Publications – complete list

The Spectrum and Regulatory Landscape of Intestinal Innate Lymphoid Cells Are Shaped by the Microbiome. Gury-BenAri M, Thaiss CA, Serafini N, Winter DR, Giladi A, Lara-Astiaso D, Levy M, Salame TM, Weiner A, David E, Shapiro H, Dori-Bachash M, Pevsner-Fischer M, Lorenzo-Vivas E, Keren-Shaul H, Paul F, Harmelin A, Eberl G, Itzkovitz S, Tanay A, Di Santo JP, Elinav E, Amit I. Cell (2016)

UMI-4C for quantitative and targeted chromosomal contact profiling. Schwartzman O, Mukamel Z, Oded-Elkayam N, Olivares-Chauvet P, Lubling Y, Landan G, Izraeli S, Tanay A. Nature Methods (2016)

The mutation spectrum in genomic late replication domains shapes mammalian GC content. Kenigsberg E, Yehuda Y, Marjavaara L, Keszthelyi A, Chabes A, Tanay A, Simon I. Nucleic Acids Research (2016)

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors. Paul F, Arkin Y, Giladi A, Jaitin DA, Kenigsberg E, Keren-Shaul H, Winter D, Lara-Astiaso D, Gury M, Weiner A, David E, Cohen N, Lauridsen FK, Haas S, Schlitzer A, Mildner A, Ginhoux F, Jung S, Trumpp A, Porse BT, Tanay A, Amit I. Cell (2016)

Single-cell Hi-C for genome-wide detection of chromatin interactions that occur simultaneously in a single cell. Nagano T, Lubling Y, Yaffe E, Wingett SW, Dean W, Tanay A, Fraser P. Nature Protocols (2015)

Single-cell epigenomics: techniques and emerging applications. Schwartzman O, Tanay A. Nature Reviews Genetics (2015)

Derivation of novel human ground state naive pluripotent stem cells. Gafni O, Weinberger L, Mansour AA, Manor YS, 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 JH. Nature (2015)

Deterministic direct reprogramming of somatic cells to pluripotency. Rais Y, Zviran A, Geula S, Gafni O, Chomsky E, Viukov S, Mansour AA, Caspi I, Krupalnik V, Zerbib M, Maza I, Mor N, Baran D, Weinberger L, Jaitin DA, Lara-Astiaso D, Blecher-Gonen R, Shipony Z, Mukamel Z, Hagai T, Gilad S, Amann-Zalcenstein D, Tanay A, Amit I, Novershtern N, Hanna JH. Nature (2015)

Comparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture. Vietri Rudan M, Barrington C, Henderson S, Ernst C, Odom DT, Tanay A, Hadjur S. Cell Reports (2015)

Cooperativity, specificity, and evolutionary stability of Polycomb targeting in Drosophila. Schuettengruber B, Oded Elkayam N, Sexton T, Entrevan M, Stern S, Thomas A, Yaffe E, Parrinello H, Tanay A, Cavalli G. Cell Reports (2014)

Intratumor DNA methylation heterogeneity reflects clonal evolution in aggressive prostate cancer. Brocks D, Assenov Y, Minner S, Bogatyrova O, Simon R, Koop C, Oakes C, Zucknick M, Lipka DB, Weischenfeldt J, Feuerbach L, Cowper-Sal Lari R, Lupien M, Brors B, Korbel J, Schlomm T, Tanay A, Sauter G, Gerhäuser C, Plass C. Cell Reports (2014)

Dynamic and static maintenance of epigenetic memory in pluripotent and somatic cells. Shipony Z, Mukamel Z, Cohen NM, Landan G, Chomsky E, Zeliger SR, Fried YC, Ainbinder E, Friedman N, Tanay A. Nature (2014)

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types. Jaitin D, Kenigsberg E, Keren-Shaul H, Elefant N, Paul F, Zaretsky I, Mildner A, Coehn N, Jung S, Tanay A, Amit I Science (2014)

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nagano T, Lubling Y, Stevens TJ, Schoenfelder S, Yaffe E, Dean W, Laue ED, Tanay A, Fraser P. Nature (2013)

Chromosomal domains: epigenetic contexts and functional implications of genomic compartmentalization. Tanay A and Cavalli G Curr Opion Gene. and Dev.(2013)

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

Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues. Landan G, Cohen NM, Mukamel Z, Bar A, Molchadsky A, Brosh R, Horn-Saban S, Zalcenstein DA, Goldfinger N, Zundelevich A, Gal-Yam EN, Rotter V, Tanay A. Nature Genetics (2012)

