Publications

All years

2025

Septal LYVE1⁺ macrophages control adipocyte stem cell adipogenic potential

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Publication category: Metabolism

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Authors: Yu X. Hu Y., Lim H. Y., Li Z., Jaitin D. A., Yang K., Kong W. T., Xu J., Bejarano D. A., Bied M., Orliaguet L., Rengasamy G., Chow Z., Lee C. Z. W., Lum J., Tian J., Zhang X. M., Liu H., Tan S. W., Chen J., See P., Loh Y. H., Malleret B., Baig S., Yassin S. M., Toh S. A. E. S., Malissen B., Fu X., Kabashima K., Ng L. G., Blériot C., Liu Z., Sheng L., Zheng D. N., Qu J., Venteclef N., Su B., Amit I., Schlitzer A., Angeli V., Ginhoux F. & Chakarov S., et al. Science | 2025 [All authors] »

Septal LYVE1⁺ macrophages control adipocyte stem cell adipogenic potential

ZEB2 is a master switch controlling the tumor-associated macrophage program

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Publication category: Cancer Immunotherapy

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Authors: Sheban F., Phan T. S., Xie K., Ingelfinger F. Gur C., Shapir Itai Y., Blecher-Gonen R., Yu C., Avellino R., Chalan P., Freitag K., Yofe I., Yutkin V., Boyeau P., Ergen C., Hong J., Mazuz K., Liu Y., Chen K., Dahan R., Kortylewski M., Yosef N., Weiner A. & Amit I., et al. Cancer Cell | 2025 [All authors] »

ZEB2 is a master switch controlling the tumor-associated macrophage program

Dissection of the immune landscape in psoriatic arthritis defines immunoproteasome up-regulation in treatment resistance

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Publication category: Autoimmunity

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Authors: Tzemach R., Gur C., Phan T. S., David E. Zada M., Shmueli M. D., Mazuz K., Sheban F., Kurilovich A., Yehuda M. B., Furer V., Polachek A., Gertel S., Snir N., Eviatar T., Nevo S., Merbl Y., Paran D., Wang S. Y., Elkayam O. & Amit I., et al. Science immunology | 2025 [All authors] »

Dissection of the immune landscape in psoriatic arthritis defines immunoproteasome up-regulation in treatment resistance

T-cell-derived IFN-γ suppresses T follicular helper cell differentiation and antibody responses

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Authors: Sala E. Nelli M., Laura C., Di Lucia P., Beccaria C. G., Bono E. B., Mangione M., Marotta D., Sperto V., Grillo M., Giustini L., Tosi F., Nie J., Kim D., Furiato G., Malpighi C., Consolo E., Becher B., David E., Cohen M., Giladi A., Amit I., Bosselut R., Guidotti L. G., Iannacone M. & Kuka M., et al. EMBO Journal | 2025 [All authors] »

T-cell-derived IFN-γ suppresses T follicular helper cell differentiation and antibody responses

Peripheral nervous system microglia-like cells regulate neuronal soma size throughout evolution

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Publication category: Brain

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Authors: Wu Z. Wang Y., Chen W. w., Sun H., Chen X., Li X., Wang Z., Liang W., Wang S. Y., Luan X., Li Y., Huang S., Liang Y., Zhang J., Chen Z. F., Wang G., Gao Y., Liu Y., Wang J., Liu Z., Shi P., Liu C., Lv L., Hou A., Wu C., Yao C., Hong Z., Dai J., Lu Z., Pan F., Chen X., Kettenmann H., Amit I., Speakman J. R., Chen Y., Ginhoux F., Cui R., Huang T. & Li H., et al. Cell | 2025 [All authors] »

Peripheral nervous system microglia-like cells regulate neuronal soma size throughout evolution

Towards the Next Generation of Data-Driven Therapeutics Using Spatially Resolved Single-Cell Technologies and Generative AI

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Publication category: Technology

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Authors: Rodov A. Baniadam H., Zeiser R., Amit I., Yosef N., Wertheimer T. & Ingelfinger F., et al. European Journal of Immunology | 2025 [All authors] »

Towards the Next Generation of Data-Driven Therapeutics Using Spatially Resolved Single-Cell Technologies and Generative AI

2024

The commitment of the human cell atlas to humanity

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Authors: Amit I. Ardlie K., Arzuaga F., Awandare G., Bader G., Bernier A., Carninci P., Donnelly S., Eils R., Forrest A. R., Greely H. T., Guigo R., Hacohen N., Haniffa M., Kirby E. S., Knoppers B. M., Kriegstein A., Lein E. S., Linnarsson S., Majumder P. P., Merad M., Meyer K., Mhlanga M. M., Nolan G., Ntusi N. A., Peer D., Prabhakar S., Raven-Adams M., Regev A., Rozenblatt-Rosen O., Saha S., Saltzman A., Shalek A. K., Shin J. W., Stunnenberg H., Teichmann S. A., Tickle T., Villani A. C., Wells C., Wold B., Yang H. & Zhuang X., et al. Nature Communications | 2024 [All authors] »

The commitment of the human cell atlas to humanity

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

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Authors: Majewska J. Agrawal A., Mayo A., Roitman L., Chatterjee R., Sekeresova Kralova J., Landsberger T., Katzenelenbogen Y., Meir-Salame T., Hagai E., Sopher I., Perez-Correa J. F., Wagner W., Maimon A., Amit I., Alon U. & Krizhanovsky V., et al. Nature Cell Biology | 2024 [All authors] »

