Publications | Department of Molecular Cell Biology

Lymphodepleting chemotherapy potentiates neoantigen-directed T cell therapy by enhancing antigen presentation

Sagie S., Babu T., Weller C., Tabachnik C., Livneh I., Quast N. P., Gumpert N., Shomuradova A., Raybould M. I., Levy R., Malko D., Alfia A., Ben Lulu T., Alon M., Herrera F., Kutuzov M., Zerbib M., Greenberg P., Wasserman-Bartov T., Benedek G., Levin Y., Stossel C., Kamer I., Golan T., Oren R., Shmueli M., Bartok O., Bar J., Cohen J., Dushek O., Deane C. M. & Samuels Y. (2025), Cell Reports Medicine. 6, 12, 102506

HLA export by melanoma cells decoys cytotoxic T cells to promote immune evasion

Chemla Y., Itzhaki O., Melamed S., Weller C., Sade Y., Manich P., Reshef K., Xenidis N., Maliah A., Levy G., Parikh R., Bartok O., Levy O., Tal I., Aziel G., Nissani A., Yunger S., Likonen D., Kliminsky V., Golan T., Capron C., Ace V., Levy R., Rasoulouniriana D., Eyal Z., Barzilay Y., Balaban R., Khateeb A., Khosravi R., Grau A., Ziv T., Greenberg P., Netanely D., Vaknin H., Wu X., Amitay Y., Brenner R., Martínez Gómez J. M., Hershkovitz D., Yardeni T., Zemser-Werner V., Kobiler O., Friedmann Y., Bassan D., Shamir R., Eisenbach L., Santana-Magal N., Milyavsky M., Eisenberg G., Keren L., Cohen M., Gur D., Barak B., Lotem M., Sprinzak D., Greenberger S., Fisher D., Besser M. J., Khaled M., Close P., Shapira R., Apcher S., Madi A., Levesque M. P., Rapino F., Carmi Y., Parikh S., Samuels Y. & Levy C. (2025), Cell

HLA export by melanoma cells decoys cytotoxic T cells to promote immune evasion

Chemla Y., Itzhaki O., Melamed S., Weller C., Sade Y., Manich P., Reshef K., Xenidis N., Maliah A., Levy G., Parikh R., Bartok O., Levy O., Tal I., Aziel G., Nissani A., Yunger S., Likonen D., Kliminsky V., Golan T., Capron C., Ace V., Levy R., Rasoulouniriana D., Eyal Z., Barzilay Y., Balaban R., Khateeb A., Khosravi R., Grau A., Ziv T., Greenberg P., Netanely D., Vaknin H., Wu X., Amitay Y., Brenner R., Martínez Gómez J. M., Hershkovitz D., Yardeni T., Zemser-Werner V., Kobiler O., Friedmann Y., Bassan D., Shamir R., Eisenbach L., Santana-Magal N., Milyavsky M., Eisenberg G., Keren L., Cohen M., Gur D., Barak B., Lotem M., Sprinzak D., Greenberger S., Fisher D., Besser M. J., Khaled M., Close P., Shapira R., Apcher S., Madi A., Levesque M. P., Rapino F., Carmi Y., Parikh S., Samuels Y. & Levy C. (2025), Cell

Recurrent Immunogenic Neoantigens and Their Cognate T-cell Receptors in Treatment-Resistant Metastatic Prostate Cancer

Gumpert N., Sagie S., Arnedo-Pac C., Babu T., Weller C., Gonzalez-Perez A., Wang Y., Michel Todó L., Levy R., Chen X., Greenberg P., Dayan-Rubinov M., Yakubovich E., Wasserman-Bartov T., Zerbib M., Gong J., Rebernick R. J., Oliveira Tercero A., Agundez Muriel L., Benedek G., Kedmi M., Oren R., Ben-Dor S., Levin Y., Troyanskaya O. G., Munzur A. D., Wyatt A. W., Cieslik M. P., Quigley D. A., Van Allen E. M., Anandasabapathy N., Mateo J., Yang X., Martínez-Jiménez F., Lopez-Bigas N. & Samuels Y. (2025), Cancer Discovery, p. OF1-OF20

A Drosophila screen of schizophrenia genes highlights neural and glial MMPs in neuronal remodeling

Keret S., Meltzer H., Marmor-Kollet N. & Schuldiner O. (2025), Life Science Alliance. 8, 12, e202503504

MMS22L is a novel key actor of normal and pathological erythropoiesis

Colin E., Ferrer-Vicens I., Brook D., Salma M., Andrieu-Soler C., Bayard E., Fernandes A., Brouzes C., Lefèvre C., Duval R., Dussiot M., Trovati T., Courtois G., Azouzi S., Zarhrate M., Lambilliotte A., Park S., Carpentier B., Colard M., Manceau S., Moshous D., Mayeux P., Gautier E. F., Miccio A., Soulier J., Vainchenker W., Shlush L., Da Costa L., Frayne J., Soler E., Hermine O. & Couronné L. (2025), HemaSphere. 9, 12, e70264

