RECOMB 2002 Proceedings

Washington, DC, United States, April 18-21, 2002

PC Chair: Gene Myers
Organization Committee: Sridhar Hannenhalli (chair), Kathy Ambrose, Liliana Florea, George Komatsoulis, Jason Miller, Morgan Park, Michelle Perry, Russell Schwartz, Brian Walenz
Keynote Speakers: Ruben Abagyan, Ali Brivanlou, Evan Eichler, Harold Garner, David Ho, Gerry Rubin, Craig Venter, Marc Vidal

List of Publications

• Using motion planning to map protein folding landscapes and analyze folding kinetics of known native structures. Nancy M. Amato, Ken A. Dill, Guang Song.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 2–11. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565198
• Stochastic roadmap simulation: an efficient representation and algorithm for analyzing molecular motion. Mehmet Serkan Apaydin, Douglas L. Brutlag, Carlos Guestrin, David Hsu, Jean-Claude Latombe.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 12–21. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565199
• Monotony of surprise and large-scale quest for unusual words. Alberto Apostolico, Mary Ellen Bock, Stefano Lonardi.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 22–31. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565200
• DNA sequence evolution with neighbor-dependent mutation. Peter F. Arndt, Christopher B. Burge, Terence Hwa.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 32–38. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565201
• A new approach to analyzing gene expression time series data. Ziv Bar-Joseph, Georg Gerber, David K. Gifford, Tommi S. Jaakkola, Itamar Simon.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 39–48. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565202
• Discovering local structure in gene expression data: the order-preserving submatrix problem. Amir Ben-Dor, Benny Chor, Richard Karp, Zohar Yakhini.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 49–57. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565203
• The restriction scaffold problem. Amir Ben-Dor, Richard M. Karp, Benno Schwikowski, Ron Shamir.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 58–66. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565204
• Comparison of minisatellites. Sèverine Bérard, Éric Rivals.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 67–76. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565205
• Trilogy: discovery of sequence-structure patterns across diverse proteins. Phil Bradley, Peter S. Kim, Bonnie Berger.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 77–88. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565206
• Provably sensitive Indexing strategies for biosequence similarity search. Jeremy Buhler.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 90–99. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565208
• Structural alignment of large-size proteins via lagrangian relaxation. Alberto Caprara, Giuseppe Lancia.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 100–108. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565209
• Designing RNA structures: natural and artificial selection. Barry Cohen, Steven Skiena.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 109–116. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565210
• Inferring domain-domain interactions from protein-protein interactions. Minghua Deng, Shipra Mehta, Fengzhu Sun, Ting Chen.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 117–126. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565211
• Analysis of gene expression profiles: class discovery and leaf ordering. Chris H. Q. Ding.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 127–136. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565212
• A bayesian approach to transcript estimation from gene array data: the BEAM technique. Ron O. Dror, Jonathan G. Murnick, Nicola A. Rinaldi, Voichita D. Marinescu, Ryan M. Rifkin, Richard A. Young.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 137–143. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565213
• Tests for gene clustering. Dannie Durand, David Sankoff.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 144–154. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565214
• Approximate matching of secondary structures. Nadia El-Mabrouk, Mathieu Raffinot.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 156–164. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565216
• Haplotyping as perfect phylogeny: conceptual framework and efficient solutions. Dan Gusfield.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 166–175. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565218
• Handling long targets and errors in sequencing by hybridization. Eran Halperin, Shay Halperin, Tzvika Hartman, Ron Shamir.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 176–185. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565219
• Sequencing by hybridization using direct and reverse cooperating spectra. Samuel A. Heath, Franco P. Preparata, Joel Young.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 186–193. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565220
• Finding motifs in the twilight zone. Uri Keich, Pavel A. Pevzner.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 195–204. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565222
• Phase-independent rhythmic analysis of genome-wide expression patterns. Christopher James Langmead, Anthony K. Yan, C. Robertson McClung, Bruce Randall Donald.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 205–215. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565223
• Significance Of inter-species matches when evolutionary rate varies. Jia Li, Webb Miller.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 216–224. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565224
• Combining pairwise sequence similarity and support vector machines for remote protein homology detection. Li Liao, William Stafford Noble.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 225–232. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565225
• Revealing protein structures: a new method for mapping antibody epitopes. Brendan M. Mumey, Brian W. Bailey, Edward A. Dratz.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 233–240. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565226
• Set association analysis of SNP case-control and microarray data. Jurg Ott, Josephine Hoh.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 241–245. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565227
• Picking alignments from (steiner) trees. Lior Pachter, Fumei Lam.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 246–253. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565228
• String barcoding: uncovering optimal virus signatures. Sam Rash, Dan Gusfield.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 254–261. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565229
• From promoter sequence to expression: a probabilistic framework. Eran Segal, Yoseph Barash, Itamar Simon, Nir Friedman, Daphne Koller.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 263–272. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565231
• Probabilistic hierarchical clustering for biological data. Eran Segal, Daphne Koller.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 273–280. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565232
• An algorithm to enumerate all sorting reversals. Adam C. Siepel.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 281–290. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565233
• Discriminative motifs. Saurabh Sinha.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 291–298. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565234
• A dimensionality reduction approach to modeling protein flexibility. Miguel L. Teodoro, George N. Phillips, Lydia E. Kavraki.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 299–308. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565235
• Deconvolving sequence variation in mixed DNA populations. Andy Wildenberg, Steven Skiena, Pavel Sumazin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 311–320. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565238
• Microarrays: how many do you need?. Alexander Zien, Juliane Fluck, Ralf Zimmer, Thomas Lengauer.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2002, pp 321–330. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/565196.565239