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2025

Helmholtz Health task force to strengthen prevention research and its translation globally.

Nature Medicine 18 April 2025 (In Press)

Transcript-specific enrichment enables profiling of rare cell states via single-cell RNA sequencing.
Abay, T., Stickels, R.R., Takizawa, M.T., Nalbant, B.N., Hsieh, Y.H., Hwang, S., Snopkowski, C., Yu, K.K.H., Abou-Mrad, Z., Tabar, V., Howitt, B.E, Ludwig, L.S., Chaligné, R., Satpathy, A.T and Lareau, C.A.
Nature Genetics 57 (2): 451-460. February 2025

Clonal driver neoantigen loss under EGFR TKI and immune selection pressures.
Al Bakir, M., Reading, J.L., Gamble, S., Rosenthal, R., Uddin, I., Rowan, A., Przewrocka, J., Rogers, A., Wong, Y.N.S., Bentzen, A.K., Veeriah, S., Ward, S., Garnett, A.T., Kalavakur, P., Martínez-Ruiz, C., Puttick, C., Huebner, A., Cook, D.E., Moore, D.A., Abbosh, C., Hiley, C.T., Naceur-Lombardelli, C., Watkins, T.B.K., Petkovic, M., Schwarz, R.F., Gálvez-Cancino, F., Litchfield, K., Meldgaard, P., Sorensen, B.S., Madsen, L.B., Jäger, D., Forster, M.D., Arkenau, T., Domingo-Vila, C., Tree, T.I.M., Kadivar, M., Hadrup, S.R., Chain, B., Quezada, S.A., McGranahan, N. and Swanton, C.
Nature 639 (639): 639. 27 March 2025

Targeting autoimmunity with CD19-CAR T cell therapy: efficacy and seroconversion in diffuse systemic sclerosis and rheumatoid arthritis.
Albach, F.N., Minopoulou, I., Wilhelm, A., Biesen, R., Kleyer, A., Wiebe, E., Fleischmann, A., Frick, M., Damm, F., Gogolok, J., Serve, S., Locher, B.N., Borie, D., Casteleyn, V., Siegert, E., Dörner, T., Alexander, T., Furth, C., Zernicke, J., Movassaghi, K., Hütter-Krönke, M.L., Schrezenmeier, E., Schneider, U., Bullinger, L., Krönke, G., Penack, O. and Simon, D.
Rheumatology : keaf077. 24 February 2025 (In Press)

Merkel cell polyomavirus infection and persistence modelled in skin organoids.
Albertini, S., Czech-Sioli, M., Guenther, T., Virdi, S., Blümke, P., Röpke, L., Brinschwitz, V., Dandri, M., Allweiss, L., Reimer, R., Schneider, C., Hansen, A., Krasemann, S., Wyler, E., Landthaler, M., Grundhoff, A. and Fischer, N.
bioRxiv : 2025.02.11.637697. 12 February 2025

Growth differentiation factor-15: a promising biomarker and target in cancer patients.
Anker, M., Bullinger, L., Keller, U. and Khan, M.S.
JACC: CardioOncology 7 (2): 153-156. February 2025

Intestinal interstitial fluid isolation provides novel insight into the human host-microbiome interface.
Avery, E.G., Haag, L.M., McParland, V., Kedziora, S.M., Zigra, G.J., Valdes, D.S., Kirchner, M., Popp, O., Geisberger, S., Nonn, O., Karlsen, T.V., N'Diaye, G., Yarritu, A., Bartolomaeus, H., Bartolomaeus, T.U.P., Tagiyeva, N.A., Wimmer, M.I., Haase, N., Zhang, Y.D., Wilhelm, A., Grütz, G., Tenstad, O., Wilck, N., Forslund, S.K., Klopfleisch, R., Kühl, A.A., Atreya, R., Kempa, S., Mertins, P., Siegmund, B., Wiig, H. and Müller, D.N.
Cardiovascular Research : cvae267. 13 January 2025 (In Press)

Epithelial OPA1 links mitochondrial fusion to inflammatory bowel disease.
Bao, L.L., Yu, Y.Q., González-Acera, M., Patankar, J.V., Giessl, A., Sturm, G., Kühl, A.A., Atreya, R., Erkert, L., Gámez-Belmonte, R., Krug, S.M., Schmid, B., Tripal, P., Chiriac, M.T., Hildner, K., Siegmund, B., Wirtz, S., Stürzl, M., Mohamed Abdou, M., Trajanoski, Z., Neurath, M.F., Zorzano, A. and Becker, C.
Science Translational Medicine 17 (781): eadn8699. January 2025

Dissecting the role of RNA-binding proteins in early herpes simplex virus 1 transcription using acute protein depletion.
Barke, N, Masser, S., Stalling, D., Wyler, E., Zinzen, R.P., Schreiner, S., Bosse, J. and Landthaler, M.
bioRxiv : 2025.02.10.637450. 11 February 2025

Identification of TTLL8, POTEE, and PKMYT1 as immunogenic cancer-associated antigens and potential immunotherapy targets in ovarian cancer.
Bassoy, E.Y., Raja, R., Rubino, T.E., Coscia, F., Goergen, K., Magtibay, P., Butler, K., Schmitt, A., Oberg, A.L. and Curtis, M.
OncoImmunology 14 (1): 2460276. 31 January 2025

SARS-CoV-2 infection of human lung ALI cultures reveals basal cells as relevant targets.
Baumgardt, M., Obermayer, B., Balázs, A., Löwa, A., Wyler, E., Teixeira Alves, L.G., Hellwig, K., Beule, D., Landthaler, M., Müller, M.A., Drosten, C., Mall, M.A., Hippenstiel, S., Hönzke, K. and Hocke, A.C.
Journal of Infectious Diseases 11 March 2025 (In Press)

Senescence-associated lineage-aberrant plasticity evokes T-cell-mediated tumor control.
Belenki, D., Richter-Pechanska, P., Shao, Z., Bhattacharya, A., Lau, A., de Freitas, J.A.N.L.F., Kandler, G., Hick, T.P., Cai, X., Scharnagl, Eva, Bittner, A., Schönlein, M., Kase, J., Pardon, K., Brzezicha, B., Thiessen, N., Bischof, O., Dörr, J.R., Reimann, M., Milanovic, M., Du, J., Yu, Y., Chapuy, B., Lee, S., Leser, U., Scheidereit, C., Wolf, J., Fan, D.N.Y. and Schmitt, C.A.
Nature Communications 16 (1): 3079. 31 March 2025

ImmuneLENS characterizes systemic immune dysregulation in aging and cancer.
Bentham, R., Jones, T.P., Black, J.R.M., Martinez-Ruiz, C., Dietzen, M., Litovchenko, M., Thol, K., Watkins, T.B.K., Bailey, C., Pich, O., Zhang, Z., Van Loo, P., Swanton, C. and McGranahan, N.
Nature Genetics 57 (3): 694-705. March 2025

Coordinated IFN-γ/TNF axis drives selective loss of activated enteric glia in inflammatory bowel diseases.
Bubeck, M., Penkert, K.A., Limberger, H., González Acera, M., Plattner, C., Ziegler, S., Muppirala, A.N., Forster, P., Jakob, M., Gamez-Belmonte, R., Erkert, L., Kulkarni, S., Günther, C., Atreya, R., Kühl, A.A., Hegazy, A., Hildner, K., Trajanoski, Z., Siegmund, B., Neurath, M.F., Rao, M., Progatzky, F., Lie, D.C., Becker, C., Romagnani, C., Ludwig, L.S., Klose, C.S.N. and Patankar, J.V.
bioRxiv : 2025.04.03.646820. 3 April 2025

Extrachromosomal circular DNA promotes inflammation and hepatocellular carcinoma development.
Chan, L.K., Shan, J., Rodriguez-Fos, E., Healy, M., Leary, P., Parrotta, R., Desboeufs, N., Semere, G., Wittstruck, N., Henssen, A. and Weber, A.
bioRxiv : 2025.01.22.634016. 24 January 2025

Genome-wide CRISPR screen in human T cells reveals regulators of FOXP3.
Chen, K.Y., Kibayashi, T., Giguelay, A., Hata, M., Nakajima, S., Mikami, N., Takeshima, Y., Ichiyama, K., Omiya, R., Ludwig, L.S., Hattori, K. and Sakaguchi, S.
Nature 26 March 2025 (In Press)

Reconstructing the three-dimensional architecture of extrachromosomal DNA with ec3D.
Chowdhury, B., Zhu, K., Li, C., Luebeck, J., Chapman, O.S., Kraft, K., Zhang, S., Chavez, L., Henssen, A.G., Mischel, P.S., Chang, H. and Bafna, V.
bioRxiv : 2025.02.01.636064. 6 February 2025

A proteogenomic view of synchronous endometrioid endometrial and ovarian cancer.
Coscia, F., Nielsen, A.B., Weigert, M., Watters, K., Javellana, M., Anglesio, M., Yamada, S.D., Lastra, R.R., Mann, M. and Lengyel, E.
Clinical Cancer Research 27 March 2025 (In Press)

Preclinical in vitro and in vivo evidence for targeting CD74 as an effective treatment strategy for cutaneous T-cell lymphomas.
Costanza, M., Giordano, C., von Brünneck, A.C., Zhao, J., Makky, A., Vinh, K., Montes-Mojarro, I.A., Reisinger, F., Forchhammer, S., Witalisz-Siepracka, A., Edtmayer, S., Stoiber, D., Yin, G., Horst, D., Fischer, A., Siebert, R., Nicolay, J.P., Yin, M., Janz, M., Fend, F., Becker, J.C., Schürch, C.M., Kenner, L., Assaf, C., Merkel, O. and Mathas, S.
British Journal of Dermatology 192 (5): 883-895. May 2025

Patient-reported outcomes with subcutaneous immunoglobulin in secondary immunodeficiency.
Cowan, J., Na, I.K., Gladiator, A., Kamieniak, M. and Mustafa, S.S.
Frontiers in Immunology 16 : 1528414. 20 March 2025

TIFA renders intestinal epithelial cells responsive to microbial ADP-heptose and drives colonic inflammation in mice.
Erkert, L., Ruder, B., Kabisch, M., Gamez Belmonte, R., Patankar, J.V., Gonzalez Acera, M., Schödel, L., Chiriac, M.T., Cineus, R., Gnafakis, S., Leupold, T., Thoma, O.M., Stolzer, I., Taut, A., Thonn, V., Zundler, S., Günther, C., Diefenbach, A., Kühl, A.A., Hegazy, A.N., Waldner, M., Basic, M., Bleich, A., Neurath, M.F., Wirtz, S. and Becker, C.
Mucosal Immunology 18 (2): 453-466. April 2025

Gene-editing in patient and humanized-mice primary muscle stem cells rescues dysferlin expression in dysferlin-deficient muscular dystrophy.
Escobar, H., Di Francescantonio, S., Smirnova, J., Graf, R., Müthel, S., Marg, A., Zhogov, A., Krishna, S., Metzler, E., Petkova, M., Daumke, O., Kühn, R. and Spuler, S.
Nature Communications 16 (1): 120. 2 January 2025

A transcriptional atlas of gut-innervating neurons reveals activation of interferon signaling and ferroptosis during intestinal inflammation.
Forster, P.M., Jakob, M.O., Yusuf, D., Bubeck, M., Limberger, H., Luo, Y., Thieme, P., Polici, A., Sterczyk, N., Boulekou, S., Bartel, L., Cosovanu, C., Witkowski, M., González-Acera, M., Kühl, A.A., Weidinger, C., Backofen, R., Hegazy, A.N., Patankar, J.V. and Klose, C.S.N.
Neuron 17 March 2025 (In Press)

Penta-ALFA-tagged substrates for self-labelling tags allow signal enhancement in microscopy.
Ghosh, S., Birke, R., Natarajan, A.K. and Broichhagen, J.
Journal of Peptide Science 31 (5): e70015. May 2025

The chromatin accessibility landscape of pediatric AML.
Giguelay, A.M. and Ludwig, L.S.
Blood 145 (11): 1109-1111. 13 March 2025

Targeting MYCN upregulates L1CAM tumor antigen in MYCN-dysregulated neuroblastoma to increase CAR T cell efficacy.
Grunewald, L., Andersch, L., Helmsauer, K., Schwiebert, S., Klaus, A., Henssen, A.G., Straka, T., Lodrini, M., Wicha, S.G., Fuchs, S., Hertwig, F., Westermann, F., Vitali, A., Caramel, C., Büchel, G., Eilers, M., Astrahantseff, K., Eggert, A., Höpken, U.E., Schulte, J.H., Blankenstein, T., Anders, K. and Künkele, A.
Pharmacological Research 212 : 107608. February 2025

Generation of a human induced pluripotent stem cell line (BIHi292-A) from PBMCs of a female patient diagnosed with Nasu-Hakola disease (NHD)/polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathy (PLOSL) carrying a novel heterozygous mutation in the TREM2 gene.
Göttert, R., Vallone, V.F., Stachelscheid, H., Metzger, J.J., Caedo, C.C., Buthut, M., Prüss, H., Endres, M., Schilling, S. and Gertz, K.
Stem Cell Research 83 : 103660. March 2025

Two-dimensional HRS condensates drive the assembly of flat clathrin lattices on endosomes.
Hakala, M., Moparthi, S.B., Ganeva, I., Gül, M., Espadas, J., Marcuello, C., Bernat-Silvestre, C., Colom, A., Kudryashev, M., Kukulski, W., Vassilopoulos, S., Kaksonen, M. and Roux, A.
bioRxiv : 2024.10.01.616068. 4 March 2025

Gonadal sex and temperature independently influence germ cell differentiation and meiotic progression in Trachemys scripta.
Hatkevich, T., Tezak, B.M., Acemel, R.D., Yee Chung, V.W., Lupiáñez, D.G. and Capel, B.
Proceedings of the National Academy of Sciences of the United States of America 122 (1): e2413191121. 7 January 2025

Extrusion of BMP2+ surface colonocytes promotes stromal remodeling and tissue regeneration.
Heuberger, J., Liu, L., Berger, H., van den Heuvel, J., Lin, M., Müllerke, S., Bayram, S., Beccaceci, G., de Jonge, H., Gherardi, E. and Sigal, M.
Nature Communications 16 (1): 4131. 3 May 2025

Serially quantifying TERT rearrangement breakpoints in circulating tumor DNA enables minimal residual disease monitoring in patients with neuroblastoma.
Hollander, J.F., Szymansky, A., Wünschel, J., Astrahantseff, K., Rosswog, C., Thorwarth, A., Thole-Kliesch, T.M., Chamorro Gonzalez, R., Hundsdörfer, P., Hauptmann, K., Schmelz, K., Gürgen, D., Rogasch, J.M.M., Henssen, A.G., Fischer, M., Schulte, J.H., Eckert, C., Eggert, A., Lodrini, M. and Deubzer, H.E.
Cancer Research Communications 5 (1): 167-177. 28 January 2025

Multimodal profiling of peripheral blood identifies proliferating circulating effector CD4(+) T cells as predictors for response to integrin α4β7-blocking therapy in inflammatory bowel disease.
Horn, V., Cancino, C.A., Steinheuer, L.M., Obermayer, B., Fritz, K., Nguyen, A.L., Juhran, K.S., Plattner, C., Bösel, D., Oldenburg, L., Burns, M., Schulz, A.R., Saliutina, M., Mantzivi, E., Lissner, D., Conrad, T., Mashreghi, M.F., Zundler, S., Sonnenberg, E., Schumann, M., Haag, L.M., Beule, D., Flatz, L., Trjanoski, Z., D'Haens, G., Weidinger, C., Mei, H.E., Siegmund, B., Thurley, K. and Hegazy, A.N.
Gastroenterology 168 (2): 327-343. February 2025

Spatial proteomics in translational and clinical research.
Horvath, P. and Coscia, F.
Molecular Systems Biology 14 April 2025 (In Press)

T cell receptors specific for an imatinib-induced mutation in BCR-ABL for adoptive T cell therapy.
Hsu, M.T., Willimsky, G., Hansmann, L. and Blankenstein, T.
Frontiers in Immunology 16 : 1518691. 27 January 2025

Leveraging large language models for data analysis automation.
Jansen, J.A., Manukyan, A., Al Khoury, N. and Akalin, A.
PLoS ONE 20 (2): e0317084. 21 February 2025

Prior chemotherapy deteriorates T-cell quality for CAR T-cell therapy in B-cell non-Hodgkin's lymphoma.
Junkuhn, C., Schiele, P., Walter, A.L., Hamm, F., Obermayer, B., Busch, D., Stroux, A., Frick, M., Penack, O., Damm, F., Polansky, J., Bullinger, L., Künkele, A., Frentsch, M. and Na, I.K.
Journal for ImmunoTherapy of Cancer 13 (4): e010709. April 2025

RIF1 integrates DNA repair and transcriptional requirements during the establishment of humoral immune responses.
Kabrani, E., Rahjouei, A., Berruezo-Llacuna, M., Ebeling, S., Saha, T., Altwasser, R., Delgado-Benito, V., Pavri, R. and Di Virgilio, M.
Nature Communications 16 (1): 777. 17 January 2025

Multicenter longitudinal quality assessment of MS-based proteomics in plasma and serum.
Kardell, O., Gronauer, T., von Toerne, C., Merl-Pham, J., König, A.C., Barth, T.K., Mergner, J., Ludwig, C., Tüshaus, J., Giesbertz, P., Breimann, S., Schweizer, L., Müller, T., Kliewer, G., Distler, U., Gomez-Zepeda, D., Popp, O., Qin, D., Teupser, D., Cox, J., Imhof, A., Küster, B., Lichtenthaler, S.F., Krijgsveld, J., Tenzer, S., Mertins, P., Coscia, F. and Hauck, S.M.
Journal of Proteome Research 24 (3): 1017-1029. 7 March 2025

Comparing functional and genomic-based precision medicine in blood cancer patients.
Kazianka, L., Pichler, A., Agreiter, C., Rohrbeck, J., Kornauth, C., Porpaczy, E., Sillaber, C., Sperr, W.R., Gleixner, K.V., Hauswirth, A., Jäger, U., Valent, P., Jonak, C., Porkert, S., Exner, R., Willenbacher, W., Wolf, D., Neumeister, P., Prochazka, K., Deutsch, A., Greil, R., Schmitt, C., Ristl, R., Mayerhoefer, M., Simonitsch-Klupp, I., Pemovska, T. and Staber, P.B.
HemaSphere 9 (4): e70129. April 2025

An integrated landscape of mRNA and protein isoforms.
Kedan, A., Zauber, H., Wang, M.R., Zhu, Q., Fang, L., Chen, W. and Selbach, M.
bioRxiv : 2025.04.16.648713. 19 April 2025

Simplified preanalytical laboratory procedures for therapeutic drug monitoring (TDM) in patients treated with high-dose methotrexate (HD-MTX) and glucarpidase.
Knörnschild, F.L., Liebig, S., Kießling, P., Prpic, M., Kim, T., Keller, U., Kappert, K., Schwartz, S. and Jahic, A.
Clinical Chemistry and Laboratory Medicine 63 (1): e11-e15. 2025

Dynamic nanoscale architecture of synaptic vesicle fusion in mouse hippocampal neurons.
Kroll, J., Kravčenko, U., Sadeghi, M., Diebolder, C.A., Ivanov, L., Lubas, M., Sprink, T., Schacherl, M., Kudryashev, M. and Rosenmund, C.
bioRxiv : 2025.02.11.635788. 12 February 2025