Dissecting endometrial cancer complexity in response to standard and targeted therapies

Vaccarella S., Bruno V., Orlandi G., Covino D. A., Frascolla C., Pulito C., Vizza R., Urbani G., Allegretti M., De Pascale V., Goeman F., Ciuffreda L., Arteni B. A. M., Di Martino S., Sacconi A., Mancini E., Bagnato A., Baiocco E., Kajal R., Vinik Y., Lev S., Fanciulli M., Vidiri A., Carosi M., Strano S., Donzelli S., Vizza E. & Blandino G. (2025), Cell Death and Disease. 16, 873

Integrated spatial proteomic analysis of breast cancer heterogeneity unravels cancer cell phenotypic plasticity

Mardamshina M., Karagach S., Mohan V., Arad G., Necula D., Golani O., Fellus-Alyagor L., Shenoy A., Krol K., Pirak D., Itzhacky N., Marin I., Shalmon B., Addadi Y., Sharan R., Gal-Yam E., Barshack I. & Geiger T. (2025), Nature Communications. 16, 10482

Single-cell transcriptomic analysis of HPV-related multiphenotypic sinonasal carcinoma uncovers MYB-HPV association

Wizel A., Spence M. D., Mints M., Britton W., Okolo O., Yu V., Cioffi I., Caruana S., Troob S. H., Faquin W. C., Lin D. T., Tirosh I., Puram S. V., Parikh A. S. & Drier Y. (2025), npj Precision Oncology. 9, 378

Unifying regulatory motifs in endocrine circuits

Raz M., Glass D. S., Milo T., Korem Kohanim Y., Karin O., Tendler A., Mayo A. & Alon U. (2025), Nature Communications. 16, 11017

Molecular Systems Biology at 20: reflecting on the past, envisioning the future

Bheda P., Hou J., Aebersold R., Alon U., Bader J. S., Bardwell L., Liu E. T., Locke J. C., Mann M., Millar A. J., Naef F., Pilpel Y., Shamir R. & Vitkup D. (2025), Molecular Systems Biology. 21, 12, p. 1667-1673

Sirt6 prevents the age-related decline of H2S through the control of one-carbon metabolism

Touitou N., Nahum L., Feldman-Trabelsi S., Avivi M. Y., Aon M. A., Naiman S., Rathaus M., Gertler A. A., Roichman A., Dvir L. B., Bernier M., Banskota N., Beck L., Nagar R., Schwartz Z., Price N. L., Harel M., Lerrer B., Ishii I., Senderowitz H., Moaddel R., Geiger T., de Cabo R. & Cohen H. Y. (2025), Proceedings of the National Academy of Sciences of the United States of America. 122, 46, e251408412

Characterization of the tumor microbiome of brain metastases and glioblastoma reveals tumor-type-specific and location-specific microbial signatures

Gigi E., Gavert N., Raijman-Nagar L., Zwang Y., Zemach H., Livyatan I., Levy-Barda A., Laviv Y., Kanner A. A., Amiel A., Siegal T., Leibovici A., Selezen I., Badran O., Zohar Y., Safadi E., Prather L. L., Helfer C. R., Castro P., Barshack I., Dadosh T., Levin-Zaidman S., Goliand I., Golani O., Horn S., Mandel J. J., Shental N., Shai A., Yust-Katz S. & Straussman R. (2025), Nature Cancer. 6, 11, p. 1761-1776

Principles of bacteriostatic and bactericidal antibiotics at subinhibitory concentrations

Vaisbourd E., Glass D. S., Yang Y., Mayo A., Bren A. & Alon U. (2025), mBio. 16, 11, e0206625

Open problems in ageing science: a roadmap for biogerontology

Talay A., Belikov A. V., To P. K. P., Alfatemi H. H., Alon U., Deelen J., Ewald C. Y., Gems D., Gorbunova V., Gruber J., Hagg S., Hemming J., Horvath S., Kaya A., Lewis C. J., Maier A. B., Marinova M. B., Pawelec G., Peleg S., Rattan S., Scheibye-Knudsen M., Schmauck-Medina T., Saroyan V., Seluanov A., Stolzing A., Teeling E., Williams R. W., White T., Unfried M. & De Magalhaes J. P. (2025), GeroScience

A spatial atlas of human gastrointestinal acute GVHD reveals epithelial and immune dynamics underlying disease pathophysiology

Azulay N., Milo I., Bussi Y., Ben-Uri R., Haran T. K., Eldar M., Elhanani O., Harnik Y., Yakubovsky O., Nachmany I., Salame T., Wartenberg M., Bertheau P., Michonneau D., Socie G. & Keren L. (2025), Science Translational Medicine. 17, 823, eadu6032

p53 regulates the expression of histone modifiers to restrict stemness and maintain differentiated luminal identity in breast cancer