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

Defining myeloid-derived suppressor cells

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Publication category: Cancer Immunotherapy

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Authors: Akkari L., Amit I. Bronte V., Fridlender Z. G., Gabrilovich D. I., Ginhoux F., Hedrick C. C. & Ostrand-Rosenberg S., et al. Nature Reviews Immunology | 2024 [All authors] »

Defining myeloid-derived suppressor cells

The CD8⁺ T cell tolerance checkpoint triggers a distinct differentiation state defined by protein translation defects

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Authors: Van Der Byl W. Nüssing S., Peters T. J., Ahn A., Li H., Ledergor G., David E., Koh A. S., Wagle M. V., Deguit C. D. T., de Menezes M. N., Travers A., Sampurno S., Ramsbottom K. M., Li R., Kallies A., Beavis P. A., Jungmann R., Bastings M. M., Belz G. T., Goel S., Trapani J. A., Crabtree G. R., Chang H. Y., Amit I., Goodnow C. C., Luciani F. & Parish I. A., et al. Immunity | 2024 [All authors] »

The CD8⁺ T cell tolerance checkpoint triggers a distinct differentiation state defined by protein translation defects

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

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Publication category: Cancer Immunotherapy

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Authors: Barboy O. Bercovich A., Li H., Lubling Y., Yalin A., Shapir Itai Y., Abadie K., Zada M., David E., Shlomi S., Katzenelenbogen Y., Adhemar D., Gur C., Yofe I., Feferman T., Cohen M., Dahan R., Newell E., Lifshitz A., Tanay A. & Amit I., et al. Nature Cancer | 2024 [All authors] »

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

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

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Publication category: Metabolism

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Authors: Landsberger T. Amit I. & Alon U., et al. GeroScience | 2024 [All authors] »

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

Time-resolved single-cell transcriptomics defines immune trajectories in glioblastoma

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Publication category: Brain , Technology

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Authors: Kirschenbaum D., Xie K., Ingelfinger F. Katzenelenbogen Y., Abadie K., Look T., Sheban F., Phan T. S., Li B., Zwicky P., Yofe I., David E., Mazuz K., Hou J., Chen Y., Shaim H., Shanley M., Becker S., Qian J., Colonna M., Ginhoux F., Rezvani K., Theis F. J., Yosef N., Weiss T., Weiner A. & Amit I., et al. Cell | 2024 [All authors] »

Time-resolved single-cell transcriptomics defines immune trajectories in glioblastoma

Regulation of lymphoid-myeloid lineage bias through regnase-1/3-mediated control of Nfkbiz

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Publication category: Development

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Authors: Uehata T. Yamada S., Ori D., Vandenbon A., Giladi A., Jelinski A., Murakawa Y., Watanabe H., Takeuchi K., Toratani K., Mino T., Kiryu H., Standley D. M., Tsujimura T., Ikawa T., Kondoh G., Landthaler M., Kawamoto H., Rodewald H. R., Amit I., Yamamoto R., Miyazaki M. & Takeuchi O., et al. Blood | 2024 [All authors] »

Regulation of lymphoid-myeloid lineage bias through regnase-1/3-mediated control of Nfkbiz

Bispecific dendritic-T cell engager potentiates anti-tumor immunity

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Publication category: Cancer Immunotherapy

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Authors: Shapir Itai Y., Barboy O. Salomon R., Bercovich A., Xie K., Winter E., Shami T., Porat Z., Erez N., Tanay A., Amit I. & Dahan R., et al. Cell | 2024 [All authors] »

Bispecific dendritic-T cell engager potentiates anti-tumor immunity

2023

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

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Publication category: Development , Brain

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Authors: Chen Q. Leshkowitz D., Li H., van Impel A., Schulte-Merker S., Amit I., Rizzoti K. & Levkowitz G., et al. Developmental Cell | 2023 [All authors] »

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

Spatial and temporal mapping of breast cancer lung metastases identify TREM2 macrophages as regulators of the metastatic boundary

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Publication category: Cancer Immunotherapy

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Authors: Yofe I. Shami T., Cohen N., Landsberger T., Sheban F., Stoler-Barak L., Yalin A., Phan T. S., Li B., Monteran L., Scharff Y., Giladi A., Elbaz M., David E., Gurevich-Shapiro A., Gur C., Shulman Z., Erez N. & Amit I., et al. Cancer Discovery | 2023 [All authors] »

Spatial and temporal mapping of breast cancer lung metastases identify TREM2 macrophages as regulators of the metastatic boundary

Cholesterol 24-hydroxylase at the choroid plexus contributes to brain immune homeostasis

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Publication category: Brain

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Authors: Tsitsou-Kampeli A. Suzzi S., Kenigsbuch M., Satomi A., Strobelt R., Singer O., Feldmesser E., Purnapatre M., Colaiuta S. P., David E., Cahalon L., Hahn O., Wyss-Coray T., Shaul Y., Amit I. & Schwartz M., et al. Cell Reports Medicine | 2023 [All authors] »

Cholesterol 24-hydroxylase at the choroid plexus contributes to brain immune homeostasis

An immune cell atlas reveals the dynamics of human macrophage specification during prenatal development

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Publication category: Development

