Publications | Department of Molecular Cell Biology

2024

Multiplexed image analysis: what have we achieved and where are we headed?

Bussi Y. & Keren L. (2024), Nature Methods. 21, p. 2212-2215

Intracellular polarization of RNAs and proteins in the human small intestinal epithelium

Novoselsky R., Harnik Y., Yakubovsky O., Katina C., Levin Y., Halpern K. B., Pencovich N., Nachmany I. & Itzkovitz S. (2024), PLoS Biology. 22, 12, e3002942

The oncogenic axis YAP/MYC/EZH2 impairs PTEN tumor suppression activity enhancing lung tumorigenicity

Lo Sardo F., Turco C., Messina B., Sacconi A., Auciello F. R., Pulito C., Strano S., Lev S. & Blandino G. (2024), Cell Death Discovery. 10, 1, 452

Identification of gut microbiome features associated with host metabolic health in a large population-based cohort

Keshet A. & Segal E. (2024), Nature Communications. 15, 9358

Crosslinking of Ly6a metabolically reprograms CD8 T cells for cancer immunotherapy

Maliah A., Santana-Magal N., Parikh S., Gordon S., Reshef K., Sade Y., Khateeb A., Richter A., Gutwillig A., Parikh R., Golan T., Krissi M., Na M., Binshtok G., Manich P., Elkoshi N., Grisaru-Tal S., Zemser-Werner V., Brenner R., Vaknine H., Nizri E., Moyal L., Amitay-Laish I., Rosemberg L., Munitz A., Kronfeld-Schor N., Shifrut E., Kobiler O., Madi A., Geiger T., Carmi Y. & Levy C. (2024), Nature Communications. 15, 8354

A modular protein language modelling approach to immunogenicity prediction

OBrien H., Salm M., Morton L. T., Szukszto M., OFarrell F., Boulton C., King L., Bola S. K., Becker P. D., Craig A., Nielsen M., Samuels Y., Swanton C., Mansour M. R., Hadrup S. R. & Quezada S. A. (2024), PLoS Computational Biology. 20, 11, e1012511

Sex-specific dietary habits and their association with weight change in healthy adults

Rein M., Elkan M., Godneva A., Dolev N. C. & Segal E. (2024), BMC Medicine. 22, 512

Phenome-wide associations of human aging uncover sex-specific dynamics

Reicher L., Bar N., Godneva A., Reisner Y., Zahavi L., Shahaf N., Dhir R., Weinberger A. & Segal E. (2024), Nature Aging. 4, 11, p. 1643-1655

Graham A. Dunn (1944-2024) - a pioneer of cell migration analysis

Jones G. E. & Bershadsky A. (2024), Journal of Cell Science. 137, 21

A Necessary Role for Cyclin D2 Induction During Colon Cancer Progression Mediated by L1

Saha A., Gavert N., Brabletz T. & Ben-Zeev A. (2024), Cells. 13, 21, 1810

Temporal BMP4 effects on mouse embryonic and extraembryonic development

Hadas R., Rubinstein H., Mittnenzweig M., Mayshar Y., Ben-Yair R., Cheng S., Aguilera-Castrejon A., Reines N., Orenbuch A., Lifshitz A., Chen D., Elowitz M. B., Zernicka-Goetz M., Hanna J. H., Tanay A. & Stelzer Y. (2024), Nature. 634, 8034, p. 652-661

Temporal BMP4 effects on mouse embryonic and extraembryonic development

TRIM46 Is Required for Microtubule Fasciculation In Vivo But Not Axon Specification or Axon Initial Segment Formation

Melton A. J., Palfini V. L., Ogawa Y., Oses Prieto J. A., Vainshtein A., Burlingame A. L., Peles E. & Rasband M. N. (2024), Journal of Neuroscience. 44, 42, e097624202

Pangenomes of human gut microbiota uncover links between genetic diversity and stress response

Shoer S., Reicher L., Zhao C., Pollard K. S., Pilpel Y. & Segal E. (2024), Cell Host and Microbe. 32, 10, p. 1744-1757.e2
Submitted Version

Multidirectional Filamented Light Biofabrication Creates Aligned and Contractile Cardiac Tissues

Jones L. S., Filippi M., Michelis M. Y., Balciunaite A., Yasa O., Aviel G., Narciso M., Freedrich S., Generali M., Tzahor E. & Katzschmann R. K. (2024), Advanced Science, 2404509

p21 regulates expression of ECM components and promotes pulmonary fibrosis via CDK4 and Rb

Papismadov N., Levi N., Roitman L., Agrawal A., Ovadya Y., Cherqui U., Yosef R., Akiva H., Gal H. & Krizhanovsky V. (2024), EMBO Journal. 43, 22, p. 5360-5380

Computational pipeline predicting cell death suppressors as targets for cancer therapy

Vinik Y., Maimon A., Mohan Raju H. R., Dubey V., Geist F., Wienke D. & Lev S. (2024), iScience. 27, 9, 110859

Endocrine gland size is proportional to its target tissue size

Raz M., Milo T., Glass D. S., Mayo A. & Alon U. (2024), iScience. 27, 9, 110625

Oncogenic Calreticulin Induces Immune Escape by Stimulating TGFβ Expression and Regulatory T-cell Expansion in the Bone Marrow Microenvironment

Schmidt D., Endres C., Hoefflin R., Andrieux G., Zwick M., Karantzelis N., Staehle H. F., Vinnakota J. M., Duquesne S., Jovein M. M., Pfeifer D., Becker H., Blazar B. R., Zähringer A., Duyster J., Brummer T., Boerries M., Baumeister J., Shoumariyeh K., Li J., Green A. R., Heidel F. H., Tirosh I., Pahl H. L., Leimkühler N., Köhler N., de Toledo M. A., Koschmieder S. & Zeiser R. (2024), Cancer Research. 84, 18, p. 2985-3003
Submitted Version

Cancer cell states: Lessons from ten years of single-cell RNA-sequencing of human tumors

Tirosh I. & Suva M. L. (2024), Cancer Cell. 42, 9, p. 1497-1506

Ferroptosis in health and disease

Berndt C., Alborzinia H., Amen V. S., Ayton S., Barayeu U., Bartelt A., Bayir H., Bebber C. M., Birsoy K., Böttcher J. P., Brabletz S., Brabletz T., Brown A. R., Brüne B., Bulli G., Bruneau A., Chen Q., DeNicola G. M., Dick T. P., Distéfano A., Dixon S. J., Engler J. B., Esser-von Bieren J., Fedorova M., Friedmann Angeli J. P., Friese M. A., Fuhrmann D. C., García-Sáez A. J., Garbowicz K., Götz M., Gu W., Hammerich L., Hassannia B., Jiang X., Jeridi A., Kang Y. P., Kagan V. E., Konrad D. B., Kotschi S., Lei P., Le Tertre M., Lev S., Liang D., Linkermann A., Lohr C., Lorenz S., Luedde T., Methner A., Michalke B., Milton A. V., Min J., Mishima E., Müller S., Motohashi H., Muckenthaler M. U., Murakami S., Olzmann J. A., Pagnussat G., Pan Z., Papagiannakopoulos T., Pedrera Puentes L., Pratt D. A., Proneth B., Ramsauer L., Rodriguez R., Saito Y., Schmidt F., Schmitt C., Schulze A., Schwab A., Schwantes A., Soula M., Spitzlberger B., Stockwell B. R., Thewes L., Thorn-Seshold O., Toyokuni S., Tonnus W., Trumpp A., Vandenabeele P., Vanden Berghe T., Venkataramani V., Vogel F. C., von Karstedt S., Wang F., Westermann F., Wientjens C., Wilhelm C., Wölk M., Wu K., Yang X., Yu F., Zou Y. & Conrad M. (2024), Redox Biology. 75, 103211

A spatial expression atlas of the adult human proximal small intestine

Harnik Y., Yakubovsky O., Hoefflin R., Novoselsky R., Bahar Halpern K., Barkai T., Korem Kohanim Y., Egozi A., Golani O., Addadi Y., Kedmi M., Keidar Haran T., Levin Y., Savidor A., Keren-Shaul H., Mayer C., Pencovich N., Pery R., Shouval D. S., Tirosh I., Nachmany I. & Itzkovitz S. (2024), Nature. 632, 8027, p. 1101-1109

A spatial expression atlas of the adult human proximal small intestine

Repurposing of glatiramer acetate to treat cardiac ischemia in rodent models

Aviel G., Elkahal J., Umansky K. B., Bueno-Levy H., Petrover Z., Kotlovski Y., Lendengolts D., Kain D., Shalit T., Zhang L., Miyara S., Kramer M. P., Merbl Y., Kozlovski S., Alon R., Aharoni R., Arnon R., Mishali D., Katz U., Nachman D., Asleh R., Amir O., Tzahor E. & Sarig R. (2024), Nature Cardiovascular Research. 3, 9, p. 1049-1066

Cohort profile: Study design and baseline characteristics of an observational longitudinal weight loss cohort and biorepository of patients undergoing sleeve gastrectomy in the USA

