RECOMB 2001 Proceedings

Montreal, Canada, 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
Keynote Speakers: George Church, Phillip Sharp, Mark Adams, Roger Brent, Franz Lang, Klaus Lindpaintner, Yvonne Martin, Mark Ptashne, Matthias Wilm
Website: https://recomb.org/recomb2001
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List of Publications

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