Image from ScienceNOW, July 14, 2005

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    Some Cornell Colleagues and Collaborators

    Carlos Bustamante
    Jason Mezey
    Andy Clark
    Chip Aquadro
    Lee Kraus
    Steve Tanksley
    Michael Stanhope

    Other Colleagues and Collaborators

    Katie Pollard
    Webb Miller
    David Haussler
    Gill Bejerano
    Rasmus Nielsen

    Publications

    1. Pollard KS, Hubisz MJ, Rosenboom K, Siepel A. Detection of non-neutral substitution rates on Mammalian phylogenies. Genome Res, 10.1101/gr.097857.109.

    2. Siepel A. Phylogenomics of primates and their ancestral populations. Genome Res, 19:1929-1941, 2009.

    3. Siepel A. Darwinian alchemy: human genes from noncoding DNA. Genome Res, 19:1693-1695, 2009.

    4. The Mammalian Gene Collection Project Team. The completion of the Mammalian Gene Collection (MGC). Genome Res, 10.1101/gr.095976.109, 2009.

    5. Zhang Y, Song G, Vinar T, Green ED, Siepel A, Miller W. Evolutionary history reconstruction for Mammalian complex gene clusters. J Comput Biol, 16(8):1051-1070, 2009.

    6. Wang Y, Diehl A, Wu F, Vrebalov J, Giovannoni J, Siepel A, Tanksley SD. Sequencing and comparative analysis of a conserved syntenic segment in the Solanaceae. Genetics, 180:391-408, 2008.

    7. Holloway A, Begun D, Siepel A, Pollard KS. Adaptive evolution drives accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster. Genome Res, 18:1592-1601, 2008.

    8. Kosiol C, Vinar T, da Fonseca RR, Hubisz MJ, Bustamante CD, Nielsen R, Siepel A. Patterns of positive selection in six mammalian genomes. PLoS Genet, 4(8):e1000144, 2008.

    9. Zhang Y, Song GT, Vinar T, Green ED, Siepel A, Miller W. Reconstructing the evolutionary history of complex human gene clusters. In Proc. 12th Int'l Conf. on Research in Computational Molecular Biology (RECOMB 2008).

    10. Siepel A, Diekhans M, Brejova B, Langton L, Stevens M, Comstock CLG, Davis C, Ewing B, Oommen S, Lau C, Yu H-C, Li J, Roe BA, Green P, Gerhard DS, Temple G, Haussler D, Brent MR. Targeted discovery of novel human exons by comparative genomics. Genome Res., 17:1763-1773, 2007.

    11. Miller W, Rosenbloom K, Hardison RC, Hou M, Taylor J, Raney B, Burhans R, King DC, Baertsch R, Blankenberg D, Kosakovsky Pond SL, Nekrutenko A, Giardine B, Harris RS, Tyekucheva S, Diekhans M, Pringle TH, Murphy WJ, Lesk A, Weinstock GM, Lindblad-Toh K, Gibbs RA, Lander ES, Siepel A, Haussler D, Kent WJ. 28-way vertebrate alignment and conservation track in the UCSC genome browser. Genome Res., 17:1797-1808, 2007.

    12. ENCODE Project Consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447:799-816, 2007.

    13. Margulies EH et al. (42 authors). Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res, 17(6):760-774, 2007.

    14. Kininis M, Chen BS, Diehl AG, Isaacs GD, Zhang T, Siepel AC, Clark AG, Kraus WL. Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters. Mol Cell Biol, 27(14):5090-104, 2007.

    15. Rhesus Macaque Genome Sequencing and Analysis Consortium. Evolutionary and biomedical insights from the rhesus macaque genome. Science, 13(316):222-234, 2007.

    16. Kuhn RM, Karolchick D, Zweig AS, Trumbower H, Thomas DJ, Thakkapallayil A, Sugnet CW, Stanke M, Smith KE, Siepel A, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pedersen JS, Hsu F, Hinrichs AS, Harte RA, Diekhans M, Clawson H, Bejerano G, Barber GP, Baertsch R, Haussler D,and Kent WJ. The UCSC genome browser database: update 2007. Nucleic Acids Res 35:D668-D673, 2007.

    17. Pollard KS, Salama SR, King B, Kern AD, Dreszer T, Katzman S, Siepel A, Pedersen JS, Bejerano G, Baertsch R, Rosenbloom KR, Kent J, and Haussler D. Forces shaping the fastest evolving regions in the human genome. PLoS Genetics, 2(10):e168, 2006.

    18. Pollard KS, Salama SR, Lambert N, Lambot M-A, Coppens S, Pedersen JS, Katzman S, King B, Onodera C, Siepel A, Kern AD, Dehay C, Igel H, Ares M, Vanderhaeghen P, and Haussler D. An RNA gene expressed during cortical development evolved rapidly in humans. Nature 443:167-172, 2006.

    19. Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, and Haussler D. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature 441: 87-90, 2006.

    20. Pedersen JK, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES, Kent J, Miller W, and Haussler D. Identification and classification of conserved RNA secondary structures in the human genome. PLoS Computational Biology 2(4): e33, 2006.

    21. Siepel A, Pollard KS, and Haussler D. New methods for detecting lineage-specific selection. In Proceedings of the 10th International Conference on Research in Computational Molecular Biology (RECOMB 2006), pp. 190-205. [reprint] [full version]

    22. Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G et al. The UCSC Genome Browser Database: update 2006. Nucleic Acids Res 34:D590-598, 2006.

    23. Siepel A, Bejerano G, Pedersen JS, Hinrichs A, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, Weinstock GM, Wilson RK, Gibbs RA, Kent WJ, Miller W, and Haussler D. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 15:1034-1050, 2005.