A phase I study of MAGE-A1-targeted T1367 T-cell receptor-based cell therapy in patients with advanced multiple myeloma.
Krüger, J., Obenaus, M., Blau, I.W., Hoser, D., Vaegler, M., Rauschenbach, H., Anagnostopoulos, I., Jöhrens, K., Scheuplein, V., Kieback, E., Böhme, J., Von Brünneck, A.C., Krönke, J., Busse, A., Willimsky, G., Blankenstein, T., Pezzutto, A., Keller, U. and Nogai, A.
Haematologica 110 (1): 244-250. January 2025

High incidence and impact of suspected exocrine pancreatic insufficiency in patients post-hematopoietic stem cell transplantation: a single-center prospective observational study.
Launspach, M., Mindermann, A., Schulz, J., Alasfar, L., Cyrull, S., Zirngibl, F., Oevermann, L., Künkele, A., Deubzer, H.E., von Bernuth, H., Pruß, A., Lang, P., Bufler, P., Eggert, A., von Stackelberg, A. and Schulte, J.H.
United European Gastroenterology Journal 13 (2): 257-267. March 2025

Macrophages recycle phagocytosed bacteria to fuel immunometabolic responses.
Lesbats, J., Brillac, A., Reisz, J.A., Mukherjee, P., Lhuissier, C., Fernández-Monreal, M., Dupuy, J.W., Sequeira, A., Tioli, G., De La Calle Arregui, C., Pinson, B., Wendisch, D., Rousseau, B., Efeyan, A., Sander, L.E., D'Alessandro, A. and Garaude, J.
Nature 640 (8058): 524-533. 10 April 2025

T cell-intrinsic lymphoproliferation as a key driver of intestinal autoimmunity in acquired generalized lipodystrophy.
Letizia, M., Omar, T., Weidner, P., Jakob, M.O., Freise, I., Krug, S.M., Löscher, B.S., Rosati, E., Obermayer, B., Gamez-Belmonte, M.D.L.R., Hecker, J., Ziegler, J.F., Weixler, B., Asbach, P., Kunkel, D., Stumvoll, M., Miehle, K., Becker, C., Klose, C.S.N., Glauben, R., Beule, D., Kühl, A., Franke, A., Sanders, A., Siegmund, B. and Weidinger, C.
medRxiv : 2025.02.19.25322160. 24 February 2025

Bone marrow breakout lesions act as key sites for tumor-immune cell diversification in multiple myeloma.
Lutz, R., Poos, A.M., Solé-Boldo, L., John, L., Wagner, J., Prokoph, N., Baertsch, M.A., Vonficht, D., Palit, S., Brobeil, A., Mechtersheimer, G., Hildenbrand, N., Hemmer, S., Steiger, S., Horn, S., Pepke, W., Spranz, D.M., Rehnitz, C., Sant, P., Mallm, J.P., Friedrich, M.J., Reichert, P., Huhn, S., Trumpp, A., Rippe, K., Haghverdi, L., Fröhling, S., Müller-Tidow, C., Hübschmann, D., Goldschmidt, H., Willimsky, G., Sauer, S., Raab, M.S., Haas, S. and Weinhold, N.
Science Immunology 10 (104): eadp6667. February 2025

Spatial-temporal diversity of extrachromosomal DNA shapes urothelial carcinoma evolution and tumor-immune microenvironment.
Lv, W., Zeng, Y., Li, C., Liang, Y., Tao, H., Zhu, Y., Sui, X., Li, Y., Jiang, S., Gao, Q., Rodriguez-Fos, E., Prasad, G., Wang, Y., Zhou, R., Xu, Z., Pan, X., Chen, L., Xiang, X., Teng, H., Sun, C., Qin, T., Dong, W., Li, Y., Lan, X., Li, X., Lin, L., Bolund, L., Yang, H., Verhaak, R.G.W., Faltas, B.M., Hansen, J.B., Wu, S., Mischel, P.S., Henssen, A.G., Bafna, V., Luebeck, J., Regenberg, B., Luo, Y., Lin, C. and Han, P.
Cancer Discovery : OF1-OF22. 7 May 2025 (In Press)

The cellular and molecular cardiac tissue responses in human inflammatory cardiomyopathies after SARS-CoV-2 infection and COVID-19 vaccination.
Maatz, H., Lindberg, E.L., Adami, E., López-Anguita, N., Perdomo-Sabogal, A., Cócera Ortega, L., Patone, G., Reichart, D., Myronova, A., Schmidt, S., Elsanhoury, A., Klein, O., Kühl, U., Wyler, E., Landthaler, M., Yousefian, S., Haas, S., Kurth, F., Teichmann, S.A., Oudit, G.Y., Milting, H., Noseda, M., Seidman, J.G., Seidman, C.E., Heidecker, B., Sander, L.E., Sawitzki, B., Klingel, K., Doeblin, P., Kelle, S., Van Linthout, S., Hubner, N. and Tschöpe, C.
Nature Cardiovascular Research 4 (3): 330-345. March 2025

Deep spatial proteomics of ovarian cancer precursor lesions delineates early disease changes and cell-of-origin signatures.
Makhmut, A., Dragomir, M.P., Fritzsche, S., Moebs, M., Schmitt, W.D., Taube, E.T. and Coscia, F.
bioRxiv : 2025.03.19.643504. 19 March 2025

Anti-CD19 CAR T cell therapy induces antibody seroconversion and complete B cell depletion in the bone marrow of a therapy-refractory patient with ANCA-associated vasculitis.
Minopoulou, I., Wilhelm, A., Albach, F., Kleyer, A., Wiebe, E., Schallenberg, S., Fleischmann, A., Frick, M., Damm, F., Gogolok, J., Serve, S., Locher, B.N., Borie, D., Casteleyn, V., Biesen, R., Dörner, T., Alexander, T., Zernicke, J., Movassaghi, K., Hütter-Krönke, M.L., Schrezenmeier, E., Schreiber, A., Schneider, U., Bullinger, L., Krönke, G., Penack, O. and Simon, D.
Annals of the Rheumatic Diseases 84 (3): e4-e7. March 2025

The macromolecular crystallography beamlines of the Helmholtz-Zentrum Berlin at the BESSY II storage ring: history, current status and future directions.
Mueller, U., Barthel, T., Benz, L.S., Bon, V., Crosskey, T., Genter Dieguez, C., Förster, R., Gless, C., Hauß, T., Heinemann, U., Hellmig, M., James, D., Lennartz, F., Oelker, M., Ovsyannikov, R., Singh, P., Wahl, M.C., Weber, G. and Weiss, M.S.
Journal of Synchrotron Radiation 32 (3) May 2025 (In Press)

Antagonistic regulation of LINE-1/Alu elements and their repressor APOBEC3B in cellular senescence.
Munot, D., Najjar, G., Singh, M., Günes, C., Sauter, D. and Arora, A.
bioRxiv : 2025.03.27.645653v2. 30 March 2025

Oncofetal reprogramming drives phenotypic plasticity in WNT-dependent colorectal cancer.
Mzoughi, S., Schwarz, M., Wang, X., Demircioglu, D., Ulukaya, G., Mohammed, K., Zorgati, H., Torre, D., Tomalin, L.E., Di Tullio, F., Company, C., Dramaretska, Y., Leushacke, M., Giotti, B., Lannagan, T.R., Lozano-Ojalvo, D., Karras, P., Vermeulen, P.B., Hasson, D., Sebra, R., Tsankov, A.M., Sansom, O.J., Marine, J.C., Barker, N., Gargiulo, G. and Guccione, E.
Nature Genetics 57 (2): 402-412. February 2025

Gauging antigen recognition by human primary T-cells featuring orthotopically exchanged TCRs of choice.
Mühlgrabner, V., Plach, A., Holler, J., Leitner, J., Steinberger, P., Dupré, L., Göhring, J. and Huppa, J.B.
Methods in Cell Biology 193 : 127-154. 5 February 2025

Engineering therapeutic regulatory T cells to overexpress G protein-coupled receptor 15 improves functional fitness for in vivo gut homing.
Müller, T.M., Liu, L.J., Wiesinger, M., Neurath, M.F., Voskens, C.J. and Zundler, S.
Gastroenterology 168 (2): 389-392. February 2025

Herpesviruses mimic zygotic genome activation to promote viral replication.
Neugebauer, E., Walter, S., Tan, J., Drayman, N., Franke, V., van Gent, M., Pennisi, S., Veratti, P., Stein, K.S., Welker, I., Tay, S., Verjans, G.M.G.M., Timmers, H.T.M., Akalin, A., Landthaler, M., Ensser, A., Wyler, E. and Full, F.
Nature Communications 16 (1): 710. 16 January 2025

Senescent syncytiotrophoblast secretion during early onset preeclampsia.
Nonn, O., Debnath, O., Valdes, D.S., Sallinger, K., Secener, A.K., Fischer, C., Tiesmeyer, S., Nimo, J., Kuenzer, T., Ulrich, J., Maxian, T., Knöfler, M., Karau, P., Bartolomaeus, H., Kroneis, T., Frolova, A., Neuper, L., Haase, N., Malt, A., Müller-Bötticher, N., Kräker, K., Kedziora, S., Forstner, D., Eils, R., Schmidt-Ullrich, R., Haider, S., Verlohren, S., Stern, C., Sugulle, M., Jones, S., Thilaganathan, B., Kaitu'u-Lino, T.J., Tong, S., Huppertz, B., El-Heliebi, A., Staff, A.C., Coscia, F., Müller, D.N., Dechend, R., Gauster, M., Ishaque, N. and Herse, F.
Hypertension 82 (5): 787-799. May 2025

Combining spatial transcriptomics and ECM imaging in 3D for mapping cellular interactions in the tumor microenvironment.
Pentimalli, T.M., Schallenberg, S., León-Periñán, D., Legnini, I., Theurillat, I., Thomas, G., Boltengagen, A., Fritzsche, S., Nimo, J., Ruff, L., Dernbach, G., Jurmeister, P., Murphy, S., Gregory, M.T., Liang, Y., Cordenonsi, M., Piccolo, S., Coscia, F., Woehler, A., Karaiskos, N., Klauschen, F. and Rajewsky, N.
Cell Systems : 101261. 11 April 2025 (In Press)

IBDome: an integrated molecular, histopathological, and clinical atlas of inflammatory bowel diseases.
Plattner, C., Sturm, G., Kühl, A.A., Atreya, R., Carollo, S., Gronauer, R., Rieder, D., Günther, M., Ormanns, S., Manzl, C., Meneghetti, A.R., Hegazy, A.N., Patankar, J., Carrero, Z.I., Neurath, M.F., Kather, J.N., Becker, C., Siegmund, B. and Trajanoski, Z.
bioRxiv : 2025.03.26.645544. 26 March 2025

Role of intestinal barrier disruption to acute-on-chronic liver failure.
Pohl, J., Aretakis, D., Tacke, F., Engelmann, C. and Sigal, M.
Seminars in Liver Disease 45 (1): 52-65. March 2025

The IBEX Knowledge-Base: a central resource for multiplexed imaging techniques.
Radtke, A.J., Anidi, I.U., Arakkal, L., Arroyo-Mejias, A.J., Beuschel, R.T., Börner, K., Chu, C.J., Clark, B., Clatworthy, M.R., Colautti, J., Coscia, F., Croteau, J., Denha, S., Dever, R., Dutra, W.O., Fritzsche, S., Fullam, S., Gerner, M.Y., Gola, A., Gollob, K.J., Hernandez, J.M., Hor, J.L., Ichise, H., Jing, Z., Jonigk, D., Kandov, E., Kastenmüller, W., Koenig, J.F.E., Kortekaas, R.K., Kothurkar, A., Kreins, A.Y., Lamborn, I.T., Lin, Y., Morais, K.L.P., Lunich, A., Luz, J.C.S., MacDonald, R.B., Makranz, C., Maltez, V.I., McDonough, J.E., Moriarty, R.V., Ocampo-Godinez, J.M., Olyntho, V.M., Oxenius, A., Padhan, K., Remmert, K., Richoz, N., Schrom, E.C., Shang, W., Shi, L., Shih, R.M., Speranza, E., Stierli, S., Teichmann, S.A., Veres, T.Z., Vierhout, M., Wachter, B.T., Wade-Vallance, A.K., Williams, M., Zangger, N., Germain, R.N. and Yaniv, Zi.
PLoS Biology 23 (3): e3003070. 19 March 2025

Metrics matter: why we need to stop using silhouette in single-cell benchmarking.
Rautenstrauch, P. and Ohler, U.
bioRxiv : 2025.01.21.634098. 24 January 2025

A kinetics-based model of hematopoiesis reveals extrinsic regulation of skewed lineage output from stem cells.
Rodriguez-Correa, E., Gruenschlaeger, F., Nizharadze, T., Anstee, N., Al-Sabah, J., Kumpost, V., Sedlmeier, A., Li, C., Ball, M., Fotopoulou, F., Jayarajan, J., Ghezzi, I., Knoch, J., Druce, M., Aurich, T., Buechler-Schaeff, M., Lux, S., Hernandez-Malmierca, P., Graesel, J., Vonficht, D., Mathioudaki, A., Zaugg, J.B., Mikut, R., Trumpp, A., Hoefer, T., Huebschmann, D., Haas, S. and Milsom, M.D.
bioRxiv : 2025.02.04.636388. 5 February 2025

Rhabdomyosarcoma of head and neck varies in aggressiveness depending on the specific site of origin.
Rohde, J., Henssen, A., Eggert, A. and Scheer, M.
Oral Oncology 164 : 107263. May 2025

Common hereditary variants of the APOE gene and posttransplant outcome in acute myeloid leukemia.
Ronnacker, J., Grau, M., Klasmeier, M., Klesse, C., Baldauf, H., Abert, S., Berdel, A.F., Füsser, F.T., Sandmann, S., Albring, J., Reicherts, C., Call, S., Marx, J., Floeth, M., Eßeling, E., Kolloch, L., Berning, P., Scheller, A., Wethmar, K., Schmidt, H., Schlüter, B., Berdel, W.E., Ostendorf, B.N., Tavazoie, S.F., Mikesch, J.H., Lenz, G., Fleischhauer, K., Schetelig, J., Stelljes, M. and Schliemann, C.
Blood 145 (17): 1943-1956. 24 April 2025

Selection of therapeutically effective T-cell receptors from the diverse tumor-bearing repertoire.
Rosenberger, L., Hansmann, L., Anastasopoulou, V., Wolf, S.P., Drousch, K., Moewes, C., Feng, X., Cao, G., Huang, J., Yew, P.Y., Strønen, E., Kato, T., Saligrama, N., Olweus, J., Nakamura, Y., Willimsky, G., Blankenstein, T., Schreiber, H. and Leisegang, M.
Journal for ImmunoTherapy of Cancer 13 (5): e011351. 2 May 2025

Characterizing uveal melanoma patients with peritoneal metastases: a retrospective single-center analysis.
Rosnev, S., Peuker, C.A., Piwonski, I., Ihlow, J., Leyvraz, S., Klingberg, J., Horst, D., Joosten, M., Möbs, M., Joussen, A.M., de Bucourt, M., Keilholz, U., Keller, U., Ochsenreither, S. and Rittig, S.M.
European Journal of Cancer 218 : 115280. 11 March 2025

Reduced monocytic IL10 expression in PD1 inhibitor-treated patients is a harbinger of severe immune-related adverse events.
Rosnev, S., Sterner, B., Schiele, P., Kolling, S., Martin, M., Flörcken, A., Erber, B., Wittenbecher, F., Kofla, G., Kurreck, A., Lang, T.J.L., von Einem, J.C., de Santis, M., Pelzer, U., Stintzing, S., Bullinger, L., Klinghammer, K., Geisel, D., Ochsenreither, S., Frentsch, M. and Na, I.K.
European Journal of Cancer 217 : 115252. 25 February 2025

The next generation of in situ multi-omics.
Salla, M., Penkert, K. and Ludwig, L.S.
Nature Methods 22 (3): 461-462. March 2025

Mapping dihydropteroate synthase evolvability through identification of a novel evolutionarily critical substructure.
Sanyal, D., Shivram, A, Pandey, D., Banerjee, S., Uversky, V.N., Muzata, D., Chivukula, A., Jasuja, R., Chattopadhyay, K. and Chowdhury, S.
International Journal of Biological Macromolecules : 143325. 18 April 2025 (In Press)

Persistence and/or senescence: not so lasting at last?
Schmitt, C.A.
Cancer Research 85 (1): 7-9. 2 January 2025

DuplexDiscoverer: a computational method for the analysis of experimental duplex RNA-RNA interaction data.
Semenchenko, E., Tsybulsky, V. and Meyer, I.M.
Nucleic Acids Research 53 (7): gkaf266. April 2025

Teclistamab in relapsed systemic sclerosis after autologous haematopoietic stem cell transplantation.
Siegert, E., Biesen, R., Dzamukova, M., Furth, C., Probst, M., Doellinger, F., Walter-Rittel, T., Fleischmann, A., Wilhelm, A., Beenken, A.E., Wiebe, E., Pecher, A.C., Henes, J., Florian, S., Simon, D., Kleyer, A., Burmester, G.R., Keller, U., Krönke, J., Krönke, G. and Alexander, T.
Annals of the Rheumatic Diseases 84 (4): 653-656. April 2025

A computational model elucidates the effect of oncogene induced expression alterations on the energy metabolism of neuroblastoma.
Simon, M., Benary, U., Baum, K., Schramm, A. and Wolf, J.
bioRxiv : 2025.02.19.639039. 24 February 2025

Outcomes with intensive treatment for acute myeloid leukemia: an analysis of two decades of data from the HARMONY Alliance.
Sobas, M.A., Turki, A.T., Ramiro, A.V., Sánchez, A.H., Elicegui, J.M., González, T., Melchor, R.A., Abáigar, M., Tur, L., Dall'Olio, D., Sträng, E., Tettero, J.M., Castellani, G., Benner, A., Döhner, K., Thiede, C., Metzeler, K.H., Haferlach, T., Damm, F., Ayala, R., Martínez-López, J., Mills, K.I., Sierra, J., Lehmann, S., Porta, M.G.D., Mayer, J., Reinhardt, D., Medina, R.V., Schulze-Rath, R., Barbus, M., Hernández-Rivas, J.M., Huntly, B.J.P., Ossenkoppele, G., Döhner, H. and Bullinger, L.
Haematologica 110 (5): 1126-1140. May 2025

Phosphoproteomics for studying signaling pathways evoked by hormones of the renin-angiotensin system: a source of untapped potential.
Souza-Silva, I.M., Carregari, V.C., Steckelings, U.M. and Verano-Braga, T.
Acta Physiologica 241 (2): e14280. February 2025

LINNAEUS: simultaneous single-cell lineage tracing and cell type identification.
Spanjaard, B. and Junker, J.P.
Methods in Molecular Biology 2886 : 243-263. 3 January 2025

Therapy adherence after interdisciplinary tumour board discussion is associated with improved outcome in soft tissue sarcoma: a Charité Comprehensive Cancer Centre analysis.
Strönisch, A., Rau, D., Wittenberg, S., Kaul, D., Koulaxouzidis, G., Öllinger, R., von Laffert, M., Jarosch, A., Schäfer, F., Keilholz, U., Bullinger, L., Märdian, S., Striefler, J. and Flörcken, A.
International Journal of Cancer 156 (4): 802-816. 15 February 2025

hnRNPA2B1 drives colorectal cancer progression via the circCDYL/EIF4A3/PHF8 axis.
Sun, Y.K., Wang, J.F., Sun, X.W. and Zhang, M.
Kaohsiung Journal of Medical Sciences 41 (3): e12943. March 2025

