Publications

All years

2021

A 3D system to model human pancreas development and its reference single-cell transcriptome atlas identify signaling pathways required for progenitor expansion

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Authors: Gonçalves C. A. Larsen M., Jung S., Stratmann J., Nakamura A., Leuschner M., Hersemann L., Keshara R., Perlman S., Lundvall L., Thuesen L. L., Hare K. J., Amit I., Jørgensen A., Kim Y. H., del Sol A. & Grapin-Botton A., et al. Nature Communications | 2021 [All authors] »

A 3D system to model human pancreas development and its reference single-cell transcriptome atlas identify signaling pathways required for progenitor expansion

Heads or tails: histone tail clipping regulates macrophage activity

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Authors: Kragesteen B. K. & Amit I. Nature Immunology | 2021 [All authors] »

Heads or tails: histone tail clipping regulates macrophage activity

Clump sequencing exposes the spatial expression programs of intestinal secretory cells

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Authors: Manco R. Averbukh I., Porat Z., Bahar Halpern K., Amit I. & Itzkovitz S., et al. Nature Communications | 2021 [All authors] »

Clump sequencing exposes the spatial expression programs of intestinal secretory cells

XCR1 + type 1 conventional dendritic cells drive liver pathology in non-alcoholic steatohepatitis

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Publication category: Cancer Immunotherapy

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Authors: Deczkowska A. David E., Ramadori P., Pfister D., Safran M., At The B., Giladi A., Jaitin D. A., Barboy O., Cohen M., Yofe I., Gur C., Shlomi-Loubaton S., Henri S., Suhail Y., Qiu M., Kam S., Hermon H., Lahat E., Ben Yakov G., Cohen-Ezra O., Davidov Y., Likhter M., Goitein D., Roth S., Weber A., Malissen B., Weiner A., Ben-Ari Z., Heikenwälder M., Elinav E. & Amit I., et al. Nature Medicine | 2021 [All authors] »

XCR1 + type 1 conventional dendritic cells drive liver pathology in non-alcoholic steatohepatitis

Deciphering the state of immune silence in fatal COVID-19 patients

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Publication category: Technology

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Authors: Bost P. De Sanctis F., Canè S., Ugel S., Donadello K., Castellucci M., Eyal D., Fiore A., Anselmi C., Barouni R. M., Trovato R., Caligola S., Lamolinara A., Iezzi M., Facciotti F., Mazzariol A., Gibellini D., De Nardo P., Tacconelli E., Gottin L., Polati E., Schwikowski B., Amit I. & Bronte V., et al. Nature Communications | 2021 [All authors] »

Deciphering the state of immune silence in fatal COVID-19 patients

NASH limits anti-tumour surveillance in immunotherapy-treated HCC

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Publication category: Cancer Immunotherapy

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Authors: Pfister D. Núñez N. G., Pinyol R., Govaere O., Pinter M., Szydlowska M., Gupta R., Qiu M., Deczkowska A., Weiner A., Müller F., Sinha A., Friebel E., Engleitner T., Lenggenhager D., Moncsek A., Heide D., Stirm K., Kosla J., Kotsiliti E., Leone V., Dudek M., Yousuf S., Inverso D., Singh I., Teijeiro A., Castet F., Montironi C., Haber P. K., Tiniakos D., Bedossa P., Cockell S., Younes R., Vacca M., Marra F., Schattenberg J. M., Allison M., Bugianesi E., Ratziu V., Pressiani T., D'Alessio A., Personeni N., Rimassa L., Daly A. K., Scheiner B., Pomej K., Kirstein M. M., Vogel A., Peck-Radosavljevic M., Hucke F., Finkelmeier F., Waidmann O., Trojan J., Schulze K., Wege H., Koch S., Weinmann A., Bueter M., Rössler F., Siebenhüner A., Dosso S. D., Mallm J., Umansky V., Jugold M., Luedde T., Schietinger A., Schirmacher P., Emu B., Augustin H. G., Billeter A., Müller-Stich B., Kikuchi H., Duda D. G., Kütting F., Waldschmidt D., Ebert M. P., Rahbari N., Mei H. E., Schulz A. R., Ringelhan M., Malek N., Spahn S., Bitzer M., Ruiz de Galarreta M., Lujambio A., Dufour J., Marron T. U., Kaseb A., Kudo M., Huang Y., Djouder N., Wolter K., Zender L., Marche P. N., Decaens T., Pinato D. J., Rad R., Mertens J. C., Weber A., Unger K., Meissner F., Roth S., Jilkova Z. M., Claassen M., Anstee Q. M., Amit I., Knolle P., Becher B., Llovet J. M. & Heikenwalder M., et al. Nature (London) | 2021 [All authors] »

NASH limits anti-tumour surveillance in immunotherapy-treated HCC

Identification of resistance pathways and therapeutic targets in relapsed multiple myeloma patients through single-cell sequencing

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Publication category: Cancer Immunotherapy

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Authors: Zada M., Wang S., Bornstein C. David E., Moshe A., Li B., Shlomi-loubaton S., Gatt M. E., Gur C., Lavi N., Ganzel C., Luttwak E., Chubar E., Rouvio O., Vaxman I., Pasvolsky O., Ballan M., Tadmor T., Nemets A., Jarchowcky-dolberg O., Shvetz O., Laiba M., Shpilberg O., Dally N., Avivi I., Weiner A. & Amit I., et al. Nature Medicine | 2021 [All authors] »

Identification of resistance pathways and therapeutic targets in relapsed multiple myeloma patients through single-cell sequencing

Meningeal lymphoid structures are activated under acute and chronic spinal cord pathologies

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Publication category: Brain

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Authors: Cohen M. Giladi A., Raposo C., Zada M., Li B., Ruckh J., Deczkowska A., Mohar B., Shechter R., Lichtenstein R. G., Amit I. & Schwartz M., et al. Life Science Alliance | 2021 [All authors] »

Meningeal lymphoid structures are activated under acute and chronic spinal cord pathologies

NF-κB activity during pancreas development regulates adult β-cell mass by modulating neonatal β-cell proliferation and apoptosis

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Publication category: Development

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Authors: Sever D. Hershko-Moshe A., Srivastava R., Eldor R., Hibsher D., Keren-Shaul H., Amit I., Bertuzzi F., Krogvold L., Dahl-Jørgensen K., Ben-Dov I. Z., Landsman L. & Melloul D., et al. Cell Death Discovery | 2021 [All authors] »

NF-κB activity during pancreas development regulates adult β-cell mass by modulating neonatal β-cell proliferation and apoptosis

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

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Publication category: Development

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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., et al. eLife | 2021 [All authors] »

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

2020

A single cell atlas of the human liver tumor microenvironment

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Publication category: Cancer Immunotherapy

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Authors: Massalha H. Bahar Halpern K., Abu-Gazala S., Jana T., Massasa E. E., Moor A. E., Buchauer L., Rozenberg M., Pikarsky E., Amit I., Zamir G. & Itzkovitz S., et al. Molecular Systems Biology | 2020 [All authors] »

A single cell atlas of the human liver tumor microenvironment

Acute liver failure is regulated by MYC- and microbiome-dependent programs

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Publication category: Metabolism

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Authors: Kolodziejczyk A. A. Federici S., Zmora N., Mohapatra G., Dori-Bachash M., Hornstein S., Leshem A., Reuveni D., Zigmond E., Tobar A., Salame T. M., Harmelin A., Shlomai A., Shapiro H., Amit I. & Elinav E., et al. Nature Medicine | 2020 [All authors] »

