Gill Bejerano

Publications

• Dispensability of mammalian DNA. McLean C, Bejerano G. Genome Res. 2008; 18 (11): 1743-51
• 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
• 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
• The UCSC genome browser database: update 2007 UCSC Genomics Group, Nucleic Acids Research. 2007: 35 D668-73
• 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
• Branch and bound computation of exact P-values G. Bejerano, Bioinformatics. 2006; 22 (17): 2158-2159
• 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
• The UCSC Genome Browser Database: Update 2006 UCSC Genomics Group, Nucleic Acids Res.. 2006: 34 D590-D598
• 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
• Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing E.A. Glazov, M. Pheasant, E.A. McGraw, G. Bejerano, J.S. Mattick, Genome Research. 2005; 15 (6): 800-808
• Computational screening of conserved genomic DNA in search of functional non-coding elements G. Bejerano, A.C. Siepel, W.J. Kent, D. Haussler, Nature Methods. 2005; 2 (7): 535-545
• 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
• Into the heart of darkness: large-scale clustering of human non-coding DNA G. Bejerano, D. Haussler, M. Blanchette, Bioinformatics. 2004: 20 I40-I48
• 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 G. Bejerano, M. Pheasant, I.V. Makunin, S. Stephen, W.J. Kent, J.S. Mattick, D. Haussler, Science. 2004; 305 (5675): 1321-1325
• 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
• 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
• Algorithms for variable length Markov chain modeling G. Bejerano, Bioinformatics. 2004; 20 (5): 788-789
• 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, EURASIP J. Applied Signal Processing. 2003: 2 93-102
• 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, Proceedings of 19th International Conference on Machine Learning. 2002 ICML
• Automated modeling of musical style O. Lartillot, S. Dubnov, G. Assayag, G. Bejerano, Proceedings of the International Computer Music Conference. 2001 ICMC
• 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
• 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
• 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
• Markovian domain fingerprinting: Statistical segmentation of protein sequences G. Bejerano,, Y. Seldin, H. Margalit, N. Tishby. Bioinformatics. 2001; 17 (10): 927-934
• 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
• Variations on probabilistic suffix trees: statistical modeling and prediction of protein families. Bejerano G, Yona G. Bioinformatics. 2001; 17 (1): 23-43
• PromEC: An updated database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sites R. Hershberg, G. Bejerano, A. Santos-Zavaleta, H. Margalit, Nucleic Acids Research. 2001; 29 (1): 277
• 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
• 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