, B. and Cha, H. and Myers, R. and van Maldegem, F. and Boumelha, J. and Veeriah, S. and Rowan, A. and Naceur-Lombardelli, C. and Karasaki, T. and Sivakumar, M. and De, S. and Caswell, D.R. and Nagano, A. and Black, J.R.M. and Martínez-Ruiz, C. and Ryu, M.H. and Huff, R.D. and Li, S. and Favé, M.J. and Magness, A. and Suárez-Bonnet, A. and Priestnall, S.L. and Lüchtenborg, M. and Lavelle, K. and Pethick, J. and Hardy, S. and McRonald, F.E. and Lin, M.H. and Troccoli, C.I. and Ghosh, M. and Miller, Y.E. and Merrick, D.T. and Keith, R.L. and Al Bakir, M. and Bailey, C. and Hill, M.S. and Saal, L.H. and Chen, Y. and George, A.M. and Abbosh, C. and Kanu, N. and Lee, S.H. and McGranahan, N. and Berg, C.D. and Sasieni, P. and Houlston, R. and Turnbull, C. and Lam, S. and Awadalla, P. and Grönroos, E. and Downward, J. and Jacks, T. and Carlsten, C. and Malanchi, I. and Hackshaw, A. and Litchfield, K. and DeGregori, J. and Jamal-Hanjani, M. and Swanton, C.
Nature 616 (7955): 159-167. 6 April 2023

A computational map of the human-SARS-CoV-2 protein-RNA interactome predicted at single-nucleotide resolution.
Horlacher, M. and Oleshko, S. and Hu, Y. and Ghanbari, M. and Cantini, G. and Schinke, P. and Vergara, E.E. and Bittner, F. and Mueller, N.S and Ohler, U. and Moyon, L. and Marsico, A.
NAR Genomics and Bioinformatics 5 (1): lqad010. March 2023

A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish.
Huljev, K. and Shamipour, S. and Pinheiro, D. and Preusser, F. and Steccari, I. and Sommer, C.M. and Naik, S. and Heisenberg, C.P.
Developmental Cell 58 (7): 582-596.e7. 10 April 2023

Synthetic genetic circuits to uncover the OCT4 trajectories of successful reprogramming of human fibroblasts.
Ilia, K. and Shakiba, N. and Bingham, T. and Jones, R.D. and Kaminski, M.M. and Aravera, E. and Bruno, S. and Palacios, S. and Weiss, R. and Collins, J.J. and Del Vecchio, D. and Schlaeger, T.M.
Science Advances 9 (48): eadg8495. December 2023

Functional analysis of structural variants in single cells using Strand-seq.
Jeong, H. and Grimes, K. and Rauwolf, K.K. and Bruch, P.M. and Rausch, T. and Hasenfeld, P. and Benito, E. and Roider, T. and Sabarinathan, R. and Porubsky, D. and Herbst, S.A. and Erarslan-Uysal, B. and Jann, J.C. and Marschall, T. and Nowak, D. and Bourquin, J.P. and Kulozik, A.E. and Dietrich, S. and Bornhauser, B. and Sanders, A.D. and Korbel, J.O.
Nature Biotechnology 41 (6): 832-844. June 2023

Pharmacological modulators of epithelial immunity uncovered by synthetic genetic tracing of SARS-CoV-2 infection responses.
Jiang, B. and Schmitt, M.J. and Rand, U. and Company, C. and Dramaretska, Y. and Grossmann, M. and Serresi, M. and Cicin-Sain, L. and Gargiulo, G.
Science Advances 9 (25): eadf4975. 23 June 2023

Oncogenic role and target properties of the lysine-specific demethylase KDM1A in chronic lymphocytic leukemia.
Jiang, Q. and Stachelscheid, J. and Bloehdorn, J. and Pacholewska, A. and Aszyk, C.M. and Grotenhuijs, F. and Müller, T.A. and Onder, O. and Wagle, P. and Herling, C.D. and Kleppe, M. and Wang, Z. and Coombes, K.R. and Robrecht, S. and Dalvi, P.S. and Plosnita, B. and Mayer, P. and Abruzzo, L.V. and Altmüller, J. and Gathof, B.S. and Persigehl, T. and Fischer, K. and Jebaraj, B.M.C. and Rienhoff, H.Y. and Ecker, R.C. and Zhao, Y. and Bruns, C.J. and Stilgenbauer, S. and Elenitoba-Johnson, K.S.J. and Hallek, M. and Schweiger, M.R. and Odenthal, M. and Vasyutina, E. and Herling, M.
Blood 142 (1): 44-61. 6 July 2023

Resolving the spatial architecture of myeloma and its microenvironment at the single-cell level.
John, L. and Poos, A.M. and Brobeil, A. and Schinke, C. and Huhn, S. and Prokoph, N. and Lutz, R. and Wagner, B. and Zangari, M. and Tirier, S.M. and Mallm, J.P. and Schumacher, S. and Vonficht, D. and Solé-Boldo, L. and Quick, S. and Steiger, S. and Przybilla, M.J. and Bauer, K. and Baumann, A. and Hemmer, S. and Rehnitz, C. and Lückerath, C. and Sachpekidis, C. and Mechtersheimer, G. and Haberkorn, U. and Dimitrakopoulou-Strauss, A. and Reichert, P. and Barlogie, B. and Müller-Tidow, C. and Goldschmidt, H. and Hillengass, J. and Rasche, L. and Haas, S.F. and van Rhee, F. and Rippe, K. and Raab, M.S. and Sauer, S. and Weinhold, N.
Nature Communications 14 (1): 5011. 17 August 2023

Spatially resolved multiomics of human cardiac niches.
Kanemaru, K. and Cranley, J. and Muraro, D. and Miranda, A.M.A. and Ho, S.Y. and Wilbrey-Clark, A. and Patrick Pett, J. and Polanski, K. and Richardson, L. and Litvinukova, M. and Kumasaka, R. and Qin, Y. and Jablonska, Z. and Semprich, C.I. and Mach, L. and Dabrowska, M. and Richoz, R. and Bolt, L. and Mamanova, L. and Kapuge, R. and Barnett, S.N. and Perera, S. and Talavera-López, C. and Mulas, I. and Mahbubani, K.T. and Tuck, Liz and Wang, Lu and Huang, M.M. and Prete, M. and Pritchard, S. and Dark, J. and Saeb-Parsy, K. and Patel, M. and Clatworthy, M.R. and Hübner, N. and Chowdhury, R.A. and Noseda, M. and Teichmann, S.A.
Nature 619 : 801-810. 27 July 2023

Evolutionary characterization of lung adenocarcinoma morphology in TRACERx.
Karasaki, T. and Moore, D.A. and Veeriah, S. and Naceur-Lombardelli, C. and Toncheva, A. and Magno, N. and Ward, S. and Bakir, M.A. and Watkins, T.B.K. and Grigoriadis, K. and Huebner, A. and Hill, M.S. and Frankell, A.M. and Abbosh, C. and Puttick, C. and Zhai, H. and Gimeno-Valiente, F. and Saghafinia, S. and Kanu, N. and Dietzen, M. and Pich, O. and Lim, E.. and Martínez-Ruiz, C. and Black, J.R.M. and Biswas, D. and Campbell, B.B. and Lee, C. and Colliver, E. and Enfield, K.S.S. and Hessey, S. and Hiley, C.T. and Zaccaria, S. and Litchfield, K. and Birkbak, N.J. and Cadieux, E.L. and Demeulemeester, J. and Van Loo, P. and Adusumilli, P.S. and Tan, K.S. and Cheema, W. and Sanchez-Vega, F. and Jones, D.R. and Rekhtman, N. and Travis, W.D. and Hackshaw, A. and Marafioti, T. and Salgado, R. and Le Quesne, J. and Nicholson, A.G. and McGranahan, N. and Swanton, C. and Jamal-Hanjani, M.
Nature Medicine 29 (4): 833-845. April 2023

iPSC-derived reactive astrocytes from patients with multiple-sclerosis protect cocultured neurons in inflammatory conditions.
Kerkering, J. and Muinjonov, B. and Rosiewicz, K.S. and Diecke, S. and Biese, C. and Schiweck, J. and Chien, C. and Zocholl, D. and Conrad, T. and Paul, F. and Alisch, M. and Siffrin, V.
Journal of Clinical Investigation 133 (13): e164637. 3 July 2023

Identification of drug candidates targeting monocyte reprogramming in people living with HIV.
Knoll, R. and Bonaguro, L. and Dos Santos, J.C. and Warnat-Herresthal, S. and Jacobs-Cleophas, M.C.P. and Blümel, E. and Reusch, N. and Horne, A. and Herbert, M. and Nuesch-Germano, M. and Otten, T. and van der Heijden, W.A. and van de Wijer, L. and Shalek, A.K. and Händler, K. and Becker, M. and Beyer, M.D. and Netea, M.G. and Joosten, L.A.B. and van der Ven, A.J.A.M. and Schultze, J.L. and Aschenbrenner, A.C.
Frontiers in Immunology 14 : 1275136. 20 November 2023

Disruption of stem cell niche-confined R-spondin 3 expression leads to impaired hematopoiesis.
Kurtova, A.V. and Heinlein, M. and Haas, S. and Velten, L. and Dijkgraaf, G.J.P. and Storm, E.E. and Kljavin, N.M. and Boumahdi, S. and Himmels, P. and Herault, A. and Mancini, A.G. and Koeppen, H. and Dail, M. and Yan, M. and Zhang, J. and Koch, U. and Radtke, F. and Modrusan, Z. and Metcalfe, C. and Piskol, R. and de Sauvage, F.J.
Blood Advances 7 (4): 491-507. 28 February 2023

Prdm16 mutation determines sex-specific cardiac metabolism and identifies two novel cardiac metabolic regulators.
Kühnisch, J. and Theisen, S. and Dartsch, J. and Fritsche-Guenther, R. and Kirchner, M. and Obermayer, B. and Bauer, A. and Kahlert, A.K. and Rothe, M. and Beule, D. and Heuser, A. and Mertins, P. and Kirwan, J.A. and Berndt, N. and MacRae, C.A. and Hubner, N. and Klaassen, S.
Cardiovascular Research 119 (18): 2902-2916. December 2023

Prdm16 mutation determines sex-specific cardiac metabolism and identifies two novel cardiac metabolic regulators.
Kühnisch, J. and Theisen, S. and Dartsch, J. and Fritsche-Guenther, R. and Kirchner, M. and Obermayer, B. and Bauer, A. and Kahlert, A.K. and Rothe, M. and Beule, D. and Heuser, A. and Mertins, P. and Kirwan, J.A. and Berndt, N. and MacRae, C.A. and Hubner, N. and Klaassen, S.
bioRxiv : 2023.01.10.523243. 10 January 2023

Single-cell multi-omics of mitochondrial DNA disorders reveals dynamics of purifying selection across human immune cells.
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Nature Genetics 55 (7): 1198-1209. July 2023

Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility.
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Nature Protocols 18 (5): 1416-1440. May 2023

Latent human herpesvirus 6 is reactivated in CAR T cells.
Lareau, C.A. and Yin, Y. and Maurer, K. and Sandor, K.D. and Daniel, B. and Yagnik, G. and Peña, J. and Crawford, J.C. and Spanjaart, A.M. and Gutierrez, J.C. and Haradhvala, N.J. and Riberdy, J.M. and Abay, T. and Stickels, R.R. and Verboon, J.M. and Liu, V. and Buquicchio, F.A. and Wang, F. and Southard, J. and Song, R. and Li, W. and Shrestha, A. and Parida, L. and Getz, G. and Maus, M.V. and Li, S. and Moore, A. and Roberts, Z.J. and Ludwig, L.S. and Talleur, A.C. and Thomas, P.G. and Dehghani, H. and Pertel, T. and Kundaje, A. and Gottschalk, S. and Roth, T.L. and Kersten, M.J. and Wu, C.J. and Majzner, R.G. and Satpathy, A.T.
Nature 623 : 608-615. 16 November 2023

Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome.
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Cell Reports Methods 3 (8): 100543. 28 August 2023

Spatiotemporal, optogenetic control of gene expression in organoids.
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Nature Methods 20 (10): 1544-1552. October 2023

A draft human pangenome reference.
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Nature 617 (7960): 312-324. 11 May 2023

Establishment of gastrointestinal assembloids to study the interplay between epithelial crypts and their mesenchymal niche.
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Nature Communications 14 (1): 3025. 25 May 2023

Human embryo models: unveiling sophisticated self-organization of stem cells during post-implantation stages.
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Signal Transduction and Targeted Therapy 8 (1): 419. 6 November 2023

Robust phenotyping of highly multiplexed tissue imaging data using pixel-level clustering.
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Nature Communications 14 (1): 4618. 1 August 2023

SLAM-Drop-seq reveals mRNA kinetic rates throughout the cell cycle.
Liu, H. and Arsiè, R. and Schwabe, D. and Schilling, M. and Minia, I. and Alles, J. and Boltengagen, A. and Kocks, C. and Falcke, M. and Friedman, N. and Landthaler, M. and Rajewsky, N.
Molecular Systems Biology 19 (10): e11427. 12 October 2023

mRNA stability and m(6)A are major determinants of subcellular mRNA localization in neurons.
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Molecular Cell 83 (15): 2709-2725. 3 August 2023

Human model of primary carnitine deficiency cardiomyopathy reveals ferroptosis as a novel mechanism.
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Stem Cell Reports 18 (11): 2123-2137. 14 November 2023

Prox2 and Runx3 vagal sensory neurons regulate esophageal motility.
Lowenstein, E.D. and Ruffault, P.L. and Misios, A. and Osman, K.L. and Li, H. and Greenberg, R.S. and Thompson, R. and Song, K. and Dietrich, S. and Li, X. and Vladimirov, N. and Woehler, A. and Brunet, J.F. and Zampieri, N. and Kühn, R. and Liberles, S.D. and Jia, S. and Lewin, G.R. and Rajewsky, N. and Lever, T.E. and Birchmeier, C.
Neuron 111 (14): 2184-2200.e7. 19 July 2023

Concomitant sequencing of accessible chromatin and mitochondrial genomes in single cells using mtscATAC-seq.
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Methods in Molecular Biology 2611 : 269-282. 2023

Platelet-derived factors dysregulate placental sphingosine-1-phosphate receptor 2 in human trophoblasts.
Lyssy, F. and Guettler, J. and Brugger, B.A. and Stern, C. and Forstner, D. and Nonn, O. and Fischer, C. and Herse, F. and Wernitznig, S. and Hirschmugl, B. and Wadsack, C. and Gauster, M.
Reproductive BioMedicine Online 47 (2): 103215. August 2023

The genomic landscape across 474 surgically accessible epileptogenic human brain lesions.
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Brain 146 (4): 1342-1356. April 2023

A comprehensive molecular profiling approach reveals metabolic alterations that steer bone tissue regeneration.
Löffler, J. and Noom, A. and Ellinghaus, A. and Dienelt, A. and Kempa, S. and Duda, G.N.
Communications Biology 6 (1): 327. 27 March 2023

Rat cytomegalovirus efficiently replicates in dendritic cells and induces changes in their transcriptional profile.
Madela-Mönchinger, J.C. and Wolf, S.A. and Wyler, E. and Bauer, A. and Mischke, M. and Möller, L. and Juranić Lisnić, V. and Landthaler, M. and Malyshkina, A. and Voigt, S.
Frontiers in Immunology 14 : 1192057. 23 November 2023

Automated reconstruction of whole-embryo cell lineages by learning from sparse annotations.
Malin-Mayor, C. and Hirsch, P. and Guignard, L. and McDole, K. and Wan, Y. and Lemon, W.C. and Kainmueller, D. and Keller, P.J. and Preibisch, S. and Funke, J.
Nature Biotechnology 44 (1): 44-49. January 2023

The little skate genome and the evolutionary emergence of wing-like fins.
Marlétaz, F. and de la Calle-Mustienes, E. and Acemel, R.D. and Paliou, C. and Naranjo, S. and Martínez-García, P.M. and Cases, I. and Sleight, V.A. and Hirschberger, C. and Marcet-Houben, M. and Navon, D. and Andrescavage, A. and Skvortsova, K. and Duckett, P.Ed. and González-Rajal, Á. and Bogdanovic, O. and Gibcus, J.H. and Yang, L. and Gallardo-Fuentes, L. and Sospedra, I. and Lopez-Rios, J. and Darbellay, F. and Visel, A. and Dekker, J. and Shubin, N. and Gabaldón, T. and Nakamura, T. and Tena, J.J. and Lupianez, D.G. and Rokhsar, D.S. and Gómez-Skarmeta, J.L.
Nature 616 (7957): 495-503. 20 April 2023

Genomic–transcriptomic evolution in lung cancer and metastasis.
Martínez-Ruiz, C. and Black, J.R.M. and Puttick, C. and Hill, M.S. and Demeulemeester, J. and Larose Cadieux, E. and Thol, K. and Jones, T.P. and Veeriah, S. and Naceur-Lombardelli, C. and Toncheva, A. and Prymas, P. and Rowan, A. and Ward, S. and Cubitt, L. and Athanasopoulou, F. and Pich, O. and Karasaki, T. and Moore, D.A. and Salgado, R. and Colliver, E. and Castignani, C. and Dietzen, M. and Huebner, A. and Al Bakir, M. and Tanić, M. and Watkins, T.B.K. and Lim, E.L. and Al-Rashed, A.M. and Lang, D. and Clements, J. and Cook, D.E. and Rosenthal, R. and Wilson, G. A. and Frankell, A.M. and de Carné Trécesson, S. and East, P. and Kanu, N. and Litchfield, K. and Birkbak, N.J. and Hackshaw, A. and Beck, S. and Van Loo, P. and Jamal-Hanjani, M. and McGranahan, N. and Swanton, C.
Nature 616 (7957): 543-552. 20 April 2023

A searchable image resource of Drosophila GAL4-driver expression patterns with single neuron resolution.
Meissner, G.W. and Nern, A. and Dorman, Z. and DePasquale, G.M. and Forster, K. and Gibney, T. and Hausenfluck, J.H. and He, Y. and Iyer, N.A. and Jeter, J. and Johnson, L. and Johnston, R.M. and Lee, K. and Melton, B. and Yarbrough, B. and Zugates, C.T. and Clements, Jody and Goina, C. and Otsuna, H. and Rokicki, K. and Svirskas, R.R. and Aso, Y. and Card, G.M. and Dickson, B.J. and Ehrhardt, E. and Goldammer, J. and Ito, M. and Kainmueller, D. and Korff, W. and Mais, L. and Minegishi, R. and Namiki, S. and Rubin, G.M. and Sterne, G.R. and Wolff, T. and Malkesman, O.
eLife 12 : e80660. 23 February 2023

Massively parallel identification of mRNA localization elements in primary cortical neurons.
Mendonsa, S. and von Kügelgen, N. and Dantsuji, S. and Ron, M. and Breimann, L. and Baranovskii, A. and Lödige, I. and Kirchner, M. and Fischer, M. and Zerna, N. and Bujanic, L. and Mertins, P. and Ulitsky, I. and Chekulaeva, M.
Nature Neuroscience 26 (3): 394-405. March 2023

Dynamic interplay between RPL3- and RPL3L-containing ribosomes modulates mitochondrial activity in the mammalian heart.
Milenkovic, I. and Santos Vieira, H.G. and Lucas, M.C. and Ruiz-Orera, J. and Patone, G. and Kesteven, S. and Wu, J. and Feneley, M. and Espadas, G. and Sabidó, E. and Hübner, N. and van Heesch, S. and Völkers, M. and Novoa, E.M.
Nucleic Acids Research 51 (11): 5301-5324. 23 June 2023

Generation of an induced pluripotent stem cell line from a Huntington's disease patient with a long HTT-PolyQ sequence.
Miller, D.C. and Lisowski, P. and Genehr, C. and Wanker, E.E. and Priller, J. and Prigione, A. and Diecke, S.
Stem Cell Research 68 : 103056. April 2023

Single-cell transcriptomics for the assessment of cardiac disease.
Miranda, A.M.A. and Janbandhu, V. and Maatz, H. and Kanemaru, K. and Cranley, J. and Teichmann, S.A. and Huebner, N. and Schneider, M.D. and Harvey, R.P. and Noseda, M.
Nature Reviews Cardiology 20 (5): 289-308. May 2023

Toward identification of functional sequences and variants in noncoding DNA.
Monti, R. and Ohler, U.
Annual Review of Biomedical Data Science 6 : 191-210. August 2023

Distinct tissue niches direct lung immunopathology via CCL18 and CCL21 in severe COVID-19.
Mothes, R. and Pascual-Reguant, A. and Koehler, R. and Liebeskind, J. and Liebheit, A. and Bauherr, S. and Philipsen, L. and Dittmayer, C. and Laue, M. and von Manitius, R. and Elezkurtaj, S. and Durek, P. and Heinrich, F. and Heinz, G.A. and Guerra, G.M. and Obermayer, B. and Meinhardt, J. and Ihlow, J. and Radke, J. and Heppner, F.L. and Enghard, P. and Stockmann, H. and Aschman, T. and Schneider, J. and Corman, V.M. and Sander, L.E. and Mashreghi, M.F. and Conrad, T. and Hocke, A.C. and Niesner, R.A. and Radbruch, H. and Hauser, A.E.
Nature Communications 14 (1): 791. 11 February 2023

Targeting the tissue factor coagulation initiation complex prevents antiphospholipid antibody development.
Mueller-Calleja, N. and Grunz, K. and Nguyen, T.S. and Posma, J. and Pedrosa, D. and Meineck, M. and Hollerbach, A. and Braun, J. and Muth, S. and Schild, H. and Saar, K. and Hübner, N. and Krishnaswamy, S. and Royce, J. and Teyton, L. and Lemmermann, N.A. and Weinmann-Menke, J. and Lackner, K.J. and Ruf, W.
Blood 143 (12): 1167-1180. 21 March 2023

Adjustments to the reference dataset design improve cell type label transfer.
Mölbert, C. and Haghverdi, L.
Frontiers in Bioinformatics 3 : 1150099. 5 April 2023

Adjustments to the reference dataset design improves cell type label transfer.
Mölbert, C. and Haghverdi, L.
bioRxiv : 2023.01.25.525533. 26 January 2023

Salt sensitivity includes effects on immune cell signalling and metabolism.
Müller, D.N. and Geisberger, S. and Kleinewietfeld, M. and Jantsch, J.
Nature Reviews Immunology 23 (6): 341-342. June 2023

A single-cell RNA labeling strategy for measuring stress response upon tissue dissociation.
Neuschulz, A. and Bakina, O. and Badillo Lisakowski, V. and Olivares-Chauvet, P. and Conrad, T. and Gotthardt, M. and Kettenmann, H. and Junker, J.P.
Molecular Systems Biology 19 (2): e11147. 10 February 2023

Antibodies against endogenous retroviruses promote lung cancer immunotherapy.
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Nature 616 (7957): 563-573. 20 April 2023

Spatial and single-cell profiling of the metabolome, transcriptome and epigenome of the aging mouse liver.
Nikopoulou, C. and Kleinenkuhnen, N. and Parekh, S. and Sandoval, T. and Ziegenhain, C. and Schneider, F. and Giavalisco, P. and Donahue, K.F. and Vesting, A.J. and Kirchner, M. and Bozukova, M. and Vossen, C. and Altmüller, J. and Wunderlich, T. and Sandberg, R. and Kondylis, V. and Tresch, A. and Tessarz, P.
Nature Aging 3 (11): 1430-1445. November 2023

Brassinosteroid gene regulatory networks at cellular resolution in the Arabidopsis root.
Nolan, T.M. and Vukašinović, N. and Hsu, C.W. and Zhang, J. and Vanhoutte, I. and Shahan, R. and Taylor, I.W. and Greenstreet, L. and Heitz, M. and Afanassiev, A. and Wang, P. and Szekely, P. and Brosnan, A. and Yin, Y. and Schiebinger, G. and Ohler, U. and Russinova, E. and Benfey, P.N.
Science 379 (6639): eadf4721. 31 March 2023

Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters.
Nouailles, G. and Adler, J.M. and Pennitz, P. and Peidli, S. and Teixeira Alves, L.G. and Baumgardt, M. and Bushe, J. and Voss, A. and Langenhagen, A. and Langner, C. and Martin Vidal, R. and Pott, F. and Kazmierski, J. and Ebenig, A. and Lange, M.V. and Mühlebach, M.D. and Goekeri, C. and Simmons, S. and Xing, N. and Abdelgawad, A. and Herwig, S. and Cichon, G. and Niemeyer, D. and Drosten, C. and Goffinet, C. and Landthaler, M. and Blüthgen, N. and Wu, H. and Witzenrath, M. and Gruber, A.D. and Praktiknjo, S.D. and Osterrieder, N. and Wyler, E. and Kunec, D. and Trimpert, J.
Nature Microbiology 8 (5): 860-874. May 2023