Antibiotic-perturbed microbiota and the role of probiotics.
Szajewska, H., Scott, K.P., de Meij, T., Forslund-Startceva, S.K., Knight, R., Koren, O., Little, P., Johnston, B.C., Łukasik, J., Suez, J., Tancredi, D.J. and Sanders, M.E.
Nature Reviews Gastroenterology & Hepatology 22 (3): 155-172. March 2025

Pronounced impairment of B cell differentiation during bone regeneration in adult immune experienced mice.
Tchouto, M.N., Bucher, C.H., Mess, A.K., Haas, S., Schmidt-Bleek, K., Duda, G.N., Beule, D. and Milek, M.
Frontiers in Immunology 16 : 1511902. 3 March 2025

Advanced disease and CD8(+) TEMRA cells predict severe infections in multiple myeloma.
Tranter, E., Busch, D., Heck, C., Blau, I.W., Nogai, A., Schiele, P., Meisel, C., Bullinger, L., Frentsch, M. and Na, I.K.
Frontiers in Immunology 16 12 February 2025

Acute promyelocytic leukemia: long-term outcomes from the HARMONY project.
Voso, M.T., Guarnera, L., Lehmann, S., Döhner, K., Döhner, H., Platzbecker, U., Russell, N.H., Dillon, R.J., Thomas, I., Ossenkoppele, G.J., Haferlach, T., Vignetti, M., La Sala, E., Piciocchi, A., Fazi, P., Villaverde Ramiro, Á., Tur Giménez, L., Gurnari, C., Bullinger, L. and Hernandez, J.M.
Blood 145 (2): 234-243. 9 January 2025

Clinical characteristics and outcomes in leptomeningeal disease with or without brain metastasis: insights from an explorative data analysis of the Charité LMD registry.
Wasilewski, D., Eitner, C., Ates, R., Murad, S., Shaked, Z., Steinle, J.A., Wetzel-Yalelis, A., Sargut, T.A., Rösler, J., Samman, M.A., Truckenmüller, P., Mertens, R., Kroneberg, D., Kowski, A., Radbruch, H., Capper, D., Ehret, F., Roohani, S., Frost, N., Nawabi, J., Onken, J., Schlaak, M., Blohmer, J.U., Pelzer, U., Keller, U., Sehouli, J., Vajkoczy, P., Keilholz, U. and Misch, M.
Journal of Neuro-Oncology 11 February 2025 (In Press)

The STRIPAK complex is required for radial sorting and laminin receptor expression in Schwann cells.
Weaver, M.R., Shkoruta, D., Pellegatta, M., Berti, C., Palmisano, M., Ferguson, S., Hurley, E., French, J., Patel, S., Belin, S., Selbach, M., Paul, F.E., Sim, F., Poitelon, Y. and Feltri, M.L.
Cell Reports 44 (3): 115401. 6 March 2025

Persistent abdominal pain and diarrhea after appendectomy-Crohn's disease versus intestinal tuberculosis.
Wizenty, J., Maibier, M. and Sigal, M.
JGH Open 9 (4): e70157. April 2025

Helicobacter pylori, microbiota and gastric cancer - principles of microorganism-driven carcinogenesis.
Wizenty, J. and Sigal, M.
Nature Reviews Gastroenterology & Hepatology 22 (5): 296-313. May 2025

Complex human hair bearing skin organoids as model for herpes simplex virus 1 infection in the skin.
Wyler, E., Albertini, S., Friedel, C.C., Manukyan, A., Huang, J., Krasemann, S., Plumbon, I., Altmüller, J., Conrad, T., Radbruch, H., Hafezi, W., Hansen, A., Grundhoff, A., Landthaler, M., Fischer, N. and Czech-Sioli, M.
bioRxiv : 2025.02.10.637415. 11 February 2025

Informationsschatz aus Umweltproben [Treasure trove of information from environmental samples].
Wyler, E. and Landthaler, M.
BIOspektrum 31 (1): 59-62. February 2025

Selective depletion of cancer cells with extrachromosomal DNA via lentiviral infection.
Yi, E., Gujar, A., Zhao, D., Suina, K., Jin, X., Pardon, K., Yu, Q., Kagermazova, L., Boeke, J.D., Henssen, A.G. and Verhaak, R.G.W.
bioRxiv : 2025.02.22.639631. 27 February 2025

Everolimus with or without mycophenolate mofetil for graft-versus-host disease prophylaxis after hematopoietic stem cell transplantation in children with acute kidney injury: a single-center retrospective Analysis.
Zirngibl, F., Gebert, P., Materne, B., Launspach, M., Künkele, A., Hundsdoerfer, P., Cyrull, S., Deubzer, H.E., Kühl, J.S., Eggert, A., Lang, P., Oevermann, L., von Stackelberg, A. and Schulte, J.H.
Transplantation and Cellular Therapy 31 (4): 257-257. April 2025

Total lesion glycolysis of primary tumor and lymphnodes is a strong predictor for development of distant metastases in oropharyngeal carcinoma patients with independent validation in automatically delineated lesions.
Zschaeck, S., Hajiyianni, M., Hausmann, P., Nikulin, P., Kukuk, E., Furth, C., Cegla, P., Lombardo, E., Kazmierska, J., Holzgreve, A., Strouthos, I., Stromberger, C., Belka, C., Baumann, M., Krause, M., Landry, G., Cholewinski, W., Kotzerke, J., Zips, D., Van den Hoff, J. and Hofheinz, F.
Cancer Imaging 25 (1): 18. 21 February 2025

Neuromuscular dysfunction in patient-derived FUS(R244RR)-ALS iPSC model via axonal downregulation of neuromuscular junction proteins.
von Kügelgen, N., Ludwik, K.A., Mendonsa, S., Römer, C., Becher, E., Breimann, L., Strauch, M., Mari, T., Mongellaz, S., Zuckerman, B., Efendic, F., Grexa, N., Oliveras-Martinez, A., Woehler, A., Selbach, M., La Bella, V., Ulitsky, I. and Chekulaeva, M.
NAR Molecular Medicine 2 (2): ugaf005. April 2025

Faecal cytolysin is associated with worse survival in patients with primary sclerosing cholangitis.
Özdirik, B., Berger, H., Tonetti, F.R., Cabré, N., Treichel, N., Clavel, T., Tacke, F., Sigal, M. and Schnabl, B.
Liver International 45 (4): e16181. April 2025

2024

Deciphering the impact of genomic variation on function.

Nature 633 (8028): 47-57. 5 September 2024

Genetic determinants of micronucleus formation in vivo.
Adams, D.J., Barlas, B., McIntyre, R.E., Salguero, I., van der Weyden, L., Barros, A., Vicente, J.R., Karimpour, N., Haider, A., Ranzani, M., Turner, G., Thompson, N.A., Harle, V., Olvera-León, R., Robles-Espinoza, C.D., Speak, A.O., Geisler, N., Weninger, W.J., Geyer, S.H., Hewinson, J., Karp, N.A., Fu, B., Yang, F., Kozik, Z., Choudhary, J., Yu, L., van Ruiten, M.S., Rowland, B.D., Lelliott, C.J., Del Castillo Velasco-Herrera, M., Verstraten, R., Bruckner, L., Henssen, A.G., Rooimans, M.A., de Lange, J., Mohun, T.J., Arends, M.J., Kentistou, K.A., Coelho, P.A., Zhao, Y., Zecchini, H., Perry, J.R.B., Jackson, S.P. and Balmus, G.
Nature 627 (8002): 130-136. 7 March 2024

Teclistamab-induced remission in refractory systemic lupus erythematosus.
Alexander, T., Krönke, J., Cheng, Q., Keller, U. and Krönke, G.
New England Journal of Medicine 391 (9): 864-866. 5 September 2024

CAR affinity modulates the sensitivity of CAR-T cells to PD-1/PD-L1-mediated inhibition.
Andreu-Saumell, I., Rodriguez-Garcia, A., Mühlgrabner, V., Gimenez-Alejandre, M., Marzal, B., Castellsagué, J., Brasó-Maristany, F., Calderon, H., Angelats, L., Colell, S., Nuding, M., Soria-Castellano, M., Barbao, P., Prat, A., Urbano-Ispizua, A., Huppa, J.B. and Guedan, S.
Nature Communications 15 (1): 3552. 26 April 2024

New cardiovascular biomarkers in patients with advanced cancer – a prospective study comparing MR-proADM, MR-proANP, copeptin, high-sensitivity troponin T and NT-proBNP.
Anker, M.S., Lück, L.C., Khan, M.S., Porthun, J., Hadzibegovic, S., Lena, A., Wilkenshoff, U., Weinländer, P., Evertz, R., Totzeck, M., Mahabadi, A.A., Rassaf, T., Anker, S.D., Bullinger, L., Keller, U., Karakas, M., Landmesser, U., Butler, J. and von Haehling, S.
European Journal of Heart Failure 26 November 2024 (In Press)

Dynamics of clonal hematopoiesis under DNA-damaging treatment in patients with ovarian cancer.
Arends, C.M., Kopp, K., Hablesreiter, R., Estrada, N., Christen, F., Moll, U.M., Zeillinger, R., Schmitt, W.D., Sehouli, J., Kulbe, H., Fleischmann, M., Ray-Coquard, I., Zeimet, A., Raspagliesi, F., Zamagni, C., Vergote, I., Lorusso, D., Concin, N., Bullinger, L., Braicu, E.I. and Damm, F.
Leukemia 38 (6): 1378-1389. June 2024

Targeted disruption of linkage-specific ubiquitylation reveals a key role of K29-linked ubiquitylation in epigenome integrity.
Arroyo-Gomez, J., Wang, J., Guérillon, C., Isaakova, E., Reverón-Gómez, N., Koutrouli, M., Rahmanto, A.S., Mitrofanov, K., Ingham, A., Schovsbo, S., Weischenfeldt, K., Coscia, F., Typas, D., Völker-Albert, M., Solis, V., Jensen, L.J., Groth, A., Mund, A., Beli, P., Shearer, R.F. and Mailand, N.
bioRxiv : 2024.10.29.620783. 2 November 2024

In situ Patch-seq analysis of microglia reveals a lack of stress genes as found in FACS-isolated microglia.
Bakina, O., Conrad, T., Mitic, N., Vidal, R.O., Obrusnik, T., Sai, S., Nolte, C., Semtner, M. and Kettenmann, H.
PLoS ONE 19 (7): e0302376. 11 July 2024

Extraembryonic gut endoderm cells undergo programmed cell death during development.
Batki, J., Hetzel, S., Schifferl, D., Bolondi, A., Walther, M., Wittler, L., Grosswendt, S., Herrmann, B.G. and Meissner, A.
Nature Cell Biology 26 (6): 868-877. June 2024

Novel human neurodevelopmental and neurodegenerative disease associated with IRF2BPL gene variants-mechanisms and therapeutic avenues.
Bauersachs, D., Bomholtz, L., Del Ray Mateos, S., Kühn, R. and Lisowski, P.
Frontiers in Neuroscience 18 : 1426177. 6 June 2024

Comparing malignant monocytosis across the updated WHO and ICC classifications of 2022.
Baumgartner, F., Baer, C., Bamopoulos, S.A., Ayoub, E., Truger, M., Meggendorfer, M., Lenk, M., Hoermann, G., Hutter, S., Müller, H., Walter, W., Mueller, M.L., Nadarajah, Ni., Blombery, P., Keller, U., Kern, W., Haferlach, C. and Haferlach, T.
Blood 143 (12): 1139-1156. 21 March 2024

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

Passenger gene coamplifications create collateral therapeutic vulnerabilities in cancer.
Bei, Y., Brame, Luca, Kirchner, M., Fritsche-Guenther, R., Kunz, S., Bhattacharya, A., Rusu, M.C., Gürgen, D., Dubois, F.P.B., Köppke, J.K.C., Proba, J., Wittstruck, N., Sidorova, O.A., Chamorro González, R., Dorado Garcia, H., Brückner, L., Xu, R., Giurgiu, M., Rodriguez-Fos, E., Yu, Q., Spanjaard, B., Koche, R.P., Schmitt, C.A., Schulte, J.H., Eggert, A., Haase, K., Kirwan, J., Hagemann, A.I., Mertins, P., Dörr, J.R. and Henssen, A.G.
Cancer Discovery 14 (3): 492-507. 1 March 2024

Virus-reactive T cells expanded in aplastic anemia eliminate hematopoietic progenitor cells by molecular mimicry.
Ben Hamza, A., Welters, C., Stadler, S., Brüggemann, M., Dietze, K., Brauns, O., Brümmendorf, T.H., Winkler, T.H., Bullinger, L., Blankenstein, T., Rosenberger, L., Leisegang, M., Kammertöns, T., Herr, W., Moosmann, A., Strobel, J., Hackstein, H., Dornmair, K., Beier, F. and Hansmann, L.
Blood 143 (14): 1365-1378. 4 April 2024

Rapid UPF1 depletion illuminates the temporal dynamics of the NMD-regulated transcriptome in human cells.
Boehm, V., Wallmeroth, D., Wulf, P.O., Teixeira Alves, L.G., Popp, O., Riedel, M., Wyler, E., Franitza, M., Gerbracht, J.V., Becker, K., Polkovnychenko, K., Del Giudice, S., Benlasfer, N., Mertins, P., Landthaler, M. and Gehring, N.H.
bioRxiv : 2024.03.04.583328. 8 March 2024

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

Assessing the efficacy and tolerability of PET-guided BrECADD versus eBEACOPP in advanced-stage, classical Hodgkin lymphoma (HD21): a randomised, multicentre, parallel, open-label, phase 3 trial.
Borchmann, P., Ferdinandus, J., Schneider, G., Moccia, A., Greil, R., Hertzberg, M., Schaub, V., Hüttmann, A., Keil, F., Dierlamm, J., Hänel, M., Novak, U., Meissner, J., Zimmermann, A., Mathas, S., Zijlstra, J.M., Fosså, A., Viardot, A., Hertenstein, B., Martin, S., Giri, P., Scholl, S., Topp, M.S., Jung, W., Vucinic, V., Beck, H.J., Kerkhoff, A., Unger, B., Rank, A., Schroers, R., zum Büschenfelde, C.M., de Wit, M., Trautmann-Grill, K., Kamper, P., Molin, D., Kreissl, S., Kaul, H., von Tresckow, B., Borchmann, S., Behringer, K., Fuchs, M., Rosenwald, A., Klapper, W., Eich, H.T., Baues, C., Zomas, A., Hallek, M., Dietlein, M., Kobe, C. and Diehl, V.
Lancet 404 (10450): 341-352. 27 July 2024

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

Imetelstat-mediated alterations in fatty acid metabolism to induce ferroptosis as a therapeutic strategy for acute myeloid leukemia.
Bruedigam, C., Porter, A.H., Song, A., Vroeg In de Wei, G., Stoll, T., Straube, J., Cooper, L., Cheng, G., Kahl, V.F.S., Sobinoff, A.P., Ling, V.Y., Jebaraj, B.M.C., Janardhanan, Y., Haldar, R., Bray, L.J., Bullinger, L., Heidel, F.H., Kennedy, G.A., Hill, M.M., Pickett, H.A., Abdel-Wahab, O., Hartel, G. and Lane, S.W.
Nature Cancer 5 (1): 47-65. January 2024

A type 1 immunity-restricted promoter of the IL-33 receptor gene directs antiviral T-cell responses.
Brunner, T.M., Serve, S., Marx, A.F., Fadejeva, J., Saikali, P., Dzamukova, M., Durán-Hernández, N., Kommer, C., Heinrich, F., Durek, P., Heinz, G.A., Höfer, T., Mashreghi, M.F., Kühn, R., Pinschewer, D.D. and Löhning, M.
Nature Immunology 25 (2): 256-267. February 2024

Making AML fly too close to the sun.
Bullinger, L. and Krönke, J.
Blood 143 (15): 1438-1439. 11 April 2024

Copy-number dosage regulates telomere maintenance and disease-associated pathways in neuroblastoma.
Burkert, M., Blanc, E., Thiessen, N., Weber, C., Toedling, J., Monti, R., Dombrowe, V.M., de Biase, M.S., Kaufmann, T.L., Haase, K., Waszak, S.M., Eggert, A., Beule, D., Schulte, J.H., Ohler, U. and Schwarz, R.F.
iScience 27 (10): 110918. 18 October 2024

Hyperphenylalaninemia and serotonin deficiency in Dnajc12-deficient mice.
Cao, Y., Popp, O., Milani, N., Qadri, F., Kühn, R., Mertins, P., Bader, M. and Alenina, N.
Communications Biology 7 (1): 1641. 18 December 2024

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

Proteomic signatures improve risk prediction for common and rare diseases.
Carrasco-Zanini, J., Pietzner, M., Davitte, J., Surendran, P., Croteau-Chonka, D.C., Robins, C., Torralbo, A., Tomlinson, C., Grünschläger, F., Fitzpatrick, N., Ytsma, C., Kanno, T., Gade, S., Freitag, D., Ziebell, F., Haas, S., Denaxas, S., Betts, J.C., Wareham, N.J., Hemingway, H., Scott, R.A. and Langenberg, C.
Nature Medicine 30 (9): 2489-2498. September 2024

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

Management of busulfan-induced lung injury in pediatric patients with high-risk neuroblastoma.
Castelli, S., Thorwarth, A., van Schewick, C., Wendt, A., Astrahantseff, K., Szymansky, A., Lodrini, M., Veldhoen, S., Gratopp, A., Mall, M.A., Eggert, A. and Deubzer, H.E.
Journal of Clinical Medicine 13 (19): 5995. 8 October 2024

Compound-SNE: comparative alignment of t-SNEs for multiple single-cell omics data visualization.
Cess, C.G. and Haghverdi, L.
Bioinformatics 40 (7): btae471. July 2024

Generation of effective and specific human TCRs against tumor/testis antigen NY-ESO-1 in mice with humanized T cell recognition system.
Chen, X.T., Leisegang, M., Gavvovidis, I., Pollack, S.M., Lorenz, F.K.M., Schumacher, T.N., Daumke, O. and Blankenstein, T.
Frontiers in Immunology 15 : 1524629. 24 December 2024

LncRNA MIR31HG fosters stemness malignant features of non-small cell lung cancer via H3K4me1- and H3K27Ace-mediated GLI2 expression.
Chen, W., Wang, F., Yu, X., Qi, J., Dong, H., Cui, B., Zhang, Q., Wu, Y., An, J., Ni, N., Liu, C., Han, Y., Zhang, S., Schmitt, C.A., Deng, J., Yu, Y. and Du, J.
Oncogene 43 (18): 1328-1340. 2 May 2024

Cancer evolution: a multifaceted affair.
Ciriello, G., Magnani, L., Aitken, S.J., Akkari, L., Behjati, S., Hanahan, D., Landau, D.A., Lopez-Bigas, N., Lupiáñez, D.G., Marine, J.C., Martin-Villalba, A., Natoli, G., Obenauf, A.C., Oricchio, E., Scaffidi, P., Sottoriva, A., Swarbrick, A., Tonon, G., 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., Schmitt, M.J., Dramaretska, Y., Serresi, M., Kertalli, S., Jiang, B., Yin, J.A., Aguzzi, A., Barozzi, I. and Gargiulo, G.
Nature Communications 15 (1): 897. 5 February 2024

