2021

Anosmia, ageusia, and other COVID-19-like symptoms in association with a positive SARS-CoV-2 test, across six national digital surveillance platforms: an observational study

Carole H Sudre, Ayya Keshet, Mark S Graham, Amit D Joshi, Smadar Shilo, Hagai Rossman, Benjamin Murray, Erika Molten, Kerstin Klaser, Liane D Canas, Michela Antonelli, Long H Nguyen, David A Drew, Marc Modat, Joan Capdevila Pujol, Sajaysurya Ganesh, Jonathan Wolf, Tomer Meir, Andrew T Chan, Claire J Steves, Tim D Spector,John S Brownstein,Eran Segal,Sebastien Ourselin,Christina M Astley

The Lancet Digital Health, 2021

Cross-reactive antibodies against human coronaviruses and the animal coronavirome suggest diagnostics for future zoonotic spillovers

Shelley Klompus, Sigal Leviatan, Thomas Vogl1,2, Roei D. Mazor3, Iris N. Kalka, Liat Stoler-Barak, Nachum Nathan, Ayelet Peres, Lihee Moss3, Anastasia Godneva, Sharon Kagan Ben Tikva, Eilat Shinar, Hadas Cohen Dvashi, Ronen Gabizon6, Nir London, Ron Diskin, Gur Yaari,Adina Weinberger,Ziv Shulman,Eran Segal1,2,*

Science Immunology, 2021

Personalized Postprandial Glucose Response–Targeting Diet Versus Mediterranean Diet for Glycemic Control in Prediabetes

Orly Ben-Yacov, Anastasia Godneva, Michal Rein, Smadar Shilo, Dmitry Kolobkov, Netta Koren, Noa Cohen Dolev, Tamara Travinsky Shmul, Bat Chen Wolf, Noa Kosower, Keren Sagiv, Maya Lotan-Pompan, Niv Zmora, Adina Weinberger, Eran Elinav, Eran Segal

Diabetes Care, 2021

Population-wide diversity and stability of serum antibody epitope repertoires against human microbiota

Thomas Vogl, Shelley Klompus, Sigal Leviatan, Iris N. Kalka, Adina Weinberger, Cisca Wijmenga, Jingyuan Fu, Alexandra Zhernakova, Rinse K. Weersma, Eran Segal

Nature Medicine, 2021

Unified platform for genetic and serological detection of COVID-19 with single-molecule technology.

Noa Furth , Shay Shilo , Niv Cohen , Nir Erez , Vadim Fedyuk , Alexander M Schrager , Adina Weinberger , Amiel A Dror , Asaf Zigron, Mona Shehadeh, Eyal Sela , Samer Srouji, Sharon Amit 8 Itzchak Levy , Eran Segal , Rony Dahan , Dan Jones, Daniel C Douek, Efrat Shema

Plos One, 2021

10 K: a large-scale prospective longitudinal study in Israel.

Smadar Shilo, Noam Bar, Ayya Keshet, Yeela Talmor-Barkan, Hagai Rossman, Anastasia Godneva, Yaron Aviv, Yochai Edlitz, Lee Reicher, Dmitry Kolobkov, Bat Chen Wolf, Maya Lotan-Pompan, Kohava Levi, Ori Cohen, Hila Saranga, Adina Weinberger, Eran Segal

European Journal of Epidemiology, 2021

COVID-19 dynamics after a national immunization program in Israel

Hagai Rossman, Smadar Shilo, Tomer Meir, Malka Gorfine, Uri Shalit, Eran Segal

Nature Medicine, 2021

Potential role of indolelactate and butyrate in multiple sclerosis revealed by integrated microbiome-metabolome analysis.

Izhak Levi, Michael Gurevich, Gal Perlman, David Magalashvili, Shay Menascu, Noam Bar, Anastasia Godneva, Liron Zahavi, Danyel Chermon, Noa Kosower, Bat Chen Wolf, Gal Malka, Maya Lotan-Pompan, Adina Weinberger, Erez Yirmiya, Daphna Rothschild, Sigal Leviatan, Avishag Tsur, Maria Didkin, Sapir Dreyer, Hen Eizikovitz, Yamit Titngi, Sue Mayost, Polina Sonis, Mark Dolev, Yael Stern, Anat Achiron and Eran Segal

Cell Reports Medicine, 2021

COVID-19 dynamics after a national immunization program in Israel.