Single-cell clonal tracking of persistent T-cells in allogeneic hematopoietic stem cell transplantation.
Obermayer, B. and Keilholz, L. and Conrad, T. and Frentsch, M. and Blau, I.W. and Vuong, L. and Lesch, S. and Movasshagi, K. and Tietze-Stolley, C. and Loyal, L. and Henze, L. and Penack, O. and Stervbo, U. and Babel, N. and Haas, S. and Beule, D. and Bullinger, L. and Wittenbecher, Friedrich and Na, I.K.
Frontiers in Immunology 14 : 1114368. 10 February 2023

Modeling of ACTN4-based podocytopathy using Drosophila nephrocytes.
Odenthal, J. and Dittrich, S. and Ludwig, V. and Merz, T. and Reitmeier, K. and Reusch, B. and Höhne, M. and Cosgun, Z.C. and Hohenadel, M. and Putnik, J. and Göbel, H. and Rinschen, M.M. and Altmüller, J. and Koehler, S. and Schermer, B. and Benzing, T. and Beck, B.B. and Brinkkötter, P.T. and Habbig, S. and Bartram, M.P.
Kidney International Reports 8 (2): 317-329. February 2023

MDC1 maintains active elongation complexes of RNA polymerase II.
Pappas, G. and Munk, S.H.N. and Watanabe, K. and Thomas, Q. and Gál, Z. and Gram, H.H. and Lee, M.H. and Gómez-Cabello, D. and Kanellis, D.C. and Olivares-Chauvet, P. and Larsen, D.H. and Gregersen, L.H. and Maya-Mendoza, A. and Galanos, P. and Bartek, J.
Cell Reports 42 (1): 111979. 31 January 2023

Protocol to dissociate healthy and infected murine- and hamster-derived lung tissue for single-cell transcriptome analysis.
Pennitz, P. and Goekeri, C. and Trimpert, J. and Wyler, E. and Ebenig, A. and Weissfuss, C. and Mühlebach, M.D. and Witzenrath, M. and Nouailles, G.
STAR Protocols 4 (1): 101957. 17 March 2023

Mitochondrial DNA mutations as natural barcodes for lineage tracing of murine tumor models.
Penter, L. and Ten Hacken, E. and Southard, J. and Lareau, C. and Ludwig, L.S. and Li, S. and Neuberg, D.S. and Livak, K.J. and Wu, C.J.
Cancer Research 83 (5): 667-672. 1 March 2023

Single-cell and spatial transcriptomics: deciphering brain complexity in health and disease.
Piwecka, M. and Rajewsky, N. and Rybak-Wolf, A.
Nature Reviews Neurology 19 (6): 346–362. June 2023

The rate of spontaneous mutations in yeast deficient for MutSβ function.
Plavskin, Y. and de Biase, M.S. and Schwarz, R.F. and Siegal, M.L.
G3 : Genes Genomes Genetics 13 (3): jkac330. March 2023

Inversion polymorphism in a complete human genome assembly.
Porubsky, D. and Harvey, W.T. and Rozanski, A.N. and Ebler, J. and Höps, W. and Ashraf, H. and Hasenfeld, P. and Paten, B. and Sanders, A.D. and Marschall, T. and Korbel, J.O. and Eichler, E.E.
Genome Biology 24 (1): 100. 30 April 2023

Gaps and complex structurally variant loci in phased genome assemblies.
Porubsky, D. and Vollger, M.R. and Harvey, W.T. and Rozanski, A.N. and Ebert, P. and Hickey, G. and Hasenfeld, P. and Sanders, A.D. and Stober, C. and Korbel, J.O. and Paten, B. and Marschall, T. and Eichler, E.E.
Genome Research 33 (4): 496-510. April 2023

What can Ribo-seq, immunopeptidomics, and proteomics tell us about the non-canonical proteome?
Prensner, J.R. and Abelin, J.G. and Kok, L.W. and Clauser, K.R. and Mudge, J.M. and Ruiz-Orera, J. and Bassani-Sternberg, M. and Moritz, R.L. and Deutsch, E.W. and van Heesch, S.
Molecular & Cellular Proteomics 22 (9): 100631. September 2023

LINC01013 is a determinant of fibroblast activation and encodes a novel fibroblast-activating micropeptide.
Quaife, N.M. and Chothani, S. and Schulz, J.F. and Lindberg, E.L. and Vanezis, K. and Adami, E. and O'Fee, K. and Greiner, J. and Litviňuková, M. and van Heesch, S. and Whiffin, N. and Hubner, N. and Schafer, S. and Rackham, O. and Cook, S.A. and Barton, P.J.R.
Journal of cardiovascular translational research 16 (1): 77-85. February 2023

Visualization and data exploration of chromosome conformation capture data using Voronoi diagrams with v3c-viz.
Race, A.M. and Fuchs, A. and Chung, H.R.
Scientific Reports 13 (1): 22020. 12 December 2023

Cell adhesion and immune response, two main functions altered in the transcriptome of seasonally regressed testes of two mammalian species.
Real, F.M. and Lao-Pérez, M. and Burgos, M. and Mundlos, S. and Lupiáñez, D.G. and Jiménez, R. and Barrionuevo, F.J.
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 340 (3): 231-244. May 2023

Mutational topography reflects clinical neuroblastoma heterogeneity.
Rodriguez-Fos, E. and Planas-Fèlix, M. and Burkert, M. and Puiggròs, M. and Toedling, J. and Thiessen, N. and Blanc, E. and Szymansky, A. and Hertwig, F. and Ishaque, N. and Beule, D. and Torrents, D. and Eggert, A. and Koche, R.P. and Schwarz, R.F. and Haase, K. and Schulte, J.H. and Henssen, A.G.
Cell Genomics 3 (10): 100402. 11 October 2023

Genomic ALK alterations in primary and relapsed neuroblastoma.
Rosswog, C. and Fassunke, J. and Ernst, A. and Schömig-Markiefka, B. and Merkelbach-Bruse, S. and Bartenhagen, C. and Cartolano, M. and Ackermann, S. and Theissen, J. and Blattner-Johnson, M. and Jones, B. and Schramm, K. and Altmüller, J. and Nürnberg, P. and Ortmann, M. and Berthold, F. and Peifer, M. and Büttner, R. and Westermann, F. and Schulte, J.H. and Simon, T. and Hero, B. and Fischer, M.
British Journal of Cancer 128 (8): 1559-1571. 12 April 2023

ACTIS: improving data efficiency by leveraging semi-supervised augmentation consistency training for instance segmentation.
Rumberger, J.L. and Franzen, J. and Hirsch, P. and Albrecht, J.P. and Kainmueller, D.
In: 2023 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW), 02-06 Oct 2023, Paris, France. 25 December 2023

Modelling viral encephalitis caused by herpes simplex virus 1 infection in cerebral organoids.
Rybak-Wolf, A. and Wyler, E. and Pentimalli, T.M. and Legnini, I. and Oliveras Martinez, A. and Glažar, P. and Loewa, A. and Kim, S.J. and Kaufer, B.B. and Woehler, A. and Landthaler, M. and Rajewsky, N.
Nature Microbiology 8 (7): 1252-1266. July 2023

Resistance to mesenchymal reprogramming sustains clonal propagation in metastatic breast cancer.
Saini, M. and Schmidleitner, L. and Moreno, H.D. and Donato, E. and Falcone, M. and Bartsch, J.M. and Vogel, V. and Würth, R. and Pfarr, N. and Espinet, E. and Lehmann, M. and Königshoff, M. and Reitberger, M. and Haas, S. and Graf, E. and Schwarzmayr, T. and Strom, T.M. and Spaich, S. and Sütterlin, M. and Schneeweiss, A. and Weichert, W. and Schotta, G. and Reichert, M. and Aceto, N. and Sprick, M.R. and Trumpp, A. and Scheel, C.H. and Klein, C.
Cell Reports 42 (6): 112533. 27 June 2023

Evolutionary origins and interactomes of human, young microproteins and small peptides translated from short open reading frames.
Sandmann, C.L. and Schulz, J.F. and Ruiz-Orera, J. and Kirchner, M. and Ziehm, M. and Adami, E. and Marczenke, M. and Christ, A. and Liebe, N. and Greiner, J. and Schoenenberger, A. and Mücke, M.B. and Liang, N. and Moritz, R.L. and Sun, Z. and Deutsch, E.W. and Gotthardt, M. and Mudge, J.M. and Prensner, J.R. and Willnow, T.E. and Mertins, P. and van Heesch, S. and Hubner, N.
Molecular Cell 83 (6): 994-1011.e18. 16 March 2023

Curvature in biological systems: its quantification, emergence and implications across the scales.
Schamberger, B. and Roschger, A. and Ziege, R. and Anselme, K. and Amar, M.B. and Bykowski, M. and Castro, A.P.G. and Cipitria, A. and Coles, R. and Dimova, R. and Eder, M. and Ehrig, S. and Escudero, L.M. and Evans, M.E. and Fernandes, P.R. and Fratzl, P. and Geris, L. and Gierlinger, N. and Hannezo, E. and Iglič, A. and Kirkensgaard, J.J.K. and Kollmannsberger, P. and Kowalewska, Ł. and Kurniawan, N.A. and Papantoniou, I. and Pieuchot, L. and Pires, T.H.V. and Renner, L. and Sageman-Furnas, A. and Schröder-Turk, G.E. and Sengupta, A. and Sharma, V.R. and Tagua, A. and Tomba, C. and Trepat, X. and Waters, S.L. and Yeo, E. and Bidan, C.M. and Dunlop, J.W.C.
Advanced Materials 35 (13): e2206110. 15 March 2023

Induction of kidney-related gene programs through co-option of SALL1 in mole ovotestes.
Schindler, M. and Osterwalder, M. and Harabula, I. and Wittler, L. and Tzika, A.C. and Dechmann, D.K.N. and Vingron, M. and Visel, A. and Haas, S. and Real, F.M.
Development 150 (17): dev201562. 1 September 2023

Transcriptional reprogramming by mutated IRF4 in lymphoma.
Schleussner, N. and Cauchy, P. and Franke, V. and Giefing, M. and Fornes, O. and Vankadari, N. and Assi, S.A. and Costanza, M. and Weniger, M.A. and Akalin, A. and Anagnostopoulos, I. and Bukur, T. and Casarotto, M.G. and Damm, F. and Daumke, O. and Edginton-White, B. and Gebhardt, J.C.M. and Grau, M. and Grunwald, S. and Hansmann, M.L. and Hartmann, S. and Huber, L. and Kärgel, E. and Lusatis, S. and Noerenberg, D. and Obier, N. and Pannicke, U. and Fischer, A. and Reisser, A. and Rosenwald, A. and Schwarz, K. and Sundararaj, S. and Weilemann, A. and Winkler, W. and Xu, W. and Lenz, G. and Rajewsky, K. and Wasserman, W.W. and Cockerill, P.N. and Scheidereit, C. and Siebert, R. and Küppers, R. and Grosschedl, R. and Janz, M. and Bonifer, C. and Mathas, S.
Nature Communications 14 (1): 6947. 7 November 2023

Homozygous loss-of-function variants in FILIP1 cause autosomal recessive arthrogryposis multiplex congenita with microcephaly.
Schnabel, F. and Schuler, E. and Al-Maawali, A. and Chaurasia, A. and Syrbe, S. and Al-Kindi, A. and Bhavani, G.S. and Shukla, A. and Altmüller, J. and Nürnberg, P. and Banka, S. and Girisha, K.M. and Li, Y. and Wollnik, B. and Yigit, G.
Human Genetics 142 (4): 543-552. April 2023

Disintegration of the NuRD complex in primary human muscle stem cells in critical illness myopathy.
Schneider, J. and Sundaravinayagam, D. and Blume, A. and Marg, A. and Grunwald, S. and Metzler, E. and Escobar, H. and Müthel, S. and Wang, H. and Wollersheim, T. and Weber-Carstens, S. and Akalin, A. and Di Virgilio, M. and Tursun, B. and Spuler, S.
International Journal of Molecular Sciences 24 (3): 2772. 1 February 2023

Treatment of adult ALL patients with third-generation CD19-directed CAR T cells: results of a pivotal trial.
Schubert, M.L. and Schmitt, A. and Hückelhoven-Krauss, A. and Neuber, B. and Kunz, A. and Waldhoff, P. and Vonficht, D. and Yousefian, S. and Jopp-Saile, L. and Wang, L. and Korell, F. and Keib, A. and Michels, B. and Haas, D. and Sauer, T. and Derigs, P. and Kulozik, A. and Kunz, J. and Pavel, P. and Laier, S. and Wuchter, P. and Schmier, J. and Bug, G. and Lang, F. and Gökbuget, N. and Casper, J. and Görner, M. and Finke, J. and Neubauer, A. and Ringhoffer, M. and Wolleschak, D. and Brüggemann, M. and Haas, S. and Ho, A.D. and Müller-Tidow, C. and Dreger, P. and Schmitt, M.
Journal of Hematology & Oncology 16 (1): 79. 22 July 2023

The cytomegalovirus M35 protein directly binds to the interferon-β enhancer and modulates transcription of (Ifnb1) and other IRF3-driven genes.
Schwanke, H. and Gonçalves Magalhães, V. and Schmelz, S. and Wyler, E. and Hennig, T. and Günther, T. and Grundhoff, A. and Dölken, L. and Landthaler, M. and van Ham, M. and Jänsch, L. and Büssow, K. and van den Heuvel, J. and Blankenfeldt, W. and Friedel, C.C. and Erhard, F. and Brinkmann, M.M.
Journal of Virology 97 (6): e0040023. 29 June 2023

The interactive complex between cytomegalovirus kinase vCDK/pUL97 and host factors CDK7-cyclin H determines individual patterns of transcription in infected cells.
Schütz, M. and Cordsmeier, A. and Wangen, C. and Horn, A.H.C. and Wyler, E. and Ensser, A. and Sticht, H. and Marschall, M.
International Journal of Molecular Sciences 24 (24): 17421. 13 December 2023

A circular RNA expressed from the FAT3 locus regulates neural development.
Seeler, S. and Andersen, M.S. and Sztanka-Toth, T. and Rybiczka-Tešulov, M. and van den Munkhof, M.H. and Chang, C.C. and Maimaitili, M. and Venø, M.T. and Hansen, T.B. and Pasterkamp, R.J. and Rybak-Wolf, A. and Denham, M. and Rajewsky, N. and Kristensen, L.S. and Kjems, J.
Molecular Neurobiology 60 (6): 3239–3260. June 2023

Mutant phosphodiesterase 3A protects the kidney from hypertension-induced damage.
Sholokh, A. and Walter, S. and Markó, L. and McMurray, B.J. and Sunaga-Franze, D.Y. and Xu, M. and Zühlke, K. and Russwurm, M. and Bartolomaeus, T.U.P. and Langanki, R. and Qadri, F. and Heuser, A. and Patzak, A. and Forslund, S.K. and Bähring, S. and Borodina, T. and Persson, P.B. and Maass, P.G. and Bader, M. and Klussmann, E.
Kidney International 104 (2): 388-393. August 2023

Systematic perturbation of chromatin factors identifies regulatory networks during healthy and malignant hematopoiesis.
Solé-Boldo, L. and Haas, S.
Nature Genetics 55 (9): 1430-1431. September 2023

CYCLeR - a novel tool for the full isoform assembly and quantification of circRNAs.
Stefanov, S.R. and Meyer, I.M.
Nucleic Acids Research 51 (2): e10. 25 January 2023

SMITH: spatially constrained stochastic model for simulation of intra-tumour heterogeneity.
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Bioinformatics 39 (3): btad102. March 2023

Stress-induced nuclear speckle reorganization is linked to activation of immediate early gene splicing.
Sung, H.M. and Schott, J. and Boss, P. and Lehmann, J.A. and Hardt, M.R. and Lindner, D. and Messens, J. and Bogeski, I. and Ohler, U. and Stoecklin, G.
Journal of Cell Biology 222 (12): e202111151. 4 December 2023

Genome architecture mapping detects transcriptionally active, multiway chromatin contacts.
Thieme, C.J. and Pombo, A.
Nature Methods 20 (7): 993-994. July 2023

Long-read sequencing identifies a common transposition haplotype predisposing for CLCNKB deletions.
Tschernoster, N. and Erger, F. and Kohl, S. and Reusch, B. and Wenzel, A. and Walsh, S. and Thiele, H. and Becker, C. and Franitza, M. and Bartram, M.P. and Kömhoff, M. and Schumacher, L. and Kukat, C. and Borodina, T. and Quedenau, C. and Nürnberg, P. and Rinschen, M.M. and Driller, J.H. and Pedersen, B.P. and Schlingmann, K.P. and Hüttel, B. and Bockenhauer, D. and Beck, B. and Altmüller, J.
Genome Medicine 15 (1): 62. 23 August 2023

e-RNA: a collection of web-servers for the prediction and visualisation of RNA secondary structure and their functional features.
Tsybulskyi, V. and Semenchenko, E. and Meyer, I.M.
Nucleic Acids Research 51 (W1): W160-W167. 5 July 2023

Efficient generation of a self-organizing neuromuscular junction model from human pluripotent stem cells.
Urzi, A. and Lahmann, I. and Nguyen, L.V.N. and Rost, B.R. and García-Pérez, A. and Lelievre, N. and Merritt-Garza, M.E. and Phan, H.C and Bassell, G.J. and Rossoll, W. and Diecke, S. and Kunz, S. and Schmitz, D. and Gouti, M.
Nature Communications 14 (1): 8043. 19 December 2023

A local subset of mesenchymal cells expressing the transcription factor Osr1 orchestrates lymph node initiation.
Vallecillo-García, P. and Orgeur, M. and Comai, G. and Poehle-Kronnawitter, S. and Fischer, C. and Gloger, M. and Dumas, C.E. and Giesecke-Thiel, C. and Sauer, S. and Tajbakhsh, S. and Höpken, U.E. and Stricker, S.
Immunity 56 (6): 1204-1219. 13 June 2023

Clonally expanded PD-1-expressing T cells are enriched in synovial fluid of juvenile idiopathic arthritis patients.
Vanni, A. and Mazzoni, A. and Semeraro, R. and Capone, M. and Maschmeyer, P. and Lamacchia, G. and Salvati, L. and Carnasciali, A. and Farahvachi, P. and Giani, T. and Simonini, G. and Filocamo, G. and Romano, M. and Liotta, F. and Mashreghi, M.F. and Cosmi, L. and Cimaz, R. and Magi, A. and Maggi, L. and Annunziato, F.
European Journal of Immunology 53 (7): 2250162. July 2023

Increased mutation and gene conversion within human segmental duplications.
Vollger, M.R. and Dishuck, P.C. and Harvey, W.T. and DeWitt, W.S. and Guitart, X. and Goldberg, M.E. and Rozanski, A.N. and Lucas, J. and Asri, M. and Munson, K.M. and Lewis, A.P. and Hoekzema, K. and Logsdon, G.A. and Porubsky, D. and Paten, B. and Harris, K. and Hsieh, P.H. and Eichler, E.E.
Nature 617 (7960): 325-334. 11 May 2023

Integrating genetics with single-cell multiomic measurements across disease states identifies mechanisms of beta cell dysfunction in type 2 diabetes.
Wang, G. and Chiou, J. and Zeng, C. and Miller, M. and Matta, I. and Han, J.Y. and Kadakia, N. and Okino, M.L. and Beebe, E. and Mallick, M. and Camunas-Soler, J. and Dos Santos, T. and Dai, X.Q. and Ellis, C. and Hang, Y. and Kim, S.K. and MacDonald, P.E. and Kandeel, F.R. and Preissl, S. and Gaulton, K.J. and Sander, M.
Nature Genetics 55 (6): 984-994. June 2023

Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity.
Watkins, T.B.K. and Colliver, E.C. and Huska, M.R. and Kaufmann, T.L. and Lim, E.L. and Duncan, C.B. and Haase, K. and Van Loo, P. and Swanton, C. and McGranahan, N. and Schwarz, R.F.
PLoS Computational Biology 19 (10): e1011379. 23 October 2023

Protocol of the Berlin Long-term Observation of Vascular Events (BeLOVE): a prospective cohort study with deep phenotyping and long-term follow up of cardiovascular high-risk patients.
Weber, J.E. and Ahmadi, M. and Boldt, L.H. and Eckardt, K.U. and Edelmann, F. and Gerhardt, H. and Grittner, U. and Haubold, K. and Hübner, N. and Kollmus-Heege, J. and Landmesser, U. and Leistner, D.M. and Mai, K. and Müller, D.N. and Nolte, C.H. and Pieske, B. and Piper, S.K. and Rattan, S. and Rauch, G. and Schmidt, S. and Schmidt-Ott, K.M. and Schönrath, K. and Schulz-Menger, J. and Schweizerhof, O. and Siegerink, B. and Spranger, J. and Ramachandran, V.S. and Witzenrath, M. and Endres, M. and Pischon, T.
BMJ Open 13 (10): e076415. 31 October 2023

Dynamic antagonism between key repressive pathways maintains the placental epigenome.
Weigert, R. and Hetzel, S. and Bailly, N. and Haggerty, C. and Ilik, I.A. and Yung, P.Y.K. and Navarro, C. and Bolondi, A. and Kumar, A.S. and Anania, C. and Brändl, B. and Meierhofer, D. and Lupianez, D.G. and Müller, F.J. and Aktas, T. and Elsässer, S.J. and Kretzmer, H. and Smith, Z.D. and Meissner, A.
Nature Cell Biology 25 : 579–591. April 2023

Heat in Germany: Health risks and preventive measures.
Winklmayr, C. and Matthies-Wiesler, F. and Muthers, S. and Buchien, S. and Kuch, B. and An der Heiden, M. and Mücke, H.G.
Journal of health monitoring 8 (S4): 3-32. 6 September 2023

Prävention von Infektionskrankheiten mit Abwasser [Prevention of Infectious Diseases with Wastewater].
Wyler, E. and Landthaler, M.
Arbeitsmedizin Sozialmedizin Umweltmedizin 58 (6): 381-384. June 2023

Mechanisms of enhancer function in neuronal systems in health and disease.
Zea Redondo, L. and Pombo, A.
Current Opinion in Systems Biology 32-33 : 100443. March 2023

Altered and allele-specific open chromatin landscape reveals epigenetic and genetic regulators of innate immunity in COVID-19.
Zhang, B. and Zhang, Z. and Koeken, V.A.C.M. and Kumar, S. and Aillaud, M. and Tsay, H.C. and Liu, Z. and Kraft, A.R.M. and Soon, C.F. and Odak, I. and Bošnjak, B. and Vlot, A. and Swertz, M.A. and Ohler, U. and Geffers, R. and Illig, T. and Huehn, J. and Saliba, A.E. and Sander, L.E. and Förster, R. and Xu, C.J. and Cornberg, M. and Schulte, L.N. and Li, Y.
Cell Genomics 3 (2): 100232. 8 February 2023

Ablation of collagen XII disturbs joint extracellular matrix organization and causes patellar subluxation.
Zhu, M. and Metzen, F. and Hopkinson, M. and Betz, J. and Heilig, J. and Sodhi, J. and Imhof, T. and Niehoff, A. and Birk, D.E. and Izu, Y. and Krüger, M. and Pitsillides, A. A. and Altmüller, J. and van Osch, G.J.V.M. and Straub, V. and Schreiber, G. and Paulsson, M. and Koch, M. and Brachvogel, B.
iScience 26 (7): 107225. 21 July 2023

Prioritization of non-coding elements involved in non-syndromic cleft lip with/without cleft palate through genome-wide analysis of de novo mutations.
Zieger, H.K. and Weinhold, L. and Schmidt, A. and Holtgrewe, M. and Juranek, S.A. and Siewert, A. and Scheer, A.B. and Thieme, F. and Mangold, E. and Ishorst, N. and Brand, F.U. and Welzenbach, J. and Beule, D. and Paeschke, K. and Krawitz, P.M. and Ludwig, K.U.
Human Genetics and Genomics Advances 4 (1): 100166. 12 January 2023

The phenotypic and genotypic spectrum of epilepsy and intellectual disability in adults: Implications for genetic testing.
von Brauchitsch, S. and Haslinger, D. and Lindlar, S. and Thiele, H. and Bernsen, N. and Zahnert, F. and Reif, P.S. and Balcik, Y. and Au, P.Y.B. and Josephson, C. and Altmüller, J. and Strzelczyk, A. and Knake, S. and Rosenow, F. and Chiocchetti, A. and Klein, K.M.
Epilepsia Open 8 (2): 497-508. June 2023

