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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 3 May 2024 (In Press)

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

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

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 4 April 2024 (In Press)

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

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

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

Frequent ZNF217 mutations lead to transcriptional deregulation of interferon signal transduction via altered chromatin accessibility in B cell lymphoma.
Briest, F. and Noerenberg, D. and Hennch, C. and Yoshida, K. and Hablesreiter, R. and Nimo, J. and Sasca, D. and Kirchner, M. and Mansouri, L. and Inoue, Y. and Wiegand, L. and Staiger, A.M. and Casadei, B. and Korkolopoulou, P. and Weiner, J. and Lopez-Guillermo, A. and Warth, A. and Schneider, T. and Nagy, Á. and Klapper, W. and Hummel, M. and Kanellis, G. and Anagnostopoulos, I. and Mertins, P. and Bullinger, L. and Rosenquist, R. and Vassilakopoulos, T.P. and Ott, G. and Ogawa, S. and Damm, F.
Leukemia 37 (11): 2237-2249. November 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.
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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

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.
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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.
Lareau, C.A. and Dubois, S.M. and Buquicchio, F.A. and Hsieh, Y.H. and Garg, K. and Kautz, P. and Nitsch, L. and Praktiknjo, S.D. and Maschmeyer, P. and Verboon, J.M. and Gutierrez, J.C. and Yin, Y. and Fiskin, E. and Luo, W. and Mimitou, E.P. and Muus, C. and Malhotra, R. and Parikh, S. and Fleming, M.D. and Oevermann, L. and Schulte, J. and Eckert, C. and Kundaje, A. and Smibert, P. and Vardhana, S.A. and Satpathy, A.T. and Regev, A. and Sankaran, V.G. and Agarwal, S. and Ludwig, L.S.
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.
Lareau, C.A. and Liu, V. and Muus, C. and Praktiknjo, S.D. and Nitsch, L. and Kautz, P. and Sandor, K. and Yin, Y. and Gutierrez, J.C. and Pelka, K. and Satpathy, A.T. and Regev, A. and Sankaran, V.G. and Ludwig, L.S.
Nature Protocols 18 (5): 1416-1440. May 2023

Latent human herpesvirus 6 is reactivated in CAR T cells.
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Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome.
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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.
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Molecular Systems Biology 19 (10): e11427. 12 October 2023

mRNA stability and m(6)A are major determinants of subcellular mRNA localization in neurons.
Loedige, I. and Baranovskii, A. and Mendonsa, S. and Dantsuji, S. and Popitsch, N. and Breimann, L. and Zerna, N. and Cherepanov, V. and Milek, M. and Ameres, S. and Chekulaeva, M.
Molecular Cell 83 (15): 2709-2725. 3 August 2023

Human model of primary carnitine deficiency cardiomyopathy reveals ferroptosis as a novel mechanism.
Loos, M. and Klampe, B. and Schulze, T. and Yin, X. and Theofilatos, K. and Ulmer, B.M. and Schulz, C. and Behrens, C.S. and van Bergen, T.D. and Adami, E. and Maatz, H. and Schweizer, M. and Brodesser, S. and Skryabin, B.V. and Rozhdestvensky, T.S. and Bodbin, S. and Stathopoulou, K. and Christ, T. and Denning, C. and Hübner, N. and Mayr, M. and Cuello, F. and Eschenhagen, T. and Hansen, A.
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.
Ludwig, L.S. and Lareau, C.A.
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.
López-Rivera, J.A. and Leu, C. and Macnee, M. and Khoury, J. and Hoffmann, L. and Coras, R. and Kobow, K. and Bhattarai, N. and Pérez-Palma, E. and Hamer, H. and Brandner, S. and Rössler, K. and Bien, C.G. and Kalbhenn, T. and Pieper, T. and Hartlieb, T. and Butler, E. and Genovese, G. and Becker, K. and Altmüller, J. and Niestroj, L.M. and Ferguson, L. and Busch, R.M. and Nürnberg, P. and Najm, I. and Blümcke, I. and Lal, D.
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

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.
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Nature Methods 20 (7): 993-994. July 2023

Long-read sequencing identifies a common transposition haplotype predisposing for CLCNKB deletions.
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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.
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Nucleic Acids Research 51 (W1): W160-W167. 5 July 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.
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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

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.
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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.
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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.
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Journal of Cell Science 135 (2): jcs258818. January 2022

Optimization of synthetic molecular reporters for a mesenchymal glioblastoma transcriptional program by integer programming.
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Bioinformatics 38 (17): 4162-4171. 1 September 2022

