Journal Publications

	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 Jan 18. doi: 10.1038/nmeth.3732.
	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 Jan.
See also: Perspective in Science
	Taking it Personally: Personalized Utilization of the Human Microbiome in Health and Disease.
	Niv Zmora, David Zeevi, Tal Korem, Eran Segal, Eran Elinav
	Cell Host Microbe, 2016 Jan., doi: 10.1016/j.chom.2015.12.016
	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 Dec., doi: 10.1016/j.cell.2015.10.048
	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 Nov., doi: 10.1016/j.cell.2015.11.001.
See also: Video, BBC, Time, NYTime, 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
	Genome Res., 2015 Sep.
See also: 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
	Science, 2015 doi:10.1126/science.aac4812
See also: Related Software, Nature Reviews Microbiology Highlight, Science perspective
	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 May
	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 Apr doi: 10.1371/journal.pgen.1005147
	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 Mar
	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, Mar. 2015, doi: 10.1101/gr.185033.114
See also: NATURE GENETICS RESEARCH HIGHLIGHTS
	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
	Gut Microbes, 2015 Mar. doi:10.1080/19490976.2015.1016690
	GenoExp: a web tool for predicting gene expression levels from single nucleotide polymorphisms
	Ehud Manor and Eran Segal
	Bioinformatics., 2015 Jun. doi:10.1093/bioinformatics/btv050
	A shared architecture for promoters and enhancers
	Weingarten-Gabbay Shira and Segal Eran
	Nature Genetics 2014 Dec. doi: 10.1038/ng.3152
	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 Oct. doi: 10.1016/j.cell.2014.09.048
	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 Oct. doi:10.1038/ncomms6172
	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 Oct. doi: 10.1101/gr.179259.114
	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 Oct. doi:10.1101/gr.168773.113
	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 Sep. doi: 10.1038/nature13793
See also: Nature News & Views, NYTimes, Wall Street Journal, Economist, Washington Post
	In pursuit of design principles of regulatory sequences
	Levo Michal, Segal Eran
	Nature Reviews Genetics 2014 Jun. 10;doi:10.1038/nrg3684
	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 Jan 30;505(7485):706-9. doi: 10.1038/nature12946
See also: Nature Reviews Genetics Highlight
	The grammar of transcriptional regulation
	Weingarten-Gabbay Shira, Segal Eran
	Human Genetics 2014 Jan 5.;PMID:24390306
	Fixated on fixation - using ChIP to interrogate the dynamics of chromatin interactions.
	Leeat Keren and Eran Segal
	Genome Biology 2013 Nov 21;14(11):138
	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 Oct. 29;9:701
	Predicting disease risk using bootstrap ranking and classification algorithms.
	Ohad Manor and Eran Segal
	PLoS Comput. Biol. 2013 Aug;9(8):e1003200.;doi: 10.1371/journal.pcbi.1003200
	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 Aug 6;110(32):13126-31. doi: 10.1073/pnas.1305548110
	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 Jul 23;110(30):E2792-801. doi: 10.1073/pnas.1222534110
	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 Jun;23(6):966-76
See also: Genome Research Cover
	Sequence features of yeast and human core promoters that are predictive of maximal promoter activity.
	Shai Lubliner, Leeat Keren, Eran Segal
	Nucleic Acids Res. 2013 Jun 1;41(11):5569-81.
	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 Apr;11(4):e1001528
	Robust prediction of expression differences among human individuals using only genotype information.
	Ohad Manor, Eran Segal
	PLoS Genet. 2013 Mar;9(3):e1003396
	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 Mar;9(3):e1002934
	Determinants of nucleosome positioning.
	Kevin Struhl and Eran Segal
	Nat. Struct Mol Biol., 2013 Mar;20(3):267-73.
	Genomics: ENCODE explained
	Joseph R. Ecker, Wendy A. Bickmore, Ines Barroso, Jonathan K. Pritchard, Yoav Gilad and Eran Segal
	Nature, 2012 Sep 6;489(7414):52-5.
	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, Sep 2012, doi:10.1016/j.molcel.2012.08.008
See also: 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
	PLoS Genetic, February 2012 ,doi:10.1371/journal.pgen.1002477
	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 Feb;11(4):658-67.
