Eran Segal

Summary

Affiliation: Weizmann Institute of Science
Country: Israel

Publications

  1. pmc Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation
    Ophir Shalem
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Mol Syst Biol 4:223. 2008
  2. pmc Modeling interactions between adjacent nucleosomes improves genome-wide predictions of nucleosome occupancy
    Shai Lubliner
    Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
    Bioinformatics 25:i348-55. 2009
  3. pmc Promoter sequence determines the relationship between expression level and noise
    Lucas B Carey
    Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
    PLoS Biol 11:e1001528. 2013
  4. pmc InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale
    Haidong Wang
    Computer Science Department, Stanford University, Serra Mall, Stanford, CA 94305, USA
    Genome Biol 8:R192. 2007
  5. pmc From DNA sequence to transcriptional behaviour: a quantitative approach
    Eran 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
  6. pmc 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
  7. pmc A genomic code for nucleosome positioning
    Eran Segal
    Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
    Nature 442:772-8. 2006
  8. pmc Poly(dA:dT) tracts: major determinants of nucleosome organization
    Eran Segal
    Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 76100, Israel
    Curr Opin Struct Biol 19:65-71. 2009
  9. pmc Distinct modes of regulation by chromatin encoded through nucleosome positioning signals
    Yair Field
    Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
    PLoS Comput Biol 4:e1000216. 2008
  10. pmc The DNA-encoded nucleosome organization of a eukaryotic genome
    Noam Kaplan
    Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
    Nature 458:362-6. 2009