Acute liver failure is regulated by MYC- and microbiome-dependent programs

Elevated Calprotectin and Abnormal Myeloid Cell Subsets Discriminate Severe from Mild COVID-19

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Publication category: Development , Technology

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Authors: Silvin A. Chapuis N., Dunsmore G., Goubet A., Dubuisson A., Derosa L., Almire C., Henon C., Kosmider O., Droin N., Rameau P., Catelain C., Alfaro A., Dussiau C., Friedrich C., Sourdeau E., Marin N., Szwebel T., Cantin D., Mouthon L., Borderie D., Deloger M., Bredel D., Mouraud S., Drubay D., Andrieu M., Lhonneur A., Saada V., Stoclin A., Willekens C., Pommeret F., Griscelli F., Ng L. G., Zhang Z., Bost P., Amit I., Barlesi F., Marabelle A., Pene F., Gachot B., Andre F., Zitvogel L., Ginhoux F., Fontenay M. & Solary E., et al. Cell | 2020 [All authors] »

Elevated Calprotectin and Abnormal Myeloid Cell Subsets Discriminate Severe from Mild COVID-19

LifeTime and improving European healthcare through cell-based interceptive medicine

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Publication category: Development

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Authors: Nikolaus Rajewsky, Geneviève Almouzni, Stanislaw A. Gorski Stein Aerts, Ido Amit, Michela G. Bertero, Christoph Bock, Annelien L. Bredenoord, Giacomo Cavalli, Susanna Chiocca, Hans Clevers, Bart De Strooper, Angelika Eggert, Jan Ellenberg, Xosé M. Fernández, Marek Figlerowicz, Susan M. Gasser, Norbert Hubner, Jørgen Kjems, Jürgen A. Knoblich, Grietje Krabbe, Peter Lichter, Sten Linnarsson, Jean-Christophe Marine, John C. Marioni, Marc A. Marti-Renom, Mihai G. Netea, Dörthe Nickel, Marcelo Nollmann, Halina R. Novak, Helen Parkinson, Stefano Piccolo, Inês Pinheiro, Ana Pombo, Christian Popp, Wolf Reik, Sergio Roman-Roman, Philip Rosenstiel, Joachim L. Schultze, Oliver Stegle, Amos Tanay, Giuseppe Testa, Dimitris Thanos, Fabian J. Theis, Maria-Elena Torres-Padilla, Alfonso Valencia, Céline Vallot, Alexander van Oudenaarden, Marie Vidal, Thierry Voet & LifeTime Community Working Groups, et al. Nature | 2020 [All authors] »

LifeTime and improving European healthcare through cell-based interceptive medicine

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

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Publication category: Cancer Immunotherapy , Technology

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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., et al. Cell | 2020 [All authors] »

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

Cancer-associated fibroblast compositions change with breast cancer progression linking the ratio of S100A4(+) and PDPN+ CAFs to clinical outcome

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Publication category: Cancer Immunotherapy

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Authors: Friedman G. Levi-Galibov O., David E., Bornstein C., Giladi A., Dadiani M., Mayo A., Halperin C., Pevsner-Fischer M., Lavon H., Mayer S., Nevo R., Stein Y., Balint-Lahat N., Barshack I., Ali H. R., Caldas C., Nili-Gal-Yam E., Alon U., Amit I. & Scherz-Shouval R., et al. Nature Cancer | 2020 [All authors] »

Cancer-associated fibroblast compositions change with breast cancer progression linking the ratio of S100A4(+) and PDPN+ CAFs to clinical outcome

Single-cell transcriptomics reveals regulators underlying immune cell diversity and immune subtypes associated with prognosis in nasopharyngeal carcinoma

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Publication category: Cancer Immunotherapy

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Authors: Chen Y. Yin J., Li W., Li H., Chen D., Zhang C., Lv J., Wang Y., Li X., Li J., Zhang P., Li Y., He Q., Yang X., Lei Y., Tang L., Zhou G., Mao Y., Wei C., Xiong K., Zhang H., Zhu S., Hou Y., Sun Y., Dean M., Amit I., Wu K., Kuang D., Li G., Liu N. & Ma J., et al. Cell Research | 2020 [All authors] »

Single-cell transcriptomics reveals regulators underlying immune cell diversity and immune subtypes associated with prognosis in nasopharyngeal carcinoma

Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19

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Publication category: Development

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Authors: Liao M. Liu Y., Yuan J., Wen Y., Xu G., Zhao J., Cheng L., Li J., Wang X., Wang F., Liu L., Amit I., Zhang S. & Zhang Z., et al. Nature Medicine | 2020 [All authors] »

Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19

The Physiology, Pathology, and Potential Therapeutic Applications of the TREM2 Signaling Pathway

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Publication category: Brain

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Authors: Deczkowska A. Weiner A. & Amit I., et al. Cell | 2020 [All authors] »

The Physiology, Pathology, and Potential Therapeutic Applications of the TREM2 Signaling Pathway

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

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Publication category: Technology

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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., et al. Cell | 2020 [All authors] »

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

Cxcl10(+) monocytes define a pathogenic subset in the central nervous system during autoimmune neuroinflammation

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Publication category: Brain

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Authors: Giladi A. Wagner L. K., Li H., Doerr D., Medaglia C., Paul F., Shemer A., Jung S., Yona S., Mack M., Leutz A., Amit I. & Mildner A., et al. Nature Immunology | 2020 [All authors] »

Cxcl10(+) monocytes define a pathogenic subset in the central nervous system during autoimmune neuroinflammation

Maternal Type-I interferon signaling adversely affects the microglia and the behavior of the offspring accompanied by increased sensitivity to stress

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Publication category: Development , Brain

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Authors: Ben-Yehuda H. Matcovitch-Natan O., Kertser A., Spinrad A., Prinz M., Amit I. & Schwartz M., et al. Molecular Psychiatry | 2020 [All authors] »

Maternal Type-I interferon signaling adversely affects the microglia and the behavior of the offspring accompanied by increased sensitivity to stress

C/EBP beta-Dependent Epigenetic Memory Induces Trained Immunity in Hematopoietic Stem Cells

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Publication category: Development

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Authors: de Laval B. Maurizio J., Kandalla P. K., Brisou G., Simonnet L., Huber C., Gimenez G., Matcovitch-Natan O., Reinhardt S., David E., Mildner A., Leutz A., Nadel B., Bordi C., Amit I., Sarrazin S. & Sieweke M. H., et al. Cell Stem Cell | 2020 [All authors] »

C/EBP beta-Dependent Epigenetic Memory Induces Trained Immunity in Hematopoietic Stem Cells

Lgr5+telocytes are a signaling source at the intestinal villus tip

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Publication category: Development

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Authors: Bahar Halpern K. Massalha H., Zwick R. K., Moor A. E., Castillo-Azofeifa D., Rozenberg M., Farack L., Egozi A., Miller D. R., Averbukh I., Harnik Y., Weinberg-Corem N., de Sauvage F. J., Amit I., Klein O. D., Shoshkes-Carmel M. & Itzkovitz S., et al. Nature Communications | 2020 [All authors] »

Lgr5+telocytes are a signaling source at the intestinal villus tip

Dissecting cellular crosstalk by sequencing physically interacting cells

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Publication category: Technology

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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., et al. Nature Biotechnology | 2020 [All authors] »

Dissecting cellular crosstalk by sequencing physically interacting cells

Bystander IFN-gamma activity promotes widespread and sustained cytokine signaling altering the tumor microenvironment

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Publication category: Cancer Immunotherapy

