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All Publications

  • Transgene-free generation of mouse post-gastrulation whole embryo models solely from naive ESCs and iPSCs

    Authors: Yilmaz A., Gurhan G., Comar M. Y., Viukov S., Serfaty I., Gayretli M., Golenchenko S., Lokshtanov D., Ashouokhi S., Polanco A., Berlad I., Ha T. W., Aguilera-Castrejon A., Tarazi S., Cohen M., Livnat N., Kumar K., Cholakkal H., Levy N., Yosef N., Khatib N., Kakun R. R., Kedmi M., Nachman I. B., Keren-Shaul H., Addadi Y., Orenbuch A. H., Korovin K., Molchadsky A., Hochedlinger K., Gafni O., Maza I., Novershtern N., Oldak B. & Hanna J. H. (2025), Cell Stem Cell.

  • Efficient Identification of Monoclonal Antibodies Against Rift Valley Fever Virus Using High-Throughput Single Lymphocyte Transcriptomics of Immunized Mice

    Authors: Rosenfeld R., Alcalay R., Yahalom-Ronen Y., Melamed S., Sarusi-Portuguez A., Noy-Porat T., Israeli O., Beth-Din A., Blecher-Gonen R., Chitlaru T., Bar-Haim E., Israely T., Zvi A. & Makdasi E. (2025), Antibodies. 14, 1, 12

  • A spatial expression atlas of the adult human proximal small intestine

    Authors: 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

  • Tuft cells and fibroblasts promote thymus regeneration through ILC2-mediated type 2 immune response

    Authors: Nevo S., Frenkel N., Kadouri N., Gome T., Rosenthal N., Givony T., Avin A., Peligero Cruz C., Kedmi M., Lindzen M., Ben Dor S., Damari G., Porat Z., Haffner-Krausz R., Keren-Shaul H., Yarden Y., Munitz A., Leshkowitz D., Goldfarb Y. & Abramson J. (2024), Science Immunology. 9, 91, eabq6930

  • SMARCA5-mediated chromatin remodeling is required for germinal center formation

    Authors: Stoler-Barak L., Schmiedel D., Sarusi-Portuguez A., Rogel A., Blecher-Gonen R., Haimon Z., Stopka T. & Shulman Z. (2024), Journal of Experimental Medicine. 221, 11, e20240433

  • Acanthamoeba polyphaga de novo transcriptome and its dynamics during Mimivirus infection

    Authors: Bickels Nuri R., Feldmesser E., Fridmann-Sirkis Y., Keren-Shaul H., Nevo R., Minsky A. & Reich Z. (2024), Scientific Reports. 14, 25894

  • Optimized single-nucleus transcriptional profiling by combinatorial indexing

    Authors: Martin B. K., Qiu C., Nichols E., Phung M., Green-Gladden R., Srivatsan S., Blecher-Gonen R., Beliveau B. J., Trapnell C., Cao J. & Shendure J. (2023), Nature protocols. 18, 1, p. 188-207

  • Complete human day 14 post-implantation embryo models from naive ES cells

    Authors: Oldak B., Wildschutz E., Bondarenko V., Comar M., Zhao C., Aguilera-Castrejon A., Tarazi S., Viukov S., Pham T. X. A., Ashouokhi S., Lokshtanov D., Roncato F., Ariel E., Rose M., Livnat N., Shani T., Joubran C., Cohen R., Addadi Y., Chemla M., Kedmi M., Keren-Shaul H., Pasque V., Petropoulos S., Lanner F., Novershtern N. & Hanna J. H. (2023), Nature. 622, 7983, p. 562-573

  • Thymic mimetic cells function beyond self-tolerance

    Authors: Givony T., Leshkowitz D., Del Castillo D., Nevo S., Kadouri N., Dassa B., Gruper Y., Khalaila R., Ben-Nun O., Gome T., Dobeš J., Ben-Dor S., Kedmi M., Keren-Shaul H., Heffner-Krausz R., Porat Z., Golani O., Addadi Y., Brenner O., Lo D. D., Goldfarb Y. & Abramson J. (2023), Nature. 622, 7981, p. 164172