Biliary microbial patterns in primary sclerosing cholangitis are linked to poorer transplant-free survival.
Özdirik, B. and Scherf, M. and Brumercek, A. and Nicklaus, J.M. and Kruis, T. and Haber, P.K. and Pratschke, J. and Tacke, F. and Sigal, M.
Hepatology Communications 7 (6): e0156. June 2023

2022

Determinants of expression of SARS-CoV-2 entry related genes in upper and lower airways.
Aliee, H. and Massip, F. and Qi, C. and de Biase, M.S. and van Nijnatten, J. and Kersten, E.T.G. and Kermani, N.Z. and Khuder, B. and Vonk, J.M. and Vermeulen, R.C.H. and Neighbors, M. and Tew, G.W. and Grimbaldeston, M.A. and Ten Hacken, N.H.T. and Hu, S. and Guo, Y. and Zhang, X. and Sun, K. and Hiemstra, P.S. and Ponder, B.A. and Mäkelä, M.J. and Malmström, K. and Rintoul, R.C. and Reyfman, P.A. and Theis, F.J. and Brandsma, C.A. and Adcock, I.M. and Timens, W. and Xu, C.J. and van den Berge, M. and Schwarz, R.F. and Koppelman, G.H. and Nawijn, M.C. and Faiz, A.
Allergy 77 (2): 690-694. February 2022

In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation.
Anania, C. and Acemel, R.D. and Jedamzick, J. and Bolondi, A. and Cova, G. and Brieske, N. and Kühn, R. and Wittler, L. and Real, F.M. and Lupiáñez, D.G.
Nature Genetics July 2022

The role of respiratory microbiota in the protection against viral diseases: respiratory commensal bacteria as next-generation probiotics for COVID-19.
Andrade, B.G.N. and Cuadrat, R.R.C. and Tonetti, F.R. and Kitazawa, H. and Villena, J.
Bioscience of Microbiota, Food and Health 41 (3): 94-102. 1 July 2022

De novo whole genome assembly of the Roborovski dwarf hamster (Phodopus roborovskii) genome, an animal model for severe/critical COVID-19.
Andreotti, S. and Altmüller, J. and Quedenau, C. and Borodina, T. and Nouailles, G. and Teixeira Alves, L.G. and Landthaler, M. and Bieniara, M. and Trimpert, J. and Wyler, E.
Genome Biology and Evolution 14 (7): evac100. July 2022

Integrative analysis of macrophage ribo-Seq and RNA-Seq data define glucocorticoid receptor regulated inflammatory response genes into distinct regulatory classes.
Ansari, S.A. and Dantoft, W. and Ruiz-Orera, J. and Syed, A.P. and Blachut, S. and van Heesch, S. and Hübner, N. and Uhlenhaut, N.H.
Computational and Structural Biotechnology Journal 20 : 5622-5638. 3 October 2022

The SPOC domain is a phosphoserine binding module that bridges transcription machinery with co- and post-transcriptional regulators.
Appel, L.M. and Grishkovskaya, I. and Benedum, J. and Franke, V. and Polyansky, A. and Neudolt, A. and Wunder, A. and Zagrovic, B. and Akalin, A. and Djinovic-Carugo, K. and Slade, D.
bioRxiv : 2022.02.26.482114. 27 February 2022

LABKIT: labeling and segmentation toolkit for big image data.
Arzt, M. and Deschamps, J. and Schmied, C. and Pietzsch, T. and Schmidt, D. and Tomancak, P. and Haase, R. and Jug, F.
Frontiers in Computer Science 4 : 777728. 10 February 2022

De novo variants of CSNK2B cause a new intellectual disability-craniodigital syndrome by disrupting the canonical Wnt signaling pathway.
Asif, M. and Kaygusuz, E. and Shinawi, M. and Nickelsen, A. and Hsieh, T.C. and Wagle, P. and Budde, B. and Hochscherf, J. and Abdullah, U. and Höning, S. and Nienberg, C. and Lindenblatt, D. and Noegel, A.A. and Altmüller, J. and Thiele, H. and Motameny, S. and Fleischer, N. and Segal, I. and Pais, L. and Tinschert, S. and Samra, N.G. and Savatt, J.M. and Rudy, N.L. and De Luca, C. and Fortugno, P. and White, S.M. and Krawitz, P. and Hurst, A.C.E. and Niefind, K. and Jose, J. and Brancati, F. and Nürnberg, P. and Hussain, M.S.
Human Genetics and Genomics Advances 3 (3): 100111. 14 July 2022

A novel missense variant of SCN4A co-segregates with congenital essential tremor in a consanguineous Kurdish family.
Asif, M. and Mocanu, I.D. and Abdullah, U. and Höhne, W. and Altmüller, J. and Makhdoom, E.U.H. and Thiele, H. and Baig, S.M. and Nürnberg, P. and Graul-Neumann, L. and Hussain, M.S.
American Journal of Medical Genetics A 188 (4): 1251-1258. April 2022

Ablation of lysophosphatidic acid receptor 1 attenuates hypertrophic cardiomyopathy in a mouse model.
Axelsson Raja, A. and Wakimoto, H. and DeLaughter, D.M. and Reichart, D. and Gorham, J. and Conner, D.A. and Lun, M. and Probst, C.K. and Sakai, N. and Knipe, R.S. and Montesi, S.B. and Shea, B. and Adam, L.P. and Leinwand, L.A. and Wan, W. and Choi, E.S. and Lindberg, E.L. and Patone, G. and Noseda, M. and Hübner, N. and Seidman, C.E. and Tager, A.M. and Seidman, J.G. and Ho, C.Y.
Proceedings of the National Academy of Sciences of the United States of America 119 (28): e2204174119. 12 July 2022

RS-FISH: precise, interactive, fast, and scalable FISH spot detection.
Bahry, E. and Breimann, L. and Zouinkhi, M. and Epstein, L. and Kolyvanov, K. and Mamrak, N. and King, B. and Long, Xi and Harrington, K.I.S. and Lionnet, T. and Preibisch, S.
Nature Methods 19 (12): 1563-1567. December 2022

Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.
Baranasic, D. and Hörtenhuber, M. and Balwierz, P.J. and Zehnder, T. and Mukarram, A.K. and Nepal, C. and Várnai, C. and Hadzhiev, Y. and Jimenez-Gonzalez, A. and Li, N. and Wragg, J. and D'Orazio, F.M. and Relic, D. and Pachkov, M. and Díaz, N. and Hernández-Rodríguez, B. and Chen, Z. and Stoiber, M. and Dong, M. and Stevens, I. and Ross, S.E. and Eagle, A. and Martin, R. and Obasaju, O. and Rastegar, S. and McGarvey, A.C. and Kopp, W. and Chambers, E. and Wang, D. and Kim, H.R. and Acemel, R.D. and Naranjo, S. and Łapiński, M. and Chong, V. and Mathavan, S. and Peers, B. and Sauka-Spengler, T. and Vingron, M. and Carninci, P. and Ohler, U. and Lacadie, S.A. and Burgess, S.M. and Winata, C. and van Eeden, F. and Vaquerizas, J.M. and Gómez-Skarmeta, J.L. and Onichtchouk, D. and Brown, B.J. and Bogdanovic, O. and van Nimwegen, E. and Westerfield, M. and Wardle, F.C and Daub, C.O. and Lenhard, B. and Müller, F.
Nature Genetics 54 (7): 1037-1050. July 2022

Multi-omics alleviates the limitations of panel sequencing for cancer drug response prediction.
Baranovskii, A. and Gündüz, I.B. and Franke, V. and Uyar, B. and Akalin, A.
Cancers 14 (22): 5604. 15 November 2022

Transcriptome analysis reveals high tumor heterogeneity with respect to re-activation of stemness and proliferation programs.
Baranovsky, A. and Ivanov, T. and Granovskaya, M. and Papatsenko, D. and Pervouchine, D.D.
PLoS ONE 17 (5): e0268626. 19 May 2022

PyZebraScope: an open-source platform for brain-wide neural activity imaging in zebrafish.
Barbara, R. and Nagathihalli Kantharaju, M. and Haruvi, R. and Harrington, K. and Kawashima, T.
Frontiers in Cell and Developmental Biology 10 : 875044. 19 May 2022

PyZebraScope: an open-source platform for brain-wide neural activity imaging in zebrafish.
Barbara, R. and Nagathihalli Kantharaju, M. and Haruvi, R. and Harrington, K. and Kawashima, T.
bioRxiv : bioRxiv. 15 February 2022

State-of-the-art analytical methods of viral infections in human lung organoids.
Baumgardt, M. and Hülsemann, M. and Löwa, A. and Fatykhova, D. and Hoffmann, K. and Kessler, M. and Mieth, M. and Hellwig, K. and Frey, D. and Langenhagen, A. and Voss, A. and Obermayer, B. and Wyler, E. and Dökel, S. and Gruber, A.D. and Tölch, U. and Hippenstiel, S. and Hocke, A.C. and Hönzke, K.
PLoS ONE 17 (12): e0276115. 20 December 2022

Investigating the role of GLUL as a survival factor in cellular adaptation to glutamine depletion via targeted stable isotope resolved metabolomics.
Bayram, S. and Razzaque, Y.S. and Geisberger, S. and Pietzke, M. and Fürst, S. and Vechiatto, C. and Forbes, M. and Mastrobuoni, G. and Kempa, S.
Frontiers in Molecular Biosciences 9 : 859787. 12 August 2022

SUMOylation of the chromodomain factor MRG-1 in C. elegans affects chromatin-regulatory dynamics.
Baytek, G. and Blume, A. and Demirel, F.G. and Bulut, S. and Popp, O. and Mertins, P. and Tursun, B.
Biotechniques 73 (1): 5-17. June 2022

Robust co-immunoprecipitation with mass spectrometry for Caenorhabditis elegans using solid-phase enhanced sample preparation.
Baytek, G. and Popp, O. and Mertins, P. and Tursun, B.
Biotechniques 72 (5): 175-184. May 2022

Sox2 levels regulate the chromatin occupancy of WNT mediators in epiblast progenitors responsible for vertebrate body formation.
Blassberg, R. and Patel, H. and Watson, T. and Gouti, M. and Metzis, V. and Delás, M.J. and Briscoe, J.
Nature Cell Biology 24 (5): 633-644. May 2022

SLM2 is a novel cardiac splicing factor involved in heart failure due to dilated cardiomyopathy.
Boeckel, J.N. and Möbius-Winkler, M. and Müller, M. and Rebs, S. and Eger, N. and Schoppe, L. and Tappu, R. and Kokot, K.E. and Kneuer, J.M. and Gaul, S. and Bordalo, D.M. and Lai, A. and Haas, J. and Ghanbari, M. and Drewe-Boss, P. and Liss, M. and Katus, H.A. and Ohler, U. and Gotthardt, M. and Laufs, U. and Streckfuss-Bömeke, K. and Meder, B.
Genomics Proteomics & Bioinformatics 20 (1): 129-146. February 2022

Inflammatory exposure drives long-lived impairment of hematopoietic stem cell self-renewal activity and accelerated aging.
Bogeska, R. and Mikecin, A.M. and Kaschutnig, P. and Fawaz, M. and Büchler-Schäff, M. and Le, D. and Ganuza, M. and Vollmer, A. and Paffenholz, S.V. and Asada, N. and Rodriguez-Correa, E. and Frauhammer, F. and Buettner, F. and Ball, M. and Knoch, J. and Stäble, S. and Walter, D. and Petri, A. and Carreño-Gonzalez, M.J. and Wagner, V. and Brors, B. and Haas, S. and Lipka, D.B. and Essers, M.A.G. and Weru, V. and Holland-Letz, T. and Mallm, J.P. and Rippe, K. and Krämer, S. and Schlesner, M. and McKinney Freeman, S. and Florian, M.C. and King, K.Y. and Frenette, P.S. and Rieger, M.A. and Milsom, M.D.
Cell Stem Cell 29 (8): 1273-1284. 4 August 2022

Full-length spatial transcriptomics reveals the unexplored isoform diversity of the myocardium post-MI.
Boileau, E. and Li, X. and Naarmann-de Vries, I.S. and Becker, C. and Casper, R. and Altmüller, J. and Leuschner, F. and Dieterich, C.
Frontiers in Genetics 13 : 912572. 22 July 2022

pTINCR microprotein promotes epithelial differentiation and suppresses tumor growth through CDC42 SUMOylation and activation.
Boix, O. and Martinez, M. and Vidal, S. and Giménez-Alejandre, M. and Palenzuela, L. and Lorenzo-Sanz, L. and Quevedo, L. and Moscoso, O. and Ruiz-Orera, J. and Ximénez-Embún, P. and Ciriaco, N. and Nuciforo, P. and Stephan-Otto Attolini, C. and Albà, M.M. and Muñoz, J. and Tian, T.V. and Varela, I. and Vivancos, A. and Ramón Y Cajal, S. and Muñoz, P. and Rivas, C. and Abad, M.
Nature Communications 13 (1): 6840. 11 November 2022

Claudin-10a deficiency shifts proximal tubular Cl(-) permeability to cation selectivity via claudin-2 redistribution.
Breiderhoff, T. and Himmerkus, N. and Meoli, L. and Fromm, A. and Sewerin, S. and Kriuchkova, N. and Nagel, O. and Ladilov, Y. and Krug, S. and Quintanova, C. and Stumpp, M. and Garbe-Schönberg, D. and Westernströer, U. and Merkel, C. and Brinkhus, M. and Altmüller, J. and Schweiger, M. and Mueller, D. and Mutig, K. and Morawski, M. and Halbritter, J. and Milatz, S. and Bleich, M. and Günzel, D.
Journal of the American Society of Nephrology 33 (4): 699-717. April 2022

The histone H4 lysine 20 demethylase DPY-21 regulates the dynamics of condensin DC binding.
Breimann, L. and Morao, A.K. and Kim, J. and Jimenez, D.S. and Maryn, N. and Bikkasani, K. and Carrozza, M.J. and Albritton, S.E. and Kramer, M. and Street, L.A. and Cerimi, K. and Schumann, V.F. and Bahry, E. and Preibisch, S. and Woehler, A. and Ercan, S.
Journal of Cell Science 135 (2): jcs258818. January 2022

Optimization of synthetic molecular reporters for a mesenchymal glioblastoma transcriptional program by integer programming.
Breitenbach, T. and Schmitt, M.J. and Dandekar, T.
Bioinformatics 38 (17): 4162-4171. 1 September 2022

Nanozyme-catalysed CRISPR assay for preamplification-free detection of non-coding RNAs.
Broto, M. and Kaminski, M.M. and Adrianus, C. and Kim, N. and Greensmith, R. and Dissanayake-Perera, S. and Schubert, A.J. and Tan, X. and Kim, H. and Dighe, A.S. and Collins, J.J. and Stevens, M.M.
Nature Nanotechnology 17 (10): 1120-1126. October 2022

The key features of SARS-CoV-2 leader and NSP1 required for viral escape of NSP1-mediated repression.
Bujanic, L. and Shevchuk, O. and von Kügelgen, N. and Kalinina, A. and Ludwik, K. and Koppstein, D. and Zerna, N. and Sickmann, A. and Chekulaeva, M.
RNA 28 (5): 766-779. May 2022

WARS1 and SARS1: two tRNA synthetases implicated in autosomal recessive microcephaly.
Bögershausen, N. and Krawczyk, H.E. and Jamra, R.A. and Lin, S.J. and Yigit, G. and Hüning, I. and Polo, A.M. and Vona, B. and Huang, K. and Schmidt, J. and Altmüller, J. and Luppe, J. and Platzer, K. and Dörgeloh, B.B. and Busche, A. and Biskup, S. and Mendes, M.I. and Smith, D.E.C. and Salomons, G.S. and Zibat, A. and Bültmann, E. and Nürnberg, P. and Spielmann, M. and Lemke, J.R. and Li, Y. and Zenker, M. and Varshney, G.K. and Hillen, H.S. and Kratz, C.P. and Wollnik, B.
Human Mutation 43 (10): 1454-1471. October 2022

Organoids as tools for fundamental discovery and translation - a Keystone Symposia report.
Cable, J. and Lutolf, M.P. and Fu, J. and Park, S.E. and Apostolou, A. and Chen, S. and Song, C.J. and Spence, J.R. and Liberali, P. and Lancaster, M. and Meier, A.B. and Pek, N.M.Q. and Wells, J.M. and Capeling, M.M. and Uzquiano, A. and Musah, S. and Huch, M. and Gouti, M. and Hombrink, P. and Quadrato, G. and Urenda, J.P.
Annals of the New York Academy of Sciences 1518 (1): 196-208. December 2022

Physical mechanisms of chromatin spatial organization.
Chiariello, A.M. and Bianco, S. and Esposito, A. and Fiorillo, L. and Conte, M. and Irani, E. and Musella, F. and Abraham, A. and Prisco, A. and Nicodemi, M.
FEBS Journal 289 (5): 1180-1190. March 2022

A high-resolution map of human RNA translation.
Chothani, S.P. and Adami, E. and Widjaja, A.A. and Langley, S.R. and Viswanathan, S. and Pua, C.J. and Zhihao, N.T. and Harmston, N. and D'Agostino, G. and Whiffin, N. and Mao, W. and Ouyang, J.F. and Lim, W.W. and Lim, S. and Lee, C.Q.E. and Grubman, A. and Chen, J. and Kovalik, J.P. and Tryggvason, K. and Polo, J.M. and Ho, L. and Cook, S.A. and Rackham, O.J.L. and Schafer, S.
Molecular Cell 82 (15): 2885-2899.e8. 4 August 2022

A novel complex genomic rearrangement affecting the KCNJ2 regulatory region causes a variant of Cooks syndrome.
Cinque, L. and Micale, L. and Manara, E. and Esposito, A. and Palumbo, O. and Chiariello, A.M. and Bianco, S. and Guerri, G. and Bertelli, M. and Giuffrida, M.G. and Bernardini, L. and Notarangelo, A. and Nicodemi, M. and Castori, M.
Human Genetics 141 (2): 217-227. February 2022

Single cell‐ and spatial 'omics revolutionize physiology.
Conrad, T. and Altmüller, J.
Acta Physiologica : e13848. 2 June 2022

Polymer models of chromatin imaging data in single cells.
Conte, M. and Chiariello, A.M. and Abraham, A. and Bianco, S. and Esposito, A. and Nicodemi, M. and Matteuzzi, T. and Vercellone, F.
Algorithms 15 (9): 330. 16 September 2022

A polymer physics model to dissect genome organization in healthy and pathological phenotypes.
Conte, M. and Fiorillo, L. and Bianco, S. and Chiariello, A.M. and Esposito, A. and Musella, F. and Flora, F. and Abraham, A. and Nicodemi, M.
Methods in Molecular Biology 2301 : 307-316. 2022

Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding.
Conte, M. and Irani, E. and Chiariello, A.M. and Abraham, A. and Bianco, S. and Esposito, A. and Nicodemi, M.
Nature Communications 13 (1): 4070. 13 July 2022

Combining callers improves the detection of copy number variants from whole-genome sequencing.
Coutelier, M. and Holtgrewe, M. and Jäger, M. and Flöttman, R. and Mensah, M.A. and Spielmann, M. and Krawitz, P. and Horn, D. and Beule, D. and Mundlos, S.
European Journal of Human Genetics 30 (2): 178-186. February 2022

Cap analysis of gene expression reveals alternative promoter usage in a rat model of hypertension.
Dahale, S. and Ruiz-Orera, J. and Silhavy, J. and Hübner, N. and van Heesch, S. and Pravenec, M. and Atanur, S.S.
Life Science Alliance 5 (4): e202101234. April 2022

Global analysis of human-to-mouse contact-dependent intercellular mRNA and lncRNA transfer in cell culture.
Dasgupta, Sandipan and Dyagi, Daniella Y. and Haimovich, Gal and Wyler, E. and Olender, Tsviya and Singer, Robert H. and Landthaler, M. and Gerst, Jeffrey E
bioRxiv : 2021.11.28.470233v2. 7 March 2022

Activated SUMOylation restricts MHC class I antigen presentation to confer immune evasion in cancer.
Demel, U.M. and Böger, M. and Yousefian, S. and Grunert, C. and Zhang, L. and Hotz, P.W. and Gottschlich, A. and Köse, H. and Isaakidis, K. and Vonficht, D. and Grünschläger, F. and Rohleder, E. and Wagner, K. and Dönig, J. and Igl, V. and Brzezicha, B. and Baumgartner, F. and Habringer, S. and Löber, J. and Chapuy, B. and Weidinger, C. and Kobold, S. and Haas, S. and Busse, A.B. and Müller, S. and Wirth, M. and Schick, M. and Keller, U.
Journal of Clinical Investigation 132 (9): e152383. 2 May 2022

A complex proinflammatory cascade mediates the activation of HSCs upon LPS exposure in vivo.
Demel, U.M. and Lutz, R. and Sujer, S. and Demerdash, Y. and Sood, S. and Grünschläger, F. and Kuck, A. and Werner, P. and Blaszkiewicz, S. and Uckelmann, H.J. and Haas, S. and Essers, M.
Blood Advances 6 (11): 3513-3528. 10 June 2022

Molecular identity of proprioceptor subtypes innervating different muscle groups in mice.
Dietrich, S. and Company, C. and Song, K. and Lowenstein, E.D. and Riedel, L. and Birchmeier, C. and Gargiulo, G. and Zampieri, N.
Nature Communications 13 (1): 6867. 11 November 2022

Hmga2 protein loss alters nuclear envelope and 3D chromatin structure.
Divisato, G. and Chiariello, A.M. and Esposito, A. and Zoppoli, P. and Zambelli, F. and Elia, M.A. and Pesole, G. and Incarnato, D. and Passaro, F. and Piscitelli, S. and Oliviero, S. and Nicodemi, M. and Parisi, S. and Russo, T.
BMC Biology 20 (1): 171. 2 August 2022

Identifying tumor cells at the single-cell level using machine learning.
Dohmen, J. and Baranovskii, A. and Ronen, J. and Uyar, B. and Franke, V. and Akalin, A.
Genome Biology 23 (1): 123. 30 May 2022

Deep learning for prediction of population health costs.
Drewe-Boss, P. and Enders, D. and Walker, J. and Ohler, U.
BMC Medical Informatics and Decision Making 22 (1): 32. 3 February 2022

C/EBPβ regulates lipid metabolism and Pparg isoform 2 expression in alveolar macrophages.
Dörr, D. and Obermayer, B. and Weiner, J.M. and Zimmermann, K. and Anania, C. and Wagner, L.K. and Lyras, E.M. and Sapozhnikova, V. and Lara-Astiaso, D. and Prósper, F. and Lang, R. and Lupiáñez, D.G. and Beule, D. and Höpken, U.E. and Leutz, A. and Mildner, A.
Science Immunology 7 (75): eabj0140. September 2022

Vaccine-associated enhanced respiratory pathology in COVID-19 hamsters after T(H)2-biased immunization.
Ebenig, A. and Muraleedharan, S. and Kazmierski, J. and Todt, D. and Auste, A. and Anzaghe, M. and Gömer, A. and Postmus, D. and Gogesch, P. and Niles, M. and Plesker, R. and Miskey, C. and Gellhorn Serra, M. and Breithaupt, A. and Hörner, C. and Kruip, C. and Ehmann, R. and Ivics, Z. and Waibler, Z. and Pfaender, S. and Wyler, E. and Landthaler, M. and Kupke, A. and Nouailles, G. and Goffinet, C. and Brown, R.J.P and Mühlebach, M.D.
Cell Reports 40 (7): 111214. 16 August 2022

Mutant phosphodiesterase 3A protects from hypertension-induced cardiac damage.
Ercu, M. and Mücke, M.B. and Pallien, T. and Markó, L. and Sholokh, A. and Schächterle, C. and Aydin, A. and Kidd, A. and Walter, S. and Esmati, Y. and McMurray, B.J. and Lato, D.F. and Sunaga-Franze, D.Y. and Dierks, P.H. and Flores, B.I.M. and Walker-Gray, R. and Gong, M. and Merticariu, C. and Zühlke, K. and Russwurm, M. and Liu, T. and Batolomaeus, T.U.P. and Pautz, S. and Schelenz, S. and Taube, M. and Napieczynska, H. and Heuser, A. and Eichhorst, J. and Lehmann, M. and Miller, D.C. and Diecke, S. and Qadri, F. and Popova, E. and Langanki, R. and Movsesian, M.A. and Herberg, F.W. and Forslund, S.K. and Müller, D.N. and Borodina, T. and Maass, P.G. and Bähring, S. and Hübner, N. and Bader, M. and Klussmann, E.
Circulation 146 (23): 1758-1778. 6 December 2022

