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Algorithms and experimental tools for integrating very large-scale single cell genomics data

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Publications

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

Author(s): Hanjie Li, Anne M. van der Leun, Ido Yofe, Yaniv Lubling, Dikla Gelbard-Solodkin, Alexander C.J. van Akkooi, Marlous van den Braber, Elisa A. Rozeman, John B.A.G. Haanen, Christian U. Blank, Hugo M. Horlings, Eyal David, Yael Baran, Akhiad Bercovich, Aviezer Lifshitz, Ton N. Schumacher, Amos Tanay, Ido Amit
Published in: Cell, Issue 176/4, 2019, Page(s) 775-789.e18, ISSN 0092-8674
DOI: 10.1016/j.cell.2018.11.043

Cnidarian Cell Type Diversity and Regulation Revealed by Whole-Organism Single-Cell RNA-Seq

Author(s): Arnau Sebé-Pedrós, Baptiste Saudemont, Elad Chomsky, Flora Plessier, Marie-Pierre Mailhé, Justine Renno, Yann Loe-Mie, Aviezer Lifshitz, Zohar Mukamel, Sandrine Schmutz, Sophie Novault, Patrick R.H. Steinmetz, François Spitz, Amos Tanay, Heather Marlow
Published in: Cell, Issue 173/6, 2018, Page(s) 1520-1534.e20, ISSN 0092-8674
DOI: 10.1016/j.cell.2018.05.019

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

Author(s): Arnau Sebé-Pedrós, Elad Chomsky, Kevin Pang, David Lara-Astiaso, Federico Gaiti, Zohar Mukamel, Ido Amit, Andreas Hejnol, Bernard M. Degnan, Amos Tanay
Published in: Nature Ecology & Evolution, Issue 2/7, 2018, Page(s) 1176-1188, ISSN 2397-334X
DOI: 10.1038/s41559-018-0575-6

Dissecting cellular crosstalk by sequencing physically interacting cells

Author(s): Amir Giladi, Merav Cohen, Chiara Medaglia, Yael Baran, Baoguo Li, Mor Zada, Pierre Bost, Ronnie Blecher-Gonen, Tomer-Meir Salame, Johannes U. Mayer, Eyal David, Franca Ronchese, Amos Tanay, Ido Amit
Published in: Nature Biotechnology, Issue 38/5, 2020, Page(s) 629-637, ISSN 1087-0156
DOI: 10.1038/s41587-020-0442-2

Single-cell analysis of clonal maintenance of transcriptional and epigenetic states in cancer cells

Author(s): Zohar Meir, Zohar Mukamel, Elad Chomsky, Aviezer Lifshitz, Amos Tanay
Published in: Nature Genetics, Issue 52/7, 2020, Page(s) 709-718, ISSN 1061-4036
DOI: 10.1038/s41588-020-0645-y

MetaCell: analysis of single-cell RNA-seq data using K-nn graph partitions

Author(s): Yael Baran, Akhiad Bercovich, Arnau Sebe-Pedros, Yaniv Lubling, Amir Giladi, Elad Chomsky, Zohar Meir, Michael Hoichman, Aviezer Lifshitz, Amos Tanay
Published in: Genome Biology, Issue 20/1, 2019, ISSN 1474-760X
DOI: 10.1186/s13059-019-1812-2