2018

Environment dominates over host genetics in shaping human gut microbiota

Daphna Rothschild, Omer Weissbrod, Elad Barkan, Alexander Kurilshikov, Tal Korem, David Zeevi, Paul I. Costea, Anastasia Godneva, Iris N. Kalka, Noam Bar, Smadar Shilo, Dar Lador, Arnau Vich Vila, Niv Zmora, Meirav Pevsner-Fischer, David Israeli, Noa Kosower, Gal Malka, Bat Chen Wolf, Tali Avnit-Sagi, Maya Lotan-Pompan, Adina Weinberger, Zamir Halpern, Shai Carmi, Jingyuan Fu, Cisca Wijmenga, Alexandra Zhernakova, Eran Elinav & Eran Segal

Nature, 2018

Unraveling the determinants of microRNA mediated regulation using a massively parallel reporter assay

Ilya Vainberg Slutskin, Shira Weingarten-Gabbay, Ronit Nir, Adina Weinberger and Eran Segal

Nature Communication, 2018

2017

Sequence features of viral and human Internal Ribosome Entry Sites predictive of their activity

Alexey A. Gritsenko, Shira Weingarten-Gabbay, Shani Elias-Kirma, Ronit Nir, Dick de Ridder, Eran Segal

PLoS, 2017

Bread Affects Clinical Parameters and Induces Gut Microbiome-Associated Personal Glycemic Responses

Tal Korem, David Zeevi, Niv Zmora, Omer Weissbrod, Noam Bar, Maya Lotan-Pompan, Tali Avnit-Sagi, Noa Kosower, Gal Malka, Michal Rein, Jotham Suez, Ben Z. Goldberg, Adina Weinberger, Avraham A. Levy, Eran Elinav, Eran Segal

Cell Metabolism, 2017

Involvement of a gut-retina axis in protection against dietary glycemia-induced age-related macular degeneration

Sheldon Rowan, Shuhong Jiang, Tal Korem, Jedrzej Szymanski, Min-Lee Chang, Jason Szelog, Christa Cassalman, Kalavathi Dasuri, Christina McGuire, Ryoji Nagai, Xue-Liang Du, Michael Brownlee, Naila Rabbani, Paul J. Thornalley, James D. Baleja, Amy A. Deik, Kerry A. Pierce, Justin M. Scott, Clary B. Clish, Donald E. Smith, Adina Weinberger, Tali Avnit-Sagi, Maya Lotan-Pompan, Eran Segal and Allen Taylor

PNAS, 2017

Systematic Investigation of Transcription Factor Activity in the Context of Chromatin Using Massively Parallel Binding and Expression Assays

Michal Levo, Tali Avnit-Sagi, Maya Lotan-Pompan, Yael Kalma, Adina Weinberger, Zohar Yakhini, Eran Segal

Molecular Cell, 2017

Large-scale mapping of gene regulatory logic reveals context-dependent repression by transcriptional activators

David van Dijk, Eilon Sharon, Maya Lotan-Pompan, Adina Weinberger, Eran Segal and Lucas B. Carey

Genome Research, 2017

2016

Microbiota Diurnal Rhythmicity Programs Host Transcriptome Oscillations

Christoph A. Thaiss, Maayan Levy, Tal Korem, Lenka Dohnalová, Hagit Shapiro, Diego A. Jaitin, Eyal David, Deborah R. Winter, Meital Gury-BenAri, Evgeny Tatirovsky, Timur Tuganbaev, Sara Federici, Niv Zmora, David Zeevi, Mally Dori-Bachash, Meirav Pevsner-Fischer, Elena Kartvelishvily, Alexander Brandis, Alon Harmelin, Oren Shibolet, Zamir Halpern, Kenya Honda, Ido Amit, Eran Segal, Eran Elinav

Cell, 2016

Persistent microbiome alterations modulate the rate of post-dieting weight regain

Christoph A. Thaiss, Shlomik Itav, Daphna Rothschild, Mariska Meijer, Maayan Levy, Claudia Moresi, Lenka Dohnalová, Sofia Braverman, Shachar Rozin, Sergey Malitsky, Mally Dori-Bachash, Yael Kuperman, Inbal Biton, Arieh Gertler, Alon Harmelin, Hagit Shapiro, Zamir Halpern, Asaph Aharoni, Eran Segal & Eran Elinav

Nature, 2016

Systematic discovery of cap-independent translation sequences in human and viral genomes