The physics of DNA folding: polymer models and phase-separation.
Esposito, A. and Abraham, A. and Conte, M. and Vercellone, F. and Prisco, A. and Bianco, S. and Chiariello, A.M.
Polymers 14 (9): 1918. 9 May 2022

Polymer physics reveals a combinatorial code linking 3D chromatin architecture to 1D chromatin states.
Esposito, A. and Bianco, S. and Chiariello, A.M. and Abraham, A. and Fiorillo, L. and Conte, M. and Campanile, R. and Nicodemi, M.
Cell Reports 38 (13): 110601. 29 March 2022

Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in severe COVID-19.
Essex, M. and Pascual-Leone, B.M. and Löber, U. and Kuhring, M. and Zhang, B. and Bruening, U. and Fritsche-Guenther, R. and Krzanowski, M. and Vernengo, F.F. and Brumhard, S. and Röwekamp, I. and Bielecka, A.A. and Lesker, T.R. and Wyler, E. and Landthaler, M. and Mantei, A. and Meisel, C. and Caesar, S. and Thiebeault, C. and Corman, V. and Marko, L. and Suttorp, N. and Strowig, T. and Kurth, F. and Sander, L.E. and Li, Y. and Kirwan, J.A. and Forslund, S.K. and Opitz, B.
bioRxiv : 2022.12.02.518860. 2 December 2022

Development of a machine learning approach for local-scale ozone forecasting: application to Kennewick, WA.
Fan, K. and Dhammapala, R. and Harrington, K. and Lamastro, R. and Lamb, B. and Lee, Y.
Frontiers in Big Data 5 : 781309. 10 February 2022

Assessing evolutionary and developmental transcriptome dynamics in homologous cell types.
Feregrino, C. and Tschopp, P.
Developmental Dynamics 251 (9): 1472-1489. September 2022

R-spondin-YAP axis promotes gastric oxyntic gland regeneration and Helicobacter pylori-associated metaplasia in mice.
Fischer, A.S. and Müllerke, S. and Arnold, A. and Heuberger, J. and Berger, H. and Lin, M. and Mollenkopf, H.J. and Wizenty, J. and Horst, D. and Tacke, F. and Sigal, M.
Journal of Clinical Investigation 132 (21): e151363. 1 November 2022

Single-cell profiling of proteins and chromatin accessibility using PHAGE-ATAC.
Fiskin, E. and Lareau, C.A. and Ludwig, L.S. and Eraslan, G. and Liu, F. and Ring, A.M. and Xavier, R.J. and Regev, A.
Nature Biotechnology 40 (3): 374-381. March 2022

Diverse but unique astrocytic phenotypes during embryonic stem cell differentiation, culturing and development.
Freitag, K. and Eede, P. and Ivanov, A. and Schneeberger, S. and Borodina, T. and Sauer, S. and Beule, D. and Heppner, F.
Research Square : rs.3.rs-1362379/v1. 28 February 2022

Spermidine reduces neuroinflammation and soluble amyloid beta in an Alzheimer’s disease mouse model.
Freitag, K. and Sterczyk, N. and Wendlinger, S. and Obermayer, B. and Schulz, J. and Farztdinov, V. and Mülleder, M. and Ralser, M. and Houtman, J. and Fleck, L. and Braeuning, C. and Sansevrino, R. and Hoffmann, C. and Milovanovic, D. and Sigrist, S.J. and Conrad, T. and Beule, D. and Heppner, F.L. and Jendrach, M.
Journal of Neuroinflammation 19 (1): 172. 2 July 2022

The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by repressing pro-differentiation genes.
Garipler, G. and Lu, C. and Morrissey, Al. and Lopez-Zepeda, L.S. and Pei, Y. and Vidal, S.E. and Zen Petisco Fiore, A.P. and Aydin, B. and Stadtfeld, M. and Ohler, U. and Mahony, S. and Sanjana, N.E. and Mazzoni, E.O.
Cell Reports 38 (11): 110524. 15 March 2022

Wie Kochsalz Mitochondrien beeinflusst.
Geisberger, S.
BIOspektrum 28 (4): 387-389. June 2022

Complement activation induces excessive T cell cytotoxicity in severe COVID-19.
Georg, P. and Astaburuaga-García, R. and Bonaguro, L. and Brumhard, S. and Michalick, L. and Lippert, L.J. and Kostevc, T. and Gäbel, C. and Schneider, M. and Streitz, M. and Demichev, V. and Gemünd, I. and Barone, M. and Tober-Lau, P. and Helbig, E.T. and Hillus, D. and Petrov, L. and Stein, J. and Dey, H.P. and Paclik, D. and Iwert, C. and Mülleder, M. and Aulakh, S.K. and Djudjaj, S. and Bülow, R.D. and Mei, H.E. and Schulz, A.R. and Thiel, A. and Hippenstiel, S. and Saliba, A.E. and Eils, R. and Lehmann, I. and Mall, M.A. and Stricker, S. and Röhmel, J. and Corman, V.M. and Beule, D. and Wyler, E. and Landthaler, M. and Obermayer, B. and von Stillfried, S. and Boor, P. and Demir, M. and Wesselmann, H. and Suttorp, N. and Uhrig, A. and Müller-Redetzky, H. and Nattermann, J. and Kuebler, W.M. and Meisel, C. and Ralser, M. and Schultze, J.L. and Aschenbrenner, A.C. and Thibeault, C. and Kurth, F. and Sander, L.E. and Blüthgen, N. and Sawitzki, B.
Cell 185 (3): 493-512. 3 February 2022

Aging-regulated TUG1 is dispensable for endothelial cell function.
Gimbel, A.T. and Koziarek, S. and Theodorou, K. and Schulz, J.F. and Stanicek, L. and Ali, T. and Günther, S. and Kumar, S. and Jo, H. and Hübner, N. and Maegdefessel, L. and Dimmeler, S. and van Heesch, S. and Boon, R.A.
bioRxiv : 2022.02.27.482212. 28 February 2022

Aging-regulated TUG1 is dispensable for endothelial cell function.
Gimbel, A.T. and Koziarek, S. and Theodorou, K. and Schulz, J.F. and Stanicek, L. and Kremer, V. and Ali, T. and Günther, S. and Kumar, S. and Jo, H. and Hübner, N. and Maegdefessel, L. and Dimmeler, S. and van Heesch, S. and Boon, R.A.
PLoS ONE 17 (9): e0265160. 29 September 2022

Rapid inflammasome activation is attenuated in post-myocardial infarction monocytes.
Giral, H. and Franke, V. and Moobed, M. and Müller, M.F. and Lübking, L. and James, D.M. and Hartung, J. and Kuschnerus, K. and Meteva, D. and Seppelt, C. and Jakob, P. and Klingenberg, R. and Kränkel, N. and Leistner, D. and Zeller, T. and Blankenberg, S. and Zimmermann, F. and Haghikia, A. and Lüscher, T.F. and Akalin, A. and Landmesser, U. and Kratzer, A.
Frontiers in Immunology 13 : 857455. 26 April 2022

Deep learning-assisted peak curation for large-scale LC-MS metabolomics.
Gloaguen, Y. and Kirwan, J.A. and Beule, D.
Analytical Chemistry 94 (12): 4930-4937. 29 March 2022

Expression of circ_Satb1 is decreased in mesial temporal lobe epilepsy and regulates dendritic spine morphology.
Gomes-Duarte, A. and Venø, M.T. and de Wit, M. and Senthilkumar, K. and Broekhoven, M.H. and van den Herik, J. and Heeres, F.R. and van Rossum, D. and Rybiczka-Tesulov, M. and Legnini, I. and van Rijen, P.C. and van Eijsden, P. and Gosselaar, P.H. and Rajewsky, N. and Kjems, J. and Vangoor, V.R. and Pasterkamp, R.J.
Frontiers in Molecular Neuroscience 15 : 832133. 3 March 2022

Epigenetic modifier balances Mapk and Wnt signalling in differentiation of goblet and Paneth cells.
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Phenotypic spectrum of BLM- and RMI1-related Bloom syndrome.
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A comparative study of graph matching algorithms in computer vision.
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A critical period of translational control during brain development at codon resolution.
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Antigen presentation safeguards the integrity of the hematopoietic stem cell pool.
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Single-cell transcriptomics reveals common epithelial response patterns in human acute kidney injury.
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Mathematical and bioinformatic tools for cell tracking.
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Tracking by weakly-supervised learning and graph optimization for whole-embryo c. elegans lineages.
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Human alveolar progenitors generate dual lineage bronchioalveolar organoids.
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Inflammation in children with chronic kidney disease linked to gut dysbiosis and metabolite imbalance.
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Integrated genomic surveillance enables tracing of person-to-person SARS-CoV-2 transmission chains during community transmission and reveals extensive onward transmission of travel-imported infections, Germany, June to July 2021.
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Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT.
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Origin and function of activated fibroblast states during zebrafish heart regeneration.
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Once upon a dish: the next frontier in engineering multicellular systems.
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Women in the European Virus Bioinformatics Center.
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Fusion moves for graph matching.
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Human lungs show limited permissiveness for SARS-CoV-2 due to scarce ACE2 levels but virus-induced expansion of inflammatory macrophages.
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Dynamics of bacteria scanning a porous environment.
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Expression of cardiovascular-related microRNAs is altered in L-arginine:glycine amidinotransferase deficient mice.
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Transient activated fibroblasts contribute to zebrafish heart regeneration.
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(RB1)-negative retinal organoids display proliferation of cone photoreceptors and loss of retinal differentiation.
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BMP feed-forward loop promotes terminal differentiation in gastric glands and is interrupted by H. pylori-driven inflammation.
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MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution.
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Nonproductive exposure of PBMCs to SARS‐CoV ‐2 induces cell‐intrinsic innate immune responses.
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Npl3 functions in mRNP assembly by recruitment of mRNP components to the transcription site and their transfer onto the mRNA.
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Urinary single-cell sequencing captures kidney injury and repair processes in human acute kidney injury.
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Association of ultra-rare coding variants with genetic generalized epilepsy: a case-control whole exome sequencing study.
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Regional gene expression patterns are associated with task-specific brain activation during reward and emotion processing measured with functional MRI.
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Identification of novel genes whose expression in adipose tissue affects body fat mass and distribution: an RNA-Seq and Mendelian Randomization study.
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Simultaneous dimensionality reduction and integration for single-cell ATAC-seq data using deep learning.
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Single-cell multi-omics allows functional characterization of structural variants.
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Nature Biotechnology 24 November 2022

Deletion in the Y chromosome of B10.BR-Y(del) mice alters transcription from MSYq genes and has moderate effect on DNA methylation.
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Sox9 is required for nail bed differentiation and digit tip regeneration.
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Editorial: Lineage tracing, hematopoietic stem cell and immune cell dynamics.
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Alport syndrome and autosomal dominant tubulointerstitial kidney disease frequently underlie end stage renal disease of unknown origin - a single center analysis.
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Spatio-temporal, optogenetic control of gene expression in organoids.
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A novel homozygous synonymous variant further expands the phenotypic spectrum of POLR3A-related pathologies.
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American Journal of Medical Genetics A 188 (1): 216-223. January 2022

Store-operated calcium entry controls innate and adaptive immune cell function in inflammatory bowel disease.
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Fly Cell Atlas: a single-nucleus transcriptomic atlas of the adult fruit fly.
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Stem cells, helicobacter pylori and mutational landscape: utility of preclinical models to understand carcinogenesis and to direct management of gastric cancer.
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Gastroenterology 162 (4): 1067-1087. April 2022

Biallelic variants in WARS1 cause a highly variable neurodevelopmental syndrome and implicate a critical exon for normal auditory function.
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Human Mutation 43 (10): 1472-1489. October 2022

Congenital anemia reveals distinct targeting mechanisms for master transcription factor GATA1.
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AntiSplodge: a neural-network-based RNA-profile deconvolution pipeline designed for spatial transcriptomics.
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Tongue immune compartment analysis reveals spatial macrophage heterogeneity.
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Renal deletion of LRRC8/VRAC channels induces proximal tubulopathy.
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SAMHD1 controls innate immunity by regulating condensation of immunogenic self RNA.
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Satellite glia of the adult dorsal root ganglia harbor stem cells that yield glia under physiological conditions and neurons in response to injury.
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In vitro Kinase-to-Phosphosite database (iKiP-DB) predicts kinase activity in phosphoproteomic datasets.
Mari, T. and Mösbauer, K. and Wyler, E. and Landthaler, M. and Drosten, C. and Selbach, M.
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The little skate genome and the evolutionary emergence of wing-like fin appendages.
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Towards reliable quantification of cell state velocities.
Marot-Lassauzaie, V. and Bouman, B.J. and Donaghy, F.D. and Demerdash, Y. and Essers, M.A.G. and Haghverdi, L.
PLoS Computational Biology 18 (9): e1010031. 28 September 2022

ATACing single cells with phages.
Maschmeyer, P. and Haas, S.
Molecular Cell 82 (2): 234-236. 20 January 2022

Despite the odds: formation of the SARS-CoV-2 methylation complex.
Matsuda, A. and Plewka, J. and Chykunova, Y. and Jones, A.N. and Pachota, M. and Rawski, M. and Mourão, A. and Karim, A. and Kresik, L. and Lis, K. and Minia, I. and Hartman, K. and Sonani, R. and Schlauderer, F. and Dubin, G. and Sattler, M. and Suder, P. and Popowicz, G. and Pyrć, K. and Czarna, A.
bioRxiv : 2022.01.25.477673. 1 March 2022

Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in zebrafish embryos.
McGarvey, A.C. and Kopp, W. and Vučićević, D. and Mattonet, K. and Kempfer, R. and Hirsekorn, A. and Bilić, I. and Gil, M. and Trinks, A. and Merks, A.M. and Panáková, D. and Pombo, A. and Akalin, A. and Junker, J.P. and Stainier, D.Y.R. and Garfield, D. and Ohler, U. and Lacadie, S.A.
Cell Genomics 2 (1): 100083. 13 January 2022

Reliable assessment of telomere maintenance mechanisms in neuroblastoma.
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A high-resolution map of small-scale inversions in the gibbon genome.
Mercuri, L. and Palmisano, D. and L'Abbate, A. and D'Addabbo, P. and Montinaro, F. and Catacchio, C.R. and Hasenfeld, P. and Ventura, M. and Korbel, J.O. and Sanders, A.D. and Maggiolini, F.A.M. and Antonacci, F.
Genome Research 32 (10): 1941-1951. October 2022

Generation of hiPSC-derived skeletal muscle cells: exploiting the potential of skeletal muscle-derived hiPSCs.
Metzler, E. and Escobar, H. and Sunaga-Franze, D.Y. and Sauer, S. and Diecke, S. and Spuler, S.
Biomedicines 10 (5): 1204. 23 May 2022

Generation of induced pluripotent stem cells from three individuals with Huntington's disease.
Miller, D.C. and Lisowski, P. and Lickfett, S. and Mlody, B. and Bünning, M. and Genehr, C. and Ulrich, C. and Wanker, E.E. and Diecke, S. and Priller, J. and Prigione, A.
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Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations.
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Nature Biotechnology 40 (7): 1030-1034. 24 February 2022

Identifying interpretable gene-biomarker associations with functionally informed kernel-based tests in 190,000 exomes.
Monti, R. and Rautenstrauch, P. and Ghanbari, M. and James, A.R. and Kirchler, M. and Ohler, U. and Konigorski, S. and Lippert, C.
Nature Communications 13 (1): 5332. 10 September 2022

Identifying interpretable gene-biomarker associations with functionally informed kernel-based tests in 190,000 exomes.
Monti, R. and Rautenstrauch, P. and Ghanbari, M. and James, A.R. and Ohler, U. and Konigorski, S. and Lippert, C.
bioRxiv : 2021.05.27.444972. 20 January 2022

Standardized annotation of translated open reading frames.
Mudge, J.M. and Ruiz-Orera, J. and Prensner, J.R. and Brunet, M.A. and Calvet, F. and Jungreis, I. and Gonzalez, Jo.M. and Magrane, M. and Martinez, T.F. and Schulz, J.F. and Yang, Y.T. and Albà, M.M. and Aspden, J.L. and Baranov, P.V. and Bazzini, A.A. and Bruford, E. and Martin, M.J. and Calviello, L. and Carvunis, A.R. and Chen, J. and Couso, J.P. and Deutsch, E.W. and Flicek, P. and Frankish, A. and Gerstein, M. and Hubner, N. and Ingolia, N.T. and Kellis, M. and Menschaert, G. and Moritz, R.L. and Ohler, U. and Roucou, X. and Saghatelian, A. and Weissman, J.S. and van Heesch, S.
Nature Biotechnology 40 (7): 994–999. July 2022

Candesartan does not activate PPAR(γ) and its target genes in early gestation trophoblasts.
Neuper, L. and Kummer, D. and Forstner, D. and Guettler, J. and Ghaffari-Tabrizi-Wizsy, N. and Fischer, C. and Juch, H. and Nonn, O. and Gauster, M.
International Journal of Molecular Sciences 23 (20): 12326. October 2022

IL11 activates pancreatic stellate cells and causes pancreatic inflammation, fibrosis and atrophy in a mouse model of pancreatitis.
Ng, B. and Viswanathan, S. and Widjaja, A.A. and Lim, W.W. and Shekeran, S.G. and Goh, J.W.T. and Tan, J. and Kuthubudeen, F. and Lim, S.Y. and Xie, C. and Schafer, S. and Adami, E. and Cook, S.A.
International Journal of Molecular Sciences 23 (7): 3549. 24 March 2022

Best practice standards for circular RNA research.
Nielsen, A.F. and Bindereif, A. and Bozzoni, I. and Hanan, M. and Hansen, T.B. and Irimia, M. and Kadener, S. and Kristensen, L.S. and Legnini, I. and Morlando, M. and Jarlstad Olesen, M.T. and Pasterkamp, R.J. and Preibisch, S. and Rajewsky, N. and Suenkel, C. and Kjems, J.
Nature Methods 19 (10): 1208-1220. October 2022

Urbanization promotes specific bacteria in freshwater microbiomes including potential pathogens.
Numberger, D. and Zoccarato, L. and Woodhouse, J. and Ganzert, L. and Sauer, S. and García Márquez, J.R. and Domisch, S. and Grossart, H.P. and Greenwood, A.D.
Science of the Total Environment 845 : 157321. 1 November 2022

Exercise blood-drop metabolic profiling links metabolism with perceived exertion.
Opialla, T. and Gollasch, B. and Kuich, P.H.J.L. and Klug, L. and Rahn, G. and Busjahn, A. and Spuler, S. and Boschmann, M. and Kirwan, J.A. and Luft, F.C. and Kempa, S.
Frontiers in Molecular Biosciences 9 : 1042231. 21 December 2022

A growth factor-expressing macrophage subpopulation orchestrates regenerative inflammation via GDF-15.
Patsalos, A. and Halasz, L. and Medina-Serpas, M.A. and Berger, W.K. and Daniel, B. and Tzerpos, P. and Kiss, M. and Nagy, G. and Fischer, C. and Simandi, Z. and Varga, T. and Nagy, L.
Journal of Experimental Medicine 219 (1): e20210420. 3 January 2022

Protective immune trajectories in early viral containment of non-pneumonic SARS-CoV-2 infection.
Pekayvaz, K. and Leunig, A. and Kaiser, R. and Joppich, M. and Brambs, S. and Janjic, A. and Popp, O. and Nixdorf, D. and Fumagalli, V. and Schmidt, N. and Polewka, V. and Anjum, A. and Knottenberg, V. and Eivers, L. and Wange, L.E. and Gold, C. and Kirchner, M. and Muenchhoff, M. and Hellmuth, J.C. and Scherer, C. and Rubio-Acero, R. and Eser, T. and Deák, F. and Puchinger, K. and Kuhl, N. and Linder, A. and Saar, K. and Tomas, L. and Schulz, C. and Wieser, A. and Enard, W. and Kroidl, I. and Geldmacher, C. and von Bergwelt-Baildon, M. and Keppler, O.T. and Munschauer, M. and Iannacone, M. and Zimmer, R. and Mertins, P. and Hubner, N. and Hoelscher, M. and Massberg, S. and Stark, K. and Nicolai, L.
Nature Communications 13 (1): 1018. 23 February 2022

A pulmonologist's guide to perform and analyse cross-species single lung cell transcriptomics.
Pennitz, P. and Kirsten, H. and Friedrich, V.D. and Wyler, E. and Goekeri, C. and Obermayer, B. and Heinz, G.A. and Mashreghi, M.F. and Büttner, M. and Trimpert, J. and Landthaler, M. and Suttorp, N. and Hocke, A.C. and Hippenstiel, S. and Tönnies, M. and Scholz, M. and Kuebler, W.M. and Witzenrath, M. and Hoenzke, K. and Nouailles, G.
European Respiratory Review 31 (165): 220056. 30 September 2022

Engineering, decoding and systems-level characterization of chimpanzee cytomegalovirus.
Phan, Q.V. and Bogdanow, B. and Wyler, E. and Landthaler, M. and Liu, F. and Hagemeier, C. and Wiebusch, L.
PLoS Pathogens 18 (1): e1010193. 4 January 2022

Tuning the 3D microenvironment of reprogrammed tubule cells enhances biomimetic modeling of polycystic kidney disease.
Pichler, R. and Rizzo, L. and Tröndle, K. and Bühler, M. and Brucker, H. and Müller, A.L. and Grand, K. and Farè, S. and Viau, A. and Kaminski, M.M. and Kuehn, E.W. and Koch, F. and Zimmermann, S. and Koltay, P. and Lienkamp, S.S.
Biomaterials 291 : 121910. December 2022

The rate of spontaneous mutations in yeast deficient for MutSβ function.
Plavskin, Y. and de Biase, M.S. and Schwarz, R.F. and Siegal, M.L.
bioRxiv : 2022.08.25.505291v2. 26 November 2022

Control of immediate early gene expression by CPEB4-repressor complex-mediated mRNA degradation.
Poetz, F. and Lebedeva, S. and Schott, J. and Lindner, D. and Ohler, U. and Stoecklin, G.
Genome Biology 23 (1): 193. 12 September 2022

Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders.
Porubsky, D. and Höps, W. and Ashraf, H. and Hsieh, P.H. and Rodriguez-Martin, B. and Yilmaz, F. and Ebler, J. and Hallast, P. and Maggiolini, F.A.M. and Harvey, W.T. and Henning, B. and Audano, P.A. and Gordon, D.S. and Ebert, P. and Hasenfeld, P. and Benito, E. and Zhu, Q. and Lee, C. and Antonacci, F. and Steinrücken, M. and Beck, C.R. and Sanders, A.D. and Marschall, T. and Eichler, E.E. and Korbel, J.O.
Cell 185 (11): 1986-2005. 26 May 2022

Long-term imaging reveals behavioral plasticity during C. elegans dauer exit.
Preusser, F. and Neuschulz, A. and Junker, J.P. and Rajewsky, N. and Preibisch, S.
BMC Biology 20 (1): 277. 13 December 2022

Long-term imaging reveals behavioral plasticity during C. elegans dauer exit.
Preusser, F. and Neuschulz, A. and Junker, J.P. and Rajewsky, N. and Preibisch, S.
bioRxiv : 2022.04.25.489360v1. 26 April 2022

Cellular hierarchies predict drug response in acute myeloid leukemia.
Raffel, S. and Velten, L. and Haas, S.
Cancer Cell 40 (9): 917-919. 12 September 2022

Liam tackles complex multimodal single-cell data integration challenges.
Rautenstrauch, P. and Ohler, U.
bioRxiv : 2022.12.21.521399. 22 December 2022

Intricacies of single-cell multi-omics data integration.
Rautenstrauch, P. and Vlot, A.H.C. and Saran, S. and Ohler, U.
Trends in Genetics 38 (2): 128-139. February 2022

EBAG9 controls CD8(+) T cell memory formation responding to tumor challenge in mice.
Rehm, A. and Wirges, A. and Hoser, D. and Fischer, C. and Herda, S. and Gerlach, K. and Sauer, S. and Willimsky, G. and Hoepken, U.E.
JCI Insight 7 (11): e155534. 8 June 2022