	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, May 2012, doi:10.1038/ng.2305
See also: 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
	Nature Biotechnology, May 2012, doi:10.1038/nbt.2205
See also: Highlight in Nature Biotechnology News and Views
	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
	Genome Res., 2011 Dec;21(12):2114-28
	Understanding the transcriptome through RNA structure.
	Yue Wan, Michael Kertesz, Robert Spitale, Eran Segal, Howard Chang
	Nature Reviews Genetics 2011, 12(9):641-55
	Computational prediction of RNA structural motifs involved in post-transcriptional regulatory processes.
	Michal Rabani, Michael Kertesz, Eran Segal
	Methods Mol Biol. 2011;714:467-79.
	How transcription factors identify regulatory sites in genomic sequence.
	Yari Field, Eilon Sharon, Eran Segal
	Subcell Biochem. 2011;52:193-204.
	High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans.
	Sevinc Ercan, Yaniv Lubling, Eran Segal, Jason D Lieb
	Genome Res., 2011 Feb;21(2):237-44
	Widespread Compensatory Evolution Conserves DNA-Encoded Nucleosome Organization in Yeast.
	Ephraim Kenigsberg, Amir Bar, Eran Segal, Amos Tanay
	PLoS Comput Biol. 2010 Dec 23;6(12):e1001039.PMID: 21203484
	Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project.
	Gerstein MB et al.
	Science 2010, 24 December 2010:24 December 2010:DOI: 10.1126/science.1196914
	Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology
	Noam Kaplan, Timothy R Hughes, Jason D Lieb, Jonathan Widom, Eran Segal
	Genome Biology 2010, 11:140 doi:10.1186/gb-2010-11-11-140
	Overlapping codes within protein-coding sequences
	Shalev Itzkovitz, Eran Hodis, Eran Segal
	Genome Res. 2010 Sep 14. [Epub ahead of print]
	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 Nature 467, 103-107 (02 September 2010) | doi:10.1038/nature09322
See also: Nature Biotechnology Review, Faculty of 1000 review
	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 Aug;17: doi-10.1101/gr.103945.109
	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 Aug;17(8):918-20
	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 DOI: 10.1126/science.1192002, Published Online July 8, 2010
	EGF Decreases the Abundance of MicroRNAs That Restrain Oncogenic Transcription Factors
	Roi Avraham, Aldema Sas-Chen, Ohad Manor, Israel Steinfeld, Reut Shalgi, Gabi Tarcic, Noa Bossel, Amit Zeisel, Ido Amit, Yaara Zwang, Espen Enerly, Hege G. Russnes, Francesca Biagioni, Marcella Mottolese, Sabrina Strano, Giovanni Blandino, Anne-Lise Børresen-Dale, Yitzhak Pilpel, Zohar Yakhini, Eran Segal, and Yosef Yarden
	Sci. Signal., 1 June 2010 Vol. 3, Issue 124, p. ra43
See also: 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
	PLoS ONE 5(2): e9129. doi:10.1371/journal.pone.0009129
	What controls nucleosome positions?
	Eran Segal & Jonathan Widom
	Trends Genet. 2009 Jul 9. [Epub ahead of print]
	From DNA sequence to transcriptional behaviour: a quantitative approach
	Eran Segal & Jonathan Widom
	Nature Reviews Genetics, advance online publication, Published online 9 June 2009 (doi:10.1038/nrg2591)
	Modeling interactions between adjacent nucleosomes improves genome-wide predictions of nucleosome occupancy
	Shai Lubliner, Eran Segal
	Bioinformatics 2009 25: i348-i355.
	Incorporating Nucleosomes into Thermodynamic Models of Transcription Regulation
	Tali Raveh-Sadka, Michal Levo, Eran Segal
	Genome Res. 2009. 19:1480-1496
	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 458, 362-366 (19 March 2009)
See also: Faculty of 1000 review
	Poly(dA:dT) tracts: major determinants of nucleosome organization
	Eran Segal and Jonathan Widom
	Curr Opin Struct Biol. 2009 Feb;19(1):65-71. Epub 2009 Feb 7
	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 Published online: 1 March 2009 | doi:10.1038/ng.324
See also: Highlight in Nature Reviews Genetics, Faculty of 1000 review.