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Authors: Thibaut R. Bost P., Milo I., Cazaux M., Lemaitre F., Garcia Z., Amit I., Breart B., Cornuot C., Schwikowski B. & Bousso P., et al. Nature Cancer | 2020 [All authors] »

Bystander IFN-gamma activity promotes widespread and sustained cytokine signaling altering the tumor microenvironment

Single-cell genomic approaches for developing the next generation of immunotherapies

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Publication category: Cancer Immunotherapy

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Authors: Yofe I., Dahan R. & Amit I. Nature Medicine | 2020 [All authors] »

Single-cell genomic approaches for developing the next generation of immunotherapies

Spatiotemporal regulation of type I interferon expression determines the antiviral polarization of CD4(+) T cells

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Publication category: Development

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Authors: De Giovanni M. Cutillo V., Giladi A., Sala E., Maganuco C. G., Medaglia C., Di Lucia P., Bono E., Cristofani C., Consolo E., Giustini L., Fiore A., Eickhoff S., Kastenmueller W., Amit I., Kuka M. & Iannacone M., et al. Nature Immunology | 2020 [All authors] »

Spatiotemporal regulation of type I interferon expression determines the antiviral polarization of CD4(+) T cells

2019

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

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Publication category: Brain

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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., et al. Cell | 2019 [All authors] »

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

ETS Proteins Bind with Glucocorticoid Receptors: Relevance for Treatment of Ewing Sarcoma

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Publication category: Cancer Immunotherapy

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Authors: Srivastava S. Nataraj N. B., Sekar A., Ghosh S., Bornstein C., Drago-Garcia D., Roth L., Romaniello D., Marrocco I., David E., Gilad Y., Lauriola M., Rotkopf R., Kimchi A., Haga Y., Tsutsumi Y., Mirabeau O., Surdez D., Zinovyev A., Delattre O., Kovar H., Amit I. & Yarden Y., et al. Cell Reports | 2019 [All authors] »

ETS Proteins Bind with Glucocorticoid Receptors: Relevance for Treatment of Ewing Sarcoma

Embrace the fat when getting old

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Publication category: Metabolism

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Authors: Adlung L. Amit I. & Elinav E., et al. AGING-US | 2019 [All authors] »

Embrace the fat when getting old

Deletion of a Csf1r enhancer selectively impacts CSF1R expression and development of tissue macrophage populations

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Publication category: Development

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Authors: Rojo R. Raper A., Ozdemir D. D., Lefevre L., Grabert K., Wollscheid-Lengeling E., Bradford B., Caruso M., Gazova I., Sanchez A., Lisowski Z. M., Alves J., Molina-Gonzalez I., Davtyan H., Lodge R. J., Glover J. D., Wallace R., Munro D. A. D., David E., Amit I., Miron V. E., Priller J., Jenkins S. J., Hardingham G. E., Blurton-Jones M., Mabbott N. A., Summers K. M., Hohenstein P., Hume D. A. & Pridans C., et al. Nature Communications | 2019 [All authors] »

Deletion of a Csf1r enhancer selectively impacts CSF1R expression and development of tissue macrophage populations

Plasmacytoid dendritic cells develop from Ly6D(+) lymphoid progenitors distinct from the myeloid lineage

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Publication category: Development

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Authors: Dress R. J. Dutertre C., Giladi A., Schlitzer A., Low I., Shadan N. B., Tay A., Lum J., Kairi M. F. B. M., Hwang Y. Y., Becht E., Cheng Y., Chevrier M., Larbi A., Newell E. W., Amit I., Chen J. & Ginhoux F., et al. Nature Immunology | 2019 [All authors] »

Plasmacytoid dendritic cells develop from Ly6D(+) lymphoid progenitors distinct from the myeloid lineage

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

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Publication category: Metabolism

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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., et al. Cell | 2019 [All authors] »

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

A niche-dependent myeloid transcriptome signature defines dormant myeloma cells

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Publication category: Cancer Immunotherapy

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Authors: Khoo W. H. Ledergor G., Weiner A., Roden D. L., Terry R. L., McDonald M. M., Chai R. C., De Veirman K., Owen K. L., Opperman K. S., Vandyke K., Clark J. R., Seckinger A., Kovacic N., Nguyen A., Mohanty S. T., Pettitt J. A., Xiao Y., Corr A. P., Seeliger C., Novotny M., Lasken R. S., Nguyen T., Oyajobi B. O., Aftab D., Swarbrick A., Parker B., Hewett D. R., Hose D., Vanderkerken K., Zannettino A. C. W., Amit I., Phan T. G. & Croucher P., et al. Blood | 2019 [All authors] »

A niche-dependent myeloid transcriptome signature defines dormant myeloma cells

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

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Publication category: Technology

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Authors: Keren-Shaul H. Kenigsberg E., Jaitin D. A., David E., Paul F., Tanay A. & Amit I., et al. Nature Protocols | 2019 [All authors] »

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

Corticosteroid signaling at the brain-immune interface impedes coping with severe psychological stress

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Publication category: Brain

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Authors: Kertser A. Baruch K., Deczkowska A., Weiner A., Croese T., Kenigsbuch M., Cooper I., Tsoory M., Ben-Hamo S., Amit I. & Schwartz M., et al. Science Advances | 2019 [All authors] »

Corticosteroid signaling at the brain-immune interface impedes coping with severe psychological stress

Cell composition analysis of bulk genomics using single-cell data

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Publication category: Technology

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Authors: Frishberg A. Peshes-Yaloz N., Cohn O., Rosentul D., Steuerman Y., Valadarsky L., Yankovitz G., Mandelboim M., Iraqi F. A., Amit I., Mayo L., Bacharach E. & Gat-Viks I., et al. Nature Methods | 2019 [All authors] »

Cell composition analysis of bulk genomics using single-cell data

DC Respond to Cognate T Cell Interaction in the Antigen-Challenged Lymph Node

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Publication category: Development

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Authors: Curato C. Bernshtein B., Zupancic E., Dufner A., Jaitin D., Giladi A., David E., Chappell-Maor L., Leshkowitz D., Knobeloch K., Amit I., Florindo H. F. & Jung S., et al. Frontiers in Immunology | 2019 [All authors] »

DC Respond to Cognate T Cell Interaction in the Antigen-Challenged Lymph Node

Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment within Human Melanoma

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Publication category: Cancer Immunotherapy

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Authors: Li H., van der Leun A. M., Yofe I., Lubling Y. Gelbard-Solodkin D., van Akkooi A. C. J., van den Braber M., Rozeman E. A., Haanen J. B. A. G., Blank C. U., Horlings H. M., David E., Baran Y., Bercovich A., Lifshitz A., Schumacher T. N., Tanay A. & Amit I., et al. Cell | 2019 [All authors] »

Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment within Human Melanoma

Deterministic Somatic Cell Reprogramming Involves Continuous Transcriptional Changes Governed by Myc and Epigenetic-Driven Modules

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Publication category: Development

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Authors: Zviran A. Mor N., Rais Y., Gingold H., Peles S., Chomsky E., Viukov S., Buenrostro J. D., Scognamiglio R., Weinberger L., Manor Y. S., Krupalnik V., Zerbib M., Hezroni H., Jaitin D. A., Larastiaso D., Gilad S., Benjamin S., Gafni O., Mousa A., Ayyash M., Sheban D., Bayerl J., Aguilera-Castrejon A., Massarwa R., Maza I., Hanna S., Stelzer Y., Ulitsky I., Greenleaf W. J., Tanay A., Trumpp A., Amit I., Pilpel Y., Novershtern N. & Hanna J. H., et al. Cell Stem Cell | 2019 [All authors] »

