RECOMB 2003 Proceedings

Berlin, Germany, April 10-14, 2003

PC Chair: Webb Miller
Organization Committee: Martin Vingron (chair), Patricia Béziat, Alexander Schliep, Rainer Spang, Thomas Steinke
Keynote Speakers: Edward Trifonov, Christiane Nüsslein-Volhard, Árpád Furka, Andrew Clark, David Haussler, Arthur Lesk, Dieter Oesterhelt, Terry Speed, Kari Stefansson

List of Publications

• Efficient extraction of mapping rules of atoms from enzymatic reaction data. Tatsuya Akutsu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 1–8. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640076
• On de novo interpretation of tandem mass spectra for peptide identification. Vineet Bafna, Nathan Edwards.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 9–18. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640077
• Haplotypes and informative SNP selection algorithms: don’t block out information. Vineet Bafna, Bjarni V. Halldorsson, Russell Schwartz, Andrew G. Clark, Sorin Istrail.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 19–27. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640078
• Modeling dependencies in protein-DNA binding sites. Yoseph Barash, Gal Elidan, Nir Friedman, Tommy Kaplan.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 28–37. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640079
• Efficient exact value computation and applications to biosequence analysis. Gill Bejerano.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 38–47. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640080
• Towards optimally multiplexed applications of universal DNA tag systems. Amir Ben-Dor, Tzvika Hartman, Benno Schwikowski, Roded Sharan, Zohar Yakhini.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 48–56. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640081
• A comparative analysis method for detecting binding sites in coding regions. Mathieu Blanchette.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 57–66. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640082
• Designing seeds for similarity search in genomic DNA. Jeremy Buhler, Uri Keich, Yanni Sun.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 67–75. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640083
• Maximum likelihood on four taxa phylogenetic trees: analytic solutions. Benny Chor, Amit Khetan, Sagi Snir.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 76–83. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640084
• Phylogenetically and spatially conserved word pairs associated with gene expression changes in yeasts. Derek Y. Chiang, Alan M. Moses, Manolis Kamvysselis, Eric S. Lander, Michael B. Eisen.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 84–93. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640085
• An integrated probabilistic model for functional prediction of proteins. Minghua Deng, Ting Chen, Fengzhu Sun.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 95–103. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640087
• Large scale reconstruction of haplotypes from genotype data. Eleazar Eskin, Eran Halperin, Richard M. Karp.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 104–113. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640088
• Optimizing exact genetic linkage computations. Ma’ayan Fishelson, Dan Geiger.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 114–121. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640089
• Finding recurrent sources in sequences. Aristides Gionis, Heikki Mannila.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 123–130. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640091
• Model-based inference of haplotype block variation. Gideon Greenspan, Dan Geiger.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 131–137. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640092
• Accurate detection of very sparse sequence motifs. Andreas Heger, Michael Lappe, Liisa Holm.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 139–147. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640094
• Engineering a scalable placement heuristic for DNA probe arrays. A. B. Kahng, I. I. Mandoiu, P. A. Pevzner, S. Reda, A. Z. Zelikovsky.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 148–156. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640095
• Whole-genome comparative annotation and regulatory motif discovery in multiple yeast species. Manolis Kamvysselis, Nick Patterson, Bruce Birren, Bonnie Berger, Eric Lander.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 157–166. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640096
• Joint classifier and feature optimization for cancer diagnosis using gene expression data. Balaji Krishnapuram, Lawrence Carin, Alexander J. Hartemink.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 167–175. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640097
• Large a polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignments. Christopher James Langmead, Anthony K. Yan, Ryan Lilien, Lincong Wang, Bruce Randall Donald.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 176–187. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640098
• A complete and effective move set for simplified protein folding. N. Lesh, M. Mitzenmacher, S. Whitesides.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 188–195. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640099
• Efficient rule-based haplotyping algorithms for pedigree data. Jing Li, Tao Jiang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 197–206. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640101
• Haplotype reconstruction from SNP alignment. Lei Li, Jong Hyun Kim, Michael S. Waterman.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 207–216. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640102
• Gene selection criterion for discriminant microarray data analysis based on extreme value distributions. Wentian Li, Ivo Grosse.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 217–223. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640103
• A multi-expert system for the automatic detection of protein domains from sequence information. Niranjan Nagarajan, Golan Yona.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 224–234. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640104
• Resolution of haplotypes and haplotype frequencies from SNP genotypes of pooled samples. Itsik Pe’er, Jacques S. Beckmann.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 237–246. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640107
• Transforming men into mice: the Nadeau-Taylor chromosomal breakage model revisited. Pavel Pevzner, Glenn Tesler.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 247–256. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640108
• Scoring two-species local alignments to try to statistically separate neutrally evolving from selected DNA segments. Krishna M. Roskin, Mark Diekhans, David Haussler.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 257–266. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640109
• Approximation of protein structure for fast similarity measures. Fabian Schwarzer, Itay Lotan.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 267–276. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640110
• Combining phylogenetic and hidden Markov models in biosequence analysis. Adam Siepel, David Haussler.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 277–286. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640111
• Using a mixture of probabilistic decision trees for direct prediction of protein function. Umar Syed, Golan Yona.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 289–300. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640114
• Modeling transcription programs: inferring binding site activity and dose-response model optimization. Amos Tanay, Ron Shamir.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 301–310. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640115
• Physical network models and multi-source data integration. Chen-Hsiang Yeang, Tommi Jaakkola.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 312–321. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640117
• Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. Gene Yeo, Christopher B. Burge.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 322–331. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640118
• Dynamic programming algorithms for haplotype block partitioning: applications to human chromosome 21 haplotype data. Kui Zhang, Fengzhu Sun, Michael S. Waterman, Ting Chen.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2003, pp 332–340. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/640075.640119