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Authors: Wang Z. Wu Z., Wang H., Feng R., Wang G., Li M., Wang S. Y., Chen X., Su Y., Wang J., Zhang W., Bao Y., Lan Z., Song Z., Wang Y., Luo X., Zhao L., Hou A., Tian S., Gao H., Miao W., Liu Y., Wang H., Yin C., Ji Z. L., Feng M., Liu H., Diao L., Amit I., Chen Y., Zeng Y., Ginhoux F., Wu X., Zhu Y. & Li H., et al. Cell | 2023 [All authors] »

An immune cell atlas reveals the dynamics of human macrophage specification during prenatal development

Cellular and metabolic characteristics of pre-leukemic hematopoietic progenitors with GATA2 haploinsufficiency

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Authors: Rein A. Geron I., Kugler E., Fishman H., Gottlieb E., Abramovich I., Giladi A., Amit I., Mulet-Lazaro R., Delwel R., Gröschel S., Levin-Zaidman S., Dezorella N., Holdengreber V., Rao T. N., Yacobovich J., Steinberg-Shemer O., Huang Q., Tan Y., Chen S., Izraeli S. & Birger Y., et al. Haematologica | 2023 [All authors] »

Cellular and metabolic characteristics of pre-leukemic hematopoietic progenitors with GATA2 haploinsufficiency

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

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Publication category: Cancer Immunotherapy

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Authors: Goldman O. Adler L. N., Hajaj E., Croese T., Darzi N., Galai S., Tishler H., Ariav Y., Lavie D., Fellus-Alyagor L., Oren R., Kuznetsov Y., David E., Jaschek R., Stossel C., Singer O., Malitsky S., Barak R., Seger R., Erez N., Amit I., Tanay A., Saada A., Golan T., Rubinek T., Sang Lee J., Ben-Shachar S., Wolf I. & Erez A., et al. Cancer Discovery | 2023 [All authors] »

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

Single-cell biology: what does the future hold?

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Authors: Polychronidou M. Hou J., Babu M. M., Liberali P., Amit I., Deplancke B., Lahav G., Itzkovitz S., Mann M., Saez-Rodriguez J., Theis F. & Eils R., et al. Molecular Systems Biology | 2023 [All authors] »

Single-cell biology: what does the future hold?

Editorial: Microglia in neuroinflammation

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Authors: Ayata P., Amit I. & Cuda C. M. Frontiers in Immunology | 2023 [All authors] »

Editorial: Microglia in neuroinflammation

The transcriptional and regulatory identity of erythropoietin producing cells

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

The transcriptional and regulatory identity of erythropoietin producing cells

Targeted delivery of tumor necrosis factor in combination with CCNU induces a T cell-dependent regression of glioblastoma

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Publication category: Cancer Immunotherapy , Brain

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Authors: Look T. Puca E., Bühler M., Kirschenbaum D., De Luca R., Stucchi R., Ravazza D., Di Nitto C., Roth P., Katzenelenbogen Y., Weiner A., Rindlisbacher L., Becher B., Amit I., Weller M., Neri D., Hemmerle T. & Weiss T., et al. Science Translational Medicine | 2023 [All authors] »

Targeted delivery of tumor necrosis factor in combination with CCNU induces a T cell-dependent regression of glioblastoma

Immunometabolism at the crossroads of obesity and cancera Keystone Symposia report

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Authors: Cable J. Rathmell J. C., Pearce E. L., Ho P. C., Haigis M. C., Mamedov M. R., Wu M. J., Kaech S. M., Lynch L., Febbraio M. A., Bapat S. P., Hong H. S., Zou W., Belkaid Y., Sullivan Z. A., Keller A., Wculek S. K., Green D. R., Postic C., Amit I., Benitah S. A., Jones R. G., Reina-Campos M., Torres S. V., Beyaz S., Brennan D., O'Neill L. A., Perry R. J. & Brenner D., et al. Annals of the New York Academy of Sciences | 2023 [All authors] »

Immunometabolism at the crossroads of obesity and cancera Keystone Symposia report

A single-cell census of mouse limb development identifies complex spatiotemporal dynamics of skeleton formation

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Publication category: Development

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Authors: Markman S., Zada M. David E., Giladi A., Amit I. & Zelzer E., et al. Developmental Cell | 2023 [All authors] »

A single-cell census of mouse limb development identifies complex spatiotemporal dynamics of skeleton formation

Fc glycoengineering of a PD-L1 antibody harnesses Fcγ receptors for increased antitumor efficacy

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Publication category: Cancer Immunotherapy

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Authors: Saban N. C., Yalin A., Landsberger T. Salomon R., Alva A., Feferman T., Amit I. & Dahan R., et al. Science immunology | 2023 [All authors] »

Fc glycoengineering of a PD-L1 antibody harnesses Fcγ receptors for increased antitumor efficacy

Author Correction: A shared disease-associated oligodendrocyte signature among multiple CNS pathologies (Nature Neuroscience, (2022), 25, 7, (876-886), 10.1038/s41593-022-01104-7)

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Publication category: Brain

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Authors: Kenigsbuch M., Bost P. Halevi S., Chang Y., Chen S., Ma Q., Hajbi R., Schwikowski B., Bodenmiller B., Fu H., Schwartz M. & Amit I., et al. Nature Neuroscience | 2023 [All authors] »