Vanegas S. M., Curado S., Gujral A., Valverde G., Parraga S., Aleman J. O., Reid M., Elbel B., Schmidt A. M., Heffron S. P., Segal E., Li H., Abrams C., Sevick M. A., Popp C., Armijos E., Merriwether E. N., Ivezaj V., Ren-Fielding C., Parikh M. & Jay M. (2024), BMJ Open. 14, 8, e081201

Probing PAC1 receptor activation across species with an engineered sensor

Cola R. B., Niethammer S. N., Rajamannar P., Gresch A., Bhat M. A., Assoumou K., Williams E. T., Hauck P., Hartrampf N., Benke D., Stoeber M., Levkowitz G., Melzer S. & Patriarchi T. (2024), eLife. 13, RP96496

Neuropeptide oxytocin facilitates its own brain-to-periphery uptake by regulating blood flow dynamics and permeability

Rajamannar P., Raz O. & Levkowitz G. (2024), BioRxiv

Guidelines for minimal information on cellular senescence experimentation in vivo

Ogrodnik M., Carlos Acosta J., Adams P. D., d'Adda di Fagagna F., Baker D. J., Bishop C. L., Chandra T., Collado M., Gil J., Gorgoulis V., Gruber F., Hara E., Jansen-Dürr P., Jurk D., Khosla S., Kirkland J. L., Krizhanovsky V., Minamino T., Niedernhofer L. J., Passos J. F., Ring N. A., Redl H., Robbins P. D., Rodier F., Scharffetter-Kochanek K., Sedivy J. M., Sikora E., Witwer K., von Zglinicki T., Yun M. H., Grillari J. & Demaria M. (2024), Cell. 187, 16, p. 4150-4175

Egr1 regulates regenerative senescence and cardiac repair

Zhang L., Elkahal J., Wang T., Rimmer R., Genzelinakh A., Bassat E., Wang J., Perez D., Kain D., Lendengolts D., Winkler R., Bueno-levy H., Umansky K. B., Mishaly D., Shakked A., Miyara S., Sarusi-Portuguez A., Goldfinger N., Prior A., Morgenstern D., Levin Y., Addadi Y., Li B., Rotter V., Katz U., Tanaka E. M., Krizhanovsky V., Sarig R. & Tzahor E. (2024), Nature Cardiovascular Research. 3, 8, p. 915-932

p16-dependent increase of PD-L1 stability regulates immunosurveillance of senescent cells

Majewska J., Agrawal A., Mayo A., Roitman L., Chatterjee R., Sekeresova Kralova J., Landsberger T., Katzenelenbogen Y., Meir-Salame T., Hagai E., Sopher I., Perez-Correa J. F., Wagner W., Maimon A., Amit I., Alon U. & Krizhanovsky V. (2024), Nature Cell Biology. 26, 8, p. 1336-1345

p16-dependent increase of PD-L1 stability regulates immunosurveillance of senescent cells

Multi-parametric atlas of the pre-metastatic liver for prediction of metastatic outcome in early-stage pancreatic cancer

Bojmar L., Zambirinis C. P., Hernandez J. M., Chakraborty J., Shaashua L., Kim J., Johnson K. E., Hanna S., Askan G., Burman J., Ravichandran H., Zheng J., Jolissaint J. S., Srouji R., Song Y., Choubey A., Kim H. S., Cioffi M., van Beek E., Sigel C., Jessurun J., Velasco Riestra P., Blomstrand H., Jönsson C., Jönsson A., Lauritzen P., Buehring W., Ararso Y., Hernandez D., Vinagolu-Baur J. P., Friedman M., Glidden C., Firmenich L., Lieberman G., Mejia D. L., Nasar N., Mutvei A. P., Paul D. M., Bram Y., Costa-Silva B., Basturk O., Boudreau N., Zhang H., Matei I. R., Hoshino A., Kelsen D., Sagi I., Scherz A., Scherz-Shouval R., Yarden Y., Oren M., Egeblad M., Lewis J. S., Keshari K., Grandgenett P. M., Hollingsworth M. A., Rajasekhar V. K., Healey J. H., Björnsson B., Simeone D. M., Tuveson D. A., Iacobuzio-Donahue C. A., Bromberg J., Vincent C. T., OReilly E. M., DeMatteo R. P., Balachandran V. P., DAngelica M. I., Kingham T. P., Allen P. J., Simpson A. L., Elemento O., Sandström P., Schwartz R. E., Jarnagin W. R. & Lyden D. (2024), Nature Medicine. 30, 8, p. 2170-2180

Egr1 regulates regenerative senescence and cardiac repair

Targeting of mutant-p53 and MYC as a novel strategy to inhibit oncogenic SPAG5 activity in triple negative breast cancer

Canu V., Vaccarella S., Sacconi A., Pulito C., Goeman F., Pallocca M., Rutigliano D., Lev S., Strano S. & Blandino G. (2024), Cell Death and Disease. 15, 603

Egr1 regulates regenerative senescence and cardiac repair

Diabetes Telemedicine Mediterranean Diet (DiaTeleMed) Study: study protocol for a fully remote randomized clinical trial evaluating personalized dietary management in individuals with type 2 diabetes

Berube L. T., Popp C. J., Curran M., Hu L., Pompeii M. L., Barua S., Bernstein E., Salcedo V., Li H., St-Jules D. E., Segal E., Bergman M., Williams N. J. & Sevick M. A. (2024), Trials. 25, 506

A hybrid epithelial/mesenchymal state in head and neck cancer: A biomarker for survival with differential prognosis by self-reported race

Mazul A. L., Barrett T. F., Colditz G., Parikh A. S., Ramadan S., Zevallos J. P., Rich J. T., Harbison R. A., Jackson R. S., Pipkorn P., Zolkind P., Tirosh I. & Puram S. V. (2024), Med. 5, 7, p. 826-831.e3

Single-cell atlas of the human brain vasculature across development, adulthood and disease

Wälchli T., Ghobrial M., Schwab M., Takada S., Zhong H., Suntharalingham S., Vetiska S., Gonzalez D. R., Wu R., Rehrauer H., Dinesh A., Yu K., Chen E. L., Bisschop J., Farnhammer F., Mansur A., Kalucka J., Tirosh I., Regli L., Schaller K., Frei K., Ketela T., Bernstein M., Kongkham P., Carmeliet P., Valiante T., Dirks P. B., Suva M. L., Zadeh G., Tabar V., Schlapbach R., Jackson H. W., De Bock K., Fish J. E., Monnier P. P., Bader G. D. & Radovanovic I. (2024), Nature. 632, 8025, p. 603-613

ASS1 metabolically contributes to the nuclear and cytosolic p53-mediated DNA damage response

Lim L. Q. J., Adler L., Hajaj E., Soria L. R., Perry R. B. T., Darzi N., Brody R., Furth N., Lichtenstein M., Bab-Dinitz E., Porat Z., Melman T., Brandis A., Aylon Y., Ben-Dor S., Orr I., Pri-Or A., Seger R., Shaul Y., Ruppin E., Oren M., Perez M., Meier J., Brunetti-Pierri N., Shema E., Ulitsky I., Erez A., Malitsky S. & Itkin M. (2024), Nature metabolism. 6, 7, p. 1294-1309

ASS1 metabolically contributes to the nuclear and cytosolic p53-mediated DNA damage response

Expression of modified FcγRI enables myeloid cells to elicit robust tumor-specific cytotoxicity

Farhat-Younis L., Na M., Zarfin A., Khateeb A., Santana-Magal N., Richter A., Gutwillig A., Rasoulouniriana D., Gleiberman A., Beck L., Giger T., Ashkenazi A., Barzel A., Rider P. & Carmi Y. (2024), eLife. 12, RP91999

Identification of senescent, TREM2-expressing microglia in aging and Alzheimers disease model mouse brain

Rachmian N., Medina S., Cherqui U., Akiva H., Deitch D., Edilbi D., Croese T., Salame T. M., Ramos J. M. P., Cahalon L., Krizhanovsky V. & Schwartz M. (2024), Nature Neuroscience. 27, 6, p. 1116-1124
Submitted Version

A snapshot into the transcriptomic landscape of apoptosis and ferroptosis in cancer

Vinik Y. & Lev S. (2024), Cell Death and Disease. 15, 371

BMP7 promotes cardiomyocyte regeneration in zebrafish and adult mice

Bongiovanni C., Bueno-Levy H., Posadas Pena D., Del Bono I., Miano C., Boriati S., Da Pra S., Sacchi F., Redaelli S., Bergen M., Romaniello D., Pontis F., Tassinari R., Kellerer L., Petraroia I., Mazzeschi M., Lauriola M., Ventura C., Heermann S., Weidinger G., Tzahor E. & D'Uva G. (2024), Cell Reports. 43, 5, 114162

Focal adhesions are controlled by microtubules through local contractility regulation

