Research Topics
Genomes and Genes | Eran SegalSummaryAffiliation: Weizmann Institute of Science Country: Israel Publications
Research Grants
| Collaborators
|
Detail Information
Publications
InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scaleHaidong Wang
Computer Science Department, Stanford University, Serra Mall, Stanford, CA 94305, USA
Genome Biol 8:R192. 2007..Several regions containing disease-causing mutations or cancer polymorphisms in human are predicted to be binding for protein pairs related to the disease, which suggests novel mechanistic hypotheses for several diseases...- From DNA sequence to transcriptional behaviour: a quantitative approachEran Segal
Department of Computer Science and Applied Mathematics and Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
Nat Rev Genet 10:443-56. 2009..It can also be used to model more complex phenomena such as transcriptional noise and the evolution of transcriptional regulation... - Poly(dA:dT) tracts: major determinants of nucleosome organizationEran Segal
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 76100, Israel
Curr Opin Struct Biol 19:65-71. 2009..Recent genome-wide studies strongly confirm these ideas and suggest that these tracts play major roles in chromatin organization and genome function. Here we review what is known about poly(dA:dT) tracts and how they work... - What controls nucleosome positions?Eran Segal
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 76100, Israel
Trends Genet 25:335-43. 2009.... - A genomic code for nucleosome positioningEran Segal
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
Nature 442:772-8. 2006..This nucleosome positioning code may facilitate specific chromosome functions including transcription factor binding, transcription initiation, and even remodelling of the nucleosomes themselves... - Distinct modes of regulation by chromatin encoded through nucleosome positioning signalsYair Field
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
PLoS Comput Biol 4:e1000216. 2008.... - Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promotersEilon Sharon
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
Nat Biotechnol 30:521-30. 2012..Our method can be used to study both cis and trans effects of genotype on transcriptional, post-transcriptional and translational control... 
Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeastTali Raveh-Sadka
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
Nat Genet 44:743-50. 2012..Overall, our results advance the understanding of the regulatory code and suggest a potential mechanism by which promoters yielding prespecified expression patterns can be designed...- The DNA-encoded nucleosome organization of a eukaryotic genomeNoam Kaplan
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
Nature 458:362-6. 2009..Our results indicate that the intrinsic DNA sequence preferences of nucleosomes have a central role in determining the organization of nucleosomes in vivo... - p53 binds preferentially to genomic regions with high DNA-encoded nucleosome occupancyEfrat Lidor Nili
Department of Molecular Cell Biology, The Weizmann Institute, Rehovot 76100, Israel
Genome Res 20:1361-8. 2010.... - Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promotersDanny Zeevi
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
Genome Res 21:2114-28. 2011..Our approach can readily be applied to uncover how transcriptional programs of other promoters are encoded... - Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organizationYair Field
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
Nat Genet 41:438-45. 2009..Our results suggest a previously unidentified genetic mechanism underlying phenotypic diversity, consisting of DNA sequence changes that directly alter the DNA-encoded nucleosome organization of promoters... - A feature-based approach to modeling protein-DNA interactionsEilon Sharon
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
PLoS Comput Biol 4:e1000154. 2008..Our FMM learning and motif finder software are available at http://genie.weizmann.ac.il/... - Incorporating nucleosomes into thermodynamic models of transcription regulationTali Raveh-Sadka
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
Genome Res 19:1480-96. 2009.... - Measurements of the impact of 3' end sequences on gene expression reveal wide range and sequence dependent effectsOphir Shalem
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
PLoS Comput Biol 9:e1002934. 2013..Altogether, our results lead to a more complete understanding of gene regulation by demonstrating that 3' end regions have a unique and sequence dependent effect on gene expression... - Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodologyNoam Kaplan
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
Genome Biol 11:140. 2010..We propose definitions and procedures for comparing nucleosome maps and discuss current agreement and disagreement on the effect of histone sequence preferences on nucleosome organization in vivo... - Predicting expression patterns from regulatory sequence in Drosophila segmentationEran Segal
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
Nature 451:535-40. 2008..Our computational framework is generally applicable to most protein-DNA interaction systems... - Using expression profiles of Caenorhabditis elegans neurons to identify genes that mediate synaptic connectivityLeehod Baruch
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
PLoS Comput Biol 4:e1000120. 2008..Notably, these predictions can be achieved using the expression patterns of only a small number of specific genes that interact in a combinatorial fashion... - Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processesMichal Rabani
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
Proc Natl Acad Sci U S A 105:14885-90. 2008..Our new RNA motif discovery tool is available online... - Computational prediction of RNA structural motifs involved in post-transcriptional regulatory processesMichal Rabani
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehoboth, Rehovot, Israel
Methods Mol Biol 714:467-79. 2011.... - Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradationOphir Shalem
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
Mol Syst Biol 4:223. 2008..Our results show genome-wide interplay between mRNA production and degradation, and that alternative modes of such interplay determine the kinetics of the transcriptome in response to stress... - Genome-wide measurement of RNA secondary structure in yeastMichael Kertesz
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
Nature 467:103-7. 2010..PARS is readily applicable to other organisms and to profiling RNA structure in diverse conditions, thus enabling studies of the dynamics of secondary structure at a genomic scale... - Widespread compensatory evolution conserves DNA-encoded nucleosome organization in yeastEphraim Kenigsberg
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
PLoS Comput Biol 6:e1001039. 2010..The model thus derived suggests that compensation is inevitable when evolution conserves quantitative and dispersed genomic functions... - Modeling interactions between adjacent nucleosomes improves genome-wide predictions of nucleosome occupancyShai Lubliner
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
Bioinformatics 25:i348-55. 2009..We present a new model that relaxes this independence assumption by modeling interactions between adjacent nucleosomes... - Overlapping codes within protein-coding sequencesShalev Itzkovitz
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
Genome Res 20:1582-9. 2010..Our results suggest that genomes may have evolved to encode extensive overlapping information within protein-coding regions... - Monoubiquitinated H2B is associated with the transcribed region of highly expressed genes in human cellsNeri Minsky
Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
Nat Cell Biol 10:483-8. 2008.... - How transcription factors identify regulatory sites in genomic sequenceYair Field
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 76100, Israel
Subcell Biochem 52:193-204. 2011..We highlight the importance of the chromatin structure context of the binding sites in this process, and its dependency on the genomic DNA sequence... 
