{ "title": "5th Annual International Conference on Research in Computational Molecular Biology", "location": "Montreal, Canada", "dates": "April 21 - 25, 2001", "pc_chair": "Thomas Lengauer", "organization_committee": "David Sankoff (chair), Nadia El-Mabrouk, Michael Hallett, François Major, Thomas Hagedorn, Theo Mevissen, Louis Pelletier, Ralf Zimmer", "keynotes": "George Church, Phillip Sharp, Mark Adams, Roger Brent, Franz Lang, Klaus Lindpaintner, Yvonne Martin, Mark Ptashne, Matthias Wilm", "website": "https://recomb.org/recomb2001", "papers": [ { "author": "Abdullah N. Arslan, Ömer Eğecioğlu, Pavel A. Pevzner", "title": "A new approach to sequence comparison: normalized sequence alignment", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 2–11. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "2–11", "proceedings_doi": "10.1145/369133.369146", "journal": "Bioinformatics", "journal_title": "A new approach to sequence comparison: normalized sequence alignment", "journal_authors": "Abdullah N. Arslan, Ömer Eğeci̇oğlu, Pavel A. Pevzner", "journal_issue_pages": "17(4): 327-337", "journal_year": "2001", "journal_doi": "10.1093/bioinformatics/17.4.327" }, { "author": "Yoseph Barash, Nir Friedman", "title": "Context-specific Bayesian clustering for gene expression data", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 12–21. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "12–21", "proceedings_doi": "10.1145/369133.369150", "journal": "Journal of Computational Biology", "journal_title": "Context-Specific Bayesian Clustering for Gene Expression Data", "journal_authors": "Yoseph Barash, Nir Friedman", "journal_issue_pages": "9(2): 169-191", "journal_year": "2002", "journal_doi": "10.1089/10665270252935403" }, { "author": "Richard Beigel, Noga Alon, Simon Kasif, Mehmet Serkan Apaydin, Lance Fortnow", "title": "An optimal procedure for gap closing in whole genome shotgun sequencing", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 22–30. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "22–30", "proceedings_doi": "10.1145/369133.369152" }, { "author": "Amir Ben-Dor, Nir Friedman, Zohar Yakhini", "title": "Class discovery in gene expression data", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 31–38. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "31–38", "proceedings_doi": "10.1145/369133.369167", "journal": "Nature Genetics", "journal_title": "Statistical benchmarking and class discovery in gene expression data", "journal_authors": "Amir Ben‐Dor, Nir Friedman, Zohar Yakhini", "journal_issue_pages": "27(S4): 96", "journal_year": "2001", "journal_doi": "10.1038/87368" }, { "author": "Yonatan Bilu, Michal Linial", "title": "On the predictive power of sequence similarity in yeast", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 39–48. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "39–48", "proceedings_doi": "10.1145/369133.369168" }, { "author": "Mathieu Blanchette", "title": "Algorithms for phylogenetic footprinting", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 49–58. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "49–58", "proceedings_doi": "10.1145/369133.369170", "journal": "Journal of Computational Biology", "journal_title": "Algorithms for Phylogenetic Footprinting", "journal_authors": "Mathieu Blanchette, Benno Schwikowski, Martin Tompa", "journal_issue_pages": "9(2): 211-223", "journal_year": "2002", "journal_doi": "10.1089/10665270252935421" }, { "author": "Phil Bradley, Lenore Cowen, Matthew Menke, Jonathan King, Bonnie Berger", "title": "Predicting the β-helix fold from protein sequence data", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 59–67. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "59–67", "proceedings_doi": "10.1145/369133.369171", "journal": "Journal of Computational Biology", "journal_title": "Predicting the Beta-Helix Fold from Protein Sequence Data", "journal_authors": "Lenore Cowen, Phil Bradley, Matthew Menke, Jonathan King, Bonnie Berger", "journal_issue_pages": "9(2): 261-276", "journal_year": "2002", "journal_doi": "10.1089/10665270252935458" }, { "author": "Jeremy Buhler, Martin Tompa", "title": "Finding motifs using random projections", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 69–76. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "69–76", "proceedings_doi": "10.1145/369133.369172", "journal": "Journal of Computational Biology", "journal_title": "Finding Motifs Using Random Projections", "journal_authors": "Jeremy Buhler, Martin Tompa", "journal_issue_pages": "9(2): 225-242", "journal_year": "2002", "journal_doi": "10.1089/10665270252935430" }, { "author": "Ralf Bundschuh", "title": "Rapid significance estimation in local sequence alignment with gaps", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 77–85. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "77–85", "proceedings_doi": "10.1145/369133.369173", "journal": "Journal of Computational Biology", "journal_title": "Rapid Significance Estimation in Local Sequence Alignment with Gaps", "journal_authors": "Ralf Bundschuh", "journal_issue_pages": "9(2): 243-260", "journal_year": "2002", "journal_doi": "10.1089/10665270252935449" }, { "author": "Harmen J. Bussemaker, Hao Li, Eric D. Siggia", "title": "Regulatory element detection using correlation with expression", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 86. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "86", "proceedings_doi": "10.1145/369133.369174", "journal": "Nature Genetics", "journal_title": "Regulatory element detection using correlation with expression", "journal_authors": "Harmen J. Bussemaker, Hao Li, Eric D. Siggia", "journal_issue_pages": "27(2): 167-171", "journal_year": "2001", "journal_doi": "10.1038/84792" }, { "author": "Ting Chen", "title": "Gene-finding via tandem mass spectrometry", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 87–94. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "87–94", "proceedings_doi": "10.1145/369133.369176" }, { "author": "Ting Chen, Jacob D. Jaffe, George M. Church", "title": "Algorithms for identifying protein cross-links via tandem mass spectrometry", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 95–102. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "95–102", "proceedings_doi": "10.1145/369133.369177", "journal": "Journal of Computational Biology", "journal_title": "Algorithms for Identifying Protein Cross-Links via Tandem Mass Spectrometry", "journal_authors": "Ting Chen, Jacob D. Jaffe, George M. Church", "journal_issue_pages": "8(6): 571-583", "journal_year": "2001", "journal_doi": "10.1089/106652701753307494" }, { "author": "Miklós Csűrös", "title": "Fast recovery of evolutionary trees with thousands of nodes", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 104–113. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "104–113", "proceedings_doi": "10.1145/369133.369178", "journal": "Journal of Computational Biology", "journal_title": "Fast Recovery of Evolutionary Trees with Thousands of Nodes", "journal_authors": "Miklós Csürös", "journal_issue_pages": "9(2): 277-297", "journal_year": "2002", "journal_doi": "10.1089/10665270252935467" }, { "author": "Alon Efrat, Frank Hoffman, Klaus Kriegel, Christof Schultz, Carola Wenk", "title": "Geometric algorithms for the analysis of 2D-electrophoresis gels", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 114–123. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "114–123", "proceedings_doi": "10.1145/369133.369181", "journal": "Journal of Computational Biology", "journal_title": "Geometric Algorithms for the Analysis of 2D-Electrophoresis Gels", "journal_authors": "Alon Efrat, Frank Hoffmann, Klaus Kriegel, Christof Schultz, Carola Wenk", "journal_issue_pages": "9(2): 299-315", "journal_year": "2002", "journal_doi": "10.1089/10665270252935476" }, { "author": "Vladimir Filkov, Steven Skiena, Jizu Zhi", "title": "Analysis techniques for microarray time-series data", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 124–131. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "124–131", "proceedings_doi": "10.1145/369133.369183", "journal": "Journal of Computational Biology", "journal_title": "Analysis Techniques for Microarray Time-Series Data", "journal_authors": "Vladimir Filkov, Steven Skiena, Jizu Zhi", "journal_issue_pages": "9(2): 317-330", "journal_year": "2002", "journal_doi": "10.1089/10665270252935485" }, { "author": "Nir Friedman, Matan Ninio, Itsik Pe'er, Tal Pupko", "title": "A structural EM algorithm for phylogenetic inference", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 132–140. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "132–140", "proceedings_doi": "10.1145/369133.369182", "journal": "Journal of Computational Biology", "journal_title": "A Structural EM Algorithm for Phylogenetic Inference", "journal_authors": "Nir Friedman, Matan Ninio, Itsik Pe’er, Tal Pupko", "journal_issue_pages": "9(2): 331-353", "journal_year": "2002", "journal_doi": "10.1089/10665270252935494" }, { "author": "Alan M. Frieze, Bjarni V. Halldórsson", "title": "Optimal sequencing by hybridization in rounds", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 141–148. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "141–148", "proceedings_doi": "10.1145/369133.369187", "journal": "Journal of Computational Biology", "journal_title": "Optimal Sequencing by Hybridization in Rounds", "journal_authors": "Alan Frieze, Bjarni V. Halldórsson", "journal_issue_pages": "9(2): 355-369", "journal_year": "2002", "journal_doi": "10.1089/10665270252935502" }, { "author": "M. T. Hallett, J. Lagergren", "title": "Efficient algorithms for lateral gene transfer problems", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 149–156. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "149–156", "proceedings_doi": "10.1145/369133.369188" }, { "author": "Daniel H. Huson, Knut Reinert, Eugene Myers", "title": "The greedy path-merging algorithm for sequence assembly", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 157–163. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "157–163", "proceedings_doi": "10.1145/369133.369190", "journal": "Journal of the ACM", "journal_title": "The greedy path-merging algorithm for contig scaffolding", "journal_authors": "Daniel H. Huson, Knut Reinert, Eugene W. Myers", "journal_issue_pages": "49(5): 603-615", "journal_year": "2002", "journal_doi": "10.1145/585265.585267" }, { "author": "Christopher James Langmead, Bruce Randall Donald", "title": "Extracting structural information using time-frequency analysis of protein NMR data", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 164–175. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "164–175", "proceedings_doi": "10.1145/369133.369191" }, { "author": "John Kececioglu, Jun Ju", "title": "Separating repeats in DNA sequence assembly", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 176–183. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "176–183", "proceedings_doi": "10.1145/369133.369192" }, { "author": "O. Kohlbacher, A. Burchardt, A. Moll, A. Hildebrandt, P. Bayer, H.-P Lenhof", "title": "A NMR-spectra-based scoring function for protein docking", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 184–192. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "184–192", "proceedings_doi": "10.1145/369133.369194" }, { "author": "Giuseppe Lancia, Robert Carr, Brian Walenz, Sorin Istrail", "title": "101 optimal PDB structure alignments: a branch-and-cut algorithm for the maximum contact map overlap problem", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 193–202. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "193–202", "proceedings_doi": "10.1145/369133.369199" }, { "author": "Wentian Li", "title": "DNA segmentation as a model selection process", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 204–210. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "204–210", "proceedings_doi": "10.1145/369133.369202", "preprint_id": "arXiv:physics/0104027", "preprint_doi": "10.48550/arXiv.physics/0104027" }, { "author": "Guo-Hui Lin, Bin Ma, Kaizhong Zhang", "title": "Edit distance between two RNA structures", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 211–220. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "211–220", "proceedings_doi": "10.1145/369133.369214", "journal": "Journal of Computational Biology", "journal_title": "A General Edit Distance between RNA Structures", "journal_authors": "Tao Jiang, Guohui Lin, Bin Ma, Kaizhong Zhang", "journal_issue_pages": "9(2): 371-388", "journal_year": "2002", "journal_doi": "10.1089/10665270252935511" }, { "author": "Gene Myers", "title": "Comparing sequence scaffolds", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 224–230. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "224–230", "proceedings_doi": "10.1145/369133.369218" }, { "author": "Gonzalo Navarro, Mathieu Raffinot", "title": "Fast and simple character classes and bounded gaps pattern matching, with application to protein searching", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 231–240. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "231–240", "proceedings_doi": "10.1145/369133.369220", "journal": "Journal of Computational Biology", "journal_title": "Fast and Simple Character Classes and Bounded Gaps Pattern Matching, with Applications to Protein Searching", "journal_authors": "Gonzalo Navarro, Mathieu Raffinot", "journal_issue_pages": "10(6): 903-923", "journal_year": "2003", "journal_doi": "10.1089/106652703322756140" }, { "author": "Lior Pachter, Marina Alexandersson, Simon Cawley", "title": "Applications of generalized pair hidden Markov models to alignment and gene finding problems", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 241–248. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "241–248", "proceedings_doi": "10.1145/369133.369227", "journal": "Journal of Computational Biology", "journal_title": "Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems", "journal_authors": "Lior Pachter, Marina Alexandersson, Simon Cawley", "journal_issue_pages": "9(2): 389-399", "journal_year": "2002", "journal_doi": "10.1089/10665270252935520" }, { "author": "Paul Pavlidis, Jason Weston, Jinsong Cai, William Noble Grundy", "title": "Gene functional classification from heterogeneous data", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 249–255. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "249–255", "proceedings_doi": "10.1145/369133.369228", "journal": "Journal of Computational Biology", "journal_title": "Learning Gene Functional Classifications from Multiple Data Types", "journal_authors": "Paul Pavlidis, Jason Weston, Jinsong Cai, William Stafford Noble", "journal_issue_pages": "9(2): 401-411", "journal_year": "2002", "journal_doi": "10.1089/10665270252935539" }, { "author": "Pavel A. Pevzner, Haixu Tang, Michael S. Waterman", "title": "A new approach to fragment assembly in DNA sequencing", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 256–267. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "256–267", "proceedings_doi": "10.1145/369133.369230" }, { "author": "Ron Shamir, Dekel Tsur", "title": "Large scale sequencing by hybridization", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 269–277. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "269–277", "proceedings_doi": "10.1145/369133.369233", "journal": "Journal of Computational Biology", "journal_title": "Large Scale Sequencing by Hybridization", "journal_authors": "Ron Shamir, Dekel Tsur", "journal_issue_pages": "9(2): 413-428", "journal_year": "2002", "journal_doi": "10.1089/10665270252935548" }, { "author": "Mona Singh, Peter S. Kim", "title": "Towards predicting coiled-coil protein interactions", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 279–286. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "279–286", "proceedings_doi": "10.1145/369133.369238" }, { "author": "Guang Song, Nancy M. Amato", "title": "Using motion planning to study protein folding pathways", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 287–296. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "287–296", "proceedings_doi": "10.1145/369133.369239", "journal": "Journal of Computational Biology", "journal_title": "Using Motion Planning to Study Protein Folding Pathways", "journal_authors": "Nancy M. Amato, Guang Song", "journal_issue_pages": "9(2): 149-168", "journal_year": "2002", "journal_doi": "10.1089/10665270252935395" }, { "author": "Mengxiang Tang, Michael Waterman, Shibu Yooseph", "title": "Zinc finger gene clusters and tandem gene duplication", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 297–304. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "297–304", "proceedings_doi": "10.1145/369133.369241", "journal": "Journal of Computational Biology", "journal_title": "Zinc Finger Gene Clusters and Tandem Gene Duplication", "journal_authors": "Mengxiang Tang, Michael S. Waterman, Shibu Yooseph", "journal_issue_pages": "9(2): 429-446", "journal_year": "2002", "journal_doi": "10.1089/10665270252935557" }, { "author": "Gert Thijs, Kathleen Marchal, Magali Lescot, Stephane Rombauts, Bart De Moor, Pierre Rouzé, Yves Moreau", "title": "A Gibbs sampling method to detect over-represented motifs in the upstream regions of co-expressed genes", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2001, pp 305–312. Association for Computing Machinery, New York, NY, USA.", "proceedings_pages": "305–312", "proceedings_doi": "10.1145/369133.369253", "journal": "Journal of Computational Biology", "journal_title": "A Gibbs Sampling Method to Detect Overrepresented Motifs in the Upstream Regions of Coexpressed Genes", "journal_authors": "Gert Thijs, Kathleen Marchal, Magali Lescot, Stéphane Rombauts, Bart De Moor, Pierre Rouzé, Yves Moreau", "journal_issue_pages": "9(2): 447-464", "journal_year": "2002", "journal_doi": "10.1089/10665270252935566" } ] }