Aylon Y., Furth N., Pirona A. C., Lavie A., Fedorova O., Hassin O., Padrão N., Steinmetz M., Sarusi-Potuguez A., Fellus-Alyagor L., Shimoni I., Dassa B., Zwart W., Shema E. & Oren M. (2025), Proceedings of the National Academy of Sciences - PNAS. 122, 44, e252264612

ProtoMol: enhancing molecular property prediction via prototype-guided multimodal learning

Wang Y., Zhang K., Huang J., Yin N., Liu S. & Segal E. (2025), Briefings in Bioinformatics. 26, 6, bbaf629

Evolutionarily conserved role of oxytocin in zebrafish social reward encoding

Kareklas K., Herrera-Castillo L., Levkowitz G. & Oliveira R. F. (2025), Biology Letters. 21, 11, 20250628

Vagal blockade of the brain-liver axis deters cancer-associated cachexia

Garrett A., Darzi N., Deshmukh A., Rosenfeld N., Goldman O., Adler L., Bab-Dinitz E., Singer O., Hassani Najafabadi A., Wong C. W., Bose S., Randon P. M., Bustamante F., Larios R., Brandis A., Mehlman T., Smaglo B., Chang P., Oliva J., Haymaker C., Nagawekar L., Wu S. R., Huang Y., Shen A., Vora A., Padilla J. F., Pfeffer A., Sutherland G., Starr M., Zimmers T., Zhu Y., Morizio J., Erez A. & Shen X. (2025), Cell. 188, 21, p. 6044-6063.e24

Towards a reference cell atlas of liver diversity over the human lifespan

Taylor S. A., Bader G. D., Macparland S., Mullen A. C., Andrews T., Cuenca A. G., Dasgupta R., Gehring A. J., Grun D., Guilliams M., Gulamhusein A., Henderson N. C., Hirschfield G., Huppert S. S., Itzkovitz S., Jiang Z. G., Lauer G. M., Mcgilvray I., Mysore K. R., Pirola C. J., Quon G., Rahbari M., Regev A., Ricciuto A., Scott C. L., Sharma A., Sookoian S., Tana M. M., Teichmann S. A., Vallier L., Vlachos I. S., Wang B. & Zhen M. (2025), Nature Reviews Gastroenterology and Hepatology. 23, 1, p. 97-109

IceQream: Quantitative chromosome accessibility analysis using physical TF models

Bercovich A., Lifshitz A., Eldar M., Cheng S., Stok Ranen R., Stelzer Y. & Tanay A. (2025), Nature Communications. 16, 8984

IceQream: Quantitative chromosome accessibility analysis using physical TF models

Bercovich A., Lifshitz A., Eldar M., Cheng S., Stok Ranen R., Stelzer Y. & Tanay A. (2025), Nature Communications. 16, 8984

CD4 T cells acquire Eomesodermin to modulate cellular senescence and aging

Elyahu Y., Feygin I., Eremenko E., Pinkas N., Zemer A., Shicht A., Berner O., Avigdory-Meiri R., Nemirovsky A., Reshef K., Roitman L., Krizhanovsky V. & Monsonego A. (2025), Nature Aging. 5, 10, p. 1970-1982

Stool shed cell transcriptomics mirrors tumor biology and enables colorectal cancer diagnosis

Bahar Halpern K., Kent I., Yakubovsky O., Ben-Moshe S., Barkai T., Fine M., Novoselsky R., Israeli A., Nachmany I. & Itzkovitz S. (2025), Scientific Reports. 15, 34413

Artificial intelligence in metabolic research

Holst J. J., Scheele C., Scherer P. E., Jia W., Segal E., Slavov N., Loos R. J. F., Vahedi G., Sun L., Babu M. M., McCradden M. D. & Jacobs P. G. (2025), Nature Metabolism. 7, 11, p. 2183-2186

Transcriptomic profiling of shed cells enables spatial mapping of cellular turnover in human organs

Barkai T., Yakubovsky O., Korem Kohanim Y., Bahar Halpern K., Shir S., Oren N., Fine M., Kelmer P., Talmon A., Israeli A., Pencovich N., Pery R., Nachmany I. & Itzkovitz S. (2025), Molecular Systems Biology. 21, 12, p. 1778-1792

Challenges and Opportunities in Spatiotemporal Models of Mammalian Gastrulation

Rubinstein H., Mayshar Y. & Stelzer Y. (2025), Annual Review of Cell and Developmental Biology. 41, 1, p. 135-158

PNKP targeting engages the autophagic machinery through STING and STAT3 to potentiate ferroptosis and chemotherapy in TNBC

Maimon A., Puzzovio P. G., Vinik Y., Hannuna G. D., Donzelli S., Rutigliano D., Blandino G. & Lev S. (2025), Redox Biology. 86, 103775

Gtf2i-encoded transcription factor Tfii-i regulates myelination via Sox10 and Mbp regulatory elements

