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  1. AU="Ido Amit"
  2. AU="Sowa, Jakub K"
  3. AU="Melore, Schuyler"
  4. AU="Ardito, Alan A"
  5. AU=Meyer Jacob
  6. AU="Nataly Ruiz-Quiñones"
  7. AU="Núñez, Marcela"
  8. AU="Poilvache, Hervé"
  9. AU="Manavalan, Preeti"
  10. AU="Kruth, Andre"
  11. AU=Kim Seong Eun
  12. AU=Leventoglu Sezai
  13. AU="Yang, Hengquan"
  14. AU="Champion, Patricia A DiGiuseppe"
  15. AU=Tomisa Antoni P
  16. AU="Charleston, Bryan"
  17. AU="Busch, Volker"
  18. AU="Fishwick, James R"
  19. AU="Obrenović-Kirćanski Biljana"
  20. AU="Ch'oe, Ok-hyang"
  21. AU="Chiaverina, Giulia"
  22. AU="Saunders, Gary I"
  23. AU="Ng, Liqi"
  24. AU="Kato, Takeshi"
  25. AU="Dalstra, Michel"
  26. AU="Ruben, Jurjen"
  27. AU="Peersman, Nele"
  28. AU=Yip Christina Y C AU=Yip Christina Y C
  29. AU=Mehan Vivek K.
  30. AU="Nara, Akina"
  31. AU=Saccente Michael
  32. AU="Wang, Xiulu" AU="Wang, Xiulu"
  33. AU="Milnes, Di"
  34. AU=Almudhi Abdulaziz
  35. AU="Kumowski, Nina"
  36. AU="Dedeke, Iyabode"
  37. AU="Srivastava, Mitul"
  38. AU=Que Jian-Yu
  39. AU="Midulla, Martina"
  40. AU="et al"
  41. AU="Pritchard, Jonathan"
  42. AU="Memeo, Lorenzo"
  43. AU="Taylan, Gokay"
  44. AU="Tijssen, Robert J. W."
  45. AU="Silva, Marcelina Jasmine"
  46. AU="Egbuna, Chukwuebuka"

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

    Giladi, Amir / Ido Amit

    Cell. 2018 Jan. 11, v. 172, no. 1-2

    2018  

    Abstract: The immunology field has invested great efforts and ingenuity to characterize the various immune cell types and elucidate their functions. However, accumulating evidence indicates that current technologies and classification schemes are limited in their ... ...

    Abstract The immunology field has invested great efforts and ingenuity to characterize the various immune cell types and elucidate their functions. However, accumulating evidence indicates that current technologies and classification schemes are limited in their ability to account for the functional heterogeneity of immune processes. Single-cell genomics hold the potential to revolutionize the way we characterize complex immune cell assemblies and study their spatial organization, dynamics, clonal distribution, pathways, function, and crosstalks. In this Perspective, we consider recent and forthcoming technological and analytical advances in single-cell genomics and the potential impact of those advances on the future of immunology research and immunotherapy.
    Schlagwörter genomics ; immunology ; immunotherapy
    Sprache Englisch
    Erscheinungsverlauf 2018-0111
    Umfang p. 14-21.
    Erscheinungsort Elsevier Inc.
    Dokumenttyp Artikel
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2017.11.011
    Datenquelle NAL Katalog (AGRICOLA)

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  2. Artikel ; Online: Clump sequencing exposes the spatial expression programs of intestinal secretory cells

    Rita Manco / Inna Averbukh / Ziv Porat / Keren Bahar Halpern / Ido Amit / Shalev Itzkovitz

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Band 13

    Abstract: Combining scRNA-seq with spatial information to enable the reconstruction of spatially-resolved cell atlases is challenging for rare cell types. Here the authors present ClumpSeq, an approach for sequencing small clumps of tissue attached cells, and ... ...

    Abstract Combining scRNA-seq with spatial information to enable the reconstruction of spatially-resolved cell atlases is challenging for rare cell types. Here the authors present ClumpSeq, an approach for sequencing small clumps of tissue attached cells, and apply it to establish spatial atlases for all secretory cell types in the small intestine.
    Schlagwörter Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2021-05-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  3. Artikel ; Online: Single‐cell biology

    Maria Polychronidou / Jingyi Hou / M Madan Babu / Prisca Liberali / Ido Amit / Bart Deplancke / Galit Lahav / Shalev Itzkovitz / Matthias Mann / Julio Saez‐Rodriguez / Fabian Theis / Roland Eils

    Molecular Systems Biology, Vol 19, Iss 7, Pp n/a-n/a (2023)

    what does the future hold?

    2023  

    Schlagwörter Biology (General) ; QH301-705.5 ; Medicine (General) ; R5-920
    Sprache Englisch
    Erscheinungsdatum 2023-07-01T00:00:00Z
    Verlag Wiley
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  4. Artikel ; Online: Physically interacting beta-delta pairs in the regenerating pancreas revealed by single-cell sequencing

    Eran Yanowski / Nancy S. Yacovzada / Eyal David / Amir Giladi / Diego Jaitin / Lydia Farack / Adi Egozi / Danny Ben-Zvi / Shalev Itzkovitz / Ido Amit / Eran Hornstein

    Molecular Metabolism, Vol 60, Iss , Pp 101467- (2022)

    2022  

    Abstract: Objectives: Until recently, communication between neighboring cells in islets of Langerhans was overlooked by genomic technologies, which require rigorous tissue dissociation into single cells. Methods: We utilize sorting of physically interacting cells ( ...