Covering hierarchical dirichlet mixture models on binary data to enhance genomic stratifications in onco-hematology.
Dall'Olio, D., Sträng, E., Turki, A.T., Tettero, J.M., Barbus, M., Schulze-Rath, R., Elicegui, J.M., Matteuzzi, T., Merlotti, A., Carota, L., Sala, C., Della Porta, M.G., Giampieri, E., Hernández-Rivas, J.M., Bullinger, L. and Castellani, G.
PLoS Computational Biology 20 (2): e1011299. 2 February 2024

Fraternal twins at work: Structures of PLD3/4 reveal mechanism for lysosomal nucleic acid breakdown.
Daumke, O. and Damme, M.
Structure 32 (6): 645-647. 6 June 2024

Systematic benchmarking of single-cell ATAC-sequencing protocols.
De Rop, F.V., Hulselmans, G., Flerin, C., Soler-Vila, P., Rafels, A., Christiaens, V., González-Blas, C.B., Marchese, D., Caratù, G., Poovathingal, S., Rozenblatt-Rosen, O., Slyper, M., Luo, W., Muus, C., Duarte, F., Shrestha, R., Bagdatli, S.T., Corces, M.R., Mamanova, L., Knights, A., Meyer, K.B., Mulqueen, R., Taherinasab, A., Maschmeyer, P., Pezoldt, J., Lambert, C.L.G., Iglesias, M., Najle, S.R., Dossani, Z.Y., Martelotto, L.G., Burkett, Z., Lebofsky, R., Martin-Subero, J.I., Pillai, S., Sebé-Pedrós, A., Deplancke, B., Teichmann, S.A., Ludwig, L.S., Braun, T.P., Adey, A.C., Greenleaf, W.J., Buenrostro, J.D., Regev, A., Aerts, S. and Heyn, H.
Nature Biotechnology 42 (6): 916-926. June 2024

Third-generation anti-CD19 CAR T cells for relapsed/refractory chronic lymphocytic leukemia: a phase 1/2 study.
Derigs, P., Schubert, M.L., Dreger, P., Schmitt, A., Yousefian, S., Haas, S., Röthemeier, C., Neuber, B., Hückelhoven-Krauss, A., Brüggemann, M., Bernhard, H., Kobbe, G., Lindemann, A., Rummel, M., Michels, B., Korell, F., Ho, A.D., Müller-Tidow, C. and Schmitt, M.
Leukemia 38 (11): 2419-2428. November 2024

High-quality peptide evidence for annotating non-canonical open reading frames as human proteins.
Deutsch, Eric W, Kok, Leron W, Mudge, Jonathan M, Ruiz-Orera, J., Fierro-Monti, Ivo, Sun, Zhi, Abelin, Jennifer G, Alba, M Mar, Aspden, Julie L, Bazzini, Ariel A, Bruford, Elspeth, Brunet, Marie A, Calviello, L., Carr, Steven A, Carvunis, Anne-Ruxandra, Chothani, Sonia, Clauwaert, Jim, Dean, Kellie, Faridi, Pouya, Frankish, Adam, Hubner, N., Ingolia, Nicholas, Magrane, Michele, Martin, Maria Jesus, Martinez, Thomas F, Menschaert, Gerben, Ohler, U., Orchard, Sandra, Rackham, Owen, Roucou, Xavier, Slavoff, Sarah A, Valen, Eivind, Wacholder, Aaron C, Weissman, Jonathan S., Wu, Wei, Xie, Zhi, Choudhary, Jyoti, Bassani-Sternberg, Michal, Vizcaino, Juan Antonio, Ternette, Nicola, Moritz, Robert L., Prensner, John and van Heesch, S.
bioRxiv : 2024.09.09.612016. 9 September 2024

Structural characterization of Thogoto Virus nucleoprotein provides insights into viral RNA encapsidation and RNP assembly.
Dick, A., Mikirtumov, V., Fuchs, J., Krupp, F., Olal, D., Bendl, E., Sprink, T., Diebolder, C., Kudryashev, M., Kochs, G., Roske, Y. and Daumke, O.
Structure 32 (8): 1068-1078. 8 August 2024

Literature review: potential non-thermal molecular effects of external radiofrequency electromagnetic fields on cancer.
Dieper, A., Scheidegger, S., Füchslin, R.M., Veltsista, P.D., Stein, U., Weyland, M., Gerster, D., Beck, M., Bengtsson, O., Zips, D. and Ghadjar, P.
International Journal of Hyperthermia 41 (1): 2379992. 17 July 2024

Comparison of R-CHOP-14 and R-mini-CHOP in older adults with diffuse large B-cell lymphoma - a retrospective multicenter cohort study.
Dilbaz, Z.G., Denker, S., Ankermann, C., Bittenbring, J.T., Kaddu-Mulindwa, D., Kunte, A.S., Hünecke, S., Poeschel, V., Stilgenbauer, S., Thurner, L., Na, I.K., Bewarder, M. and Christofyllakis, K.
European Journal of Haematology 113 (5): 675-684. November 2024

Orientation regulation of class-switch recombination in human B cells.
Du, L., Oksenych, V., Wan, H., Ye, X., Dong, J., Ye, A.Y., Abolhassani, H., Vlachiotis, S., Zhang, X., de la Rosa, K., Hammarström, L., van der Burg, M., Alt, F.W. and Pan-Hammarström, Q.
Journal of Immunology 213 (8): 1093-1104. 15 October 2024

Effective symptom relief through continuous integration of palliative care in advanced renal cell carcinoma patients: comprehensive measurement using the palliative care base assessment.
Dörr, A., Vogel, I., Wittenbecher, F., Westermann, J., Thuss-Patience, P., Ahn, J., Pelzer, U., Hardt, J., Bullinger, L. and Flörcken, A.
Palliative Care and Social Practice 18 : 26323524241260424. 24 June 2024

Thrombus or tumor? A case report of a rare sarcoma entity: intimal sarcoma of the pulmonary arteries.
Dörr, A., Flörcken, A, Bullinger, L., Capper, D., Von Deimling, A., Kaul, D., Märdian, S., Starck, C., Horst, D., Dragomir, M.P., Schäfer, F.M. and Jarosch, A.
Molecular Biology Reports 51 : 568. 24 April 2024

Detection of Bombali virus in a Mops condylurus bat in Kyela, Tanzania.
Düx, A., Lwitiho, S.E., Ayouba, A., Röthemeier, C., Merkel, K., Weiss, S., Thaurignac, G., Lander, A., Kouadio, L., Nowak, K., Corman, V., Drosten, C., Couacy-Hymann, E., Krüger, D.H., Kurth, A., Calvignac-Spencer, S., Peeters, M., Ntinginya, N.E., Leendertz, F.H. and Mangu, C.
Viruses 16 (8): 1227. August 2024

CAR-mediated targeting of NK cells overcomes tumor immune escape caused by ICAM-1 downregulation.
Eitler, J., Rackwitz, W., Wotschel, N., Gudipati, V., Murali Shankar, N., Sidorenkova, A., Huppa, J.B., Ortiz-Montero, P., Opitz, C., Künzel, S.R., Michen, S., Temme, A., Loureiro, L.R., Feldmann, A., Bachmann, M., Boissel, L., Klingemann, H., Wels, W.S. and Tonn, T.
Journal for ImmunoTherapy of Cancer 12 (2): e008155. 27 February 2024

Targeted perturb-seq reveals EGR1 and FOS as key regulators of the transcriptional RAF-MAPK response.
El Kassem, G., Sieber, A., Klinger, B., Uhlitz, F., Steinbrecht, D., van Bentum, M., Hillmer, J., von Schlichting, J., Schäfer, R., Blüthgen, N. and Boettcher, M.
bioRxiv : 2024.01.13.575500. 15 January 2024

MACC1 regulates LGR5 to promote cancer stem cell properties in colorectal cancer.
Erdem, M., Lee, K.H., Hardt, M., Regan, J.L., Kobelt, D., Walther, W., Mokrizkij, M., Regenbrecht, C. and Stein, U.
Cancers 16 (3): 604. 31 January 2024

Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in COVID-19.
Essex, M., Millet Pascual-Leone, B.L., Löber, U., Kuhring, M., Zhang, B., Brüning, U., Fritsche-Guenther, R., Krzanowski, M., Fiocca Vernengo, F., Brumhard, S., Röwekamp, I., Bielecka, A.A., Lesker, T.R., Wyler, E., Landthaler, M., Mantei, A., Meisel, C., Caesar, S., Thibeault, C., Corman, V.M., Marko, L., Suttorp, N., Strowig, T., Kurth, F., Sander, L.E., Li, Y., Kirwan, J.A., Forslund, S.K. and Opitz, B.
NPJ Biofilms and Microbiomes 10 (1): 66. 1 August 2024

In vivo sequential mutagenesis in germinal center B cells using a dual-recombinase approach: FOXO1 re-expression upon FOXO1 knockout rescues class switch recombination.
Farré Díaz, C., Kabrani, E., Winkler, W., Salomon, C., Wunderlich, F.T., Janz, M. and Rajewsky, K.
bioRxiv : 2024.05.17.592915. 22 May 2024

The C-terminus of the prototypical M2 muscarinic receptor localizes to the mitochondria and regulates cell respiration under stress conditions.
Fasciani, I., Petragnano, F., Wang, Z., Edwards, R., Telugu, N., Pietrantoni, I., Zabel, U., Zauber, H., Grieben, M., Terzenidou, M.E., Di Gregorio, J., Pellegrini, C., Santini, S., Taddei, A.R., Pohl, B., Aringhieri, S., Carli, M., Aloisi, G., Marampon, F., Charlesworth, E., Roman, A., Diecke, S., Flati, V., Giorgi, F., Amicarelli, F., Tobin, A.B., Scarselli, M., Tokatlidis, K., Rossi, M., Lohse, M.J., Annibale, P. and Maggio, R.
PLoS Biology 22 (4): e3002582. 29 April 2024

Wie weiblich ist die Onkologie in Deutschland? [How feminine is oncology in Germany?].
Fehm, T., Behrens, B., Friebe, V., Krawczyk, N., Bleckmann, A., Höpken, U., Wardelmann, E., Heinrich, K., Duda, A., Gögel, S., Wesselmann, S., Nothacker, M., Schmalfeldt, B. and Hasenburg, A.
Forum 39 : 212-216. June 2024

IGF1R is protective in pneumococcal pneumonia.
Felten, M., Teixeira Alves, L.G., Letsiou, E., Arnedo, E.A., Piñeiro-Hermida, S., López, I.P., Dietert, K., Firsching, T., Gruber, A.D., Fatykhova, D., Hocke, A., Lingscheid, T., Lienau, J., Rohde, G., Pichel, J.G. and Witzenrath, M.
bioRxiv : 2024.09.11.612370. 11 September 2024

Impact of individualized treatment on recovery from fatigue and return to work in survivors of advanced stage Hodgkin Lymphoma: results from the randomized international GHSG HD18 trial.
Ferdinandus, J., Müller, H., Damaschin, C., Jacob, A.S., Meissner, J., Krasniqi, F., Mey, U., Schöndube, D., Thiemer, J., Mathas, S., Zijlstra, J., Greil, R., Feuring-Buske, M., Markova, J., Rüffer, J.U., Kobe, C., Eich, H.T., Baues, C., Fuchs, M., Borchmann, P. and Behringer, K.
Annals of Oncology 35 (3): 276-284. March 2024

Feasibility analysis of using patient-derived tumour organoids for treatment decision guidance in locally advanced head and neck squamous cell carcinoma.
Fischer, A.S., Pestana, A., Sachse, V., Doll, C., Hofmann, E., Heiland, M., Obermueller, T., Heidemann, J., Dommerich, S., Schoppe, D., Schallenberg, S., Piwonski, I., Blanc, E. and Tinhofer, I.
European Journal of Cancer 213 : 115100. December 2024

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

Neural network-assisted humanisation of COVID-19 hamster transcriptomic data reveals matching severity states in human disease.
Friedrich, V.D., Pennitz, P., Wyler, E., Adler, J.M., Postmus, D., Müller, K., Teixeira Alves, L.G., Prigann, J., Pott, F., Vladimirova, D., Hoefler, T., Goekeri, C., Landthaler, M., Goffinet, C., Saliba, A.E., Scholz, M., Witzenrath, M., Trimpert, J., Kirsten, H. and Nouailles, G.
EBioMedicine 108 : 105312. October 2024

Association of an impaired GH‑IGF‑I axis with cardiac wasting in patients with advanced cancer.
Fröhlich, A.K., Porthun, J., Talha, K.M., Lena, A., Hadzibegovic, S., Wilkenshoff, U., Sonntag, F., Nikolski, A., Ramer, L.V., Zeller, T., Keller, U., Bullinger, L., Anker, S.D., Haverkamp, W., von Haehling, S., Doehner, W., Rauch, U., Skurk, C., Cleland, J.G.F., Butler, J., Coats, A.J.S., Landmesser, U., Karakas, M. and Anker, M.S.
Clinical Research in Cardiology 8 April 2024 (In Press)

Follow-up of the GHSG HD16 trial of PET-guided treatment in early-stage favorable Hodgkin lymphoma.
Fuchs, M., Jacob, A.S., Kaul, H., Kobe, C., Kuhnert, G., Pabst, T., Greil, R., Bröckelmann, P.J., Topp, M.S., Just, M., Hertenstein, B., Soekler, M., Vogelhuber, M., Zijlstra, J.M., Keller, U.B., Krause, S.W., Dührsen, U., Meissner, J., Viardot, A., Eich, H.T., Baues, C., Diehl, V., Rosenwald, A., Buehnen, I., von Tresckow, B., Dietlein, M., Borchmann, P., Engert, A. and Eichenauer, D.A.
Leukemia 38 (1): 160-167. January 2024

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

The NSP3 protein of SARS-CoV-2 binds fragile X mental retardation proteins to disrupt UBAP2L interactions.
Garvanska, D.H., Alvarado, R.E., Mundt, F.O., Lindqvist, R., Duel, J.K., Coscia, F., Nilsson, E., Lokugamage, K., Johnson, B.A., Plante, J.A., Morris, D.R., Vu, M.N., Estes, L.K., McLeland, A.M., Walker, J., Crocquet-Valdes, P.A., Mendez, B.L., Plante, K.S., Walker, D.H., Weisser, M.B., Överby, A.K., Mann, M., Menachery, V.D. and Nilsson, J.
EMBO Reports 25 (2): 902-926. 13 February 2024

BTK inhibition limits microglia‑perpetuated CNS inflammation and promotes myelin repair.
Geladaris, A., Torke, S., Saberi, D., Alankus, Y.B., Streit, F., Zechel, S., Stadelmann-Nessler, C., Fischer, A., Boschert, U., Häusler, D. and Weber, M.S.
Acta Neuropathologica 147 (1): 75. 24 April 2024

Epstein-Barr virus-driven B cell lymphoma mediated by a direct LMP1-TRAF6 complex.
Giehler, F., Ostertag, M.S., Sommermann, T., Weidl, D., Sterz, K.R., Kutz, H., Moosmann, A., Feller, S.M., Geerlof, A., Biesinger, B., Popowicz, G.M., Kirchmair, J. and Kieser, A.
Nature Communications 15 (1): 414. 10 January 2024

Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil.
Giurgiu, M., Wittstruck, N., Rodriguez-Fos, E., Chamorro González, R., Brückner, L., Krienelke-Szymansky, A., Helmsauer, K., Hartebrodt, A., Euskirchen, P., Koche, R.P., Haase, K., Reinert, K. and Henssen, A.G.
Genome Research 34 (9): 1355-1364. September 2024

Decoil: reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data.
Giurgiu, M., Wittstruck, N., Rodriguez-Fos, E., Chamorro González, R., Brückner, L., Krienelke-Szymansky, A., Helmsauer, K., Hartebrodt, A., Euskirchen, P., Koche, R.P., Haase, K., Reinert, K. and Henssen, A.G.
Lecture Notes in Computer Science 14758 : 406-411. 17 May 2024

CRISPR-enabled point-of-care genotyping for APOL1 genetic risk assessment.
Greensmith, R., Lape, I.T., Riella, C.V., Schubert, A.J., Metzger, J.J., Dighe, A.S., Tan, X., Hemmer, B., Rau, J., Wendlinger, S., Diederich, N., Schütz, A., Riella, L.V. and Kaminski, M.M.
EMBO Molecular Medicine 16 (10): 2619-2637. 14 October 2024

Cell-type-specific consequences of mosaic structural variants in hematopoietic stem and progenitor cells.
Grimes, K., Jeong, H., Amoah, A., Xu, N., Niemann, J., Raeder, B., Hasenfeld, P., Stober, C., Rausch, T., Benito, E., Jann, J.C., Nowak, D., Emini, R., Hoenicka, M., Liebold, A., Ho, A., Shuai, S., Geiger, H., Sanders, A.D. and Korbel, J.O.
Nature Genetics 56 (6): 1134-1146. June 2024

Therapy-related AML: long-term outcome in a large cohort of AML-patients with intensive and non-intensive therapy.
Gross, S., Ihlow, J., Busack, L., Adamiak, K., Schrezenmeier, J., Jesse, J., Schwarz, M., Flörcken, A., Vuong, L.G., Rieger, K., Krönke, J., le Coutre, P., Boldt, V., von Brünneck, A.C., Horst, D., Burmeister, T., Blau, I.W., Keller, U., Bullinger, L. and Westermann, J.
Blood Cancer Journal 14 (1): 160. 16 September 2024

Placental growth factor promotes neural invasion and predicts disease prognosis in resectable pancreatic cancer.
Göhrig, A., Hilfenhaus, G., Rosseck, F., Welzel, M., Moser, B., Barbone, G., Kunze, C.A., Rein, J., Wilken, G., Böhmig, M., Malinka, T., Tacke, F., Bahra, M., Detjen, K.M. and Fischer, C.
Journal of Experimental & Clinical Cancer Research 43 (1): 153. 30 May 2024

A prospective observational study of real-world treatment and outcome in secondary CNS lymphoma.
Habringer, S., Demel, U.M., Fietz, A.K., Lammer, F., Schroers, R., Hofer, S., Bairey, O., Braess, J., Meier-Stiegen, A.S., Stuhlmann, R., Schmidt-Hieber, M., Hoffmann, J., Zinngrebe, B., Kaiser, U., Reimer, P., Möhle, R., Fix, P., Höffkes, H.G., Langenkamp, U., Büschenfelde, C.M.Z., Hopfer, O., Stoltefuß, A., La Rosée, P., Blasberg, H., Jordan, K., Kaun, S., Meurer, A., Unteroberdörster, M., von Brünneck, A.C., Capper, D., Heppner, F.L., Chapuy, B., Janz, M., Schwartz, S., Konietschke, F., Vajkoczy, P., Korfel, A. and Keller, U.
European Journal of Cancer 196 : 113436. January 2024

A diagnostic challenge of KIT p.V559D and BRAF p.G469A mutations in a paragastric mass.
Habringer, S., Ihlow, J., Kleo, K., Klostermann, A., Schmidt, M., Chai, L., Knödler, M., Leyvraz, S., Sigler, C., Sinn, B., Maschmeyer, G., Jegodka, Y., Benary, M., Ott, C.E., Tinhofer, I., Schäfer, R., Möbs, M., Keller, U., Keilholz, U. and Rieke, D.T.
Oncologist 29 (10): 908-912. October 2024

