Works by Tanay, Amos

Results: 38

Functional Anatomy of Polycomb and Trithorax Chromatin Landscapes in Drosophila Embryos.

Published in:

PLoS Biology, 2009, v. 7, n. 1, p. e1000013, doi. 10.1371/journal.pbio.1000013

By:

Leblanc, Benjamin;
Portoso, Manuela;
Jaschek, Rami;
Tolhuis, Bas;
Van Lohuizen, Maarten;
Tanay, Amos;
Cavalli, Giacomo

Publication type:

Article

Single cell Hi-C identifies plastic chromosome conformations underlying the gastrulation enhancer landscape.

Published in:

Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-39549-4

By:

Rappoport, Nimrod;
Chomsky, Elad;
Nagano, Takashi;
Seibert, Charlie;
Lubling, Yaniv;
Baran, Yael;
Lifshitz, Aviezer;
Leung, Wing;
Mukamel, Zohar;
Shamir, Ron;
Fraser, Peter;
Tanay, Amos

Publication type:

Article

MARS-seq2.0: an experimental and analytical pipeline for indexed sorting combined with single-cell RNA sequencing.

Published in:

Nature Protocols, 2019, v. 14, n. 6, p. 1841, doi. 10.1038/s41596-019-0164-4

By:

Keren-Shaul, Hadas;
Kenigsberg, Ephraim;
Jaitin, Diego Adhemar;
David, Eyal;
Paul, Franziska;
Tanay, Amos;
Amit, Ido

Publication type:

Article

Cohesin-mediated interactions organize chromosomal domain architecture.

Published in:

EMBO Journal, 2013, v. 32, n. 24, p. 3119, doi. 10.1038/emboj.2013.237

By:

Sofueva, Sevil;
Yaffe, Eitan;
Chan, Wen-Ching;
Georgopoulou, Dimitra;
Vietri Rudan, Matteo;
Mira-Bontenbal, Hegias;
Pollard, Steven M;
Schroth, Gary P;
Tanay, Amos;
Hadjur, Suzana

Publication type:

Article

Integrative analysis of genome-wide experiments in the context of a large high-throughput data compendium.

Published in:

Molecular Systems Biology, 2005, v. 1, n. 1, p. E1, doi. 10.1038/msb4100005

By:

Tanay, Amos;
Steinfeld, Israel;
Kupiec, Martin;
Shamir, Ron

Publication type:

Article

A global view of pleiotropy and phenotypically derived gene function in yeast.

Published in:

Molecular Systems Biology, 2005, v. 1, n. 1, p. E1, doi. 10.1038/msb4100004

By:

Dudley, Aimée Marie;
Janse, Daniel Maarten;
Tanay, Amos;
Shamir, Ron;
Church, George McDonald

Publication type:

Article

Widespread Compensatory Evolution Conserves DNAEncoded Nucleosome Organization in Yeast.

Published in:

PLoS Computational Biology, 2010, v. 6, n. 12, p. 1, doi. 10.1371/journal.pcbi.1001039

By:

Kenigsberg, Ephraim;
Bar, Amir;
Segal, Eran;
Tanay, Amos

Publication type:

Article

Evolution and Selection in Yeast Promoters: Analyzing the Combined Effect of Diverse Transcription Factor Binding Sites.

Published in:

PLoS Computational Biology, 2008, v. 4, n. 1, p. e7, doi. 10.1371/journal.pcbi.0040007

By:

Raijman, Daniela;
Shamir, Ron;
Tanay, Amos

Publication type:

Article

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure.

Published in:

Nature, 2013, v. 502, n. 7469, p. 59, doi. 10.1038/nature12593

By:

Nagano, Takashi;
Lubling, Yaniv;
Stevens, Tim J.;
Schoenfelder, Stefan;
Yaffe, Eitan;
Dean, Wendy;
Laue, Ernest D.;
Tanay, Amos;
Fraser, Peter

Publication type:

Article

MinReg: A Scalable Algorithm for Learning Parsimonious Regulatory Networks in Yeast and Mammals.

