@article{Akutsu2004,
  author = {Tatsuya Akutsu},
  title = {Efficient Extraction of Mapping Rules of Atoms from Enzymatic Reaction Data},
  journal = {Journal of Computational Biology},
  volume = {11},
  number = {2-3},
  pages = {449--462},
  year = {2004},
  doi = {10.1089/1066527041410337},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 1–8. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {1--8},
  proceedings_doi = {10.1145/640075.640076}
}

@inproceedings{Bafna2003,
  author = {Vineet Bafna, Nathan Edwards},
  title = {On de novo interpretation of tandem mass spectra for peptide identification},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2003, pp 9–18. Association for Computing Machinery, New York, NY, USA.},
  pages = {9--18},
  year = {2003},
  doi = {10.1145/640075.640077},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 9–18. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {9--18},
  proceedings_doi = {10.1145/640075.640077}
}

@inproceedings{Bafna2003,
  author = {Vineet Bafna, Bjarni V. Halldorsson, Russell Schwartz, Andrew G. Clark, Sorin Istrail},
  title = {Haplotypes and informative SNP selection algorithms: don't block out information},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2003, pp 19–27. Association for Computing Machinery, New York, NY, USA.},
  pages = {19--27},
  year = {2003},
  doi = {10.1145/640075.640078},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 19–27. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {19--27},
  proceedings_doi = {10.1145/640075.640078}
}

@inproceedings{Barash2003,
  author = {Yoseph Barash, Gal Elidan, Nir Friedman, Tommy Kaplan},
  title = {Modeling dependencies in protein-DNA binding sites},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2003, pp 28–37. Association for Computing Machinery, New York, NY, USA.},
  pages = {28--37},
  year = {2003},
  doi = {10.1145/640075.640079},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 28–37. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {28--37},
  proceedings_doi = {10.1145/640075.640079}
}

@inproceedings{Bejerano2003,
  author = {Gill Bejerano},
  title = {Efficient exact value computation and applications to biosequence analysis},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2003, pp 38–47. Association for Computing Machinery, New York, NY, USA.},
  pages = {38--47},
  year = {2003},
  doi = {10.1145/640075.640080},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 38–47. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {38--47},
  proceedings_doi = {10.1145/640075.640080}
}

@article{Ben‐Dor2004,
  author = {Amir Ben‐Dor, Tzvika Hartman, Richard M. Karp, Benno Schwikowski, Roded Sharan, Zohar Yakhini},
  title = {Towards Optimally Multiplexed Applications of Universal Arrays},
  journal = {Journal of Computational Biology},
  volume = {11},
  number = {2-3},
  pages = {476--492},
  year = {2004},
  doi = {10.1089/1066527041410373},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 48–56. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {48--56},
  proceedings_doi = {10.1145/640075.640081}
}

@inproceedings{Blanchette2003,
  author = {Mathieu Blanchette},
  title = {A comparative analysis method for detecting binding sites in coding regions},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2003, pp 57–66. Association for Computing Machinery, New York, NY, USA.},
  pages = {57--66},
  year = {2003},
  doi = {10.1145/640075.640082},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 57–66. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {57--66},
  proceedings_doi = {10.1145/640075.640082}
}

@article{Buhler2005,
  author = {Jeremy Buhler, Uri Keich, Yanni Sun},
  title = {Designing seeds for similarity search in genomic DNA},
  journal = {Journal of Computer and System Sciences},
  volume = {70},
  number = {3},
  pages = {342--363},
  year = {2005},
  doi = {10.1016/j.jcss.2004.12.003},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 67–75. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {67--75},
  proceedings_doi = {10.1145/640075.640083}
}

@article{Chor2005,
  author = {Benny Chor, Michael D. Hendy, Sagi Snir},
  title = {Maximum Likelihood Jukes-Cantor Triplets: Analytic Solutions},
  journal = {Molecular Biology and Evolution},
  volume = {23},
  number = {3},
  pages = {626--632},
  year = {2005},
  doi = {10.1093/molbev/msj069},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 76–83. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {76--83},
  proceedings_doi = {10.1145/640075.640084}
}