Genomic characterization of AML with aberrations of chromosome 7: a multinational cohort of 519 patients.
Halik, A., Tilgner, M., Silva, P., Estrada, N., Altwasser, R., Jahn, E., Heuser, M., Hou, H.A., Pratcorona, M., Hills, R.K., Metzeler, K.H., Fenwarth, L., Dolnik, A., Terre, C., Kopp, K., Blau, O., Szyska, M., Christen, F., Krönke, J., Vasseur, L., Löwenberg, B., Esteve, J., Valk, P.J.M., Duchmann, M., Chou, W.C., Linch, D.C., Döhner, H., Gale, R.E., Döhner, K., Bullinger, L., Yoshida, K. and Damm, F.
Journal of Hematology & Oncology 17 (1): 70. 19 August 2024

p53 terminates the regenerative fetal-like state after colitis-associated injury.
Hartl, K., Bayram, Ş., Wetzel, A., Harnack, C., Lin, M., Fischer, A.S., Liu, L., Beccacec, G., Mastrobuoni, G., Geisberger, S., Forbes, M., Monteiro, B.J.E., Macino, M., Flores, R.E., Engelmann, C., Mollenkopf, H.J., Schupp, M., Tacke, F., Sanders, A.D., Kempa, S., Berger, H. and Sigal, M.
Science Advances 10 (43): eadp8783. 25 October 2024

Insights, opportunities and challenges provided by large cell atlases.
Hemberg, M., Marini, F., Ghazanfar, S., Al Ajami, A., Abassi, N., Anchang, B., Benayoun, B.A., Cao, Y., Chen, K., Cuesta-Astroz, Y., DeBruine, Z., Dendrou, K.A., De Vlaminck, I., Imkeller, K., Korsunsky, I., Lederer, A.R., Meysman, P., Miller, C., Mullan, K., Ohler, U., Patikas, N., Schuck, N., Siu, J.H.Y., Triche, T.J., Tsankov, A., van der Laan, S.W., Yajima, M., Yang, J., Zanini, F. and Jelic, I.
arXiv : 2408.06563. 13 August 2024

Rearrangements involving 11q23.3/KMT2A in adult AML: mutational landscape and prognostic implications - a HARMONY study.
Hernández-Sánchez, A., González, T., Sobas, M., Sträng, E., Castellani, G., Abáigar, M., Valk, P.J.M., Villaverde Ramiro, Á., Benner, A., Metzeler, K.H., Azibeiro, R., Tettero, J.M., Martínez-López, J., Pratcorona, M., Martínez Elicegui, J., Mills, K.I., Thiede, C., Sanz, G., Döhner, K., Heuser, M., Haferlach, T., Turki, A.T., Reinhardt, D., Schulze-Rath, R., Barbus, M., Hernández-Rivas, J.M., Huntly, B., Ossenkoppele, G., Döhner, H. and Bullinger, L.
Leukemia 38 (9): 1929-1937. September 2024

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

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

Coordinated inheritance of extrachromosomal DNAs in cancer cells.
Hung, K.L., Jones, M.G., Wong, I.T.L., Curtis, E.J., Lange, J.T., He, B.J., Luebeck, J., Schmargon, R., Scanu, E., Brückner, L., Yan, X., Li, R., Gnanasekar, A., Chamorro González, R., Belk, J.A., Liu, Z., Melillo, B., Bafna, V., Dörr, J.R., Werner, B., Huang, W., Cravatt, B.F., Henssen, A.G., Mischel, P.S and Chang, H.Y.
Nature 635 (8037): 201-209. 7 November 2024

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

Structure of tetrameric forms of the serotonin-gated 5-HT3(A) receptor ion channel.
Introini, B., Cui, W., Chu, X., Zhang, Y., Alves, A.C., Eckhardt-Strelau, L., Golusik, S., Tol, M., Vogel, H., Yuan, S. and Kudryashev, M.
EMBO Journal 4 September 2024

Extensive folding variability between homologous chromosomes in mammalian cells.
Irastorza-Azcarate, I., Kukalev, A., Kempfer, R., Thieme, C.J., Mastrobuoni, G., Markowski, J., Loof, G., Sparks, T.M., Brookes, E., Natarajan, K.N., Sauer, S., Fisher, A.G., Nicodemi, M., Ren, B., Schwarz, R.F., Kempa, S. and Pombo, A.
bioRxiv : 2024.05.08.591087. 10 May 2024

In vitro functionality and endurance of GMP-compliant point-of-care BCMA.CAR-T cells at different timepoints of cryopreservation.
Jiang, G., Neuber, B., Hückelhoven-Krauss, A., Höpken, U., Ding, Y., Sedloev, D., Wang, L., Reichman, A., Eberhardt, F., Wermke, M., Rehm, A., Müller-Tidow, C., Schmitt, A. and Schmitt, M.
International Journal of Molecular Sciences 25 (3): 1394. 23 January 2024

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

Abklärung und OP-Indikationen bei malignen Lymphknoten des unteren GI-Traktes.
Keller, U. and Merz, I.
In: Chirurgie des unteren Gastrointestinaltrakts und Allgemeine Chirurgie. Springer Reference Medizin . Springer, Berlin, Heidelberg, 177-185. ISBN 978-3-662-63355-7 31 July 2024

The other site of rhabdomyosarcoma.
Kern, L., Henssen, A., Eggert, A. and Scheer, M.
Cancer Medicine 13 (20): e70348. October 2024

Intestinal retinol saturase is implicated in the development of obesity and epithelial homeostasis upon injury.
Kiefer, M.F., Meng, Y., Yang, N., Vahrenbrink, M., Wulff, S., Li, C., Wowro, S.J., Petricek, K.M., Sommerfeld, M., Flores, R.E., Obermayer, B., Piepelow, K., Klaus, S., Hartl, K., Guillot, A., Tacke, F., Sigal, M. and Schupp, M.
American Journal of Physiology Endocrinology and Metabolism 327 (2): E203-E216. August 2024

Aggressive lymphoma after CD19 CAR T-cell therapy.
Kobbe, G., Brüggemann, M., Baermann, B.N., Wiegand, L., Trautmann, H., Yousefian, S., Libertini, S., Menssen, H.D., Maier, H.J., Ulrich, P., Gao, J., Bruch, P.M., Liebers, N., Radujkovic, A., Seifert, M., Schniederjohann, C., Paramasivam, N., Fitzgerald, D., Seidel, M., Esposito, I., Germing, U., Cadeddu, R.P., Nachtkamp, K., Jäger, P., Ulrych, T., Fischer, J.C., Rox, J.M., Giesel, F., Koch, R., Antoch, G., Distler, J.H.W., Meuth, S.G., Jacobsen, M., Hübschmann, D., Lu, J., Iaccarino, I., Haas, S., Damm, F. and Dietrich, S.
New England Journal of Medicine 391 (13): 1217-1226. 3 October 2024

Synthetic lethality by PARP inhibitors: new mechanism uncovered based on unresolved transcription-replication conflicts.
Kolesnichenko, M. and Scheidereit, C.
Signal Transduction and Targeted Therapy 9 (1): 179. 29 July 2024

Interpreting deep neural networks for the prediction of translation rates.
Korbel, F., Eroshok, E. and Ohler, U.
BMC Genomics 25 (1): 1061. 9 November 2024

Unlocking the secrets of structural variants in a healthy tissue.
Korbel, J.O. and Sanders, A.D.
Nature Genetics 56 (6): 1047-1048. June 2024

Frequent, high density expression of surface CD38 as a potential therapeutic target in adult T-lineage acute lymphoblastic leukemia.
Koslowski, S., Glauben, R., Habringer, S., Burmeister, T., Keller, U., Brüggemann, M., Gökbuget, N. and Schwartz, S.
Haematologica 109 (2): 661-665. February 2024

Molecular architecture of synaptic vesicles.
Kravčenko, U., Ruwolt, M., Kroll, J., Yushkevich, A., Zenkner, M., Ruta, J., Lotfy, R., Wanker, E.E., Rosenmund, C., Liu, F. and Kudryashev, M.
Proceedings of the National Academy of Sciences of the United States of America 121 (49): e2407375121. 3 December 2024

A high proportion of germline variants in pediatric chronic myeloid leukemia.
Krumbholz, M., Dolnik, A., Sträng, E., Ghete, T., Skambraks, S., Hutter, S., Simonis, A., Stegelmann, F., Suttorp, M., Horn, A.H.C., Sticht, H., Haferlach, T., Bullinger, L. and Metzler, M.
Molecular Cancer 23 (1): 206. 26 September 2024

In vitro testing of drug response in primary multiple myeloma cells using a microwell-based technology.
Krüger, J., Blau, I.W., Blau, O., Bettelli, A., Rocchi, L., Bocchi, M., Krönke, J., Bullinger, L., Keller, U. and Nogai, A.
Leukemia Research 147 : 107599. December 2024

The big chill: growth of in situ structural biology with cryo-electron tomography.
Kudryashev, M.
QRB Discovery 5 : e10. 13 December 2024

Delphi hackathon – a new approach to develop Core Outcome Sets for blood cancers.
Lang, K.M., de Waal, E., Bereczky, T., Dawoud, D., Geissler, J., Bolanos, N., Sanz, G., Guillevic, Y., Rivas, J.M.H., van den Berg, L., Barbus, M., Schulze-Rath, R. and Bullinger, L.
Research Square : rs-3961968/v1. 30 April 2024

Mapping lineage-traced cells across time points with moslin.
Lange, M., Piran, Z., Klein, M., Spanjaard, B., Klein, D., Junker, J.P., Theis, F.J. and Nitzan, M.
Genome Biology 25 (1): 277. 21 October 2024

Artifacts in single-cell mitochondrial DNA mutation analyses misinform phylogenetic inference.
Lareau, C.A., Chapman, M.S., Penter, L., Nawy, T., Pe’er, D. and Ludwig, L.S.
bioRxiv : 2024.07.28.605517v2. 5 October 2024

SARS-CoV-2 neutralization and protection of hamsters via nasal administration of a humanized neutralizing antibody.
Lebedin, M., Petrovsky, N., Tabynov, K., Tabynov, K. and Lebedin, Y.
bioRxiv : 2024.07.08.602557. 8 July 2024

Diversification of antibodies: from V(D)J recombination to somatic exon shuffling.
Lebedin, M. and de la Rosa, K.
Annual Review of Cell and Developmental Biology 40 (1): 265-281. October 2024

Soluble ACE2 correlates with severe COVID-19 and can impair antibody responses.
Lebedin, M., Ratswohl, C., Garg, A., Schips, M., Vazquez Garcia, C., Spatt, L., Thibeault, C., Obermayer, B., Weiner, J., Moreno Velásquez, I., Gerhard, C., Stubbemann, P., Hanitsch, L.G., Pischon, T., Witzenrath, M., Sander, L.E., Kurth, F., Meyer-Hermann, M. and de la Rosa, K.
iScience 27 (3): 109330. 15 March 2024

Spatial single cell profiling using imaging mass cytometry: inflammatory versus penetrating Crohn's disease.
Lehmann, M., Weixler, B., Elezkurtaj, S., Loddenkemper, C., Kühl, A.A. and Siegmund, B.
Journal of Crohn's & Colitis 18 (8): 1305-1318. August 2024

Single-cell multiomics analysis reveals dynamic clonal evolution and targetable phenotypes in acute myeloid leukemia with complex karyotype.
Leppä, A.M., Grimes, K., Jeong, H., Huang, F.Y., Andrades, A., Waclawiczek, A., Boch, T., Jauch, A., Renders, S., Stelmach, P., Müller-Tidow, C., Karpova, D., Sohn, M., Grünschläger, F., Hasenfeld, P., Benito Garagorri, E., Thiel, V., Dolnik, A., Rodriguez-Martin, B., Bullinger, L., Mrózek, K., Eisfeld, A.K., Krämer, A., Sanders, A.D., Korbel, J.O. and Trumpp, A.
Nature Genetics 56 (12): 2790-2803. December 2024

mTORC1 regulates cell survival under glucose starvation through 4EBP1/2-mediated translational reprogramming of fatty acid metabolism.
Levy, T., Voeltzke, K., Hruby, L., Alasad, K., Bas, Z., Snaebjörnsson, M., Marciano, R., Scharov, K., Planque, M., Vriens, K., Christen, S., Funk, C.M., Hassiepen, C., Kahler, A., Heider, B., Picard, D., Lim, J.K.M., Stefanski, A., Bendrin, K., Vargas-Toscano, A., Kahlert, U.D., Stühler, K., Remke, M., Elkabets, M., Grünewald, T.G.P., Reichert, A.S., Fendt, S.M., Schulze, A., Reifenberger, G., Rotblat, B. and Leprivier, G.
Nature Communications 15 (1): 4083. 14 May 2024

Microscopy image reconstruction with physics-informed denoising diffusion probabilistic model.
Li, R., Della Maggiora, G., Andriasyan, V., Petkidis, A., Yushkevich, A., Deshpande, N., Kudryashev, M. and Yakimovich, A.
Communications Engineering 3 (1): 186. 29 December 2024

Solving the inverse problem of microscopy deconvolution with a residual Beylkin-Coifman-Rokhlin neural network.
Li, R., Kudryashev, M. and Yakimovich, A.
Lecture Notes in Computer Science 15133 : 378-395. 1 November 2024

Denoising, deblurring, and optical deconvolution for cryo-ET and light microscopy with a physics-informed deep neural network DeBCR.
Li, R., Yushkevich, A., Chu, X., Kudryashev, M. and Yakimovich, A.
bioRxiv : 2024.07.12.603278. 16 July 2024

Expansion and precise CRISPR-Cas9 gene repair of autologous T memory stem cells from patients with T cell immunodeficiencies.
Li, X., Chu, V.T., Kocks, C. and Rajewsky, K.
Bio-protocol 14 (20): e5085. 20 October 2024

Precise CRISPR-Cas9 gene repair in autologous memory T cells to treat familial hemophagocytic lymphohistiocytosis.
Li, X., Wirtz, T., Weber, T., Lebedin, M., Lowenstein, E.D., Sommermann, T., Zach, A., Yasuda, T., de la Rosa, K., Chu, V.T., Schulte, J.H., Müller, I., Kocks, C. and Rajewsky, K.
Science Immunology 9 (92): eadi0042. 2 February 2024

Effective inhibitor removal from wastewater samples increases sensitivity of RT-dPCR and sequencing analyses and enhances the stability of wastewater-based surveillance.
Linzner, N., Bartel, A., Schumacher, V., Grau, J.H., Wyler, E., Preuß, H., Garske, S., Bitzegeio, J., Kirst, E.B., Liere, K., Hoppe, S., Borodina, T.A., Altmüller, J., Landthaler, M., Meixner, M., Sagebiel, D. and Böckelmann, U.
Microorganisms 12 (12): 2475. December 2024

Mutant huntingtin impairs neurodevelopment in human brain organoids through CHCHD2-mediated neurometabolic failure.
Lisowski, P., Lickfett, S., Rybak-Wolf, A., Menacho, C., Le, S., Pentimalli, T.M., Notopoulou, S., Dykstra, W., Oehler, D., López-Calcerrada, S., Mlody, B., Otto, M., Wu, H., Richter, Y., Roth, P., Anand, R., Kulka, L.A.M., Meierhofer, D., Glazar, P., Legnini, I., Telugu, N.S., Hahn, T., Neuendorf, N., Miller, D.C., Böddrich, A., Polzin, A., Mayatepek, E., Diecke, S., Olzscha, H., Kirstein, J., Ugalde, C., Petrakis, S., Cambridge, S., Rajewsky, N., Kühn, R., Wanker, E.E., Priller, J., Metzger, J.J. and Prigione, A.
Nature Communications 15 (1): 7027. 22 August 2024

CD19-targeting CAR T cells protect from ANCA-induced acute kidney injury.
Lodka, D., Zschummel, M., Bunse, M., Rousselle, A., Sonnemann, J., Kettritz, R., Höpken, U.E. and Schreiber, A.
Annals of the Rheumatic Diseases 83 (4): 499-507. 12 March 2024

Taste mapping: navigating the spatiotemporal link between diet and colorectal cancer.
Luo, Q., Liu, Y., Bi, M., Kuai, X., Tian, Q., Sun, Y. and Zhuang, S.
IEEE Access 12 : 17735 - 17747. 30 January 2024

Marsupial genomes reveal how a skin membrane for gliding evolved.
Lupiáñez, D.G.
Nature 629 (8010): 43-44. 2 May 2024

Multiple myeloma long-term survivors exhibit sustained immune alterations decades after first-line therapy.
Lutz, R., Grünschläger, F., Simon, M., Awwad, M.H.S., Bauer, M., Yousefian, S., Beumer, N., Jopp-Saile, L., Sedlmeier, A., Solé-Boldo, L., Avanesyan, B., Vonficht, D., Stelmach, P., Steinbuss, G., Boch, T., Steiger, S., Baertsch, M.A., Prokoph, N., Rippe, K., Durie, B.G.M., Wickenhauser, C., Trumpp, A., Müller-Tidow, C., Hübschmann, D., Weinhold, N., Raab, M.S., Brors, B., Goldschmidt, H., Imbusch, C.D., Hundemer, M. and Haas, S.
Nature Communications 15 (1): 10396. 29 November 2024

An automated and fast sample preparation workflow for laser microdissection guided ultrasensitive proteomics.
Makhmut, A., Qin, D., Hartlmayr, D., Seth, A. and Coscia, F.
Molecular & Cellular Proteomics 23 (5): 100750. May 2024

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

Structure-based humanization of a therapeutic antibody for multiple myeloma.
Marino, S.F. and Daumke, O.
Journal of Molecular Medicine 102 (9): 1151-1161. September 2024

Identifying cancer cells from calling single-nucleotide variants in scRNA-seq data.
Marot-Lassauzaie, V., Beneyto-Calabuig, S., Obermayer, B., Velten, L., Beule, D. and Haghverdi, L.
Bioinformatics 40 (9): btae512. September 2024

Despite the odds: formation of the SARS-CoV-2 methylation complex.
Matsuda, A., Plewka, J., Rawski, M., Mourão, A., Zajko, W., Siebenmorgen, T., Kresik, L., Lis, K., Jones, A.N., Pachota, M., Karim, A., Hartman, K., Nirwal, S., Sonani, R., Chykunova, Y., Minia, I., Mak, P., Landthaler, M., Nowotny, M., Dubin, G., Sattler, M., Suder, P., Popowicz, G.M., Pyrć, K. and Czarna, A.
Nucleic Acids Research 52 (11): 6441-6458. 24 June 2024

Structure-based mapping of the histone-binding pocket of KDM4D using functionalized tetrazole and pyridine core compounds.
Małecki, P.H., Fassauer, G.M., Rüger, N., Schulig, L., Link, A., Krylova, O., Heinemann, U. and Weiss, M.S.
European Journal of Medicinal Chemistry 276 : 116642. 5 October 2024

Ongoing genome doubling promotes evolvability and immune dysregulation in ovarian cancer.
McPherson, A.W., Vázquez-Garcia, I., Myers, M.A., Zatzman, M., Al-Rawi, D.H., Weiner, A.C., Freeman, S.S., Mohibullah, N., Satas, G., Williams, M.J., Ceglia, N., Zhang, A.W., Li, J., Lim, J.L.P., Wu, M., Choi, S., Havasov, E., Grewal, D., Shi, H., Kim, M., Schwarz, R.F., Kaufmann, T.L., Dinh, K.N., Uhlitz, F., Tran, J., Wu, Y., Patel, R., Ramakrishnan, S., Kim, D., Clarke, J., Green, H., Ali, E., DiBona, M., Varice, N., Kundra, R., Broach, V., Gardner, G.J., Long Roche, K., Sonoda, Y., Zivanovic, O., Kim, S.H., Grisham, R.N., Liu, Y.L., Viale, A., Rusk, N., Lakhman, Y., Ellenson, L.H., Tavare, S., Aparicio, S.A.J.R., Chi, D.S., Aghajanian, C., Abu-Rustum, N.R., Friedman, C.F., Bakhoum, S.F., Zamarin, D., Weigelt, B. and Shah, S.P.
bioRxiv : 2024.07.11.602772v2. 15 July 2024