Published in:

Journal of Machine Learning Research, 2006, v. 7, n. 2, p. 167

By:

Pe'er, Dana;
Tanay, Amos;
Regev, Aviv;
Jaakkola, Tommi

Publication type:

Article

MCProj: metacell projection for interpretable and quantitative use of transcriptional atlases.

Published in:

Genome Biology, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s13059-023-03069-7

By:

Ben-Kiki, Oren;
Bercovich, Akhiad;
Lifshitz, Aviezer;
Raz, Ofir;
Brook, Dror;
Tanay, Amos

Publication type:

Article

Single-cell Hi-C for genome-wide detection of chromatin interactions that occur simultaneously in a single cell.

Published in:

Nature Protocols, 2015, v. 10, n. 12, p. 1986, doi. 10.1038/nprot.2015.127

By:

Takashi Nagano;
Lubling, Yaniv;
Yaffe, Eitan;
Wingett, Steven W.;
Dean, Wendy;
Tanay, Amos;
Fraser, Peter

Publication type:

Article

Combgap Promotes Ovarian Niche Development and Chromatin Association of EcR-Binding Regions in BR-C.

Published in:

PLoS Genetics, 2016, v. 12, n. 11, p. 1, doi. 10.1371/journal.pgen.1006330

By:

Hitrik, Anna;
Popliker, Malka;
Gancz, Dana;
Mukamel, Zohar;
Lifshitz, Aviezer;
Schwartzman, Omer;
Tanay, Amos;
Gilboa, Lilach

Publication type:

Article

Dynamic and static maintenance of epigenetic memory in pluripotent and somatic cells.

Published in:

Nature, 2014, v. 513, n. 7516, p. 115, doi. 10.1038/nature13458

By:

Shipony, Zohar;
Mukamel, Zohar;
Cohen, Netta Mendelson;
Landan, Gilad;
Tanay, Amos;
Chomsky, Elad;
Zeliger, Shlomit Reich;
Friedman, Nir;
Fried, Yael Chagit;
Ainbinder, Elena

Publication type:

Article

Metacell-2: a divide-and-conquer metacell algorithm for scalable scRNA-seq analysis.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02667-1

By:

Ben-Kiki, Oren;
Bercovich, Akhiad;
Lifshitz, Aviezer;
Tanay, Amos

Publication type:

Article

Robust 4C-seq data analysis to screen for regulatory DNA interactions.

Published in:

Nature Methods, 2012, v. 9, n. 10, p. 969, doi. 10.1038/nmeth.2173

By:

van de Werken, Harmen J G;
Landan, Gilad;
Holwerda, Sjoerd J B;
Hoichman, Michael;
Klous, Petra;
Chachik, Ran;
Splinter, Erik;
Valdes-Quezada, Christian;
Öz, Yuva;
Bouwman, Britta A M;
Verstegen, Marjon J A M;
de Wit, Elzo;
Tanay, Amos;
de Laat, Wouter

Publication type:

Article

Minreg: Inferring an active regulator set.

Published in:

Bioinformatics, 2002, v. 18, p. S258

By:

Pe'er, Dana;
Regev, Aviv;
Tanay, Amos

Publication type:

Article

Discovering statistically significant biclusters in gene expression data.

Published in:

Bioinformatics, 2002, v. 18, p. S136, doi. 10.1093/bioinformatics/18.suppl_1.S136

By:

Tanay, Amos;
Sharan, Roded;
Shamir, Ron

Publication type:

Article

Computational expansion of genetic networks.

Published in:

Bioinformatics, 2001, v. 17, p. 270, doi. 10.1093/bioinformatics/17.suppl_1.s270

By:

Tanay, Amos;
Shamir, Ron

Publication type:

Article

Single-cell epigenomics: techniques and emerging applications.

Published in:

2015

By:

Schwartzman, Omer;
Tanay, Amos

Publication type:

journal article

Dissecting cellular crosstalk by sequencing physically interacting cells.

