RECOMB 2001 Proceedings

Montreal, Canada, April 22-25, 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

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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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