Deep learning-driven neuromorphogenesis screenings identify repurposable drugs for mitochondrial disease.
Menacho, C., Okawa, S., Alvarez-Merz, I., Wittich, A., Muñoz-Oreja, M., Lisowski, P., Pentimalli, T.M., Rybak-Wolf, A., Inak, G., Zakin, S., Thevandavakkam, M., Petersilie, L., Zaliani, A., Mlody, B., Seibt, A., Donnelly, J., Woleben, K., Fernandez-Checa, J., Herebian, D., Mayatepek, E., Rajewsky, N., Spinazzola, A., Schuelke, M., Perlstein, E., Rossi, A., Distelmaier, F., Holt, I.J., Pless, O., Rose, C., Del Sol, A. and Prigione, A.
bioRxiv : 2024.07.08.602501. 12 July 2024

CD3 aptamers promote expansion and persistence of tumor-reactive T cells for adoptive T cell therapy in cancer.
Menon, A.P., Villanueva, H., Meraviglia-Crivelli, D., van Santen, H.M., Hellmeier, J., Zheleva, A., Nonateli, F., Peters, T., Wachsmann, T.L.A., Hernandez-Rueda, M., Huppa, J.B., Schütz, G.J., Sevcsik, E., Moreno, B. and Pastor, F.
Molecular Therapy Nucleic Acids 35 (2): 102198. 11 June 2024

A single-dose MCMV-based vaccine elicits long-lasting immune protection in mice against distinct SARS-CoV-2 variants.
Metzdorf, K., Jacobsen, H., Kim, Y., Teixeira Alves, L.G., Kulkarni, U., Brdovčak, M.C., Materljan, J., Eschke, K., Chaudhry, M.Z., Hoffmann, M., Bertoglio, F., Ruschig, M., Hust, M., Šustić, M., Krmpotić, A., Jonjić, S., Widera, M., Ciesek, S., Pöhlmann, S., Landthaler, M. and Čičin-Šain, L.
Frontiers in Immunology 15 : 1383086. 25 July 2024

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

Sodium as an important regulator of immunometabolism.
Miyauchi, H., Geisberger, S., Luft, F.C., Wilck, N., Stegbauer, J., Wiig, H., Dechend, R., Jantsch, J., Kleinewietfeld, M., Kempa, S. and Mueller, D.N.
Hypertension 81 (3): 426-435. March 2024

Proteomic profiling reveals ACSS2 facilitating metabolic support in acute myeloid leukemia.
Mochmann, L.H., Treue, D., Bockmayr, M., Silva, P., Zasada, C., Mastrobuoni, G., Bayram, S., Forbes, M., Jurmeister, P., Liebig, S., Blau, O., Schleich, K., Splettstoesser, B., Nordmann, T.M., von der Heide, E.K., Isaakidis, K., Schulze, V., Busch, C., Siddiq, H., Schlee, C., Hester, S., Fransecky, L., Neumann, M., Kempa, S., Klauschen, F. and Baldus, C.D.
Cancer Gene Therapy 31 (9): 1344-1356. September 2024

Impact of the PI3Kalpha inhibitor alpelisib on everolimus resistance and somatostatin receptor expression in an orthotopic pancreatic NEC xenograft mouse model.
Mohan, A.M., Prasad, S., Schmitz-Peiffer, F., Lange, C., Lukas, M., Koziolek, E.J., Albrecht, J., Messroghli, D., Stein, U., Ilmer, M., Wang, K., Schober, L., Reul, A., Maurer, J., Friemel, J., Weber, A., Zuellig, R.A., Hantel, C., Fritsch, R., Reincke, M., Pacak, K., Grossman, A.B., Auernhammer, C.J., Beuschlein, F., Brenner, W., Beindorff, N. and Nölting, S.
Endocrine-Related Cancer 31 (1): e230041. January 2024

Identification of drug-like molecules targeting the ATPase activity of dynamin-like EHD4.
Mohd, S., Oder, A., Specker, E., Neuenschwander, M., von Kries, J.P. and Daumke, O.
PLoS ONE 19 (7): e0302704. 29 July 2024

CXCR4 has a dual role in improving the efficacy of BCMA redirected CAR-NK cells in multiple myeloma.
Moles, M.W., Erdlei, H., Menzel, L., Massaro, M., Fiori, A., Bunse, M., Schrimpf, M., Gerlach, K., Gudipati, V., Reiser, J., Mathavan, K., Goodrich, J., Huppa, J.B., Kroenke, J., Valamehr, B., Höpken, U.E. and Rehm, A.
Frontiers in Immunology 15 : 1383136. 24 June 2024

AHRR and SFRP2 in primary versus recurrent high-grade serous ovarian carcinoma and their prognostic implication.
Monjé, N., Dragomir, M.P., Sinn, B.V., Hoffmann, I., Makhmut, A., Simon, T., Kunze, C.A., Ihlow, J., Schmitt, W.D., Pohl, J., Piwonski, I., Marchenko, S., Keunecke, C., Calina, T.G., Tiso, F., Kulbe, H., Kreuzinger, C., Cacsire Castillo-Tong, D., Sehouli, J., Braicu, E.I., Denkert, C., Darb-Esfahani, S., Kübler, K., Capper, D., Coscia, F., Morkel, M., Horst, D., Sers, C. and Taube, E.T.
British Journal of Cancer 13 (8): 1249-1260. 3 May 2024

Evaluation of polygenic scoring methods in five biobanks shows larger variation between biobanks than methods and finds benefits of ensemble learning.
Monti, R., Eick, L., Hudjashov, G., Läll, K., Kanoni, S., Wolford, B.N., Wingfield, B., Pain, O., Wharrie, S., Jermy, B., McMahon, A., Hartonen, T., Heyne, H., Mars, N., Lambert, S., Hveem, K., Inouye, M., van Heel, D.A., Mägi, R., Marttinen, P., Ripatti, S., Ganna, A. and Lippert, C.
American Journal of Human Genetics 111 (7): 1431-1447. 11 July 2024

Successful generation of fully human, second generation, anti-CD19 CAR T cells for clinical use in patients with diverse autoimmune disorders.
Mougiakakos, D., Sengupta, R., Gold, R., Schroers, R., Haghikia, A., Lorente, M., Pendleton, M., Register, A., Heesen, C., Kröger, N., Schett, G., Mackensen, A., Podoll, A., Gutman, J., Furie, R., Bayer, R., Distler, J.H.W., Dietrich, S., Krönke, G., Bullinger, L. and Walker, K.
Cytotherapy 27 (2): 236-246. February 2024

Natural proteome diversity links aneuploidy tolerance to protein turnover.
Muenzner, J., Trébulle, P., Agostini, F., Zauber, H., Messner, C.B., Steger, M., Kilian, C., Lau, K., Barthel, N., Lehmann, A., Textoris-Taube, K., Caudal, E., Egger, A.S., Amari, F., De Chiara, M., Demichev, V., Gossmann, T.I., Mülleder, M., Liti, G., Schacherer, J., Selbach, M., Berman, J. and Ralser, M.
Nature 630 (8015): 149-157. 6 June 2024

MatK impacts differential chloroplast translation by limiting spliced tRNA-K(UUU) abundance.
Muino, J.M., Ruwe, H., Qu, Y., Maschmann, S., Chen, W., Zoschke, R., Ohler, U., Kaufmann, K. and Schmitz-Linneweber, C.
Plant Journal 119 (6): 2737-2752. September 2024

Mice with renal-specific alterations 1 of stem cell-associated signaling develop symptoms of chronic kidney disease but surprisingly no tumors.
Myszczyszyn, A., Popp, O., Kunz, S., Sporbert, A., Jung, S., Penning, L.C., Fendler, A., Mertins, P. and Birchmeier, W.
PLoS ONE 19 (3): e0282938. 21 March 2024

TCR/CD3-based synthetic antigen receptors (TCC) convey superior antigen sensitivity combined with high fidelity of activation.
Mühlgrabner, V., Peters, T., Velasco Cárdenas, R.M.H., Salzer, B., Göhring, J., Plach, A., Höhrhan, M., Perez, I.D., Goncalves, V.D.R., Farfán, J.S., Lehner, M., Stockinger, H., Schamel, W.W., Schober, K., Busch, D.H., Hudecek, M., Dushek, O., Minguet, S., Platzer, R. and Huppa, J.B.
Science Advances 10 (36): eadj4632. 6 September 2024

Arginine methylation of the p30 C/EBPα oncoprotein regulates progenitor proliferation and myeloid differentiation.
Nguyen, L.T., Zimmermann, K., Kowenz-Leutz, E., Dörr, D., Schütz, A., Schönheit, J., Mildner, A. and Leutz, A.
iScience 27 (11): 111199. 15 November 2024

Mitochondrial genetics through the lens of single-cell multi-omics.
Nitsch, L., Lareau, C.A. and Ludwig, L.S.
Nature Genetics 56 (7): 1355-1365. July 2024

Topological reaction coordinate captures the folding transition state ensemble in a pierced lasso protein.
Noel, J.K. and Haglund, E.
Journal of Physical Chemistry B 128 (1): 117-124. 11 January 2024

Genetic characterization of primary mediastinal B-cell lymphoma: pathogenesis and patient outcomes.
Noerenberg, D., Briest, F., Hennch, C., Yoshida, K., Hablesreiter, R., Takeuchi, Y., Ueno, H., Staiger, A.M., Ziepert, M., Asmar, F., Locher, B.N., Toth, E., Weber, T., Amini, R.M., Klapper, W., Bouzani, M., Poeschel, V., Rosenwald, A., Held, G., Campo, E., Ishaque, N., Stamatopoulos, K., Kanellis, G., Anagnostopoulos, I., Bullinger, L., Goldschmidt, N., Zinzani, P.L., Bödör, C., Rosenquist, R., Vassilakopoulos, T.P., Ott, G., Ogawa, S. and Damm, F.
Journal of Clinical Oncology 42 (4): 452-466. 1 February 2024

Update and European consensus on a patient-centered core outcome set for multiple myeloma in clinical practice and research.
Oerlemans, S., De Rooij, B.H., Bennink, C., Bullinger, L., Broijl, A., D'Agostino, M., Laane, E., Lupo-Stanghellini, M.T., Perrot, A., Wester, R., Cursaru, V., Scheurer, H., Vesseur, J., Dalal, M., Sen, R., Stamm, T., Ludwig, H. and Sonneveld, P.
Haematologica 109 (6): 1956-1959. June 2024

Recapitulating the tumor microenvironment in a dish, one cell type at a time.
Ostendorf, B.N.
Cell Reports Methods 4 (6): 100800. 17 June 2024

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

GIMAP5 deficiency reveals a mammalian ceramide-driven longevity assurance pathway.
Park, A.Y., Leney-Greene, M., Lynberg, M., Gabrielski, J.Q., Xu, X., Schwarz, B., Zheng, L., Balasubramaniyam, A., Ham, H., Chao, B., Zhang, Y., Matthews, H.F., Cui, J., Yao, Y., Kubo, S., Chanchu, J.M., Morawski, A.R., Cook, S.A., Jiang, P., Ravell, J.C., Cheng, Y.H., George, A., Faruqi, A., Pagalilauan, A.M., Bergerson, J.R.E., Ganesan, S., Chauvin, S.D., Aluri, J., Edwards-Hicks, J., Bohrnsen, E., Tippett, C., Omar, H., Xu, L., Butcher, G.W., Pascall, J., Karakoc-Aydiner, E., Kiykim, A., Maecker, H., Tezcan, İ., Esenboga, S., Heredia, R.J., Akata, D., Tekin, S., Kara, A., Kuloglu, Z., Unal, E., Kendirli, T., Dogu, F., Karabiber, E., Atkinson, T.P., Cochet, C., Filhol, O., Bosio, C.M., Davis, M.M., Lifton, R.P., Pearce, E.L., Daumke, O., Aytekin, C., Şahin, G.E., Aksu, A.Ü., Uzel, G., Koneti Rao, V., Sari, S., Boztug, K., Cagdas, D., Haskologlu, S., Ikinciogullari, A., Schwefel, D., Vilarinho, S., Baris, S., Ozen, A., Su, H.C. and Lenardo, M.J.
Nature Immunology 25 (2): 282-293. February 2024

Increased abundance of Firmicutes and depletion of Bacteroidota predicts poor outcome in chronic lymphocytic leukemia.
Paziewska, M., Szelest, Mo., Kiełbus, M., Masternak, M., Zaleska, J., Wawrzyniak, E., Kotkowska, A., Siemieniuk-Ryś, M., Morawska, M., Kalicińska, E., Jabłonowska, P., Wróbel, T., Wolska-Washer, A., Błoński, J.Z., Robak, T., Bullinger, L. and Giannopoulos, K.
Oncology letters 28 (5): 552. November 2024

Single-cell-resolved interspecies comparison shows a shared inflammatory axis and a dominant neutrophil-endothelial program in severe COVID-19.
Peidli, S., Nouailles, G., Wyler, E., Adler, J.M., Kunder, S., Voß, A., Kazmierski, J., Pott, F., Pennitz, P., Postmus, D., Teixeira Alves, L.G., Goffinet, C., Gruber, A.D., Blüthgen, N., Witzenrath, M., Trimpert, J., Landthaler, M. and Praktiknjo, S.D.
Cell Reports 43 (6): 114328. 25 June 2024

Tracking rare single donor and recipient immune and leukemia cells after allogeneic hematopoietic cell transplantation using mitochondrial DNA mutations.
Penter, L., Cieri, N., Maurer, K., Kwok, M., Lyu, H., Lu, W.S., Oliveira, G., Gohil, S.H., Leshchiner, I., Lareau, C.A., Ludwig, L.S., Neuberg, D.S., Kim, H.T., Li, S., Bullinger, L., Ritz, J., Getz, G., Garcia, J.S., Soiffer, R.J., Livak, K.J. and Wu, C.J.
Blood Cancer Discovery 5 (6): 442-459. 1 November 2024

Pial collaterals develop through mosaic colonization of capillaries by arterial and microvascular endothelial cells.
Perovic, T., Hollfinger, I., Mayer, S., Lips, J., Dopatka, M., Harms, C. and Gerhardt, H.
bioRxiv : 2023.10.09.561542v3. 7 February 2024

Rewired type I IFN signaling is linked to age-dependent differences in COVID-19.
Petrov, L., Brumhard, S., Wisniewski, S., Georg, P., Hillus, D., Hiller, A., Astaburuaga-García, R., Blüthgen, N., Wyler, E., Vogt, K., Dey, H.P., von Stillfried, S., Iwert, C., Bülow, R.D., Märkl, B., Maas, L., Langner, C., Meyer, T., Loske, J., Eils, R., Lehmann, I., Ondruschka, B., Ralser, M., Trimpert, J., Boor, P., Bedoui, S., Meisel, C., Mall, M.A., Corman, V.M., Sander, L.E., Röhmel, J. and Sawitzki, B.
bioRxiv : 2024.10.23.619479. 23 October 2024

Spontaneous single-nucleotide substitutions and microsatellite mutations have distinct distributions of fitness effects.
Plavskin, Y., de Biase, M.S., Ziv, N., Janská, L., Zhu, Y.O., Hall, D.W., Schwarz, R.F., Tranchina, D. and Siegal, M.L.
PLoS Biology 22 (7): e3002698. 1 July 2024

Distinct roles for MNK1 and MNK2 in social and cognitive behavior through kinase-specific regulation of the synaptic proteome and phosphoproteome.
Proce, R.O., Uddström, E., Steinecker, M., Wüsthoff, S., Teixeira Alves, L.G., Popp, O., Maxwell, K., Hortmann, L., Mertins, P., Landthaler, M., Bunina, D. and Hörnberg, H.
bioRxiv : 2024.12.18.628637. 20 December 2024

Novel ectopic expression of zona pellucida 3 glycoprotein in lung cancer promotes tumor growth.
Pulawska-Moon, K., Ponikwicka-Tyszko, D., Lebiedzinska, W., Pilaszewicz-Puza, A., Bernaczyk, P., Koda, M., Lupu, O., Milewska, G., Huang, C.C.J., Zheng, H., Schiele, P., Na, I.K., Frentsch, M., Li, X., Toppari, J., Wolczynski, S., Coelingh Bennink, H.J.T., Huhtaniemi, I. and Rahman, N.A.
International Journal of Cancer 155 (10): 1846-1857. 15 November 2024

Elimusertib has antitumor activity in preclinical patient-derived pediatric solid tumor models.
Pusch, F.F., Dorado Garcia, H., Xu, R., Gürgen, D., Bei, Y., Brückner, L., Röefzaad, C., von Stebut, J., Bardinet, V., Chamorro Gonzalez, R., Eggert, A., Schulte, J.H., Hundsdörfer, P., Seifert, G., Haase, K., Schäfer, B.W., Wachtel, M., Kühl, A.A., Ortiz, M.V., Wengner, A.M., Scheer, M. and Henssen, A.G.
Molecular Cancer Therapeutics 23 (4): 507-519. 2 April 2024

MHC Hammer reveals genetic and non-genetic HLA disruption in cancer evolution.
Puttick, C., Jones, T.P., Leung, M.M., Galvez-Cancino, F., Liu, J., Varas-Godoy, M., Rowan, A., Pich, O., Martinez-Ruiz, C., Bentham, R., Dijkstra, K.K., Black, J.R.M., Rosenthal, R., Kanu, N., Litchfield, K., Salgado, R., Moore, D.A., Van Loo, P., Jamal-Hanjani, M., Quezada, S.A., Swanton, C. and McGranahan, N.
Nature Genetics 56 (10): 2121-2131. October 2024

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

Metadata-guided feature disentanglement for functional genomics.
Rakowski, A., Monti, R., Huryn, V., Lemanczyk, M., Ohler, U. and Lippert, C.
Bioinformatics 40 (Suppl 2): ii4-ii10. September 2024

TransferGWAS of T1-weighted brain MRI data from UK Biobank.
Rakowski, A., Monti, R. and Lippert, C.
PLoS Genetics 20 (12): e1011332. 13 December 2024

The proteogenomic landscape of multiple myeloma reveals insights into disease biology and therapeutic opportunities.
Ramberger, E., Sapozhnikova, V., Ng, Y.L.D., Dolnik, A., Ziehm, M., Popp, O., Sträng, E., Kull, M., Grünschläger, F., Krüger, J., Benary, M., Müller, S., Gao, X., Murgai, A., Haji, M., Schmidt, A., Lutz, R., Nogai, A., Braune, J., Laue, D., Langer, C., Khandanpour, C., Bassermann, F., Döhner, H., Engelhardt, M., Straka, C., Hundemer, M., Beule, D., Haas, S., Keller, U., Einsele, H., Bullinger, L., Knop, S., Mertins, P. and Krönke, J.
Nature Cancer 5 (8): 1267-1284. August 2024