Deterministic Somatic Cell Reprogramming Involves Continuous Transcriptional Changes Governed by Myc and Epigenetic-Driven Modules

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

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Publication category: Development , Technology

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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., et al. Cell Systems | 2019 [All authors] »

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

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

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Publication category: Brain

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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., et al. Nature Communications | 2019 [All authors] »

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

2018

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

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Publication category: Cancer Immunotherapy

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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., et al. Nature Medicine | 2018 [All authors] »

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

Impaired immune surveillance accelerates accumulation of senescent cells and aging

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Publication category: Metabolism

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Authors: Ovadya Y., Landsberger T. Leins H., Vadai E., Gal H., Biran A., Yosef R., Sagiv A., Agrawal A., Shapira A., Windheim J., Tsoory M., Schirmbeck R., Amit I., Geiger H. & Krizhanovsky V., et al. Nature Communications | 2018 [All authors] »

Impaired immune surveillance accelerates accumulation of senescent cells and aging

Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting

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Publication category: Development

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Authors: Cohen M., Giladi A., Gorki A. Galbard Solodkin D., Zada M., Hladik A., Miklosi A., Salame T., Halpern K. B., David E., Itzkovitz S., Harkany T., Knapp S. & Amit I., et al. Cell | 2018 [All authors] »

Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting

From the Human Cell Atlas to dynamic immune maps in human disease

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Publication category: Technology

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Authors: Adlung L. & Amit I. Nature Reviews Immunology | 2018 [All authors] »

From the Human Cell Atlas to dynamic immune maps in human disease

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

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Publication category: Development

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Authors: Alyagor I., Berkun V. Keren-Shaul H., Marmor-Kollet N., David E., Mayseless O., Issman-Zecharya N., Amit I. & Schuldiner O., et al. Developmental Cell | 2018 [All authors] »

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

Paired-cell sequencing enables spatial gene expression mapping of liver endothelial cells

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Publication category: Metabolism , Technology

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Authors: Halpern K. B. Shenhav R., Massalha H., Toth B., Egozi A., Massasa E. E., Medgalia C., David E., Giladi A., Moor A. E., Porat Z., Amit I. & Itzkovitz S., et al. Nature Biotechnology | 2018 [All authors] »

Paired-cell sequencing enables spatial gene expression mapping of liver endothelial cells

Early metazoan cell type diversity and the evolution of multicellular gene regulation

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Publication category: Development

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Authors: Sebe-Pedros A. Chomsky E., Pang K., Lara-Astiaso D., Gaiti F., Mukamel Z., Amit I., Hejnol A., Degnan B. M. & Tanay A., et al. Nature ecology & evolution | 2018 [All authors] »

Early metazoan cell type diversity and the evolution of multicellular gene regulation

Single-cell characterization of haematopoietic progenitors and their trajectories in homeostasis and perturbed haematopoiesis

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Publication category: Development

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Authors: Giladi A., Paul F. Herzog Y., Lubling Y., Weiner A., Yofe I., Jaitin D., Cabezas-Wallscheid N., Dress R., Ginhoux F., Trumpp A., Tanay A. & Amit I., et al. Nature Cell Biology | 2018 [All authors] »

Single-cell characterization of haematopoietic progenitors and their trajectories in homeostasis and perturbed haematopoiesis

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

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Publication category: Development

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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., et al. European Journal of Immunology | 2018 [All authors] »

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

Single-cell mapping of the thymic stroma identifies IL-25-producing tuft epithelial cells

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Publication category: Development

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Authors: Bornstein C., Nevo S., Giladi A. Kadouri N., Pouzolles M., Gerbe F., David E., Machado A., Chuprin A., Toth B., Goldberg O., Itzkovitz S., Taylor N., Jay P., Zimmermann V. S., Abramson J. & Amit I., et al. Nature | 2018 [All authors] »

Single-cell mapping of the thymic stroma identifies IL-25-producing tuft epithelial cells

Differences in Cell Cycle Status Underlie Transcriptional Heterogeneity in the HSC Compartment

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Publication category: Development

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Authors: Lauridsen F. K. B. Jensen T. L., Rapin N., Aslan D., Wilhelmson A. S., Pundhir S., Rehn M., Paul F., Giladi A., Hasemann M. S., Serup P., Amit I. & Porse B. T., et al. Cell Reports | 2018 [All authors] »

Differences in Cell Cycle Status Underlie Transcriptional Heterogeneity in the HSC Compartment

Dissection of Influenza Infection In Vivo by Single-Cell RNA Sequencing

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Publication category: Technology

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Authors: Steuerman Y., Cohen M. Peshes-Yaloz N., Valadarsky L., Cohn O., David E., Frishberg A., Mayo L., Bacharach E., Amit I. & Gat-Viks I., et al. Cell Systems | 2018 [All authors] »

Dissection of Influenza Infection In Vivo by Single-Cell RNA Sequencing

Trained Memory of Human Uterine NK Cells Enhances Their Function in Subsequent Pregnancies

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Publication category: Development

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Authors: Gamliel M. Goldman-Wohl D., Isaacson B., Gur C., Stein N., Yamin R., Berger M., Grunewald M., Keshet E., Rais Y., Bornstein C., David E., Jelinski A., Eisenberg I., Greenfield C., Ben-David A., Imbar T., Gilad R., Haimov-Kochman R., Mankuta D., Elami-Suzin M., Amit I., Hanna J. H., Yagel S. & Mandelboim O., et al. Immunity | 2018 [All authors] »

Trained Memory of Human Uterine NK Cells Enhances Their Function in Subsequent Pregnancies

Disease-Associated Microglia: A Universal Immune Sensor of Neurodegeneration

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Publication category: Brain

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Authors: Deczkowska A., Keren-Shaul H., Weiner A. Colonna M., Schwartz M. & Amit I., et al. Cell | 2018 [All authors] »

Disease-Associated Microglia: A Universal Immune Sensor of Neurodegeneration

Microglial immune checkpoint mechanisms

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Publication category: Brain

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Authors: Deczkowska A., Amit I. & Schwartz M. Nature Neuroscience | 2018 [All authors] »

Microglial immune checkpoint mechanisms

Salient experiences are represented by unique transcriptional signatures in the mouse brain

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Publication category: Brain

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Authors: Mukherjee D. Ignatowska-Jankowska B. M., Itskovits E., Gonzales B. J., Turm H., Izakson L., Haritan D., Bleistein N., Cohen C., Amit I., Shay T., Grueter B., Zaslaver A. & Citri A., et al. eLife | 2018 [All authors] »

Salient experiences are represented by unique transcriptional signatures in the mouse brain

A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies

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Publication category: Cancer Immunotherapy

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Authors: Bahr C. von Paleske L., Slu V. V. U., Emeseiro S. R., Takayama N., Ng S. W., Murison A., Langenfeld K., Petretich M., Scognamiglio R., Zeisberger P., Benk A. S., Amit I., Zandstra P. W., Lupien M., Dick J. E., Trumpp A. & Spitz F., et al. Nature | 2018 [All authors] »

A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies

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

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Publication category: Development , Brain

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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., et al. Cell | 2018 [All authors] »

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

Single-Cell Genomics: A Stepping Stone for Future Immunology Discoveries

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Publication category: Technology

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Authors: Giladi A. & Amit I. Cell | 2018 [All authors] »

Single-Cell Genomics: A Stepping Stone for Future Immunology Discoveries

2017

Spatial reconstruction of immune niches by combining photoactivatable reporters and scRNA-seq

