Single-cell analysis of human non-small cell lung cancer lesions refines tumor classification and patient stratification. Andrew M Leader, John A Grout, Barbara B Maier, Barzin Y Nabet, Matthew D Park, Alexandra Tabachnikova, Christie Chang, Laura Walker, Alona Lansky, Jessica Le Berichel, Leanna Troncoso, Nausicaa Malissen, Melanie Davila, Jerome C Martin, Giuliana Magri, Kevin Tuballes, Zhen Zhao, Francesca Petralia, Robert Samstein, Natalie Roy D’Amore, Gavin Thurston, Alice O Kamphorst, Andrea Wolf, Raja Flores, Pei Wang, Sören Müller, Ira Mellman, Mary Beth Beasley, Hélène Salmon, Adeeb H Rahman, Thomas U Marron, Ephraim Kenigsberg, Miriam Merad. Cancer Cell 2021

DNA methylation disruption reshapes the hematopoietic differentiation landscape.Franco Izzo, Stanley C. Lee, Asaf Poran, Ronan Chaligne, Federico Gaiti, Baptiste Gross, Rekha R. Murali, Sunil D. Deochand, Chelston Ang, Philippa Wyndham Jones, Anna S. Nam, Kyu-Tae Kim, Steven Kothen-Hill, Rafael C. Schulman, Michelle Ki, Priscillia Lhoumaud, Jane A. Skok, Aaron D. Viny, Ross L. Levine, Ephraim Kenigsberg, Omar Abdel-Wahab, Dan A. Landau. Nature Genetics 2020

Single-cell analysis of Crohn’s disease lesions identifies a pathogenic cellular module associated with resistance to anti-TNF therapy. Jerome C. Martin, Christie Chang, Gilles Boschetti, Ryan Ungaro, Mamta Giri, John A. Grout, Kyle Gettler, Ling-shiang Chuang, Shikha Nayar, Alexander J. Greenstein, Marla Dubinsky, Laura Walker, Andrew Leader, Jay S. Fine, Charles E. Whitehurst, M Lamine Mbow, Subra Kugathasan¹⁰, Lee A. Denson, Jeffrey S. Hyams, Joshua R. Friedman, Prerak T. Desai, Huaibin M. Ko, Ilaria Laface^1,2,8, Guray Akturk, Eric E. Schadt, Helene Salmon, Sacha Gnjatic, Adeeb H. Rahman, Miriam Merad*, Judy H. Cho*, Ephraim Kenigsberg*. Cell 2019

MARS-seq2. 0: an experimental and analytical pipeline for indexed sorting combined with single-cell RNA sequencing. Hadas Keren-Shaul, Ephraim Kenigsberg, Diego Adhemar Jaitin, Eyal David, FranziskaPaul, Amos Tanay, Ido Amit. Nature Protocols 2019

The mutation spectrum in genomic late replication domains shapes mammalian GC content. Ephraim Kenigsberg*, Yishai Yehuda*, Lisette Marjavaara, Andrea Keszthelyi, Andrei Chabes, Amos Tanay, Itamar Simon. NAR 2016

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors. Franziska Paul, Ya’ara Arkin, Amir Giladi, Diego Adhemar Jaitin, Ephraim Kenigsberg, Hadas Keren-Shaul, Deborah Winter, David Lara-Astiaso, Meital Gury, Assaf Weiner, Eyal David, Nadav Cohen, Felicia Kathrine Bratt Lauridsen, Simon Haas, Andreas Schlitzer, Alexander Mildner, Florent Ginhoux, Steffen Jung, Andreas Trumpp, Bo Torben Porse, Amos Tanay, Ido Amit. Cell 2015

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types. Diego Adhemar Jaitin*, Ephraim Kenigsberg*, Hadas Keren-Shaul*, Naama Elefant, Franziska Paul, Irina Zaretsky, Alexander Mildner, Nadav Cohen, Steffen Jung, Amos Tanay, Ido Amit. Science 2014

Drosophila Functional Elements Are Embedded in Structurally Constrained Sequences. Ephraim Kenigsberg and Amos Tanay. PLoS Genetics 2013

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome. Tom Sexton*, Eitan Yaffe*, Ephraim Kenigsberg, Frederic Bantignies, Benjamin Leblanc, Michael Hoichman, Hugues Parrinello, Amos Tanay, and Giacomo Cavalli. Cell 2012

Primate CpG Islands Are Maintained by Heterogeneous Evolutionary Regimes Involving Minimal Selection. Netta Mendelson Cohen, Ephraim Kenigsberg, and Amos Tanay. Cell 2011

Widespread Compensatory Evolution Conserves DNA-Encoded Nucleosome Organization in Yeast. Ephraim Kenigsberg, Amir Bar, Eran Segal, Amos Tanay. PLoS Comp Bio 2010

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