Shira Weingarten-Gabbay, Shani Elias-Kirma, Ronit Nir, Alexey A. Gritsenko, Noam Stern-Ginossar, Zohar Yakhini, Adina Weinberger, Eran Segal

Science, 2016

Massively Parallel Interrogation of the Effects of Gene Expression Levels on Fitness

Leeat Keren, Jean Hausser, Maya Lotan-Pompan, Ilya Vainberg Slutskin, Hadas Alisar, Sivan Kaminski, Adina Weinberger, Uri Alon, Ron Milo, Eran Segal

Cell, 2016

Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace

Kun Qu, Sara Garamszegi, Felix Wu, Helga Thorvaldsdottir, Ted Liefeld, Marco Ocana, Diego Borges-Rivera, Nathalie Pochet, James T Robinson, Barry Demchak, Tim Hull, Gil Ben-Artzi, Daniel Blankenberg, Galt P Barber, Brian T Lee, Robert M Kuhn, Anton Nekrutenko, Eran Segal, Trey Ideker, Michael Reich, Aviv Regev, Howard Y Chang & Jill P Mesirov.

Nature Methods, 2016

2015

Microbiota-Modulated Metabolites Shape the Intestinal Microenvironment by Regulating NLRP6 Inflammasome Signaling.

Maayan Levy, Christoph A. Thaiss, David Zeevi, Lenka Dohnalov, Gili Zilberman-Schapira, Jemal Ali Mahdi, Eyal David, Alon Savidor, Tal Korem, Yonatan Herzig, Meirav Pevsner-Fischer, Hagit Shapiro, Anette Christ, Alon Harmelin, Zamir Halpern, Eicke Latz, Richard A. Flavell, Ido Amit, Eran Segal, Eran Elinav

Cell, 2015

Personalized Nutrition by Prediction of Glycemic Responses.

David Zeevi, Tal Korem, Niv Zmora, David Israeli, Daphna Rothschild, Adina Weinberger, Orly Ben-Yacov, Dar Lador, Tali Avnit-Sagi, Maya Lotan-Pompan, Jotham Suez, Jemal Ali Mahdi, Elad Matot, Gal Malka, Noa Kosower, Michal Rein, Gili Zilberman-Schapira, Lenka Dohnalov, Meirav Pevsner-Fischer, Rony Bikovsky, Zamir Halpern, Eran Elinav, Eran Segal

Cell, 2015

Noise in gene expression is coupled to growth rate

Leeat Keren, David van Dijk, Shira Weingarten-Gabbay Dan Davidi, Ghil Jona, Adina Weinberger, Ron Milo and Eran Segal

Genome Res., 2015

Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples

Tal Korem, David Zeevi, Jotham Suez, Adina Weinberger, Tali Avnit-Sagi, Maya Pompan-Lotan, Elad Matot, Ghil Jona, Alon Harmelin, Nadav Cohen, Alexandra Sirota-Madi, Christoph A. Thaiss, Meirav Pevsner-Fischer, Rotem Sorek, Ramnik Xavier, Eran Elinav, Eran Segal

Science, 2015

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Core promoter sequence in yeast is a major determinant of expression level

Shai Lubliner, Ifat Regev, Maya Lotan-Pompan, Sarit Edelheit, Adina Weinberger and Eran Segal

Genome Res., 2015

Systematic dissection of the sequence determinants of gene 3' end mediated expression control

Ophir Shalem, Eilon Sharon , Shai Lubliner, Ifat Regev, Maya Lotan-Pompan, Zohar Yakhini and Eran Segal

PLoS Gen. 2015

Non-caloric artificial sweeteners and the microbiome: findings and challenges

Jotham Sueza, Tal Korem, Gili Zilberman-Schapiraa, Eran Segal and Eran Elinav

Gut Microbes. 2015

Unraveling determinants of transcription factor binding outside the core binding site

Michal Levo, Einat Zalckvar, Eilon Sharon, Ana Carolina Dantas Machado, Yael Kalma, Maya Lotam-Pompan, Adina Weinberger, Zohar Yakhini, Remo Rohs and Eran Segal

Genome Research, 2015

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2014

Transkingdom Control of Microbiota Diurnal Oscillations Promotes Metabolic Homeostasis

Thaiss CA, Zeevi David, Levy M, Zilberman-Schapira G, Suez J, Tengeler AC, Abramson L, Katz MN,Korem Tal, Zmora N, Kuperman Y, Biton I, Gilad S, Harmelin A, Shapiro H, Halpern Z, Segal Eran, Elinav E

Cell, 2014

Host-parasite network structure is associated with community-level immunogenetic diversity

Pilosof S, Fortuna MA, Cosson JF, Galan M, Kittipong C, Ribas A, Segal Eran, Krasnov BR, Morand S, Bascompte J.