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Publication category: Technology

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Authors: Medaglia C., Giladi A., Stoler-Barak L. De Giovanni M., Salame T. M., Biram A., David E., Li H., Iannacone M., Shulman Z. & Amit I., et al. Science | 2017 [All authors] »

Spatial reconstruction of immune niches by combining photoactivatable reporters and scRNA-seq

Science Forum: The Human Cell Atlas

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Publication category: Development

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Authors: Regev A., Teichmann S. A., Lander E. S., Amt I. Benoist C., Birney E., Bodenmiller B., Campbell P., Carninci P., Clatworthy M., Clevers H., Deplancke B., Dunham I., Eberwine J., Elis R., Enard W., Farmer A., Fugger L., Gottgens B., Hacohen N., Haniffa M., Hemberg M., Kim S., Klenerman P., Kriegstein A., Lein E. D., Linnarsson S., Lundberg E., Lundeberg J., Majumder P., Marioni J. C., Merad M., Mhlanga M., Nawijin M., Netea M., Nolan G., Pe'er D., Phillipakis A., Ponting C. P., Quake S., Reik W., Rozenblatt-Rosen O., Sanes J., Satija R., Schumacher T. N., Shalek A., Shapiro E., Sharma P., Shin J. W., Stegle O. & , et al. eLife | 2017 [All authors] »

Science Forum: The Human Cell Atlas

Mef2C restrains microglial inflammatory response and is lost in brain ageing in an IFN-I-dependent manner

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Publication category: Brain

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Authors: Deczkowska A., Matcovitch-Natan O. Tsitsou-Kampeli A., Ben-Hamo S., Dvir-Szternfeld R., Spinrad A., Singer O., David E., Winter D. R., Smith L. K., Kertser A., Baruch K., Rosenzweig N., Terem A., Prinz M., Villeda S., Citri A., Amit I. & Schwartz M., et al. Nature Communications | 2017 [All authors] »

Mef2C restrains microglial inflammatory response and is lost in brain ageing in an IFN-I-dependent manner

Immunology, one cell at a time

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Publication category: Technology

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Authors: Giladi A. & Amit I. Nature | 2017 [All authors] »

Immunology, one cell at a time

MicroRNA-142 controls thymocyte proliferation

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Publication category: Development , Autoimmunity

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Authors: Mildner A. Chapnik E., Varol D., Aychek T., Lampl N., Rivkin N., Bringmann A., Paul F., Boura-Halfon S., Hayoun Y. S., Barnett Itzhaki I. Z., Amit I., Hornstein E. & Jung S., et al. European Journal of Immunology | 2017 [All authors] »

MicroRNA-142 controls thymocyte proliferation

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

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Publication category: Brain

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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., et al. Cell | 2017 [All authors] »

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

Dicer Deficiency Differentially Impacts Microglia of the Developing and Adult Brain

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Publication category: Development , Brain

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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., et al. Immunity | 2017 [All authors] »

Dicer Deficiency Differentially Impacts Microglia of the Developing and Adult Brain

Innate Immune Landscape in Early Lung Adenocarcinoma by Paired Single-Cell Analyses

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Publication category: Cancer Immunotherapy

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Authors: Lavin Y. Kobayashi S., Leader A., Amir E. D., Elefant N., Bigenwald C., Remark R., Sweeney R., Becker C. D., Levine J. H., Meinhof K., Chow A., Kim-Shulze S., Wolf A., Medaglia C., Li H., Rytlewski J. A., Emerson R. O., Solovyov A., Greenbaum B. D., Sanders C., Vignali M., Beasley M. B., Flores R., Gnjatic S., Pe'er D., Rahman A., Amit I. & Merad M., et al. Cell | 2017 [All authors] »

Innate Immune Landscape in Early Lung Adenocarcinoma by Paired Single-Cell Analyses

Genomic Characterization of Murine Monocytes Reveals C/EBP beta Transcription Factor Dependence of Ly6C(-) Cells

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Publication category: Development

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Authors: Mildner A. Schoenheit J., Giladi A., David E., Lara Astiaso A. D., Lorenzo Vivas V. E., Paul F., Chappell-Maor L., Priller J., Leutz A., Amit I. & Jung S., et al. Immunity | 2017 [All authors] »

Genomic Characterization of Murine Monocytes Reveals C/EBP beta Transcription Factor Dependence of Ly6C(-) Cells

Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression

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Publication category: Cancer Immunotherapy

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Authors: Fiziev P. Akdemir K. C., Miller J. P., Keung E. Z., Samant N. S., Sharma S., Natale C. A., Terranova C. J., Maitituoheti M., Amin S. B., Martinez-Ledesma E., Dhamdhere M., Axelrad J. B., Shah A., Cheng C. S., Mahadeshwar H., Seth S., Barton M. C., Protopopov A., Tsai K. Y., Davies M. A., Garcia B. A., Amit I., Chin L., Ernst J. & Rai K., et al. Cell Reports | 2017 [All authors] »

Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression

Single-cell transcriptome conservation in cryopreserved cells and tissues

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Publication category: Technology

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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., et al. GENOME BIOLOGY | 2017 [All authors] »

Single-cell transcriptome conservation in cryopreserved cells and tissues

Systemic Human ILC Precursors Provide a Substrate for Tissue ILC Differentiation

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Publication category: Development

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Authors: Lim A. I. Li Y., Lopez-Lastra S., Stadhouders R., Paul F., Casrouge A., Serafini N., Puel A., Bustamante J., Surace L., Masse-Ranson G., David E., Strick-Marchand H., Le Bourhis B. L., Cocchi R., Topazio D., Graziano P., Muscarella L. A., Rogge L., Norel X., Sallenave J., Allez M., Graf T., Hendriks R. W., Casanova J., Amit I., Yssel H. & Di Santo S. J. P., et al. Cell | 2017 [All authors] »

Systemic Human ILC Precursors Provide a Substrate for Tissue ILC Differentiation

Single-cell spatial reconstruction reveals global division of labour in the mammalian liver

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Publication category: Metabolism , Technology

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Authors: Halpern K. B., Shenhav R. Matcovitch-Natan O., Toth B., Lemze D., Golan M., Massasa E. E., Baydatch S., Landen S., Moor A. E., Brandis A., Giladi A., Stokar-Avihail A., David E., Amit I. & Itzkovitz S., et al. Nature | 2017 [All authors] »

Single-cell spatial reconstruction reveals global division of labour in the mammalian liver

Transcriptional programs that control expression of the autoimmune regulator gene Aire

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Publication category: Development

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Authors: Herzig Y. Nevo S., Bornstein C., Brezis M. R., Ben-Hur S., Shkedy A., Eisenberg-Bord M., Levi B., Delacher M., Goldfarb Y., David E., Weinberger L., Viukov S., Ben-Dor S., Giraud M., Hanna J. H., Breiling A., Lyko F., Amit I., Feuerer M. & Abramson J., et al. Nature Immunology | 2017 [All authors] »

Transcriptional programs that control expression of the autoimmune regulator gene Aire

Autonomous TNF is critical for in vivo monocyte survival in steady state and inflammation

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Publication category: Development

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Authors: Wolf Y. Shemer A., Polonsky M., Gross-Vered M., Mildner A., Yona S., David E., Kim K., Goldmann T., Amit I., Heikenwalder M., Nedospasov S., Prinz M., Friedman N. & Jung S., et al. Journal of Experimental Medicine | 2017 [All authors] »

Autonomous TNF is critical for in vivo monocyte survival in steady state and inflammation

CD74 is a novel transcription regulator

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Publication category: Development