    24. Bejerano G, Siepel AC, Kent WJ, and Haussler D. Computational screening of conserved genomic DNA in search of functional noncoding elements. Nature Methods 2(7):535-545, 2005 [reprint]

    25. Siepel A and Haussler D. Phylogenetic hidden Markov models. In R. Nielsen, editor, Statistical Methods in Molecular Evolution, pp. 325-351, Springer, New York, 2005. [reprint]

    26. International Chicken Genome Sequencing Consortium. Sequencing and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695-716, 2004.

    27. International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 431:931-945, 2004.

    28. ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306:636-640, 2004.

    29. Jojic V, Jojic N, Meek C, Geiger D, Siepel A, Haussler D, and Heckerman D. Efficient approximations for learning phylogenetic HMM models from data. In Intelligent Systems for Molecular Biology 2004 and Bioinformatics 20:i161-168, 2004.

    30. Siepel A and Haussler D. Computational identification of evolutionarily conserved exons. Proc. 8th Int'l Conf. on Research in Computational Molecular Biology, pp. 177-186, 2004. [reprint]

    31. Siepel A and Haussler D. Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol Biol Evol 21:468-488, 2004. [supplementary data]

    32. Thomas JW et al (71 authors). Comparative analyses of multi-species sequences from targeted genomic regions. Nature 424:788-793, 2003.

    33. Siepel A and Haussler D. Combining phylogenetic and hidden Markov models in biosequence analysis. J Comput Biol 11:413-428, 2004. [reprint]

    34. Siepel A and Haussler D. Combining phylogenetic and hidden Markov models in biosequence analysis. Proc. 7th Int'l Conf. on Research in Computational Molecular Biology (RECOMB '03), pp. 277-286, 2003. [reprint]

    35. Siepel A. An algorithm to enumerate sorting reversals for signed permutations. J Comput Biol 10:575-597, 2003. [reprint]

    36. Moret BME, Siepel AC, Tang J, and Liu T. Inversion medians outperform breakpoint medians in phylogeny reconstruction from gene-order data. Proc. 2nd Int'l Workshop on Algorithms in Bioinformatics, Lecture Notes in Computer Science, vol. 2452, 2002. [reprint]

    37. Siepel A. An algorithm to find all sorting reversals. Proc. 6th Int'l Conf. on Research in Computational Molecular Biology (RECOMB '02), pp. 281-290, 2002. [reprint]

    38. Sobral BW, Mangalam H, Siepel A, Mendes P, Pecherer R, and McLaren G. Bioinformatics for rice resources. Novartis Found Symp 236:59-81, 2001.

    39. Siepel AC and Moret BME. Finding an optimal inversion median: Experimental results. Proc. 1st Int'l Workshop on Algorithms in Bioinformatics, Lecture Notes in Computer Science, vol. 2149, pp. 189-203, 2001. [reprint]

    40. Siepel A, Tolopko A, Farmer A, Steadman P, Schilkey F, Perry BD, and Beavis W. An integration platform for heterogeneous bioinformatics software components. IBM Systems Journal 40:570-591, 2001. [reprint]

    41. Siepel A, Farmer A, Tolopko A, Zhuang M, Mendes P, Beavis W, and Sobral B. ISYS: A decentralized, component-based approach to the integration of heterogeneous bioinformatics resources. Bioinformatics 17:83-94, 2001.

    42. Skupski MP, Booker M, Farmer A, Harpold M, Huang W, Inman J, Kiphart D, Kodira C, Root S, Schilkey F, Schwertfeger J, Siepel A, Stamper D, Thayer N, Thompson R, Wortman J, Zhuang JJ, Harger C. The Genome Sequence DataBase: towards an integrated functional genomics resource. Nucleic Acids Res 27(1):35-38, 1999.

    43. Harger C, Skupski M, Bingham J, Farmer A, Hoisie S, Hraber P, Kiphart D, Krakowski L, McLeod M, Schwertfeger J, Seluja G, Siepel A, Singh G, Stamper D, Steadman P, Thayer N, Thompson R, Wargo P, Waugh M, Zhuang JJ, Schad PA. The Genome Sequence DataBase (GSDB): improving data quality and data access. Nucleic Acids Res 26(1):21-26, 1998.

    44. Harger C, Skupski M, Allen E, Clark C, Crowley D, Dickinson E, Easley D, Espinosa-Lujan A, Farmer A, Fields C, Flores L, Harris L, Keen G, Manning M, McLeod M, O'Neill J, Pumilia M, Reinert R, Rider D, Rohrlich J, Romero Y, Schwertfeger J, Seluja G, Siepel A, Schad PA. The Genome Sequence DataBase version 1.0 (GSDB): from low pass sequences to complete genomes. Nucleic Acids Res 25(1):18-23, 1997.

    45. Siepel AC, Halpern AL, Macken C, and Korber B. A computer program designed to screen rapidly for HIV Type 1 intersubtype recombinant sequences. AIDS Res Hum Retroviruses 11:1413-1416, 1995.

    Theses and Unpublished manuscripts

    1. Siepel A. Comparative mammalian genomics: models of evolution and detection of functional elements. Ph.D. dissertation, University of California, Santa Cruz, 2005.

    2. Siepel A. Expectation maximization for combined phylogenetic and hidden Markov models. UC Santa Cruz, 2002.

    3. Siepel A. A probabilistic approach to the reconciliation of gene and species trees. UC Santa Cruz, 2002.

    4. Siepel A. Exact algorithms for the reversal median problem. Master's thesis, University of New Mexico, 2001.