Levy G., Rokach M., Fischer I., Kimchi-Feldhorn O., Shoob S., Bar E., Rosenberg T., Bartman J., Parnas H., Grad M., Israel-Elgali I., Sfadia G. E., Trangle S. S., Vainshtein A., Eisenbach Y. E., Jahn O., Siems S. B., Werner H. B., Shomron N., Assaf Y., Peles E., Slutsky I., Marco A. & Barak B. (2025), Nature Communications. 16, 8518

The Biodiversity Cell Atlas: mapping the tree of life at cellular resolution

Sebé-Pedrós A., Tanay A., Lawniczak M. K., Arendt D., Aerts S., Archibald J., Arnone M. I., Blaxter M., Cleves P., Coelho S. M., Dias M., Dunn C., Elek A., Frazer J., Gabaldón T., Gillis J., Grau-Bové X., Guigó R., Hobert O. & Huerta-Cepas J. (2025), Nature. 645, 8082, p. 877-885

Disruption of the developmental factor Otp in the adult forebrain reveals its diverse physiological functions

Tahor M., Kuperman Y., Nahum T., Tsoory M., Bejar B., Regev E., Blechman J., Biran J., Chen A. & Levkowitz G. (2025), BioRxiv

Fibro predict a machine learning risk score for advanced liver fibrosis in the general population using Israeli electronic health records

Kalka I. N., Hazzan R., Yacovzada N. S., Igbaria S., Segal E., Weinberger A. & Neeman Z. (2025), Scientific Reports. 15, 32035

Long-term Hyperbaric Oxygen Treatment Enhances Nerve Regeneration and Remyelination in a Rat Sciatic Nerve Graft Model

Kedar D. J., Shani N., Fliss E., Bracha G., Zvi E., Rosen R., Greenberg O., Eshed Eisenbach Y., Peles E. & Gur E. (2025), Plastic and Reconstructive Surgery - Global Open. 13, 8, p. e7039

Hyperbaric Oxygen Therapy for PTSD: Threshold Effect for Sustained Symptom Improvement in a Biologically Based Treatment

Danan D., Grosskopf Y., Mayo A., Efrati S., Kutz I., Lang E., Alon U. & Doenyas-Barak K. (2025), Brain and Behavior. 15, 8, e70757

Immune surveillance of senescent cells in aging and disease

Majewska J. & Krizhanovsky V. (2025), Nature Aging. 5, p. 1415-1424

RNA editing deficiency models differential immunogenicity of pancreatic α- and β-cells

Peleg S., Zamashanski L., Belin J., Novoselsky R., Cohen-Fultheim R., Knebel U. E., Glaser B., Itzkovitz S., Kaestner K. H., Powers A. C., Levanon E. Y., Klochendler A. & Dor Y. (2025), Molecular Metabolism. 98, 102183

The Nodes of Ranvier: Mechanisms of Assembly and Maintenance

Rasband M. N. & Peles E. (2025), Cold Spring Harbor perspectives in biology. 17, 8, a041361

Multimodal AI correlates of glucose spikes in people with normal glucose regulation, pre-diabetes and type 2 diabetes

Carletti M., Pandit J., Gadaleta M., Chiang D., Delgado F., Quartuccio K., Fernandez B., Raygoza Garay J. A., Torkamani A., Miotto R., Rossman H., Berk B., Baca-Motes K., Kheterpal V., Segal E., Topol E. J., Ramos E. & Quer G. (2025), Nature Medicine. 31, 9, p. 3121-3127

Subtypes and proliferation patterns of small intestine neuroendocrine tumors revealed by single-cell RNA sequencing

Somech E., Halder D., Spitzer A., Barbolin C., Tyler M., Halperin R., Biton M., Tirosh A. & Tirosh I. (2025), eLife. 13, RP101153

Deep phenotyping of health-disease continuum in the Human Phenotype Project

Reicher L., Shilo S., Godneva A., Lutsker G., Zahavi L., Shoer S., Krongauz D., Rein M., Kohn S., Segev T., Schlesinger Y., Barak D., Levine Z., Keshet A., Shaulitch R., Lotan-Pompan M., Elkan M., Talmor-Barkan Y., Aviv Y., Dadiani M., Tsodyks Y., Gal-Yam E. N., Leibovitzh H., Werner L., Tzadok R., Maharshak N., Koga S., Glick-Gorman Y., Stossel C., Raitses-Gurevich M., Golan T., Dhir R., Reisner Y., Weinberger A., Rossman H., Song L., Xing E. P. & Segal E. (2025), Nature Medicine. 31, 9, p. 3191-3203

Generative AI enables medical image segmentation in ultra low-data regimes

Zhang L., Jindal B., Alaa A., Weinreb R., Wilson D., Segal E., Zou J. & Xie P. (2025), Nature Communications. 16, 6486

Mapping circulating hematopoietic stem cells for non-invasive, blood-based diagnostics

Furer N. & Shlush L. (2025), Nature Medicine

Crohns disease and ulcerative colitis exhibit prediagnostic antibody signatures with shared and divergent changes towards disease onset