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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., et al. Proceedings of the National Academy of Sciences of the United States of America | 2017 [All authors] »

CD74 is a novel transcription regulator

2016

Microbiota Diumal Rhythmicity Programs Host Transcriptome Oscillations

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Publication category: Metabolism

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Authors: Thaiss C., Levy M. Korem T., Dohnalova L., Shapiro H., Jaitin D., David E., Winter D., Gury-BenAri M., Tatirovsky E., Tuganbaev T., Federici S., Zmora N., Zeevi D., Dori-Bachash M., Pevsner-Fischer M., Kartvelishvily E., Brandis A., Harmelin A., Shibolet O., Halpern Z., Honda K., Amit I., Segal E. & Elinav E., et al. Cell | 2016 [All authors] »

Microbiota Diumal Rhythmicity Programs Host Transcriptome Oscillations

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

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Publication category: Technology

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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., et al. Cell | 2016 [All authors] »

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

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

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Publication category: Development

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Authors: Talmi-Frank D. Altboum Z., Solomonov I., Ziv T., Amit I. & Sagi I., et al. Cell Host & Microbe | 2016 [All authors] »

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

Distinct biological events generated by ECM proteolysis by two homologous collagenases

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Publication category: Development

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Authors: Solomonov I. Zehorai E., Talmi-Frank D., Wolf S. G., Shainskaya A., Zhuravlev A., Kartvelishvily E., Visse R., Levin Y., Kampf N., Jaitin D. A., David E., Amit I., Nagase H. & Sagi I., et al. Proceedings of the National Academy of Sciences of the United States of America | 2016 [All authors] »

Distinct biological events generated by ECM proteolysis by two homologous collagenases

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

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Publication category: Metabolism

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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., et al. Cell | 2016 [All authors] »

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

Co-ChIP enables genome-wide mapping of histone mark co-occurrence at single-molecule resolution.

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Publication category: Technology

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Authors: Weiner A., Lara Astiaso A. D. Krupalnik V., Gafni O., David E., Winter D. R., Hanna J. H. & Amit I., et al. Nature Biotechnology | 2016 [All authors] »

Co-ChIP enables genome-wide mapping of histone mark co-occurrence at single-molecule resolution.

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

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Publication category: Development

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Authors: Barzilai S., Blecher-Gonen R. Barnett Itzhaki Z., Zauberman A., Lebel-Haziv Y., Amit I. & Alon R., et al. Journal of Leukocyte Biology | 2016 [All authors] »

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

Microglia development follows a stepwise program to regulate brain homeostasis.

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Publication category: Development , Brain

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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., et al. Science (New York, N.Y.) | 2016 [All authors] »

Microglia development follows a stepwise program to regulate brain homeostasis.

Voices Of Biotech

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Publication category: Technology

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Authors: Amit I. Baker D., Barker R., Berger B., Bertozzi C., Bhatia S., Biffi A., Demichelis F., Doudna J., Dowdy S. F., Endy D., Helmstaedter M., Junca H., June C., Kamb S., Khvorova A., Kim D., Kim J., Krishnan Y., Lakadamyali M., Lappalainen T., Lewin S., Liao J., Loman N., Lundberg E., Lynd L., Martin C., Mellman I., Miyawaki A., Mummery C., Nelson K., Paz J., Peralta-Yahya P., Picotti P., Polyak K., Prather K., Qin J., Quake S., Regev A., Rogers J. A., Shetty R., Sommer M., Stevens M., Stolovitzky G., Takahashi M., Tang F., Teichmann S., Torres-Padilla M., Tripathi L., Vemula P., Verdine G., Vollmer F., Wang J., Ying J. Y., Zhang F. & Zhang T., et al. Nature Biotechnology | 2016 [All authors] »

Voices Of Biotech

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

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Publication category: Technology

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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., et al. Nature Immunology | 2016 [All authors] »

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

PD-1 immune checkpoint blockade reduces pathology and improves memory in mouse models of Alzheimer's disease

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Publication category: Brain

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Authors: Baruch K. Deczkowska A., Rosenzweig N., Tsitsou-Kampeli A., Sharif A. M., Matcovitch-Natan O., Kertser A., David E., Amit I. & Schwartz M., et al. Nature Medicine | 2016 [All authors] »

PD-1 immune checkpoint blockade reduces pathology and improves memory in mouse models of Alzheimer's disease

The role of the local environment and epigenetics in shaping macrophage identity and their effect on tissue homeostasis

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Publication category: Development

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Authors: Amit I., Winter D. R. & Jung S. Nature Immunology | 2016 [All authors] »

The role of the local environment and epigenetics in shaping macrophage identity and their effect on tissue homeostasis

2015

Microbiota-Modulated Metabolites Shape the Intestinal Microenvironment by Regulating NLRP6 Inflammasome Signaling.

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Publication category: Metabolism

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Authors: Levy M., Thaiss C. A. Zeevi D., Dohnalova L., Zilberman-Schapira G., Mahdi J. A., David E., Savidor A., Korem T., Herzig Y., Pevsner-Fischer M., Shapiro H., Christ A., Harmelin A., Halpern Z., Latz E., Flavell R. A., Amit I., Segal E. & Elinav E., et al. Cell | 2015 [All authors] »

Microbiota-Modulated Metabolites Shape the Intestinal Microenvironment by Regulating NLRP6 Inflammasome Signaling.

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

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Publication category: Development , Technology

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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., et al. Cell | 2015 [All authors] »

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

From mass cytometry to cancer prognosis

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Publication category: Cancer Immunotherapy , Technology

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Authors: Winter D. R., Ledergor G. & Amit I. Nature Biotechnology | 2015 [All authors] »

From mass cytometry to cancer prognosis

Making the case for chromatin profiling: a new tool to investigate the immune-regulatory landscape

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Publication category: Development , Technology

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Authors: Winter D. R., Jung S. & Amit I. Nature Reviews Immunology | 2015 [All authors] »

Making the case for chromatin profiling: a new tool to investigate the immune-regulatory landscape

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

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Publication category: Development

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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., et al. Immunity | 2015 [All authors] »

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

DCs are ready to commit

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Publication category: Development

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Authors: Winter D. & Amit I. Nature Immunology | 2015 [All authors] »

DCs are ready to commit

Derivation of novel human ground state naive pluripotent stem cells (vol 504, pg 282, 2013)

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Publication category: Development

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Authors: Gafni O., Weinberger L., Mansour A. A. Manor Y. S., Chomsky E., Ben-Yosef D., Kalma Y., Viukov S., Maza I., Zviran A., Rais Y., Shipony Z., Mukamel Z., Krupalnik V., Zerbib M., Geula S., Caspi I., Schneir D., Shwartz T., Gilad S., Amann-Zalcenstein D., Benjamin S., Amit I., Tanay A., Massarwa R., Novershtern N. & Hanna J. H., et al. Nature | 2015 [All authors] »

Derivation of novel human ground state naive pluripotent stem cells (vol 504, pg 282, 2013)

Simultaneous measurement of genome-wide transcription elongation speeds and rates of RNA polymerase II transition into active elongation with 4sUDRB-seq

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Publication category: Technology

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Authors: Fuchs G. Voichek Y., Rabani M., Benjamin S., Gilad S., Amit I. & Oren M., et al. Nature Protocols | 2015 [All authors] »

Simultaneous measurement of genome-wide transcription elongation speeds and rates of RNA polymerase II transition into active elongation with 4sUDRB-seq

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

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Publication category: Development

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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., et al. Nature | 2015 [All authors] »

