Gill Bejerano

Publications

• Enhancers: five essential questions. Pennacchio LA, Bickmore W, Dean A, Nobrega MA, Bejerano G. Nat Rev Genet. 2013; 14 (4): 288-95
• Evolutionary biology for the 21st century. Losos JB, Arnold SJ, Bejerano G, Brodie ED, Hibbett D, Hoekstra HE, Mindell DP, Monteiro A, Moritz C, Orr HA, Petrov DA, Renner SS, Ricklefs RE, Soltis PS, Turner TL. PLoS Biol. 2013; 11 (1): e1001466
• PRISM offers a comprehensive genomic approach to transcription factor function prediction. Wenger AM, Clarke SL, Guturu H, Chen J, Schaar BT, McLean CY, Bejerano G. Genome Res. 2013; 23 (5): 889-904
• A "forward genomics" approach links genotype to phenotype using independent phenotypic losses among related species. Hiller M, Schaar BT, Indjeian VB, Kingsley DM, Hagey LR, Bejerano G. Cell Rep. 2012; 2 (4): 817-23
• A novel 13 base pair insertion in the sonic hedgehog ZRS limb enhancer (ZRS/LMBR1) causes preaxial polydactyly with triphalangeal thumb. Laurell T, Vandermeer JE, Wenger AM, Grigelioniene G, Nordenskjöld A, Arner M, Ekblom AG, Bejerano G, Ahituv N, Nordgren A. Hum Mutat. 2012; 33 (7): 1063-6
• Coding exons function as tissue-specific enhancers of nearby genes. Birnbaum RY, Clowney EJ, Agamy O, Kim MJ, Zhao J, Yamanaka T, Pappalardo Z, Clarke SL, Wenger AM, Nguyen L, Gurrieri F, Everman DB, Schwartz CE, Birk OS, Bejerano G, Lomvardas S, Ahituv N. Genome Res. 2012; 22 (6): 1059-68
• Human developmental enhancers conserved between deuterostomes and protostomes. Clarke SL, VanderMeer JE, Wenger AM, Schaar BT, Ahituv N, Bejerano G. PLoS Genet. 2012; 8 (8): e1002852
• Hundreds of conserved non-coding genomic regions are independently lost in mammals. Hiller M, Schaar BT, Bejerano G. Nucleic Acids Res. 2012; 40 (22): 11463-76
• PESNPdb: a comprehensive database of SNPs studied in association with pre-eclampsia. Tuteja G, Cheng E, Papadakis H, Bejerano G. Placenta. 2012; 33 (12): 1055-7
• Control of pelvic girdle development by genes of the Pbx family and Emx2. Capellini TD, Handschuh K, Quintana L, Ferretti E, Di Giacomo G, Fantini S, Vaccari G, Clarke SL, Wenger AM, Bejerano G, Sharpe J, Zappavigna V, Selleri L. Dev Dyn. 2011; 240 (5): 1173-89
• Human-specific loss of regulatory DNA and the evolution of human-specific traits. McLean CY, Reno PL, Pollen AA, Bassan AI, Capellini TD, Guenther C, Indjeian VB, Lim X, Menke DB, Schaar BT, Wenger AM, Bejerano G, Kingsley DM. Nature. 2011; 471 (7337): 216-9
• Noninvasive monitoring of placenta-specific transgene expression by bioluminescence imaging. Fan X, Ren P, Dhal S, Bejerano G, Goodman SB, Druzin ML, Gambhir SS, Nayak NR. PLoS One. 2011; 6 (1): e16348
• Endangered species hold clues to human evolution. Lowe CB, Bejerano G, Salama SR, Haussler D. J Hered. 2010 Jul-Aug; 101 (4): 437-47
• GREAT improves functional interpretation of cis-regulatory regions. McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, Wenger AM, Bejerano G. Nat Biotechnol. 2010; 28 (5): 495-501
• Dispensability of mammalian DNA. McLean C, Bejerano G. Genome Res. 2008; 18 (11): 1743-51
• Comparative genomic analysis using the UCSC genome browser. Karolchik D, Bejerano G, Hinrichs AS, Kuhn RM, Miller W, Rosenbloom KR, Zweig AS, Haussler D, Kent WJ. Methods Mol Biol. 2007: 395 17-34
• Human genome ultraconserved elements are ultraselected. Katzman S, Kern AD, Bejerano G, Fewell G, Fulton L, Wilson RK, Salama SR, Haussler D. Science. 2007; 317 (5840): 915
• Thousands of human mobile element fragments undergo strong purifying selection near developmental genes C.B. Lowe, G. Bejerano, D. Haussler. Proc. Nat’l Acad. Sci. USA. 2007; 104 (19): 8005-8010
• A Distal Enhancer and an Ultraconserved Exon are Derived From a Novel Retroposon G. Bejerano, C.B. Lowe, N. Ahituv, B. King, A. Siepel, S.R. Salama, E.M. Rubin, W.J. Kent, D. Haussler. Nature. 2006; 441 (7089): 87-90
• Branch and bound computation of exact p-values. Bejerano G, Bioinformatics. 2006; 22 (17): 2158-9
• Forces Shaping the Fastest Evolving Regions in the Human Genome K.S. Pollard, S.R. Salama, B. King, A.D. Kern, T. Dreszer, S. Katzman, A.Siepel, J.S. Pedersen, G. Bejerano, R. Baertsch, K.R. Rosenbloom, J. Kent and D. Haussler. PLoS Genetics. 2006; 2 (10): e168
• Identification and classification of conserved RNA secondary structures in the human genome. Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES, Kent J, Miller W, Haussler D. PLoS Comput Biol. 2006; 2 (4): e33
• The UCSC Genome Browser Database: update 2006. Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H, Diekhans M, Furey TS, Harte RA, Hsu F, Hillman-Jackson J, Kuhn RM, Pedersen JS, Pohl A, Raney BJ, Rosenbloom KR, Siepel A, Smith KE, Sugnet CW, Sultan-Qurraie A, Thomas DJ, Trumbower H, Weber RJ, Weirauch M, Zweig AS, Haussler D, Kent WJ. Nucleic Acids Res. 2006; 34 (Database issue): D590-8
