4. RECOMB 2000: Tokyo, Japan

• Tatsuya Akutsu, Hiroki Arimura, Shinichi Shimozono:
  On approximation algorithms for local multiple alignment. 1-7
  
• Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara:
  Algorithms for identifying Boolean networks and related biological networks based on matrix multiplication and fingerprint function. 8-14
  
• Ernst Althaus, Oliver Kohlbacher, Hans-Peter Lenhof, Peter Müller:
  A combinatorial approach to protein docking with flexible side-chains. 15-24
  
• Alberto Apostolico, Gill Bejerano:
  Optimal amnesic probabilistic automata or how to learn and classify proteins in linear time and space. 25-32
  
• Christopher Bailey-Kellogg, Alik Widge, John J. Kelley, Marcelo J. Berardi, John H. Bushweller, Bruce Randall Donald:
  The NOESY jigsaw: automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data. 33-44
  
• Serafim Batzoglou, Bonnie Berger, Jill P. Mesirov, Eric S. Lander:
  Sequencing a genome by walking with clone-end sequences: a mathematical analysis (abstract). 45
  
• Serafim Batzoglou, Lior Pachter, Jill P. Mesirov, Bonnie Berger, Eric S. Lander:
  Human and mouse gene structure: comparative analysis and application to exon prediction. 46-53
  
• Amir Ben-Dor, Laurakay Bruhn, Nir Friedman, Iftach Nachman, Michèl Schummer, Zohar Yakhini:
  Tissue classification with gene expression profiles. 54-64
  
• Amir Ben-Dor, Richard M. Karp, Benno Schwikowski, Zohar Yakhini:
  Universal DNA tag systems: a combinatorial design scheme. 65-75
  
• Jadwiga R. Bienkowska, Lihua Yu, Sophia Zarakhovich, Robert G. Rogers, Temple F. Smith:
  Comprehensive statistical method for protein fold recognition. 76-85
  
• Ralf Bundschuh:
  An analytic approach to significance assessment in local sequence alignment with gaps. 86-95
  
• Kevin Chen, Dannie Durand, Martin Farach-Colton:
  Notung: dating gene duplications using gene family trees. 96-106
  
• Xin Chen, Sam Kwong, Ming Li:
  A compression algorithm for DNA sequences and its applications in genome comparison. 107
  
• Benny Chor, Michael D. Hendy, Barbara R. Holland, David Penny:
  Multiple maxima of likelihood in phylogenetic trees: an analytic approach. 108-117
  
• Richard Desper, Martin Vingron:
  Tree fitting: an algebraic approach using profile distances. 119-126
  
• Nir Friedman, Michal Linial, Iftach Nachman, Dana Pe'er:
  Using Bayesian networks to analyze expression data. 127-135
  
• Walter Gilbert:
  Invited presentation: introns and modules in ancient conserved genes (abstract only). 136
  
• Takashi Gojobori, T. Daniel Andrews, Takeshi Itoh:
  Evolutionary features of genomes as disclosed by comparative analysis of complete genome sequences (abstract only). 137
  
• Michael T. Hallett, Jens Lagergren:
  New algorithms for the duplication-loss model. 138-146
  
• Reece Hart, Ajay K. Royyuru, Gustavo Stolovitzky, Andrea Califano:
  Systematic and automated discovery of patterns in PROSITE families. 147-154
  
• Steffen Heber, Jens Stoye, Jörg D. Hoheisel, Martin Vingron:
  Contig selection in physical mapping. 155-164
  
• Steffen Hennig, Ralf Herwig, Matthew Clark, Pia Aanstad, A. Musa, John O'Brien, C. Bull, Uwe Radelof, Georgia Panopoulou, Albert J. Poustka, Hans Lehrach:
  A data-analysis pipeline for large-scale gene expression analysis. 165-173
  