Pathogenic variants damage cell composition and single cell transcription in cardiomyopathies.
Reichart, D. and Lindberg, E.L. and Maatz, H. and Miranda, A.M.A. and Viveiros, A. and Shvetsov, N. and Gärtner, A. and Nadelmann, E.R. and Lee, M. and Kanemaru, K. and Ruiz-Orera, J. and Strohmenger, V. and DeLaughter, D.M. and Patone, G. and Zhang, H. and Woehler, A. and Lippert, C. and Kim, Y. and Adami, E. and Gorham, J.M. and Barnett, S.N. and Brown, K. and Buchan, R.J. and Chowdhury, R.A. and Constantinou, C. and Cranley, J. and Felkin, L.E. and Fox, H. and Ghauri, A. and Gummert, J. and Kanda, M. and Li, R. and Mach, L. and McDonough, B. and Samari, S. and Shahriaran, F. and Yapp, C. and Stanasiuk, C. and Theotokis, P.I. and Theis, F.J. and van den Bogaerdt, A. and Wakimoto, H. and Ware, J.S. and Worth, C.L. and Barton, P.J.R. and Lee, Y.A. and Teichmann, S.A. and Milting, H. and Noseda, M. and Oudit, G.Y. and Heinig, M. and Seidman, J.G. and Hubner, N. and Seidman, C.E.
Science 377 (6606): eabo1984. 5 August 2022

MAGED2 controls vasopressin-induced aquaporin-2 expression in collecting duct cells.
Reusch, B. and Bartram, M.P. and Dafinger, C. and Palacio-Escat, N. and Wenzel, A. and Fenton, R.A. and Saez-Rodriguez, J. and Schermer, B. and Benzing, T. and Altmüller, J. and Beck, B.B. and Rinschen, M.M.
Journal of Proteomics 252 : 104424. 10 February 2022

Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes.
Ringel, A.R. and Szabo, Q. and Chiariello, A.M. and Chudzik, K. and Schöpflin, R. and Rothe, P. and Mattei, A.L. and Zehnder, To. and Harnett, D. and Laupert, V. and Bianco, S. and Hetzel, S. and Glaser, J. and Phan, M.H.Q. and Schindler, M. and Ibrahim, D.M. and Paliou, C. and Esposito, A. and Prada-Medina, C.A. and Haas, S.A. and Giere, P. and Vingron, M. and Wittler, L. and Meissner, A. and Nicodemi, M. and Cavalli, G. and Bantignies, F. and Mundlos, S. and Robson, M.I.
Cell 185 (20): 3689-3704. 29 September 2022

Prevalence of cancer predisposition germline variants in male breast cancer patients: results of the German Consortium for Hereditary Breast and Ovarian Cancer.
Rolfes, M. and Borde, J. and Möllenhoff, K. and Kayali, M. and Ernst, C. and Gehrig, A. and Sutter, C. and Ramser, J. and Niederacher, D. and Horváth, J. and Arnold, N. and Meindl, A. and Auber, B. and Rump, A. and Wang-Gohrke, S. and Ritter, J. and Hentschel, J. and Thiele, H. and Altmüller, J. and Nürnberg, P. and Rhiem, K. and Engel, C. and Wappenschmidt, B. and Schmutzler, R.K. and Hahnen, E. and Hauke, J.
Cancers 14 (13): 3292. 5 July 2022

The trispecific DARPin ensovibep inhibits diverse SARS-CoV-2 variants.
Rothenberger, S. and Hurdiss, D.L. and Walser, M. and Malvezzi, F. and Mayor, J. and Ryter, S. and Moreno, H. and Liechti, N. and Bosshart, A. and Iss, C. and Calabro, V. and Cornelius, A. and Hospodarsch, T. and Neculcea, A. and Looser, T. and Schlegel, A. and Fontaine, S. and Villemagne, D. and Paladino, M. and Schiegg, D. and Mangold, S. and Reichen, C. and Radom, F. and Kaufmann, Y. and Schaible, D. and Schlegel, I. and Zitt, C. and Sigrist, G. and Straumann, M. and Wolter, J. and Comby, M. and Sacarcelik, F. and Drulyte, I. and Lyoo, H. and Wang, C. and Li, W. and Du, W. and Binz, H.K. and Herrup, R. and Lusvarghi, S. and Neerukonda, S.N. and Vassell, R. and Wang, W. and Adler, J.M. and Eschke, K. and Nascimento, M. and Abdelgawad, A. and Gruber, A.D. and Bushe, J. and Kershaw, O. and Knutson, C.G. and Balavenkatraman, K.K. and Ramanathan, K. and Wyler, E. and Teixeira Alves, L.G. and Lewis, S. and Watson, R. and Haeuptle, M.A. and Zürcher, A. and Dawson, K.M. and Steiner, D. and Weiss, C.D. and Amstutz, P. and van Kuppeveld, F.J.M. and Stumpp, M.T. and Bosch, B.J. and Engler, O. and Trimpert, J.
Nature Biotechnology 40 (12): 1845-1854. December 2022

Panoptic segmentation with highly imbalanced semantic labels.
Rumberger, J.L. and Baumann, E. and Hirsch, P. and Janowczyk, A. and Zlobec, I. and Kainmueller, D.
In: 2022 IEEE International Symposium on Biomedical Imaging Challenges (ISBIC), 28-31 March 2022, Kolkata, India. 17 August 2022

Panoptic segmentation with highly imbalanced semantic labels.
Rumberger, J.L. and Baumann, E. and Hirsch, P. and Janowczyk, A. and Zlobec, I. and Kainmueller, D.
arXiv : 2203.11692. 19 April 2022

How shift equivariance impacts metric learning for instance segmentation.
Rumberger, J.L. and Yu, X. and Hirsch, P. and Dohmen, M. and Guarino, V.E. and Mokarian, A. and Mais, L. and Funke, J. and Kainmueller, D.
In: 2021 IEEE/CVF International Conference on Computer Vision (ICCV), 10-17 Oct 2021, Montreal, QC, Canada. 28 February 2022

Clonal expansion and epigenetic inheritance of long-lasting NK cell memory.
Rückert, T. and Lareau, C.A. and Mashreghi, M.F. and Ludwig, L.S. and Romagnani, C.
Nature Immunology 23 (11): 1551-1563. November 2022

Epigenetic targeting of transposon relics: beating the dead horses of the genome?
Sammarco, I. and Pieters, J. and Salony, S. and Toman, I. and Zolotarov, G. and Lafon Placette, C.
Epigenetics 17 (11): 1331-1344. November 2022

Adolescence is a sensitive period for prefrontal microglia to act on cognitive development.
Schalbetter, S.M. and von Arx, A.S. and Cruz-Ochoa, N. and Dawson, K. and Ivanov, A. and Mueller, F.S. and Lin, H.Y. and Amport, R. and Mildenberger, W. and Mattei, D. and Beule, D. and Földy, C. and Greter, M. and Notter, T. and Meyer, U.
Science Advances 8 (9): eabi6672. 4 March 2022

Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice.
Schepanski, S. and Chini, M. and Sternemann, V. and Urbschat, C. and Thiele, K. and Sun, T. and Zhao, Y. and Poburski, M. and Woestemeier, A. and Thieme, M.T. and Zazara, D.E. and Alawi, M. and Fischer, N. and Heeren, J. and Vladimirov, N. and Woehler, A. and Puelles, V.G. and Bonn, S. and Gagliani, N. and Hanganu-Opatz, I.L. and Arck, P.C.
Nature Communications 13 (1): 4571. 5 August 2022

Somatic mosaicism in STAG2-associated cohesinopathies: Expansion of the genotypic and phenotypic spectrum.
Schmidt, J. and Dreha-Kulaczewski, S. and Zafeiriou, M.P. and Schreiber, M.K. and Wilken, B. and Funke, R. and Neuhofer, C.M. and Altmüller, J. and Thiele, H. and Nürnberg, P. and Biskup, S. and Li, Y. and Zimmermann, W.H. and Kaulfuß, S. and Yigit, G. and Wollnik, B.
Frontiers in Cell and Developmental Biology 10 : 1025332. 16 November 2022

Familial cleft tongue caused by a unique translation initiation codon variant in TP63.
Schmidt, J. and Schreiber, G. and Altmüller, J. and Thiele, H. and Nürnberg, P. and Li, Y. and Kaulfuß, S. and Funke, R. and Wilken, B. and Yigit, G. and Wollnik, B.
European Journal of Human Genetics 30 (2): 211-218. February 2022

In prostate cancer cells cytokines are early responders to gravitational changes occurring in parabolic flights.
Schulz, H. and Dietrichs, D. and Wehland, M. and Corydon, T.J. and Hemmersbach, R. and Liemersdorf, C. and Melnik, D. and Hübner, N. and Saar, K. and Infanger, M. and Grimm, D.
International Journal of Molecular Sciences 23 (14): 7876. 17 July 2022

Data augmentation via partial nonlinear registration for brain-age prediction.
Schulz, M.A. and Koch, A. and Guarino, V.E. and Kainmueller, D. and Ritter, K.
Lecture Notes in Computer Science 13596 : 169-178. 2022

SARS-CoV-2 infection dynamics revealed by wastewater sequencing analysis and deconvolution.
Schumann, V.F. and de Castro Cuadrat, R.R. and Wyler, E. and Wurmus, R. and Deter, A. and Quedenau, C. and Dohmen, J. and Faxel, M. and Borodina, T. and Blume, A. and Freimuth, J. and Meixner, M. and Grau, J.H. and Liere, K. and Hackenbeck, T. and Zietzschmann, F. and Gnirss, R. and Böckelmann, U. and Uyar, B. and Franke, V. and Barke, N. and Altmüller, J. and Rajewsky, N. and Landthaler, M. and Akalin, A.
Science of the Total Environment 853 : 158931. 20 December 2022

Highly conserved interaction profiles between clinically relevant mutants of the cytomegalovirus CDK-like kinase pUL97 and human cyclins: functional significance of cyclin H.
Schütz, M. and Müller, R. and Socher, E. and Wangen, C. and Full, F. and Wyler, E. and Wong, D. and Scherer, M. and Stamminger, T. and Chou, S. and Rawlinson, W.D. and Hamilton, S.T. and Sticht, H. and Marschall, M.
International Journal of Molecular Sciences 23 (19): 11814. 5 October 2022

Pathogenic variants in cardiomyopathy disorder genes underlie pediatric myocarditis - Further impact of heterozygous immune disorder gene variants?
Seidel, F. and Laser, K.T. and Klingel, K. and Dartsch, J. and Theisen, S. and Pickardt, T. and Holtgrewe, M. and Gärtner, A. and Berger, F. and Beule, D. and Milting, H. and Schubert, S. and Klaassen, S. and Kühnisch, J.
Journal of Cardiovascular Development and Disease 9 (7): 216. 5 July 2022

Optocoder: computational decoding of spatially indexed bead arrays.
Senel, E. and Rajewsky, N. and Karaiskos, N.
NAR Genomics and Bioinformatics 4 (2): lqac042. June 2022

A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants.
Shahan, R. and Hsu, C.W. and Nolan, T.M. and Cole, B.J. and Taylor, I.W. and Greenstreet, L. and Zhang, S. and Afanassiev, A. and Vlot, A.H.C. and Schiebinger, G. and Benfey, P.N. and Ohler, U.
Developmental Cell 57 (4): 543-560. 28 February 2022

A single-cell atlas of de novo β-cell regeneration reveals the contribution of hybrid β/δ-cells to diabetes recovery in zebrafish.
Singh, S.P. and Chawla, P. and Hnatiuk, A. and Kamel, M. and Silva, L.D. and Spanjaard, B. and Eski, S.E. and Janjuha, S. and Olivares-Chauvet, P. and Kayisoglu, O. and Rost, F. and Bläsche, J. and Kränkel, A. and Petzold, A. and Kurth, T. and Reinhardt, S. and Junker, J.P. and Ninov, N.
Development 149 (2): dev199853. January 2022

A single-cell atlas of de novo β-cell regeneration reveals the contribution of hybrid β/δ cells to diabetes recovery in zebrafish.
Singh, S.P. and Chawla, P. and Hnatiuk, A. and Kamel, M. and Silva, L.D. and Spanjard, B. and Eski, S.E. and Janjuha, S. and Olivares, P. and Kayisoglu, O. and Rost, F. and Bläsche, J. and Kränkel, A. and Petzold, A. and Kurth, T. and Reinhardt, S. and Junker, J.P. and Ninov, N.
bioRxiv : 2021.06.24.449704. 31 January 2022

Mechanisms of IRF2BPL-related disorders and identification of a potential therapeutic strategy.
Sinha Ray, S. and Dutta, D. and Dennys, C. and Powers, S. and Roussel, F. and Lisowski, P. and Glažar, P. and Zhang, X. and Biswas, P. and Caporale, J.R. and Rajewsky, N. and Bickle, M. and Wein, N. and Bellen, H.J. and Likhite, S. and Marcogliese, P.C. and Meyer, K.C.
Cell Reports 41 (10): 111751. 6 December 2022

Single-cell sequencing of human midbrain reveals glial activation and a Parkinson-specific neuronal state.
Smajić, S. and Prada-Medina, C.A. and Landoulsi, Z. and Ghelfi, J. and Delcambre, S. and Dietrich, C. and Jarazo, J. and Henck, J. and Balachandran, S. and Pachchek, S. and Morris, C.M. and Antony, P. and Timmermann, B. and Sauer, S. and Pereira, S.L. and Schwamborn, J.C. and May, P. and Grünewald, A. and Spielmann, M.
Brain 145 (3): 964-978. March 2022

SMITH: spatially constrained stochastic model for simulation of intra-tumour heterogeneity.
Streck, A. and Kaufmann, T. and Schwarz, R.F.
bioRxiv : 2022.07.22.501136. 24 July 2022

Cell type diversity in a developing octopus brain.
Styfhals, R. and Zolotarov, G. and Hulselmans, G. and Spanier, K.I. and Poovathingal, S. and Elagoz, A.M. and De Winter, S. and Deryckere, A. and Rajewsky, N. and Ponte, G. and Fiorito, G. and Aerts, S. and Seuntjens, E.
Nature Communications 13 (1): 7392. 30 November 2022

Male carriers of HLA-C*04:01 have increased risk of cardiac injury in COVID-19.
Suwalski, P. and Violano, M. and Müller, M. and Patriki, D. and Thibeault, C. and Quedenau, C. and Wang, X. and Karadeniz, Z. and Saccomanno, J. and Doehn, J.M. and Hübner, R.H. and Hinzmann, B. and Beer, H.J. and Wiggli, B. and Siemann, S. and Suttorp, N. and Witzenrath, M. and Hippenstiel, S. and Skurk, C. and Poller, W. and Sander, L.E. and Kurth, F. and Borodina, T. and Guettouche, T. and Landmesser, U. and Heidecker, B.
Journal of Cardiovascular Aging 2 (3): 33. 27 June 2022

Spacemake: processing and analysis of large-scale spatial transcriptomics data.
Sztanka-Toth, T.R. and Jens, M. and Karaiskos, N. and Rajewsky, N.
GigaScience 11 : giac064. 19 July 2022

S100A4 is a strong negative prognostic marker and potential therapeutic target in adenocarcinoma of the stomach and esophagus.
Treese, C. and Hartl, K. and Pötzsch, M. and Dahlmann, M. and von Winterfeld, M. and Berg, E. and Hummel, M. and Timm, L. and Rau, B. and Walther, W. and Daum, S. and Kobelt, D. and Stein, U.
Cells 11 (6): 1056. 21 March 2022

Cancer stem cells: The adventurous journey from hematopoietic to leukemic stem cells.
Trumpp, A. and Haas, S.
Cell 185 (8): 1266-1270. 14 April 2022

Enzyme self-label-bound ATTO700 in single-molecule and super-resolution microscopy.
Trumpp, M. and Oliveras, A. and Gonschior, H. and Ast, J. and Hodson, D.J. and Knaus, P. and Lehmann, M. and Birol, M. and Broichhagen, J.
Chemical Communications 58 (99): 13724-13727. 13 December 2022

Unraveling structural rearrangements of the CFH gene cluster in atypical hemolytic uremic syndrome patients using molecular combing and long-fragment targeted sequencing.
Tschernoster, N. and Erger, F. and Walsh, P.R. and McNicholas, B. and Fistrek, M. and Habbig, S. and Schumacher, L. and Folz-Donahue, K. and Kukat, C. and Toliat, M.R. and Becker, C. and Thiele, H. and Kavanagh, D. and Nürnberg, P. and Beck, B. and Altmüller, J.
Journal of Molecular Diagnostics 24 (6): 619-631. June 2022

ShapeSorter: a fully probabilistic method for detecting conserved RNA structure features supported by SHAPE evidence.
Tsybulskyi, V. and Meyer, I.M.
Nucleic Acids Research 50 (15): e85. 26 August 2022

Transcriptome analysis reveals putative genes involved in the lipid metabolism of chaulmoogra oil biosynthesis in Carpotroche brasiliensis (Raddi) A.Gray, a tropical tree species.
Vasconcelos, L.M. and Bittencourt, F. and Vidal, R.O. and Silva, E.M.A. and Costa, E.A. and Micheli, F. and Kirst, M. and Pirovani, C.P. and Gaiotto, F.A
Forests 13 (11): 1806. 29 October 2022

Cluster-independent marker feature identification from single-cell omics data using SEMITONES.
Vlot, A.H.C. and Maghsudi, S. and Ohler, U.
Nucleic Acids Research 50 (18): e107. 14 October 2022

Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection clusters based on integrated genomic surveillance, outbreak analysis and contact tracing in an urban setting.
Walker, A. and Houwaart, T. and Finzer, P. and Ehlkes, L. and Tyshaieva, A. and Damagnez, M. and Strelow, D. and Duplessis, A. and Nicolai, J. and Wienemann, T. and Tamayo, T. and Kohns Vasconcelos, M. and Hülse, L. and Hoffmann, K. and Lübke, N. and Hauka, S. and Andree, M. and Däumer, M.P. and Thielen, A. and Kolbe-Busch, S. and Göbels, K. and Zotz, R. and Pfeffer, K. and Timm, J. and Dilthey, A.T.
Clinical Infectious Diseases 74 (6): 1039-1046. 15 March 2022

A neutralizing IL-11 antibody improves renal function and increases lifespan in a mouse model of alport syndrome.
Widjaja, A.A. and Shekeran, S. and Adami, E. and Goh, J. and Tan, J. and Viswanathan, S. and Lim, S.Y. and Tan, P.H. and Hübner, N. and Coffman, T. and Cook, S.
Journal of the American Society of Nephrology 33 (4): 718-730. April 2022

Targeting endogenous kidney regeneration using anti-IL11 therapy in acute and chronic models of kidney disease.
Widjaja, A.A. and Viswanathan, S. and Shekeran, S.G. and Adami, E. and Lim, W.W. and Chothani, S. and Tan, J. and Goh, J.W.T. and Chen, H.M. and Lim, S.Y. and Boustany-Kari, C.M. and Hawkins, J. and Petretto, E. and Hübner, N. and Schafer, S. and Coffman, T.M. and Cook, S.A.
Nature Communications 13 (1): 7497. 5 December 2022

Can fractal dimensions objectivize gastropod shell morphometrics? A case study from Lake Lugu (SW China).
Wiese, R. and Harrington, K. and Hartmann, K. and Hethke, M. and Rintelen, T. and Zhang, H. and Zhang, L.J. and Riedel, F.
Ecology and Evolution 12 (3): e8622. February 2022

Gastric stem cells promote inflammation and gland remodeling in response to Helicobacter pylori via Rspo3-Lgr4 axis.
Wizenty, J. and Müllerke, S. and Kolesnichenko, M. and Heuberger, J. and Lin, M. and Fischer, A.S. and Mollenkopf, H.J. and Berger, H. and Tacke, F. and Sigal, M.
EMBO Journal 41 (13): e109996. 4 July 2022

Mutations in TAF8 cause a neurodegenerative disorder.
Wong, K.M. and Jepsen, W.M. and Efthymiou, S. and Salpietro, V. and Sanchez-Castillo, M. and Yip, J. and Kriouile, Y. and Diegmann, S. and Dreha-Kulaczewski, S. and Altmüller, J. and Thiele, H. and Nürnberg, P. and Toosi, M.B. and Akhondian, J. and Ghayoor Karimiani, E. and Hummel-Abmeier, H. and Huppke, B. and Houlden, H. and Gärtner, J. and Maroofian, R. and Huppke, P.
Brain 145 (9): 3022-3034. September 2022

A local human Vδ1 T cell population is associated with survival in nonsmall-cell lung cancer.
Wu, Y. and Biswas, D. and Usaite, I. and Angelova, M. and Boeing, S. and Karasaki, T. and Veeriah, S. and Czyzewska-Khan, J. and Morton, C. and Joseph, M. and Hessey, S. and Reading, J. and Georgiou, A. and Al-Bakir, M. and McGranahan, N. and Jamal-Hanjani, M. and Hackshaw, A. and Quezada, S.A. and Hayday, A.C. and Swanton, C.
Nature Cancer 3 (6): 696-709. June 2022

The transcription factor EB (TFEB) sensitizes the heart to chronic pressure overload.
Wundersitz, S. and Pablo Tortola, C. and Schmidt, S. and Oliveira Vidal, R. and Kny, M. and Hahn, A. and Zanders, L. and Katus, H.A. and Sauer, S. and Butter, C. and Luft, F.C. and Müller, O.J. and Fielitz, J.
International Journal of Molecular Sciences 23 (11): 5943. 25 May 2022

Key benefits of dexamethasone and antibody treatment in COVID-19 hamster models revealed by single cell transcriptomics.
Wyler, E. and Adler, J.M. and Eschke, K. and Teixeira Alves, G. and Peidli, S. and Pott, F. and Kazmierski, J. and Michalick, L. and Kershaw, O. and Bushe, J. and Andreotti, S. and Pennitz, P. and Abdelgawad, A. and Postmus, D. and Goffinet, C. and Kreye, J. and Reincke, S.M. and Prüss, H. and Blüthgen, N. and Gruber, A.D. and Kuebler, W.M. and Witzenrath, M. and Landthaler, M. and Nouailles, G. and Trimpert, J.
Molecular Therapy 30 (5): 1952-1965. 4 May 2022

Analysis of copy number variation in men with non-obstructive azoospermia.
Wyrwoll, M.J. and Wabschke, R. and Röpke, A. and Wöste, M. and Ruckert, C. and Perrey, S. and Rotte, N. and Hardy, J. and Astica, L. and Lupianez, D.G. and Wistuba, J. and Westernströer, B. and Schlatt, S. and Berman, A.J. and Müller, A.M. and Kliesch, S. and Yatsenko, A.N. and Tüttelmann, F. and Friedrich, C.
Andrology 10 (8): 1593-1604. November 2022

A noncoding single-nucleotide polymorphism at 8q24 drives IDH1-mutant glioma formation.
Yanchus, C. and Drucker, K.L. and Kollmeyer, T.M. and Tsai, R. and Winick-Ng, W. and Liang, M. and Malik, A. and Pawling, J. and De Lorenzo, S.B. and Ali, A. and Decker, P.A. and Kosel, M.L. and Panda, A. and Al-Zahrani, K.N. and Jiang, L. and Browning, J.W.L. and Lowden, C. and Geuenich, M. and Hernandez, J.J. and Gosio, J.T. and Ahmed, M. and Loganathan, S.K. and Berman, J. and Trcka, D. and Michealraj, K.A. and Fortin, J. and Carson, B. and Hollingsworth, E.W. and Jacinto, S. and Mazrooei, P. and Zhou, L. and Elia, A. and Lupien, M. and He, H.H. and Murphy, D.J. and Wang, L. and Abyzov, A. and Dennis, J.W. and Maass, P.G. and Campbell, K. and Wilson, M.D. and Lachance, D.H. and Wrensch, M. and Wiencke, J. and Mak, T. and Pennacchio, L.A. and Dickel, D.E. and Visel, A. and Wrana, J. and Taylor, M.D. and Zadeh, G. and Dirks, P. and Eckel-Passow, J.E. and Attisano, L. and Pombo, A. and Ida, C.M. and Kvon, E.Z. and Jenkins, R.B. and Schramek, D.
Science 378 (6615): 68-78. 7 October 2022

Analysis of single-cell transcriptome data in drosophila.
Yousefian, S. and Musillo, M.J. and Bageritz, J.
Methods in Molecular Biology 2540 (3): 93-111. 19 August 2022

Novel targets, treatments, and advanced models for intracerebral haemorrhage.
Zille, M. and Farr, T.D. and Keep, R.F. and Römer, C. and Xi, G. and Boltze, J.
EBioMedicine 76 : 103880. 12 February 2022

