RECOMB 1999 Proceedings

Lyon, France, April 11-14, 1999

PC Chair: Sorin Istrail
Organization Committee: Mireille Regnier (chair), Florence Balax, Daniel Kahn, Gregory Kucherov, Sophie Schbath, Annick Theis-Viémont
Keynote Speakers: Peer Bork, Cyrus Chothia, Daniel Cohen, John Moult, Gene Myers, Piotr Slonimski, E. M. Southern, Peter Willett, John Wooley

List of Publications

• Algorithms for whole genome shotgun sequencing. Eric Anson, Gene Myers.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 1–9. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299442
• Classifying proteins by family using the product of correlated p-values. Timothy L. Bailey, William Noble Grundy.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 10–14. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299444
• Modeling protein families using probabilistic suffix trees. Gill Bejerano, Golan Yona.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 15–24. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299445
• A method for optimal design of a threading scoring function. Jadwiga R. Bieńkowska, Robert G. Rogers, Temple F. Smith.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 25–32. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299446
• Clustering gene expression patterns. Amir Ben-Dor, Zohar Yakhini.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 33–42. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299448
• Searching gene transfers on Bacillus subtilis using hidden Markov models. Laurent Bize, Florence Muri, Franck Samson, François Rodolphe, S. Dusko Ehrlich, Bernard Prum, Philippe Bessières.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 43–49. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299449
• Winnowing sequences from a database search. Piotr Berman, Zheng Zhang, Yuri I. Wolf, Eugene V. Koonin, Webb Miller.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 50–58. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299451
• Faster reliable phylogenetic analysis. Vincent Berry, David Bryant.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 59–68. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299457
• An analytic study of the phase transition line in local sequence alignment with gaps. R. Bundschuh, T. Hwa.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 70–76. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.349874
• q-gram based database searching using a suffix array (QUASAR). Stefan Burkhardt, Andreas Crauser, Paolo Ferragina, Hans-Peter Lenhof, Eric Rivals, Martin Vingron.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 77–83. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299460
• Formulations and hardness of multiple sorting by reversals. Alberto Caprara.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 84–93. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299461
• Identifying gene regulatory networks from experimental data. Ting Chen, Vladimir Filkov, Steven S. Skiena.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 94–103. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299462
• Fast detection of common geometric substructure in proteins. L. Paul Chew, Dan Huttenlocher, Klara Kedem, Jon Kleinberg.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 104–113. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299464
• Computing physical maps of chromosomes with nonoverlapping probes by branch-and-cut. Thomas Christof, John Kececioglu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 115–123. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299465
• Optimizing combinatorial library construction via split synthesis. Barry Cohen, Steven Skiena.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 124–133. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299467
• De Novo peptide sequencing via tandem mass spectrometry: a graph-theoretical approach. Vlado Dančík, Theresa A. Addona, Karl R. Clauser, James E. Vath.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 135–144. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299471
• A solvation potential with improved contact definitions and optimized by extensive threading. Alan A. Dombkowski, Gordon M. Crippen.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 145–153. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299474
• Reconstructing the pre-doubling genome. Nadia El-Mabrouk, David Bryant, David Sankoff.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 154–163. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299475
• Sequence homology detection through large scale pattern discovery. Aris Floratos, Isidore Rigoutsos, Laxmi Parida, Gustova Stolovitzky, Yuan Gao.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 164–173. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299477
• Evolution of metabolisms: a new method for the comparison of metabolic pathways. Christian V. Forst, Klaus Schulten.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 174–181. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299481
• Significance testing for genomic mismatch scanning. G. R. Grant, R. S. Spielman, E. Manduchi, V. G. Cheung, W. J. Ewens.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 182–187. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299482
• An algorithm for clustering cDNAs for gene expression analysis. Erez Hartuv, Armin Schmitt, Jörg Lange, Sebastian Meier-Ewert, Hans Lehrach, Ron Shamir.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 188–197. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299483
• Obtaining highly accurate topology estimates of evolutionary trees from very short sequences. Daniel H. Huson, Scott Nettles, Tandy J. Warnow.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 198–207. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299484
• Algorithms for choosing differential gene expression experiments. Richard M. Karp, Roland Stoughton, Ka Yee Yeung.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 208–217. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299485
• Recognition of remote protein homologies using three-dimensional information to generate a position specific scoring matrix in the program 3D-PSSM. Lawrence A. Kelley, Robert M. MacCallum, Michael J. E. Sternberg.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 218–225. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299486
• Efficient algorithms for protein sequence design and the analysis of certain evolutionary fitness landscapes. Jon M. Kleinberg.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 226–237. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299487
• An anytime algorithm for gapped block protein threading with pair interactions. Richard H. Lathrop.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 238–249. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299488
• Efficient database screening for rational drug design using pharmacophore-constrained conformational search. Steven M. LaValle, Paul W. Finn, Lydia E. Kavraki, Jeal-Claude Latombe.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 250–260. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299489
• Internal loops in RNA secondary structure prediction. Rune B. Lyngsø, Michael Zuker, Christian N. S. Pedersen.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 260–267. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299490
• Construction of physical maps from oligonucleotide fingerprints data. Guy Mayraz, Ron Shamir.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 268–277. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299497
• Coupled optimization in protein docking. Julie C. Mitchell, J. Ben Rosen, Andrew T. Phillips, Lynn F. Ten Eyck.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 280–284. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299502
• A dictionary based approach for gene annotation. Lior Pachter, Serafim Batzoglou, Valentin I. Spitkovsky, William S. Beebee, Eric S. Lander, Bonnie Berger, Daniel J. Kleitman.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 285–294. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299504
• On the power of universal bases in sequencing by hybridization. Franco P. Preparata, Alan M. Frieze, Eli Upfal.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 295–301. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299505
• Probability models for genome rearrangement and linear invariants for phylogenetic inference. David Sankoff, Mathieu Blanchette.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 302–309. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299506
• Derivation of sensitive discrimination potential for virtual ligand screening. Maxim Totrov, Ruben Abagyan.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 312–320. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299509
• Computational analysis of molecular diversity for drug discovery. Martin J. Bayley, Valerie J. Gillet, Peter Willett, John Bradshaw, Darren V. S. Green.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 1999, pp 321–330. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/299432.299510