Author Correction: A shared disease-associated oligodendrocyte signature among multiple CNS pathologies (Nature Neuroscience, (2022), 25, 7, (876-886), 10.1038/s41593-022-01104-7)

Cerebrospinal fluid proteomics indicates immune dysregulation and neuronal dysfunction in antibody associated autoimmune encephalitis

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Publication category: Brain , Autoimmunity

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Authors: Räuber S. Schroeter C. B., Strippel C., Nelke C., Ruland T., Dik A., Golombeck K. S., Regner-Nelke L., Paunovic M., Esser D., Münch C., Rosenow F., van Duijn M., Henes A., Ruck T., Amit I., Leypoldt F., Titulaer M. J., Wiendl H., Meuth S. G., Meyer zu Hörste G. & Melzer N., et al. Journal of Autoimmunity | 2023 [All authors] »

Cerebrospinal fluid proteomics indicates immune dysregulation and neuronal dysfunction in antibody associated autoimmune encephalitis

Neighbor-specific gene expression revealed from physically interacting cells during mouse embryonic development

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Publication category: Development , Technology

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Authors: Kim J. Rothová M. M., Madan E., Rhee S., Weng G., Palma A. M., Liao L., David E., Amit I., Hajkarim M. C., Vudatha V., Gutiérrez-García A., Moreno E., Winn R., Trevino J., Fisher P. B., Brickman J. M., Gogna R. & Won K. J., et al. Proceedings of the National Academy of Sciences - PNAS | 2023 [All authors] »

Neighbor-specific gene expression revealed from physically interacting cells during mouse embryonic development

In Synergy: Optimizing CAR T Development and Personalizing Patient Care Using Single-Cell Technologies

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Publication category: Cancer Immunotherapy

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Authors: Barboy O. Katzenelenbogen Y., Shalita R. & Amit I., et al. Cancer Discovery | 2023 [All authors] »

In Synergy: Optimizing CAR T Development and Personalizing Patient Care Using Single-Cell Technologies

2022

Time-resolved single-cell RNA-seq using metabolic RNA labelling

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Publication category: Technology

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Authors: Erhard F. Saliba A., Lusser A., Toussaint C., Hennig T., Prusty B. K., Kirschenbaum D., Abadie K., Miska E. A., Friedel C. C., Amit I., Micura R. & Doelken L., et al. Nature Reviews Methods Primers | 2022 [All authors] »

Time-resolved single-cell RNA-seq using metabolic RNA labelling

Distinct gene programs underpinning disease tolerance and resistance in influenza virus infection

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Authors: Cohn O. Yankovitz G., Peshes-Yaloz N., Steuerman Y., Frishberg A., Brandes R., Mandelboim M., Hamilton J. R., Hagai T., Amit I., Netea M. G., Hacohen N., Iraqi F. A., Bacharach E. & Gat-Viks I., et al. Cell Systems | 2022 [All authors] »

Distinct gene programs underpinning disease tolerance and resistance in influenza virus infection

A spatiotemporally resolved single-cell atlas of the Plasmodium liver stage

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Authors: Afriat A. Zuzarte-Luis V., Halpern K. B., Buchauer L., Marques S., Chora A. F., Lahree A., Amit I., Mota M. M. & Itzkovitz S., et al. Nature | 2022 [All authors] »

A spatiotemporally resolved single-cell atlas of the Plasmodium liver stage

Microglia states and nomenclature: A field at its crossroads

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Publication category: Brain

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Authors: Paolicelli R. C. Sierra A., Stevens B., Tremblay M., Aguzzi A., Ajami B., Amit I., Audinat E., Bechmann I., Bennett M., Bennett F., Bessis A., Biber K., Bilbo S., Blurton-Jones M., Boddeke E., Brites D., Brône B., Brown G. C., Butovsky O., Carson M. J., Castellano B., Colonna M., Cowley S. A., Cunningham C., Davalos D., De Jager P. L., de Strooper B., Denes A., Eggen B. J., Eyo U., Galea E., Garel S., Ginhoux F., Glass C. K., Gokce O., Gomez-Nicola D., González B., Gordon S., Graeber M. B., Greenhalgh A. D., Gressens P., Greter M., Gutmann D. H., Haass C., Heneka M. T., Heppner F. L., Hong S., Hume D. A., Jung S., Kettenmann H., Kipnis J., Koyama R., Lemke G., Lynch M., Majewska A., Malcangio M., Malm T., Mancuso R., Masuda T., Matteoli M., McColl B. W., Miron V. E., Molofsky A. V., Monje M., Mracsko E., Nadjar A., Neher J. J., Neniskyte U., Neumann H., Noda M., Peng B., Peri F., Perry V. H., Popovich P. G., Pridans C., Priller J., Prinz M., Ragozzino D., Ransohoff R. M., Salter M. W., Schaefer A., Schafer D. P., Schwartz M., Simons M., Smith C. J., Streit W. J., Tay T. L., Tsai L., Verkhratsky A., von Bernhardi R., Wake H., Wittamer V., Wolf S. A., Wu L. & Wyss-Coray T., et al. Neuron | 2022 [All authors] »

Microglia states and nomenclature: A field at its crossroads

The industrial genomic revolution: A new era in neuroimmunology

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Publication category: Brain , Technology

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Authors: Shalita R. & Amit I. Neuron | 2022 [All authors] »

