Publications

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

Single-cell analysis of Crohn’s disease lesions identifies a pathogenic cellular module associated with resistance to anti TNF therapy, Jerome Christophe Martin, Gilles Boschetti, Christie Chang, Ryan Ungaro, Mamta Giri, Ling-Shiang Chuang, Shikha Nayar, Alexander Greenstein, Marla Dubinsky, Laura Walker, Andrew Leader, Jay Fine, Charles Whitehurst, Lamine Mbow, Subra Kugathasan, Lee Denson, Jeffrey Hyams, Joshua Friedman, Prerak Desai, Mabel Ko, Ilaria Laface, Guray Akturk, Eric Schadt, Sacha Gnjatic, Adeeb Rahman, Miriam Merad, Judy Cho, Ephraim Kenigsberg. bioRxiv 2018

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 ProgenitorsFranziska 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 TypesDiego 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 SequencesEphraim Kenigsberg and Amos Tanay. PLoS Genetics 2013

Three-Dimensional Folding and Functional Organization Principles of the Drosophila GenomeTom 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