Published in:

Nature Biotechnology, 2020, v. 38, n. 5, p. 629, doi. 10.1038/s41587-020-0442-2

By:

Giladi, Amir;
Cohen, Merav;
Medaglia, Chiara;
Baran, Yael;
Li, Baoguo;
Zada, Mor;
Bost, Pierre;
Blecher-Gonen, Ronnie;
Salame, Tomer-Meir;
Mayer, Johannes U.;
David, Eyal;
Ronchese, Franca;
Tanay, Amos;
Amit, Ido

Publication type:

Article

Inferring Divergence of Context-Dependent Substitution Rates in Drosophila Genomes with Applications to Comparative Genomics.

Published in:

Molecular Biology & Evolution, 2012, v. 29, n. 7, p. 1769, doi. 10.1093/molbev/mss056

By:

Chachick, Ran;
Tanay, Amos

Publication type:

Article

The mutation spectrum in genomic late replication domains shapes mammalian GC content.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4222, doi. 10.1093/nar/gkw268

By:

Kenigsberg, Ephraim;
Yishai Yehuda;
Marjavaara, Lisette;
Keszthelyi, Andrea;
Chabes, Andrei;
Tanay, Amos;
Simon, Itamar

Publication type:

Article

Global DNA methylation reflects spatial heterogeneity and molecular evolution of lung adenocarcinomas.

Published in:

International Journal of Cancer, 2019, v. 144, n. 5, p. 1061, doi. 10.1002/ijc.31939

By:

Dietz, Steffen;
Lifshitz, Aviezer;
Kazdal, Daniel;
Harms, Alexander;
Endris, Volker;
Winter, Hauke;
Stenzinger, Albrecht;
Warth, Arne;
Sill, Martin;
Tanay, Amos;
Sültmann, Holger

Publication type:

Article

Deciphering the molecular mechanisms underlying the three-dimensional folding of the Drosophila genome into physical domains.

Published in:

2013

By:

Jacquier, Caroline;
Sexton, Tom;
Yaffe, Eitan;
Kenigsberg, Ephraim;
Bantignies, Frédéric;
Leblanc, Benjamin;
Hoichman, Michael;
Parrinello, Hugues;
Tanay, Amos;
Cavalli, Giacomo

Publication type:

Abstract

Cell-Autonomous Function of Runx1 Transcriptionally Regulates Mouse Megakaryocytic Maturation

Published in:

PLoS ONE, 2013, v. 8, n. 5, p. 1, doi. 10.1371/journal.pone.0064248

By:

Pencovich, Niv;
Jaschek, Ram;
Dicken, Joseph;
Amit, Ayelet;
Lotem, Joseph;
Tanay, Amos;
Groner, Yoram

Publication type:

Article

<i>Drosophila</i> Functional Elements Are Embedded in Structurally Constrained Sequences

Published in:

PLoS Genetics, 2013, v. 9, n. 5, p. 1, doi. 10.1371/journal.pgen.1003512

By:

Kenigsberg, Ephraim;
Tanay, Amos

Publication type:

Article

Hypomethylation marks enhancers within transposable elements.

Published in:

Nature Genetics, 2013, v. 45, n. 7, p. 717, doi. 10.1038/ng.2680

By:

Mukamel, Zohar;
Tanay, Amos

Publication type:

Article

Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues.

Published in:

Nature Genetics, 2012, v. 44, n. 11, p. 1207, doi. 10.1038/ng.2442

By:

Landan, Gilad;
Cohen, Netta Mendelson;
Mukamel, Zohar;
Bar, Amir;
Molchadsky, Alina;
Brosh, Ran;
Horn-Saban, Shirley;
Zalcenstein, Daniela Amann;
Goldfinger, Naomi;
Zundelevich, Adi;
Gal-Yam, Einav Nili;
Rotter, Varda;
Tanay, Amos

Publication type:

Article

Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture.