Aureille J., Prabhu S. S., Barnett S. F., Farrugia A. J., Arnal I., Lafanechère L., Low B. C., Kanchanawong P., Mogilner A. & Bershadsky A. D. (2024), EMBO Journal. 43, 13, p. 2715-2732

Mutant p53 reactivation restricts the protumorigenic consequences of wild type p53 loss of heterozygosity in Li-Fraumeni syndrome patient-derived fibroblasts

Agarwal H., Tal P., Goldfinger N., Chattopadhyay E., Malkin D., Rotter V. & Attery A. (2024), Cell Death and Differentiation. 31, 7, p. 855-867

Integrative spatial analysis reveals a multi-layered organization of glioblastoma

Greenwald A. C., Darnell N. G., Hoefflin R., Simkin D., Mount C. W., Gonzalez Castro L. N., Harnik Y., Dumont S., Hirsch D., Nomura M., Talpir T., Kedmi M., Goliand I., Medici G., Laffy J., Li B., Mangena V., Keren-Shaul H., Weller M., Addadi Y., Neidert M. C., Suvà M. L. & Tirosh I. (2024), Cell. 187, 10, p. 2485-2501.e26
Submitted Version

TM7SF3 controls TEAD1 splicing to prevent MASH-induced liver fibrosis

Isaac R., Bandyopadhyay G., Rohm T. V., Kang S., Wang J., Pokhrel N., Sakane S., Zapata R., Libster A. M., Vinik Y., Berhan A., Kisseleva T., Borok Z., Zick Y., Telese F., Webster N. J. & Olefsky J. M. (2024), Cell Metabolism. 36, 5, p. 1030-1043.e7

Competitive fungal commensalism mitigates candidiasis pathology

Sekeresova Kralova J., Donic C., Dassa B., Livyatan I., Jansen P. M., Ben-Dor S., Fidel L., Trzebanski S., Narunsky-Haziza L., Asraf O., Brenner O., Dafni H., Jona G., Boura-Halfon S., Stettner N., Segal E., Brunke S., Pilpel Y., Straussman R., Zeevi D., Bacher P., Hube B., Shlezinger N. & Jung S. (2024), Journal of Experimental Medicine. 221, 5, e20231686

Competitive fungal commensalism mitigates candidiasis pathology

Membrane Tilt Drives Phase Separation of Adhesion Receptors

Lin S. Z., Changede R., Farrugia A. J., Bershadsky A. D., Sheetz M. P., Prost J. & Rupprecht J. F. (2024), Physical Review Letters. 132, 18, 188402

The caloric value of food intake structurally adjusts a neuronal mushroom body circuit mediating olfactory learning in Drosophila

Çoban B., Poppinga H., Rachad E. Y., Geurten B., Vasmer D., Jimenez F. J. R., Gadgil Y., Deimel S. H., Alyagor I., Schuldiner O., Grunwald Kadow I. C., Riemensperger T. D., Widmann A. & Fiala A. (2024), Learning and Memory. 31, 5, p. 1-15

Modeling T cell temporal response to cancer immunotherapy rationalizes development of combinatorial treatment protocols

Barboy O., Bercovich A., Li H., Lubling Y., Yalin A., Shapir Itai Y., Abadie K., Zada M., David E., Shlomi S., Katzenelenbogen Y., Adhemar D., Gur C., Yofe I., Feferman T., Cohen M., Dahan R., Newell E., Lifshitz A., Tanay A. & Amit I. (2024), Nature Cancer. 5, 5, p. 742-759

ARTS and small-molecule ARTS mimetics upregulate p53 levels by promoting the degradation of XIAP

Abbas R., Hartmann O., Asiss D. T., Abbas R., Kagan J., Kim H. T., Oren M., Diefenbacher M., Orian A. & Larisch S. (2024), Apoptosis. 29, 7-8, p. 1145-1160

ATF3 characterizes aggressive drug-tolerant persister cells in HGSOC

Böpple K., Oren Y., Henry W. S., Dong M., Weller S., Thiel J., Kleih M., Gaißler A., Zipperer D., Kopp H. G., Aylon Y., Oren M., Essmann F., Liang C. & Aulitzky W. E. (2024), Cell Death and Disease. 15, 290

Targeting SRSF2 mutations in leukemia with RKI-1447: A strategy to impair cellular division and nuclear structure

Su M., Fleischer T., Grosheva I., Horev M. B., Olszewska M., Mattioli C. C., Barr H., Plotnikov A., Carvalho S., Moskovich Y., Minden M. D., Chapal-Ilani N., Wainstein A., Papapetrou E. P., Dezorella N., Cheng T., Kaushansky N., Geiger B. & Shlush L. I. (2024), iScience. 27, 4, 109443

Continuous glucose monitoring and intrapersonal variability in fasting glucose

Shilo S., Keshet A., Rossman H., Godneva A., Talmor-Barkan Y., Aviv Y. & Segal E. (2024), Nature Medicine. 30, 5, p. 1424-1431

Genome-wide CRISPR screens identify novel regulators of wild-type and mutant p53 stability

Lü Y. Q., Cho T., Mukherjee S., Suarez C. F., Gonzalez-Foutel N. S., Malik A., Martinez S., Dervovic D., Oh R. H., Langille E., Al-Zahrani K. N., Hoeg L., Lin Z. Y., Tsai R., Mbamalu G., Rotter V., Ashton-Prolla P., Moffat J., Chemes L. B., Gingras A. C., Oren M., Durocher D. & Schramek D. (2024), Molecular Systems Biology. 20, 6, p. 719-740

Genome-wide CRISPR screens identify novel regulators of wild-type and mutant p53 stability

Mutant IDH inhibitors induce lineage differentiation in IDH-mutant oligodendroglioma

Spitzer A., Gritsch S., Nomura M., Jucht A., Fortin J., Raviram R., Weisman H. R., Gonzalez Castro L. N., Druck N., Chanoch-Myers R., Lee J. J., Mylvaganam R., Lee Servis R., Fung J. M., Lee C. K., Nagashima H., Miller J. J., Arrillaga-Romany I., Louis D. N., Wakimoto H., Pisano W., Wen P. Y., Mak T. W., Sanson M., Touat M., Landau D. A., Ligon K. L., Cahill D. P., Suvà M. L. & Tirosh I. (2024), Cancer Cell. 42, 5, p. 904-914.e9

From the Inside Out: Exposing the Roles of Urea Cycle Enzymes in Tumors and Their Micro and Macro Environments

Hajaj E., Pozzi S. & Erez A. (2024), Cold Spring Harbor perspectives in medicine. 14, 4, a041538

Geroprotective interventions converge on gene expression programs of reduced inflammation and restored fatty acid metabolism

Landsberger T., Amit I. & Alon U. (2024), GeroScience. 46, 2, p. 1627-1639
Submitted Version

Embracing cancer complexity: Hallmarks of systemic disease

Swanton C., Bernard E., Abbosh C., André F., Auwerx J., Balmain A., Bar-Sagi D., Bernards R., Bullman S., DeGregori J., Elliott C., Erez A., Evan G., Febbraio M. A., Hidalgo A., Jamal-Hanjani M., Joyce J. A., Kaiser M., Lamia K., Locasale J. W., Loi S., Malanchi I., Merad M., Musgrave K., Patel K. J., Quezada S., Wargo J. A., Weeraratna A., White E., Winkler F., Wood J. N., Vousden K. H. & Hanahan D. (2024), Cell. 187, 7, p. 1589-1616

p53: A tale of complexity and context

Oren M. & Prives C. (2024), Cell. 187, 7, p. 1569-1573

How Can Young Extracellular Matrix Promote Cardiac Regeneration? Versi-Can!

Bassat E. & Tzahor E. (2024), Circulation. 149, 13, p. 1016-1018

Longitudinal hair cortisol in bipolar disorder and a mechanism based on HPA dynamics

Milo T., Maimon L., Cohen B., Haran D., Segman D., Danon T., Bren A., Mayo A., Rappaport G. C., McInnis M. & Alon U. (2024), iScience. 27, 3, 109234

Programming a Ferroptosis-to-Apoptosis Transition Landscape Revealed Ferroptosis Biomarkers and Repressors for Cancer Therapy

Vinik Y., Maimon A., Dubey V., Raj H., Abramovitch I., Malitsky S., Itkin M., Ma'ayan A., Westermann F., Gottlieb E., Ruppin E. & Lev S. (2024), Advanced Science. 11, 17, 2307263

Age-related micro-environmental changes as drivers of clonal hematopoiesis

Bacharach T., Kaushansky N. & Shlush L. I. (2024), Current Opinion in Hematology. 31, 2, p. 53-57

MinD-RNase E interplay controls localization of polar mRNAs in E. coli

Kannaiah S., Goldberger O., Alam N., Barnabas G., Pozniak Y., Nussbaum-Shochat A., Schueler-Furman O., Geiger T. & Amster-Choder O. (2024), EMBO Journal. 43, 4, p. 637-662

A synthetic differentiation circuit in Escherichia coli for suppressing mutant takeover