The industrial genomic revolution: A new era in neuroimmunology

Anti-CTLA-4 antibodies drive myeloid activation and reprogram the tumor microenvironment through FcγR engagement and type I interferon signaling

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Publication category: Cancer Immunotherapy

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Authors: Yofe I., Landsberger T., Yalin A. Solomon I., Costoya C., Demane D. F., Shah M., David E., Borenstein C., Barboy O., Matos I., Peggs K. S., Quezada S. A. & Amit I., et al. Nature Cancer | 2022 [All authors] »

Anti-CTLA-4 antibodies drive myeloid activation and reprogram the tumor microenvironment through FcγR engagement and type I interferon signaling

Spatiotemporal Omics-Refining the landscape of precision medicine

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Publication category: Technology

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Authors: Zhang J. Yin J., Heng Y., Xie K., Chen A., Amit I., Bian X. & Xu X., et al. Life Medicine | 2022 [All authors] »

Spatiotemporal Omics-Refining the landscape of precision medicine

Human microglia development in the embryonic brain

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Publication category: Brain

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Authors: Li B. Li Y., Li Z., Jiao J. & Amit I., et al. Life Medicine | 2022 [All authors] »

Human microglia development in the embryonic brain

DestVI identifies continuums of cell types in spatial transcriptomics data

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Publication category: Technology

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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., et al. Nature biotechnology | 2022 [All authors] »

DestVI identifies continuums of cell types in spatial transcriptomics data

Dual ontogeny of disease-associated microglia and disease inflammatory macrophages in aging and neurodegeneration

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Publication category: Brain

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Authors: Silvin' A. Uderhardt S., Piot C., Da Mesquita S., Yang K., Geirsdottir L., Mulder K., David E., Liu Z., Bridlance C., Thion M. S., Zhang X., Ting Kong W., Deloger M., Fontes V., Weiner A., Ee R., Dress R., Wen Hang J., Balachander A., Chakarov S., Malleret B., Dunsmore G., Cexus O., Chen J., Garel S., Dutertre C. A., Amit I., Kipnis J. & Ginhoux F., et al. Immunity | 2022 [All authors] »

Dual ontogeny of disease-associated microglia and disease inflammatory macrophages in aging and neurodegeneration

A shared disease-associated oligodendrocyte signature among multiple CNS pathologies

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Publication category: Brain

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Authors: Kenigsbuch M., Bost P., Halevi S. Chang Y., Chen S., Ma Q., Hajbi R., Schwikowski B., Bodenmiller B., Fu H., Schwartz M. & Amit I., et al. Nature Neuroscience | 2022 [All authors] »

A shared disease-associated oligodendrocyte signature among multiple CNS pathologies

Identification of the central intermediate in the extra-embryonic to embryonic endoderm transition through single-cell transcriptomics

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Publication category: Development

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Authors: Rothová M. M. Nielsen A. V., Proks M., Wong Y. F., Riveiro A. R., Linneberg-Agerholm M., David E., Amit I., Trusina A. & Brickman J. M., et al. Nature Cell Biology | 2022 [All authors] »

Identification of the central intermediate in the extra-embryonic to embryonic endoderm transition through single-cell transcriptomics

Physically interacting beta-delta pairs in the regenerating pancreas revealed by single-cell sequencing

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Authors: Yanowski E. Yacovzada N. S., David E., Giladi A., Jaitin D., Farack L., Egozi A., Ben-Zvi D., Itzkovitz S., Amit I. & Hornstein E., et al. Molecular metabolism (Germany) | 2022 [All authors] »

Physically interacting beta-delta pairs in the regenerating pancreas revealed by single-cell sequencing

LGR5 expressing skin fibroblasts define a major cellular hub perturbed in scleroderma

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Publication category: Autoimmunity

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Authors: Gur C., Wang S. Sheban F., Zada M., Li B., Kharouf F., Peleg H., Aamar S., Yalin A., Kirschenbaum D., Braun-Moscovici Y., Jaitin D. A., Meir-Salame T., Hagai E., Kragesteen B. K., Avni B., Grisariu S., Bornstein C., Shlomi-Loubaton S., David E., Shreberk-Hassidim R., Molho-Pessach V., Amar D., Tzur T., Kuint R., Gross M., Barboy O., Moshe A., Fellus-Alyagor L., Hirsch D., Addadi Y., Erenfeld S., Biton M., Tzemach T., Elazary A., Naparstek Y., Tzemach R., Weiner A., Giladi A., Balbir-Gurman A. & Amit I., et al. Cell | 2022 [All authors] »

LGR5 expressing skin fibroblasts define a major cellular hub perturbed in scleroderma

MYCN mediates cysteine addiction and sensitizes neuroblastoma to ferroptosis

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Publication category: Cancer Immunotherapy

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Authors: Alborzinia H. Flórez A. F., Kreth S., Brückner L. M., Yildiz U., Gartlgruber M., Odoni D. I., Poschet G., Garbowicz K., Shao C., Klein C., Meier J., Zeisberger P., Nadler-Holly M., Ziehm M., Paul F., Burhenne J., Bell E., Shaikhkarami M., Würth R., Stainczyk S. A., Wecht E. M., Kreth J., Büttner M., Ishaque N., Schlesner M., Nicke B., Stresemann C., Llamazares-Prada M., Reiling J. H., Fischer M., Amit I., Selbach M., Herrmann C., Wölfl S., Henrich K., Höfer T., Trumpp A. & Westermann F., et al. Nature Cancer | 2022 [All authors] »

