RECOMB 2000 Proceedings

Tokyo, Japan, April 8 - 11, 2000

PC Chair: Ron Shamir
Organization Committee: Satoru Miyano (chair), Tatsuya Akutsu, Nir Friedman, Osamu Maruyama, Kenta Nakai, Asako Suzuki, Toshihisa Takagi, Ayako Tomiyasu
Keynote Speakers: Minoru Kanehisa, Hans Lehrach, Svante Paabo, Eric Davidson, Takashi Gojobori, Leroy Hood, Walter Gilbert, Yusuke Nakamura
Website: https://recomb.org/recomb2000
Export: JSON | BibTeX

List of Publications

• On approximation algorithms for local multiple alignment. Tatsuya Akutsu, Hiroki Arimura, Shinichi Shimozono.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2000, pp 1–7. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/332306.332311
• Algorithms for identifying Boolean networks and related biological networks based on matrix multiplication and fingerprint function. Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2000, pp 8–14. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/332306.332317
  • Journal: Algorithms for Identifying Boolean Networks and Related Biological Networks Based on Matrix Multiplication and Fingerprint Function. Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara. Journal of Computational Biology, 7(3-4): 331-343, 2000.
    • DOI: 10.1089/106652700750050817
• A combinatorial approach to protein docking with flexible side-chains. E. Althaus, O. Kohlbacher, H.-P. Lenhof, P. Müller.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2000, pp 15–24. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/332306.332319
  • Journal: A Combinatorial Approach to Protein Docking with Flexible Side Chains. Ernst Althaus, Oliver Kohlbacher, Hans‐Peter Lenhof, Peter Müller. Journal of Computational Biology, 535(4): 15-24, 2000.
    • DOI: 10.1089/106652702760277336
• Optimal amnesic probabilistic automata or how to learn and classify proteins in linear time and space. Alberto Apostolico, Gill Bejerano.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2000, pp 25–32. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/332306.332321
  • Journal: Optimal Amnesic Probabilistic Automata or How to Learn and Classify Proteins in Linear Time and Space. Alberto Apostolico, Gill Bejerano. Journal of Computational Biology, 7(3-4): 381-393, 2000.
    • DOI: 10.1089/106652700750050844
• The NOESY jigsaw: automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data. Chris Bailey-Kellogg, Alik Widge, John J. Kelley, Marcelo J. Berardi, John H. Bushweller, Bruce Randall Donald.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2000, pp 33–44. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/332306.332323
  • Journal: The NOESY Jigsaw: Automated Protein Secondary Structure and Main-Chain Assignment from Sparse, Unassigned NMR Data. Chris Bailey‐Kellogg, Alik S. Widge, John J. Kelley, Marcelo J. Berardi, John H. Bushweller, Bruce R. Donald. Journal of Computational Biology, 7(3-4): 537-558, 2000.
    • DOI: 10.1089/106652700750050934
• Sequencing a genome by walking with clone-end sequences: a mathematical analysis. Serafim Batzoglou, Bonnie Berger, Jill Mesirov, Eric S. Lander.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2000, pp 45. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/332306.332325
  • Journal: Sequencing a Genome by Walking with Clone-End Sequences: A Mathematical Analysis. Serafim Batzoglou, Bonnie Berger, Jill P. Mesirov, Eric S. Lander. Genome Research, 9(12): 1163-1174, 1999.
    • DOI: 10.1101/gr.9.12.1163
• Human and mouse gene structure: comparative analysis and application to exon prediction. Serafim Batzoglou, Lior Pachter, Jill Mesirov, Bonnie Berger, Eric S. Lander.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2000, pp 46–53. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/332306.332326
  • Journal: Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction. Serafim Batzoglou, Lior Pachter, Jill P. Mesirov, Bonnie Berger, Eric S. Lander. Genome Research, 10(7): 950-958, 2000.