Bourgonje A. R., Andreu-Sánchez S., Gacesa R., Innocenti G., Kalka I. N., Klompus S., Leviatan S., Schlesinger Y., Krongauz D., Weinberger A., Van Der Vegt B., Fu J., Segal E., Zhernakova A., Vogl T. & Weersma R. K. (2025), Gut. 74, 12, p. 1977-1988, 334362

High-Throughput Single-Cell Proteomics of In Vivo Cells

Karagach S., Smollich J., Atrakchi O., Mohan V. & Geiger T. (2025), Molecular and Cellular Proteomics. 24, 7, 101018

From bench to business: translating academic advances into industry innovations

Abilez O. J., Javali A., Jones J., Rellán-Álvarez R., Sozzani R. & Tzahor E. (2025), Development. 152, 13, dev205007

Baseline Characteristics of Weight-Loss Success in a Personalized Nutrition Intervention: A Secondary Analysis

Popp C. J., Wang C., Berube L., Curran M., Hu L., Pompeii M. L., Barua S., Li H., St-Jules D. E., Schoenthaler A., Segal E., Bergman M. & Sevick M. A. (2025), Nutrients. 17, 13, 2178

A reference model of circulating hematopoietic stem cells across the lifespan with applications to diagnostics

Furer N., Rappoport N., Milman O., Tavor S., Lifshitz A., Bercovich A., Ben-Kiki O., Danin A., Kedmi M., Shipony Z., Lipson D., Meiri E., Yanai G., Shapira S., Arber N., Berdichevsky S., Tyner J., Joshi S., Landau D., Ganesan S., Dusaj N., Chamely P., Kaushansky N., Chapal-Ilani N., Shamir R., Tanay A. & Shlush L. (2025), Nature Medicine. 31, 7, p. 2442-2451

A reference model of circulating hematopoietic stem cells across the lifespan with applications to diagnostics

Furer N., Rappoport N., Milman O., Tavor S., Lifshitz A., Bercovich A., Ben-Kiki O., Danin A., Kedmi M., Shipony Z., Lipson D., Meiri E., Yanai G., Shapira S., Arber N., Berdichevsky S., Tyner J., Joshi S., Landau D., Ganesan S., Dusaj N., Chamely P., Kaushansky N., Chapal-Ilani N., Shamir R., Tanay A. & Shlush L. (2025), Nature Medicine. 31, 7, p. 2442-2451

Protocol for predicting suppressors of cell-death pathways based on transcriptomic and vulnerability data

Vinik Y., Maimon A. & Lev S. (2025), STAR Protocols. 6, 2, 103855

The Society for Immunotherapy of Cancer Perspective on Liquid Biopsy and Radiomics-Based Technologies for Immuno-oncology Biomarker Discovery and Application

Monette A., Aguilar-Mahecha A., Altinmakas E., Angelos M. G., Assad N., Batist G., Bommareddy P. K., Bonilla D. L., Borchers C. H., Church S. E., Ciliberto G., Cogdill A. P., Fattore L., Hacohen N., Haris M., Lacasse V., Lie W. R., Mehta A., Ruella M., Sater S., Spatz A., Taouli B., Tarhoni I., Gonzalez-Kozlova E., Tirosh I., Wang X. & Gnjatic S. (2025), Clinical Cancer Research. 31, 12, p. 2278-2293

Curating a single-cell data atlas for a deeper understanding of intra-tumor heterogeneity

Tyler M. & Tirosh I. (2025), Nature Cancer. 6, 6, p. 922-923

Esophageal microbiome correlates with post-esophagectomy anastomotic leak in cancer patients

Naddaf R., Shmilovich H., Carasso S., Keshet-David R., Herren R., Gefen T., Goshen-Lago T., Zwang Y., Livyatan I., Shental N., Haberfeld O., Straussman R., Markar S. R., Nilsson M., Kashtan H., Ben-Aharon I. & Geva-Zatorsky N. (2025), ESMO Gastrointestinal Oncology. 8, 100172

Clonal hematopoiesis-associated motoric deficits caused by monocyte-derived microglia accumulating in aging mice

Kim J., Trzebanski S., Shin S., Schori L., Frumer Friedman G. R., Ilani N. C., Kadam A., Vicario R., Aust O., Bugaeva P., Piatek S., Ismajli L. K., Hoffmann C. J., Scheller M., Boura-Halfon S., Kaushansky N., Golani O., Solomon A., Liu Z., Amann L., Böhm-Sturm P., Koch S. P., Wenger N., Ginhoux F., Prinz M., Avraham R., Harms C., Geissmann F., Müller-Tidow C., Uderhardt S., Milenkovic I., Shlush L. & Jung S. (2025), Cell Reports. 44, 5, 115609

Erratum: Interactions between cancer cells and immune cells drive transitions to mesenchymal-like states in glioblastoma (Cancer Cell (2021) 39(6) (779792.e11), (S1535610821002683), (10.1016/j.ccell.2021.05.002))