MYCN mediates cysteine addiction and sensitizes neuroblastoma to ferroptosis

Brain metastases: Not all tumors are created equal

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Publication category: Cancer Immunotherapy , Brain

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Authors: Kirschenbaum D. & Amit I. Neuron | 2022 [All authors] »

Brain metastases: Not all tumors are created equal

Single-cell immunology: Past, present, and future

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Publication category: Technology

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Authors: Ginhoux F., Yalin A. Dutertre C. A. & Amit I., et al. Immunity | 2022 [All authors] »

Single-cell immunology: Past, present, and future

The interaction of CD4⁺ helper T cells with dendritic cells shapes the tumor microenvironment and immune checkpoint blockade response

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Publication category: Cancer Immunotherapy

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Authors: Cohen M. Giladi A., Barboy O., Hamon P., Li B., Zada M., Gurevich-Shapiro A., Beccaria C. G., David E., Maier B. B., Buckup M., Kamer I., Deczkowska A., Le Berichel J., Bar J., Iannacone M., Tanay A., Merad M. & Amit I., et al. Nature Cancer | 2022 [All authors] »

The interaction of CD4⁺ helper T cells with dendritic cells shapes the tumor microenvironment and immune checkpoint blockade response

Bispecific antibodies increase the therapeutic window of CD40 agonists through selective dendritic cell targeting

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Publication category: Cancer Immunotherapy

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Authors: Salomon R., Rotem H., Katzenelenbogen Y. Weiner A., Cohen Saban N., Feferman T., Amit I. & Dahan R., et al. Nature Cancer | 2022 [All authors] »

Bispecific antibodies increase the therapeutic window of CD40 agonists through selective dendritic cell targeting

Fatal cytokine release syndrome by an aberrant FLIP/STAT3 axis

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Authors: Musiu C. Caligola S., Fiore A., Lamolinara A., Frusteri C., Del Pizzo F. D., De Sanctis F., Cane S., Adamo A., Hofer F., Barouni R. M., Grilli A., Zilio S., Serafini P., Tacconelli E., Donadello K., Gottin L., Polati E., Girelli D., Polidoro I., Iezzi P. A., Angelucci D., Capece A., Chen Y., Shi Z., Murray P. J., Chilosi M., Amit I., Bicciato S., Iezzi M., Bronte V. & Ugel S., et al. Cell Death and Differentiation | 2022 [All authors] »

Fatal cytokine release syndrome by an aberrant FLIP/STAT3 axis

Publisher Correction: XCR1 ⁺ type 1 conventional dendritic cells drive liver pathology in non-alcoholic steatohepatitis (Nature Medicine, (2021), 27, 6, (1043-1054), 10.1038/s41591-021-01344-3)

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Publication category: Cancer Immunotherapy

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Authors: Deczkowska A. David E., Ramadori P., Pfister D., Safran M., Li 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 | 2022 [All authors] »

Publisher Correction: XCR1 ⁺ type 1 conventional dendritic cells drive liver pathology in non-alcoholic steatohepatitis (Nature Medicine, (2021), 27, 6, (1043-1054), 10.1038/s41591-021-01344-3)

Early antitumor activity of oral Langerhans cells is compromised by a carcinogen

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Publication category: Cancer Immunotherapy

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Authors: Saba Y. Aizenbud I., Matanes D., Koren N., Barel O., Zubeidat K., Capucha T., David E., Eli-Berchoer L., Stoitzner P., Wilensky A., Amit I., Czerninski R., Yona S. & Hovav A., et al. Proceedings of the National Academy of Sciences of the United States of America | 2022 [All authors] »

Early antitumor activity of oral Langerhans cells is compromised by a carcinogen

Alzheimers disease modification mediated by bone marrow-derived macrophages via a TREM2-independent pathway in mouse model of amyloidosis

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Publication category: Brain

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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., et al. Nature Aging | 2022 [All authors] »

Alzheimers disease modification mediated by bone marrow-derived macrophages via a TREM2-independent pathway in mouse model of amyloidosis

2021

Clump sequencing exposes the spatial expression programs of intestinal secretory cells

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Publication category: Technology

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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

Dichotomous metabolic networks govern human ILC2 proliferation and function

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Authors: Surace L. Doisne J., Croft C. A., Thaller A., Escoll P., Marie S., Petrosemoli N., Guillemot V., Dardalhon V., Topazio D., Cama A., Buchrieser C., Taylor N., Amit I., Musumeci O. & Di Santo J. P., et al. Nature Immunology | 2021 [All authors] »

Dichotomous metabolic networks govern human ILC2 proliferation and function

Single-cell analysis of regions of interest (SCARI) using a photosensitive tag

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Publication category: Technology

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Authors: van der Leun A. M. Hoekstra M. E., Reinalda L., Scheele C. L. G. J., Toebes M., van de Graaff M. J., Chen L. Y. Y., Li H., Bercovich A., Lubling Y., David E., Thommen D. S., Tanay A., van Rheenen J., Amit I., van Kasteren S. I. & Schumacher T. N., et al. Nature Chemical Biology | 2021 [All authors] »

Single-cell analysis of regions of interest (SCARI) using a photosensitive tag

Tumor cells in light-chain amyloidosis and myeloma show distinct transcriptional rewiring of normal plasma cell development