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

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

  • The transcriptional and regulatory identity of erythropoietin producing cells

    Authors: Kragesteen B. K., Giladi A., David E., Halevi S., Geirsdóttir L., Lempke O. M., Li B., Bapst A. M., Xie K., Katzenelenbogen Y., Dahl S. L., Sheban F., Gurevich-Shapiro A., Zada M., Phan T. S., Avellino R., Wang S., Barboy O., Shlomi-Loubaton S., Winning S., Markwerth P. P., Dekalo S., Keren-Shaul H., Kedmi M., Sikora M., Fandrey J., Korneliussen T. S., Prchal J. T., Rosenzweig B., Yutkin V., Racimo F., Willerslev E., Gur C., Wenger R. H. & Amit I. (2023), Nature Medicine. 29, p. 1191-1200

  • Meso-seq for in-depth transcriptomics in ultra-low amounts of FACS-purified neuronal nuclei

    Authors: Apelblat D., Roethler O., Bitan L., Keren-Shaul H. & Spiegel I. (2022), Cell Reports Methods. 2, 8, 100259

  • DestVI identifies continuums of cell types in spatial transcriptomics data

    Authors: Lopez R., Li B., Keren-Shaul H., Boyeau P., Kedmi M., Pilzer D., Jelinski A., Yofe I., David E., Wagner A., Ergen C., Addadi Y., Golani O., Ronchese F., Jordan M. I., Amit I. & Yosef N. (2022), Nature biotechnology. 40, 9, p. 1360-1369

  • The continuum of Drosophila embryonic development at single-cell resolution

    Authors: Calderon D., Blecher-Gonen R., Huang X., Secchia S., Kentro J., Daza R. M., Martin B., Dulja A., Schaub C., Trapnell C., Larschan E., OConnor-Giles K. M., Furlong E. E. & Shendure J. (2022), Science. 377, 6606, eabn5800

  • Exploring differential exon usage via short- and long-read RNA sequencing strategies

    Authors: Leshkowitz D., Kedmi M., Fried Y., Pilzer D., Keren-Shaul H., Ainbinder E. & Dassa B. (2022), Open Biology. 12, 9, 220206

  • Ex utero mouse embryogenesis from pre-gastrulation to late organogenesis

    Authors: Aguilera-Castrejon A., Shani T., Ghanem N., Itzkovich C., Slomovich S., Tarazi S., Bayerl J., Chugaeva V., Ayyash M., Ashouokhi S., Sheban D., Livnat N., Lasman L., Viukov S., Zerbib M., Addadi Y., Rais Y., Cheng S., Keren-Shaul H., Stelzer Y., Shlomo R., Massarwa R., Novershtern N. & Hanna J. H. (2021), Nature (London). 593, 7857, p. 119-124

  • Dissection of floral transition by single-meristem transcriptomes at high temporal resolution

    Authors: Meir Z., Aviezer I., Chongloi G. L., Ben-Kiki O., Bronstein R., Mukamel Z., Keren-Shaul H., Jaitin D., Tal L., Shalev-Schlosser G., Harel T. H., Tanay A. & Eshed Y. (2021), Nature Plants. 7, 6, p. 800-813

  • Dissecting cellular crosstalk by sequencing physically interacting cells

    Authors: Giladi A., Cohen M., Medaglia C., Baran Y., Li B., Zada M., Bost P., Blecher-Gonen R., Salame T., Mayer J. U., David E., Ronchese F., Tanay A. & Amit I. (2020), Nature Biotechnology. 38, 5, p. 629-637

  • Coupled scRNA-Seq and Intracellular Protein Activity Reveal an Immunosuppressive Role of TREM2 in Cancer

