RECOMB 2004 Proceedings

San Diego, CA, United States, March 27-31, 2004

PC Chair: Dan Gusfield
Organization Committee: Philip E. Bourne (chair), Kristine Briedis, Apostol Gramada, Stephanie Hagstrom, Nancy Jensen, Dana Jermanis, Chris Smith, Peggy Wagner
Keynote Speakers: Carlos D. Bustamante, Russell Doolittle, Andrew Fire, Richard Karp, William McGinnis, Deborah Nickerson, Martin Nowak, Christine Orengo, Elizabeth Winzeler

List of Publications

• Maximum likelihood resolution of multi-block genotypes. Gad Kimmel, Ron Shamir.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 2–9. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974616
  • Journal: GERBIL: genotype resolution and block identification using likelihood. Gad Kimmel, Ron Shamir. Proc Natl Acad Sci USA, 102 (1) 158-162, 2005.
    • DOI: 10.1073/pnas.0404730102
• Perfect phylogeny and haplotype assignment. Eran Halperin, Richard M. Karp.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 10–19. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974617
• An exact solution for finding minimum recombinant haplotype configurations on pedigrees with missing data by integer linear programming. Jing Li, Tao Jiang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 20–29. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974618
  • Journal: Computing the minimum recombinant haplotype configuration from incomplete genotype data on a pedigree by integer linear programming. Jing Li, Tao Jiang. Journal of Computational Biology, 12(6): 719-739, 2005.
    • DOI: 10.1089/cmb.2005.12.719
• Chromosomal breakpoint re-use in the inference of genome sequence rearrangement. David Sankoff, Phil Trinh.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 30–35. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974619
  • Journal: Chromosomal breakpoint reuse in genome sequence rearrangement. David Sankoff, Phil Trinh. Journal of Computational Biology, 12(6): 812-821, 2005.
    • DOI: 10.1089/cmb.2005.12.812
• Learning multiple evolutionary pathways from cross-sectional data. Niko Beerenwinkel, Jörg Rahnenführer, Martin Däumer, Daniel Hoffmann, Rolf Kaiser, Joachim Selbig, Thomas Lengauer.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 36–44. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974620
  • Journal: Learning multiple evolutionary pathways from cross-sectional data. Niko Beerenwinkel, Jörg Rahnenführer, Martin Däumer, Daniel Hoffmann, Rolf Kaiser, Joachim Selbig, Thomas Lengauer. Journal of Computational Biology, 12(6): 584-598, 2005.
    • DOI: 10.1089/cmb.2005.12.584
• A novel ensemble-based scoring and search algorithm for protein redesign, and its application to modify the substrate specificity of the gramicidin synthetase A phenylalanine adenylation enzyme. Ryan H. Lilien, Brian W. Stevens, Amy C. Anderson, Bruce R. Donald.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 46–57. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974622
• A random graph approach to NMR sequential assignment. Chris Bailey-Kellogg, Sheetal Chainraj, Gopal Pandurangan.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 58–67. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974623
  • Journal: A random graph approach to NMR sequential assignment. Chris Bailey-Kellogg, Sheetal Chainraj, Gopal Pandurangan. Journal of Computational Biology, 12(6): 569–583, 2005.
    • DOI: 10.1089/cmb.2005.12.569
• Finding short DNA motifs using permuted markov models. Xiaoyue Zhao, Haiyan Huang, Terence P. Speed.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 68–75. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974624
• Designing multiple simultaneous seeds for DNA similarity search. Yanni Sun, Jeremy Buhler.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 76–84. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974625
• Aligning alignments exactly. John Kececioglu, Dean Starrett.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 85–96. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974626
• Stochastic models inspired by hybridization theory for short oligonucleotide arrays. Zhijin Wu, Rafael A. Irizarry.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 98–106. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974628
• Checking homogeneity of motifs’ distribution in heterogenous sequences. Sabrina Ledent, Stéphane Robin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 107–114. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974629
• From profiles to patterns and back again: a branch and bound algorithm for finding near optimal motif profiles. Eleazar Eskin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 115–124. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974630
• Finding motifs for insufficient number of sequences with strong binding to transcription facto. Francis Y. L. Chin, Henry C. M. Leung, S. M. Yiu, T. W. Lam, Roni Rosenfeld, W. W. Tsang, David K. Smith, Y. Jiang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 125–132. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974631
• Structured motifs search. Alberto Policriti, Nicola Vitacolonna, Michele Morgante, Andrea Zuccolo.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 133–139. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974632
• A discriminative model for identifying spatial cis-regulatory modules. Eran Segal, Roded Sharan.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 141–149. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974634