Glass D. S., Bren A., Vaisbourd E., Mayo A. & Alon U. (2024), Cell. 187, 4, p. 931-944.e12
Submitted Version

Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domains

Zwick R. K., Kasparek P., Palikuqi B., Viragova S., Weichselbaum L., McGinnis C. S., McKinley K. L., Rathnayake A., Vaka D., Nguyen V., Trentesaux C., Reyes E., Gupta A. R., Gartner Z. J., Locksley R. M., Gardner J. M., Itzkovitz S., Boffelli D. & Klein O. D. (2024), Nature Cell Biology. 26, 2, p. 250-262

Quantification of beta cell carrying capacity in prediabetes

Woller A., Tamir Y., Bar A., Mayo A., Rein M., Godneva A., Cohen N. M., Segal E., Toledano Y., Shilo S., Gonze D. & Alon U. (2024), BioRxiv

Quantification of beta cell carrying capacity in prediabetes

Woller A., Tamir Y., Bar A., Mayo A., Rein M., Godneva A., Cohen N. M., Segal E., Toledano Y., Shilo S., Gonze D. & Alon U. (2024), BioRxiv

Endocrinology in the multi-omics era

Shilo S. & Segal E. (2024), Nature Reviews Endocrinology. 20, p. 73-74

Immune profiling and tracking of two-dimensional transition metal dichalcogenides in cells and tissues

Gazzi A., Fusco L., Orecchioni M., Keshavan S., Shin Y., Grivel J. C., Rinchai D., Ahmed E. I., Elhanani O., Furesi G., Rauner M., Keren L., Ley K., Casiraghi C., Bedognetti D., Fadeel B. & Delogu L. G. (2024), Nano Today. 54, 102084

Bispecific dendritic-T cell engager potentiates anti-tumor immunity

Shapir Itai Y., Barboy O., Salomon R., Bercovich A., Xie K., Winter E., Shami T., Porat Z., Erez N., Tanay A., Amit I. & Dahan R. (2024), Cell. 187, 2, p. 375-389.e18

Genome-wide association studies and polygenic risk score phenome-wide association studies across complex phenotypes in the human phenotype project

Levine Z., Kalka I., Kolobkov D., Rossman H., Godneva A., Shilo S., Keshet A., Weissglas-Volkov D., Shor T., Diament A., Talmor-Barkan Y., Aviv Y., Sharon T., Weinberger A. & Segal E. (2024), Med. 5, 1, p. 90-101.e4

Melanoma and microbiota: Current understanding and future directions

Routy B., Jackson T., Mählmann L., Baumgartner C. K., Blaser M., Byrd A., Corvaia N., Couts K., Davar D., Derosa L., Hang H. C., Hospers G., Isaksen M., Kroemer G., Malard F., McCoy K. D., Meisel M., Pal S., Ronai Z., Segal E., Sepich-Poore G. D., Shaikh F., Sweis R. F., Trinchieri G., van den Brink M., Weersma R. K., Whiteson K., Zhao L., McQuade J., Zarour H. & Zitvogel L. (2024), Cancer Cell. 42, 1, p. 16-34

Longitudinal machine learning uncouples healthy aging factors from chronic disease risks

Cohen N. M., Lifshitz A., Jaschek R., Rinott E., Balicer R., Shlush L. I., Barbash G. I. & Tanay A. (2024), Nature Aging. 4, 1, p. 129-144

Longitudinal machine learning uncouples healthy aging factors from chronic disease risks

Cohen N. M., Lifshitz A., Jaschek R., Rinott E., Balicer R., Shlush L. I., Barbash G. I. & Tanay A. (2024), Nature Aging. 4, 1, p. 129-144

2023

p53 deficient breast cancer cells reprogram preadipocytes toward tumor-protective immunomodulatory cells

Hassin O., Sernik M., Seligman A., Vogel F. C., Wellenstein M. D., Smollich J., Halperin C., Pirona A. C., Toledano L. N., Caballero C. D., Schlicker L., Salame T. M., Portuguez A. S., Aylon Y., Scherz-Shouval R., Geiger T., de Visser K. E., Schulze A. & Oren M. (2023), Proceedings of the National Academy of Sciences of the United States of America. 120, 52, e231146012

p53 deficient breast cancer cells reprogram preadipocytes toward tumor-protective immunomodulatory cells

Lung dendritic-cell metabolism underlies susceptibility to viral infection in diabetes

Nobs S. P., Kolodziejczyk A. A., Adler L., Horesh N., Botscharnikow C., Herzog E., Mohapatra G., Hejndorf S., Hodgetts R. J., Spivak I., Schorr L., Fluhr L., Kviatcovsky D., Zacharia A., Njuki S., Barasch D., Stettner N., Dori-Bachash M., Harmelin A., Brandis A., Mehlman T., Erez A., He Y., Ferrini S., Puschhof J., Shapiro H., Kopf M., Moussaieff A., Abdeen S. K. & Elinav E. (2023), Nature. 624, 7992, p. 645-652

Tradeoffs in bacterial physiology determine the efficiency of antibiotic killing

Bren A., Glass D. S., Kohanim Y. K., Mayo A. & Alon U. (2023), Proceedings of the National Academy of Sciences of the United States of America. 120, 51, e231265112

Systems Medicine: Physiological Circuits and the Dynamics of Disease

Alon U. (2023)

Breaking the performance ceiling for neoantigen immunogenicity prediction

OBrien H., Salm M., Morton L., Szukszto M., OFarrell F., Boulton C., Becker P. D., Samuels Y., Swanton C., Mansour M. R., Reker Hadrup S. & Quezada S. A. (2023), Nature Cancer. 4, 12, p. 1618-1621

Neural plate progenitors give rise to both anterior and posterior pituitary cells

Chen Q., Leshkowitz D., Li H., van Impel A., Schulte-Merker S., Amit I., Rizzoti K. & Levkowitz G. (2023), Developmental Cell. 58, 23, p. 2652-2665.e6

Clonal evolution of leukemia from G6PD studies

Bacharach T. & Shlush L. I. (2023), Haematologica. 108, 12, p. 3191-3192

Histone exchange sensors reveal variant specific dynamics in mouse embryonic stem cells

Dunjic M., Jonas F., Yaakov G., More R., Mayshar Y., Rais Y., Barkai N. & Stelzer Y. (2023), Nature Communications. 14, 1, 3791

Major depressive disorder and bistability in an HPA-CNS toggle switch

Ron Mizrachi B., Tendler A., Karin O., Milo T., Haran D., Mayo A. & Alon U. (2023), PLoS Computational Biology. 19, 12, e1011645

MCProj: metacell projection for interpretable and quantitative use of transcriptional atlases

Ben-Kiki O., Bercovich A., Lifshitz A., Raz O., Brook D. & Tanay A. (2023), GENOME BIOLOGY. 24, 1, 220

TAZ facilitates breast tumor growth by promoting an immune-suppressive tumor microenvironment

Gershoni A., Hassin O., Nataraj N. B., Baruch S., Avioz-Seligman A., Pirona A. C., Fellus-Alyagor L., Meir Salame T., Mukherjee S., Mallel G., Yarden Y., Aylon Y. & Oren M. (2023), Molecular Oncology. 17, 12, p. 2675-2693

Damage dynamics and the role of chance in the timing of E. coli cell death

Yang Y., Karin O., Mayo A., Song X., Chen P., Santos A. L., Lindner A. B. & Alon U. (2023), Nature Communications. 14, 2209

Excitable dynamics of flares and relapses in autoimmune diseases

Lebel Y., Milo T., Bar A., Mayo A. & Alon U. (2023), iScience. 26, 11, 108084

Targeting ribosome biogenesis reinforces ERK-dependent senescence in pancreatic cancer

Rowell M. C., Deschênes-Simard X., Lopes-Paciencia S., Le Calvé B., Kalegari P., Mignacca L., Fernandez-Ruiz A., Guillon J., Lessard F., Bourdeau V., Igelmann S., Duman A. M., Stanom Y., Kottakis F., Deshpande V., Krizhanovsky V., Bardeesy N. & Ferbeyre G. (2023), Cell Cycle. 22, 19, p. 2172-2193
Submitted Version

Clinical trial links oncolytic immunoactivation to survival in glioblastoma

Ling A. L., Solomon I. H., Landivar A. M., Nakashima H., Woods J. K., Santos A., Masud N., Fell G., Mo X., Yilmaz A. S., Grant J., Zhang A., Bernstock J. D., Torio E., Ito H., Liu J., Shono N., Nowicki M. O., Triggs D., Halloran P., Piranlioglu R., Soni H., Stopa B., Bi W. L., Peruzzi P., Chen E., Malinowski S. W., Prabhu M. C., Zeng Y., Carlisle A., Rodig S. J., Wen P. Y., Lee E. Q., Nayak L., Chukwueke U., Gonzalez Castro L. N., Dumont S. D., Batchelor T., Kittelberger K., Tikhonova E., Miheecheva N., Tabakov D., Shin N., Gorbacheva A., Shumskiy A., Frenkel F., Aguilar-Cordova E., Aguilar L. K., Krisky D., Wechuck J., Manzanera A., Matheny C., Tak P. P., Barone F., Kovarsky D., Tirosh I., Suvà M. L., Wucherpfennig K. W., Ligon K., Reardon D. A. & Antonio Chiocca E. (2023), Nature. 623, 7985, p. 157-166