Published in:

Nature Genetics, 2011, v. 43, n. 11, p. 1059, doi. 10.1038/ng.947

By:

Yaffe, Eitan;
Tanay, Amos

Publication type:

Article

DNA methylation landscapes of 1538 breast cancers reveal a replication-linked clock, epigenomic instability and cis-regulation.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-25661-w

By:

Batra, Rajbir Nath;
Lifshitz, Aviezer;
Vidakovic, Ana Tufegdzic;
Chin, Suet-Feung;
Sati-Batra, Ankita;
Sammut, Stephen-John;
Provenzano, Elena;
Ali, H. Raza;
Dariush, Ali;
Bruna, Alejandra;
Murphy, Leigh;
Purushotham, Arnie;
Ellis, Ian;
Green, Andrew;
Garrett-Bakelman, Francine E.;
Mason, Chris;
Melnick, Ari;
Aparicio, Samuel A. J. R.;
Rueda, Oscar M.;
Tanay, Amos

Publication type:

Article

Recurrent deletions in clonal hematopoiesis are driven by microhomology-mediated end joining.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-22803-y

By:

Feldman, Tzah;
Bercovich, Akhiad;
Moskovitz, Yoni;
Chapal-Ilani, Noa;
Mitchell, Amanda;
Medeiros, Jessie J. F.;
Biezuner, Tamir;
Kaushansky, Nathali;
Minden, Mark D.;
Gupta, Vikas;
Milyavsky, Michael;
Livneh, Zvi;
Tanay, Amos;
Shlush, Liran I.

Publication type:

Article

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

Published in:

Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1812-2

By:

Baran, Yael;
Bercovich, Akhiad;
Sebe-Pedros, Arnau;
Lubling, Yaniv;
Giladi, Amir;
Chomsky, Elad;
Meir, Zohar;
Hoichman, Michael;
Lifshitz, Aviezer;
Tanay, Amos

Publication type:

Article

A systematic approach to understand the functional consequences of non-protein coding risk regions.

Published in:

Cell Cycle, 2010, v. 9, n. 2, p. 256, doi. 10.4161/cc.9.2.10419

By:

Coetzee, Gerhard A.;
Li Jia;
Frenkel, Baruch;
Henderson, Brian E.;
Tanay, Amos;
Haiman, Christopher A.;
Freedman, Matthew L.

Publication type:

Article

EXPANDER -- an integrative program suite for microarray data analysis.

Published in:

BMC Bioinformatics, 2005, v. 6, p. 1, doi. 10.1186/1471-2105-6-232

By:

Shamir, Ron;
Maron-Katz, Adi;
Tanay, Amos;
Linhart, Chaim;
Steinfeld, Israel;
Sharan, Roded;
Shiloh, Yosef;
Elkon, Ran

Publication type:

Article

Comparative Analysis of DNA Replication Timing Reveals Conserved Large-Scale Chromosomal Architecture.

Published in:

PLoS Genetics, 2010, v. 6, n. 7, p. 1, doi. 10.1371/journal.pgen.1001011

By:

Yaffe, Eitan;
Farkash-Amar, Shlomit;
Polten, Andreas;
Yakhini, Zohar;
Tanay, Amos;
Simon, Itamar

Publication type:

Article

Functional Enhancers at the Gene-Poor 8q24 Cancer- Linked Locus.

Published in:

PLoS Genetics, 2009, v. 5, n. 8, p. 1, doi. 10.1371/journal.pgen.1000597

By:

Li Jia;
Landan, Gilad;
Pomerantz, Mark;
Jaschek, Rami;
Herman, Paula;
Reich, David;
Chunli Yan;
Khalid, Omar;
Kantoff, Phil;
Oh, William;
Manak, J. Robert;
Berman, Benjamin P.;
Henderson, Brian E.;
Frenkel, Baruch;
Haiman, Christopher A.;
Freedman, Matthew;
Tanay, Amos;
Coetzee, Gerhard A.

Publication type:

Article

Constitutive Nucleosome Depletion and Ordered Factor Assembly at the GRP78 Promoter Revealed by Single Molecule Footprinting.

Published in:

PLoS Genetics, 2006, v. 3, n. 3, p. e160, doi. 10.1371/journal.pgen.0020160

By:

Gal-Yam, Einav Nili;
Jeong, Shinwu;
Tanay, Amos;
Egger, Gerda;
Lee, Amy S.;
Jones, Peter A.

Publication type:

Article