Hara T., Chanoch-Myers R., Mathewson N. D., Myskiw C., Atta L., Bussema L., Eichhorn S. W., Greenwald A. C., Kinker G. S., Rodman C., Gonzalez Castro L. N., Wakimoto H., Rozenblatt-Rosen O., Zhuang X., Fan J., Hunter T., Verma I. M., Wucherpfennig K. W., Regev A., Suvà M. L. & Tirosh I. (2025), Cancer Cell. 43, 6, p. 1175-1176

Characterizing the metabolome of children with growth hormone deficiency

Shilo S., Keshet A., Halloun R., Bar N., Cohen M., Gal S., Oren M., Glantz-Gashai Y., Malitsky S., Itkin M., Lotan-Pompan M., Godneva A., Weinberger A., Tiosano D. & Segal E. (2025), Journal of Pediatric Endocrinology and Metabolism. 38, 8, p. 815-823

Proliferating Microglia Exhibit Unique Transcriptional and Functional Alterations in Alzheimers Disease

Villacampa N., Sarlus H., Martorell P., Bhalla K., Gomez-Castro S., Vieira-Saecker A., Slutzkin I., Händler K., Venegas C., McManus R., Ulas T., Beyer M., Segal E. & Heneka M. T. (2025), ASN Neuro. 17, 1, 2506406

Translation dysregulation in cancer as a source for targetable antigens

Weller C., Bartok O., McGinnis C. S., Palashati H., Chang T. G., Malko D., Shmueli M. D., Nagao A., Hayoun D., Murayama A., Sakaguchi Y., Poulis P., Khatib A., Erlanger Avigdor B., Gordon S., Cohen Shvefel S., Zemanek M. J., Nielsen M. M., Boura-Halfon S., Sagie S., Gumpert N., Yang W., Alexeev D., Kyriakidou P., Yao W., Zerbib M., Greenberg P., Benedek G., Litchfield K., Petrovich-Kopitman E., Nagler A., Oren R., Ben-Dor S., Levin Y., Pilpel Y., Rodnina M., Cox J., Merbl Y., Satpathy A. T., Carmi Y., Erhard F., Suzuki T., Buskirk A. R., Olweus J., Ruppin E., Schlosser A. & Samuels Y. (2025), Cancer Cell. 43, 5, p. 823-840.e18

Deciphering the longitudinal trajectories of glioblastoma ecosystems by integrative single-cell genomics

Spitzer A., Johnson K. C., Nomura M., Garofano L., Nehar-belaid D., Darnell N. G., Greenwald A. C., Bussema L., Oh Y. T., Varn F. S., DAngelo F., Gritsch S., Anderson K. J., Migliozzi S., Gonzalez Castro L. N., Chowdhury T., Robine N., Reeves C., Park J. B., Lipsa A., Hertel F., Golebiewska A., Niclou S. P., Nusrat L., Kellet S., Das S., Moon H. E., Paek S. H., Bielle F., Laurenge A., Di Stefano A. L., Mathon B., Picca A., Sanson M., Tanaka S., Saito N., Ashley D. M., Keir S. T., Ligon K. L., Huse J. T., Yung W. K., Lasorella A., Iavarone A., Verhaak R. G., Tirosh I. & Suvà M. L. (2025), Nature Genetics. 57, 5, p. 1168-1178, 1088

The multilayered transcriptional architecture of glioblastoma ecosystems

Nomura M., Spitzer A., Johnson K. C., Garofano L., Nehar-belaid D., Galili Darnell N., Greenwald A. C., Bussema L., Oh Y. T., Varn F. S., DAngelo F., Gritsch S., Anderson K. J., Migliozzi S., Gonzalez Castro L. N., ChowdhFury T., Robine N., Reeves C., Park J. B., Lipsa A., Hertel F., Golebiewska A., Niclou S. P., Nusrat L., Kellet S., Das S., Moon H. E., Paek S. H., Bielle F., Laurenge A., Di Stefano A. L., Mathon B., Picca A., Sanson M., Tanaka S., Saito N., Ashley D. M., Keir S. T., Ligon K. L., Huse J. T., Yung W. K., Lasorella A., Verhaak R. G., Iavarone A., Suvà M. L. & Tirosh I. (2025), Nature Genetics. 57, 5, p. 1155-1167, 3406

The Curated Cancer Cell Atlas provides a comprehensive characterization of tumors at single-cell resolution

Tyler M., Gavish A., Barbolin C., Tschernichovsky R., Hoefflin R., Mints M., Puram S. V. & Tirosh I. (2025), Nature Cancer. 6, 6, p. 1088-1101

Proteomic and lipidomic analysis of low-density lipoprotein identifies potential biomarkers of early estrogen receptor-positive breast cancer

