Challenge Bejerano Lab

Publications

In ascending chronological order. 

Most full texts available via http://bejerano.stanford.edu/publications.html

Refereed journal papers

  1. A. Apostolico and G. Bejerano. Optimal amnesic probabilistic automata, or, how to learn and classify proteins in linear time and space, J. Computational Biology, 7(3-4): 381-393, 2000. [pdf]

  2. R. Hershberg, G. Bejerano, A. Santos-Zavaleta and H. Margalit. PromEC: An updated database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sites, Nucleic Acids Research, 29(1): 277, 2001. [pdf] [website]

  3. G. Bejerano and G. Yona. Variations on probabilistic suffix trees - a new tool for statistical modeling and prediction of protein families, Bioinformatics, 17(1): 23-43, 2001. [pdf] [code]

  4. L. Argaman, R. Hershberg, J. Vogel, G. Bejerano, G. Wagner, H. Margalit and S. Altuvia. Novel small RNA-encoding genes in Escherichia coli, Current Biology, 11(12): 941-950, 2001. [pubmed]

  5. G. Bejerano, Y. Seldin, H. Margalit and N. Tishby. Markovian domain fingerprinting: Statistical segmentation of protein sequences, Bioinformatics 17(10): 927-934, 2001. [pdf] [poster]

  6. N. Slonim, G. Bejerano, S. Fine and N. Tishby. Discriminative feature selection via multiclass variable memory Markov models, EURASIP J. Applied Signal Processing, 2: 93-102, 2003. [pdf]

  7. O. Lartillot, S. Dubnov, G. Assayag and G. Bejerano. A system for computer music generation by learning and improvisation in a particular style, IEEE Computer J., 36(10): 73-80, 2003. [pdf] [music]

  8. G. Bejerano. Algorithms for variable length Markov chain modeling. Bioinformatics, 20(5): 788-789, 2004. [pdf] [code]

  9. G. Bejerano, M. Pheasant, I.V. Makunin, S. Stephen, W.J. Kent, J.S. Mattick and D. Haussler. Ultraconserved elements in the human genome. Science, 304(5675): 1321-1325, 2004. Quoted by Science in Breakthrough of the Year, 5th runner up.[pdf] [suppl] [website]

  10. G. Bejerano, D. Haussler and M. Blanchette. Into the heart of darkness: large-scale clustering of human non-coding DNA. Bioinformatics, 20: I40-I48, 2004. [pdf] [website]

  11. International Chicken Genome Sequencing Consortium. Sequencing and comparative analysis of the chicken genome, Nature, 432(7018): 695-716, 2004. [pubmed]

  12. G. Bejerano, N. Friedman and N. Tishby. Efficient exact p-value computation for small sample, sparse and surprising categorical data, J. Computational Biology, 11(5): 867-886, 2004. [pdf] [code]

  13. E.A. Glazov, M. Pheasant, E.A. McGraw, G. Bejerano and J.S. Mattick. Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing. Genome Research, 15(6):800-808, 2005. [pubmed]

  14. 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, and D. Haussler. Evolutionarily Conserved Elements in Vertebrate, Fly, Worm, and Yeast Genomes. Genome Research, 15(8):1034-1050, 2005. [pubmed]

  15. G. Bejerano, A.C. Siepel, W.J. Kent and D. Haussler. Computational screening of conserved genomic DNA in search of functional non-coding elements. Nature Methods, 2(7):535-545, 2005. [pdf]

  16. UCSC Genomics Group. The UCSC Genome Browser Database: Update 2006. Nucleic Acids Res., 34:D590-D598, 2006. [pubmed]

  17. J.S. Pedersen, G. Bejerano, A. Siepel, K. Rosenbloom, K. Lindblad-Toh, E.S. Lander, W.J. Kent, W. Miller and D. Haussler. Identification and Classification of Conserved RNA Secondary Structures in the Human Genome. PLoS Computational Biology, 2(4):e33, 2006. [pubmed]

  18. G. Bejerano, C.B. Lowe, N. Ahituv, B. King, A. Siepel, S.R. Salama, E.M. Rubin, W.J. Kent and D. Haussler. A Distal Enhancer and an Ultraconserved Exon are Derived From a Novel Retroposon. Nature, 441(7089):87-90, 2006. [pdf] [suppl] [website]