    Abstract Objectives: Until recently, communication between neighboring cells in islets of Langerhans was overlooked by genomic technologies, which require rigorous tissue dissociation into single cells. Methods: We utilize sorting of physically interacting cells (PICs) with single-cell RNA-sequencing to systematically map cellular interactions in the endocrine pancreas after pancreatectomy. Results: The pancreas cellular landscape features pancreatectomy associated heterogeneity of beta-cells, including an interaction-specific program between paired beta and delta-cells. Conclusions: Our analysis suggests that the particular cluster of beta-cells that pairs with delta-cells benefits from stress protection, implying that the interaction between beta- and delta-cells might safeguard against pancreatectomy associated challenges. The work encourages testing the potential relevance of physically-interacting beta-delta-cells also in diabetes mellitus.
    Schlagwörter Islet of Langerhans ; Endocrine pancreas ; Single-cell RNA-sequencing ; Single-cell transcriptome sequencing ; scRNA-seq ; beta-delta cell pair ; Internal medicine ; RC31-1245
    Thema/Rubrik (Code) 612
    Sprache Englisch
    Erscheinungsdatum 2022-06-01T00:00:00Z
    Verlag Elsevier
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  5. Artikel ; Online: CRISPECTOR provides accurate estimation of genome editing translocation and off-target activity from comparative NGS data

    Ido Amit / Ortal Iancu / Alona Levy-Jurgenson / Gavin Kurgan / Matthew S. McNeill / Garrett R. Rettig / Daniel Allen / Dor Breier / Nimrod Ben Haim / Yu Wang / Leon Anavy / Ayal Hendel / Zohar Yakhini

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Band 11

    Abstract: The control of off-target activity is a challenge for adapting CRISPR to therapeutic use. Here the authors present CRISPECTOR, a software tool to detect, evaluate and quantify editing activity, including translocations, from NGS data. ...

    Abstract The control of off-target activity is a challenge for adapting CRISPR to therapeutic use. Here the authors present CRISPECTOR, a software tool to detect, evaluate and quantify editing activity, including translocations, from NGS data.
    Schlagwörter Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2021-05-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  6. Artikel ; Online: A single cell atlas of the human liver tumor microenvironment

    Hassan Massalha / Keren Bahar Halpern / Samir Abu‐Gazala / Tamar Jana / Efi E Massasa / Andreas E Moor / Lisa Buchauer / Milena Rozenberg / Eli Pikarsky / Ido Amit / Gideon Zamir / Shalev Itzkovitz

    Molecular Systems Biology, Vol 16, Iss 12, Pp n/a-n/a (2020)

    2020  

    Abstract: Abstract Malignant cell growth is fueled by interactions between tumor cells and the stromal cells composing the tumor microenvironment. The human liver is a major site of tumors and metastases, but molecular identities and intercellular interactions of ... ...

    Abstract Abstract Malignant cell growth is fueled by interactions between tumor cells and the stromal cells composing the tumor microenvironment. The human liver is a major site of tumors and metastases, but molecular identities and intercellular interactions of different cell types have not been resolved in these pathologies. Here, we apply single cell RNA‐sequencing and spatial analysis of malignant and adjacent non‐malignant liver tissues from five patients with cholangiocarcinoma or liver metastases. We find that stromal cells exhibit recurring, patient‐independent expression programs, and reconstruct a ligand–receptor map that highlights recurring tumor–stroma interactions. By combining transcriptomics of laser‐capture microdissected regions, we reconstruct a zonation atlas of hepatocytes in the non‐malignant sites and characterize the spatial distribution of each cell type across the tumor microenvironment. Our analysis provides a resource for understanding human liver malignancies and may expose potential points of interventions.
    Schlagwörter human cell atlas ; liver cancer ; single cell RNAseq ; spatial transcriptomics ; tumor‐stroma interactions ; Biology (General) ; QH301-705.5 ; Medicine (General) ; R5-920
    Thema/Rubrik (Code) 610
    Sprache Englisch
    Erscheinungsdatum 2020-12-01T00:00:00Z
    Verlag Wiley
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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

    Carla A. Gonçalves / Michael Larsen / Sascha Jung / Johannes Stratmann / Akiko Nakamura / Marit Leuschner / Lena Hersemann / Rashmiparvathi Keshara / Signe Perlman / Lene Lundvall / Lea Langhoff Thuesen / Kristine Juul Hare / Ido Amit / Anne Jørgensen / Yung Hae Kim / Antonio del Sol / Anne Grapin-Botton

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Band 17

    Abstract: From single-cell transcriptome analyses to defining culture media for spheroids, the authors provide a census of information to understand the development of human pancreatic progenitors. This approach identifies signalling pathways (EGF and FGF) ... ...