Abu Mohsen Y., Twitto-Greenberg R., Cohen A., Leichner G. S., Mahler L., Cohen H., Kamari Y., Shaish A., Harari A., Leikin-Frenkel A., Glick Saar E., Geiger T., Malitsky S., Itkin M., Harats D. & Keshet R. (2025), Cancer & Metabolism. 13, 20

Precision nutrition for cardiometabolic diseases

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Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC

Smith B. J., Zhao C., Dubinkina V., Jin X., Zahavi L., Shoer S., Moltzau-Anderson J., Segal E. & Pollard K. S. (2025), Genome Research. 35, 5, p. 1247-1260

GMP-like and MLP-like Subpopulations of Hematopoietic Stem and Progenitor Cells Harboring Mutated EZH2 and TP53 at Diagnosis Promote Acute Myeloid Leukemia Relapse: Data of Combined Molecular, Functional, and Genomic Single-Stem-Cell Analyses

Shahar Gabay T., Stolero N., Rabhun N., Sabah R., Raz O., Neumeier Y., Marx Z., Tao L., Biezuner T., Amir S., Adar R., Levy R., Chapal-Ilani N., Evtiugina N., Shlush L. I., Shapiro E., Yehudai-Resheff S. & Zuckerman T. (2025), International Journal of Molecular Sciences. 26, 9, 4224

ARID5A promotes inflammation and fibrosis during cardiac aging: Cardiac aging

Miyara S. & Tzahor E. (2025), Nature Cardiovascular Research. 4, 5, p. 508-510

Chemoresistome mapping in individual breast cancer patients unravels diversity in dynamic transcriptional adaptation

Dadiani M., Friedlander G., Perry G., Balint-Lahat N., Gilad S., Morzaev-Sulzbach D., Shenoy A., Bossel Ben-Moshe N., Pavlovsky A., Bernstein-Molho R., Domany E., Barshack I., Geiger T., Kaufman B. & Gal-Yam E. N. (2025), Molecular Oncology. 19, 12, p. 3665-3684

Re-epithelialization of cancer cells increases autophagy and DNA damage: Implications for breast cancer dormancy and relapse

Drago-Garcia D., Giri S., Chatterjee R., Simoni-Nieves A., Abedrabbo M., Genna A., Uribe Rios M. L., Lindzen M., Sekar A., Gupta N., Aharoni N., Bhandari T., Mayalagu A., Schwarzmüller L., Tarade N., Zhu R., Mohan-Raju H. R., Karatekin F., Roncato F., Eyal-Lubling Y., Keidar T., Nof Y., Nataraj N. B., Bernshtein K. S., Wagner B., Nair N. U., Sanghvi N., Alon R., Seger R., Pikarsky E., Donzelli S., Blandino G., Wiemann S., Lev S., Prywes R., Barkan D., Rueda O. M., Caldas C., Ruppin E., Shiloh Y., Dahlhoff M. & Yarden Y. (2025), Science Signaling. 18, 883, eado3473

Neuropeptide oxytocin facilitates its own brain-to-periphery uptake

Rajamannar P., Blechman J., Raz O. & Levkowitz G. (2025), Cell Reports. 44, 4, 115491

Deciphering the complex clonal heterogeneity of polycythemia vera and the response to interferon alfa

Kalmer M., Grasshoff M., Maié T., Pannen K., Toledo M. A., Vieri M., Olschok K., Lemanzyk R., Lazarevic J., Junge B., Baumeister J., Galauner A., Ilani N. C., Bar D., Colin E., Cheng M., Schifflers J., Kricheldorf K., Schemionek M., Brümmendorf T. H., Weiskirchen R., Shlush L., Zenke M., Chatain N., Costa I. G. & Koschmieder S. (2025), Blood advances. 9, 8, p. 1873-1887

Development of antibiotic resistome in premature infants

Keshet A., Hochwald O., Lavon A., Borenstein-Levin L., Shoer S., Godneva A., Glantz-Gashai Y., Cohen-Dolev N., Timstut F., Lotan-Pompan M., Solt I., Weinberger A., Segal E. & Shilo S. (2025), Cell Reports. 44, 4, 115515

Preventing Multimer Formation in Commonly Used Synthetic Biology Plasmids

Vaisbourd E., Bren A., Alon U. & Glass D. S. (2025), ACS Synthetic Biology. 14, 4, p. 1309-1315

A single-cell atlas of Schwannoma across genetic backgrounds and anatomic locations

Gonzalez Castro L. N., Gavish A., Bussema L., Mount C. W., Neftel C., Nomura M., Chiocca E. A., Bi W. L., Arnaout O., Barker F. G., Brown J. M., Jordan J. T., Batchelor T. T., Stemmer-Rachamimov A., Plotkin S. R., Tirosh I. & Suvà M. L. (2025), Genome Medicine. 17, 37

Compression of morbidity by interventions that steepen the survival curve

Yang Y., Mayo A., Levy T., Raz N., Shenhar B., Jarosz D. F. & Alon U. (2025), Nature Communications. 16, 3340

