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

Systematic interrogation of human promoters

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

Functional characterization of the p53 "mutome"

Eran Kotler, Eran Segal & Moshe Oren

The Helix Twist: Damage and Repair Follows the DNA Minor Groove

Eran Kotler, Eran Segal

Regularization Learning Networks: Deep Learning for Tabular Datasets

Ira Shavitt, Eran Segal

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

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

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

Host genetics and microbiome associations through the lens of genome wide association studies

Omer Weissbrod, Daphna Rothschild, Elad Barkan, Eran Segal

Role of the gut microbiota in nutrition and health

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

Editorial overview: Systems biology: Data, discovery, delivery

Nathan D Price, EranSegal

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

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

Towards utilization of the human genome and microbiome for personalized nutrition

Stavros Bashiardes, Anastasia Godneva, EranElinav, EranSegal

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

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

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

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

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

van Dijk D, Sharon E, Lotan-Pompan M, Weinberger A, Segal E, Carey LB

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

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

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

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

Perspective in Science, Faculty of 1000 review, Highlight in Cell Systems

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

Taking it Personally: Personalized Utilization of the Human Microbiome in Health and Disease

Niv Zmora, David Zeevi, Tal Korem, Eran Segal, Eran Elinav

Toward a systematic understanding of translational regulatory elements in human and viruses

Shira Weingarten-Gabbay, Eran Segal

A Minimalistic Resource Allocation Model to Explain Ubiquitous Increase in Protein Expression with Growth Rate

Uri Barenholz, Leeat Keren, Eran Segal, Ron Milo

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.

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

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

Video, BBC, Time, NYTimes, Nature

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

Nature Reviews Genetics Highlight

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

Nature Reviews Microbiology Highlight, Science perspective

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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

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

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

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

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

NATURE GENETICS RESEARCH HIGHLIGHTS

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A day in the life of the meta-organism: diurnal rhythms of the intestinal microbiome and its host

Christoph A Thaissa, David Zeevi, Maayan Levy, Eran Segal and Eran Elinav

GenoExp: a web tool for predicting gene expression levels from single nucleotide polymorphisms

Ehud Manor and Eran Segal

A shared architecture for promoters and enhancers

Weingarten-Gabbay Shira and Segal Eran

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

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.

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

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

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 News & Views, NYTimes, Wall Street Journal, Economist, Washington Post

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 Reviews Genetics Highlight

The grammar of transcriptional regulation

Weingarten-Gabbay Shira, Segal Eran

link

In pursuit of design principles of regulatory sequences

Levo Michal, Segal Eran

Fixated on fixation - using ChIP to interrogate the dynamics of chromatin interactions.

Leeat Keren and Eran Segal

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

Predicting disease risk using bootstrap ranking and classification algorithms.

Ohad Manor and Eran Segal

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

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

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 Research Cover

Sequence features of yeast and human core promoters that are predictive of maximal promoter activity.

Shai Lubliner, Leeat Keren, Eran Segal

Promoter sequence determines the relationship between expression level and noise

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

Robust prediction of expression differences among human individuals using only genotype information.

Ohad Manor, Eran Segal

link

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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

Determinants of nucleosome positioning.

Kevin Struhl and Eran Segal

Genomics: ENCODE explained

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

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

Faculty of 1000 review

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

New insights into replication origin characteristics in metazoans

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

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

Related link, Faculty of 1000 review, News and Views in Nature Generics

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

Highlight in Nature Biotechnology News and Views

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Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promoters.

Zeevi D, Sharon E, Lotan-Pompan M, Lubling Y, Shipony Z, Raveh-Sadka T, Keren L, Levo M, Weinberger A, Segal E

Understanding the transcriptome through RNA structure.

Yue Wan, Michael Kertesz, Robert Spitale, Eran Segal, Howard Chang

Computational prediction of RNA structural motifs involved in post-transcriptional regulatory processes.

Michal Rabani, Michael Kertesz, Eran Segal

How transcription factors identify regulatory sites in genomic sequence.

Yair Field, Eilon Sharon, Eran Segal

High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans.

Sevinc Ercan, Yaniv Lubling, Eran Segal, Jason D Lieb

Widespread Compensatory Evolution Conserves DNA-Encoded Nucleosome Organization in Yeast.

Ephraim Kenigsberg, Amir Bar, Eran Segal, Amos Tanay

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project.

Gerstein MB et al.

Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology

Noam Kaplan, Timothy R Hughes, Jason D Lieb, Jonathan Widom, Eran Segal

Overlapping codes within protein-coding sequences

Shalev Itzkovitz, Eran Hodis, Eran Segal

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 Biotechnology Review, Faculty of 1000 review

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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

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

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

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

Faculty of 1000 review

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

What controls nucleosome positions?

Eran Segal & Jonathan Widom

From DNA sequence to transcriptional behaviour: a quantitative approach

Eran Segal & Jonathan Widom

Modeling interactions between adjacent nucleosomes improves genome-wide predictions of nucleosome occupancy

Shai Lubliner, Eran Segal

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Incorporating Nucleosomes into Thermodynamic Models of Transcription Regulation

Tali Raveh-Sadka, Michal Levo, Eran Segal

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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

Faculty of 1000 review

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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

Highlight in Nature Reviews Genetics, Faculty of 1000 review

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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

Stemness, cancer, and cancer stem cells

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

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

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Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation

Ophir Shalem, Orna Dahan, Michal Levo, Maria Rodriguez Martinez, Itay Furman, Eran Segal & Yitzhak Pilpel

Faculty of 1000 review

Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes

Michal Rabani, Michael Kertesz, Eran Segal

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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

A Feature-Based Approach to Modeling Protein-DNA Interactions

Eilon Sharon, Shai Lubliner, Eran Segal.