    • DOI: 10.1101/gr.10.7.950
• Tissue classification with gene expression profiles. Amir Ben-Dor, Laurakay Bruhn, Nir Friedman, Iftach Nachman, Michèel Schummer, Zohar Yakhini.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2000, pp 54–64. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/332306.332328
  • Journal: Tissue Classification with Gene Expression Profiles. Amir Ben‐Dor, Laurakay Bruhn, Nir Friedman, Iftach Nachman, Michèl Schummer, Zohar Yakhini. Journal of Computational Biology, 7(3-4): 559-583, 2000.
    • DOI: 10.1089/106652700750050943
• Universal DNA tag systems: a combinatorial design scheme. Amir Ben-Dor, Richard Karp, Benno Schwikowski, Zohar Yakhini.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2000, pp 65–75. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/332306.332346
  • Journal: Universal DNA Tag Systems: A Combinatorial Design Scheme. Amir Ben‐Dor, Richard M. Karp, Benno Schwikowski, Zohar Yakhini. Journal of Computational Biology, 7(3-4): 503-519, 2000.
    • DOI: 10.1089/106652700750050916
• Comprehensive statistical method for protein fold recognition. Jadwiga R. Bieńkowska, Lihua Yu, Sophia Zarakhovich, Robert G. Rogers, Temple F. Smith.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2000, pp 76–85. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/332306.332347
• An analytic approach to significance assessment in local sequence alignment with gaps. Ralf Bundschuh.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2000, pp 86–95. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/332306.332350
  • 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
• Notung: dating gene duplications using gene family trees. Kevin Chen, Dannie Durand, Martin Farach-Colton.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2000, pp 96–106. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/332306.332351
  • Journal: NOTUNG: A Program for Dating Gene Duplications and Optimizing Gene Family Trees. Kevin Chen, Dannie Durand, Martı́n Farach-Colton. Journal of Computational Biology, 7(3-4): 429-447, 2000.
    • DOI: 10.1089/106652700750050871
• A compression algorithm for DNA sequences and its applications in genome comparison. Xin Chen, Sam Kwong, Ming Li.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2000, pp 107. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/332306.332352
• Multiple maxima of likelihood in phylogenetic trees: an analytic approach. Benny Chor, Michael D. Hendy, Barbara R. Holland, David Penny.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2000, pp 108–117. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/332306.332353
  • Journal: Multiple Maxima of Likelihood in Phylogenetic Trees: An Analytic Approach. Benny Chor, Michael D. Hendy, Barbara R. Holland, David Penny. Molecular Biology and Evolution, 17(10): 1529-1541, 2000.
    • DOI: 10.1093/oxfordjournals.molbev.a026252
• Tree fitting: an algebraic approach using profile distances. Richard Desper, Martin Vingron.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2000, pp 119–126. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/332306.332354
• Using Bayesian networks to analyze expression data. Nir Friedman, Michal Linial, Iftach Nachman, Dana Pe’er.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2000, pp 127–135. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/332306.332355
  • Journal: Using Bayesian Networks to Analyze Expression Data. Nir Friedman, Michal Linial, Iftach Nachman, Dana Pe’er. Journal of Computational Biology, 7(3-4): 601-620, 2000.
    • DOI: 10.1089/106652700750050961
• New algorithms for the duplication-loss model. Michael T. Hallett, Jens Lagergren.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2000, pp 138–146. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/332306.332359
  • Journal: New algorithms for the duplication-loss model. Michael Hallett, Jens Lagergren. Repository for Publications and Research Data (ETH Zurich), 330, 1999.
    • DOI: 10.3929/ethz-a-006653457
• Systematic and automated discovery of patterns in PROSITE families. Reece Hart, Ajay K. Royyuru, Gustavo Stolovitzky, Andrea Califano.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2000, pp 147–154. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/332306.332360
  • Journal: Systematic and Fully Automated Identification of Protein Sequence Patterns. Reece K. Hart, Ajay K. Royyuru, Gustavo Stolovitzky, Andrea Califano. Journal of Computational Biology, 7(3-4): 585-600, 2000.