• Discovering temporal relations in molecular pathways using protein-protein interactions. Martin Farach-Colton, Yang Huang, John L. L. Woolford.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 150–156. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974635
• Comparing in situ mRNA expression patterns of drosophila embryos. Hanchuan Peng, Eugene W. Myers.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 157–166. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974636
• Probabilistic discovery of overlapping cellular processes and their regulation. Alexis Battle, Eran Segal, Daphne Koller.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 167–176. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974637
• Computational identification of evolutionarily conserved exons. Adam Siepel, David Haussler.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 177–186. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974638
• Multiple organism gene finding by collapsed gibbs sampling. Sourav Chatterji, Lior Pachter.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 187–193. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974639
  • Journal: Large Multiple Organism Gene Finding by Collapsed Gibbs Sampling. Sourav Chatterji, Lior Pachter. Journal of Computational Biology, 12(6): 599–608, 2005.
    • DOI: 10.1089/cmb.2005.12.609
• Protein similarity from knot theory and geometric convolution. Michael A. Erdmann.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 195–204. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974641
• Interface surfaces for protein-protein complexes. Yih-En Andrew Ban, Herbert Edelsbrunner, Johannes Rudolph.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 205–212. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974642
• De novo repeat classification and fragment assembly. Pavel A. Pevzner, Haixu Tang, Glenn Tesler.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 213–222. Association for Computing Machinery, New York, NY, USA.
    • DOI: 11/974614.974643
• Finding approximate tandem repeats in genomic sequences. Ydo Wexler, Zohar Yakhini, Yechezkel Kashi, Dan Geiger.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 223–232. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974644
• Finding anchors for genomic sequence comparison. Ross A. Lippert, Xiaoyue Zhao, Liliana Florea, Clark Mobarry, Sorin Istrail.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 233–241. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974645
• Faster genome annotation of non-coding RNA families without loss of accuracy. Zasha Weinberg, Walter L. Ruzzo.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 243–251. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974647
• Using motion planning to study RNA folding kinetics. Xinyu Tang, Bonnie Kirkpatrick, Shawna Thomas, Guang Song, Nancy M. Amato.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 252–261. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974648
• A class of edit kernels for SVMs to predict translation initiation sites in eukaryotic mRNAs. Haifeng Li, Tao Jiang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 262–271. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974649
• Identifying conserved gene clusters in the presence of orthologous groups. Xin He, Michael H. Goldwasser.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 272–280. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974650
• Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. Roded Sharan, Trey Ideker, Brian P. Kelley, Ron Shamir, Richard M. Karp.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 282–289. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974652
• The evolutionary capacity of protein structures. Leonid Meyerguz, David Kempe, Jon Kleinberg, Ron Elber.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 290–297. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974653
• Wrap-and-pack: a new paradigm for beta structural motif recognition with application to recognizing beta trefoils. Matthew Menke, Eben Scanlon, Jonathan King, Bonnie Berger, Lenore Cowen.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 298–307. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974654
• Mining protein family specific residue packing patterns from protein structure graphs. Jun Huan, Wei Wang, Deepak Bandyopadhyay, Jack Snoeyink, Jan Prins, Alexander Tropsha.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 308–315. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974655
• Reconciliation problems for duplication, loss and horizontal gene transfer. Pawel Górecki.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 316–325. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974656
• Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution. Lars Arvestad, Ann-Charlotte Berglund, Jens Lagergren, Bengt Sennblad.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 326–335. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974657
• Reconstructing reticulate evolution in species: theory and practice. Luay Nakhleh, Tandy Warnow, C. Randal Linder.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 337–346. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974659
• Simultaneous identification of duplications and lateral transfers. Mike Hallett, Jens Lagergren, Ali Tofigh.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2004, pp 347–356. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/974614.974660