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Geometric constraints on neuronal connectivity facilitate a concise synaptic adhesive code

Shalev Itzkovitz, Leehod Baruch, Ehud Shapiro, and Eran Segal

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

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

Module map of stem cell genes guides creation of epithelial cancer stem cells

Wong DJ, Liu H, Ridky TW, Cassarino D, Segal E, Chang HY.

Faculty of 1000 review

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Predicting expression patterns from regulatory sequence in Drosophila segmentation

Eran Segal, Tali Raveh-Sadka, Mark Schroeder, Ulrich Unnerstall & Ulrike Gaul

Editor Summary

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Monoubiquitinated H2B is associated with the transcribed region of highly expressed genes in human cells

Neri Minsky, Efrat Shema, Yair Field, Meromit Schuster, Eran Segal & Moshe Oren

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

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

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.

Reversal of aging by NFkappaB blockade

Adler AS, Kawahara TL, Segal E, Chang HY

Faculty of 1000 review

Motif module map reveals enforcement of aging by continual NF-{kappa}B activity

Adler AS, Sinha S, Kawahara TL, Zhang JY, Segal E, Chang HY

Genes & Development Cover, Faculty of 1000 review

The role of site accessibility in microRNA target recognition

Michael Kertesz, Nicola Iovino, Ulrich Unnerstall, Ulrike Gaul & Eran Segal

News & Views, Research Highlights

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InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale

Haidong Wang, Eran Segal, Asa Ben-Hur, Qianru Li, Marc Vidal and Daphne Koller

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.

News & Views, Faculty of 1000 review.

A Transcriptional Program Mediating Entry into Cellular Quiescence

Liu H, Adler AS, Segal E, Chang HY

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

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Zinc-ion binding and cytokine activity regulation pathways predicts outcome in relapsing-remitting multiple sclerosis

Achiron A, Gurevich M, Snir Y, Segal E, Mandel M

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

A Feature-Based Approach to Modeling Protein-DNA Interactions

E. Sharon and E. Segal

A Genomic Code for Nucleosome Positioning

E. Segal,Y. Fondufe-Mittendorf, L. Chen, A. Thastrom, Y. Field, I. K. Moore, J. Z. Wang, J. Widom.

ESI Hot Paper, NY Times, Nature cover, News & Views, Nature Reviews Genetics, Faculty of 1000 review, Codes and Enigmas, TheScientist and about the authors.

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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.

Efficient Bundle Sorting

Y. Matias,E. Segal, J.S. Vitter

From Signature to Models: Understanding Cancer Using Microarrays

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

Learning Module Networks

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

*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.

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.

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

A Module Map Showing Conditional Activity of Expression Modules in Cancer

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

Genome Biology highlight, Faculty of 1000 review

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Disruption of Yeast Forkhead-Associated Cell Cycle Transcription by Oxidative Stress

M. Shapira, E. Segal and D. Botstein.

A Transcriptional Profile of Aging in the Human Kidney

G.J. Rodwell, R. Sonu, J.M. Zahn, J.Lund, J. Wilhelmy, L. Wang, W. Xiao, M. Mindrinos, E. Crane, E. Segal, B.D. Myers, J.D. Brooks, R.W. Davis, J. Higgins, A.B. Owen, S.K. Kim.

Sfp1 is a Stress- and Nutrient-Sensitive Regulator of Ribosomal Protein Gene Expression

R.M. Marion, A. Regev, E. Segal, Y. Barash, N. Friedman, D. Koller, and E. O'Shea.

Identifying Protein-Protein Interaction Sites on a Genome-Wide Scale

H. Wang, E. Segal, A. Ben-Hur, D. Brutlag, and D. Koller.

GeneXPress: A Visualization and Statistical Analysis Tool for Gene Expression and Sequence Data

E. Segal, R. Yelensky, A. Kaushal, T. Pham, A. Regev, D. Koller, and N. Friedman.

Module Networks: Identifying Regulatory Modules and their Condition Specific Regulators from Gene Expression Data

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

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A Gene Co-Expression Network for Global Discovery of Conserved Genetics Modules

J. Stuart­*, E. Segal*, D. Koller, and S.Kim. (*equal contribution)

Science highlight, Faculty of 1000 review, Nature Reviews Genetics.

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

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

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.

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.

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Decomposing Gene Expression into Cellular Processes

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

Boosting Density Estimation

S. Rosset,E. Segal.

From Promoter Sequence to Expression: A Probabilistic Framework

E. Segal, Y. Barash, I. Simon, N. Friedman, and D. Koller.

Probabilistic Hierarchical Clustering for Biological Data

E. Segal, D.Koller.

Probabilistic Abstraction Hierarchies

E. Segal, D. Koller, D. Ormoneit.

Probabilistic Classification and Clustering in Relational Data

B. Taskar, E. Segal, and D. Kollerp

Exact Inference in Networks with Discrete Children of Continuous Parents

U. Lerner, E. Segal and D. Koller

Probabilistic Models of Text and Link Structure for Hypertext Classification

L. Getoor,E. Segal, B. Taskar and D. Koller