Nature Communication, 2014

Molecular dissection of the genetic mechanisms that underlie expression conservation in orthologous yeast ribosomal promoters

Zeevi Danny, Lubliner Shai, Lotan-Pompan Maya, Hodis Eran, Vesterman R, Weinberger Adina and Segal Eran

Genome Research, 2014

Probing the effect of promoters on noise in gene expression using thousands of designed sequences

Sharon Eilon, van-Dijk David, Kalma Yael, Keren Leeat, Manor Ohad, Yakhini Z, and Segal Eran

Genome Research, 2014

Artificial sweeteners induce glucose intolerance by altering the gut microbiota

Suez J, Korem Tal, Zeevi David, Zilberman-Schapira G, Thaiss CA, Maza O, Israeli D, Zmora N, Gilad S, Weinberger Adina, Kuperman Y, Harmelin A, Kolodkin-Gal I, Shapiro H, Halpern Z, Segal Eran, Elinav E.

Nature, 2014

Landscape and variation of RNA secondary structure across the human transcriptome

Wan Y, Qu K, Zhang QC, Flynn RA, Manor Ohad, Ouyang Z, Zhang J, Spitale RC, Snyder MP, Segal Eran, Chang HY.

Nature, 2014

2013

Promoters maintain their relative activity levels under different growth conditions

Leeat Keren, Ora Zackay, Maya Lotan-Pompan, Uri Barenholz, Erez Dekel, Vered Sasson, Guy Aidelberg, Anat Bren, Danny Zeevi, Adina Weinberger, Uri Alon, Ron Milo and Eran Segal

Molecular Systems Biology, 2013

Nucleosome maps of the human cytomegalovirus genome reveal a temporal switch in chromatin organization linked to a major IE protein.

Einat Zalckvara, Christina Paulus, Desiree Tilloa, Alexandra Asbach-Nitzschec, Yaniv Lubling, Carla Winterling, Nicholas Strieder, Katrin Mucke,Felicia Goodrum, Eran Segal and Michael Nevels

Proc. Natl. Acad. Sci., 2013

Deciphering the rules by which 5'-UTR sequences affect protein expression in yeast.

Shlomi Dvir, Lars Velten, Eilon Sharon, Danny Zeevi, Lucas B. Careya, Adina Weinberger and Eran Segal

Proc. Natl. Acad. Sci., 2013

Two DNA-encoded strategies for increasing expression with opposing effects on promoter dynamics and transcriptional noise.

Maya Dadiani, David van Dijk, Barak Segal, Yair Field, Gil Ben-Artzi, Tali Raveh-Sadka, Michal Levo, Irene M. Kaplow, Adina Weinberger, Eran Segal.

Genome Res., 2013

Promoter sequence determines the relationship between expression level and noise

Lucas B Carey , David van Dijk, Sloot PM, Kaandorp JA, Eran Segal

PLoS Biol., 2013

Measurements of the impact of 3' end sequences on gene expression reveal wide range and sequence dependent effects

Ophir Shalem, Lucas Carey, Danny Zeevi, Eilon Sharon, Leeat Keren, Adina Weinberger, Orna Dahan, Yitzhak Pilpel and Eran Segal

PLoS Comput Biol., 2013

2012

Genomics: ENCODE explained

Joseph R. Ecker, Wendy A. Bickmore, Ines Barroso, Jonathan K. Pritchard, Yoav Gilad and Eran Segal

Nature, 2012

Genome-wide Measurement of RNA Folding Energies

Yue Wan, Kun Qu, Zhengqing Ouyang, Michael Kertesz, Jun Li, Robert Tibshirani, Debora L. Makino, Robert C. Nutter, Eran Segal, Howard Y. Chang

Molecular Cell, 2012

Cell lineage analysis of the mammalian female germline

Yitzhak Reizel, Shalev Itzkovitz, Rivka Adar, Judith Elbaz, Adrian Jinich, Noa Chapal-Ilani, Yosef E. Maruvka, Nava Nevo, Zipora Marx, Inna Horovitz, Adam Wasserstrom, Avi Mayo, Irena Shur, Dafna Benayahu, Karl Skorecki, Eran Segal, Nava Dekel and Ehud Shapiro