@article{Chiang2003,
  author = {Derek Y. Chiang, Alan M Moses, Manolis Kellis, Eric S. Lander, Michael B. Eisen},
  title = {Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts},
  journal = {Genome Biology},
  volume = {4},
  number = {7},
  pages = {R43},
  year = {2003},
  doi = {10.1186/gb-2003-4-7-r43},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 84–93. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {84--93},
  proceedings_doi = {10.1145/640075.640085}
}

@article{Deng2004,
  author = {Minghua Deng, Ting Chen, Fengzhu Sun},
  title = {An Integrated Probabilistic Model for Functional Prediction of Proteins},
  journal = {Journal of Computational Biology},
  volume = {11},
  number = {2-3},
  pages = {463--475},
  year = {2004},
  doi = {10.1089/1066527041410346},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 95–103. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {95--103},
  proceedings_doi = {10.1145/640075.640087}
}

@article{Halperin2004,
  author = {Eran Halperin, Eleazar Eskin},
  title = {Haplotype reconstruction from genotype data using Imperfect Phylogeny},
  journal = {Bioinformatics},
  volume = {20},
  number = {12},
  pages = {1842--1849},
  year = {2004},
  doi = {10.1093/bioinformatics/bth149},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 104–113. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {104--113},
  proceedings_doi = {10.1145/640075.640088}
}

@article{Fishelson2004,
  author = {M. Fishelson, Dan Geiger},
  title = {Optimizing Exact Genetic Linkage Computations},
  journal = {Journal of Computational Biology},
  volume = {11},
  number = {2-3},
  pages = {263--275},
  year = {2004},
  doi = {10.1089/1066527041410409},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 114–121. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {114--121},
  proceedings_doi = {10.1145/640075.640089}
}

@inproceedings{Gionis2003,
  author = {Aristides Gionis, Heikki Mannila},
  title = {Finding recurrent sources in sequences},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2003, pp 123–130. Association for Computing Machinery, New York, NY, USA.},
  pages = {123--130},
  year = {2003},
  doi = {10.1145/640075.640091},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 123–130. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {123--130},
  proceedings_doi = {10.1145/640075.640091}
}

@article{Greenspan2004,
  author = {Gideon Greenspan, Dan Geiger},
  title = {Model-Based Inference of Haplotype Block Variation},
  journal = {Journal of Computational Biology},
  volume = {11},
  number = {2-3},
  pages = {493--504},
  year = {2004},
  doi = {10.1089/1066527041410300},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 131–137. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {131--137},
  proceedings_doi = {10.1145/640075.640092}
}

@article{Heger2004,
  author = {Andreas Heger, Michael Lappé, Liisa Holm},
  title = {Accurate Detection of Very Sparse Sequence Motifs},
  journal = {Journal of Computational Biology},
  volume = {11},
  number = {5},
  pages = {843--857},
  year = {2004},
  doi = {10.1089/cmb.2004.11.843},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 139–147. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {139--147},
  proceedings_doi = {10.1145/640075.640094}
}

@article{Kahng2004,
  author = {Andrew B. Kahng, Ion Măndoiu, Pavel A. Pevzner, Sherief Reda, Alex Zelikovsky},
  title = {Scalable Heuristics for Design of DNA Probe Arrays},
  journal = {Journal of Computational Biology},
  volume = {11},
  number = {2-3},
  pages = {429--447},
  year = {2004},
  doi = {10.1089/1066527041410391},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 148–156. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {148--156},
  proceedings_doi = {10.1145/640075.640095}
}

@inproceedings{Kamvysselis2003,
  author = {Manolis Kamvysselis, Nick Patterson, Bruce Birren, Bonnie Berger, Eric Lander},
  title = {Whole-genome comparative annotation and regulatory motif discovery in multiple yeast species},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2003, pp 157–166. Association for Computing Machinery, New York, NY, USA.},
  pages = {157--166},
  year = {2003},
  doi = {10.1145/640075.640096},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 157–166. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {157--166},
  proceedings_doi = {10.1145/640075.640096}
}