    Abstract From single-cell transcriptome analyses to defining culture media for spheroids, the authors provide a census of information to understand the development of human pancreatic progenitors. This approach identifies signalling pathways (EGF and FGF) regulating progenitor proliferation.
    Schlagwörter Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2021-05-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  8. Artikel ; Online: Bi-fated tendon-to-bone attachment cells are regulated by shared enhancers and KLF transcription factors

    Shiri Kult / Tsviya Olender / Marco Osterwalder / Svetalana Markman / Dena Leshkowitz / Sharon Krief / Ronnie Blecher-Gonen / Shani Ben-Moshe / Lydia Farack / Hadas Keren-Shaul / Tomer-Meir Salame / Terence D Capellini / Shalev Itzkovitz / Ido Amit / Axel Visel / Elazar Zelzer

    eLife, Vol

    2021  Band 10

    Abstract: The mechanical challenge of attaching elastic tendons to stiff bones is solved by the formation of a unique transitional tissue. Here, we show that murine tendon-to-bone attachment cells are bi-fated, activating a mixture of chondrocyte and tenocyte ... ...

    Abstract The mechanical challenge of attaching elastic tendons to stiff bones is solved by the formation of a unique transitional tissue. Here, we show that murine tendon-to-bone attachment cells are bi-fated, activating a mixture of chondrocyte and tenocyte transcriptomes, under regulation of shared regulatory elements and Krüppel-like factors (KLFs) transcription factors. High-throughput bulk and single-cell RNA sequencing of humeral attachment cells revealed expression of hundreds of chondrogenic and tenogenic genes, which was validated by in situ hybridization and single-molecule ISH. ATAC sequencing showed that attachment cells share accessible intergenic chromatin areas with either tenocytes or chondrocytes. Epigenomic analysis revealed enhancer signatures for most of these regions. Transgenic mouse enhancer reporter assays verified the shared activity of some of these enhancers. Finally, integrative chromatin and motif analyses and transcriptomic data implicated KLFs as regulators of attachment cells. Indeed, blocking expression of both Klf2 and Klf4 in developing limb mesenchyme impaired their differentiation.
    Schlagwörter musculoskeletal system ; cartilage ; tendon ; enthesis ; mouse ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
    Sprache Englisch
    Erscheinungsdatum 2021-01-01T00:00:00Z
    Verlag eLife Sciences Publications Ltd
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  9. Artikel ; Online: PD-1/PD-L1 checkpoint blockade harnesses monocyte-derived macrophages to combat cognitive impairment in a tauopathy mouse model

    Neta Rosenzweig / Raz Dvir-Szternfeld / Afroditi Tsitsou-Kampeli / Hadas Keren-Shaul / Hila Ben-Yehuda / Pierre Weill-Raynal / Liora Cahalon / Alex Kertser / Kuti Baruch / Ido Amit / Assaf Weiner / Michal Schwartz

    Nature Communications, Vol 10, Iss 1, Pp 1-

    2019  Band 15

    Abstract: Blocking the PD-1 pathway was shown to be effective in amyloid beta mouse models, yet little is known about its therapeutic potential in models of tauopathy. The authors show here that blocking PD-L1, a PD-1 ligand, is similarly effective, and that both ... ...

    Abstract Blocking the PD-1 pathway was shown to be effective in amyloid beta mouse models, yet little is known about its therapeutic potential in models of tauopathy. The authors show here that blocking PD-L1, a PD-1 ligand, is similarly effective, and that both treatments reversed cognitive deficiencies, and modified disease pathology not only in an animal model of AD, but also in the DM-hTAU mouse tauopathy model, through a mechanism that involves monocyte-derived macrophages.
    Schlagwörter Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2019-01-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  10. Artikel ; Online: Deciphering the state of immune silence in fatal COVID-19 patients

    Pierre Bost / Francesco De Sanctis / Stefania Canè / Stefano Ugel / Katia Donadello / Monica Castellucci / David Eyal / Alessandra Fiore / Cristina Anselmi / Roza Maria Barouni / Rosalinda Trovato / Simone Caligola / Alessia Lamolinara / Manuela Iezzi / Federica Facciotti / Annarita Mazzariol / Davide Gibellini / Pasquale De Nardo / Evelina Tacconelli /
    Leonardo Gottin / Enrico Polati / Benno Schwikowski / Ido Amit / Vincenzo Bronte

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Band 15

    Abstract: Integrated studies of matched tissue sites and cell types in COVID-19 patients are important to define the immune mechanisms of pathology. Here, the authors describe an immune signature in fatal COVID-19 patients harmonizing single-cell RNA sequencing of ...

    Abstract Integrated studies of matched tissue sites and cell types in COVID-19 patients are important to define the immune mechanisms of pathology. Here, the authors describe an immune signature in fatal COVID-19 patients harmonizing single-cell RNA sequencing of blood and matched BAL cells with deep clinical, immunological and functional data.
    Schlagwörter Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2021-03-01T00:00:00Z
    Verlag Nature Portfolio
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