    Authors: Katzenelenbogen Y., Sheban F., Yalin A., Yofe I., Svetlichnyy D., Jaitin D. A., Bornstein C., Moshe A., Keren-Shaul H., Cohen M., Wang S., Li B., David E., Salame T., Weiner A. & Amit I. (2020), Cell. 182, 4, p. 872-885.e19

  • Pan-cancer single-cell RNA-seq identifies recurring programs of cellular heterogeneity

    Authors: Kinker G. S., Greenwald A. C., Tal R., Orlova Z., Cuoco M. S., McFarland J. M., Warren A., Rodman C., Roth J. A., Bender S. A., Kumar B., Rocco J. W., Fernandes P. A., Mader C. C., Keren-Shaul H., Plotnikov A., Barr H., Tsherniak A., Rozenblatt-Rosen O., Krizhanovsky V., Puram S. V., Regev A. & Tirosh I. (2020), Nature Genetics. 52, 11, p. 1208-1218

  • A human cell atlas of fetal gene expression

    Authors: Cao J., ODay D. R., Pliner H. A., Kingsley P. D., Deng M., Daza R. M., Zager M. A., Aldinger K. A., Blecher-Gonen R., Zhang F., Spielmann M., Palis J., Doherty D., Steemers F. J., Glass I. A., Trapnell C. & Shendure J. (2020), Science. 370, 6518, eaba7721

  • Host-Viral Infection Maps Reveal Signatures of Severe COVID-19 Patients

    Authors: Bost P., Giladi A., Liu Y., Bendjelal Y., Xu G., David E., Blecher-Gonen R., Cohen M., Medaglia C., Li H., Deczkowska A., Zhang S., Schwikowski B., Zhang Z. & Amit I. (2020), Cell. 181, 7, p. 1475-1488

  • Cross-Species Single-Cell Analysis Reveals Divergence of the Primate Microglia Program

    Authors: Geirsdottir L., David E., Keren-Shaul H., Weiner A., Bohlen S. C., Neuber J., Balic A., Giladi A., Sheban F., Dutertre C., Pfeifle C., Peri F., Raffo-Romero A., Vizioli J., Matiasek K., Scheiwe C., Meckel S., Maetz-Rensing K., van der Meer F., Thormodsson F. R., Stadelmann C., Zilkha N., Kimchi T., Ginhoux F., Ulitsky I., Erny D., Amit I. & Prinz M. (2019), Cell. 179, 7, p. 1609-1622.e16

  • Lipid-Associated Macrophages Control Metabolic Homeostasis in a Trem2-Dependent Manner

    Authors: Jaitin D. A., Adlung L., Thaiss C. A., Weiner A., Li B., Descamps H., Lundgren P., Bleriot C., Liu Z., Deczkowska A., Keren-Shaul H., David E., Zmora N., Eldar S. M., Lubezky N., Shibolet O., Hill D. A., Lazar M. A., Colonna M., Ginhoux F., Shapiro H., Elinav E. & Amit I. (2019), Cell. 178, 3, p. 686-698.e14

  • PD-1/PD-L1 checkpoint blockade harnesses monocyte-derived macrophages to combat cognitive impairment in a tauopathy mouse model

    Authors: Rosenzweig N., Dvir-Szternfeld R., Tsitsou-Kampeli A., Keren-Shaul H., Ben-Yehuda H., Weill-Raynal P., Cahalon L., Kertser A., Baruch K., Amit I., Weiner A. & Schwartz M. (2019), Nature Communications. 10, 1, 465

  • MARS-seq2.0: an experimental and analytical pipeline for indexed sorting combined with single-cell RNA sequencing

    Authors: Keren-Shaul H., Kenigsberg E., Jaitin D. A., David E., Paul F., Tanay A. & Amit I. (2019), Nature Protocols. 14, 6, p. 1841-1862

  • Correction:: The 'TranSeq' 3 '-end sequencing method for high-throughput transcriptomics and gene space refinement in plant genomes (vol 96, pg 223, 2018)