The role of site accessibility in microRNA target recognitionMichael Kertesz
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
Nat Genet 39:1278-84. 2007..Our study thus demonstrates that target accessibility is a critical factor in microRNA function...- Geometric constraints on neuronal connectivity facilitate a concise synaptic adhesive codeShalev Itzkovitz
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
Proc Natl Acad Sci U S A 105:9278-83. 2008..Our study suggests an additional advantage of these prominent topological features--the facilitation of the ability to genetically encode neuronal networks given constraints on the number of addresses... - A module of negative feedback regulators defines growth factor signalingIdo Amit
Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 76100, Israel
Nat Genet 39:503-12. 2007..More generally, our study proposes a mechanistic description of the cellular response to growth factors by defining architectural motifs that underlie the function of signaling networks... - Systematic functional characterization of cis-regulatory motifs in human core promotersSaurabh Sinha
Department of Computer Science, University of Illinois Urbana Champaign, Urbana, Illinois 61801, USA
Genome Res 18:477-88. 2008..Our analysis thus provides a concrete framework for uncovering the biological function of cis-regulatory motifs genome wide... - A gene-coexpression network for global discovery of conserved genetic modulesJoshua M Stuart
Stanford Medical Informatics, 251 Campus Drive, Medical School Office Building X 215, Stanford, CA 94305 5329, USA
Science 302:249-55. 2003..By assembling these links into a gene-coexpression network, we found several components that were animal-specific as well as interrelationships between newly evolved and ancient modules... - Preferentially quantized linker DNA lengths in Saccharomyces cerevisiaeJi Ping Wang
Department of Statistics, Northwestern University, Evanston, Illinois, United States of America
PLoS Comput Biol 4:e1000175. 2008..This 10 bp periodicity implies an ordered superhelical intrinsic structure for the average chromatin fiber in yeast... - A discriminative model for identifying spatial cis-regulatory modulesEran Segal
Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10021
J Comput Biol 12:822-34. 2005..Thus, our results provide one of the first comprehensive compendiums of putative cis-regulatory modules in human... - Module networks: identifying regulatory modules and their condition-specific regulators from gene expression dataEran Segal
Computer Science Department, Stanford University, Stanford, California, 94305, USA
Nat Genet 34:166-76. 2003..We present microarray experiments supporting three novel predictions, suggesting regulatory roles for previously uncharacterized proteins... - Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expressionRosa M Marion
Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, 600 16th Street, Genentech Hall, Room GH S472D, University of California, San Francisco, CA 94143 2240, USA
Proc Natl Acad Sci U S A 101:14315-22. 2004..We conclude that Sfp1 integrates information from nutrient- and stress-responsive signaling pathways to help control RP gene expression... - From signatures to models: understanding cancer using microarraysEran Segal
Center for Studies in Physics and Biology, Rockefeller University, New York, USA
Nat Genet 37:S38-45. 2005..We conclude by discussing the challenges of generalizing these methods from cells to tissues and the opportunities they offer to improve cancer diagnosis and management... - Disruption of yeast forkhead-associated cell cycle transcription by oxidative stressMichael Shapira
Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
Mol Biol Cell 15:5659-69. 2004..The apparent involvement of a forkhead protein in HP-induced cell cycle arrest, similar to that reported for Caenorhabditis elegans and human, describes a potentially novel stress response pathway in yeast... - Probabilistic discovery of overlapping cellular processes and their regulationAlexis Battle
Computer Science Department, Stanford University, Stanford, CA 94305 9010, USA
J Comput Biol 12:909-27. 2005.... - Module map of stem cell genes guides creation of epithelial cancer stem cellsDavid J Wong
Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
Cell Stem Cell 2:333-44. 2008..Thus, activation of an ESC-like transcriptional program in differentiated adult cells may induce pathologic self-renewal characteristic of cancer stem cells... - The modular era of functional genomicsEran Segal
Computer Science Department, Stanford University, Stanford, CA 94305, USA
Genome Biol 4:317. 2003..A report on the Keystone Symposium 'Functional Genomics: Global Analysis of Complex Biological Systems', Santa Fe, USA, 20-24 February 2003... - ISCB honors Temple F. Smith and Eran SegalMerry Maisel
San Diego, California, United States of America
PLoS Comput Biol 3:e128. 2007 - Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAsJohn L Rinn
Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
Cell 129:1311-23. 2007..Thus, transcription of ncRNA may demarcate chromosomal domains of gene silencing at a distance; these results have broad implications for gene regulation in development and disease states... - Evidence for an instructive mechanism of de novo methylation in cancer cellsIlana Keshet
Department of Cellular Biochemistry and Human Genetics, Hebrew University, Jerusalem, Israel
Nat Genet 38:149-53. 2006..In addition, many are already repressed in normal cells. These results are consistent with the hypothesis that cancer-related de novo methylation may come about through an instructive mechanism...
Research Grants
- Genome-wide analysis of regulated chromosomal domains: From mechanisms to cancerEran Segal; Fiscal Year: 2010..abstract_text> ..
- Genome-wide analysis of regulated chromosomal domains: From mechanisms to cancerEran Segal; Fiscal Year: 2007....