Robust 4C-seq data analysis to screen for regulatory DNA interactions. van de Werken HG*, Landan G*, Holwerda SJ, Hoichman M, Klous P, Chachik R, Splinter E, Quezada CV, Öz Y, Bouwma B, Verstegen M, de Wit E, Tanay A*, de Laat W* Nature Methods (2012)

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

Inferring divergence of context dependent substitution rates in drosophila genomes with applications to comparative genomics. Chachick R and Tanay A. Mol Biol Evol(2012)

Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture.
Yaffe E and Tanay A. Nature Genetics(2011)

Primate CpG Islands Are Maintained by Heterogeneous Evolutionary Regimes Involving Minimal Selection.
Mendelson Cohen N, Kenigsberg E, and Tanay A. Cell (2011)

Dynamic combinatorial interactions of RUNX1 and cooperating partners regulates megakaryocytic differentiation in cell line models
Pencovich N, Jaschek R, Tanay A, Groner Y. Blood. 2011 Jan 6;117(1):e1-e14..

Widespread Compensatory Evolution Conserves DNA-Encoded Nucleosome Organization in Yeast.
Kenigsberg E, Bar A, Segal E, Tanay A. PLoS Comput Biol (2010),

H2A.Z maintenance during mitosis reveals nucleosome shifting on mitotically silenced genes.
Kelly TK, Miranda TB, Liang G, Berman BP, Lin JC, Tanay A, Jones PA Mol Cell. 2010 Sep 24;39(6):901-11

Comparative Analysis of DNA Replication Timing Reveals Conserved Large-Scale Chromosomal Architecture.
Yaffe E, Farkash-Amar S, Polten A, Yakhini Z, Tanay A, Simon I. PLoS Genetics (2010).

Infering complex substitution dynamics given flanking nucleotides, G+C content and recombination rate.
Tanay, A. TR 2010-1.

Expander: from expression microarrays to networks and functions.
Ulitsky I, Maron-Katz A, Shavit S, Sagir D, Linhart C, Elkon R, Tanay A, Sharan R, Shiloh Y, Shamir R. Nat Protoc. 2010;5(2):303-22. Epub 2010 Jan 28.

A systematic approach to understand the functional consequences of non-protein coding risk regions
Coetzee GA, Jia L, Frenkel B, Henderson BE, Tanay A, Haiman CA, Freedman ML. .Cell Cycle. 2010 Jan 15;9(2):256-9. Epub 2010 Jan 23.

DNA methylation programming and reprogramming in primate embryonic stem cells.
Cohen NM, Dighe V, Landan G, Reynisdóttir S, Palsson A, Mitalipov S, Tanay A. Genome Res 2009.

Functional enhancers at the gene-poor 8q24 cancer linked region.
Li Jia*, Gilad Landan*, Mark Pomeranz, Rami Jaschek, Paula Herman, David Reich, Chunli Yan, Omar Khalid, Phil Kanthoff, William Oh, Robert Manak, Benjamim Berman, Brian Henderson, Baruch Franekl, Christopher Haiman, Mathew Friedman, Amos Tanay, Gerhard Coetzee. PLoS Genet, 2009.

Spatial Clustering of Multivariate Genomic and Epigenomic Information.
Rami Jaschek, Amos Tanay. RECOMB 2009: 170-183

Functional anatomy of polycomb and trithorax chromatin landscapes in Drosophila embryos.
Schuettengruber B, Ganapathi M, Leblanc B, Portoso M, Jaschek R, Tolhuis B, van Lohuizen M, Tanay A, Cavalli G. PLoS Biol. 2009 Jan 13;7(1):e13.

Frequent switching of Polycomb repressive marks and DNA hypermethylation in the PC3 prostate cancer cell line.
Einav Nili Gal-Yam, Gerda Egger, Leo Iniguez, Heather Holster, Steingrimur Einarsson, Xinmin Zhang, Joy C. Lin, Gangning Liang, Peter A. Jones and Amos Tanay. PNAS September 2, 2008 vol. 105 no. 35 12979-12984

Sequence contexts affect the rate of short insertions and deletions in flies and primates.
Amos Tanay and Eric Siggia. Genome Biolgoy. 2008.