	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 Aug 18;106(33):13785-90. Epub 2009 Aug 3
	Stemness, cancer, and cancer stem cells
	David J. Wong, Eran Segal and Howard Y. Chang
	Cell Cycle. 2008 Dec 2;7(23). [Epub ahead of print]Click here to read
	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 4(11): e1000216. doi:10.1371/journal.pcbi.1000216
	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
	Molecular Systems Biology 4 Article number: 4 doi:10.1038/msb.2008.59, Published online: 14 October 2008
See also: Faculty of 1000 review
	Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes
	Michal Rabani, Michael Kertesz, Eran Segal
	Proc Natl Acad Sci U S A. 2008 Sep 24. [Epub ahead of print]
	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, September 12;4(9):e1000175
	A Feature-Based Approach to Modeling Protein-DNA Interactions
	Eilon Sharon, Shai Lubliner, Eran Segal.
	PLoS Comput Biol 2008, August 22;4(8):e1000154
	Geometric constraints on neuronal connectivity facilitate a concise synaptic adhesive code
	Shalev Itzkovitz, Leehod Baruch, Ehud Shapiro, and Eran Segal
	Proc Natl Acad Sci U S A. 2008 Jun 26. [Epub ahead of print]
	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 Apr 11;4(4):e1000058
	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 Apr 9;3(4):e1939
	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.
	Cell Stem Cell. 2008 Apr 10;2(4):333-44.
See also: Faculty of 1000 review
	Predicting expression patterns from regulatory sequence in Drosophila segmentation
	Eran Segal, Tali Raveh-Sadka, Mark Schroeder, Ulrich Unnerstall & Ulrike Gaul
	Nature 451, 535-540 (31 January 2008)
See also: Editor Summary
	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
	Nature Cell Biology Published online: 16 March 2008, doi:10.1038/ncb1712
	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. 18:477-488, 2008, Published online before print February 6, 2008, 10.1101/gr.6828808
	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 Jan 15;68(2):369-78.
	Reversal of aging by NFkappaB blockade
	Adler AS, Kawahara TL, Segal E, Chang HY
	Cell Cycle. 2007 Dec 26;7(5) [Epub ahead of print]
See also: 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 Dev. 2007 Dec 15;21(24):3244-57. Epub 2007 Nov 30.
See also: 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
	Nature Genetics 39, 1278 - 1284 (2007).
See also: News & Views, Research Highlights
	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
	Genome Biology, 2007 8:R192 ( 14 September 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 Jun 29;129(7):1311-23.
See also: News & Views, Faculty of 1000 review.
	A Transcriptional Program Mediating Entry into Cellular Quiescence
	Liu H, Adler AS, Segal E, Chang HY
	PLoS Genet. 2007 Jun 8;3(6):e91 [Epub ahead of print]
	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 25, 675 - 680 (2007)
	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
	Clin Exp Immunol. 2007 May 4
	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, 39, 503 - 512 (2007).
	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.
	Nature, 2006 July, 442(7104):772-8
See also: ESI Hot Paper, NY Times, Nature cover, News & Views, Nature Reviews Genetics, Faculty of 1000 review, Codes and Enigmas, TheScientist and about the authors.
	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 February, 38(2): 149-53.
	Efficient Bundle Sorting
	Y. Matias,E. Segal, J.S. Vitter
	SIAM Journal on Computing, 36(2):394-410, 2006.
	From Signature to Models: Understanding Cancer Using Microarrays
	E. Segal,N. Friedman, N. Kaminski, A. Regev, and D. Koller.
	Nature Genetics, 2005 June, 37(6 Suppl): S38-45.
	A Module Map Showing Conditional Activity of Expression Modules in Cancer
	E. Segal, N. Friedman, D. Koller, and A. Regev.
	Nature Genetics, 2004 October, 36(10): 1090-8.
See also: Genome Biology highlight, Faculty of 1000 review.
	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.
	Nature Genetics, 2003 June, 34(2): 166-76.