Glioma synapses recruit mechanisms of adaptive plasticity

Taylor K. R., Barron T., Hui A., Spitzer A., Yalçin B., Ivec A. E., Geraghty A. C., Hartmann G. G., Arzt M., Gillespie S. M., Kim Y. S., Maleki Jahan S., Zhang H., Shamardani K., Su M., Ni L., Du P. P., Woo P. J., Silva-Torres A., Venkatesh H. S., Mancusi R., Ponnuswami A., Mulinyawe S., Keough M. B., Chau I., Aziz-Bose R., Tirosh I., Suvà M. L. & Monje M. (2023), Nature. 623, 7986, p. 366-374

Glucocorticoid-sensitive period of corticotroph development - Implications for mechanisms of early life stress

Peles G., Swaminathan A. & Levkowitz G. (2023), Journal of Neuroendocrinology. 35, 11, e13229

The cellular states and fates of shed intestinal cells

Bahar Halpern K., Korem Kohanim Y., Biram A., Harnik Y., Egozi A., Yakubovsky O., Shulman Z. & Itzkovitz S. (2023), Nature metabolism. 5, 11, p. 1858-1869
Submitted Version

Bacterial SNPs in the human gut microbiome associate with host BMI

Zahavi L., Lavon A., Reicher L., Shoer S., Godneva A., Leviatan S., Rein M., Weissbrod O., Weinberger A. & Segal E. (2023), Nature Medicine. 29, 11, p. 2785-2792

The total mass, number, and distribution of immune cells in the human body

Sender R., Weiss Y., Navon Y., Milo I., Azulay N., Keren L., Fuchs S., Ben-Zvi D., Noor E. & Milo R. (2023), Proceedings of the National Academy of Sciences. 120, 44, e230851112

Antibody-directed extracellular proximity biotinylation reveals that Contactin-1 regulates axo-axonic innervation of axon initial segments

Ogawa Y., Lim B. C., George S., Oses-Prieto J. A., Rasband M. N., Eshed-Eisenbach Y., Hamdan H., Nair S., Boato F., Peles E., Burlingame A. L., Van Aelst L. & Rasband M. N. (2023), Nature Communications. 14, 1, 6797

Complement-membrane regulatory proteins are absent from the nodes of Ranvier in the peripheral nervous system

Karbian N., Eshed-Eisenbach Y., Zeibak M., Tabib A., Sukhanov N., Vainshtein A., Morgan B. P., Fellig Y., Peles E. & Mevorach D. (2023), Journal of Neuroinflammation. 20, 245

Dissecting the cellular states and fates of shed mouse intestinal cells

Itzkovitz S. & Halpern K. B. (2023), Nature metabolism

Compression of sickspan by interventions that steepen the survival curve

Yang Y., Mayo A., Levy T., Jarosz D. & Alon U. (2023), BioRxiv

A clinical evaluation of an ex vivo organ culture system to predict patient response to cancer therapy

Golan S., Bar V., Salpeter S. J., Neev G., Creiderman G., Kedar D., Aharon S., Turovsky L., Zundelevich A., Shahar H., Shapira H., Mallel G., Stossel E., Gavert N., Straussman R., Dotan Z., Berger R., Stossel C., Golan T., Halperin S., Leibovici D., Breuer S., Rottenberg Y., Applebaum L., Hubert A., Nechushtan H., Peretz T., Zick A., Chertin B., Koulikov D., Sonnenblick A. & Rosenbaum E. (2023), Frontiers in Medicine. 10, 1221484

The tumor microenvironment shows a hierarchy of cell-cell interactions dominated by fibroblasts

Mayer S., Milo T., Isaacson A., Halperin C., Miyara S., Stein Y., Lior C., Pevsner-Fischer M., Tzahor E., Mayo A., Alon U. & Scherz-Shouval R. (2023), Nature Communications. 14, 1, 5810

The tumor microenvironment shows a hierarchy of cell-cell interactions dominated by fibroblasts

Mayer S., Milo T., Isaacson A., Halperin C., Miyara S., Stein Y., Lior C., Pevsner-Fischer M., Tzahor E., Mayo A., Alon U. & Scherz-Shouval R. (2023), Nature Communications. 14, 1, 5810

Chiral growth of adherent filopodia

Li W., Chung W. L., Kozlov M. M., Medalia O., Geiger B. & Bershadsky A. D. (2023), Biophysical Journal. 122, 18, p. 3704-3721

Experimental and theoretical model for the origin of coiling of cellular protrusions around fibers

Sadhu R. K., Hernandez-Padilla C., Eisenbach Y. E., Penič S., Zhang L., Vishwasrao H. D., Behkam B., Konstantopoulos K., Shroff H., Iglič A., Peles E., Nain A. S. & Gov N. S. (2023), Nature Communications. 14, 1, 5612

Single-cell multi-omics defines the cell-type-specific impact of splicing aberrations in human hematopoietic clonal outgrowths

Cortés-López M., Chamely P., Hawkins A. G., Stanley R. F., Swett A. D., Ganesan S., Mouhieddine T. H., Dai X., Kluegel L., Chen C., Batta K., Furer N., Vedula R. S., Beaulaurier J., Drong A. W., Hickey S., Dusaj N., Mullokandov G., Stasiw A. M., Su J., Chaligné R., Juul S., Harrington E., Knowles D. A., Potenski C. J., Wiseman D. H., Tanay A., Shlush L., Lindsley R. C., Ghobrial I. M., Taylor J., Abdel-Wahab O., Gaiti F. & Landau D. A. (2023), Cell Stem Cell. 30, 9, p. 1262-1281.e8
Submitted Version

Single-cell multi-omics defines the cell-type-specific impact of splicing aberrations in human hematopoietic clonal outgrowths

Impact of dietary interventions on pre-diabetic oral and gut microbiome, metabolites and cytokines

Shoer S., Shilo S., Godneva A., Ben-Yacov O., Rein M., Wolf B. C., Lotan-Pompan M., Bar N., Weiss E. I., Houri-Haddad Y., Pilpel Y., Weinberger A. & Segal E. (2023), Nature Communications. 14, 1, 5384

An Increase in Mucin2 Expression Is Required for Colon Cancer Progression Mediated by L1

Saha A., Gavert N., Brabletz T. & Ben-Zeev A. (2023), International Journal of Molecular Sciences. 24, 17, 13418

PYK2, a hub of signaling networks in breast cancer progression

Gil-Henn H., Girault J. A. & Lev S. (2023), Trends in Cell Biology. 34, 4, p. 312-326

Spectrum of Response to Platinum and PARP Inhibitors in <i>Germline</i> BRCAAssociated Pancreatic Cancer in the Clinical and Preclinical Setting

Stossel C., Raitses-Gurevich M., Atias D., Beller T., Glick Gorman Y., Halperin S., Peer E., Denroche R. E., Zhang A., Notta F., Wilson J. M., O'Kane G. M., Haimov Talmoud E., Amison N., Schvimer M., Salpeter S. J., Bar V., Zundelevich A., Tirosh I., Tal R., Dinstag G., Kinar Y., Eliezer Y., Ben-David U., Gavert N. S., Straussman R., Gallinger S. J., Berger R. & Golan T. (2023), Cancer Discovery. 13, 8, p. 1826-1843

Spectrum of Response to Platinum and PARP Inhibitors in <i>Germline</i> BRCAAssociated Pancreatic Cancer in the Clinical and Preclinical Setting

Deoxyhypusine hydroxylase: A novel therapeutic target differentially expressed in short-term vs long-term survivors of glioblastoma

Ofek P., Yeini E., Arad G., Danilevsky A., Pozzi S., Luna C. B., Dangoor S. I., Grossman R., Ram Z., Shomron N., Brem H., Hyde T. M., Geiger T. & Satchi-Fainaro R. (2023), International Journal of Cancer. 153, 3, p. 654-668

Gut microbiome modulates the effects of a personalised postprandial-targeting (PPT) diet on cardiometabolic markers: a diet intervention in pre-diabetes

Ben-Yacov O., Godneva A., Rein M., Shilo S., Lotan-Pompan M., Weinberger A. & Segal E. (2023), Gut. 72, 8, p. 1486-1496

A randomized clinical trial comparing low-fat with precision nutritionbased diets for weight loss: impact on glycemic variability and HbA1c

Kharmats A. Y., Popp C., Hu L., Berube L., Curran M., Wang C., Pompeii M. L., Li H., Bergman M., St-Jules D. E., Segal E., Schoenthaler A., Williams N., Schmidt A. M., Barua S. & Sevick M. A. (2023), American Journal of Clinical Nutrition. 118, 2, p. 443-451

Neoantigens in cancer immunotherapy: quantity vs. quality

Wolf Y. & Sameuls Y. (2023), Molecular Oncology. 17, 8, p. 1457-1459

A spatially resolved timeline of the human maternalfetal interface

Greenbaum S., Averbukh I., Soon E., Rizzuto G., Baranski A., Greenwald N. F., Kagel A., Bosse M., Jaswa E. G., Khair Z., Kwok S., Warshawsky S., Piyadasa H., Goldston M., Spence A., Miller G., Schwartz M., Graf W., Van Valen D., Winn V. D., Hollmann T., Keren L., van de Rijn M. & Angelo M. (2023), Nature. 619, 7970, p. 595-605

CellSighter: a neural network to classify cells in highly multiplexed images

Amitay Y., Bussi Y., Feinstein B., Bagon S., Milo I. & Keren L. (2023), Nature Communications. 14, 4302

Single-cell biology: what does the future hold?