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

High-Resolution Chromatin Dynamics during a Yeast Stress Response

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Publication category: Technology

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Authors: Weiner A., Hsieh T. S., Appleboim A. Chen H. V., Rahat A., Amit I., Rando O. J. & Friedman N., et al. Molecular Cell | 2015 [All authors] »

High-Resolution Chromatin Dynamics during a Yeast Stress Response

Transcription factor binding dynamics during human ES cell differentiation

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Publication category: Development

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Authors: Tsankov A. M. Gu H., Akopian V., Ziller M. J., Donaghey J., Amit I., Gnirke A. & Meissner A., et al. Nature | 2015 [All authors] »

Transcription factor binding dynamics during human ES cell differentiation

m(6)A mRNA methylation facilitates resolution of naive pluripotency toward differentiation

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Publication category: Development , Technology

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Authors: Geula S., Moshitch-Moshkovitz S., Dominissini D. Mansour A. A., Kol N., Salmon-Divon M., Hershkovitz V., Peer E., Mor N., Manor Y. S., Ben-Haim M., Eyal E., Yunger S., Pinto Y., Jaitin D. A., Viukov S., Rais Y., Krupalnik V., Chomsky E., Zerbib M., Maza I., Rechavi Y., Massarwa R., Hanna S., Amit I., Levanon E. Y., Amariglio N., Stern-Ginossar N., Novershtern N., Rechavi G. & Hanna J. H., et al. Science | 2015 [All authors] »

m(6)A mRNA methylation facilitates resolution of naive pluripotency toward differentiation

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

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Publication category: Technology

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Authors: Jaitin D. A., Keren-Shaul H., Elefant N. & Amit I. Seminars in Immunology | 2015 [All authors] »

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

2014

A Negative Feedback Loop of Transcription Factors Specifies Alternative Dendritic Cell Chromatin States

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Publication category: Development

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Authors: Bornstein C., Winter D. Barnett Itzhaki I. Z., David E., Kadri S., Garber M. & Amit I., et al. Molecular Cell | 2014 [All authors] »

A Negative Feedback Loop of Transcription Factors Specifies Alternative Dendritic Cell Chromatin States

Chronic exposure to TGF beta 1 regulates myeloid cell inflammatory response in an IRF7-dependent manner

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Publication category: Development , Brain

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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., et al. EMBO Journal | 2014 [All authors] »

Chronic exposure to TGF beta 1 regulates myeloid cell inflammatory response in an IRF7-dependent manner

Tissue-Resident Macrophage Enhancer Landscapes Are Shaped by the Local Microenvironment

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Publication category: Development

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Authors: Lavin Y., Winter D. Blecher-Gonen R., David E., Keren-Shaul H., Merad M., Jung S. & Amit I., et al. Cell | 2014 [All authors] »

Tissue-Resident Macrophage Enhancer Landscapes Are Shaped by the Local Microenvironment

High-Resolution Sequencing and Modeling Identifies Distinct Dynamic RNA Regulatory Strategies

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Publication category: Technology

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Authors: Rabani M. Raychowdhury R., Jovanovic M., Rooney M., Stumpo D. J., Pauli A., Hacohen N., Schier A. F., Blackshear P. J., Friedman N., Amit I. & Regev A., et al. Cell | 2014 [All authors] »

High-Resolution Sequencing and Modeling Identifies Distinct Dynamic RNA Regulatory Strategies

Sequential Feedback Induction Stabilizes the Phosphate Starvation Response in Budding Yeast

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Publication category: Technology

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Authors: Vardi N. Levy S., Gurvich Y., Polacheck T., Carmi M., Jaitin D., Amit I. & Barkai N., et al. Cell Reports | 2014 [All authors] »

Sequential Feedback Induction Stabilizes the Phosphate Starvation Response in Budding Yeast

Plasticity in the transcriptional and epigenetic circuits regulating dendritic cell lineage specification and function

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Publication category: Development

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Authors: Paul F. & Amit I. Current Opinion in Immunology | 2014 [All authors] »

Plasticity in the transcriptional and epigenetic circuits regulating dendritic cell lineage specification and function

Aging-induced immunological signature of the brain's choroid plexus negatively regulates neurogenesis and cognitive function

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Publication category: Brain

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Authors: Deczkowska A., Baruch K. David E., Castellano J. M., Miller O., Kertser A., Berkutzki T., Barnett Itzhaki I. Z., Bezalel D., Wyss-coray T., Amit I. & Schwartz M., et al. Journal of Neuroimmunology | 2014 [All authors] »

Aging-induced immunological signature of the brain's choroid plexus negatively regulates neurogenesis and cognitive function

Aging-induced type I interferon response at the choroid plexus negatively affects brain function

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Publication category: Brain

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Authors: Baruch K., Deczkowska A. David E., Castellano J. M., Miller O., Kertser A., Berkutzki T., Barnett Itzhaki I. Z., Bezalel D., Wyss-Coray T., Amit I. & Schwartz M., et al. Science | 2014 [All authors] »

Aging-induced type I interferon response at the choroid plexus negatively affects brain function

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

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Publication category: Brain

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Authors: Orit Matcovitch; Merav Cohen; Eyal David; Zohar Barnettitzhaki; Hadas Keren-Shaul; Ronnie Blecher-gonen; Diego Adhemar Jaitin; Antonio Sica; Ido Amit; Michal Schwartz Journal of Neuroimmunology | 2014 [All authors] »

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

The role of chromatin dynamics in immune cell development

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Publication category: Development

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Authors: Winter D. R. & Amit I. Immunological Reviews | 2014 [All authors] »

The role of chromatin dynamics in immune cell development

Analysis of the transcriptional networks underpinning the activation of murine macrophages by inflammatory mediators

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Publication category: Development

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Authors: Raza S. Barnett M. W., Barnett Itzhaki I. Z., Amit I., Hume D. A. & Freeman T. C., et al. Journal of Leukocyte Biology | 2014 [All authors] »

Analysis of the transcriptional networks underpinning the activation of murine macrophages by inflammatory mediators

Chromatin state dynamics during blood formation

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Publication category: Development , Technology

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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., et al. Science | 2014 [All authors] »

Chromatin state dynamics during blood formation

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

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Publication category: Technology

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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., et al. Science | 2014 [All authors] »

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

Digital cell quantification identifies global immune cell dynamics during influenza infection

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Publication category: Development , Technology

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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., et al. Molecular Systems Biology | 2014 [All authors] »

Digital cell quantification identifies global immune cell dynamics during influenza infection

4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells

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Publication category: Technology

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Authors: Fuchs G., Voichek Y. Benjamin S., Gilad S., Amit I. & Oren M., et al. GENOME BIOLOGY | 2014 [All authors] »

4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells

2013

Derivation of novel human ground state naive pluripotent stem cells

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Publication category: Development

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Authors: Gafni O., Weinberger L., Mansour A. A. Manor Y. S., Chomsky E., Ben-Yosef D., Kalma Y., Viukov S., Maza I., Zviran A., Rais Y., Shipony Z., Mukamel Z., Krupalnik V., Zerbib M., Geula S., Caspi I., Schneir D., Shwartz T., Gilad S., Amann Zalcenstein D., Benjamin S., Amit I., Tanay A., Massarwa R., Novershtern N. & Hanna J. (., et al. Nature | 2013 [All authors] »

Derivation of novel human ground state naive pluripotent stem cells

Deterministic direct reprogramming of somatic cells to pluripotency

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Publication category: Development

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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. (., et al. Nature | 2013 [All authors] »