• Leroy E. Hood:
  Computing life and global technologies (abstract only). 174
  
• Henrik Kaessmann, Ingo Ebersberger, Victor Wiebe, Rikard Erlandsson, Jim F. Wilson, Carsten Schwarz, Michaela Winkler, Svante Pääbo:
  DNA sequence variation among humans and apes (abstract only). 175
  
• Minoru Kanehisa:
  Sequence comparison to graph comparison--a new generation of algorithms for network analysis of interacting molecules (abstract only). 176
  
• Maricel Kann, Richard A. Goldstein:
  Optimizing for success: a new score function for distantly related protein sequence comparison. 177-182
  
• John D. Kececioglu, Sanjay Shete, Jonathan Arnold:
  Reconstructing distances in physical maps of chromosomes with nonoverlapping probes. 183-192
  
• Adam Liwo, Jaroslaw Pillardy, Cezary Czaplewski, Jooyoung Lee, Daniel R. Ripoll, Malgorzata Groth, Sylwia Rodziewicz-Motowidlo, Rajmund Kazmierkiewicz, Ryszard J. Wawak, Stanislaw Oldziej, Harold A. Scheraga:
  UNRES: a united-residue force field for energy-based prediction of protein structure - orgin and significance of multibody terms. 193-200
  
• Rune B. Lyngsø, Christian N. S. Pedersen:
  Pseudoknots in RNA secondary structures. 201-209
  
• Laurent Marsan, Marie-France Sagot:
  Extracting structured motifs using a suffix tree - algorithms and application to promoter consensus identification. 210-219
  
• Yvonne C. Martin, Mark G. Bures:
  Molecular diversity: strategies and concerns (abstract only). 220
  
• Yusuke Nakamura:
  Human genome analysis and medicine in the 21st century (abstract only). 221-222
  
• Y. Zenmei Ohkubo, Gordon M. Crippen:
  Determining contact energy function for continuous state models of globular protein conformations. 223-230
  
• Pavel A. Pevzner, Vlado Dancík, Chris L. Tang:
  Mutation-tolerant protein identification by mass-spectrometry. 231-236
  
• Elon Portugaly, Michal Linial:
  Probabilities for having a new fold on the basis of a map of all protein sequences. 237-244
  
• Franco P. Preparata, Eli Upfal:
  Sequencing-by-hybridization at the information-theory bound: an optimal algorithm. 245-253
  
• David Sankoff, David Bryant, Mélanie Deneault, B. Franz Lang, Gertraud Burger:
  Early eukaryote evolution based on mitochondrial gene order breakpoints. 254-262
  
• Donna K. Slonim, Pablo Tamayo, Jill P. Mesirov, Todd R. Golub, Eric S. Lander:
  Class prediction and discovery using gene expression data. 263-272
  
• Jon M. Sorenson, Teresa Head-Gordon:
  Matching simulation and experiment (extended abstract): a new simplified model for simulating protein folding. 273-282
  
• Sarah A. Teichmann, Cyrus Chothia, George M. Church, Jong Park:
  PDB_ISL: an intermediate sequence library for protein structure assignment. 283-289
  
• Masaru Tomita, Kenta Hashimoto, Koichi Takahashi, Yuri Matsuzaki, Ryo Matsushima, Katsuyuki Yugi, Fumihiko Miyoshi, Hisako Nakano, Yusuke Saito, S. Shimizu, Yoichi Nakayama:
  The E-CELL project: towards integrative simulation of cellular processes. 290-298
  
• Ying Xu, Dong Xu, Oakley H. Crawford, J. Ralph Einstein, Engin Serpersu:
  Protein structure determination using protein threading and sparse NMR data (extended abstract). 299-307
  
• Golan Yona, Michael Levitt:
  A unified sequence-structure classification of protein sequences: combining sequence and structure in a map of the protein space. 308-317
  
• Alexander Zien, Ralf Zimmer, Thomas Lengauer:
  A simple iterative approach to parameter optimization. 318-327
  

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