Polychronidou M., Hou J., Babu M. M., Liberali P., Amit I., Deplancke B., Lahav G., Itzkovitz S., Mann M., Saez-Rodriguez J., Theis F. & Eils R. (2023), Molecular Systems Biology. 19, 7, e11799

Unifying design principles of endocrine gland mass and its regulatory circuits

Raz M., Milo T., Kohanim Y. K., Karin O., Tendler A., Bar A., Glass D. S., Mayo A. & Alon U. (2023), BioRxiv

Early Infiltration of Innate Immune Cells to the Liver Depletes HNF4α and Promotes Extrahepatic Carcinogenesis

Goldman O., Adler L. N., Hajaj E., Croese T., Darzi N., Galai S., Tishler H., Ariav Y., Lavie D., Fellus-Alyagor L., Oren R., Kuznetsov Y., David E., Jaschek R., Stossel C., Singer O., Malitsky S., Barak R., Seger R., Erez N., Amit I., Tanay A., Saada A., Golan T., Rubinek T., Sang Lee J., Ben-Shachar S., Wolf I. & Erez A. (2023), Cancer Discovery. 13, 7, p. 1616-1635

Early Infiltration of Innate Immune Cells to the Liver Depletes HNF4α and Promotes Extrahepatic Carcinogenesis

MYC Induces Immunotherapy and IFNg Resistance Through Downregulation of JAK2

Markovits E., Harush O., Baruch E. N., Shulman E. D., Debby A., Itzhaki O., Anafi L., Danilevsky A., Shomron N., Ben-Betzalel G., Asher N., Shapira-Frommer R., Schachter J., Barshack I., Geiger T., Elkon R., Besser M. J. & Markel G. (2023), Cancer Immunology Research. 11, 7, p. 909-924

Functional Impact of Protein-RNA Variation in Clinical Cancer Analyses

Arad G. & Geiger T. (2023), Molecular & cellular proteomics : MCP. 22, 7, 100587

Nodes of Ranvier in health and disease

Eshed-Eisenbach Y., Brophy P. J. & Peles E. (2023), Journal of the Peripheral Nervous System. 28, S3, p. S3-S11

The landscape of T cell antigens for cancer immunotherapy

Peri A., Salomon N., Wolf Y., Kreiter S., Diken M. & Samuels Y. (2023), Nature Cancer. 4, 7, p. 937-954
Submitted Version

Clonal hematopoiesis in the donor does not adversely affect long-term outcomes following allogeneic hematopoietic stem cell transplantation: result from a 13-year follow-up

Kim K. H., Kim T., Novitzky-Basso I., Lee H., Yoo Y., Ahn J., Pasic I., Law A., Lam W., Michelis F. V., Gerbitz A., Viswabandya A., Lipton J., Kumar R., Mattsson J., Zhang Z., Kaushansky N., Brilon Y., Chapal-Ilani N., Biezuner T., Shlush L. I. & Kim D. D. H. (2023), Haematologica. 108, 7, p. 1817-1826

Single cell Hi-C identifies plastic chromosome conformations underlying the gastrulation enhancer landscape

Rappoport N., Chomsky E., Nagano T., Seibert C., Lubling Y., Baran Y., Lifshitz A., Leung W., Mukamel Z., Shamir R., Fraser P. & Tanay A. (2023), Nature Communications. 14, 1, 3844

Hallmarks of transcriptional intratumour heterogeneity across a thousand tumours

Gavish A., Tyler M., Greenwald A. C., Hoefflin R., Simkin D., Tschernichovsky R., Galili Darnell N., Somech E., Barbolin C., Antman T., Kovarsky D., Barrett T., Gonzalez Castro L. N., Halder D., Chanoch-Myers R., Laffy J., Mints M., Wider A., Tal R., Spitzer A., Hara T., Raitses-Gurevich M., Stossel C., Golan T., Tirosh A., Suvà M. L., Puram S. V. & Tirosh I. (2023), Nature. 618, 7965, p. 598-606

Phage display sequencing reveals that genetic, environmental, and intrinsic factors influence variation of human antibody epitope repertoire

Andreu-Sánchez S., Bourgonje A. R., Vogl T., Kurilshikov A., Leviatan S., Ruiz-Moreno A. J., Hu S., Sinha T., Vich Vila A., Klompus S., Kalka I. N., de Leeuw K., Arends S., Jonkers I., Withoff S., Brouwer E., Weinberger A., Wijmenga C., Segal E. & Weersma R. K. (2023), Immunity. 56, 6, p. 1376-1392
Submitted Version

Phage-display immunoprecipitation sequencing of the antibody epitope repertoire in inflammatory bowel disease reveals distinct antibody signatures

Bourgonje A. R., Andreu-Sánchez S., Vogl T., Hu S., Vich Vila A., Gacesa R., Leviatan S., Kurilshikov A., Klompus S., Kalka I. N., van Dullemen H. M., Weinberger A., Visschedijk M. C., Festen E. A., Faber K. N., Wijmenga C., Dijkstra G., Segal E., Fu J., Zhernakova A. & Weersma R. K. (2023), Immunity. 56, 6, p. 1393-1409.e6

Time-aligned hourglass gastrulation models in rabbit and mouse

Mayshar Y., Raz O., Cheng S., Ben-Yair R., Hadas R., Reines N., Mittnenzweig M., Ben-Kiki O., Lifshitz A., Tanay A. & Stelzer Y. (2023), Cell. 186, 12, p. 2610-2627.e18
Submitted Version

Time-aligned hourglass gastrulation models in rabbit and mouse

Mayshar Y., Raz O., Cheng S., Ben-Yair R., Hadas R., Reines N., Mittnenzweig M., Ben-Kiki O., Lifshitz A., Tanay A. & Stelzer Y. (2023), Cell. 186, 12, p. 2610-2627.e18
Submitted Version

GATA6-AS1 Regulates Intestinal Epithelial Mitochondrial Functions, and its Reduced Expression is Linked to Intestinal Inflammation and Less Favourable Disease Course in Ulcerative Colitis

Sosnovski K. E., Braun T., Amir A., Moshel D., BenShoshan M., VanDussen K. L., Levhar N., Abbas-Egbariya H., Beider K., Ben-Yishay R., Asad Ali S., Moore S. R., Kugathasan S., Abramovich I., Saar E. G., Weiss B., Barshack I., Gottlieb E., Geiger T., Ben-Horin S., Ulitsky I., Hyams J. S., Denson L. A. & Haberman Y. (2023), Journal of Crohn's and Colitis. 17, 6, p. 960-971

Single-cell atlas of the human neonatal small intestine affected by necrotizing enterocolitis

Egozi A., Olaloye O., Werner L., Silva T., McCourt B., Pierce R. W., An X., Wang F., Chen K., Pober J. S., Shouval D., Itzkovitz S. & Konnikova L. (2023), PLoS Biology. 21, 5, e3002124

Interplay between calcium and sarcomeres directs cardiomyocyte maturation during regeneration

Nguyen P. D., Gooijers I., Campostrini G., Verkerk A. O., Honkoop H., Bouwman M., de Bakker D. E. M., Koopmans T., Vink A., Lamers G. E. M., Shakked A., Mars J., Mulder A. A., Chocron S., Bartscherer K., Tzahor E., Mummery C. L., de Boer T. P., Bellin M. & Bakkers J. (2023), Science (New York, N.Y.). 380, 6646, p. 758-764

Pregnancy and postpartum dynamics revealed by an atlas of millions of lab tests

Bar A., Mendelsohn-Cohen N., Kohanim Y. K., Mayo A., Toledano Y. & Alon U. (2023), BioRxiv

CGMap: Characterizing continuous glucose monitor data in thousands of non-diabetic individuals: Characterizing continuous glucose monitor data in thousands of non-diabetic individuals

Keshet A., Shilo S., Godneva A., Talmor-Barkan Y., Aviv Y., Segal E. & Rossman H. (2023), Cell Metabolism. 35, 5, p. 758-769.e3
Submitted Version