    Authors: Tzfadia O., Bocobza S., Defoort J., Almekias-Siegl E., Panda S., Levy M., Storme V., Rombauts S., Adhemar D., Keren-Shaul, Van de Peer Y. & Aharoni A. (2019),

  • Disease-Associated Microglia: A Universal Immune Sensor of Neurodegeneration

    Authors: Deczkowska A., Keren-Shaul H., Weiner A., Colonna M., Schwartz M. & Amit I. (2018), Cell. 173, 5, p. 1073-1081

  • Combining Developmental and Perturbation-Seq Uncovers Transcriptional Modules Orchestrating Neuronal Remodeling

    Authors: Alyagor I., Berkun V., Keren-Shaul H., Marmor-Kollet N., David E., Mayseless O., Issman-Zecharya N., Amit I. & Schuldiner O. (2018), Developmental Cell. 47, 1, p. 38-52

  • Single cell dissection of plasma cell heterogeneity in symptomatic and asymptomatic myeloma

    Authors: Ledergor G., Weiner A., Zada M., Wang S., Cohen Y. C., Gatt M. E., Snir N., Magen H., Koren-Michowitz M., Herzog-Tzarfati K., Keren-Shaul H., Bornstein C., Rotkopf R., Yofe I., David E., Yellapantula V., Kay S., Salai M., Ben Yehuda D., Nagler A., Shvidel L., Orr-Urtreger A., Halpern K. B., Itzkovitz S., Landgren O., San-Miguel J., Paiva B., Keats J. J., Papaemmanuil E., Avivi I., Barbash G. I., Tanay A. & Amit I. (2018), Nature Medicine. 24, 12, p. 1867-1876

  • Microbiome Influences Prenatal and Adult Microglia in a Sex-Specific Manner

    Authors: Thion M. S., Low D., Silvin A., Chen J., Grisel P., Schulte-Schrepping J., Blecher R., Ulas T., Squarzoni P., Hoeffel G., Coulpier F., Siopi E., David F. S., Scholz C., Shihui F., Lum J., Amoyo A. A., Larbi A., Poidinger M., Buttgereit A., Lledo P., Greter M., Chan J. K. Y., Amit I., Beyer M., Schultze J. L., Schlitzer A., Pettersson S., Ginhoux F. & Garel S. (2018), Cell. 172, 3, p. 500-516.e16

  • The bone marrow is patrolled by NK cells that are primed and expand in response to systemic viral activation

    Authors: Milo I., Blecher-Gonen R., Barnett-Itzhaki Z., Bar-Ziv R., Tal O., Gurevich I., Feferman T., Drexler I., Amit I., Bousso P. & Shakhar G. (2018), European Journal of Immunology. 48, 7, p. 1137-1152

  • The 'TranSeq' 3 '-end sequencing method for high-throughput transcriptomics and gene space refinement in plant genomes

    Authors: Tzfadia O., Bocobza S., Defoort J., Almekias-Siegl E., Panda S., Levy M., Storme V., Rombauts S., Jaitin D. A., Keren-Shaul H., Van de Peer Y. & Aharoni A. (2018), Plant Journal. 96, 1, p. 223-232

  • CD74 is a novel transcription regulator

    Authors: Gil-Yarom N., Radomir L., Sever L., Kramer M. P., Lewinsky H., Bornstein C., Blecher-Gonen R., Barnett Itzhaki Z., Mirkin V., Friedlander G., Shvidel L., Herishanu Y., Lolis E. J., Becker Herman S., Amit I. & Shachar I. (2017), Proceedings of the National Academy of Sciences of the United States of America. 114, 3, p. 562-567

  • Evolution and dissemination of the Klebsiella pneumoniae clonal group 258 throughout Israeli post-acute care hospitals, 2008-13

    Authors: Adler A., Lifshitz Z., Gordon M., Ben-David D., Khabra E., Masarwa S., Zion O., Schwaber M. J. & Carmeli Y. (2017), Journal of Antimicrobial Chemotherapy. 72, 8, p. 2219-2224, dkx135