@article{Krishnapuram2004,
  author = {Balaji Krishnapuram, Lawrence Carin, Alexander J. Hartemink},
  title = {Joint Classifier and Feature Optimization for Comprehensive Cancer Diagnosis Using Gene Expression Data},
  journal = {Journal of Computational Biology},
  volume = {11},
  number = {2-3},
  pages = {227--242},
  year = {2004},
  doi = {10.1089/1066527041410463},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 167–175. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {167--175},
  proceedings_doi = {10.1145/640075.640097}
}

@article{Langmead2004,
  author = {Christopher J. Langmead, Anthony K. Yan, Ryan Lilien, Lincong Wang, Bruce R. Donald},
  title = {A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments},
  journal = {Journal of Computational Biology},
  volume = {11},
  number = {2-3},
  pages = {277--298},
  year = {2004},
  doi = {10.1089/1066527041410436},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 176–187. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {176--187},
  proceedings_doi = {10.1145/640075.640098}
}

@inproceedings{Lesh2003,
  author = {N. Lesh, M. Mitzenmacher, S. Whitesides},
  title = {A complete and effective move set for simplified protein folding},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2003, pp 188–195. Association for Computing Machinery, New York, NY, USA.},
  pages = {188--195},
  year = {2003},
  doi = {10.1145/640075.640099},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 188–195. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {188--195},
  proceedings_doi = {10.1145/640075.640099}
}

@inproceedings{Li2003,
  author = {Jing Li, Tao Jiang},
  title = {Efficient rule-based haplotyping algorithms for pedigree data},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2003, pp 197–206. Association for Computing Machinery, New York, NY, USA.},
  pages = {197--206},
  year = {2003},
  doi = {10.1145/640075.640101},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 197–206. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {197--206},
  proceedings_doi = {10.1145/640075.640101}
}

@article{Li2004,
  author = {Lei M. Li, Jong Hyun Kim, Michael S. Waterman},
  title = {Haplotype Reconstruction from SNP Alignment},
  journal = {Journal of Computational Biology},
  volume = {11},
  number = {2-3},
  pages = {505--516},
  year = {2004},
  doi = {10.1089/1066527041410454},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 207–216. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {207--216},
  proceedings_doi = {10.1145/640075.640102}
}

@article{Li2004,
  author = {Wentian Li, Fengzhu Sun, Ivo Große},
  title = {Extreme Value Distribution Based Gene Selection Criteria for Discriminant Microarray Data Analysis Using Logistic Regression},
  journal = {Journal of Computational Biology},
  volume = {11},
  number = {2-3},
  pages = {215--226},
  year = {2004},
  doi = {10.1089/1066527041410445},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 217–223. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {217--223},
  proceedings_doi = {10.1145/640075.640103},
  preprint_id = {arXiv:q-bio/0403038},
  preprint_doi = {10.48550/arXiv.q-bio/0403038}
}

@article{Nagarajan2004,
  author = {Niranjan Nagarajan, Golan Yona},
  title = {Automatic prediction of protein domains from sequence information using a hybrid learning system},
  journal = {Bioinformatics},
  volume = {20},
  number = {9},
  pages = {1335--1360},
  year = {2004},
  doi = {10.1093/bioinformatics/bth086},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 224–234. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {224--234},
  proceedings_doi = {10.1145/640075.640104}
}

@inproceedings{Pe'er2003,
  author = {Itsik Pe'er, Jacques S. Beckmann},
  title = {Resolution of haplotypes and haplotype frequencies from SNP genotypes of pooled samples},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2003, pp 237–246. Association for Computing Machinery, New York, NY, USA.},
  pages = {237--246},
  year = {2003},
  doi = {10.1145/640075.640107},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 237–246. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {237--246},
  proceedings_doi = {10.1145/640075.640107}
}