Apoptotic cell death in diseaseCurrent understanding of the NCCD 2023

Vitale I., Pietrocola F., Guilbaud E., Aaronson S. A., Abrams J. M., Adam D., Agostini M., Agostinis P., Alnemri E. S., Altucci L., Amelio I., Andrews D. W., Aqeilan R. I., Arama E., Baehrecke E. H., Balachandran S., Bano D., Barlev N. A., Bartek J., Bazan N. G., Becker C., Bernassola F., Bertrand M. J., Bianchi M. E., Blagosklonny M. V., Blander J. M., Blandino G., Blomgren K., Borner C., Bortner C. D., Bove P., Boya P., Brenner C., Broz P., Brunner T., Damgaard R. B., Calin G. A., Campanella M., Candi E., Carbone M., Carmona-Gutierrez D., Cecconi F., Chan F. K., Chen G. Q., Chen Q., Chen Y. H., Cheng E. H., Chipuk J. E., Cidlowski J. A., Ciechanover A., Ciliberto G., Conrad M., Cubillos-Ruiz J. R., Czabotar P. E., DAngiolella V., Daugaard M., Dawson T. M., Dawson V. L., De Maria R., De Strooper B., Debatin K. M., Deberardinis R. J., Degterev A., Del Sal G., Deshmukh M., Di Virgilio F., Diederich M., Dixon S. J., Dynlacht B. D., El-Deiry W. S., Elrod J. W., Engeland K., Fimia G. M., Galassi C., Ganini C., Garcia-Saez A. J., Garg A. D., Garrido C., Gavathiotis E., Gerlic M., Ghosh S., Green D. R., Greene L. A., Gronemeyer H., Häcker G., Hajnóczky G., Hardwick J. M., Haupt Y., He S., Heery D. M., Hengartner M. O., Hetz C., Hildeman D. A., Ichijo H., Inoue S., Jäättelä M., Janic A., Joseph B., Jost P. J., Kanneganti T. D., Karin M., Kashkar H., Kaufmann T., Kelly G. L., Kepp O., Kimchi A., Kitsis R. N., Klionsky D. J., Kluck R., Krysko D. V., Kulms D., Kumar S., Lavandero S., Lavrik I. N., Lemasters J. J., Liccardi G., Linkermann A., Lipton S. A., Lockshin R. A., López-Otín C., Luedde T., MacFarlane M., Madeo F., Malorni W., Manic G., Mantovani R., Marchi S., Marine J. C., Martin S. J., Martinou J. C., Mastroberardino P. G., Medema J. P., Mehlen P., Meier P., Melino G., Melino S., Miao E. A., Moll U. M., Muñoz-Pinedo C., Murphy D. J., Niklison-Chirou M. V., Novelli F., Núñez G., Oberst A., Ofengeim D., Opferman J. T., Oren M., Pagano M., Panaretakis T., Pasparakis M., Penninger J. M., Pentimalli F., Pereira D. M., Pervaiz S., Peter M. E., Pinton P., Porta G., Prehn J. H., Puthalakath H., Rabinovich G. A., Rajalingam K., Ravichandran K. S., Rehm M., Ricci J. E., Rizzuto R., Robinson N., Rodrigues C. M., Rotblat B., Rothlin C. V., Rubinsztein D. C., Rudel T., Rufini A., Ryan K. M., Sarosiek K. A., Sawa A., Sayan E., Schroder K., Scorrano L., Sesti F., Shao F., Shi Y., Sica G. S., Silke J., Simon H. U., Sistigu A., Stephanou A., Stockwell B. R., Strapazzon F., Strasser A., Sun L., Sun E., Sun Q., Szabadkai G., Tait S. W., Tang D., Tavernarakis N., Troy C. M., Turk B., Urbano N., Vandenabeele P., Vanden Berghe T., Vander Heiden M. G., Vanderluit J. L., Verkhratsky A., Villunger A., von Karstedt S., Voss A. K., Vousden K. H., Vucic D., Vuri D., Wagner E. F., Walczak H., Wallach D., Wang R., Wang Y., Weber A., Wood W., Yamazaki T., Yang H. T., Zakeri Z., Zawacka-Pankau J. E., Zhang L., Zhang H., Zhivotovsky B., Zhou W., Piacentini M., Kroemer G. & Galluzzi L. (2023), Cell Death and Differentiation. 30, 5, p. 1097-1154

Local angiogenic interplay of Vegfc/d and Vegfa controls brain region-specific emergence of fenestrated capillaries

Parab S., Card O. A., Chen Q., America M., Buck L. D., Quick R. E., Horrigan W. F., Levkowitz G., Vanhollebeke B. & Matsuoka R. L. (2023), eLife. 12, e86066

The proteasome regulator PSME4 drives immune evasion and abrogates anti-tumor immunity in NSCLC

Javitt A., Shmueli M., Kramer M., Kolodziejczyk A., Cohen I., Kamer I., Litchfield K., Bab-Dinitz E., Zadok O., Neiens V., Ulman A., Radomir L., Wolf-Levy H., Eisenberg-Lerner A., Kacen A., Alon M., Toste Rêgo A., Stacher-Priehse E., Lindner M., Koch I., Bar J., Swanton C., Samuels Y., Levin Y., da Fonseca P. C. A., Elinav E., Friedman N., Meiners S. & Merbl Y. (2023), bioArxiv
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Submitted Version

miR-4734 conditionally suppresses ER stress-associated proinflammatory responses

Michael D., Feldmesser E., Gonen C., Furth N., Maman A., Heyman O., Argoetti A., Tofield A., Baichman-Kass A., Ben-Dov A., Benbenisti D., Hen N., Rotkopf R., Ganci F., Blandino G., Ulitsky I. & Oren M. (2023), FEBS Letters. 597, 9, p. 1233-1245

Autoimmune thyroid diseases as a cost of physiological autoimmune surveillance

Milo T., Kohanim Y. K., Toledano Y. & Alon U. (2023), Trends in Immunology. 44, 5, p. 365-371
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The proteasome regulator PSME4 modulates proteasome activity and antigen diversity to abrogate antitumor immunity in NSCLC

Javitt A., Shmueli M. D., Kramer M. P., Kolodziejczyk A. A., Cohen I. J., Radomir L., Sheban D., Kamer I., Litchfield K., Bab-Dinitz E., Zadok O., Neiens V., Ulman A., Wolf-Levy H., Eisenberg-Lerner A., Kacen A., Alon M., Rêgo A. T., Stacher-Priehse E., Lindner M., Koch I., Bar J., Swanton C., Samuels Y., Levin Y., da Fonseca P. C., Elinav E., Friedman N., Meiners S. & Merbl Y. (2023), Nature Cancer. 4, 5, p. 629-647
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Sex-dependent control of pheromones on social organization within groups of wild house mice

Zilkha N., Chuartzman S. G., Sofer Y., Pen Y., Cum M., Mayo A., Alon U. & Kimchi T. (2023), Current Biology. 33, 8, p. 1407-1420.e4
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p21 facilitates chronic lung inflammation via epithelial and endothelial cells

Levi N., Papismadov N., Majewska J., Roitman L., Wigoda N., Eilam R., Tsoory M., Rotkopf R., Ovadya Y., Akiva H., Regev O. & Krizhanovsky V. (2023), Aging (Albany, NY.). 15, 7, p. 2395-2417

Inflammatory signals from fatty bone marrow support DNMT3A driven clonal hematopoiesis

Zioni N., Bercovich A. A., Chapal-Ilani N., Bacharach T., Rappoport N., Solomon A., Avraham R., Kopitman E., Porat Z., Sacma M., Hartmut G., Scheller M., Muller-Tidow C., Lipka D., Shlush E., Minden M., Kaushansky N. & Shlush L. I. (2023), Nature Communications. 14, 1, 2070

Large-Scale Immunopeptidome Analysis Reveals Recurrent Posttranslational Splicing of Cancer- and Immune-Associated Genes

Levy R., Alter Regev T., Paes W., Gumpert N., Cohen Shvefel S., Bartok O., Dayan-Rubinov M., Alon M., Shmueli M., Levin Y., Merbl Y., Ternette N. & Samuels Y. (2023), Molecular and Cellular Proteomics. 22, 4, 100519

Wearable and digital devices to monitor and treat metabolic diseases

Keshet A., Reicher L., Bar N. & Segal E. (2023), Nature metabolism. 5, 4, p. 563-571
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Redifferentiated cardiomyocytes retain residual dedifferentiation signatures and are protected against ischemic injury

Shakked A., Petrover Z., Aharonov A., Ghiringhelli M., Umansky K., Kain D., Elkahal J., Divinsky Y., Nguyen P. D., Miyara S., Friedlander G., Savidor A., Zhang L., Perez D. E., Sarig R., Lendengolts D., Bueno-Levy H., Kastan N., Levin Y., Bakkers J., Gepstein L. & Tzahor E. (2023), Nature Cardiovascular Research. 2, 4, p. 383-398
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Cellular states are coupled to genomic and viral heterogeneity in HPV-related oropharyngeal carcinoma