Evolution and selection in yeast promoters: analyzing the combined effect of diverse transcription factor binding sites.
Daniela Raijman, Ron Shamir and Amos Tanay. PloS Computational Biology 2008

Hyperconserved CpG domains underlie polycomb binding sites.
Amos Tanay, Anne Odonnel, Marc Damelin and Timothy H. Bestor. Proc Nat Acad Sci USA 2007 104(13):5521-6.

Einav Nili GalYam, Shinwu Jeong, Amos Tanay, Gerda Egger, Amy Lee and Peter A. Jones. Constitutive nucleosome depletion and stress induced, ordered factor assembly at the GRP78 core promoter revealed by single molecule resolution footprinting. PloS Genetics, 2006 Sep 22;2(9).

Extensive Low-affinity Transcriptional Interactions in the Yeast Genome.
Amos Tanay. Genome Research, 2006 Aug;16(8):962-72.

Archana Belle, Amos Tanay, Ledion Bitincka, Ron Shamir and Erin OShea. Quantification of protein half-lives in the budding yeast proteome. Proc Nat Acad Sci USA 2006 Aug 29;103(35):13004-9.

Irit Gat-Viks, Amos Tanay, Daniela Raijman and Ron Shamir. A probabilistic methodology for integrating knowledge and experiments on biological networks. J Comput Biol. 2006 Mar;13(2):165-81.

Dana Pe’er, Amos Tanay, Aviv Regev. “Minreg: A Scalable Algorithm for Learning Parsimonious Regulatory networks in Yeast and Mammals”, Journal of Machine Learning Research, in press.

Ron Shamir, Adi Maron-Katz, Amos Tanay, Chaim Linhart, Israel Steinfeld, Roded Sharan, Yosi Shiloh, Rani Elkon. EXPANDER–an integrative program suite for microarray data analysis. BMC Bioinformatics. 2005 Sep 21;6:232.

Amos Tanay, Aviv Regev and Ron Shamir. “Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast”. Proc Nat Acad Sci USA 102 (20):7203-8, 2005.

Amos Tanay, Israel Steinfeld, Martin Kupiec and Ron Shamir. “Integrative analysis of genome-wide experiments in the context of a large high-throughput data compendium”. Mol. Syst. Biol., doi: 10.1038/msb4100005, 2005.

Aimee M. Dudley, Daniel M. Janse, Amos Tanay, Ron Shamir and George M. Church. “A global view of pleitropy and phenotypically derived gene function in yeast”. Mol. Syst. Biol. doi 10.1038/msb4100004, 2005.

Amos Tanay, Irit Gat-Viks and Ron Shamir. A Global View of the Selection Forces in the Evolution of Yeast Cis-Regulation. Genome Research 14: 829-834, 2004.

Amos Tanay, Roded Sharan, Martin Kupiec and Ron Shamir. Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data. Proc. National Academy of Science USA 101 (9), 2981-2986 (2004).

Irit Gat-Viks*, Amos Tanay* and Ron Shamir. Modeling and Analysis of Heterogeneous Regulation in Biological Network. To appear in Journal of Computational Biology. (* equal contribution)

Amos Tanay and Ron Shamir. Multi-level Modeling and Inference of Transcription Regulation. Journal of Computational Biology, 11(2-3), 357-75 (2004).

Amos Tanay, Roded Sharan and Ron Shamir. Discovering Statistically Significant Biclusters in Gene Expression Data. Bioinformatics 18 Supp 1, S136-44 (2002) (Proceedings of ISMB 2002).

Dana Pe’er, Amos Tanay and Aviv Regev. “Minreg: inferring an active regulator set”. Bioinformatics 18 Supp 1, S258-671 (2002) (Proceedings of ISMB 2002)

Amos Tanay and Ron Shamir. “Computational Expansion of Genetic Networks”. Bioinformatics 17 Supp 1 S270-S278 (2001) (Proceedings of ISMB 2001).

Peer reviewed Conferences:

Irit Gat-Viks, Amos Tanay and Ron Shamir. Biological Networks Involving Metabolic Pathways and Gene Regulation: Modeling and Inference”. The first RECOMB satellite meeting on regulatory genomics, University of California, San Diego, March 26-27, 2004.

Amos Tanay and Ron Shamir. Modeling transcription programs: inferring binding site activity and dose-response model optimization. Proceedings of RECOMB 2003, pp. 301-310 (Journal version published in J. Comp Biol).

Irit Gat-Viks, Amos Tanay, Daniela Raijman and Ron Shamir. “The Factor Graph Network Model for biological systems”. Proceeding of RECOMB 2005 (Journal version published in J Comp Biol).