Single-cell genomics-based immune and disease monitoring in blood malignancies.
Rathgeber, A.C., Ludwig, L.S. and Penter, L.
Clinical Hematology International 6 (2): 62-84. 14 June 2024

Liam tackles complex multimodal single-cell data integration challenges.
Rautenstrauch, P. and Ohler, U.
Nucleic Acids Research 52 (12): e52. 8 July 2024

JUN mediates the senescence associated secretory phenotype and immune cell recruitment to prevent prostate cancer progression.
Redmer, T., Raigel, M., Sternberg, C., Ziegler, R., Probst, C., Lindner, D., Aufinger, A., Limberger, T., Trachtova, K., Kodajova, P., Högler, S., Schlederer, M., Stoiber, S., Oberhuber, M., Bolis, M., Neubauer, H.A., Miranda, S., Tomberger, M., Harbusch, N.S., Garces de Los Fayos Alonso, I., Sternberg, F., Moriggl, R., Theurillat, J.P., Tichy, B., Bystry, V., Persson, J.L., Mathas, S., Aberger, F., Strobl, B., Pospisilova, S., Merkel, O., Egger, G., Lagger, S. and Kenner, L.
Molecular Cancer 23 (1): 114. 29 May 2024

Cellular senescence: neither irreversible nor reversible.
Reimann, M., Lee, S. and Schmitt, C.A.
Journal of Experimental Medicine 221 (4): e20232136. 1 April 2024

Abnormal biomarkers predict complex FAS or FADD defects missed by exome sequencing.
Rensing-Ehl, A., Lorenz, M.R., Führer, M., Willenbacher, W., Willenbacher, E., Sopper, S., Abinun, M., Maccari, M.E., König, C., Haegele, P., Fuchs, S., Castro, C., Kury, P., Pelle, O., Klemann, C., Heeg, M., Thalhammer, J., Wegehaupt, O., Fischer, M., Goldacker, S., Schulte, B., Biskup, S., Chatelain, P., Schuster, V., Warnatz, K., Grimbacher, B., Meinhardt, A., Holzinger, D., Oommen, P.T., Hinze, T., Hebart, H., Seeger, K., Lehmberg, K., Leahy, T.R., Claviez, A., Vieth, S., Schilling, F.H., Fuchs, I., Groß, M., Rieux-Laucat, F., Magerus, A., Speckmann, C., Schwarz, K. and Ehl, S.
Journal of Allergy and Clinical Immunology 153 (1): 297-308. January 2024

Renal extramedullary hematopoiesis in mast cell leukemia with bone marrow fibrosis.
Rieke, D.T., Schmalbrock, L.K., Ihlow, J., Kleo, K., von Brünneck, A.C., Nolte, F., Keller, U. and Ochsenreither, S.
Case Reports in Hematology 2024 : 1-6. 3 January 2024

Structural analysis of PLD3 reveals insights into the mechanism of lysosomal 5' exonuclease-mediated nucleic acid degradation.
Roske, Y., Cappel, C., Cremer, N., Hoffmann, P., Koudelka, T., Tholey, A., Heinemann, U., Daumke, O. and Damme, M.
Nucleic Acids Research 52 (1): 370-384. 11 January 2024

Sociality shapes mitochondrial adaptations supporting hypoxia tolerance.
Rossi, A., Ruwolt, M., Kakouri, P., Kosten, T., Kunz, S., Puchkov, D., Reznick, J., Purfürst, B., Omerbašić, D., Méndez Aranda, D., Carai, G., Mastrobuoni, G., Hart, D.W., Carraro, M., Tommasin, L., Bennett, N.C., Bégay, V., Faelber, K., Daumke, O., Bernardi, P., Park, T.J., Kempa, S., Liu, F. and Lewin, G.R.
bioRxiv : 2024.09.30.615914. 2 October 2024

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

Measurable residual disease monitoring in AML with FLT3-ITD treated with intensive chemotherapy plus midostaurin.
Rücker, F.G., Bullinger, L., Cocciardi, S., Skambraks, S., Luck, T.J., Weber, D., Krzykalla, J., Pozek, E., Schneider, I.J., Corbacioglu, A., Gaidzik, V.I., Meid, A., Aicher, S., Stegelmann, F., Schrade, A., Theis, F., Fiedler, W., Salih, H.R., Wulf, G.G., Salwender, H.J., Schroeder, T., Götze, K.S., Kühn, M.W.M., Lübbert, M., Schlenk, R.F., Benner, A., Thol, F.R., Heuser, M., Ganser, A., Döhner, H. and Döhner, K.
Blood Advances 8 (23): 6067-6080. 10 December 2024

Refinement of the prognostic impact of somatic CEBPA bZIP domain mutations in acute myeloid leukemia: Results of the AML Study Group (AMLSG).
Rücker, F.G., Corbacioglu, A., Krzykalla, J., Cocciardi, S., Lengerke, C., Germing, U., Wulf, G., Samra, M.A., Teichmann, L.L., Lübbert, M., Kühn, M.W.M., Bentz, M., Westermann, J., Bullinger, L., Gaidzik, V.I., Meid, A., Aicher, S., Stegelmann, F., Weber, D., Schrade, A., Thol, F., Heuser, M., Ganser, A., Benner, A., Döhner, H. and Döhner, K.
HemaSphere 8 (7): e123. July 2024

Cell-type specific prediction of RNA stability from RNA-protein interactions.
Saran, S., Lebedeva, S., Hirsekorn, A. and Ohler, U.
bioRxiv : 2024.11.19.624283. 19 November 2024

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

Review of preclinical data on hyperthermia treatment in lymphomas and its potential for clinical application.
Scharr, M.V., Damm, F., Krahl, P., Dieper, A., Veltsista, P.D., Hansch, A., Beck, M., Gerster, D., Giovannelli, A.C., Bullinger, L., Zips, D. and Ghadjar, P.
International Journal of Hyperthermia 41 (1): 2418427. 3 November 2024

Flow cytometric assessment of FcγRIIIa-V158F polymorphisms and NK cell mediated ADCC revealed reduced NK cell functionality in colorectal cancer patients.
Schiele, P., Kolling, S., Rosnev, S., Junkuhn, C., Walter, A.L., Von Einem, J.C., Stintzing, S., Schöning, W., Sauer, I.M., Modest, D.P., Heinrich, K., Weiss, L., Heinemann, V., Bullinger, L., Frentsch, M. and Na, I.K.
Cells 14 (1): 32. 31 December 2024

Comparative single-cell analyses reveal evolutionary repurposing of a conserved gene program in bat wing development.
Schindler, M., Feregrino, C., Aldrovandi, S., Lo, B.W., Monaco, A.A., Ringel, A.R., Morales, A., Zehnder, T., Behncke, R.Y., Glaser, J., Barclay, A., Andrey, G., Kragesteen, B.K., Hägerling, R., Haas, S., Vingron, M., Ulitsky, I., Marti-Renom, M., Hechavarria, J., Fasel, N., Hiller, M., Lupianez, D.G., Mundlos, S. and Real, F.M.
bioRxiv : 2024.10.10.617585. 13 October 2024

A biomathematical model of SARS-CoV-2 in Syrian hamsters.
Schirm, S., Nouailles, G., Kirsten, H., Trimpert, J., Wyler, E., Teixeira Alves, L.G., Landthaler, M., Ahnert, P., Suttorp, N., Witzenrath, M. and Scholz, M.
Scientific Reports 14 (1): 30541. 18 December 2024

Oncogene inactivation-induced senescence facilitates tumor relapse.
Schmitt, P., Hönig, K., Milojkovic, A., Anders, K., Schröck, E., Sauer, S., Uyar, B., Akalin, A., Martínez-Reyes, I. and Blankenstein, T.
bioRxiv : 2024.07.13.603369. 17 July 2024

High-dose chemotherapy and autologous haematopoietic stem-cell transplantation in older, fit patients with primary diffuse large B-cell CNS lymphoma (MARTA): a single-arm, phase 2 trial.
Schorb, E., Isbell, L.K., Kerkhoff, A., Mathas, S., Braulke, F., Egerer, G., Röth, A., Schliffke, S., Borchmann, P., Brunnberg, U., Kroschinsky, F., Möhle, R., Rank, A., Wellnitz, D., Kasenda, B., Pospiech, L., Wendler, J., Scherer, F., Deckert, M., Henkes, E., von Gottberg, P., Gmehlin, D., Backenstraß, M., Jensch, A., Burger-Martin, E., Grishina, O., Fricker, H., Malenica, N., Orbán, A., Duyster, J., Ihorst, G., Finke, J. and Illerhaus, G.
Lancet Haematology 11 (3): e196-e205. March 2024

Measurement of forces acting on single T-cell receptors.
Schrangl, L., Göhring, J., Kellner, F., Huppa, J.B. and Schütz, G.J.
Methods in Molecular Biology 2800 : 147-165. 7 May 2024

Advanced quantification of receptor-ligand interaction lifetimes via single-molecule FRET microscopy.
Schrangl, L., Mühlgrabner, V., Platzer, R., Kellner, F., Wieland, J., Obst, R., Toca-Herrera, J.L., Huppa, J.B., Schütz, G.J. and Göhring, J.
Biomolecules 14 (8): 1001. 13 August 2024

Induction of circulating ABCB1 transcripts under platinum-based chemotherapy indicates poor prognosis and a bone micrometastatic phenotype in ovarian cancer patients.
Schwarz, F.M., Kuhlmann, J.D., Kämpfer, J., Klimova, A., Klotz, D.M., Freitag, L., Herrmann, P., Zinnow, V., Smith, J., Scheller, T., Walther, W., Wimberger, P. and Stein, U.
Molecular Cancer 23 (1): 174. 23 August 2024

MACC1 revisited - an in-depth review of a master of metastasis.
Schöpe, P.C., Torke, S., Kobelt, D., Kortüm, B., Treese, C., Dumbani, M., Güllü, N., Walther, W. and Stein, U.
Biomarker Research 12 (1): 146. 23 November 2024

Transcriptional dosage of oncogenic KRAS drives lung adenocarcinoma cell states, progression and metastasis.
Serresi, M., Cetin, A.O., Dramaretska, Y., Kertalli, S., Schmitt, M.J., Naumann, H., Zschummel, M., Liesse-Labat, M., Maciel, L.F., Declercq, J., Marine, J.C. and Gargiulo, G.
bioRxiv : 2024.12.29.630643. 30 December 2024

A mouse model of X-linked chronic granulomatous disease for the development of CRISPR/Cas9 gene therapy.
Sevim-Wunderlich, S., Dang, T., Rossius, J., Schnütgen, F. and Kuehn, R.
Genes 15 (6): 706. June 2024

Safety and efficacy of glofitamab for relapsed/refractory large B-cell lymphoma in a multinational real-world study.
Shumilov, E., Wurm-Kuczera, R., Kerkhoff, A., Wang, M., Melchardt, T., Holtick, U., Bacher, U., Staber, P.B., Mazzeo, P., Leng, C., Böckle, D., Hölscher, A.S., Kauer, J., Rotter, N., Vucinic, V., Rudzki, J.D., Nachbaur, D., Bücklein, V.L., Schnetzke, U., Krämer, I., Wille, K., Hasse, A., von Tresckow, B., Hänel, M., Koenecke, C., Velazquez, G.F., Viardot, A., Schmid, C., Thurner, L., Wolf, D., Subklewe, M., Dreyling, M., Dreger, P., Dietrich, S., Keller, U., Jäger, U., Greil, R., Pabst, T., Lenz, G. and Chapuy, B.
Blood Advances : bloodadvances.2024014903. 11 December 2024 (In Press)

From regulation of cell fate decisions towards patient-specific treatments, insights from mechanistic models of signalling pathways.
Simon, M., Konrath, F. and Wolf, J.
Current Opinion in Systems Biology 39 : 100533. December 2024

Architecture of the Sap S-layer of Bacillus anthracis revealed by integrative structural biology.
Sogues, A., Leigh, K., Halingstad, E.V., Van der Verren, S.E., Cecil, A.J., Fioravanti, A., Pak, A.J., Kudryashev, M. and Remaut, H.
Proceedings of the National Academy of Sciences of the United States of America 121 (51): e2415351121. 17 December 2024

Targeted H3K9 acetylation at lncSox1 promoter by cell type-specific epigenome editing promotes intermediate progenitor proliferation in developing mouse cortex.
Sokpor, Godwin, Ulmke, P.A., Nguyen, H.D., Pham, L., Kakani, P., Chu, V.T., Arnold, S.J., Brand-Saberi, B., Nguyen, H.P. and Tuoc, T.
bioRxiv : 2024.11.05.621758. 5 November 2024

Pyjacker identifies enhancer hijacking events in acute myeloid leukemia including MNX1 activation via deletion 7q.
Sollier, E., Riedel, A., Toprak, U.H., Wierzbinska, J.A., Weichenhan, D., Schmid, J.P., Hakobyan, M., Touzart, A., Jahn, E., Vick, B., Brown-Burke, F., Kelly, K., Kelekci, S., Pejkovska, A., Goyal, A., Baehr, M., Breuer, K., Chen, M.J.M., Llamazares-Prada, M., Hartmann, M., Schoenung, M., Correia, N., Trumpp, A., Abdullah, Y., Klingmueller, U., Mughal, S.S., Brors, B., Westermann, F., Schlesner, M., Vosberg, S., Herold, T., Greif, P.A., Pfeifer, D., Luebbert, M., Fischer, T., Heidel, F., Gebhard, C., Walter, W., Haferlach, T., Eisfeld, A.K., Mrozek, K., Nicolet, D., Bullinger, L., Smeenk, L., Erpelinck, C., Mulet-Lazaro, R., Delwel, R., Ernst, A., Scherer, M., Lutsik, P., Jeremias, I., Doehner, K., Doehner, H., Lipka, D.B. and Plass, C.
bioRxiv : 2024.09.11.611224. 13 September 2024

Targeting KDM1A in neuroblastoma with NCL-1 induces a less aggressive phenotype and suppresses angiogenesis.
Sprüssel, A., Suzuki, T., Miyata, N., Astrahantseff, K., Szymansky, A., Toedling, J., Thole-Kliesch, T.M., Ballagee, A., Lodrini, M., Künkele, A., Truss, M., Heukamp, L.C., Mathia, S., Hertwig, F., Rosenberger, C., Eggert, A., Deubzer, H.E. and Schulte, J.H.
Journal of Clinical Medicine 13 (20): 6081. October 2024

Subcellular mRNA kinetic modeling reveals nuclear retention as rate-limiting.
Steinbrecht, D., Minia, I., Milek, M., Meisig, J., Blüthgen, N. and Landthaler, M.
Molecular Systems Biology 20 (12): 1346-1371. 2 December 2024

CNSistent integration and feature extraction from somatic copy number profiles.
Streck, A. and Schwarz, R.F.
bioRxiv : 2024.12.23.630118. 23 December 2024

Intercellular extrachromosomal DNA copy-number heterogeneity drives neuroblastoma cell state diversity.
Stöber, M.C., Chamorro González, R., Brückner, L., Conrad, T., Wittstruck, N., Szymansky, A., Eggert, A., Schulte, J.H., Koche, R.P., Henssen, A.G., Schwarz, R.F. and Haase, K.
Cell Reports 43 (9): 114711. 24 September 2024

Molecular subtyping of head and neck cancer - Clinical applicability and correlations with morphological characteristics.
Stögbauer, F., Otto, R., Jöhrens, K., Tinhofer, I., Keilholz, U., Poremba, C., Keller, U., Leser, U., Weichert, W., Boxberg, M. and Klinghammer, K.
Oral Oncology 149 : 106678. February 2024

Herpes simplex virus type 1 modifies the protein composition of extracellular vesicles to promote neurite outgrowth and neuroinfection.
Sun, G., Kropp, K.A., Kirchner, M., Plückebaum, N., Selich, A., Serrero, M., Dhingra, A., Cabrera, J.R., Ritter, B., Bauerfeind, R., Wyler, E., Landthaler, M., Schambach, A., Sodeik, B., 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., Agostinho, M., Bury, J., Cook, S., Durinx, C., Ender, A., van Luenen, H., Lund, A.H., Medema, R.H., Miączyńska, M., Nickel, D., Pelicci, P.G., Puisieux, A., Ripatti, S., Sander, M., Schubeler, D., Serrano, L., Sommer, T., Sonne-Hansen, K., Tomančák, P., Vives, J., Vontas, J. and Bettencourt-Dias, M.
FEBS Letters 598 (7): 719-724. April 2024

DNA virus infections shape transposable elements activity in vitro and in vivo.
Tan, J., Franke, V., Neugebauer, E., Lagisquet, J., Kuderna, A.K., Walter, S., Landthaler, M., Ensser, A., Stamminger, T., Gramberg, T., Akalin, A., Wyler, E. and Full, F.
bioRxiv : 2024.04.18.589901. 19 April 2024

Arabidopsis uses a molecular grounding mechanism and a biophysical circuit breaker to limit floral abscission signaling.
Taylor, I.W., Patharkar, O.R., Mijar, M., Hsu, C.W., Baer, J., Niederhuth, C.E., Ohler, U., Benfey, P.N. and Walker, J.C.
Proceedings of the National Academy of Sciences of the United States of America 121 (44): e2405806121. 29 October 2024

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

Acute myeloid leukemia: does sex matter?
Tettero, J.M., Cloos, J. and Bullinger, L.
Leukemia 38 (11): 2329-2331. November 2024

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

Immune response and metastasis-links between the metastasis driver MACC1 and cancer immune escape strategies.
Torke, S., Walther, W. and Stein, U.
Cancers 16 (7): 1330. 28 March 2024

Long-term follow-up of the prospective randomized AATT study (autologous or allogeneic transplantation in patients with peripheral T-cell lymphoma).
Tournilhac, O., Altmann, B., Friedrichs, B., Bouabdallah, K., Leclerc, M., Cartron, G., Turlure, P., Reimer, P., Wagner-Drouet, E., Sanhes, L., Houot, R., Roussel, M., Kroschinsky, F., Dreger, P., Viardot, A., de Leval, L., Rosenwald, A., Gaulard, P., Wulf, G., Villate, A., Latiere, C., Elmaagacli, A., Glass, B., Poeschel, V., Damaj, G., Sibon, D., Durot, E., Bilger, K., Banos, A., Haenel, M., Dreyling, M., Keller, U., Tiab, M., Drenou, B., Cornillon, J., Nguyen, S., Robin, M., Nickelsen, M., Trümper, L., Lenz, G., Ziepert, M. and Schmitz, N.
Journal of Clinical Oncology 42 (32): 3788-3794. 10 November 2024

In vivo CRISPR/Cas9-mediated screen reveals a critical function of TFDP1 and E2F4 transcription factors in hematopoiesis.
Tran, N.T., Graf, R., Acevedo-Ochoa, E., Trombke, J., Weber, T., Sommermann, T., Salomon, C., Kühn, R., Rajewsky, K. and Chu, V.T.
Leukemia 38 (9): 2003-2015. September 2024

Comparable CD8(+) T-cell responses to SARS-CoV-2 vaccination in single-cell transcriptomics of recently allogeneic transplanted patients and healthy individuals.
Tranter, E., Frentsch, M., Hütter-Krönke, M.L., Vuong, G.L., Busch, D., Loyal, L., Henze, L., Rosnev, S., Blau, I.W., Thiel, A., Beule, D., Bullinger, L., Obermayer, B. and Na, I.K.
Journal of Medical Virology 96 (3): e29539. March 2024