PLoS Genetic, 2012

New insights into replication origin characteristics in metazoans

Christelle Cayrou, Philippe Coulombe, Aurore Puy, Stephanie Rialle, Noam Kaplan, Eran Segal and Marcel Mechali

Cell Cycle, 2012

Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast

Tali Raveh-Sadka, Michal Levo, Uri Shabi, Boaz Shany, Leeat Keren, Maya Lotan-Pompan, Danny Zeevi, Eilon Sharon, Adina Weinberger & Eran Segal

Nature Genetics, 2012

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

Eilon Sharon, Yael Kalma, Ayala Sharp, Tali Raveh-Sadka, Michal Levo, Danny Zeevi, Leeat Keren, Zohar Yakhini, Adina Weinberger & Eran Segal

Nature Biotechnology, 2012

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2010

Overlapping codes within protein-coding sequences

Shalev Itzkovitz, Eran Hodis, Eran Segal

Genome Res., 2010

Genome-wide measurement of RNA secondary structure in yeast

Michael Kertesz, Yue Wan, Elad Mazor, John L.Rinn, Robert C.Nutter, Howard Y.Chang, Eran Segal

Nature, 2010

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p53 binds preferentially to genomic region with high DNA-encoded nucleosome occupancy

Efrat Lidor Nili, Yair Field, Yaniv Lubling Jonathan Widom, Moshe Oren, Eran Segal

Genome Research., 2010

Nucleosome sequence preferences influence in vivo nucleosome organization

Noam Kaplan, Irene Moore, Yvonne Fondufe-Mittendorf, Andrea J Gossett, Desiree Tillo, Yair Field, Timothy R Hughes, Jason D Lieb, Jonathan Widom & Eran Segal

Nat Struct Mol Biol., 2010

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

Miao-Chih Tsai, Ohad Manor, Yue Wan, Nima Mosammaparast, Jordon K. Wang, Fei Lan, Yang Shi, Eran Segal, Howard Y. Chang

Science, 2010

EGF Decreases the Abundance of MicroRNAs That Restrain Oncogenic Transcription Factors

Roi Avraham, Aldema Sas-Chen, Ohad Manor, Israel Steinfeld, Reut Shalgi, Gabi Tarcic, Noa Bossel, Amit Zeisel, Ido Amit, Yaara Zwang, Espen Enerly, Hege G. Russnes, Francesca Biagioni, Marcella Mottolese, Sabrina Strano, Giovanni Blandino, Anne-Lise Børresen-Dale, Yitzhak Pilpel, Zohar Yakhini, Eran Segal, and Yosef Yarden

Sci. Signal.,2010

High Nucleosome Occupancy Is Encoded at Human Regulatory Sequences

Desiree Tillo, Noam Kaplan, Irene K. Moore, Yvonne Fondufe-Mittendorf, Andrea J. Gossett, Yair Field, Jason D. Lieb, Jonathan Widom, Eran Segal, Timothy R. Hughes

PLoS ONE, 2010

2009

The DNA-encoded nucleosome organization of a eukaryotic genome

Noam Kaplan, Irene K. Moore, Yvonne Fondufe-Mittendorf, Andrea J. Gossett, Desiree Tillo, Yair Field, Emily M. LeProust, Timothy R. Hughes, Jason D. Lieb, Jonathan Widom & Eran Segal

Nature, 2009

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Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization

Yair Field, Yvonne Fondufe-Mittendorf, Irene K. Moore, Piotr Mieczkowski, Noam Kaplan, Yaniv Lubling, Jason D. Lieb, Jonathan Widom & Eran Segal

Nature Genetics, 2009

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Proteome-wide prediction of acetylation substrates

Amrita Basu, Kristie L. Rose, Junmei Zhang, Ronald C. Beavis, Beatrix Ueberheide, Benjamin A. Garcia, Brian Chait, Yingming Zhao, Donald F. Hunt, Eran Segal, C. David Allis and Sandra B. Hake

Proc Natl Acad Sci U S A.,2009

2008

Stemness, cancer, and cancer stem cells

David J. Wong, Eran Segal and Howard Y. Chang

Cell Cycle.,2008

Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals

Yair Field, Noam Kaplan, Yvonne Fondufe-Mittendorf, Irene K. Moore, Eilon Sharon, Yaniv Lubling, Jonathan Widom, Eran Segal

PLoS Comput Biol, 2008

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Preferentially Quantized Linker DNA Lengths in Saccharomyces cerevisiae