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Publication category: Cancer Immunotherapy

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Authors: Alameda D. Goicoechea I., Vicari M., Arriazu E., Nevone A., Rodríguez S., Lasa M., Puig N., Cedena M., Alignani D., Garate S., Lara-Astiaso D., Vilas-Zornoza A., Sarvide S., Ocio E. M., Lecumberri R., Garcia de Coca A., Labrador J., Gonzalez M., Palomera L., Gironella M., Cabañas V., Casanova M., Oriol A., Krsnik I., Pérez-Montaña A., de la Rubia J., de la Puerta J., de Arriba F., Fazio V. M., Martinez-Lopez J., Lahuerta J., Mateos M., Odero M. D., Prosper F., Weiner A., Amit I., Nuvolone M., San-Miguel J. F. F. & Paiva B., et al. Blood | 2021 [All authors] »

Tumor cells in light-chain amyloidosis and myeloma show distinct transcriptional rewiring of normal plasma cell development

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

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Authors: Deczkowska A. David E., Ramadori P., Pfister D., Safran M., Li 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

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

Multi-tissue single-cell analysis deconstructs the complex programs of mouse natural killer and type 1 innate lymphoid cells in tissues and circulation

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Authors: McFarland A. P., Yalin A., Wang S. Cortez V. S., Landsberger T., Sudan R., Peng V., Miller H. L., Ricci B., David E., Faccio R., Amit I. & Colonna M., et al. Immunity (Cambridge, Mass.) | 2021 [All authors] »

Multi-tissue single-cell analysis deconstructs the complex programs of mouse natural killer and type 1 innate lymphoid cells in tissues and circulation

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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Publication category: Technology

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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

CRISPECTOR provides accurate estimation of genome editing translocation and off-target activity from comparative NGS data

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Authors: Amit I. Iancu O., Levy-Jurgenson A., Kurgan G., McNeill M. S., Rettig G. R., Allen D., Breier D., Ben Haim N., Wang Y., Anavy L., Hendel A. & Yakhini Z., et al. Nature Communications | 2021 [All authors] »

CRISPECTOR provides accurate estimation of genome editing translocation and off-target activity from comparative NGS data

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., DAlessio 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., De Dosso S., Mallm J. P., 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. T., 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. F., Marron T. U., Kaseb A., Kudo M., Huang Y. H., 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

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

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

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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

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

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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

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

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

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

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 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

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

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

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

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

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

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

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

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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/EBPβ-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

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

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

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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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

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

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

Cell composition analysis of bulk genomics using single-cell data

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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

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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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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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

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

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

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

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

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

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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

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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Authors: Deczkowska A. Amit I. & Schwartz M., et al. 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

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

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

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

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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

2017

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

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

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: 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

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

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

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 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

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

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

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 Diurnal 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 Diurnal 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

The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery

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Authors: Stunnenberg H. G. Abrignani S., Adams D., de Almeida M., Altucci L., Amin V., Amit I., Antonarakis S. E., Aparicio S., Arima T., Arrigoni L., Arts R., Asnafi V., Badosa M. E., Bae J. B., Bassler K., Beck S., Berkman B., Bernstein B. E., Bilenky M., Bird A., Bock C., Boehm B., Bourque G., Breeze C. E., Brors B., Bujold D., Burren O., Bussemakers M. J., Butterworth A., Campo E., Carrillo-de-Santa-Pau E., Chadwick L., Chan K. M., Chen W., Cheung T. H., Chiapperino L., Choi N. H., Chung H. R., Clarke L., Connors J. M., Cronet P., Danesh J., Dermitzakis M., Drewes G., Durek P., Dyke S., Dylag T., Eaves C. J., Ebert P., Eils R., Eils J., Ennis C. A., Enver T., Feingold E. A., Felder B., Ferguson-Smith A., Fitzgibbon J., Flicek P., Foo R. S., Fraser P., Frontini M., Furlong E., Gakkhar S., Gasparoni N., Gasparoni G., Geschwind D. H., Glažar P., Graf T., Grosveld F., Guan X. Y., Guigo R., Gut I. G., Hamann A., Han B. G., Harris R. A., Heath S., Helin K., Hengstler J. G., Heravi-Moussavi A., Herrup K., Hill S., Hilton J. A., Hitz B. C., Horsthemke B., Hu M., Hwang J. Y., Ip N. Y., Ito T., Javierre B. M., Jenko S., Jenuwein T., Joly Y., Jones S. J., Kanai Y., Kang H. G., Karsan A., Kiemer A. K., Kim S. C., Kim B. J., Kim H. H., Kimura H., Kinkley S., Klironomos F., Koh I. U., Kostadima M., Kressler C., Kreuzhuber R., Kundaje A., Küppers R., Larabell C., Lasko P., Lathrop M., Lee D. H., Lee S., Lehrach H., Leitão E., Lengauer T., Lernmark Å., Leslie R. D., Leung G. K., Leung D., Loeffler M., Ma Y., Mai A., Manke T., Marcotte E. R., Marra M. A., Martens J. H., Martin-Subero J. I., Maschke K., Merten C., Milosavljevic A., Minucci S., Mitsuyama T., Moore R. A., Müller F., Mungall A. J., Netea M. G., Nordström K., Norstedt I., Okae H., Onuchic V., Ouellette F., Ouwehand W., Pagani M., Pancaldi V., Pap T., Pastinen T., Patel R., Paul D. S., Pazin M. J., Pelicci P. G., Phillips A. G., Polansky J., Porse B., Pospisilik J. A., Prabhakar S., Procaccini D. C., Radbruch A., Rajewsky N., Rakyan V., Reik W., Ren B., Richardson D., Richter A., Rico D., Roberts D. J., Rosenstiel P., Rothstein M., Salhab A., Sasaki H., Satterlee J. S., Sauer S., Schacht C., Schmidt F., Schmitz G., Schreiber S., Schröder C., Schübeler D., Schultze J. L., Schulyer R. P., Schulz M., Seifert M., Shirahige K., Siebert R., Sierocinski T., Siminoff L., Sinha A., Soranzo N., Spicuglia S., Spivakov M., Steidl C., Strattan J. S., Stratton M., Südbeck P., Sun H., Suzuki N., Suzuki Y., Tanay A., Torrents D., Tyson F. L., Ulas T., Ullrich S., Ushijima T., Valencia A., Vellenga E., Vingron M., Wallace C., Wallner S., Walter J., Wang H., Weber S., Weiler N., Weller A., Weng A., Wilder S., Wiseman S. M., Wu A. R., Wu Z., Xiong J., Yamashita Y., Yang X., Yap D. Y., Yip K. Y., Yip S., Yoo J. I., Zerbino D., Zipprich G. & Hirst M., et al. Cell | 2016 [All authors] »