HDLBP binds ER-targeted mRNAs by multivalent interactions to promote protein synthesis of transmembrane and secreted proteins.
Zinnall, U. and Milek, M. and Minia, I. and Vieira-Vieira, C.H. and Müller, S. and Mastrobuoni, G. and Hazapis, O.G. and Del Giudice, S. and Schwefel, D. and Bley, N. and Voigt, F. and Chao, J.A. and Kempa, S. and Hüttelmaier, S. and Selbach, M. and Landthaler, M.
Nature Communications 13 (1): 2727. 18 May 2022

MicroRNAs are deeply linked to the emergence of the complex octopus brain.
Zolotarov, G. and Fromm, B. and Legnini, I. and Ayoub, S. and Polese, G. and Maselli, V. and Chabot, P.J. and Vinther, J. and Styfhals, R. and Seuntjens, E. and Di Cosmo, A. and Peterson, K.J. and Rajewsky, N.
Science Advances 8 (47): eadd9938. 25 November 2022

Mammalian splicing divergence is shaped by drift, buffering in trans, and a scaling law.
Zou, X. and Schaefke, B. and Li, Y. and Jia, F. and Sun, W. and Li, G. and Liang, W. and Reif, T. and Heyd, F. and Gao, Q. and Tian, S. and Li, Y. and Tang, Y. and Fang, L. and Hu, Y. and Chen, W.
Life Science Alliance 5 (4): e202101333. April 2022

Naïve-like pluripotency to pave the way for saving the northern white rhinoceros from extinction.
Zywitza, V. and Rusha, E. and Shaposhnikov, D. and Ruiz-Orera, J. and Telugu, N. and Rishko, V. and Hayashi, M. and Michel, G. and Wittler, L. and Stejskal, J. and Holtze, S. and Göritz, F. and Hermes, R. and Wang, J. and Izsvák, Z. and Colleoni, S. and Lazzari, G. and Galli, C. and Hildebrandt, T.B. and Hayashi, K. and Diecke, S. and Drukker, M.
Scientific Reports 12 (1): 3100. 8 March 2022

Altered nuclear architecture in blood cells from Huntington's disease patients.
de Castro, I.J. and Toner, B. and Xie, S.Q. and Swingland, J. and Hodges, A. and Tabrizi, S.J. and Turkheimer, F. and Pombo, A. and Khalil, A.
Neurological Sciences 43 (1): 379-385. January 2022

Soluble urokinase plasminogen activator receptor levels are associated with severity of fibrosis in patients with primary sclerosing cholangitis.
Özdirik, B. and Maibier, M. and Scherf, M. and Nicklaus, J.M. and Frohme, J. and Puengel, T. and Meyer Zum Büschenfelde, D. and Tacke, F. and Mueller, T. and Sigal, M.
Journal of Clinical Medicine 11 (9): 2479. 28 April 2022

2021

Age-related and disease locus-specific mechanisms contribute to early remodelling of chromatin structure in Huntington's disease mice.
Alcalá-Vida, R. and Seguin, J. and Lotz, C. and Molitor, A.M. and Irastorza-Azcarate, I. and Awada, A. and Karasu, N. and Bombardier, A. and Cosquer, B. and Skarmeta, J.L.G. and Cassel, J.C. and Boutillier, A.L. and Sexton, T. and Merienne, K.
Nature Communications 12 (1): 364. 13 January 2021

Rapid nuclear deadenylation of mammalian messenger RNA.
Alles, J. and Legnini, I. and Pacelli, M. and Rajewsky, N.
bioRxiv : 2021.11.16.468655. 18 November 2021

In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation.
Anania, C. and Acemel, R.D. and Jedamzick, J. and Bolondi, A. and Cova, G. and Brieske, N. and Kuehn, R. and Wittler, L. and Real, F.M. and Lupianez, D.G.
bioRxiv : 2021.04.14.439779. 14 April 2021

Putative mobilized colistin resistance genes in the human gut microbiome.
Andrade, B.G.N. and Goris, T. and Afli, H. and Coutinho, F.H. and Dávila, A.M.R. and Cuadrat, R.R.C.
BMC Microbiology 21 : 220. 22 July 2021

PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC.
Appel, L.M. and Franke, V. and Bruno, M. and Grishkovskaya, I. and Kasiliauskaite, A. and Kaufmann, T. and Schoeberl, U.E. and Puchinger, M.G. and Kostrhon, S. and Ebenwaldner, C. and Sebesta, M. and Beltzung, E. and Mechtler, K. and Lin, G. and Vlasova, A. and Leeb, M. and Pavri, R. and Stark, A. and Akalin, A. and Stefl, R. and Bernecky, C. and Djinovic-Carugo, K. and Slade, D.
Nature Communications 12 (1): 6078. 19 October 2021

Inhibiting PHGDH with NCT-503 reroutes glucose-derived carbons into the TCA cycle, independently of its on-target effect.
Arlt, B. and Mastrobuoni, G. and Wuenschel, J. and Astrahantseff, K. and Eggert, A. and Kempa, S. and Deubzer, H.E.
Journal of Enzyme Inhibition and Medicinal Chemistry 36 (1): 1282-1289. 30 June 2021

SNT: a unifying toolbox for quantification of neuronal anatomy.
Arshadi, C. and Günther, U. and Eddison, M. and Harrington, K.I.S. and Ferreira, T.A.
Nature Methods 18 : 374-377. April 2021

Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients.
Aschenbrenner, A.C. and Mouktaroudi, M. and Krämer, B. and Oestreich, M. and Antonakos, N. and Nuesch-Germano, M. and Gkizeli, K. and Bonaguro, L. and Reusch, N. and Baßler, K. and Saridaki, M. and Knoll, R. and Pecht, T. and Kapellos, T.S. and Doulou, S. and Kröger, C. and Herbert, M. and Holsten, L. and Horne, A. and Gemünd, I.D. and Rovina, N. and Agrawal, S. and Dahm, K. and van Uelft, M. and Drews, A. and Lenkeit, L. and Bruse, N. and Gerretsen, J. and Gierlich, J. and Becker, M. and Händler, K. and Kraut, M. and Theis, H. and Mengiste, S. and Domenico, E. and Schulte-Schrepping, J. and Seep, L. and Raabe, J. and Hoffmeister, C. and ToVinh, M. and Keitel, V. and Rieke, G. and Talevi, V. and Skowasch, D. and Aziz, N.A. and Pickkers, P. and van de Veerdonk, F.L. and Netea, M.G. and Schultze, J.L. and Kox, M. and Breteler, M.M.B. and Nattermann, J. and Koutsoukou, A. and Giamarellos-Bourboulis, E.J. and Ulas, T.
Genome Medicine 13 (1): 7. 13 January 2021

RS-FISH: Precise, interactive, fast, and scalable FISH spot detection.
Bahry, E. and Breimann, L. and Zouinkhi, M. and Epstein, L. and Kolyvanov, K. and Long, X. and Harrington, K.I.S. and Lionnet, T. and Preibisch, S.
bioRxiv : 2021.03.09.434205v2. 18 October 2021

Extracellular matrix in heart Failure: role of ADAMTS5 in proteoglycan remodeling.
Barallobre-Barreiro, J. and Radovits, T. and Fava, M. and Mayr, U. and Lin, W.Y. and Ermolaeva, E. and Martínez-López, D. and Lindberg, E.L. and Duregotti, E. and Daróczi, L. and Hasman, M. and Schmidt, L.E. and Singh, B. and Lu, R. and Baig, F. and Siedlar, A.M. and Cuello, F. and Catibog, N. and Theofilatos, K. and Shah, A.M. and Crespo-Leiro, M.G. and Doménech, N. and Hübner, N. and Merkely, B. and Mayr, M.
Circulation 144 (25): 2021-2034. 21 December 2021

SUMOylation of the chromodomain factor MRG-1 in C. elegans affects chromatin-regulatory dynamics.
Baytek, G. and Blume, A. and Gerceker Demirel, F. and Bulut, S. and Mertins, P. and Tursun, B.
bioRxiv : 2021.02.14.431134. 14 February 2021

Using DNA sequencing data to quantify T cell fraction and therapy response.
Bentham, R. and Litchfield, K. and Watkins, T.B.K. and Lim, E.L. and Rosenthal, R. and Martínez-Ruiz, C. and Hiley, C.T. and Bakir, M.A. and Salgado, R. and Moore, D.A. and Jamal-Hanjani, M. and Swanton, C. and McGranahan, N.
Nature 597 (7877): 555-560. 23 September 2021

SARS-CoV-2 in humans.
Binder, M. and Wyler, E.
Berliner und Munchener Tierarztliche Wochenschrift 134 : 1-13. 30 April 2021

Uncovering de novo gene birth in yeast using deep transcriptomics.
Blevins, W.R. and Ruiz-Orera, J. and Messeguer, X. and Blasco-Moreno, B. and Villanueva-Cañas, J.L. and Espinar, L. and Díez, J. and Carey, L.B. and Albà, M.M.
Nature Communications 12 (1): 604. 27 January 2021

A comparison of metabolic labeling and statistical methods to infer genome-wide dynamics of RNA turnover.
Boileau, E. and Altmüller, J. and Naarmann-de Vries, I.S. and Dieterich, C.
Briefings in Bioinformatics 22 (6): bbab219. November 2021

The H4K20 demethylase DPY-21 regulates the dynamics of condensin DC binding.
Breimann, L. and Morao, A.K. and Kim, J. and Jimenez, D. and Maryn, N. and Bikkasani, K. and Carrozza, M.J. and Albritton, S.E. and Kramer, M. and Street, L.A. and Cerimi, K. and Schumann, V.F. and Bahry, E. and Preibisch, S. and Woehler, A. and Ercan, S.
bioRxiv : 2021.04.11.438056. 24 September 2021

Mitochondrial respiratory chain function promotes extracellular matrix integrity in cartilage.
Bubb, K. and Holzer, T. and Nolte, J.L. and Krüger, M. and Wilson, R. and Schlötzer-Schrehardt, U. and Brinckmann, J. and Altmüller, J. and Aszodi, A. and Fleischhauer, L. and Clausen-Schaumann, H. and Probst, K. and Brachvogel, B.
Journal of Biological Chemistry 297 (4): 101224. October 2021

Systematic identification of A-to-I RNA editing in zebrafish development and adult organs.
Buchumenski, I. and Holler, K. and Appelbaum, L. and Eisenberg, E. and Junker, J.P. and Levanon, E.Y.
Nucleic Acids Research 49 (8): 4325-4337. 7 May 2021

Non-coding RNAs: lncRNAs, miRNAs, and piRNAs in sexual development.
Burgos, M. and Hurtado, A. and Jiménez, R. and Barrionuevo, F.J.
Sexual Development 15 (5-6): 335-350. December 2021

Single cell biology - a Keystone Symposia report.
Cable, J. and Elowitz, M.B. and Domingos, A.I. and Habib, N. and Itzkovitz, S. and Hamidzada, H. and Balzer, M.S. and Yanai, I. and Liberali, P. and Whited, J. and Streets, A. and Cai, L. and Stergachis, A.B. and Hong, C.K.Y. and Keren, L. and Guilliams, M. and Alon, U. and Shalek, A.K. and Hamel, R. and Pfau, S.J. and Raj, A. and Quake, S.R. and Zhang, N.R. and Fan, J. and Trapnell, C. and Wang, B. and Greenwald, N.F. and Vento-Tormo, R. and Santos, S.D.M. and Spencer, S.L. and Garcia, H.G. and Arekatla, G. and Gaiti, F. and Arbel-Goren, R. and Rulands, S. and Junker, J.P. and Klein, A.M. and Morris, S.A. and Murray, J.I. and Galloway, K.E. and Ratz, M. and Romeike, M.
Annals of the New York Academy of Sciences 1506 (1): 74-97. December 2021

DDX3 depletion represses translation of mRNAs with complex 5' UTRs.
Calviello, L. and Venkataramanan, S. and Rogowski, K.J. and Wyler, E. and Wilkins, K. and Tejura, M. and Thai, B. and Krol, J. and Filipowicz, W. and Landthaler, M. and Floor, S.N.
Nucleic Acids Research 49 (9): 5336-5350. May 2021

Ecological factors influence balancing selection on leaf chemical profiles of a wildflower.
Carley, L.N. and Mojica, J.P. and Wang, B. and Chen, C.Y. and Lin, Y.P. and Prasad, K.V.S.K and Chan, E. and Hsu, C.W. and Keith, R. and Nuñez, C.L. and Olson-Manning, C.F. and Rushworth, C.A. and Wagner, M.R. and Wang, J. and Yeh, P.M. and Reichelt, M. and Ghattas, K. and Gershenzon, J. and Lee, C.R. and Mitchell-Olds, T.
Nature Ecology & Evolution 5 : 1135-1144. August 2021

Dynamic and equilibrium properties of finite-size polymer models of chromosome folding.
Conte, M. and Fiorillo, L. and Annunziatella, C. and Esposito, A. and Musella, F. and Abraham, A. and Bianco, S. and Chiariello, A.M.
Physical Review E 104 (5): 054402. 10 November 2021

Impairment of the ER/mitochondria compartment in human cardiomyocytes with PLN p.Arg14del mutation.
Cuello, F. and Knaust, A.E. and Saleem, U. and Loos, M. and Raabe, J. and Mosqueira, D. and Laufer, S. and Schweizer, M. and Kraak, P. and Flenner, F. and Ulmer, B.M and Braren, I. and Yin, X. and Theofilatos, K. and Ruiz-Orera, J. and Patone, G. and Klampe, B. and Schulze, T. and Piasecki, A. and Pinto, Y. and Vink, A. and Hübner, N. and Harding, S. and Mayr, M. and Denning, C. and Eschenhagen, T. and Hansen, A.
EMBO Molecular Medicine 13 (6): e13074. 7 June 2021

Elevated Flt3L predicts long-term survival in patients with high-grade gastroenteropancreatic neuroendocrine neoplasms.
Detjen, K.M. and Otto, R. and Giesecke, Y. and Geisler, L. and Riemer, P. and Jann, H. and Grötzinger, C. and Sers, C. and Pascher, A. and Lüdde, T. and Leser, U. and Wiedenmann, B. and Sigal, M. and Tacke, F. and Roderburg, C. and Hammerich, L.
Cancers 13 (17): 4463. 1 September 2021

Modeling Structure-Activity Relationship of AMPK Activation.
Drewe, J. and Küsters, E. and Hammann, F. and Kreuter, M. and Boss, P. and Schöning, V.
Molecules 26 (21): 6508. 1 November 2021

Evaluation of aggression and fearfulness in domestic dog (Canis familiaris).
Dyjak, M. and Boruta, A. and Adamkiewicz, E. and Walasek, A. and Bury-Burzymski, P. and Lisowski, P.
Animal Science Papers and Reports 39 (4): 407-418. 2021

Complex population dynamics in a spatial microbial ecosystem with Physarum polycephalum.
Epstein, L. and Dubois, Z. and Smith, J. and Lee, Y. and Harrington, K.
Biosystems 208 : 104483. October 2021

Complex population dynamics in a spatial microbial ecosystem with Physarum polycephalum.
Epstein, L. and Dubois, Z. and Smith, J. and Lee, Y. and Harrington, K.
bioRxiv : 2021.03.14.435300. 15 March 2021

Polymer models are a versatile tool to study chromatin 3D organization.
Esposito, A. and Bianco, S. and Fiorillo, L. and Conte, M. and Abraham, A. and Musella, F. and Nicodemi, M. and Prisco, A. and Chiariello, A.M.
Biochemical Society Transactions 49 (4): 1675-1684. August 2021

Humane neuromuskuläre Organoide - Anwendung und Perspektive [Human neuromuscular organoids - Application and perspective].
Faustino Martins, J.M. and Nguyen, L.V.N. and Gouti, M.
BIOspektrum 27 (2): 135-138. March 2021

Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin.
Fiorillo, L. and Musella, F. and Conte, M. and Kempfer, R. and Chiariello, A.M. and Bianco, S. and Kukalev, A. and Irastorza-Azcarate, I. and Esposito, A. and Abraham, A. and Prisco, A. and Pombo, A. and Nicodemi, M.
Nature Methods 18 (5): 482-490. May 2021

Truncated titin proteins and titin haploinsufficiency are targets for functional recovery in human cardiomyopathy due to TTN mutations.
Fomin, A. and Gärtner, A. and Cyganek, L. and Tiburcy, M. and Tuleta, I. and Wellers, L. and Folsche, L. and Hobbach, A.J. and von Frieling-Salewsky, M. and Unger, A. and Hucke, A. and Koser, F. and Kassner, A. and Sielemann, K. and Streckfuß-Bömeke, K. and Hasenfuss, G. and Goedel, A. and Laugwitz, K.L. and Moretti, A. and Gummert, J.F. and Dos Remedios, C.G. and Reinecke, H. and Knöll, R. and van Heesch, S. and Hubner, N. and Zimmermann, W.H. and Milting, H. and Linke, W.A.
Science Translational Medicine 13 (618): eabd3079. 3 November 2021

The SEQC2 epigenomics quality control (EpiQC) study.
Foox, J. and Nordlund, J. and Lalancette, C. and Gong, T. and Lacey, M. and Lent, S. and Langhorst, B.W. and Ponnaluri, V.K.C. and Williams, L. and Padmanabhan, K.R. and Cavalcante, R. and Lundmark, A. and Butler, D. and Mozsary, C. and Gurvitch, J. and Greally, J.M. and Suzuki, M. and Menor, M. and Nasu, M. and Alonso, A. and Sheridan, C. and Scherer, A. and Bruinsma, S. and Golda, G. and Muszynska, A. and Łabaj, P.P. and Campbell, M.A. and Wos, F. and Raine, A. and Liljedahl, U. and Axelsson, T. and Wang, C. and Chen, Z. and Yang, Z. and Li, J. and Yang, X. and Wang, H. and Melnick, A. and Guo, S. and Blume, A. and Franke, V. and Ibanez de Caceres, I. and Rodriguez-Antolin, C. and Rosas, R. and Davis, J.W. and Ishii, J. and Megherbi, D.B. and Xiao, W. and Liao, W. and Xu, J. and Hong, H. and Ning, B. and Tong, W. and Akalin, A. and Wang, Y. and Deng, Y. and Mason, C.E.
Genome Biology 22 (1): 332. 6 December 2021

CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression.
Franke, M. and De la Calle-Mustienes, E. and Neto, A. and Almuedo-Castillo, M. and Irastorza-Azcarate, I. and Acemel, R.D. and Tena, J.J. and Santos-Pereira, J.M. and Gómez-Skarmeta, J.L.
Nature Communications 12 (1): 5415. 13 September 2021

Diverse but unique astrocytic phenotypes during embryonic stem cell differentiation, culturing and aging.
Freitag, K. and Eede, P. and Ivanov, A. and Schneeberger, S. and Borodina, T. and Sauer, S. and Beule, D. and Heppner, F.L.
bioRxiv : 2021.08.02.454573v1. 28 November 2021

Optimized workflow for on-line derivatization for targeted metabolomics approach by gas chromatography-mass spectrometry.
Fritsche-Guenther, R. and Gloaguen, Y. and Bauer, A. and Opialla, T. and Kempa, S. and Fleming, C.A. and Redmond, H.P. and Kirwan, J.A.
Metabolites 11 (12): 888. 18 December 2021

Estimation of C. elegans cell- and tissue volumes.
Froehlich, J.J. and Rajewsky, N. and Ewald, C.Y.
microPublication Biology : 000345. 4 January 2021

Parallel genetics of regulatory sequences using scalable genome editing in vivo.
Froehlich, J.J. and Uyar, B. and Herzog, M. and Theil, K. and Glažar, P. and Akalin, A. and Rajewsky, N.
Cell Reports 35 (2): 108988. 13 April 2021

RNA-binding proteins regulate aldosterone homeostasis in human steroidogenic cells.
Fu, R. and Wellman, K. and Baldwin, A. and Rege, J. and Walters, K. and Hirsekorn, A. and Riemondy, K. and Rainey, W.E and Mukherjee, N.
RNA 27 (8): 933-945. August 2021

SARS-CoV-2-mediated dysregulation of metabolism and autophagy uncovers host-targeting antivirals.
Gassen, N.C. and Papies, J. and Bajaj, T. and Emanuel, J. and Dethloff, F. and Chua, R.L. and Trimpert, J. and Heinemann, N. and Niemeyer, C. and Weege, F. and Hönzke, K. and Aschman, T. and Heinz, D.E. and Weckmann, K. and Ebert, T. and Zellner, A. and Lennarz, M. and Wyler, E. and Schroeder, S. and Richter, A. and Niemeyer, D. and Hoffmann, K. and Meyer, T.F. and Heppner, F.L. and Corman, V.M. and Landthaler, M. and Hocke, A.C. and Morkel, M. and Osterrieder, N. and Conrad, C. and Eils, R. and Radbruch, H. and Giavalisco, P. and Drosten, C. and Müller, M.A.
Nature Communications 12 (1): 3818. 21 June 2021

Salt transiently inhibits mitochondrial energetics in mononuclear phagocytes.
Geisberger, S. and Bartolomaeus, H. and Neubert, P. and Willebrand, R. and Zasada, C. and Bartolomaeus, T. and McParland, V. and Swinnen, D. and Geuzens, A. and Maifeld, A. and Krampert, L. and Vogl, M. and Mähler, A. and Wilck, N. and Marko, L. and Tilic, E. and Forslund, S.K. and Binger, K.J. and Stegbauer, J. and Dechend, R. and Kleinewietfeld, M. and Jantsch, J. and Kempa, S. and Müller, D.N.
Circulation 144 (2): 144-158. 13 July 2021

Complement activation induces excessive T cell cytotoxicity in severe COVID-19.
Georg, P. and Astaburuaga-García, R. and Bonaguro, L. and Brumhard, S. and Michalick, L. and Lippert, L.J. and Kostevc, T. and Gäbel, C. and Schneider, M. and Streitz, M. and Demichev, V. and Gemünd, I. and Barone, M. and Tober-Lau, P. and Helbig, E.T. and Stein, J. and Dey, H.P. and Paclik, D. and Mülleder, M. and Aulakh, S.K. and Mei, H.E. and Schulz, A.R. and Hippenstiel, S. and Corman, V.M. and Beule, D. and Wyler, E. and Landthaler, M. and Obermayer-Wasserscheid, B. and Boor, P. and Demir, M. and Wesselmann, H. and Suttorp, N. and Uhrig, A. and Müller-Redetzky, H. and Nattermann, J. and Kuebler, W.M. and Meisel, C. and Ralser, M. and Schultze, J.L. and Aschenbrenner, A.C. and Thibeault, C. and Kurth, F. and Sander, L.E. and Blüthgen, N. and Sawitzki, B.
medRxiv : 2021.06.08.21258481. 11 June 2021

Assessing genome-wide dynamic changes in enhancer activity during early mESC differentiation by FAIRE-STARR-seq.
Glaser, L.V. and Steiger, M. and Fuchs, A. and van Bömmel, A. and Einfeldt, E. and Chung, H.R. and Vingron, M. and Meijsing, S.H.
Nucleic Acids Research 49 (21): 12178-12195. 2 December 2021

Assessing genome-wide dynamic changes in enhancer activity during early mESC differentiation by FAIRE-STARR-seq.
Glaser, L.V. and Steiger, M. and Fuchs, A. and van Bömmel, A. and Einfeldt, E. and Chung, H.R. and Vingron, M. and Meijsing, S.H.
bioRxiv : 2021.06.04.446899. 6 June 2021

The zinc finger antiviral protein ZAP restricts human cytomegalovirus and selectively binds and destabilizes viral UL4/UL5 transcripts.
Gonzalez-Perez, A.C. and Stempel, M. and Wyler, E. and Urban, C. and Piras, A. and Hennig, T. and Ganskih, S. and Wei, Y. and Heim, A. and Landthaler, M. and Pichlmair, A. and Dölken, L. and Munschauer, M. and Erhard, F. and Brinkmann, M.M.
mBio 12 (3): e02683-20. 4 May 2021

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.
Grapotte, M. and Saraswat, M. and Bessière, C. and Menichelli, C. and Ramilowski, J.A. and Severin, J. and Hayashizaki, Y. and Itoh, M. and Tagami, M. and Murata, M. and Kojima-Ishiyama, M. and Noma, S. and Noguchi, S. and Kasukawa, T. and Hasegawa, A. and Suzuki, H. and Nishiyori-Sueki, H. and Frith, M.C. and Chatelain, C. and Carninci, P. and de Hoon, M.J.L. and Wasserman, W.W. and Bréhélin, L. and Lecellier, C.H.
Nature Communications 12 (1): 3297. 2 June 2021

