{ "title": "7th Annual International Conference on Research in Computational Molecular Biology", "location": "Berlin, Germany", "dates": "April 10 - 14, 2003", "pc_chair": "Webb Miller", "organization_committee": "Martin Vingron (chair), Patricia Béziat, Alexander Schliep, Rainer Spang, Thomas Steinke", "keynotes": "Edward Trifonov, Christiane Nüsslein-Volhard, Árpád Furka, Andrew Clark, David Haussler, Arthur Lesk, Dieter Oesterhelt, Terry Speed, Kari Stefansson", "website": "https://recomb.org/recomb2003", "papers": [ { "author": "Tatsuya Akutsu", "title": "Efficient extraction of mapping rules of atoms from enzymatic reaction data", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 1–8. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "1–8", "proceedings_doi": "10.1145/640075.640076", "journal": "Journal of Computational Biology", "journal_title": "Efficient Extraction of Mapping Rules of Atoms from Enzymatic Reaction Data", "journal_authors": "Tatsuya Akutsu", "journal_issue_pages": "11(2-3): 449-462", "journal_year": "2004", "journal_doi": "10.1089/1066527041410337" }, { "author": "Vineet Bafna, Nathan Edwards", "title": "On de novo interpretation of tandem mass spectra for peptide identification", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 9–18. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "9–18", "proceedings_doi": "10.1145/640075.640077" }, { "author": "Vineet Bafna, Bjarni V. Halldorsson, Russell Schwartz, Andrew G. Clark, Sorin Istrail", "title": "Haplotypes and informative SNP selection algorithms: don't block out information", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 19–27. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "19–27", "proceedings_doi": "10.1145/640075.640078" }, { "author": "Yoseph Barash, Gal Elidan, Nir Friedman, Tommy Kaplan", "title": "Modeling dependencies in protein-DNA binding sites", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 28–37. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "28–37", "proceedings_doi": "10.1145/640075.640079" }, { "author": "Gill Bejerano", "title": "Efficient exact value computation and applications to biosequence analysis", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 38–47. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "38–47", "proceedings_doi": "10.1145/640075.640080" }, { "author": "Amir Ben-Dor, Tzvika Hartman, Benno Schwikowski, Roded Sharan, Zohar Yakhini", "title": "Towards optimally multiplexed applications of universal DNA tag systems", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 48–56. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "48–56", "proceedings_doi": "10.1145/640075.640081", "journal": "Journal of Computational Biology", "journal_title": "Towards Optimally Multiplexed Applications of Universal Arrays", "journal_authors": "Amir Ben‐Dor, Tzvika Hartman, Richard M. Karp, Benno Schwikowski, Roded Sharan, Zohar Yakhini", "journal_issue_pages": "11(2-3): 476-492", "journal_year": "2004", "journal_doi": "10.1089/1066527041410373" }, { "author": "Mathieu Blanchette", "title": "A comparative analysis method for detecting binding sites in coding regions", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 57–66. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "57–66", "proceedings_doi": "10.1145/640075.640082" }, { "author": "Jeremy Buhler, Uri Keich, Yanni Sun", "title": "Designing seeds for similarity search in genomic DNA", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 67–75. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "67–75", "proceedings_doi": "10.1145/640075.640083", "journal": "Journal of Computer and System Sciences", "journal_title": "Designing seeds for similarity search in genomic DNA", "journal_authors": "Jeremy Buhler, Uri Keich, Yanni Sun", "journal_issue_pages": "70(3): 342-363", "journal_year": "2005", "journal_doi": "10.1016/j.jcss.2004.12.003" }, { "author": "Benny Chor, Amit Khetan, Sagi Snir", "title": "Maximum likelihood on four taxa phylogenetic trees: analytic solutions", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 76–83. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "76–83", "proceedings_doi": "10.1145/640075.640084", "journal": "Molecular Biology and Evolution", "journal_title": "Maximum Likelihood Jukes-Cantor Triplets: Analytic Solutions", "journal_authors": "Benny Chor, Michael D. Hendy, Sagi Snir", "journal_issue_pages": "23(3): 626-632", "journal_year": "2005", "journal_doi": "10.1093/molbev/msj069" }, { "author": "Derek Y. Chiang, Alan M. Moses, Manolis Kamvysselis, Eric S. Lander, Michael B. Eisen", "title": "Phylogenetically and spatially conserved word pairs associated with gene expression changes in yeasts", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 84–93. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "84–93", "proceedings_doi": "10.1145/640075.640085", "journal": "Genome Biology", "journal_title": "Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts", "journal_authors": "Derek Y. Chiang, Alan M Moses, Manolis Kellis, Eric S. Lander, Michael B. Eisen", "journal_issue_pages": "4(7): R43", "journal_year": "2003", "journal_doi": "10.1186/gb-2003-4-7-r43" }, { "author": "Minghua Deng, Ting Chen, Fengzhu Sun", "title": "An integrated probabilistic model for functional prediction of proteins", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 95–103. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "95–103", "proceedings_doi": "10.1145/640075.640087", "journal": "Journal of Computational Biology", "journal_title": "An Integrated Probabilistic Model for Functional Prediction of Proteins", "journal_authors": "Minghua Deng, Ting Chen, Fengzhu Sun", "journal_issue_pages": "11(2-3): 463-475", "journal_year": "2004", "journal_doi": "10.1089/1066527041410346" }, { "author": "Eleazar Eskin, Eran Halperin, Richard M. Karp", "title": "Large scale reconstruction of haplotypes from genotype data", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 104–113. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "104–113", "proceedings_doi": "10.1145/640075.640088", "journal": "Bioinformatics", "journal_title": "Haplotype reconstruction from genotype data using Imperfect Phylogeny", "journal_authors": "Eran Halperin, Eleazar Eskin", "journal_issue_pages": "20(12): 1842-1849", "journal_year": "2004", "journal_doi": "10.1093/bioinformatics/bth149" }, { "author": "Ma'ayan Fishelson, Dan Geiger", "title": "Optimizing exact genetic linkage computations", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 114–121. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "114–121", "proceedings_doi": "10.1145/640075.640089", "journal": "Journal of Computational Biology", "journal_title": "Optimizing Exact Genetic Linkage Computations", "journal_authors": "M. Fishelson, Dan Geiger", "journal_issue_pages": "11(2-3): 263-275", "journal_year": "2004", "journal_doi": "10.1089/1066527041410409" }, { "author": "Aristides Gionis, Heikki Mannila", "title": "Finding recurrent sources in sequences", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 123–130. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "123–130", "proceedings_doi": "10.1145/640075.640091" }, { "author": "Gideon Greenspan, Dan Geiger", "title": "Model-based inference of haplotype block variation", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 131–137. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "131–137", "proceedings_doi": "10.1145/640075.640092", "journal": "Journal of Computational Biology", "journal_title": "Model-Based Inference of Haplotype Block Variation", "journal_authors": "Gideon Greenspan, Dan Geiger", "journal_issue_pages": "11(2-3): 493-504", "journal_year": "2004", "journal_doi": "10.1089/1066527041410300" }, { "author": "Andreas Heger, Michael Lappe, Liisa Holm", "title": "Accurate detection of very sparse sequence motifs", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 139–147. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "139–147", "proceedings_doi": "10.1145/640075.640094", "journal": "Journal of Computational Biology", "journal_title": "Accurate Detection of Very Sparse Sequence Motifs", "journal_authors": "Andreas Heger, Michael Lappé, Liisa Holm", "journal_issue_pages": "11(5): 843-857", "journal_year": "2004", "journal_doi": "10.1089/cmb.2004.11.843" }, { "author": "A. B. Kahng, I. I. Mandoiu, P. A. Pevzner, S. Reda, A. Z. Zelikovsky", "title": "Engineering a scalable placement heuristic for DNA probe arrays", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 148–156. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "148–156", "proceedings_doi": "10.1145/640075.640095", "journal": "Journal of Computational Biology", "journal_title": "Scalable Heuristics for Design of DNA Probe Arrays", "journal_authors": "Andrew B. Kahng, Ion Măndoiu, Pavel A. Pevzner, Sherief Reda, Alex Zelikovsky", "journal_issue_pages": "11(2-3): 429-447", "journal_year": "2004", "journal_doi": "10.1089/1066527041410391" }, { "author": "Manolis Kamvysselis, Nick Patterson, Bruce Birren, Bonnie Berger, Eric Lander", "title": "Whole-genome comparative annotation and regulatory motif discovery in multiple yeast species", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 157–166. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "157–166", "proceedings_doi": "10.1145/640075.640096" }, { "author": "Balaji Krishnapuram, Lawrence Carin, Alexander J. Hartemink", "title": "Joint classifier and feature optimization for cancer diagnosis using gene expression data", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 167–175. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "167–175", "proceedings_doi": "10.1145/640075.640097", "journal": "Journal of Computational Biology", "journal_title": "Joint Classifier and Feature Optimization for Comprehensive Cancer Diagnosis Using Gene Expression Data", "journal_authors": "Balaji Krishnapuram, Lawrence Carin, Alexander J. Hartemink", "journal_issue_pages": "11(2-3): 227-242", "journal_year": "2004", "journal_doi": "10.1089/1066527041410463" }, { "author": "Christopher James Langmead, Anthony K. Yan, Ryan Lilien, Lincong Wang, Bruce Randall Donald", "title": "Large a polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignments", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 176–187. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "176–187", "proceedings_doi": "10.1145/640075.640098", "journal": "Journal of Computational Biology", "journal_title": "A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments", "journal_authors": "Christopher J. Langmead, Anthony K. Yan, Ryan Lilien, Lincong Wang, Bruce R. Donald", "journal_issue_pages": "11(2-3): 277-298", "journal_year": "2004", "journal_doi": "10.1089/1066527041410436" }, { "author": "N. Lesh, M. Mitzenmacher, S. Whitesides", "title": "A complete and effective move set for simplified protein folding", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 188–195. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "188–195", "proceedings_doi": "10.1145/640075.640099" }, { "author": "Jing Li, Tao Jiang", "title": "Efficient rule-based haplotyping algorithms for pedigree data", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 197–206. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "197–206", "proceedings_doi": "10.1145/640075.640101" }, { "author": "Lei Li, Jong Hyun Kim, Michael S. Waterman", "title": "Haplotype reconstruction from SNP alignment", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 207–216. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "207–216", "proceedings_doi": "10.1145/640075.640102", "journal": "Journal of Computational Biology", "journal_title": "Haplotype Reconstruction from SNP Alignment", "journal_authors": "Lei M. Li, Jong Hyun Kim, Michael S. Waterman", "journal_issue_pages": "11(2-3): 505-516", "journal_year": "2004", "journal_doi": "10.1089/1066527041410454" }, { "author": "Wentian Li, Ivo Grosse", "title": "Gene selection criterion for discriminant microarray data analysis based on extreme value distributions", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 217–223. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "217–223", "proceedings_doi": "10.1145/640075.640103", "preprint_id": "arXiv:q-bio/0403038", "preprint_doi": "10.48550/arXiv.q-bio/0403038", "journal": "Journal of Computational Biology", "journal_title": "Extreme Value Distribution Based Gene Selection Criteria for Discriminant Microarray Data Analysis Using Logistic Regression", "journal_authors": "Wentian Li, Fengzhu Sun, Ivo Große", "journal_issue_pages": "11(2-3): 215-226", "journal_year": "2004", "journal_doi": "10.1089/1066527041410445" }, { "author": "Niranjan Nagarajan, Golan Yona", "title": "A multi-expert system for the automatic detection of protein domains from sequence information", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 224–234. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "224–234", "proceedings_doi": "10.1145/640075.640104", "journal": "Bioinformatics", "journal_title": "Automatic prediction of protein domains from sequence information using a hybrid learning system", "journal_authors": "Niranjan Nagarajan, Golan Yona", "journal_issue_pages": "20(9): 1335-1360", "journal_year": "2004", "journal_doi": "10.1093/bioinformatics/bth086" }, { "author": "Itsik Pe'er, Jacques S. Beckmann", "title": "Resolution of haplotypes and haplotype frequencies from SNP genotypes of pooled samples", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 237–246. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "237–246", "proceedings_doi": "10.1145/640075.640107" }, { "author": "Pavel Pevzner, Glenn Tesler", "title": "Transforming men into mice: the Nadeau-Taylor chromosomal breakage model revisited", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 247–256. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "247–256", "proceedings_doi": "10.1145/640075.640108", "journal": "Proceedings of the National Academy of Sciences", "journal_title": "Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution", "journal_authors": "Pavel Pevzner, Glenn Tesler", "journal_issue_pages": "100 (13) 7662-7667", "journal_year": "2003", "journal_doi": "10.1073/pnas.1330369100" }, { "author": "Krishna M. Roskin, Mark Diekhans, David Haussler", "title": "Scoring two-species local alignments to try to statistically separate neutrally evolving from selected DNA segments", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 257–266. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "257–266", "proceedings_doi": "10.1145/640075.640109" }, { "author": "Fabian Schwarzer, Itay Lotan", "title": "Approximation of protein structure for fast similarity measures", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 267–276. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "267–276", "proceedings_doi": "10.1145/640075.640110", "journal": "Journal of Computational Biology", "journal_title": "Approximation of Protein Structure for Fast Similarity Measures", "journal_authors": "Itay Lotan, Fabian Schwarzer", "journal_issue_pages": "11(2-3): 299-317", "journal_year": "2004", "journal_doi": "10.1089/1066527041410355" }, { "author": "Adam Siepel, David Haussler", "title": "Combining phylogenetic and hidden Markov models in biosequence analysis", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 277–286. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "277–286", "proceedings_doi": "10.1145/640075.640111", "journal": "Journal of Computational Biology", "journal_title": "Combining Phylogenetic and Hidden Markov Models in Biosequence Analysis", "journal_authors": "Adam Siepel, David Haussler", "journal_issue_pages": "11(2-3): 413-428", "journal_year": "2004", "journal_doi": "10.1089/1066527041410472" }, { "author": "Umar Syed, Golan Yona", "title": "Using a mixture of probabilistic decision trees for direct prediction of protein function", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 289–300. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "289–300", "proceedings_doi": "10.1145/640075.640114" }, { "author": "Amos Tanay, Ron Shamir", "title": "Modeling transcription programs: inferring binding site activity and dose-response model optimization", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 301–310. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "301–310", "proceedings_doi": "10.1145/640075.640115" }, { "author": "Chen-Hsiang Yeang, Tommi Jaakkola", "title": "Physical network models and multi-source data integration", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 312–321. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "312–321", "proceedings_doi": "10.1145/640075.640117", "journal": "Journal of Computational Biology", "journal_title": "Physical Network Models", "journal_authors": "Chen‐Hsiang Yeang, Trey Ideker, Tommi Jaakkola", "journal_issue_pages": "11(2-3): 243-262", "journal_year": "2004", "journal_doi": "10.1089/1066527041410382" }, { "author": "Gene Yeo, Christopher B. Burge", "title": "Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 322–331. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "322–331", "proceedings_doi": "10.1145/640075.640118", "journal": "Journal of Computational Biology", "journal_title": "Maximum Entropy Modeling of Short Sequence Motifs with Applications to RNA Splicing Signals", "journal_authors": "G Yeo, Christopher B. Burge", "journal_issue_pages": "11(2-3): 377-394", "journal_year": "2004", "journal_doi": "10.1089/1066527041410418" }, { "author": "Kui Zhang, Fengzhu Sun, Michael S. Waterman, Ting Chen", "title": "Dynamic programming algorithms for haplotype block partitioning: applications to human chromosome 21 haplotype data", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2003, pp 332–340. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "332–340", "proceedings_doi": "10.1145/640075.640119", "journal": "The American Journal of Human Genetics", "journal_title": "Haplotype Block Partition with Limited Resources and Applications to Human Chromosome 21 Haplotype Data", "journal_authors": "Kui Zhang, Fengzhu Sun, Michael S. Waterman, Ting Chen", "journal_issue_pages": "73(1): 63-73", "journal_year": "2003", "journal_doi": "10.1086/376437" } ] }