The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery

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

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Publication category: Development

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Authors: Talmi-Frank D. Altboum Z., Solomonov I., Udi Y., Jaitin D. A., Klepfish M., David E., Zhuravlev A., Keren-Shaul H., Winter D. R., Gat-Viks I., Mandelboim M., Ziv T., Amit I. & Sagi I., et al. Cell Host & Microbe | 2016 [All authors] »

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

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

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

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 | 2016 [All authors] »

Microglia development follows a stepwise program to regulate brain homeostasis

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

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

Voices of biotech

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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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Authors: Decque A. Joffre O., Magalhaes J. G., Cossec J. C., Blecher-Gonen R., Lapaquette P., Silvin A., Manel N., Joubert P. E., Seeler J. S., Albert M. L., Amit I., Amigorena S. & Dejean A., 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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Authors: Amit I. Winter D. R. & Jung S., et al. 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

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

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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

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

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

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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

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

High-resolution chromatin dynamics during a yeast stress response

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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

Derivation of novel human ground state naive pluripotent stem cells (vol 504, pg 282, 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. H., et al. Nature | 2015 [All authors] »

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

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

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

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

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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

Transcription factor binding dynamics during human ES cell differentiation

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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

m⁶A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation

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Publication category: Development

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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] »

m⁶A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation

2014

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

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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 TGFβ1 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 TGFβ1 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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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

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

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

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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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

Digital cell quantification identifies global immune cell dynamics during influenza infection

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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

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

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

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

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

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

2012

Nanowire-mediated delivery enables functional interrogation of primary immune cells: Application to the analysis of chronic lymphocytic leukemia

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Authors: Shalek A. K. Gaublomme J. T., Wang L., Yosef N., Chevrier N., Andersen M. S., Robinson J. T., Pochet N., Neuberg D., Gertner R. S., Amit I., Brown J. R., Hacohen N., Regev A., Wu C. J. & Park H., et al. Nano Letters | 2012 [All authors] »

Nanowire-mediated delivery enables functional interrogation of primary immune cells: Application to the analysis of chronic lymphocytic leukemia

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

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Authors: Garber M. Yosef N., Goren A., Raychowdhury R., Thielke A., Guttman M., Robinson J., Minie B., Chevrier N., Itzhaki Z., Blecher-Gonen R., Bornstein C., Amann Zalcenstein D., Weiner A., Friedrich D., Meldrim J., Ram O., Cheng C., Gnirke A., Fisher S., Friedmann N., Wong B., Bernstein B. E., Nusbaum C., Hacohen N., Regev A. & Amit I., et al. Molecular Cell | 2012 [All authors] »

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

The H3K27 demethylase Utx regulates somatic and germ cell epigenetic reprogramming

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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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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

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

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

2011

Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells

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Authors: Ram O. Goren A., Amit I., Shoresh N., Yosef N., Ernst J., Kellis M., Gymrek M., Issner R., Coyne M., Durham T., Zhang X., Donaghey J., Epstein C. B., Regev A. & Bernstein B. E., et al. Cell | 2011 [All authors] »

Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells

Strategies to discover regulatory circuits of the mammalian immune system

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

Strategies to discover regulatory circuits of the mammalian immune system

Systematic discovery of TLR signaling components delineates viral-sensing circuits

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Authors: Chevrier N. Mertins P., Artyomov M. N., Shalek A. K., Iannacone M., Ciaccio M. F., Gat-Viks I., Tonti E., DeGrace M. M., Clauser K. R., Garber M., Eisenhaure T. M., Yosef N., Robinson J., Sutton A., Andersen M. S., Root D. E., von Andrian U., Jones R. B., Park H., Carr S. A., Regev A., Amit I. & Hacohen N., et al. Cell | 2011 [All authors] »

Systematic discovery of TLR signaling components delineates viral-sensing circuits

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

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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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

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

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