Rare variant analysis in eczema identifies exonic variants in DUSP1, NOTCH4 and SLC9A4.
Grosche, S. and Marenholz, I. and Esparza-Gordillo, J. and Arnau-Soler, A. and Pairo-Castineira, E. and Rüschendorf, F. and Ahluwalia, T.S. and Almqvist, C. and Arnold, A. and Baurecht, H. and Bisgaard, H. and Bønnelykke, K. and Brown, S.J. and Bustamante, M. and Curtin, J.A. and Custovic, A. and Dharmage, S.C. and Esplugues, A. and Falchi, M. and Fernandez-Orth, D. and Ferreira, M.A.R. and Franke, A. and Gerdes, S. and Gieger, C. and Hakonarson, H. and Holt, P.G. and Homuth, G. and Hubner, N. and Hysi, P.G. and Jarvelin, M.R. and Karlsson, R. and Koppelman, G.H. and Lau, S. and Lutz, M. and Magnusson, P.K.E. and Marks, G.B. and Müller-Nurasyid, M. and Nöthen, M.M. and Paternoster, L. and Pennell, C.E. and Peters, A. and Rawlik, K. and Robertson, C.F. and Rodriguez, E. and Sebert, S. and Simpson, A. and Sleiman, P.M.A. and Standl, M. and Stölzl, D. and Strauch, K. and Szwajda, A. and Tenesa, A. and Thompson, P.J. and Ullemar, V. and Visconti, A. and Vonk, J.M. and Wang, C.A. and Weidinger, S. and Wielscher, M. and Sargent, C.L. and Xu, C.J. and Lee, Y.A.
Nature Communications 12 (1): 6618. 16 November 2021

How to find genomic regions relevant for gene regulation.
Guo, X. and Ohler, U. and Yildirim, F.
Medizinische Genetik 33 (2): 157-165. 14 August 2021

The dynamics of chromatin architecture in brain development and function.
Harabula, I. and Pombo, A.
Current Opinion in Genetics & Development 67 : 84-93. April 2021

Timed global reorganization of protein synthesis during neocortex neurogenesis at codon resolution.
Harnett, D. and Ambrozkiewicz, M.C. and Zinnall, U. and Borisova, E. and Rusanova, A. and Dannenberg, R. and Imami, K. and Münster-Wandowski, A. and Fauler, B. and Mielke, T. and Selbach, M. and Landthaler, M. and Spahn, C.M.T. and Tarabykin, V. and Ohler, U. and Kraushar, M.L.
bioRxiv : 2021.06.23.449626. 24 June 2021

Genome-wide analysis of actively translated open reading frames using riboTaper/ORFquant.
Harnett, D. and Meerdink, E. and Calviello, L. and Sydow, D. and Ohler, U.
Methods in Molecular Biology 2252 : 331-346. 2021

A comparison of nine machine learning mutagenicity models and their application for predicting pyrrolizidine alkaloids.
Helma, C. and Schöning, V. and Drewe, J. and Boss, P.
Frontiers in Pharmacology 12 : 708050. 22 July 2021

High Yap and Mll1 promote a persistent regenerative cell state induced by Notch signaling and loss of p53.
Heuberger, J. and Grinat, J. and Kosel, F. and Liu, L. and Kunz, S. and Vidal, R.O. and Keil, M. and Haybaeck, J. and Robine, S. and Louvard, D. and Regenbrecht, C. and Sporbert, A. and Sauer, S. and von Eyss, B. and Sigal, M. and Birchmeier, W.
Proceedings of the National Academy of Sciences of the United States of America 118 (22): e2019699118. 1 June 2021

Epithelial response to IFN-γ promotes SARS-CoV-2 infection.
Heuberger, J. and Trimpert, J. and Vladimirova, D. and Goosmann, C. and Lin, M. and Schmuck, R. and Mollenkopf, H.J. and Brinkmann, V. and Tacke, F. and Osterrieder, N. and Sigal, M.
EMBO Molecular Medicine 13 (4): e13191. 9 April 2021

HNRNPM controls circRNA biogenesis and splicing fidelity to sustain cancer cell fitness.
Ho, J.S. and Di Tullio, F. and Schwarz, M. and Low, D. and Incarnato, D. and Gay, F. and Tabaglio, T. and Zhang, J.X. and Wollmann, H. and Chen, L. and An, O. and Chan, T.H.M. and Hall Hickman, A. and Zheng, S. and Roudko, V. and Chen, S. and Karz, A. and Ahmed, M. and He, H.H. and Greenbaum, B.D. and Oliviero, S. and Serresi, M. and Gargiulo, G. and Mann, K.M. and Hernando, E. and Mulholland, D. and Marazzi, I. and Wee, D.K.B. and Guccione, E.
eLife 10 : e59654. 2 June 2021

Spatio-temporal mRNA tracking in the early zebrafish embryo.
Holler, K. and Neuschulz, A. and Drewe-Boß, P. and Mintcheva, J. and Spanjaard, B. and Arsiè, R. and Ohler, U. and Landthaler, M. and Junker, J.P.
Nature Communications 12 : 3358. 7 June 2021

Mit Einzelzell-Genomik die Entscheidungen von Zellen verfolgen [Deciphering cell fate decisions using single cell genomics].
Hu, B. and Junker, J.P.
BIOspektrum 27 (1): 25-27. February 2021

Cellular drivers of injury response and regeneration in the adult zebrafish heart.
Hu, B. and Lelek, S. and Spanjaard, B. and Simões, M.G. and Aliee, H. and Schäfer, R. and Theis, F. and Panáková, D. and Junker, J.P.
bioRxiv : 2021.01.07.425670. 7 January 2021

CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains.
Huang, H. and Zhu, Q. and Jussila, A. and Han, Y. and Bintu, B. and Kern, C. and Conte, M. and Zhang, Y. and Bianco, S. and Chiariello, A.M. and Yu, M. and Hu, R. and Tastemel, M. and Juric, I. and Hu, M. and Nicodemi, M. and Zhuang, X. and Ren, B.
Nature Genetics 53 (7): 1064-1074. July 2021

Apple peel and flesh contain pro-neurogenic compounds.
Ichwan, M. and Walker, T.L. and Nicola, Z. and Ludwig-Müller, J. and Böttcher, C. and Overall, R.W. and Adusumilli, V.S. and Bulut, M. and Sykes, A.M. and Hübner, N. and Ramirez-Rodriguez, G. and Ortiz-López, L. and Lugo-Hernández, E.A. and Kempermann, G.
Stem Cell Reports 16 (3): 548-565. 9 March 2021

Genomic aberrations after short-term exposure to colibactin-producing E. coli transform primary colon epithelial cells.
Iftekhar, A. and Berger, H. and Bouznad, N. and Heuberger, J. and Boccellato, F. and Dobrindt, U. and Hermeking, H. and Sigal, M. and Meyer, T.F.
Nature Communications 12 (1): 1003. 12 February 2021

Defence and adaptation mechanisms of the intestinal epithelium upon infection.
Iftekhar, A. and Sigal, M.
International Journal of Medical Microbiology 311 (3): 151486. April 2021

MACC1 regulates clathrin-mediated endocytosis and receptor recycling of transferrin receptor and EGFR in colorectal cancer.
Imbastari, F. and Dahlmann, M. and Sporbert, A. and Ciolli Mattioli, C. and Mari, T. and Scholz, F. and Timm, L. and Twamley, S. and Migotti, R. and Walther, W. and Dittmar, G. and Rehm, A. and Stein, U.
Cellular and Molecular Life Sciences 78 (7): 3525-3542. April 2021

Defective metabolic programming impairs early neuronal morphogenesis in neural cultures and an organoid model of Leigh syndrome.
Inak, G. and Rybak-Wolf, A. and Lisowski, P. and Pentimalli, T.M. and Jüttner, R. and Glažar, P. and Uppal, K. and Bottani, E. and Brunetti, D. and Secker, C. and Zink, A. and Meierhofer, D. and Henke, M.T. and Dey, M. and Ciptasari, U. and Mlody, B. and Hahn, T. and Berruezo-Llacuna, M. and Karaiskos, N. and Di Virgilio, M. and Mayr, J.A. and Wortmann, S.B. and Priller, J. and Gotthardt, M. and Jones, D.P. and Mayatepek, E. and Stenzel, W. and Diecke, S. and Kühn, R. and Wanker, E.E. and Rajewsky, N. and Schuelke, M. and Prigione, A.
Nature Communications 12 (1): 1929. 26 March 2021

Dolosigranulum pigrum modulates immunity against SARS-CoV-2 in respiratory epithelial cells.
Islam, M.A. and Albarracin, L. and Melnikov, V. and Andrade, B.G.N. and Cuadrat, R.R.C. and Kitazawa, H. and Villena, J.
Pathogens 10 (6): 634. 21 May 2021

Immunobiotic Lactobacilli improve resistance of respiratory epithelial cells to SARS-CoV-2 infection.
Islam, M.A. and Albarracin, L. and Tomokiyo, M. and Valdez, J.C. and Sacur, J. and Vizoso-Pinto, M.G. and Andrade, B.G.N. and Cuadrat, R.C. and Kitazawa, H. and Villena, J.
Pathogens 10 (9): 1197. September 2021

Functional analysis of a gene-edited mouse model to gain insights into the disease mechanisms of a titin missense variant.
Jiang, H. and Hooper, C. and Kelly, M. and Steeples, V. and Simon, J.N. and Beglov, J. and Azad, A.J. and Leinhos, L. and Bennett, P. and Ehler, E. and Kalisch-Smith, J.I. and Sparrow, D.B. and Fischer, R. and Heilig, R. and Isackson, H. and Ehsan, M. and Patone, G. and Huebner, N. and Davies, B. and Watkins, H. and Gehmlich, K.
Basic Research in Cardiology 116 (1): 14. 26 February 2021

Self-sustaining interleukin-8 loops drive a prothrombotic neutrophil phenotype in severe COVID-19.
Kaiser, R. and Leunig, A. and Pekayvaz, K. and Popp, O. and Joppich, M. and Polewka, V. and Escaig, R. and Anjum, A. and Hoffknecht, M.L. and Gold, C. and Brambs, S. and Engel, A. and Stockhausen, S. and Knottenberg, V. and Titova, A. and Haji, M. and Scherer, C. and Muenchhoff, M. and Hellmuth, J.C. and Saar, K. and Schubert, B. and Hilgendorff, A. and Schulz, C. and Kääb, S. and Zimmer, R. and Hübner, N. and Massberg, S. and Mertins, P. and Nicolai, L. and Stark, K.
JCI Insight 6 (18): e150862. 22 September 2021

CRISPR-based diagnostics.
Kaminski, M.M. and Abudayyeh, O.O. and Gootenberg, J.S. and Zhang, F. and Collins, J.J.
Nature Biomedical Engineering 5 (7): 643-656. July 2021

MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution.
Kaufmann, T.L. and Petkovic, M. and Watkins, T.B.K. and Colliver, E.C. and Laskina, S. and Thapa, N. and Minussi, D.C. and Navin, N. and Swanton, C. and Van Loo, P. and Haase, K. and Tarabichi, M. and Schwarz, R.F.
bioRxiv : 2021.02.28.433227. 6 September 2021

Profiling of sub-lethal in vitro effects of multi-walled carbon nanotubes reveals changes in chemokines and chemokine receptors.
Keshavan, S. and Andón, F.T. and Gallud, A. and Chen, W. and Reinert, K. and Tran, L. and Fadeel, B.
Nanomaterials 11 (4): 883. 30 March 2021

Transcriptional repression of NFKBIA triggers constitutive IKK- and proteasome-independent p65/RelA activation in senescence.
Kolesnichenko, M. and Mikuda, N. and Höpken, U.E. and Kärgel, E. and Uyar, B. and Tufan, A.B. and Milanovic, M. and Sun, W. and Krahn, I. and Schleich, K. and von Hoff, L. and Hinz, M. and Willenbrock, M. and Jungmann, S. and Akalin, A. and Lee, S. and Schmidt-Ullrich, R. and Schmitt, C.A. and Scheidereit, C.
EMBO Journal 40 (6): e104296. 15 March 2021

Simultaneous dimensionality reduction and integration for single-cell ATAC-seq data using deep learning.
Kopp, W. and Akalin, A. and Ohler, U.
bioRxiv : 2021.05.11.443540. 12 May 2021

Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19.
Krämer, B. and Knoll, R. and Bonaguro, L. and ToVinh, M. and Raabe, J. and Astaburuaga-García, R. and Schulte-Schrepping, J. and Kaiser, K.M. and Rieke, G.J. and Bischoff, J. and Monin, M.B. and Hoffmeister, C. and Schlabe, S. and De Domenico, E. and Reusch, N. and Händler, K. and Reynolds, G. and Blüthgen, N. and Hack, G. and Finnemann, C. and Nischalke, H.D. and Strassburg, C.P. and Stephenson, E. and Su, Y. and Gardner, L. and Yuan, D. and Chen, D. and Goldman, J. and Rosenstiel, P. and Schmidt, S.V. and Latz, E. and Hrusovsky, K. and Ball, A.J. and Johnson, J.M. and Koenig, P.A. and Schmidt, F.I. and Haniffa, M. and Heath, J.R. and Kümmerer, B.M. and Keitel, V. and Jensen, B. and Stubbemann, P. and Kurth, F. and Sander, L.E. and Sawitzki, B. and Aschenbrenner, A.C. and Schultze, J.L. and Nattermann, J.
Immunity 54 (11): 2650-2669. 9 November 2021

Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation.
Kubo, N. and Ishii, H. and Xiong, X. and Bianco, S. and Meitinger, F. and Hu, R. and Hocker, J.D. and Conte, M. and Gorkin, D. and Yu, M. and Li, B. and Dixon, J.R. and Hu, M. and Nicodemi, M. and Zhao, H. and Ren, B.
Nature Structural & Molecular Biology 28 (2): 152-161. February 2021

Health workforce response to Covid-19: What pandemic preparedness planning and action at the federal and state levels in Germany? Germany's health workforce responses to Covid-19.
Köppen, J. and Hartl, K. and Maier, C.B.
International Journal of Health Planning and Management 36 (S1): 71-91. May 2021

Generation of human brain organoids for mitochondrial disease modeling.
Le, S. and Petersilie, L. and Inak, G. and Menacho-Pando, C. and Kafitz, K.W. and Rybak-Wolf, A. and Rajewsky, N. and Rose, C.R. and Prigione, A.
Journal of Visualized Experiments (172): e62756. 21 June 2021

Virus-induced senescence is driver and therapeutic target in COVID-19.
Lee, S. and Yu, Y. and Trimpert, J. and Benthani, F. and Mairhofer, M. and Richter-Pechanska, P. and Wyler, E. and Belenki, D. and Kaltenbrunner, S. and Pammer, M. and Kausche, L. and Firsching, T.C. and Dietert, K. and Schotsaert, M. and Martínez-Romero, C. and Singh, G. and Kunz, S. and Niemeyer, D. and Ghanem, R. and Salzer, H.J.F. and Paar, C. and Mülleder, M. and Uccellini, M. and Michaelis, E.G. and Khan, A. and Lau, A. and Schönlein, M. and Habringer, A. and Tomasits, J. and Adler, J.M. and Kimeswenger, S. and Gruber, A.D. and Hoetzenecker, W. and Steinkellner, H. and Purfuerst, B. and Motz, R. and Di Pierro, F. and Lamprecht, B. and Osterrieder, N. and Landthaler, M. and Drosten, C. and García-Sastre, A. and Langer, R. and Ralser, M. and Eils, R. and Reimann, M. and Fan, D.N.Y. and Schmitt, C.A.
Nature 599 : 283-289. 11 November 2021

Nuclei isolation from adult mouse kidney for single-nucleus RNA-sequencing.
Leiz, J. and Hinze, C. and Boltengagen, A. and Braeuning, C. and Kocks, C. and Rajewsky, N. and Schmidt-Ott, K.M.
Journal of Visualized Experiments (175): e62901. September 2021

The Collaborative Research Center FONDA.
Leser, U. and Hilbrich, M. and Draxl, C. and Eisert, P. and Grunske, L. and Hostert, P. and Kainmüller, D. and Kao, O. and Kehr, B. and Kehrer, T. and Koch, C. and Markl, V. and Meyerhenke, H. and Rabl, T. and Reinefeld, A. and Reinert, K. and Ritter, K. and Scheuermann, B. and Schintke, F. and Schweikardt, N. and Weidlich, M.
Datenbank-Spektrum 21 : 255-260. November 2021

Predicting lethal courses in critically ill COVID-19 patients using a machine learning model trained on patients with non-COVID-19 viral pneumonia.
Lichtner, G. and Balzer, F. and Haufe, S. and Giesa, N. and Schiefenhövel, F. and Schmieding, M. and Jurth, C. and Kopp, W. and Akalin, A. and Schaller, S.J. and Weber-Carstens, S. and Spies, C. and von Dincklage, F.
Scientific Reports 11 (1): 13205. 24 June 2021

Gene expression analysis and next-generation sequencing.
Lindberg, E.L. and Hübner, N.
In: Encyclopedia of Molecular Pharmacology : Third Edition. Springer, Cham, 684-688. ISBN 978-3-030-57400-0 2021

Analysis of correlation and ionization from pair distributions in many-electron systems.
López-Rosa, S. and Angulo, J. C. and Martín, A. L. and Antolín, J.
European Physical Journal Plus 136 (7): 763. 22 July 2021

PatchPerPixMatch for automated 3d search of neuronal morphologies in light microscopy.
Mais, L. and Hirsch, P. and Managan, C. and Wang, K. and Rokicki, K. and Svirskas, R.R. and Dickson, B.J. and Korff, W. and Rubin, G.M. and Ihrke, G. and Meissner, G.W. and Kainmueller, D.
bioRxiv : 2021.07.23.453511. 26 July 2021

Automated reconstruction of whole-embryo cell lineages by learning from sparse annotations.
Malin-Mayor, C. and Hirsch, P. and Guignard, L. and McDole, K. and Wan, Y. and Lemon, W.C. and Keller, P.J. and Preibisch, S. and Funke, J.
bioRxiv : 2021.07.28.454016. 29 July 2021

Induced neurons from germ cells in Caenorhabditis elegans.
Marchal, I. and Tursun, B.
Frontiers in Neuroscience 15 : 771687. 3 December 2021

Locus specific epigenetic modalities of random allelic expression imbalance.
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Nature Communications 12 (1): 5330. 9 September 2021

GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data.
Markowski, J. and Kempfer, R. and Kukalev, A. and Irastorza-Azcarate, I. and Loof, G. and Kehr, B. and Pombo, A. and Rahmann, S. and Schwarz, R.F.
Bioinformatics 37 (19): 3128–3135. 1 October 2021

NF1 regulates mesenchymal glioblastoma plasticity and aggressiveness through the AP-1 transcription factor FOSL1.
Marques, C. and Unterkircher, T. and Kroon, P. and Oldrini, B. and Izzo, A. and Dramaretska, Y. and Ferrarese, R. and Kling, E. and Schnell, O. and Nelander, S. and Wagner, E.F. and Bakiri, L. and Gargiulo, G. and Carro, M.S. and Squatrito, M.
eLife 10 : e64846. 17 August 2021

The relevance of the SH2 domain for c-Src functionality in triple-negative breast cancer cells.
Mayoral-Varo, V. and Sánchez-Bailón, M.P. and Calcabrini, A. and García-Hernández, M. and Frezza, V. and Martín, M.E. and González, V.M. and Martín-Pérez, J.
Cancers 13 (3): 462. 26 January 2021

Identification of disease-relevant modulators of the SHH pathway in the developing brain.
Mecklenburg, N. and Kowalczyk, I. and Witte, F. and Görne, J. and Laier, A. and Mamo, T.M. and Gonschior, H. and Lehmann, M. and Richter, M. and Sporbert, A. and Purfürst, B. and Hübner, N. and Hammes, A.
Development 148 (17): dev199307. September 2021

Charcot-Marie-Tooth mutation in glycyl-tRNA synthetase stalls ribosomes in a pre-accommodation state and activates integrated stress response.
Mendonsa, S. and von Kuegelgen, N. and Bujanic, L. and Chekulaeva, M.
Nucleic Acids Research 49 (17): 10007-10017. 27 September 2021

Lymphocyte access to lymphoma is impaired by high endothelial venule regression.
Menzel, L. and Zschummel, M. and Crowley, T. and Franke, V. and Grau, M. and Ulbricht, C. and Hauser, A. and Siffrin, V. and Bajénoff, M. and Acton, S.E. and Akalin, A. and Lenz, G. and Willimsky, G. and Höpken, U.E. and Rehm, A.
Cell Reports 37 (4): 109878. 26 October 2021

Inferring time series chromatin states for promoter-enhancer pairs based on Hi-C data.
Miko, H. and Qiu, Y. and Gaertner, B. and Sander, M. and Ohler, U.
BMC Genomics 22 (1): 84. 28 January 2021

Mitochondrial variant enrichment from high-throughput single-cell RNA-seq resolves clonal populations.
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bioRxiv : 2021.03.08.434450. 9 March 2021

Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells.
Mimitou, E.P. and Lareau, C.A. and Chen, K.Y. and Zorzetto-Fernandes, A.L. and Hao, Y. and Takeshima, Y. and Luo, W. and Huang, T.S. and Yeung, B.Z. and Papalexi, E. and Thakore, P.I. and Kibayashi, T. and Wing, J.B. and Hata, M. and Satija, R. and Nazor, K.L. and Sakaguchi, S. and Ludwig, L.S. and Sankaran, V.G. and Regev, A. and Smibert, P.
Nature Biotechnology 39 (10): 1246-1258. October 2021

Single-cell genomics to study developmental cell fate decisions in zebrafish.
Moreno-Ayala, R. and Junker, J.P.
Briefings in Functional Genomics 20 (6): 420–426. November 2021

Variability of an early developmental cell population underlies stochastic laterality defects.
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Cell Reports 34 (2): 108606. 12 January 2021

NovoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport.
Moriel, N. and Senel, E. and Friedman, N. and Rajewsky, N. and Karaiskos, N. and Nitzan, M.
Nature Protocols 16 (9): 4177-4200. September 2021

Impact of uORFs in mediating regulation of translation in stress conditions.
Moro, S.G. and Hermans, C. and Ruiz-Orera, J. and Albà, M.M.
BMC Molecular and Cell Biology 22 (1): 29. 16 May 2021

A community-driven roadmap to advance research on translated open reading frames detected by Ribo-seq.
Mudge, J.M. and Ruiz-Orera, J. and Prensner, J.R. and Brunet, M.A. and Gonzalez, J.M. and Magrane, M. and Martinez, T. and Schulz, J.F. and Yang, Y.T. and Albà, M.M. and Baranov, P.V. and Bazzini, A. and Bruford, E. and Martin, M.J. and Carvunis, A.R. and Chen, J. and Couso, J.P. and Flicek, P. and Frankish, A. and Gerstein, M. and Hubner, N. and Ingolia, N.T. and Menschaert, G. and Ohler, U. and Roucou, X. and Saghatelian, A. and Weissman, J. and van Heesch, S.
bioRxiv : 2021.06.10.447896. 10 June 2021

Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics.
Muus, C. and Luecken, M.D. and Eraslan, G. and Sikkema, L. and Waghray, A. and Heimberg, G. and Kobayashi, Y. and Vaishnav, E.D. and Subramanian, A. and Smillie, C. and Jagadeesh, K.A. and Duong, E.T. and Fiskin, E. and Triglia, E.T. and Ansari, M. and Cai, P. and Lin, B. and Buchanan, J. and Chen, S. and Shu, J. and Haber, A.L. and Chung, H. and Montoro, D.T. and Adams, T. and Aliee, H. and Allon, S.J. and Andrusivova, Z. and Angelidis, I. and Ashenberg, O. and Bassler, K. and Bécavin, C. and Benhar, I. and Bergenstråhle, J. and Bergenstråhle, L. and Bolt, L. and Braun, E. and Bui, L.T. and Callori, S. and Chaffin, M. and Chichelnitskiy, E. and Chiou, J. and Conlon, T.M. and Cuoco, M.S. and Cuomo, A.S.E. and Deprez, M. and Duclos, G. and Fine, D. and Fischer, D.S. and Ghazanfar, S. and Gillich, A. and Giotti, B. and Gould, J. and Guo, M. and Gutierrez, A.J. and Habermann, A.C. and Harvey, T. and He, P. and Hou, X. and Hu, L. and Hu, Y. and Jaiswal, A. and Ji, L. and Jiang, P. and Kapellos, T.S. and Kuo, C.S. and Larsson, L. and Leney-Greene, M.A. and Lim, K. and Litviňuková, M. and Ludwig, L.S. and Lukassen, S. and Luo, W. and Maatz, H. and Madissoon, E. and Mamanova, L. and Manakongtreecheep, K. and Leroy, S. and Mayr, C.H. and Mbano, I.M. and McAdams, A.M. and Nabhan, A.N. and Nyquist, S.K. and Penland, L. and Poirion, O.B. and Poli, S. and Qi, C.C. and Queen, R. and Reichart, D. and Rosas, I. and Schupp, J.C. and Shea, C.V. and Shi, X. and Sinha, R. and Sit, R.V. and Slowikowski, K. and Slyper, M. and Smith, N.P. and Sountoulidis, A. and Strunz, M. and Sullivan, T.B. and Sun, D. and Talavera-López, C. and Tan, P. and Tantivit, J. and Travaglini, K.J. and Tucker, N.R. and Vernon, K.A. and Wadsworth, M.H. and Waldman, J. and Wang, X. and Xu, K. and Yan, W. and Zhao, W. and Ziegler, C.G.K.
Nature Medicine 27 (3): 546-559. 2 March 2021