	A Gene Co-Expression Network for Global Discovery of Conserved Genetics Modules
	J. Stuart­*, E. Segal*, D. Koller, and S.Kim. (*equal contribution)
	Science, 2003 October, 302(5643): 249-55.
See also: Science highlight, Faculty of 1000 review, Nature Reviews Genetics.
	Learning Module Networks
	E. Segal, D. Pe'er, A. Regev, D. Koller, and N. Friedman.
	Journal of Machine Learning Research (JMLR), 2005 April, 6(Apr): 557-88.
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, 12(6): 822-34, August 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, 12(7): 909-27, September 2005.
An earlier version appeared at the 8th Inter. Conf. on Research in Computational Molecular Biology (RECOMB)
	Genome-wide Discovery of Transcriptional Modules from DNA Sequence and Gene Expression
	E. Segal, R. Yelensky, and D. Koller.
	Bioinformatics, 2003; 19(Suppl 1): 273-82.
	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; 19(Suppl 1): 264-272.
	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; 17 Suppl 1: S243-252.
	Disruption of Yeast Forkhead-Associated Cell Cycle Transcription by Oxidative Stress
	M. Shapira, E. Segal and D. Botstein.
	Molecular Biology of the Cell, 34(2): 166-76, October 2004.
	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.
	PLoS Biology, 2(12): e427, November 2004.
	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.
	PNAS, 2004 October, 101(40):14315-22.

Conference Publications

< 2010 Dec 22.tr> 2010 Dec 22.

	A Feature-Based Approach to Modeling Protein-DNA Interactions
	E. Sharon and E. Segal
	In 11th Inter. Conf. on Research in Computational Molecular Biology (RECOMB), 2007
	Identifying Protein-Protein Interaction Sites on a Genome-Wide Scale
	H. Wang, E. Segal, A. Ben-Hur, D. Brutlag, and D. Koller.
	In Proc. 18th Inter. Conf. on Neural Information Processing Systems (NIPS), Vancouver, British Columbia, Canada, 2004
	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.
	Proceedings of the 11th Inter. Conf. on Intelligent Systems for Molecular Biology (ISMB), 2004
	Decomposing Gene Expression into Cellular Processes
	E. Segal, A. Battle, D. Koller.
	In Proc. 8th Pacific Symposium on Biocomputing (PSB), Kaua'i, January 2003
	Boosting Density Estimation
	S. Rosset,E. Segal.
	In Proc. 16th Inter. Conf. on Neural Information Processing Systems (NIPS), Vancouver, British Columbia, Canada, 2002
	From Promoter Sequence to Expression: A Probabilistic Framework
	E. Segal, Y. Barash, I. Simon, N. Friedman, and D. Koller.
	In Proc. 6th Inter. Conf. on Research in Computational Molecular Biology (RECOMB), Washington, DC, April 2002.
	Probabilistic Hierarchical Clustering for Biological Data
	E. Segal, D.Koller.
	In Proc. 6th Inter. Conf. on Research in Computational Molecular Biology (RECOMB), Washington, DC, April 2002
	Probabilistic Abstraction Hierarchies
	E. Segal, D. Koller, D. Ormoneit.
	In Proc. 15th International Conference on Neural Information Processing Systems (NIPS), Vancouver, British Columbia, Canada, 2001
	Probabilistic Classification and Clustering in Relational Data
	B. Taskar, E. Segal, and D. Koller
	In Proc. 17th Inter. Joint Conference on Artificial Intelligence (IJCAI), Seattle, Washington, August 2001
	Exact Inference in Networks with Discrete Children of Continuous Parents
	U. Lerner, E. Segal and D. Koller
	In Proc. 17th Conf. on Uncertainty in Artificial Intelligence (UAI), Seattle, Washington, August 2001
	Probabilistic Models of Text and Link Structure for Hypertext Classification
	L. Getoor,E. Segal, B. Taskar and D. Koller
	In IJCAI Workshop on "Text Learning: Beyond Supervision", Seattle, Washington, August 2001
	Efficient Bundle Sorting
	Y. Matias,E. Segal, J.S. Vitter
	In Proc. 11th Annual SIAM/ACM Symposium on Discrete Algorithms (SODA), San-Francisco, California, January 2000