Hagai Rossman, Smadar Shilo, Tomer Meir, Malka Gorfine, Uri Shalit and Eran Segal

Nature Medicine, 2021

Hospital load and increased COVID-19 related mortality in Israel.

Hagai Rossman, Tomer Meir, Jonathan Somer, Smadar Shilo, Rom Gutman, Asaf Ben Arie, Eran Segal, Uri Shalit and Malka Gorfine

Nature Communications, 2021

Diversity and functional landscapes in the microbiota of animals in the wild.

Doron Levin, Neta Raab1,Yishay Pinto1,Daphna Rothschild, Gal Zanir1,Anastasia Godneva, Nadav Mellul, David Futorian, Doran Gal1, Sigal Leviatan, David Zeevi,Ido Bachelet and Eran Segal

Science, 2021

Prediction of Childhood Obesity from Nationwide Health Records.

Rossman, Hagai, Smadar Shilo, Shiri Barbash-Hazan, Nitzan Shalom Artzi, Eran Hadar, Ran D. Balicer, Becca Feldman, Arnon Wiznitzer, and Eran Segal

The Journal of Pediatrics, 2021

2020

Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome

Ruben A.T.Mars, Yi Yang, Tonya Ward, Mo Houtti, Sambhawa Priya, Heather R.Lekatz, Xiaojia Tang, Zhifu Sun, Krishna R.Kalari, Tal Korem, Yogesh Bhattarai, Tenghao Zheng, Noam Bar, Gary Frost, Abigail J.Johnson Willvan, Treuren ShuoHan, Tamas Ordog, Madhusudan Grover, Justin Sonnenburg, Mauro D’Amato, Michael Camilleri, Eran Elinav, Eran Segal, Ran Blekhman, Gianrico Farrugia, Jonathan R.Swann, Dan Knights, Purna C.Kashyap

Cell, 2020

The road ahead in genetics and genomics

Amy L. McGuire, Stacey Gabriel, Sarah A. Tishkoff, Ambroise Wonkam, Aravinda Chakravarti, Eileen E. M. Furlong, Barbara Treutlein, Alexander Meissner, Howard Y. Chang, N?ria L?pez-Bigas, Eran Segal ,Jin-Soo Kim

Nature Reviews Genetics, 2020

Rationale and design of a randomised controlled trial testing the effect of personalised diet in individuals with pre-diabetes or type 2 diabetes mellitus treated with metformin

Thaw D Htet, Anastasia Godneva, Zhixin Liu, Eliza Chalmers, Dmitry Kolobkov, Jennifer R Snaith, Renee Richens, Krisztina Toth,Mark Danta, Tien-Ming Hng , Eran Elinav , Eran Segal ,Jerry R Greenfield , Dorit Samocha-Bonet

BMJ Open, 2020

A prediction model to prioritize individuals for SARS-CoV-2 test built from national symptom surveys

Saar Shoer, Tal Karady, Ayya Keshet, Smadar Shilo, Hagai Rossman, Amir Gavrieli, Tomer Meir, Amit Lavon, Dmitry Kolobkov, Iris Kalka, Anastasia Godneva, Ori Cohen, Adam Kariv, Ori Hoch, Mushon Zer-Aviv, Noam Castel Carole Sudre, Anat Ekka, Zohar Angela Irony, Tim Spector, Benjamin Geiger, Dorit Hizi, Varda Shalev, Ran Balicer, Eran Segal

Med, 2020

Visualizing the structure and motion of the long noncoding RNA HOTAIR

Rachel Spokoini-Stern, Dimitar Stamov, Hadass Jessel, Lior Aharoni, Heiko Haschke, Jonathan Giron, Ron Unger, Eran Segal, Almogit Abu-Horowitz, Ido Bachelet

RNA Journal, 2020

A framework for identifying regional outbreak and spread of COVID-19 from one-minute population-wide surveys

