Publications

25. C. McLean and G. Bejerano. Dispensability of mammalian DNA. Genome Res. 18(11):1743-1751, 2008. [pdf] [suppl]

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]

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]

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]

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

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]

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

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]

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]

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

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]

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]

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]

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

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]

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]

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

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]

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]

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]

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]

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]

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]

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]

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.

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]

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.

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

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.

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.

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.

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]

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.

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