End-User Confidence in Artificial Intelligence-Based Predictions Applied to Biomedical Data

Kam Z., Peracchio L. & Nicora G. (2025), International Journal of Neural Systems. 35, 4, 2550017

Clinical translation of microbiome research

Gilbert J. A., Azad M. B., Bäckhed F., Blaser M. J., Byndloss M., Chiu C. Y., Chu H., Dugas L. R., Elinav E., Gibbons S. M., Gilbert K. E., Henn M. R., Ishaq S. L., Ley R. E., Lynch S. V., Segal E., Spector T. D., Strandwitz P., Suez J., Tropini C., Whiteson K. & Knight R. (2025), Nature Medicine. 31, 4, p. 1099-1113

Metabolic interplays between the tumour and the host shape the tumour macroenvironment

Altea-Manzano P., Decker-Farrell A., Janowitz T. & Erez A. (2025), Nature Reviews Cancer. 25, 4, p. 274-292, 387014

Pregnancy and postpartum dynamics revealed by millions of lab tests

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High-dimensional imaging using combinatorial channel multiplexing and deep learning

Ben-Uri R., Ben Shabat L., Shainshein D., Bar-Tal O., Bussi Y., Maimon N., Keidar Haran T., Milo I., Goliand I., Addadi Y., Salame T. M., Rochwarger A., Schürch C. M., Bagon S., Elhanani O. & Keren L. (2025), Nature Biotechnology, eaar7042

Cold and hot fibrosis define clinically distinct cardiac pathologies

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Cold and hot fibrosis define clinically distinct cardiac pathologies

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Hormone circuit explains why most HPA drugs fail for mood disorders and predicts the few that work

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Temporal Genomic Analysis of Homogeneous Tumor Models Reveals Key Regulators of Immune Evasion in Melanoma

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Members of the DIP and Dpr adhesion protein families use cis inhibition to shape neural development in Drosophila

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Phenome-wide associations of sleep characteristics in the Human Phenotype Project

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Submitted Version

Emerging clinical applications of single-cell RNA sequencing in oncology

Boxer E., Feigin N., Tschernichovsky R., Darnell N. G., Greenwald A. R., Hoefflin R., Kovarsky D., Simkin D., Turgeman S., Zhang L. & Tirosh I. (2025), Nature Reviews Clinical Oncology. 22, 5, p. 315-326, 2285

What is the main bottleneck in deriving biological understanding from spatial transcriptomic profiling?

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Editorial A Journal that Promotes Excellence Through Uncompromising Review Process: Reflection of freedom of speech and scientific publication

Kam Z. & Nicora G. (2025), International Journal of Neural Systems. 35, 13, 2502001

The Society for Immunotherapy of Cancer Perspective on Tissue-Based Technologies for Immuno-Oncology Biomarker Discovery and Application

Monette A., Aguilar-Mahecha A., Altinmakas E., Angelos M. G., Assad N., Batist G., Bommareddy P. K., Bonilla D. L., Borchers C. H., Church S. E., Ciliberto G., Cogdill A. P., Fattore L., Hacohen N., Haris M., Lacasse V., Lie W. R., Mehta A., Ruella M., Sater H. A., Spatz A., Taouli B., Tarhoni I., Gonzalez-Kozlova E., Tirosh I., Wang X. & Gnjatic S. (2025), Clinical Cancer Research. 31, 3, p. 439-456

GD3 ganglioside checkpoints in immune surveillance of senescent cells: Immune surveillance

Majewska J. & Krizhanovsky V. (2025), Nature Aging. 5, 2, p. 182-183, 5435

Glioblastoma Cortical Organoids Recapitulate Cell-State Heterogeneity and Intercellular Transfer

Mangena V., Chanoch-Myers R., Sartore R., Paulsen B., Gritsch S., Weisman H., Hara T., Breakefield X. O., Breyne K., Regev A., Chung K., Arlotta P., Tirosh I. & Suvà M. L. (2025), Cancer Discovery. 15, 2, p. 299-315

International consensus statement on microbiome testing in clinical practice

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Submitted Version

Oncogenic IDH1mut drives robust loss of histone acetylation and increases chromatin heterogeneity

Furth N., Cohen N., Spitzer A., Salame T. M., Dassa B., Mehlman T., Brandis A., Moussaieff A., Friedmann-Morvinski D., Castro M. G., Fortin J., Suvà M. L., Tirosh I., Erez A., Ron G. & Shema E. (2025), Proceedings of the National Academy of Sciences - PNAS. 122, 1, e240386212

Oncogenic IDH1mut drives robust loss of histone acetylation and increases chromatin heterogeneity

Furth N., Cohen N., Spitzer A., Salame T. M., Dassa B., Mehlman T., Brandis A., Moussaieff A., Friedmann-Morvinski D., Castro M. G., Fortin J., Suvà M. L., Tirosh I., Erez A., Ron G. & Shema E. (2025), Proceedings of the National Academy of Sciences - PNAS. 122, 1, e240386212