Ji-Ping Wang, Yvonne Fondufe-Mittendorf, Liqun Xi, Guei-Feng Tsai, Eran Segal, Jonathan Widom

PLoS Comput Biol, 2008

Estimating cell depth from somatic mutations

Adam Wasserstrom, Dan Frumkin, Rivka Adar, Shalev Itzkovitz, Tomer Stern, Shai Kaplan, Gabi Shefer, Irena Shur, Lior Zangi, Yitzhak Reizel, Alon Harmelin, Yuval Dor, Nava Dekel, Yair Reisner, Dafna Benayahu, Eldad Tzahor, Eran Segal, Ehud Shapiro

PLoS Comput Biol., 2008

Reconstruction of Cell Lineage Trees in Mice

Adam Wasserstrom, Rivka Adar, Gabi Shefer, Dan Frumkin, Shalev Itzkovitz, Tomer Stern, Irena Shur, Lior Zangi, Shai Kaplan, Alon Harmelin, Yair Reisner, Dafna Benayahu, Eldad Tzahor, Eran Segal, Ehud Shapiro

PLoS ONE, 2008

Systematic functional characterization of cis-regulatory motifs in human core promoters

Saurabh Sinha, Adam S. Adler, Yair Field, Howard Y. Chang, Eran Segal

Genome Res., 2008

Revealing Targeted Therapy for Human Cancer by Gene Module Maps

Wong DJ, Nuyten DS, Regev A, Lin M, Adler AS, Segal E, van de Vijver MJ, Chang HY.

Cancer Res., 2008

2007

Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs

Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, Goodnough LH, Helms JA, Farnham PJ, Segal E, Chang HY.

Cell, 2007

Decoding global gene expression programs in liver cancer by noninvasive imaging

Segal E, Sirlin CB, Ooi C, Adler AS, Gollub J, Chen X, Chan BK, Matcuk GR, Barry CT, Chang HY, Kuo MD

Nature Biotechnology, 2007

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A module of negative feedback regulators defines growth factor signaling

Amit I, Citri A, Shay T, Lu Y, Katz M, Zhang F, Tarcic G, Siwak D, Lahad J, Jacob-Hirsch J, Amariglio N, Vaisman N, Segal E, Rechavi G, Alon U, Mills GB, Domany E, Yarden Y

Nature Genetics, 2007

2006

Evidence for an instructive mechanism of de novo methylation in cancer cells.

I. Keshet., Y. Schlesinger, S. Farkash, E. Rand, M. Hecht, E. Segal, E. Pikarski, R.A. Young, A. Niveleau, H. Cedar, I. Simon.

Nature Genetics, 2006

2005

From Signature to Models: Understanding Cancer Using Microarrays

E. Segal,N. Friedman, N. Kaminski, A. Regev, and D. Koller.

Nature Genetics, 2005

Learning Module Networks

E. Segal, D. Pe'er, A. Regev, D. Koller, and N. Friedman.

Journal of Machine Learning Research (JMLR), 2005

*An earlier version appeared in Proc. 19th Conference on Uncertainty in Artificial Intelligence (UAI)

A Discriminative Model for Identifying Spatial Cis-Regulatory Modules

E. Segal, R. Sharan.

Journal of Computational Biology, 2005

Recipient of the Best Paper by a Young Scientist Award at the 8th Inter. Conf. on Research in Computational Molecular Biology (RECOMB)

Probabilistic Discovery of Overlapping Cellular Processes and their Regulation Using Gene Expression Data

A. Battle, E. Segal, and D. Koller.

Journal of Computational Biology, 2005

**An earlier version appeared at the 8th Inter. Conf. on Research in Computational Molecular Biology (RECOMB)

2003

Genome-wide Discovery of Transcriptional Modules from DNA Sequence and Gene Expression

E. Segal, R. Yelensky, and D. Koller.

Bioinformatics, 2003

Recipient of the Best Paper Award at the 11th Inter. Conf. on Intelligent Systems for Molecular Biology (ISMB)

Discovering Molecular Pathways from Protein Interaction and Gene Expression Data

E. Segal, H. Wang, and D. Koller.

Bioinformatics, 2003

Recipient of the Best Student Paper Award at the 11th Inter. Conf. on Intelligent Systems for Molecular Biology (ISMB)

Rich Probabilistic Models for Gene Expression

E. Segal, B. Taskar, A. Gasch, N. Friedman, and D. Koller.

Bioinformatics, 2003

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