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

Plasmapheresis effectively abrogates severe liver toxicity of pegaspargase in a patient with acute lymphoblastic leukemia.
Tölle, M., Gökbuget, N., Habringer, S., Keller, U. and Schwartz, S.
Annals of Hematology 103 (8): 3269-3271. August 2024

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

Poxviruses induce a nuclear environment in the cytoplasm to promote viral replication.
Veratti, P., Wyler, E., Read, C., Scherer, M., Tan, J., Walther, P., Wider, S., Weidl, D. and Full, F.
bioRxiv : 2024.11.21.624458. 22 November 2024

Expression of mGluR5 in pediatric Hodgkin and Non-Hodgkin lymphoma-a comparative analysis of immunohistochemical and clinical findings regarding the association between tumor and paraneoplastic neurological disease.
Viezens, I., Knierim, E., Deubzer, H.E., Hauptmann, K., Fassbender, J., Morales-Gonzalez, S., Kaindl, A.M., Schuelke, M. and Nikolaus, M.
Cancers 16 (13): 2452. 4 July 2024

Sensitive dissection of a genomic regulatory landscape using bulk and targeted single-cell activation.
Vučićević, D., Hsu, C.W., Lopez Zepeda, L.S., Burkert, M., Hirsekorn, A., Bilić, I., Kastelić, N., Landthaler, M., Lacadie, S.A. and Ohler, U.
bioRxiv : 2024.09.12.612198. 12 September 2024

Breakthrough infections in SARS-CoV-2-vaccinated multiple myeloma patients improve cross-protection against omicron variants.
Wagner, A., Garner-Spitzer, E., Auer, C., Gattinger, P., Zwazl, I., Platzer, R., Orola-Taus, M., Pichler, P., Amman, F., Bergthaler, A., Huppa, J.B., Stockinger, H., Zielinski, C.C., Valenta, R., Kundi, M. and Wiedermann, U.
Vaccines 12 (5): 518. 9 May 2024

Editorial: The MACC1 network in cancer.
Walther, W., Siegel, F. and Stein, U.
Frontiers in Oncology 13 : 1343812. 5 July 2024

TransTACs: novel heterobispecific antibodies for targeted protein degradation in cancer therapy.
Walther, W., Torke, S. and Stein, U.
Signal Transduction and Targeted Therapy 9 (1): 331. 26 November 2024

K48- and K63-linked ubiquitin chain interactome reveals branch- and length-specific ubiquitin interactors.
Waltho, A., Popp, O., Lenz, C., Pluska, L., Lambert, M., Dötsch, V., Mertins, P. and Sommer, T.
Life Science Alliance 7 (8): e202402740. August 2024

Cross-platform clinical proteomics using the Charité Open Standard for Plasma Proteomics (OSPP).
Wang, Z., Farztdinov, V., Sinn, L.R., Tober-Lau, P., Ludwig, D., Freiwald, A., Amari, F., Textoris-Taube, K., Niewienda, A., Welter, A.S., Wei, A.A.J., Luckau, L., Kurth, F., Selbach, M., Hartl, J., Mülleder, M. and Ralser, M.
medRxiv : 2024.05.10.24307167. 10 May 2024

Anti-angiogenesis and anti-immunosuppression gene therapy through targeting COUP-TFII in an in situ glioblastoma mouse model.
Wang, F., Zhang, S., Sun, F., Chen, W., Liu, C., Dong, H., Cui, B., Li, L., Sun, C., Du, W., Liu, B., Fan, W., Deng, J., Schmitt, C.A., Wang, X. and Du, J.
Cancer Gene Therapy 31 (8): 1135-1150. August 2024

Altered enhancer-promoter interaction leads to MNX1 expression in pediatric acute myeloid leukemia with t(7;12)(q36;p13).
Weichenhan, D., Riedel, A., Sollier, E., Toprak, U.H., Hey, J., Breuer, K.H., Wierzbinska, J.A., Touzart, A., Lutsik, P., Bähr, M., Östlund, A., Nilsson, T., Jacobsson, S., Waraky, A., Behrens, Y.L., Göhring, G., Schlegelberger, B., Steinek, C., Harz, H., Leonhardt, H., Dolnik, A., Reinhardt, D., Bullinger, L., Palmqvist, L., Lipka, D.B. and Plass, C.
Blood Advances 8 (19): 5100-5111. 8 October 2024

Structural insights into the activation mechanism of antimicrobial GBP1.
Weismehl, M., Chu, X., Kutsch, M., Lauterjung, P., Herrmann, C., Kudryashev, M. and Daumke, O.
EMBO Journal 43 (4): 615-636. 15 February 2024

Combining Data Independent Acquisition with spike-in SILAC (DIA-SiS) improves proteome coverage and quantification.
Welter, A.S., Gerwien, M., Kerridge, R., Alp, K.M., Mertins, P. and Selbach, M.
Molecular & Cellular Proteomics 23 (10): 100839. October 2024

HLA-C*04:09N is expressed at the cell surface and triggers peptide-specific T-cell activation.
Welters, C., Welters, M.L., Stadler, S., Bullinger, L., Strobel, J., Hackstein, H., Dhamodaran, A., Blankenstein, T. and Hansmann, L.
Haematologica 109 (4): 1121-1127. April 2024

Oligonucleotide library screening for identification of virus-specific T-cell receptors.
Welters, M.L., Stadler, S., Anastasopoulou, V., Bullinger, L., Leisegang, M., Kammertöns, T., Welters, C. and Hansmann, L.
European Journal of Immunology 56 (6): e2350908. June 2024

Tissue-specific apparent mtDNA heteroplasmy and its relationship with ageing and mtDNA gene expression.
Wengert, S., Giannoulis, X., Kreitmaier, P., Kautz, P., Ludwig, L.S., Prokisch, H., Casale, F.P., Heinig, M. and Cai, N.
bioRxiv : 2024.12.11.627989. 16 December 2024

CXCR4-gerichtete Theranostics in der Hämato-Onkologie: Möglichkeiten und Herausforderungen [CXCR4-targeted theranostics in hematooncology: opportunities and challenges].
Werner, R., Haug, A., Buske, C., Heidegger, S., Illert, A.L., Bassermann, F., Herhaus, P., Buck, A., Duell, J., Topp, M.S., Kraus, S., Einsele, H., Lapa, C., Raderer, M., Lenz, G., Habringer, S., von Tresckow, B. and Keller, U.
Nuklearmedizin 63 (2): 57-61. April 2024

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

A hypoxia-epigenetics axis drives EMT in pancreatic cancer.
Wirth, M. and Schneider, G.
Cancer Research 84 (11): 1739-1741. 1 June 2024

Gastric stem cell biology and helicobacter pylori infection.
Wizenty, J. and Sigal, M.
Current Topics in Microbiology and Immunology 444 : 1-24. 18 January 2024

Single-cell RNA-sequencing of RVFV infection.
Wyler, E.
Methods in Molecular Biology 2824 : 361-372. August 2024

Pathogen dynamics and discovery of novel viruses and enzymes by deep nucleic acid sequencing of wastewater.
Wyler, E., Lauber, C., Manukyan, A., Deter, A., Quedenau, C., Teixeira Alves, L.G., Wylezich, C., Borodina, T., Seitz, S., Altmüller, J. and Landthaler, M.
Environment International 190 : 108875. August 2024

Spatial omics of acute myocardial infarction reveals a novel mode of immune cell infiltration.
Wünnemann, F., Sicklinger, F., Bestak, K., Nimo, J., Thiemann, T., Amrute, J., Nordbeck, M., Hartmann, N., Ibarra-Arellano, M.A., Tanevski, J., Heine, C., Frey, N., Lavine, K.J., Coscia, F., Saez-Rodriguez, J., Leuschner, F. and Schapiro, D.
bioRxiv : 2024.05.20.594955. 21 May 2024

PDGFRA is a conserved HAND2 effector during early cardiac development.
Xu, Y., Gehlot, R., Capon, S.J., Albu, M., Gretz, J., Bloomekatz, J., Mattonet, K., Vucicevic, D., Talyan, S., Kikhi, K., Günther, S., Looso, M., Firulli, B.A., Sanda, M., Firulli, A.B., Lacadie, S.A., Yelon, D. and Stainier, D.Y.R.
Nature Cardiovascular Research 3 (12): 1531-1548. December 2024

Cellular atlases are unlocking the mysteries of the human body.
Yanai, I., Haas, S., Lippert, C. and Kretzmer, H.
Nature 635 (8039): 553-555. November 2024

The IBEX imaging Knowledge-Base: a community resource enabling adoption and development of immunofluoresence imaging methods.
Yaniv, Z., Anidi, I.U., Arakkal, L., Arroyo-Mejías, A.J., Beuschel, R.T., Börner, K., Chu, C.J., Clark, B., Clatworthy, M.R., Colautti, J., Coscia, F., Croteau, J., Denha, S., Dever, R., Dutra, W.O., Fritzsche, S., Fullam, S., Gerner, M.Y., Gola, A., Gollob, K.J., Hernandez, J.M., Hor, J.L., Ichise, H., Jing, Z., Jonigk, D., Kandov, E., Kastenmüller, W., Koenig, J.F.E., Kothurkar, A., Kortekaas, R.K., Kreins, A.Y., Lamborn, I.T., Lin, Y., Morais, K.L.P., Lunich, A., Luz, J.C.S., MacDonald, R.B., Makranz, C., Maltez, V.I., McDonough, J.E., Moriarty, R.V., Ocampo-Godinez, J.M., Olyntho, V.M., Oxenius, A., Padhan, K., Remmert, K., Richoz, N., Schrom, E.C., Shang, W., Shi, L., Shih, R.M., Speranza, E., Stierli, S., Teichmann, S.A., Veres, T.Z., Vierhout, M., Wachter, B.T., Williams, M., Zangger, N., Germain, R.N. and Radtke, A.J.
arXiv : 2412.12965. 17 December 2024

Insights into therapeutic discovery through the Kelch domain structure of Keap1 at ambient temperature.
Yilmaz, M., Sever, B., Kutlu, Y., Gul, M., Okuducu, C., Tavli, S., Otsuka, M., Fujita, M., Haliloglu, T., Ciftci, H. and DeMirci, H.
bioRxiv : 2024.07.30.605796. 2 August 2024

Grainyhead-like 2 deficiency and kidney cyst growth in a mouse model.
Yurtdas, Z.Y., Kilic, E., Boor, P., Wyler, E., Landthaler, M., Jung, K. and Schmidt-Ott, K.M.
Journal of the American Society of Nephrology 35 (7): 838-853. July 2024

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

Everolimus and mycophenolate mofetil effectively prevent GvHD in children with severe acute kidney injury undergoing allogeneic HSCT.
Zirngibl, F., Gebert, P., Materne, B., Launspach, M., Künkele, A., Hundsdoerfer, P., Cyrull, S., Deubzer, H.E., Kühl, J.S., Eggert, A., Lang, P., Oevermann, L., von Stackelberg, A. and Schulte, J.H.
medRxiv : 2024.03.14.24304155. 16 March 2024

Integrative analysis reveals a macrophage-predominant, immunosuppressive immune microenvironment and subtype-specific therapeutic vulnerabilities in advanced salivary gland cancer.
Zuljan, E., von der Emde, B., Piwonski, I., Afonseca Pestana, A.C., Klinghammer, K., Mock, A., Horak, P., Heining, C., Klauschen, F., Pretzell, I., Boerries, M., Brandts, C.H., Kreutzfeldt, S., Teleanu, M.V., Hübschmann, D., Morris, L.G.T., Keller, U., Glimm, H., Fröhling, S., Ochsenreither, S., Keilholz, U., Blanc, E., Beule, D. and Rieke, D.T.
medRxiv : 2024.06.11.24308538v2. 14 June 2024

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

New coronavirus vaccine and method for designing and obtaining a virus vaccine.
Max Delbrueck Centrum fuer Molekulare in der Helmholtz Gemeinschaft.
EP-4396198-A2. 10 July 2024

LONG-read sequencing of human immunoglobulin gene introns to define a biomarker for in vivo DNA break repair.
Max Delbrueck Centrum fuer Molekulare in der Helmholtz Gemeinschaft.
WO-2024194255-A1. 26 September 2024

Spike-in enhanced phosphoproteomics uncovers synergistic signaling responses to MEK inhibition in colon cancer cells.
van Bentum, M., Klinger, B., Sieber, A., Lehmann, N., Haji, M., Naghiloo, S., Niquet, S., Mertins, P., Blüthgen, N. and Selbach, M.
bioRxiv : 2024.05.13.593849. 15 May 2024

Neuromuscular dysfunction in patient-derived FUS(R244RR)-ALS iPSC model via axonal downregulation of neuromuscular junction proteins.
von Kuegelgen, N., Ludwik, K., Mendonsa, S., Roemer, C., Becher, E., Breimann, L., Strauch, M., Mari, T., Mongellaz, S., Zuckerman, B., Grexa, N., Oliveras-Martinez, A., Woehler, A., Selbach, M., La Bella, V., Ulitsky, I. and Chekulaeva, M.
bioRxiv : 2024.08.17.607965. 17 August 2024

Long-term impact of scheduled regular endoscopic interventions for patients with primary sclerosing cholangitis.
Özdirik, B., Veltzke-Schlieker, W., Nicklaus, J.M., Berger, H., Schmidt, D., Leonhardt, S., Penndorf, V., Adler, A., Müller, T., Wree, A., Tacke, F. and Sigal, M.
Hepatology Communications 8 (9): e0494. September 2024

2023

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

MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange.
Abualrous, E.T., Stolzenberg, S., Sticht, J., Wieczorek, M., Roske, Y., Günther, M., Dähn, S., Boesen, B.B., Calvo, M.M., Biese, C., Kuppler, F., Medina-García, Á., Álvaro-Benito, M., Höfer, T., Noé, F. and Freund, C.
Nature Chemical Biology 19 (10): 1196-1204. October 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 evolution of non-small cell lung cancer metastases in TRACERx.
Al Bakir, M., Huebner, A., Martínez-Ruiz, C., Grigoriadis, K., Watkins, T.B.K., Pich, O., Moore, D.A., Veeriah, S., Ward, S., Laycock, J., Johnson, D., Rowan, A., Razaq, M., Akther, M., Naceur-Lombardelli, C., Prymas, P., Toncheva, A., Hessey, S., Dietzen, M., Colliver, E., Frankell, A.M., Bunkum, A., Lim, E.L., Karasaki, T., Abbosh, C., Hiley, C.T., Hill, M.S., Cook, D.E., Wilson, G.A., Salgado, R., Nye, E., Stone, R.K., Fennell, D.A., Price, G., Kerr, K.M., Naidu, B., Middleton, G., Summers, Y., Lindsay, C.R., Blackhall, F.H., Cave, J., Blyth, K.G., Nair, A., Ahmed, A., Taylor, M.N., Procter, A.J., Falzon, M., Lawrence, D., Navani, N., Thakrar, R.M., Janes, S.M., Papadatos-Pastos, D., Forster, M.D., Lee, S.M., Ahmad, T., Quezada, S.A., Peggs, K.S., Van Loo, P., Dive, C., Hackshaw, A., Birkbak, N.J., Zaccaria, S., Jamal-Hanjani, M., McGranahan, N. and Swanton, C.
Nature 616 (7957): 534-542. April 2023

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

Clinically relevant glioblastoma patient-derived xenograft models to guide drug development and identify molecular signatures.
Alcaniz, J., Winkler, L., Dahlmann, M., Becker, M., Orthmann, A., Haybaeck, J., Krassnig, S., Skofler, C., Kratzsch, T., Kuhn, S.A., Jödicke, A., Linnebacher, M., Fichtner, I., Walther, W. and Hoffmann, J.
Frontiers in Oncology 13 : 1129627. 11 April 2023

Patient-reported ability to walk 4 m and to wash: New clinical endpoints and predictors of survival in patients with pre-terminal cancer.
Anker, M.S., Lena, A., Roeland, E.J., Porthun, J., Schmitz, S., Hadzibegovic, S., Sikorski, P., Wilkenshoff, U., Fröhlich, A.K., Ramer, L.V., Rose, M., Eucker, J., Rassaf, T., Totzeck, M., Lehmann, L.H., von Haehling, S., Coats, A.J.S., Friede, T., Butler, J., Anker, S.D., Riess, H., Landmesser, U., Bullinger, L., Keller, U. and Ahn, J.
Journal of Cachexia Sarcopenia and Muscle 14 (4): 1670-1681. August 2023

Cardiovascular health-related quality of life in cancer: a prospective study comparing the ESC HeartQoL and EORTC QLQ-C30 questionnaire.
Anker, M.S., Potthoff, S.K., Lena, A., Porthun, J., Hadzibegovic, S., Evertz, R., Denecke, C., Fröhlich, A.K., Sonntag, F., Regitz-Zagrosek, V., Rosen, S.D., Lyon, A.R., Lüscher, T.F., Spertus, J.A., Anker, S.D., Karakas, M., Bullinger, L., Keller, U., Landmesser, U., Butler, J. and von Haehling, S.
European Journal of Heart Failure 25 (9): 1635-1647. September 2023

Associations of clonal hematopoiesis with recurrent vascular events and death in patients with incident ischemic stroke.
Arends, C.M., Liman, T.G., Strzelecka, P.M., Kufner, A., Löwe, P., Huo, S., Stein, C.M., Piper, S.K., Tilgner, M., Sperber, P.S., Dimitriou, S., Heuschmann, P., Hablesreiter, R., Harms, C., Bullinger, L., Weber, J.E., Endres, M. and Damm, F.
Blood 141 (7): 787-799. 16 February 2023

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

Immune phenotypes and checkpoint molecule expression of clonally expanded lymph node-infiltrating T cells in classical Hodgkin lymphoma.
Ballhausen, A., Ben Hamza, A., Welters, C., Dietze, K., Bullinger, L., Rahn, H.P., Hartmann, S., Hansmann, M.L. and Hansmann, L.
Cancer Immunology Immunotherapy 72 (2): 515-521. February 2023

Streamlined structure determination by cryo-electron tomography and subtomogram averaging using TomoBEAR.
Balyschew, N., Yushkevich, A., Mikirtumov, V., Sanchez, R.M., Sprink, T. and Kudryashev, M.
Nature Communications 14 (1): 6543. 17 October 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

Proteomic profiling of colorectal adenomas identifies a predictive risk signature for development of metachronous advanced colorectal neoplasia.
Bech, J.M., Terkelsen, T., Bartels, A.S., Coscia, F., Doll, S., Zhao, S., Zhang, Z., Brünner, N., Lindebjerg, J., Madsen, G.I., Fang, X., Mann, M. and Moreira, J.M.A.
Gastroenterology 165 (1): 121-132.e5. July 2023

Establishment and thorough characterization of xenograft (PDX) models derived from patients with pancreatic cancer for molecular analyses and chemosensitivity testing.
Behrens, D., Pfohl, U., Conrad, T., Becker, M., Brzezicha, B., Büttner, B., Wagner, S., Hallas, C., Lawlor, R., Khazak, V., Linnebacher, M., Wartmann, T., Fichtner, I., Hoffmann, J., Dahlmann, M. and Walther, W.
Cancers 15 (24): 5753. 8 December 2023

Leveraging large language models for decision support in personalized oncology.
Benary, M., Wang, X.D., Schmidt, M., Soll, D., Hilfenhaus, G., Nassir, M., Sigler, C., Knödler, M., Keller, U., Beule, D., Keilholz, U., Leser, U. and Rieke, D.T.
JAMA Network Open 6 (11): e2343689. November 2023

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