• Computational screening of conserved genomic DNA in search of functional noncoding elements. Bejerano G, Siepel AC, Kent WJ, Haussler D. Nat Methods. 2005; 2 (7): 535-45
• Evolutionarily Conserved Elements in Vertebrate, Fly, Worm, and Yeast Genomes A. Siepel, G. Bejerano, J.S. Pedersen, A. Hinrichs, M. Hou, K. Rosenbloom, H. Clawson, J. Spieth, L.W. Hillier, S. Richards, G.M. Weinstock, R.K. Wilson, R.A. Gibbs, W.J. Kent, W. Miller, D. Hausler. Genome Research. 2005; 15 (8): 1034-1050
• Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing. Glazov EA, Pheasant M, McGraw EA, Bejerano G, Mattick JS. Genome Res. 2005; 15 (6): 800-8
• Algorithms for variable length Markov chain modeling. Bejerano G, Bioinformatics. 2004; 20 (5): 788-9
• Efficient exact p-value computation for small sample, sparse and surprising categorical data G. Bejerano, N. Friedman, N. Tishby, J. Computational Biology. 2004; 11 (5675): 867-886
• Extremely conserved non-coding sequences in the vertebrate genomes I.V. Makunin, S. Stephen, M. Pheasant, G. Bejerano, W.J. Kent, D. Haussler, J.S. Mattick, Proceedings of 4th International Conference on Bioinformatics of Genome Regulation and Structure. 2004 BGRS
• Into the heart of darkness: large-scale clustering of human non-coding DNA. Bejerano G, Haussler D, Blanchette M. Bioinformatics. 2004: 20 Suppl 1 i40-8
• Sequencing and comparative analysis of the chicken genome International Chicken Genome Sequencing Consortium, Nature. 2004; 432 (7018): 695-716
• Ultraconserved elements in the human genome. Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D. Science. 2004; 304 (5675): 1321-5
• A system for computer music generation by learning and improvisation in a particular style O. Lartillot, S. Dubnov, G. Assayag, G. Bejerano, IEEE Computer J.. 2003; 36 (10): 73-80
• Discriminative feature selection via multiclass variable memory Markov models N. Slonim, G. Bejerano, S. Fine, N. Tishby, EURASIP J. Applied Signal Processing. 2003: 2 93-102
• Efficient exact p-value computation and applications to biosequence analysis G. Bejerano, Proceedings of the 7th annual international conference on research in computational molecular biology. 2003 RECOMB
• Discriminative feature selection via multiclass variable memory Markov models N. Slonim, G. Bejerano, S. Fine, N. Tishby, Proceedings of 19th International Conference on Machine Learning. 2002 ICML
• A Simple Hyper-Geometric Approach for Discovering Putative Transcription Factor Binding Sites, 1st Workshop on Algorithms in Bioinformatics Y. Barash, G. Bejerano, N. Friedman, Lecture Notes in Computer Science. 2001; WABI (2149): 278-293
• A variable memory Markovian modeling approach to unsupervised sequence segmentation Y. Seldin, G. Bejerano, N. Tishby, Proceedings of 33rd Symposium on the Interface of Computing Science and Statistics. 2001 INTERFACE
• Automated modeling of musical style O. Lartillot, S. Dubnov, G. Assayag, G. Bejerano, Proceedings of the International Computer Music Conference. 2001 ICMC
• Markovian domain fingerprinting: statistical segmentation of protein sequences. Bejerano G, Seldin Y, Margalit H, Tishby N. Bioinformatics. 2001; 17 (10): 927-34
• Novel small RNA-encoding genes in Escherichia coli L. Argaman, R. Hershberg, J. Vogel, G. Bejerano, G. Wagner, H. Margalit, S. Altuvia, Current Biology. 2001; 11 (12): 941-950
• Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H, Altuvia S. Curr Biol. 2001; 11 (12): 941-50
• PromEC: An updated database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sites. Hershberg R, Bejerano G, Santos-Zavaleta A, Margalit H. Nucleic Acids Res. 2001; 29 (1): 277
• Unsupervised sequence segmentation by a mixture of switching variable memory Markov sources Y. Seldin, G. Bejerano, N. Tishby, Proceedings of 18th International Conference on Machine Learning. 2001 IMCL
• Variations on probabilistic suffix trees: statistical modeling and prediction of protein families. Bejerano G, Yona G. Bioinformatics. 2001; 17 (1): 23-43
• Optimal amnesic probabilistic automata, or, how to learn and classify proteins in linear time and space A. Apostolico, G. Bejerano, J. Computational Biology. 2000; 7 (3-4): 381-393
• Optimal amnesic probabilistic automata, or, how to learn and classify proteins in linear time and space A. Apostolico, G. Bejerano, Proceedings of the 4th annual international conference on research in computational molecular biology. 2000 RECOMB
• Modeling protein families using probabilistic suffix trees, Proceedings of the 3rd annual international conference on research in computational molecular biology G. Bejerano, G. Yona. RECOMB. 1999