Nanozyme-catalysed CRISPR assay for preamplification-free detection of non-coding RNAs.
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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.
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WARS1 and SARS1: two tRNA synthetases implicated in autosomal recessive microcephaly.
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Organoids as tools for fundamental discovery and translation - a Keystone Symposia report.
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Annals of the New York Academy of Sciences 1518 (1): 196-208. December 2022

Physical mechanisms of chromatin spatial organization.
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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.
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Single cell‐ and spatial 'omics revolutionize physiology.
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Acta Physiologica : e13848. 2 June 2022

Polymer models of chromatin imaging data in single cells.
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A polymer physics model to dissect genome organization in healthy and pathological phenotypes.
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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.
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Nature Communications 13 (1): 4070. 13 July 2022

Combining callers improves the detection of copy number variants from whole-genome sequencing.
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Cap analysis of gene expression reveals alternative promoter usage in a rat model of hypertension.
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Life Science Alliance 5 (4): e202101234. April 2022

Global analysis of human-to-mouse contact-dependent intercellular mRNA and lncRNA transfer in cell culture.
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Activated SUMOylation restricts MHC class I antigen presentation to confer immune evasion in cancer.
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Journal of Clinical Investigation 132 (9): e152383. 2 May 2022

A complex proinflammatory cascade mediates the activation of HSCs upon LPS exposure in vivo.
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Blood Advances 6 (11): 3513-3528. 10 June 2022

Molecular identity of proprioceptor subtypes innervating different muscle groups in mice.
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Nature Communications 13 (1): 6867. 11 November 2022

Hmga2 protein loss alters nuclear envelope and 3D chromatin structure.
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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.
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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.
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Polymers 14 (9): 1918. 9 May 2022

Polymer physics reveals a combinatorial code linking 3D chromatin architecture to 1D chromatin states.
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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.
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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.
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Single-cell profiling of proteins and chromatin accessibility using PHAGE-ATAC.
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Nature Biotechnology 40 (3): 374-381. March 2022

Diverse but unique astrocytic phenotypes during embryonic stem cell differentiation, culturing and development.
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Research Square : rs.3.rs-1362379/v1. 28 February 2022

Spermidine reduces neuroinflammation and soluble amyloid beta in an Alzheimer’s disease mouse model.
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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.
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Complement activation induces excessive T cell cytotoxicity in severe COVID-19.
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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.
Grinat, J. and Kosel, F. and Goveas, N. and Kranz, A. and Alexopoulou, D. and Rajewsky, K. and Sigal, M. and Stewart, A.F. and Heuberger, J.
Life Science Alliance 5 (4): e202101187. April 2022

Phenotypic spectrum of BLM- and RMI1-related Bloom syndrome.
Gönenc, I.I. and Elcioglu, N.H. and Martinez Grijalva, C. and Aras, S. and Großmann, N. and Praulich, I. and Altmüller, J. and Kaulfuß, S. and Li, Y. and Nürnberg, P. and Burfeind, P. and Yigit, G. and Wollnik, B.
Clinical Genetics 101 (5-6): 559-564. May 2022

A comparative study of graph matching algorithms in computer vision.
Haller, S. and Feineis, L. and Hutschenreiter, L. and Bernard, F. and Rother, C. and Kainmüller, D. and Swoboda, P. and Savchynskyy, B.
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A critical period of translational control during brain development at codon resolution.
Harnett, D. and Ambrozkiewicz, M.C. and Zinnall, U. and Rusanova, A. and Borisova, E. and Drescher, A.N. and Couce-Iglesias, M. and Villamil, G. 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.
Nature Structural & Molecular Biology 29 (12): 1277-1290. December 2022

Antigen presentation safeguards the integrity of the hematopoietic stem cell pool.
Hernández-Malmierca, P. and Vonficht, D. and Schnell, A. and Uckelmann, H.J. and Bollhagen, A. and Mahmoud, M.A.A. and Landua, S.L. and van der Salm, E. and Trautmann, C. and Raffel, S. and Grünschläger, F. and Lutz, R. and Ghosh, M. and Renders, S. and Correia, N. and Donato, E. and Dixon, K.O. and Hirche, C. and Andresen, C. and Robens, Cl. and Werner, P.S. and Boch, T. and Eisel, D. and Osen, W. and Pilz, F. and Przybylla, A. and Klein, C. and Buchholz, F. and Milsom, M.D. and Essers, M.A.G. and Eichmüller, S.B. and Hofmann, W.K. and Nowak, D. and Hübschmann, D. and Hundemer, M. and Thiede, C. and Bullinger, L. and Müller-Tidow, C. and Armstrong, S.A. and Trumpp, A. and Kuchroo, V.K. and Haas, S.
Cell Stem Cell 29 (5): 760-775. 5 May 2022