Deterministic direct reprogramming of somatic cells to pluripotency

Semiconductor-based DNA sequencing of histone modification states

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Publication category: Technology

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Authors: Cheng C. S. Rai K., Garber M., Hollinger A., Robbins D., Anderson S., Macbeth A., Tzou A., Carneiro M. O., Raychowdhury R., Russ C., Hacohen N., Gershenwald J. E., Lennon N., Nusbaum C., Chin L., Regev A. & Amit I., et al. Nature Communications | 2013 [All authors] »

Semiconductor-based DNA sequencing of histone modification states

Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli

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Publication category: Technology

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Authors: Gat-Viks I. Chevrier N., Wilentzik R., Eisenhaure T., Raychowdhury R., Steuerman Y., Shalek A. K., Hacohen N., Amit I. & Regev A., et al. Nature Biotechnology | 2013 [All authors] »

Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli

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

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Publication category: Technology

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Authors: Blecher-Gonen R. Barnett Itzhaki Z., Jaitin D., Amann Zalcenstein D., Lara Astiaso D. & Amit I., et al. Nature Protocols | 2013 [All authors] »

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

Mononuclear phagocyte miRNome analysis identifies miR-142 as critical regulator of murine dendritic cell homeostasis

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Publication category: Development

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Authors: Mildner A. Chapnik E., Manor O., Yona S., Kim K., Aychek T., Varol D., Beck G., Itzhaki Z. B., Feldmesser E., Amit I., Hornstein E. & Jung S., et al. Blood | 2013 [All authors] »

Mononuclear phagocyte miRNome analysis identifies miR-142 as critical regulator of murine dendritic cell homeostasis

2012

The H3K27 demethylase Utx regulates somatic and germ cell epigenetic reprogramming

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Publication category: Development

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Authors: Mansour A. A. Gafni O., Weinberger L., Zviran A., Ayyash M., Rais Y., Krupalnik V., Zerbib M., Amann Zalcenstein D., Maza I., Geula S., Viukov S., Holtzman L., Pribluda A., Canaani E., Horn-Saban S., Amit I., Novershtern N. & Hanna J. H., et al. Nature | 2012 [All authors] »

The H3K27 demethylase Utx regulates somatic and germ cell epigenetic reprogramming

Expression Noise and Acetylation Profiles Distinguish HDAC Functions

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Publication category: Technology

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Authors: Weinberger L., Voichek Y. Tirosh I., Hornung G., Amit I. & Barkai N., et al. Molecular Cell | 2012 [All authors] »

Expression Noise and Acetylation Profiles Distinguish HDAC Functions

EGR1 and the ERK-ERF axis drive mammary cell migration in response to EGF

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Publication category: Development

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Authors: Tarcic G. Avraham R., Pines G., Amit I., Shay T., Lu Y., Zwang Y., Katz M., Ben Chetrit C. N., Jacob-Hirsch J., Virgilio L., Rechavi G., Mavrothalassitis G., Mills G. B., Domany E. & Yarden Y., et al. FASEB Journal | 2012 [All authors] »

EGR1 and the ERK-ERF axis drive mammary cell migration in response to EGF

M(odu)LLating the Innate Response

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Publication category: Technology

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Authors: Blecher-Gonen R. & Amit I. Immunity | 2012 [All authors] »

M(odu)LLating the Innate Response

2011

Strategies to discover regulatory circuits of the mammalian immune system

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Publication category: Technology

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Authors: Amit I., Regev A. & Hacohen N. Nature Reviews Immunology | 2011 [All authors] »

Strategies to discover regulatory circuits of the mammalian immune system

2010

EGF Decreases the Abundance of MicroRNAs That Restrain Oncogenic Transcription Factors

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Publication category: Development

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Authors: Avraham R. Sas-Chen A., Manor O., Steinfeld I., Shalgi R., Tarcic G., Bossel N., Zeisel A., Amit I., Zwang Y., Enerly E., Russnes H. G., Biagioni F., Mottolese M., Strano S., Blandino G., Borresen-Dale A., Pilpel Y. & Yakhini Z., et al. Science Signaling | 2010 [All authors] »

EGF Decreases the Abundance of MicroRNAs That Restrain Oncogenic Transcription Factors

2007

Evolvable signaling networks of receptor tyrosine kinases: relevance of robustness to malignancy and to cancer therapy

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Publication category: Development

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Authors: Amit I., Wides R. & Yarden Y. Molecular Systems Biology | 2007 [All authors] »

Evolvable signaling networks of receptor tyrosine kinases: relevance of robustness to malignancy and to cancer therapy

Systems approach to growth factor signaling and to therapeutic intervention

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Publication category: Development

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Authors: Yarden Y. & Amit I. Ejc Supplements | 2007 [All authors] »

Systems approach to growth factor signaling and to therapeutic intervention

A reciprocal tensin-3-cten switch mediates EGF-driven mammary cell migration

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Publication category: Development

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Authors: Katz M. Amit I., Citri A., Shay T., Carvalho S., Lavi S., Milanezi F., Lyass L., Amariglio N., Jacob-Hirsch J., Ben Chetrit C. N., Tarcic G., Lindzen M., Avraham R., Liao Y., Trusk P., Lyass A., Rechavi G. & Spector N. L., et al. Nature Cell Biology | 2007 [All authors] »

A reciprocal tensin-3-cten switch mediates EGF-driven mammary cell migration

Regulation of MAPKs by growth factors and receptor tyrosine kinases

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Publication category: Development

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Authors: Katz M., Amit I. & Yarden Y. Biochimica Et Biophysica Acta-Molecular Cell Research | 2007 [All authors] »

Regulation of MAPKs by growth factors and receptor tyrosine kinases

A module of negative feedback regulators defines growth factor signaling

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Publication category: Development

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Authors: Amit I. Citri A., Shay T., Lu Y., Katz M., Zhang F., Tarcic G., Siwak D., Lahad J., Jacob-Hirsch J., Amariglio N., Vaisman N., Segal E., Rechavi G., Alon U., Mills G. B., Domany E. & Yarden Y., et al. Nature Genetics | 2007 [All authors] »

A module of negative feedback regulators defines growth factor signaling

2005

Suppressors of cytokine signaling 4 and 5 regulate epidermal growth factor receptor signaling

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Publication category: Development

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Authors: Kario E. Marmor M., Adamsky K., Citri A., Amit I., Amariglio N., Rechavi G. & Yarden Y., et al. Journal of Biological Chemistry | 2005 [All authors] »

Suppressors of cytokine signaling 4 and 5 regulate epidermal growth factor receptor signaling

2004

LRIG1 restricts growth factor signaling by enhancing receptor ubiquitylation and degradation

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Publication category: Development

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Authors: Gur G. Rubin C., Katz M., Amit I., Citri A., Nilsson J., Amariglio N., Henriksson R., Rechavi G., Hedman H., Wides R. & Yarden Y., et al. EMBO Journal | 2004 [All authors] »

LRIG1 restricts growth factor signaling by enhancing receptor ubiquitylation and degradation

Tal, a Tsg101-specific E3 ubiquitin ligase, regulates receptor endocytosis and retrovirus budding

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Publication category: Development

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Authors: Amit I. Yakir L., Katz M., Zwang Y., Marmor M., Citri A., Shtiegman K., Alroy I., Tuvia S., Reiss Y., Roubini E., Cohen M., Wides R., Bacharach E., Schubert U. & Yarden Y., et al. GENES & DEVELOPMENT | 2004 [All authors] »

Tal, a Tsg101-specific E3 ubiquitin ligase, regulates receptor endocytosis and retrovirus budding