Puram S. V., Mints M., Pal A., Qi Z., Reeb A., Gelev K., Barrett T. F., Gerndt S., Liu P., Parikh A. S., Ramadan S., Law T., Mroz E. A., Rocco J. W., Adkins D., Thorstad W. L., Gay H. A., Ding L., Paniello R. C., Pipkorn P., Jackson R. S., Wang X., Mazul A., Chernock R., Zevallos J. P., Silva-Fisher J. & Tirosh I. (2023), Nature Genetics. 55, 4, p. 640-650

Deciphering the involvement of the Hippo pathway co-regulators, YAP/TAZ in invadopodia formation and matrix degradation

Venghateri J. B., Dassa B., Morgenstern D., Shreberk-Shaked M., Oren M. & Geiger B. (2023), Cell Death and Disease. 14, 4, 290

Evolutionarily conserved role of oxytocin in social fear contagion in zebrafish

Akinrinade I., Kareklas K., Teles M. C., Reis T. K., Gliksberg M., Petri G., Levkowitz G. & Oliveira R. F. (2023), Science. 379, 6638, p. 1232-1237

Neuronal excitability as a regulator of circuit remodeling

Mayseless O., Shapira G., Rachad E. Y., Fiala A. & Schuldiner O. (2023), Current Biology. 33, 5, p. 981-989.e3

Spatial profiling technologies illuminate the tumor microenvironment

Elhanani O., Ben-Uri R. & Keren L. (2023), Cancer Cell. 41, 3, p. 404-420

Tackling tumor complexity with single-cell proteomics

Geiger T. (2023), Nature Methods. 20, 3, p. 324-326

Instruction of epigenetic states from DNA sequences

Stelzer Y. (2023), Nature reviews. Molecular cell biology. 24, 3, p. 164

Actin-dependent astrocytic infiltration is a key step for axon defasciculation during remodeling

Marmor-Kollet N., Berkun V., Cummings G., Keren-Shaul H., David E., Addadi Y. & Schuldiner O. (2023), Cell Reports. 42, 2, 112117

LGI3/2ADAM23 interactions cluster Kv1 channels in myelinated axons to regulate refractory period

Kozar-Gillan N., Velichkova A., Kanatouris G., Eshed-Eisenbach Y., Steel G., Jaegle M., Aunin E., Peles E., Torsney C. & Meijer D. N. (2023), Journal of Cell Biology. 222, 4, e202211031

Rules for body fat interventions based on an operating point mechanism

Bar A., Karin O., Mayo A., Ben-Zvi D. & Alon U. (2023), iScience. 26, 2, 106047

Induced epigenetic changes memorized across generations in mice

Cheng S., Mayshar Y. & Stelzer Y. (2023), Cell. 186, 4, p. 683-685

Proteomic signature for detection of high-grade ovarian cancer in germline BRCA mutation carriers

Bahar-Shany K., Barnabas G. D., Deutsch L., Deutsch N., Glick-Saar E., Dominissini D., Sapoznik S., Helpman L., Perri T., Blecher A., Katz G., Yagel I., Rosenblatt O., Shai D., Brandt B., Meyer R., Mohr-Sasson A., Volodarsky-Perel A., Zilberman I., Armon S., Jakobson-Setton A., Eitan R., Kadan Y., Beiner M., Josephy D., Brodsky M., Friedman E., Anafi L., Molchanov Y., Korach J., Geiger T. & Levanon K. (2023), International Journal of Cancer. 152, 4, p. 781-793

Distal fecal wash host transcriptomics identifies inflammation throughout the colon and terminal ileum

Dan S., Ungar B., Ben-Moshe S., Halpern K. B., Yavzori M., Fudim E., Picard O., Abitbol C. M., Harnik S., Barshack I., Kopylov U., Ben-Horin S. & Itzkovitz S. (2023), Cellular and Molecular Gastroenterology and Hepatology. 16, 1, p. 1-15

Actin polymerisation and crosslinking drive left-right asymmetry in single cell and cell collectives

Tee Y. H., Goh W. J., Yong X., Ong H. T., Hu J., Tay I. Y. Y., Shi S., Jalal S., Barnett S. F., Kanchanawong P., Huang W., Yan J., Lim Y. A. B., Thiagarajan V., Mogilner A. & Bershadsky A. D. (2023), Nature Communications. 14, 1, 776

Post-translational modifications reshape the antigenic landscape of the MHC I immunopeptidome in tumors

Kacen A., Javitt A., Kramer M. P., Morgenstern D., Tsaban T., Shmueli M. D., Teo G. C., Leprevost F. d. V., Barnea E., Yu F., Admon A., Eisenbach L., Samuels Y., Schueler-Furman O., Levin Y., Nesvizhskii A. & Merbl Y. (2023), Nature Biotechnology. 41, 2, p. 239-251
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Publisher Correction: Nascent Ribo-Seq measures ribosomal loading time and reveals kinetic impact on ribosome density (Nature Methods, (2021), 18, 9, (1068-1074), 10.1038/s41592-021-01250-z)

Schott J., Reitter S., Lindner D., Grosser J., Bruer M., Shenoy A., Geiger T., Mathes A., Dobreva G. & Stoecklin G. (2023), Nature Methods. 20, 2, p. 316

Drugging p53 in cancer: one protein, many targets

Hassin O. & Oren M. (2023), Nature reviews. Drug discovery. 22, 2, p. 127-144

Stress resilience is established during development and is regulated by complement factors

Swaminathan A., Gliksberg M., Anbalagan S., Wigoda N. & Levkowitz G. (2023), Cell Reports. 42, 1, 111973

Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies

Kennedy K. M., de Goffau M. C., Perez-Muñoz M. E., Arrieta M., Bäckhed F., Bork P., Braun T., Bushman F. D., Dore J., de Vos W. M., Earl A. M., Eisen J. A., Elovitz M. A., Ganal-Vonarburg S. C., Gänzle M. G., Garrett W. S., Hall L. J., Hornef M. W., Huttenhower C., Konnikova L., Lebeer S., Macpherson A. J., Massey R. C., McHardy A. C., Koren O., Lawley T. D., Ley R. E., O'Mahony L., O'Toole P. W., Pamer E. G., Parkhill J., Raes J., Rattei T., Salonen A., Segal E., Segata N., Shanahan F., Sloboda D. M., Smith G. C. S., Sokol H., Spector T. D., Surette M. G., Tannock G. W., Walker A. W., Yassour M. & Walter J. (2023), Nature. 613, 7945, p. 639-649
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Author Correction: Breast cancer plasticity is restricted by a LATS1-NCOR1 repressive axis (doi 10.1038/s41467-022-34863-9 , 28 Nov, 2022)

Aylon Y., Furth N., Mallel G., Friedlander G., Nataraj N. B., Dong M., Hassin O., Zoabi R., Cohen B., Drendel V., Salame T. M., Mukherjee S., Harpaz N., Johnson R., Aulitzky W. E., Yarden Y., Shema E. & Oren M. (2023), Nature Communications. 14, 1, 133

An enhancer-based gene-therapy strategy for spatiotemporal control of cargoes during tissue repair

Yan R., Cigliola V., Oonk K. A., Petrover Z., DeLuca S., Wolfson D. W., Vekstein A., Mendiola M. A., Devlin G., Bishawi M., Gemberling M. P., Sinha T., Sargent M. A., York A. J., Shakked A., DeBenedittis P., Wendell D. C., Ou J., Kang J., Goldman J. A., Baht G. S., Karra R., Williams A. R., Bowles D. E., Asokan A., Tzahor E., Gersbach C. A., Molkentin J. D., Bursac N., Black B. L. & Poss K. D. (2023), Cell Stem Cell. 30, 1, p. 96-111.e6

Germline TP53 mutations undergo copy number gain years prior to tumor diagnosis

Light N., Layeghifard M., Attery A., Subasri V., Zatzman M., Anderson N. D., Hatkar R., Blay S., Chen D., Novokmet A., Fuligni F., Tran J., de Borja R., Agarwal H., Waldman L., Abegglen L. M., Albertson D., Finlay J. L., Hansford J. R., Behjati S., Villani A., Gerstung M., Alexandrov L. B., Somers G. R., Schiffman J. D., Rotter V., Malkin D. & Shlien A. (2023), Nature Communications. 14, 1, 77

An autocrine signaling circuit in hepatic stellate cells underlies advanced fibrosis in nonalcoholic steatohepatitis

Wang S., Li K., Pickholz E., Dobie R., Matchett K. P., Henderson N. C., Carrico C., Driver I., Borch Jensen M., Chen L., Petitjean M., Bhattacharya D., Fiel M. I., Liu X., Kisseleva T., Alon U., Adler M., Medzhitov R. & Friedman S. L. (2023), Science Translational Medicine. 15, 677, eadd3949
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Head-to-head efficacy and safety of rivaroxaban, apixaban, and dabigatran in an observational nationwide targeted trial

Talmor-Barkan Y., Yacovzada N., Rossman H., Witberg G., Kalka I., Kornowski R. & Segal E. (2023), European heart journal. Cardiovascular pharmacotherapy. 9, 1, p. 26-37