Isolation of nuclei from mammalian cells and tissues for single-nucleus molecular profiling.
Nadelmann, E.R. and Gorham, J.M. and Reichart, D. and Delaughter, D.M. and Wakimoto, H. and Lindberg, E.L. and Litviňuková, M. and Maatz, H. and Curran, J.J. and Ischiu Gutierrez, D. and Hübner, N. and Seidman, C.E. and Seidman, J G
Current Protocols 1 (5): e132. May 2021

Deep learning is widely applicable to phenotyping embryonic development and disease.
Naert, T. and Çiçek, Ö. and Ogar, P. and Bürgi, M. and Shaidani, N.I. and Kaminski, M.M. and Xu, Y. and Grand, K. and Vujanovic, M. and Prata, D. and Hildebrandt, F. and Brox, T. and Ronneberger, O. and Voigt, F.F. and Helmchen, F. and Loffing, J. and Horb, M.E. and Willsey, H.R. and Lienkamp, S.S.
Development 148 (21): dev199664. 1 November 2021

Vascular tissue specific miRNA profiles reveal novel correlations with risk factors in coronary artery disease.
Neiburga, K. and Vilne, B. and Bauer, S. and Bongiovanni, D. and Ziegler, T. and Lachmann, M. and Wengert, S. and Hawe, J. and Güldener, U. and Westerlund, A. and Li, L. and Pang, S. and Yang, C. and Saar, K. and Huebner, N. and Maegdefessel, L. and Lange, R. and Krane, M. and Schunkert, H. and von Scheidt, M.
Biomolecules 11 (11): 1683. 12 November 2021

Maternal angiotensin increases placental leptin in early gestation via an alternative renin-angiotensin system pathway: suggesting a link to preeclampsia.
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Hypertension 77 (5): 1723-1736. May 2021

Endophilin A2 deficiency protects rodents from autoimmune arthritis by modulating T cell activation.
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Nature Communications 12 (1): 610. 27 January 2021

Temporal omics analysis in Syrian hamsters unravel cellular effector responses to moderate COVID-19.
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Nature Communications 12 (1): 4869. 11 August 2021

Longitudinal omics in Syrian hamsters integrated with human data unravel cellular effector responses to moderate COVID-19.
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The C. elegans pseudogene sspt-16 (F55A3.7) is required to safeguard germ cells against reprogramming.
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Protective immune trajectories in early viral containment of non-pneumonic SARS-CoV-2 infection.
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bioRxiv : 2021.02.03.429351. 3 February 2021

Longitudinal single-cell dynamics of chromatin accessibility and mitochondrial mutations in chronic lymphocytic leukemia mirror disease history.
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Cancer Discovery 11 (12): 3048-3063. December 2021

Variant profiling of colorectal adenomas from three patients of two families with MSH3-related adenomatous polyposis.
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PLoS ONE 16 (11): e0259185. 29 November 2021

Engineering, decoding and systems-level characterization of chimpanzee cytomegalovirus.
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bioRxiv : 2021.07.20.453063. 20 July 2021

RNF219 attenuates global mRNA decay through inhibition of CCR4-NOT complex-mediated deadenylation.
Poetz, F. and Corbo, J. and Levdansky, Y. and Spiegelhalter, A. and Lindner, D. and Magg, V. and Lebedeva, S. and Schweiggert, J. and Schott, J. and Valkov, E. and Stoecklin, G.
Nature Communications 12 (1): 7175. 9 December 2021

Single-cell analysis of arthritogenic alphavirus-infected human synovial fibroblasts links low abundance of viral RNA to induction of innate immunity and arthralgia-associated gene expression.
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Emerging Microbes & Infections 10 (1): 2151-2168. 16 November 2021

Single-cell transcriptomic analysis of antiviral responses and viral antagonism in Chikungunya virus-infected synovial fibroblasts.
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bioRxiv : 2020.06.07.138610. 11 June 2021

FRC-QE: a robust and comparable 3D microscopy image quality metric for cleared organoids.
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Integrated multi-omics analysis of RB-loss identifies widespread cellular programming and synthetic weaknesses.
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Communications Biology 4 (1): 977. 17 August 2021

Investigating the concept of accessibility for predicting novel RNA-RNA interactions.
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bioRxiv : 2021.06.03.446902. 3 June 2021

Chromothripsis followed by circular recombination drives oncogene amplification in human cancer.
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Nature Genetics 53 (12): 1673–1685. December 2021

Probabilistic deep learning for instance segmentation.
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Lecture Notes in Computer Science 12535 : 445-457. 2021

RNA dynamics in Alzheimer’s disease.
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Molecules 26 (17): 5113. 1 September 2021

Neurodegeneration in human brain organoids infected with herpes simplex virus type 1.
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bioRxiv : 2021.03.05.434122. 7 March 2021

Viruses and endogenous retroviruses as roots for neuroinflammation and neurodegenerative diseases.
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Frontiers in Neuroscience 15 : 648629. 12 March 2021

Dataset for: Modeling chemotherapy induced neurotoxicity with human induced pluripotent stem cell (iPSC)-derived sensory neurons.
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Modeling chemotherapy induced neurotoxicity with human induced pluripotent stem cell (iPSC)-derived sensory neurons.
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Neurobiology of Disease 155 : 105391. July 2021

Spatial and temporal intratumour heterogeneity has potential consequences for single biopsy-based neuroblastoma treatment decisions.
Schmelz, K. and Toedling, J. and Huska, M. and Cwikla, M.C. and Kruetzfeldt, L.M. and Proba, J. and Ambros, P.F. and Ambros, I.M. and Boral, S. and Lodrini, M. and Chen, C.Y. and Burkert, M. and Guergen, D. and Szymansky, A. and Astrahantseff, K. and Kuenkele, A. and Haase, K. and Fischer, M. and Deubzer, H.E. and Hertwig, F. and Hundsdoerfer, P. and Henssen, A.G. and Schwarz, R.F. and Schulte, J.H. and Eggert, A.
Nature Communications 12 (1): 6804. 23 November 2021

Biallelic variants in YRDC cause a developmental disorder with progeroid features.
Schmidt, J. and Goergens, J. and Pochechueva, T. and Kotter, A. and Schwenzer, N. and Sitte, M. and Werner, G. and Altmueller, J. and Thiele, H. and Nürnberg, P. and Isensee, J. and Li, Y. and Müller, C. and Leube, B. and Reinhardt, H.C. and Hucho, T. and Salinas, G. and Helm, M. and Jachimowicz, R.D. and Wieczorek, D. and Kohl, T. and Lehnart, S.E. and Yigit, G. and Wollnik, B.
Human Genetics 140 (12): 1679-1693. December 2021

The neuroinflammatory interleukin-12 signaling pathway drives Alzheimer's disease-like pathology by perturbing oligodendrocyte survival and neuronal homeostasis.
Schneeberger, S. and Kim, S.J. and Eede, P. and Boltengagen, A. and Braeuning, C. and Andreadou, M. and Becher, B. and Karaiskos, N. and Kocks, C. and Rajewsky, N. and Heppner, F.L.
bioRxiv : 2021.04.25.441313. 27 April 2021

Multifunctional RNA-binding proteins influence mRNA abundance and translational efficiency of distinct sets of target genes.
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PLoS Computational Biology 17 (12): e1009658. 8 December 2021

Multifunctional RNA-binding proteins influence mRNA abundance and translational efficiency of distinct sets of target genes.
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bioRxiv : 2021.04.13.439465. 6 July 2021

Dual-function RNA-binding proteins influence mRNA abundance and translational efficiency of distinct sets of target genes.
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bioRxiv : 2021.04.13.439465. 13 April 2021

Pathogenic variants associated with dilated cardiomyopathy predict outcome in pediatric myocarditis.
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Circulation Genomic and Precision Medicine 14 (4): e003250. 4 August 2021

TUNAR lncRNA encodes a microprotein that regulates neural differentiation and neurite formation by modulating calcium dynamics.
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Functional antagonism of chromatin modulators regulates epithelial-mesenchymal transition.
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Science Advances 7 (9): eabd7974. 24 February 2021

Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain.
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eLife 10 : e62719. 9 July 2021

Crowdsourcing digital health measures to predict Parkinson's disease severity: the Parkinson's Disease Digital Biomarker DREAM Challenge.
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Wie das Immunsystem SARS-CoV-2 den Weg ebnet [How the immune system paves the way for SARS-CoV-2].
Sigal, M.
Hygiene und Medizin 46 (3): 22-23. 2021

SARS-CoV-2 infection paralyzes cytotoxic and metabolic functions of the immune cells.
Singh, Y. and Trautwein, C. and Fendel, R. and Krickeberg, N. and Berezhnoy, G. and Bissinger, R. and Ossowski, S. and Salker, M.S. and Casadei, N. and Riess, O.
Heliyon 7 (6): e07147. June 2021

CYCLeR - a novel tool for the full isoform assembly and quantification of circRNAs.
Stefanov, S.R. and Meyer, I.M.
bioRxiv : 2021.04.27.441578. 28 April 2021

Light sheet fluorescence microscopy.
Stelzer, E.H.K. and Strobl, F. and Chang, B.J. and Preusser, F. and Preibisch, S. and McDole, K. and Fiolka, R.
Nature Reviews Methods Primers 1 (1): 73. 3 November 2021

Single-nuclei RNA-sequencing of plant tissues using a nanowell-based system.
Sunaga-Franze, D. and Muino, J.M. and Braeuning, C. and Xu, X. and Zong, M. and Smaczniak, C. and Yan, W. and Fischer, C. and Vidal, R. and Kliem, M. and Kaufmann, K. and Sauer, S.
Plant Journal 108 (3): 859-869. 5 November 2021

Single-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell states.
Triana, S. and Vonficht, D. and Jopp-Saile, L. and Raffel, S. and Lutz, R. and Leonce, D. and Antes, M. and Hernández-Malmierca, P. and Ordoñez-Rueda, D. and Ramasz, B. and Boch, T. and Jann, J.C. and Nowak, D. and Hofmann, W.K. and Müller-Tidow, C. and Hübschmann, D. and Alexandrov, T. and Benes, V. and Trumpp, A. and Paulsen, M. and Velten, L. and Haas, S.
Nature Immunology 22 (12): 1577-1589. December 2021

Single-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell states.
Triana, S.H. and Vonficht, D. and Jopp-Saile, L. and Raffel, S. and Lutz, R. and Leonce, D. and Ordoñez-Rueda, D. and Ramasz, B. and Boch, T. and Jann, J.C. and Nowak, D. and Hofmann, W.K. and Müller-Tidow, C. and Hübschmann, D. and Alexandrov, T. and Benes, V. and Trumpp, A. and Paulsen, M. and Velten, L. and Haas, S.
bioRxiv : 2021.03.18.435922. 2 September 2021

Mitogen-activated protein kinase activity drives cell trajectories in colorectal cancer.
Uhlitz, F. and Bischoff, P. and Peidli, S. and Sieber, A. and Trinks, A. and Lüthen, M. and Obermayer, B. and Blanc, E. and Ruchiy, Y. and Sell, T. and Mamlouk, S. and Arsie, R. and Wei, T.T. and Klotz-Noack, K. and Schwarz, R.F. and Sawitzki, B. and Kamphues, C. and Beule, D. and Landthaler, M. and Sers, C. and Horst, D. and Blüthgen, N. and Morkel, M.
EMBO Molecular Medicine 13 (10): e14123. 7 October 2021

Identification of leukemic and pre-leukemic stem cells by clonal tracking from single-cell transcriptomics.
Velten, L. and Story, B.A. and Hernández-Malmierca, P. and Raffel, S. and Leonce, D.R. and Milbank, J. and Paulsen, M. and Demir, A. and Szu-Tu, C. and Frömel, R. and Lutz, C. and Nowak, D. and Jann, J.C. and Pabst, C. and Boch, T. and Hofmann, W.K. and Müller-Tidow, C. and Trumpp, A. and Haas, S. and Steinmetz, L.M.
Nature Communications 12 (1): 1366. 1 March 2021

Dual-view light-sheet imaging through a tilted glass interface using a deformable mirror.
Vladimirov, N. and Preusser, F. and Wisniewski, J. and Yaniv, Z. and Desai, R.A. and Woehler, A. and Preibisch, S.
Biomedical Optics Express 12 (4): 2186-2203. 1 April 2021

Cannabidiol converts NF(κ)B into a tumor suppressor in glioblastoma with defined antioxidative properties.
Volmar, M.N.M. and Cheng, J. and Alenezi, H. and Richter, S. and Haug, A. and Hassan, Z. and Goldberg, M. and Li, Y. and Hou, M. and Herold-Mende, C. and Maire, C.L. and Lamszus, K. and Flüh, C. and Held-Feindt, J. and Gargiulo, G. and Topping, G.J. and Schilling, F. and Saur, D. and Schneider, G. and Synowitz, M. and Schick, J.A. and Kälin, R.E. and Glass, R.
Neuro-Oncology 23 (11): 1898-1910. November 2021

A biallelic variant in CLRN2 causes non-syndromic hearing loss in humans.
Vona, B. and Mazaheri, N. and Lin, S.J. and Dunbar, L.A. and Maroofian, R. and Azaiez, H. and Booth, K.T. and Vitry, S. and Rad, A. and Rüschendorf, F. and Varshney, P. and Fowler, B. and Beetz, C. and Alagramam, K.N. and Murphy, D. and Shariati, G. and Sedaghat, A. and Houlden, H. and Petree, C. and VijayKumar, S. and Smith, R.J.H. and Haaf, T. and El-Amraoui, A. and Bowl, M.R. and Varshney, G.K. and Galehdari, H.
Human Genetics 140 (6): 915-931. June 2021

Herpesviral induction of germline transcription factor DUX4 is critical for viral gene expression.
Walter, S. and Franke, V. and Drayman, N. and Wyler, E. and Tay, S. and Landthaler, M. and Akalin, A. and Ensser, A. and Full, F.
bioRxiv : 2021.03.24.436599. 24 March 2021

KDD Health Day/DSHealth 2021: Joint KDD 2021 Health Day and 2021 KDD Workshop on Applied Data Science for Healthcare: state of XAI and trustworthiness in health.
Wang, F. and Chakraborty, P. and Xu, T. and Hsueh, P.Y.S. and Sun, X. and Stiglic, G. and Crane, G. and Bian, J. and Haghverdi, L. and Yao, L. and Buettner, F.
In: KDD '21: The 27th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, 14-18 Aug 2021, Virtual Event Singapore. 14 August 2021

Swarm Learning for decentralized and confidential clinical machine learning.
Warnat-Herresthal, S. and Schultze, H. and Shastry, K.L. and Manamohan, S. and Mukherjee, S. and Garg, V. and Sarveswara, R. and Händler, K. and Pickkers, P. and Aziz, N.A. and Ktena, S. and Tran, F. and Bitzer, M. and Ossowski, S. and Casadei, N. and Herr, C. and Petersheim, D. and Behrends, U. and Kern, F. and Fehlmann, T. and Schommers, P. and Lehmann, C. and Augustin, M. and Rybniker, J. and Altmüller, J. and Mishra, N. and Bernardes, J.P. and Krämer, B. and Bonaguro, L. and Schulte-Schrepping, J. and De Domenico, E. and Siever, C. and Kraut, M. and Desai, M. and Monnet, B. and Saridaki, M. and Siegel, C.M. and Drews, A. and Nuesch-Germano, M. and Theis, H. and Heyckendorf, J. and Schreiber, S. and Kim-Hellmuth, S. and Nattermann, J. and Skowasch, D. and Kurth, I. and Keller, A. and Bals, R. and Nürnberg, P. and Rieß, O. and Rosenstiel, P. and Netea, M.G. and Theis, F. and Mukherjee, S. and Backes, M. and Aschenbrenner, A.C. and Ulas, T. and Breteler, M.M.B. and Giamarellos-Bourboulis, E.J. and Kox, M. and Becker, M. and Cheran, S. and Woodacre, M.S. and Goh, E.L. and Schultze, J.L.
Nature 594 (7862): 265-270. 10 June 2021

Rbm10 facilitates heterochromatin assembly via the Clr6 HDAC complex.
Weigt, M. and Gao, Q. and Ban, H. and He, H. and Mastrobuoni, G. and Kempa, S. and Chen, W. and Li, F.
Epigenetics & Chromatin 14 (1): 8. 19 January 2021

Increased risk of severe clinical course of COVID-19 in carriers of HLA-C*04:01.
Weiner, J. and Suwalski, P. and Holtgrewe, M. and Rakitko, A. and Thibeault, C. and Müller, M. and Patriki, D. and Quedenau, C. and Krüger, U. and Ilinsky, V. and Popov, I. and Balnis, J. and Jaitovich, A. and Helbig, E.T. and Lippert, L.J. and Stubbemann, P. and Real, L.M. and Macías, J. and Pineda, J.A. and Fernandez-Fuertes, M. and Wang, X. and Karadeniz, Z. and Saccomanno, J. and Doehn, J.M. and Hübner, R.H. and Hinzmann, B. and Salvo, M. and Blueher, A. and Siemann, S. and Jurisic, S. and Beer, J.H. and Rutishauser, J. and Wiggli, B. and Schmid, H. and Danninger, K. and Binder, R. and Corman, V.M. and Mühlemann, B. and Arjun Arkal, R. and Fragiadakis, G.K. and Mick, E. and Calfee, C.S. and Erle, D.J. and Hendrickson, C.M. and Kangelaris, K.N. and Krummel, M.F. and Woodruff, P.G. and Langelier, C.R. and Venkataramani, U. and García, F. and Zyla, J. and Drosten, C. and Braun, A. and Jones, T.C. and Suttorp, N. and Witzenrath, M. and Hippenstiel, S. and Zemojtel, T. and Skurk, C. and Wolfgang, P. and Borodina, T. and Ripke, S. and Sander, L.E. and Beule, D. and Landmesser, U. and Guettouche, T. and Kurth, F. and Heidecker, B.
EClinicalMedicine 40 : 101099. October 2021

SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis.
Wendisch, D. and Dietrich, O. and Mari, T. and von Stillfried, S. and Ibarra, I.L. and Mittermaier, M. and Mache, C. and Chua, R.L. and Knoll, R. and Timm, S. and Brumhard, S. and Krammer, T. and Zauber, H. and Hiller, A.L. and Pascual-Reguant, A. and Mothes, R. and Bülow, R.D. and Schulze, J. and Leipold, A.M. and Djudjaj, S. and Erhard, F. and Geffers, R. and Pott, F. and Kazmierski, J. and Radke, J. and Pergantis, P. and Baßler, K. and Conrad, C. and Aschenbrenner, A.C. and Sawitzki, B. and Landthaler, M. and Wyler, E. and Horst, D. and Hippenstiel, S. and Hocke, A. and Heppner, F.L. and Uhrig, A. and Garcia, C. and Machleidt, F. and Herold, S. and Elezkurtaj, S. and Thibeault, C. and Witzenrath, M. and Cochain, C. and Suttorp, N. and Drosten, C. and Goffinet, C. and Kurth, F. and Schultze, J.L. and Radbruch, H. and Ochs, M. and Eils, R. and Müller-Redetzky, H. and Hauser, A.E. and Luecken, M.D. and Theis, F.J. and Conrad, C. and Wolff, T. and Boor, P. and Selbach, M. and Saliba, A.E. and Sander, L.E.
Cell 184 (26): 6243-6261. 22 December 2021

Cell-type specialization is encoded by specific chromatin topologies.
Winick-Ng, W. and Kukalev, A. and Harabula, I. and Zea-Redondo, L. and Szabó, D. and Meijer, M. and Serebreni, L. and Zhang, Y. and Bianco, S. and Chiariello, A.M. and Irastorza-Azcarate, I. and Thieme, C.J. and Sparks, T.M. and Carvalho, S. and Fiorillo, L. and Musella, F. and Irani, E. and Triglia, E.T. and Kolodziejczyk, A.A. and Abentung, A. and Apostolova, G. and Paul, E.J. and Franke, V. and Kempfer, R. and Akalin, A. and Teichmann, S.A. and Dechant, G. and Ungless, M.A. and Nicodemi, M. and Welch, L. and Castelo-Branco, G. and Pombo, A.
Nature 599 (7886): 684-691. 25 November 2021

A trans locus causes a ribosomopathy in hypertrophic hearts that affects mRNA translation in a protein length-dependent fashion.
Witte, F. and Ruiz-Orera, J. and Ciolli Mattioli, C. and Blachut, S. and Adami, E. and Schulz, J.F. and Schneider-Lunitz, V. and Hummel, O. and Patone, G. and Mücke, M.B. and Šilhavý, Jan and Heinig, M. and Bottolo, L. and Sanchis, D. and Vingron, M. and Chekulaeva, M. and Pravenec, M. and Hubner, N. and van Heesch, S.
Genome Biology 22 (1): 191. 28 June 2021

Ythdf is a N6-methyladenosine reader that modulates Fmr1 target mRNA selection and restricts axonal growth in Drosophila.
Worpenberg, L. and Paolantoni, C. and Longhi, S. and Mulorz, M.M. and Lence, T. and Wessels, H.H. and Dassi, E. and Aiello, G. and Sutandy, F.X.R. and Scheibe, M. and Edupuganti, R.R. and Busch, A. and Möckel, M.M. and Vermeulen, M. and Butter, F. and König, J. and Notarangelo, M. and Ohler, U. and Dieterich, C. and Quattrone, A. and Soldano, A. and Roignant, J.Y.
EMBO Journal 40 (4): e104975. 15 February 2021

Transcriptomic profiling of SARS-CoV-2 infected human cell lines identifies HSP90 as target for COVID-19 therapy.
Wyler, E. and Mösbauer, K. and Franke, V. and Diag, A. and Gottula, L.T. and Arsiè, R. and Klironomos, F. and Koppstein, D. and Hönzke, K. and Ayoub, S. and Buccitelli, C. and Hoffmann, K. and Richter, A. and Legnini, I. and Ivanov, A. and Mari, T. and Del Giudice, S. and Papies, J. and Praktiknjo, S. and Meyer, T.F. and Müller, M.A. and Niemeyer, D. and Hocke, A. and Selbach, M. and Akalin, A. and Rajewsky, N. and Drosten, C. and Landthaler, M.
iScience 24 (3): 102151. 19 March 2021

CRNKL1 is a highly selective regulator of intron-retaining HIV-1 and cellular mRNAs.
Xiao, H. and Wyler, E. and Milek, M. and Grewe, B. and Kirchner, P. and Ekici, A. and Silva, A.B.O.V. and Jungnickl, D. and Full, F. and Thomas, M. and Landthaler, M. and Ensser, A. and Überla, K.
mBio 12 (1): e02525-20. 19 January 2021

Decline in IGF1 in the bone marrow microenvironment initiates hematopoietic stem cell aging.
Young, K. and Eudy, E. and Bell, R. and Loberg, M.A. and Stearns, T. and Sharma, D. and Velten, L. and Haas, S. and Filippi, M.D. and Trowbridge, J.J.
Cell Stem Cell 28 (8): 1473-1482. 5 August 2021

SPLICE-q: a Python tool for genome-wide quantification of splicing efficiency.
de Melo Costa, V.R. and Pfeuffer, J. and Louloupi, A. and Ørom, U.A.V. and Piro, R.M.
BMC Bioinformatics 22 (1): 368. 15 July 2021

This list was generated on Sun May 26 02:17:22 2024 CEST.
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