  • M-sec regulates polarized secretion of inflammatory endothelial chemokines and facilitates CCL2-mediated lymphocyte transendothelial migration

    Authors: Barzilai S., Blecher-Gonen R., Barnett Itzhaki Z., Zauberman A., Lebel-Haziv Y., Amit I. & Alon R. (2016), Journal of Leukocyte Biology. 99, 6, p. 1045-1055

  • Extracellular Matrix Proteolysis by MT1-MMP Contributes to Influenza-Related Tissue Damage and Mortality

    Authors: Talmi-Frank D., Altboum Z., Solomonov I., Udi Y., Jaitin D. A., Klepfish M., David E., Zhuravlev A., Keren-Shaul H., Winter D. R., Gat-Viks I., Mandelboim M., Ziv T., Amit I. & Sagi I. (2016), Cell Host & Microbe. 20, 4, p. 458-470

  • The Spectrum and Regulatory Landscape of Intestinal Innate Lymphoid Cells Are Shaped by the Microbiome

    Authors: Gury-BenAri M., Thaiss C. A., Serafini N., Winter D. R., Giladi A., Lara Astiaso A. D., Levy M., Salame T. M., Weiner A., David E., Shapiro H., Dori-Bachash M., Pevsner-Fischer M., Lorenzo Vivas V. E., Keren-Shaul H., Paul F., Harmelin A., Eberl G., Itzkovitz S., Tanay A., Di Santo S. J. P., Elinav E. & Amit I. (2016), Cell. 166, 5, p. 1231-1246.e13

  • Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq

    Authors: Jaitin D. A., Weiner A., Yofe I., Lara Astiaso D., Keren-Shaul H., David E., Salame T. M., Tanay A., van Oudenaarden A. & Amit I. (2016), Cell. 167, 7, p. 1883-1896.e15

  • Microglia development follows a stepwise program to regulate brain homeostasis

    Authors: Matcovitch-Natan O., Winter D. R., Giladi A., Vargas Aguilar A. S., Spinrad A., Sarrazin S., Ben-Yehuda H., David E., Zelada Gonzalez G. F., Perrin P., Keren-Shaul H., Gury M., Lara-Astaiso D., Thaiss C. A., Cohen M., Bahar Halpern H. K., Baruch K., Deczkowska A., Lorenzo Vivas V. E., Itzkovitz S., Elinav E., Sieweke M. H., Schwartz M. & Amit I. (2016), Science. 353, 6301, aad8670

  • Sumoylation coordinates the repression of inflammatory and anti-viral gene-expression programs during innate sensing

    Authors: Decque A., Joffre O., Magalhaes J. G., Cossec J. C., Blecher-Gonen R., Lapaquette P., Silvin A., Manel N., Joubert P. E., Seeler J. S., Albert M. L., Amit I., Amigorena S. & Dejean A. (2016), Nature Immunology. 17, 2, p. 140-149

  • Deterministic direct reprogramming of somatic cells to pluripotency (vol 502, pg 65, 2013): Deterministic direct reprogramming of somatic cells to pluripotency (Nature (2013) 502 (65-70) DOI: 10.1038/nature12587)

    Authors: Rais Y., Zviran A., Geula S., Gafni O., Chomsky E., Viukov S., Mansour A. A., Caspi I., Krupalnik V., Zerbib M., Maza I., Mor N., Baran D., Weinberger L., Jaitin D. A., Lara-Astiaso D., Blecher-Gonen R., Shipony Z., Mukamel Z., Hagai T., Gilad S., Amann-Zalcenstein D., Tanay A., Amit I., Novershtern N. & Hanna J. H. (2015), Nature. 520, 7549, p. 710-710

  • Each cell counts: Hematopoiesis and immunity research in the era of single cell genomics

    Authors: Jaitin D. A., Keren-Shaul H., Elefant N. & Amit I. (2015), Seminars in Immunology. 27, 1, p. 67-71

  • Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

    Authors: Paul F., Arkin Y., Giladi A., Jaitin D. A., Kenigsberg E., Keren-Shaul H., Winter D., Lara-Astiaso D., Gury M., Weiner A., David E., Cohen N., Lauridsen F. K. B., Haas S., Schlitzer A., Mildner A., Ginhoux F., Jung S., Trumpp A., Porse B. T., Tanay A. & Amit I. (2015), Cell. 163, 7, p. 1663-1677

  • Chromatin state dynamics during blood formation

    Authors: Lara Astiaso A. D., Weiner A., Lorenzo Vivas V. E., Zaretsky I., Jaitin D. A., David E., Keren-Shaul H., Mildner A., Winter D., Jung S., Friedman N. & Amit I. (2014), Science. 345, 6199, p. 943-949

  • Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment

    Authors: Lavin Y., Winter D., Blecher-Gonen R., David E., Keren-Shaul H., Merad M., Jung S. & Amit I. (2014), Cell. 159, 6, p. 1312-1326

  • Chronic exposure to TGFβ1 regulates myeloid cell inflammatory response in an IRF7-dependent manner

    Authors: Cohen M., Matcovitch O., David E., Barnett Itzhaki I. Z., Keren-Shaul H., Blecher-Gonen R., Jaitin D. A., Sica A., Amit I. & Schwartz M. (2014), EMBO Journal. 33, 24, p. 2906-2921

  • Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types

    Authors: Jaitin D. A., Kenigsberg E., Keren-Shaul H., Elefant N., Paul F., Zaretsky I., Mildner A., Cohen N., Jung S., Tanay A. & Amit I. (2014), Science. 343, 6172, p. 776-779

  • The central nervous system microenvironment imprints microglial inability to switch from pro- to anti-inflammatory phenotype

    Authors: Matcovitch O., Cohen M., David E., Barnettitzhaki Z., Keren-Shaul H., Blecher-gonen R., Jaitin D. A., Sica A., Amit I. & Schwartz M. (2014),

  • Digital cell quantification identifies global immune cell dynamics during influenza infection

    Authors: Altboum Z., Steuerman Y., David E., Barnett Itzhaki I. Z., Valadarsky L., Keren-Shaul H., Meningher T., Mendelson E., Mandelboim M., Gat-Viks I. & Amit I. (2014), Molecular Systems Biology. 10, 2, 134947

  • Deterministic direct reprogramming of somatic cells to pluripotency

    Authors: Rais Y., Zviran A., Geula S., Gafni O., Chomsky E., Viukov S., Mansour A. A., Caspi I., Krupalnik V., Zerbib M., Maza I., Mor N., Baran D., Weinberger L., Jaitin D. A., Lara Astiaso A. D., Blecher-Gonen R., Shipony Z., Mukamel Z., Hagai T., Gilad S., Amann Zalcenstein D., Tanay A., Amit I., Novershtern N. & Hanna J. (. (2013), Nature. 502, 7469, p. 65-70

  • High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states

    Authors: Blecher-Gonen R., Barnett Itzhaki Z., Jaitin D., Amann Zalcenstein D., Lara Astiaso D. & Amit I. (2013), Nature protocols. 8, 3, p. 539-554

  • M(odu)LLating the Innate Response

    Authors: Blecher-Gonen R. & Amit I. (2012),

  • A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals

    Authors: Garber M., Yosef N., Goren A., Raychowdhury R., Thielke A., Guttman M., Robinson J., Minie B., Chevrier N., Itzhaki Z., Blecher-Gonen R., Bornstein C., Amann Zalcenstein D., Weiner A., Friedrich D., Meldrim J., Ram O., Cheng C., Gnirke A., Fisher S., Friedmann N., Wong B., Bernstein B. E., Nusbaum C., Hacohen N., Regev A. & Amit I. (2012), Molecular Cell. 47, 5, p. 810-822