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
Website: https://recomb.org/recomb2003
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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
  • Journal: Efficient Extraction of Mapping Rules of Atoms from Enzymatic Reaction Data. Tatsuya Akutsu. Journal of Computational Biology, 11(2-3): 449-462, 2004.
    • DOI: 10.1089/1066527041410337
• 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
  • Journal: Towards Optimally Multiplexed Applications of Universal Arrays. Amir Ben‐Dor, Tzvika Hartman, Richard M. Karp, Benno Schwikowski, Roded Sharan, Zohar Yakhini. Journal of Computational Biology, 11(2-3): 476-492, 2004.
    • DOI: 10.1089/1066527041410373
• 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
  • Journal: Designing seeds for similarity search in genomic DNA. Jeremy Buhler, Uri Keich, Yanni Sun. Journal of Computer and System Sciences, 70(3): 342-363, 2005.
    • DOI: 10.1016/j.jcss.2004.12.003
• 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
  • Journal: Maximum Likelihood Jukes-Cantor Triplets: Analytic Solutions. Benny Chor, Michael D. Hendy, Sagi Snir. Molecular Biology and Evolution, 23(3): 626-632, 2005.
    • DOI: 10.1093/molbev/msj069
• 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
  • Journal: Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts. Derek Y. Chiang, Alan M Moses, Manolis Kellis, Eric S. Lander, Michael B. Eisen. Genome Biology, 4(7): R43, 2003.
    • DOI: 10.1186/gb-2003-4-7-r43
• 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
  • Journal: An Integrated Probabilistic Model for Functional Prediction of Proteins. Minghua Deng, Ting Chen, Fengzhu Sun. Journal of Computational Biology, 11(2-3): 463-475, 2004.
    • DOI: 10.1089/1066527041410346
• 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
  • Journal: Haplotype reconstruction from genotype data using Imperfect Phylogeny. Eran Halperin, Eleazar Eskin. Bioinformatics, 20(12): 1842-1849, 2004.
    • DOI: 10.1093/bioinformatics/bth149
• 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
  • Journal: Optimizing Exact Genetic Linkage Computations. M. Fishelson, Dan Geiger. Journal of Computational Biology, 11(2-3): 263-275, 2004.
    • DOI: 10.1089/1066527041410409
• 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
  • Journal: Model-Based Inference of Haplotype Block Variation. Gideon Greenspan, Dan Geiger. Journal of Computational Biology, 11(2-3): 493-504, 2004.
    • DOI: 10.1089/1066527041410300
• 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
  • Journal: Accurate Detection of Very Sparse Sequence Motifs. Andreas Heger, Michael Lappé, Liisa Holm. Journal of Computational Biology, 11(5): 843-857, 2004.
    • DOI: 10.1089/cmb.2004.11.843
• 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
  • Journal: Scalable Heuristics for Design of DNA Probe Arrays. Andrew B. Kahng, Ion Măndoiu, Pavel A. Pevzner, Sherief Reda, Alex Zelikovsky. Journal of Computational Biology, 11(2-3): 429-447, 2004.
    • DOI: 10.1089/1066527041410391
• 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
  • Journal: Joint Classifier and Feature Optimization for Comprehensive Cancer Diagnosis Using Gene Expression Data. Balaji Krishnapuram, Lawrence Carin, Alexander J. Hartemink. Journal of Computational Biology, 11(2-3): 227-242, 2004.
    • DOI: 10.1089/1066527041410463
• 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
  • Journal: A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments. Christopher J. Langmead, Anthony K. Yan, Ryan Lilien, Lincong Wang, Bruce R. Donald. Journal of Computational Biology, 11(2-3): 277-298, 2004.
    • DOI: 10.1089/1066527041410436
• 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
  • Journal: Haplotype Reconstruction from SNP Alignment. Lei M. Li, Jong Hyun Kim, Michael S. Waterman. Journal of Computational Biology, 11(2-3): 505-516, 2004.
    • DOI: 10.1089/1066527041410454
• 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
  • Preprint: arXiv:q-bio/0403038
  • Journal: Extreme Value Distribution Based Gene Selection Criteria for Discriminant Microarray Data Analysis Using Logistic Regression. Wentian Li, Fengzhu Sun, Ivo Große. Journal of Computational Biology, 11(2-3): 215-226, 2004.
    • DOI: 10.1089/1066527041410445
• 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
  • Journal: Automatic prediction of protein domains from sequence information using a hybrid learning system. Niranjan Nagarajan, Golan Yona. Bioinformatics, 20(9): 1335-1360, 2004.
    • DOI: 10.1093/bioinformatics/bth086
• 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
  • Journal: Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution. Pavel Pevzner, Glenn Tesler. Proceedings of the National Academy of Sciences, 100 (13) 7662-7667, 2003.
    • DOI: 10.1073/pnas.1330369100
• 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
  • Journal: Approximation of Protein Structure for Fast Similarity Measures. Itay Lotan, Fabian Schwarzer. Journal of Computational Biology, 11(2-3): 299-317, 2004.
    • DOI: 10.1089/1066527041410355
• 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
  • Journal: Combining Phylogenetic and Hidden Markov Models in Biosequence Analysis. Adam Siepel, David Haussler. Journal of Computational Biology, 11(2-3): 413-428, 2004.
    • DOI: 10.1089/1066527041410472
• 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
  • Journal: Physical Network Models. Chen‐Hsiang Yeang, Trey Ideker, Tommi Jaakkola. Journal of Computational Biology, 11(2-3): 243-262, 2004.
    • DOI: 10.1089/1066527041410382
• 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
  • Journal: Maximum Entropy Modeling of Short Sequence Motifs with Applications to RNA Splicing Signals. G Yeo, Christopher B. Burge. Journal of Computational Biology, 11(2-3): 377-394, 2004.
    • DOI: 10.1089/1066527041410418
• 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
  • Journal: Haplotype Block Partition with Limited Resources and Applications to Human Chromosome 21 Haplotype Data. Kui Zhang, Fengzhu Sun, Michael S. Waterman, Ting Chen. The American Journal of Human Genetics, 73(1): 63-73, 2003.
    • DOI: 10.1086/376437