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All Publications

  • 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

  • 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

  • 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

  • Post-Gastrulation Synthetic Embryos Generated Ex Utero from Mouse Naֳ¯ve ESCs

    Authors: Tarazi S., Aguilera Castrejon A., Joubran C., Ghanem N., Ashouokhi S., Roncato F., Wildschutz E., Haddad M., Oldak B., Gomez-Cesar E., Livnat N., Viukov S., Lukshtanov D., Naveh Tassa S., Rose M., Issaq - Hanna S., Raanan C., Brenner O. J., Kedmi M., Keren-Shaul H., Lapidot T., Maza I., Novershtern N. & Hanna J. (. (2022), Cell. 185, 18, p. 3290-3306.e25

  • Alzheimerג€™s disease modification mediated by bone marrow-derived macrophages via a TREM2-independent pathway in mouse model of amyloidosis

    Authors: Dvir-Szternfeld R., Castellani G., Arad M., Cahalon L., Colaiuta S. P., Keren-Shaul H., Croese T., Burgaletto C., Baruch K., Ulland T., Colonna M., Weiner A., Amit I. & Schwartz M. (2022), Nature Aging. 2, p. 60-73

  • 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

  • NF-־÷B activity during pancreas development regulates adult ־²-cell mass by modulating neonatal ־²-cell proliferation and apoptosis

    Authors: Sever D., Hershko-Moshe A., Srivastava R., Eldor R., Hibsher D., Keren-Shaul H., Amit I., Bertuzzi F., Krogvold L., Dahl-Jֳ¸rgensen K., Ben-Dov I. Z., Landsman L. & Melloul D. (2021), Cell Death Discovery. 7, 1, 2

  • 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).

  • Bi-fated tendon-to-bone attachment cells are regulated by shared enhancers and KLF transcription factors

    Authors: Kult S., Olender T., Osterwalder M., Markman S., Leshkowitz D., Krief S., Blecher-Gonen R., Ben-Moshe S., Farack L., Keren-Shaul H., Salame T. M., Capellini T. D., Itzkovitz S., Amit I., Visel A. & Zelzer E. (2021), eLife. 10, 55361

  • Transneuronal Dpr12/DIP-־´ interactions facilitate compartmentalized dopaminergic innervation of Drosophila mushroom body axons

    Authors: Bornstein B., Meltzer H., Adler R., Alyagor I., Berkun V., Cummings G., Reh F., Keren-Shaul H., David E., Riemensperger T. & Schuldiner O. (2021), The EMBO Journal. e105763

  • 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

  • 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

  • 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

  • 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. 5, p. 629-+

  • 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, 465

  • 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),

  • 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

  • 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

  • Single-Cell Analysis of Diverse Pathogen Responses Defines a Molecular Roadmap for Generating Antigen-Specific Immunity

    Authors: Blecher-Gonen R., Bost P., Hilligan K. L., David E., Salame T. M., Roussel E., Connor L. M., Mayer J. U., Halpern K. B., Toth B., Itzkovitz S., Schwikowski B., Ronchese F. & Amit I. (2019), Cell Systems. 8, 2, p. 109-121.e6

  • 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-+

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • Single-cell transcriptome conservation in cryopreserved cells and tissues

    Authors: Guillaumet-Adkins A., Rodriguez-Esteban G., Mereu E., Mendez-Lago M., Jaitin D. A., Villanueva A., Vidal A., Martinez-Marti A., Felip E., Vivancos A., Keren-Shaul H., Heath S., Gut M., Amit I., Gut I. & Heyn H. (2017), GENOME BIOLOGY. 18, 45

  • A Unique Microglia Type Associated with Restricting Development of Alzheimer's Disease

    Authors: Keren-Shaul H., Spinrad A., Weiner A., Matcovitch-Natan O., Dvir-Szternfeld R., Ulland T. K., David E., Baruch K., Lara-Astaiso D., Toth B., Itzkovitz S., Colonna M., Schwartz M. & Amit I. (2017), Cell. 169, 7, p. 1276-+

  • Dicer Deficiency Differentially Impacts Microglia of the Developing and Adult Brain

    Authors: Varol D., Mildner A., Blank T., Shemer A., Barashi N., Yona S., David E., Boura-Halfon S., Segal-Hayoun Y., Chappell-Maor L., Keren-Shaul H., Leshkowitz D., Hornstein E., Fuhrmann M., Amit I., Maggio N., Prinz M. & Jung S. (2017), Immunity. 46, 6, p. 1030-+

  • 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 (New York, N.Y.). 353, 6301, p. aad8670

  • 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

  • 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-+

  • 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., Blecher-Gonen R., Lapaquette P., Silvin' A., Mane N., Joubert P. -., Seeler J., Albert M. L., Amit I., Amigorena S. & Dejean A. (2016), Nature Immunology. 17, 2, p. 140-149

  • 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

  • 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

  • Distinct Murine Mucosal Langerhans Cell Subsets Develop from Pre-dendritic Cells and Monocytes

    Authors: Capucha T., Mizraji G., Segev H., Blecher-Gonen R., Winter D., Khalaileh A., Tabib Y., Attal T., Nassar M., Zelentsova K., Kisos H., Zenke M., Sere K., Hieronymus T., Burstyn-Cohen T., Amit I., Wilensky A. & Hovav A. (2015), Immunity. 43, 2, p. 369-381

  • Deterministic direct reprogramming of somatic cells to pluripotency (vol 502, pg 65, 2013)

    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

  • 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

  • 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

  • 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),

  • Chronic exposure to TGF beta 1 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

  • 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

  • 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

  • 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-+

  • 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. (2012), Molecular Cell. 47, 5, p. 810-822

  • M(odu)LLating the Innate Response

    Authors: Blecher-Gonen R. & Amit I. (2012), Immunity. 36, 4, p. 551-552