Single-cell transcriptomics reveals common epithelial response patterns in human acute kidney injury.
Hinze, C. and Kocks, C. and Leiz, J. and Karaiskos, N. and Boltengagen, A. and Cao, S. and Skopnik, C.M. and Klocke, J. and Hardenberg, J.H. and Stockmann, H. and Gotthardt, I. and Obermayer, B. and Haghverdi, L. and Wyler, E. and Landthaler, M. and Bachmann, S. and Hocke, A.C. and Corman, V. and Busch, J. and Schneider, W. and Himmerkus, N. and Bleich, M. and Eckardt, K.U. and Enghard, P. and Rajewsky, N. and Schmidt-Ott, K.M.
Genome Medicine 14 (1): 103. 9 September 2022

Mathematical and bioinformatic tools for cell tracking.
Hirsch, P. and Epstein, L. and Guignard, L.
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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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Development 149 (20): dev200744. 15 October 2022

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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Semi-automated assembly of high-quality diploid human reference genomes.
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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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Epilepsia 63 (3): 723-735. March 2022

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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European Journal of Human Genetics 11 August 2022 (In Press)

Simultaneous dimensionality reduction and integration for single-cell ATAC-seq data using deep learning.
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Nature Machine Intelligence 4 (2): 162-168. February 2022

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.
Lareau, C.A. and Romagnani, C. and Ludwig, L.S.
Frontiers in Immunology 13 : 1062415. 18 October 2022

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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bioRxiv : 2021.09.26.461850v3. 9 February 2022

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.
Liabeuf, D. and Oshima, M. and Stange, D.E. and Sigal, M.
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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Blood 139 (16): 2534-2546. 21 April 2022

AntiSplodge: a neural-network-based RNA-profile deconvolution pipeline designed for spatial transcriptomics.
Lund, J.B. and Lindberg, E.L. and Maatz, H. and Pottbaecker, F. and Hübner, N. and Lippert, C.
NAR Genomics and Bioinformatics 4 (4): lqac073. December 2022

Tongue immune compartment analysis reveals spatial macrophage heterogeneity.
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eLife 11 : 77490. 24 June 2022

Renal deletion of LRRC8/VRAC channels induces proximal tubulopathy.
López-Cayuqueo, K.I. and Planells-Cases, R. and Pietzke, M. and Oliveras, A. and Kempa, S. and Bachmann, S. and Jentsch, T.J.
Journal of the American Society of Nephrology 33 (8): 1528-1545. August 2022

SAMHD1 controls innate immunity by regulating condensation of immunogenic self RNA.
Maharana, S. and Kretschmer, S. and Hunger, S. and Yan, X. and Kuster, D. and Traikov, S. and Zillinger, T. and Gentzel, M. and Elangovan, S. and Dasgupta, P. and Chappidi, N. and Lucas, N. and Maser, K.I. and Maatz, H. and Rapp, A. and Marchand, V. and Chang, Y.T. and Motorin, Y. and Hubner, N. and Hartmann, G. and Hyman, A.A. and Alberti, S. and Lee-Kirsch, M.A.
Molecular Cell 82 (19): 3712-3728.e10. 6 October 2022

Satellite glia of the adult dorsal root ganglia harbor stem cells that yield glia under physiological conditions and neurons in response to injury.
Maniglier, M. and Vidal, M. and Bachelin, Corinne and Deboux, C. and Chazot, J. and Garcia-Diaz, B. and Baron-Van Evercooren, A.
Stem Cell Reports 17 (11): 2467-2483. 8 November 2022

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.
Journal of Proteome Research 21 (6): 1575-1587. 3 June 2022

The little skate genome and the evolutionary emergence of wing-like fin appendages.
Marletaz, F. and de la Calle-Mustienes, E. and Acemel, R.D. and Nakamura, T. and Paliou, C. and Naranjo, S. and Martinez-Garcia, 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.E. and Gonzalez-Rajal, A. 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 Gabaldon, T. and Tena, J.J. and Lupianez, D.G. and Rokhsar, D.S. and Gomez-Skarmeta, J.L.
bioRxiv : 2022.03.21.485123. 22 March 2022

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