    • DOI: 10.1089/106652700750050952
• Contig selection in physical mapping. Steffan Heber, Jens Stoye, Jörg Hoheisel, Martin Vingron.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2000, pp 155–164. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/332306.332361
  • Journal: Contig Selection in Physical Mapping. Steffen Heber, Jens Stoye, Marcus Frohme, Jörg D. Hoheisel, Martin Vingron. Journal of Computational Biology, 7(3-4): 395-408, 2000.
    • DOI: 10.1089/106652700750050853
• Optimizing for success: a new score function for distantly related protein sequence comparison. Maricel Kann, Richard A. Goldstein.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2000, pp 177–182. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/332306.332536
• Reconstructing distances in physical maps of chromosomes with nonoverlapping probes. John Krececioglu, Sanjay Shete, Jonathan Arnold.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2000, pp 183–192. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/332306.332540
• UNRES: a united-residue force field for energy-based prediction of protein structure—orgin and significance of multibody terms. Adam Liwo, Jaroslaw Pillardy, Cezary Czaplewski, Jooyoung Lee, Daniel R. Ripoll, Malgorzata Groth, Sylwia Rodziewicz-Motowidlo, Rajmund Kamierkiewicz, Ryszard J. Wawak, Stanislaw Oldziej, Harold A. Scheraga.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2000, pp 193–200. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/332306.332544
• Pseudoknots in RNA secondary structures. Rune B. Lyngsø, Christian N. S. Pedersen.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2000, pp 201–209. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/332306.332551
  • Journal: Pseudoknots in RNA Secondary Structures. Rune B. Lyngsø, Christian N. S. Pedersen. BRICS Report Series, 7(1), 2000.
    • DOI: 10.7146/brics.v7i1.20129
• Extracting structured motifs using a suffix tree—algorithms and application to promoter consensus identification. Laurent Marsan, Marie-France Sagot.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2000, pp 210–219. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/332306.332553
  • Journal: Algorithms for Extracting Structured Motifs Using a Suffix Tree with an Application to Promoter and Regulatory Site Consensus Identification. Laurent Marsan, Marie-France Sagot. Journal of Computational Biology, 7(3-4): 345-362, 2000.
    • DOI: 10.1089/106652700750050826
• The E-CELL project: towards integrative simulation of cellular processes. Masaru Tomita, Kenta Hashimoto, Koichi Takahashi, Yuri Matsuzaki, Ryo Matsushima, Katsuyuki Yugi, Fumihiko Miyoshi, Hisako Nakano, Yusuke Saito, S. Shimizu, Yoichi Nakayama.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2000, pp 290–298. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/332306.332567
  • Journal: The E-CELL project: Towards integrative simulation of cellular processes. Masaru Tomita, Kenta Hashimoto, Koichi Takahashi, Yuri Matsuzaki, Ryo Matsushima, Kanako Saito, Katsuyuki Yugi, Fumihiko Miyoshi, Hisako Nakano, Sakura Tanida, Yûsuke Saito, Akiko Kawase, Naoko Watanabe, Thomas S. Simizu, Yoichi Nakayama. New Generation Computing, 18(1): 1-12, 2000.
    • DOI: 10.1007/bf03037563
• Protein structure determination using protein threading and sparse NMR data. Ying Xu, Dong Xu, Oakley H. Crawford, J. Ralph Einstein, Engin Serpersu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2000, pp 299–307. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/332306.332568
• A unified sequence-structure classification of protein sequences: combining sequence and structure in a map of the protein space. Golan Yona, Michael Levitt.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2000, pp 308–317. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/332306.332569
• A simple iterative approach to parameter optimization. Alexander Zein, Ralf Zimmer, Thomas Lengauer.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2000, pp 318–327. Association for Computing Machinery, New York, NY, USA.
    • DOI: 10.1145/332306.332570
  • Journal: A Simple Iterative Approach to Parameter Optimization. Alexander Zien, Ralf Zimmer, Thomas Lengauer. Journal of Computational Biology, 7(3-4): 483-501, 2000.
    • DOI: 10.1089/106652700750050907