@article{Pevzner2003,
  author = {Pavel Pevzner, Glenn Tesler},
  title = {Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution},
  journal = {Proceedings of the National Academy of Sciences},
  volume = {100 (13) 7662-7667},
  year = {2003},
  doi = {10.1073/pnas.1330369100},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 247–256. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {247--256},
  proceedings_doi = {10.1145/640075.640108}
}

@inproceedings{Roskin2003,
  author = {Krishna M. Roskin, Mark Diekhans, David Haussler},
  title = {Scoring two-species local alignments to try to statistically separate neutrally evolving from selected DNA segments},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2003, pp 257–266. Association for Computing Machinery, New York, NY, USA.},
  pages = {257--266},
  year = {2003},
  doi = {10.1145/640075.640109},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 257–266. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {257--266},
  proceedings_doi = {10.1145/640075.640109}
}

@article{Lotan2004,
  author = {Itay Lotan, Fabian Schwarzer},
  title = {Approximation of Protein Structure for Fast Similarity Measures},
  journal = {Journal of Computational Biology},
  volume = {11},
  number = {2-3},
  pages = {299--317},
  year = {2004},
  doi = {10.1089/1066527041410355},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 267–276. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {267--276},
  proceedings_doi = {10.1145/640075.640110}
}

@article{Siepel2004,
  author = {Adam Siepel, David Haussler},
  title = {Combining Phylogenetic and Hidden Markov Models in Biosequence Analysis},
  journal = {Journal of Computational Biology},
  volume = {11},
  number = {2-3},
  pages = {413--428},
  year = {2004},
  doi = {10.1089/1066527041410472},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 277–286. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {277--286},
  proceedings_doi = {10.1145/640075.640111}
}

@inproceedings{Syed2003,
  author = {Umar Syed, Golan Yona},
  title = {Using a mixture of probabilistic decision trees for direct prediction of protein function},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2003, pp 289–300. Association for Computing Machinery, New York, NY, USA.},
  pages = {289--300},
  year = {2003},
  doi = {10.1145/640075.640114},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 289–300. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {289--300},
  proceedings_doi = {10.1145/640075.640114}
}

@inproceedings{Tanay2003,
  author = {Amos Tanay, Ron Shamir},
  title = {Modeling transcription programs: inferring binding site activity and dose-response model optimization},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2003, pp 301–310. Association for Computing Machinery, New York, NY, USA.},
  pages = {301--310},
  year = {2003},
  doi = {10.1145/640075.640115},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 301–310. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {301--310},
  proceedings_doi = {10.1145/640075.640115}
}

@article{Yeang2004,
  author = {Chen‐Hsiang Yeang, Trey Ideker, Tommi Jaakkola},
  title = {Physical Network Models},
  journal = {Journal of Computational Biology},
  volume = {11},
  number = {2-3},
  pages = {243--262},
  year = {2004},
  doi = {10.1089/1066527041410382},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 312–321. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {312--321},
  proceedings_doi = {10.1145/640075.640117}
}

@article{Yeo2004,
  author = {G Yeo, Christopher B. Burge},
  title = {Maximum Entropy Modeling of Short Sequence Motifs with Applications to RNA Splicing Signals},
  journal = {Journal of Computational Biology},
  volume = {11},
  number = {2-3},
  pages = {377--394},
  year = {2004},
  doi = {10.1089/1066527041410418},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 322–331. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {322--331},
  proceedings_doi = {10.1145/640075.640118}
}

@article{Zhang2003,
  author = {Kui Zhang, Fengzhu Sun, Michael S. Waterman, Ting Chen},
  title = {Haplotype Block Partition with Limited Resources and Applications to Human Chromosome 21 Haplotype Data},
  journal = {The American Journal of Human Genetics},
  volume = {73},
  number = {1},
  pages = {63--73},
  year = {2003},
  doi = {10.1086/376437},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2003, pp 332–340. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {332--340},
  proceedings_doi = {10.1145/640075.640119}
}