Hagai Rossman, Ayya Keshet, Smadar Shilo, Amir Gavrieli, Tal Bauman, Ori Cohen, Esti Shelly, Ran Balicer, Benjamin Geiger, Yuval Dor, Eran Segal

Nature Medicine, 2020

Prediction of gestational diabetes based on nationwide electronic health records

Nitzan Shalom Artzi, Smadar Shilo, Eran Hadar, Hagai Rossman, Shiri Barbash-Hazan, Avi Ben-Haroush, Ran D. Balicer, Becca Feldman, Arnon Wiznitzer & Eran Segal

Nature Medicine, 2020

2019

The pros, cons, and many unknowns of probiotics

Jotham Suez, Niv Zmora, Eran Segal & Eran Elinav

Nature Medicine, 2019

Potential roles of gut microbiome and metabolites in modulating ALS in mice

Eran Blacher, Stavros Bashiardes, Hagit Shapiro, Daphna Rothschild, Uria Mor, Mally Dori-Bachash, Christian Kleimeyer, Claudia Moresi, Yotam Harnik, Maya Zur, Michal Zabari, Rotem Ben-Zeev Brik, Denise Kviatcovsky, Niv Zmora, Yotam Cohen, Noam Bar, Izhak Levi, Nira Amar, Tevie Mehlman, Alexander Brandis, Inbal Biton, Yael Kuperman, Michael Tsoory, Leenor Alfahel, Alon Harmelin, Michal Schwartz, Adrian Israelson, Liisa Arike, Malin E. V. Johansson, Gunnar C. Hansson, Marc Gotkine, Eran Segal & Eran Elinav

Nature, 2019

Structural variation in the gut microbiome associates with host health

David Zeevi, Tal Korem, Anastasia Godneva, Noam Bar, Alexander Kurilshikov, Maya Lotan-Pompan, Adina Weinberger, Jingyuan Fu, Cisca Wijmenga, Alexandra Zhernakova and Eran Segal

Nature, 2019

Systematic interrogation of human promoters

Shira Weingarten-Gabbay, Ronit Nir, Shai Lubliner, Eilon Sharon, Yael Kalma, Adina Weinberger and Eran Segal

Genome Research, 2019

2018

Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT

Jotham Suez, Niv Zmora, Gili Zilberman-Schapira, Uria Mor, Mally Dori-Bachash, Stavros Bashiardes, Maya Zur, Dana Regev-Lehavi, Rotem Ben-Zeev Brik, Sara Federici, Max Horn, Yotam Cohen, Andreas E.Moor, David Zeevi, Tal Korem, Eran Kotler, Alon Harmelin, Shalev Itzkovitz, Meirav Pevsner-Fischer, Hagit Shapiro, Itai Sharon, Zamir Halpern, Eran Segal, Eran Elinav

Cell, 2018

Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features

Niv Zmora, Gili Zilberman-Schapira, Jotham Suez, Uria Mor, Mally Dori-Bachash, Stavros Bashiardes, Eran Kotler, Maya Zur, Dana Regev-Lehavi, Rotem Ben-Zeev Brik, Sara Federici, Yotam Cohen, Raquel Linevsky, Daphna Rothschild, Andreas E.Moor, Shani Ben-Moshe, Alon Harmelin, halev Itzkovitz, Nitsan Maharshak, Oren Shibolet, Hagit Shapiro, Meirav Pevsner-Fischer, Itai Sharon, Zamir Halpern, Eran Segal, Eran Elinav

Cell, 2018

A Systematic p53 Mutation Library Links Differential Functional Impact to Cancer Mutation Pattern and Evolutionary Conservation

Eran Kotler ,Odem Shani, Guy Goldfeld, Maya Lotan-Pompan, Ohad Tarcic, Anat Gershoni, Thomas A.Hopf, Debora S.Marks, Moshe Oren, Eran Segal

Molecular Cell, 2018

Role of the gut microbiota in nutrition and health

Ana M Valdes, Jens Walter, Eran Segal, Tim D Spector

BMJ, 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 Dohnalov?, 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 Dohnalov?, 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

Related software

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

Related software

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

Related software

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

Related software

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 B?rresen-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

Related software

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

Related software

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

Related software

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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