Collaborators

Detail Information

Publications56

  1. pmc Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation
    Ophir 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...
  2. pmc Modeling interactions between adjacent nucleosomes improves genome-wide predictions of nucleosome occupancy
    Shai 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...
  3. pmc Promoter sequence determines the relationship between expression level and noise
    Lucas B Carey
    Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
    PLoS Biol 11:e1001528. 2013
    ..Taken together, we show that the precise amount by which noise changes with expression is specific to the regulatory mechanism of transcription and translation that acts at each gene...
  4. pmc InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale
    Haidong 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...
  5. pmc From DNA sequence to transcriptional behaviour: a quantitative approach
    Eran 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...
  6. pmc 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
    ....
  7. pmc A genomic code for nucleosome positioning
    Eran 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...
  8. pmc Poly(dA:dT) tracts: major determinants of nucleosome organization
    Eran 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...
  9. pmc Distinct modes of regulation by chromatin encoded through nucleosome positioning signals
    Yair Field
    Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
    PLoS Comput Biol 4:e1000216. 2008
    ....
  10. pmc The DNA-encoded nucleosome organization of a eukaryotic genome
    Noam 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...
  11. pmc Incorporating nucleosomes into thermodynamic models of transcription regulation
    Tali Raveh-Sadka
    Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
    Genome Res 19:1480-96. 2009
    ....
  12. pmc Two DNA-encoded strategies for increasing expression with opposing effects on promoter dynamics and transcriptional noise
    Maya Dadiani
    Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
    Genome Res 23:966-76. 2013
    ..Our study thus demonstrates the effect of cis-regulatory elements on expression variability and points to concrete types of sequence changes that may allow partial decoupling of expression level and noise...
  13. pmc Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters
    Eilon 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...
  14. doi request reprint Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast
    Tali 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...
  15. pmc Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization
    Yair 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...
  16. pmc Measurements of the impact of 3' end sequences on gene expression reveal wide range and sequence dependent effects
    Ophir 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...
  17. pmc p53 binds preferentially to genomic regions with high DNA-encoded nucleosome occupancy
    Efrat Lidor Nili
    Department of Molecular Cell Biology, The Weizmann Institute, Rehovot 76100, Israel
    Genome Res 20:1361-8. 2010
    ....
  18. pmc A feature-based approach to modeling protein-DNA interactions
    Eilon 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/...
  19. pmc Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promoters
    Danny 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...
  20. doi request reprint Predicting expression patterns from regulatory sequence in Drosophila segmentation
    Eran 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...
  21. pmc Deciphering the rules by which 5'-UTR sequences affect protein expression in yeast
    Shlomi Dvir
    Departments of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
    Proc Natl Acad Sci U S A 110:E2792-801. 2013
    ....
  22. pmc Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology
    Noam 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...
  23. pmc Using expression profiles of Caenorhabditis elegans neurons to identify genes that mediate synaptic connectivity
    Leehod 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...
  24. pmc Sequence features of yeast and human core promoters that are predictive of maximal promoter activity
    Shai Lubliner
    Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
    Nucleic Acids Res 41:5569-81. 2013
    ..We further show that human core promoters also contain features that are indicative of maximal promoter activity; thus, our results emphasize the important role of the core promoter sequence in transcriptional regulation...
  25. pmc Promoters maintain their relative activity levels under different growth conditions
    Leeat Keren
    1 Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel 2 Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel 3 Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
    Mol Syst Biol 9:701. 2013
    ..It suggests that many changes in expression across conditions result from global effects and not specific regulation, and provides means for quantitative interpretation of expression profiles...
  26. pmc Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes
    Michal 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...
  27. pmc The grammar of transcriptional regulation
    Shira Weingarten-Gabbay
    Department of Computer Science, Applied Mathematics and Department of Molecular Cell Biology, Weizmann Institute of Science, 76100, Rehovot, Israel
    Hum Genet 133:701-11. 2014
    ..We review different methods that are used to study the grammar of transcription regulation, highlight gaps in current understanding, and discuss how recent technological advances may be utilized to bridge them. ..
  28. pmc Predicting disease risk using bootstrap ranking and classification algorithms
    Ohad Manor
    Dept of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
    PLoS Comput Biol 9:e1003200. 2013
    ..Overall, our results show that improving disease risk prediction from genotypic information may be a tangible goal, with potential implications for personalized disease screening and treatment. ..
  29. doi request reprint Computational prediction of RNA structural motifs involved in post-transcriptional regulatory processes
    Michal Rabani
    Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehoboth, Rehovot, Israel
    Methods Mol Biol 714:467-79. 2011
    ....
  30. pmc Widespread compensatory evolution conserves DNA-encoded nucleosome organization in yeast
    Ephraim 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...
  31. pmc Overlapping codes within protein-coding sequences
    Shalev 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...
  32. pmc Nucleosome maps of the human cytomegalovirus genome reveal a temporal switch in chromatin organization linked to a major IE protein
    Einat Zalckvar
    Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
    Proc Natl Acad Sci U S A 110:13126-31. 2013
    ..These results provide a framework of spatial and temporal nucleosome organization across the genome of a major human pathogen and suggest that an hCMV major IE protein governs overall viral chromatin structure and function. ..
  33. pmc Genome-wide measurement of RNA secondary structure in yeast
    Michael 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...
  34. doi request reprint Monoubiquitinated H2B is associated with the transcribed region of highly expressed genes in human cells
    Neri Minsky
    Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    Nat Cell Biol 10:483-8. 2008
    ....
  35. ncbi request reprint The role of site accessibility in microRNA target recognition
    Michael 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...
  36. pmc Robust prediction of expression differences among human individuals using only genotype information
    Ohad Manor
    Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
    PLoS Genet 9:e1003396. 2013
    ....
  37. pmc Cell lineage analysis of the mammalian female germline
    Yitzhak Reizel
    Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
    PLoS Genet 8:e1002477. 2012
    ..Overall, our study sheds light on substantial novel aspects of female germline preservation and development...
  38. doi request reprint How transcription factors identify regulatory sites in genomic sequence
    Yair 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...
  39. pmc Geometric constraints on neuronal connectivity facilitate a concise synaptic adhesive code
    Shalev 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...
  40. ncbi request reprint In pursuit of design principles of regulatory sequences
    Michal Levo
    Department of Molecular Cell Biology, and Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
    Nat Rev Genet 15:453-68. 2014
    ..We discuss how understanding different aspects of the sequence-encoded regulation can help to unravel the genotype-phenotype relationship, which would lead to a more accurate and mechanistic interpretation of personal genome sequences. ..
  41. pmc Estimating cell depth from somatic mutations
    Adam Wasserstrom
    Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
    PLoS Comput Biol 4:e1000058. 2008
    ..Our method for depth estimation opens a window for revealing tissue turnover rates in animals, including humans, which has important implications for our knowledge of the body under physiological and pathological conditions...
  42. ncbi request reprint A module of negative feedback regulators defines growth factor signaling
    Ido 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...
  43. ncbi request reprint A discriminative model for identifying spatial cis-regulatory modules
    Eran 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...
  44. pmc Systematic functional characterization of cis-regulatory motifs in human core promoters
    Saurabh 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...
  45. pmc Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae
    Ji 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...
  46. ncbi request reprint A gene-coexpression network for global discovery of conserved genetic modules
    Joshua 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...
  47. ncbi request reprint Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data
    Eran 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...
  48. ncbi request reprint From signatures to models: understanding cancer using microarrays
    Eran 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...
  49. pmc Module map of stem cell genes guides creation of epithelial cancer stem cells
    David 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...
  50. ncbi request reprint Evidence for an instructive mechanism of de novo methylation in cancer cells
    Ilana 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...
  51. pmc The modular era of functional genomics
    Eran 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...
  52. pmc Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs
    John 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...
  53. pmc ISCB honors Temple F. Smith and Eran Segal
    Merry Maisel
    San Diego, California, United States of America
    PLoS Comput Biol 3:e128. 2007
  54. pmc Disruption of yeast forkhead-associated cell cycle transcription by oxidative stress
    Michael 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...
  55. pmc Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression
    Rosa 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...
  56. ncbi request reprint Probabilistic discovery of overlapping cellular processes and their regulation
    Alexis Battle
    Computer Science Department, Stanford University, Stanford, CA 94305 9010, USA
    J Comput Biol 12:909-27. 2005
    ....