  19. G. Bejerano. Branch and bound computation of exact P-values, Bioinformatics, 22(17):2158-2159, 2006. [pdf] [code]

  20. 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. Forces Shaping the Fastest Evolving Regions in the Human Genome. PLoS Genetics 2(10): e168, 2006. [pubmed]

  21. UCSC Genomics Group. The UCSC genome browser database: update 2007. Nucleic Acids Research, 35:D668-73, 2007. [pubmed]

  22. C.B. Lowe, G. Bejerano and D. Haussler. Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc. Nat’l Acad. Sci. USA. 104(19):8005-8010, 2007. [pdf] [suppl] [website]

  23. S. Katzman, A.D. Kern, G. Bejerano, G. Fewell, L. Fulton, R.K. Wilson, S.R. Salama, and  D. Haussler. Human genome ultraconserved elements are ultraselected.Science 317(5840):915, 2007. [pubmed]

  24. D. Karolchik, G. Bejerano, A.S. Hinrichs, R.M. Kuhn, W. Miller, K.R. Rosenbloom, A.S Zweig, D. Haussler and W.J. Kent. Comparative Genomic Analysis Using the UCSC Genome Browser. Methods Mol Biol. 2007;395:17-34, 2007. [pubmed]

Refereed conference papers (8-12 pages)

  1. G. Bejerano and G. Yona. Modeling protein families using probabilistic suffix trees, Proceedings of the 3rd annual international conference on research in computational molecular biology (RECOMB), 1999. Best paper by a young scientist award. [pdf]

  2. A. Apostolico and G. Bejerano. Optimal amnesic probabilistic automata, or, how to learn and classify proteins in linear time and space, Proceedings of the 4th annual international conference on research in computational molecular biology (RECOMB), 2000.

  3. Y. Seldin, G. Bejerano and N. Tishby. A variable memory Markovian modeling approach to unsupervised sequence segmentation, Proceedings of 33rd Symposium on the Interface of Computing Science and Statistics (Interface), 2001.

  4. Y. Seldin, G. Bejerano and N. Tishby. Unsupervised sequence segmentation by a mixture of switching variable memory Markov sources, Proceedings of 18th International Conference on Machine Learning (ICML), 2001.

  5. Y. Barash, G. Bejerano and N. Friedman. A Simple Hyper-Geometric Approach for Discovering Putative Transcription Factor Binding Sites, 1st Workshop on Algorithms in Bioinformatics (WABI), 2001. Lecture Notes in Computer Science, 2149: 278-293.

  6. O. Lartillot, S. Dubnov, G. Assayag, and G. Bejerano. Automated modeling of musical style, Proceedings of the International Computer Music Conference (ICMC), 2001.

  7. N. Slonim, G. Bejerano, S. Fine and N. Tishby. Discriminative feature selection via multiclass variable memory Markov models, Proceedings of 19th International Conference on Machine Learning (ICML), 2002.

  8. G. Bejerano. Efficient exact p-value computation and applications to biosequence analysis. Proceedings of the 7th annual international conference on research in computational molecular biology (RECOMB), 2003. Best paper by a young scientist award. [pdf]

  9. I.V. Makunin, S. Stephen, M. Pheasant, G. Bejerano, W.J. Kent, D. Haussler and J.S. Mattick. Extremely conserved non-coding sequences in the vertebrate genomes. Proceedings of 4th International Conference on Bioinformatics of Genome Regulation and Structure (BGRS), 2004.

Book Chapters

  1. D. Karolchik, G. Bejerano, A.S. Hinrichs, R.M. Kuhn, W. Miller, A.S. Zweig, D. Haussler, W.J. Kent. Comparative Genomics Analysis Using the UCSC Genome Browser. Methods in Molecular Biology series, ed. Nicholas Bergman, Comparative Genomics volume 1, to appear, Humana Press.

Patents

  1. N. Tishby, Y. Seldin, G. Bejerano and H. Margalit. Markovian Domain Fingerprinting In Statistical Segmentation Of Protein Sequences. [link]

Ph.D. Thesis

G. Bejerano. Automata learning and stochastic modeling for biosequence analysis. Hebrew University, Israel, 2003. [pdf]
      [last modified 01/25/08 08:45] Bejerano Lab • Department of Developmental Biology and Department of Computer Science • Stanford University