@article{Kimmel2005,
  author = {Gad Kimmel, Ron Shamir},
  title = {GERBIL: genotype resolution and block identification using likelihood},
  journal = {Proc Natl Acad Sci USA},
  volume = {102 (1) 158-162},
  year = {2005},
  doi = {10.1073/pnas.0404730102},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 2–9. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {2--9},
  proceedings_doi = {10.1145/974614.974616}
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@inproceedings{Halperin2004,
  author = {Eran Halperin, Richard M. Karp},
  title = {Perfect phylogeny and haplotype assignment},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2004, pp 10–19. Association for Computing Machinery, New York, NY, USA.},
  pages = {10--19},
  year = {2004},
  doi = {10.1145/974614.974617},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 10–19. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {10--19},
  proceedings_doi = {10.1145/974614.974617}
}

@article{Li2005,
  author = {Jing Li, Tao Jiang},
  title = {Computing the minimum recombinant haplotype configuration from incomplete genotype data on a pedigree by integer linear programming},
  journal = {Journal of Computational Biology},
  volume = {12},
  number = {6},
  pages = {719--739},
  year = {2005},
  doi = {10.1089/cmb.2005.12.719},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 20–29. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {20--29},
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@article{Sankoff2005,
  author = {David Sankoff, Phil Trinh},
  title = {Chromosomal breakpoint reuse in genome sequence rearrangement},
  journal = {Journal of Computational Biology},
  volume = {12},
  number = {6},
  pages = {812--821},
  year = {2005},
  doi = {10.1089/cmb.2005.12.812},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 30–35. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {30--35},
  proceedings_doi = {10.1145/974614.974619}
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@article{Beerenwinkel2005,
  author = {Niko Beerenwinkel, Jörg Rahnenführer, Martin Däumer, Daniel Hoffmann, Rolf Kaiser, Joachim Selbig, Thomas Lengauer},
  title = {Learning multiple evolutionary pathways from cross-sectional data},
  journal = {Journal of Computational Biology},
  volume = {12},
  number = {6},
  pages = {584--598},
  year = {2005},
  doi = {10.1089/cmb.2005.12.584},
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  proceedings_pages = {36--44},
  proceedings_doi = {10.1145/974614.974620}
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@article{Lilien2005,
  author = {Ryan Lilien, Brian W. Stevens, Amy C. Anderson, Bruce R. Donald},
  title = {A Novel Ensemble-Based Scoring and Search Algorithm for Protein Redesign and Its Application to Modify the Substrate Specificity of the Gramicidin Synthetase A Phenylalanine Adenylation Enzyme},
  journal = {Journal of Computational Biology},
  volume = {12},
  number = {6},
  pages = {740--761},
  year = {2005},
  doi = {10.1089/cmb.2005.12.740},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 46–57. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {46--57},
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@article{Bailey-Kellogg2005,
  author = {Chris Bailey-Kellogg, Sheetal Chainraj, Gopal Pandurangan},
  title = {A random graph approach to NMR sequential assignment},
  journal = {Journal of Computational Biology},
  volume = {12},
  number = {6},
  pages = {569--583},
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  doi = {10.1089/cmb.2005.12.569},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 58–67. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {58--67},
  proceedings_doi = {10.1145/974614.974623}
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@article{Zhao2005,
  author = {Xiaoyue Zhao, Haiyan Huang, Terence P. Speed},
  title = {Finding Short DNA Motifs Using Permuted Markov Models},
  journal = {Journal of Computational Biology},
  volume = {12},
  number = {6},
  pages = {894--906},
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  doi = {10.1089/cmb.2005.12.894},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 68–75. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {68--75},
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@article{Sun2005,
  author = {Yanni Sun, Jeremy Buhler},
  title = {Designing Multiple Simultaneous Seeds for DNA Similarity Search},
  journal = {Journal of Computational Biology},
  volume = {12},
  number = {6},
  pages = {847--861},
  year = {2005},
  doi = {10.1089/cmb.2005.12.847},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 76–84. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {76--84},
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@inproceedings{Kececioglu2004,
  author = {John Kececioglu, Dean Starrett},
  title = {Aligning alignments exactly},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2004, pp 85–96. Association for Computing Machinery, New York, NY, USA.},
  pages = {85--96},
  year = {2004},
  doi = {10.1145/974614.974626},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 85–96. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {85--96},
  proceedings_doi = {10.1145/974614.974626}
}

@article{Wu2005,
  author = {Zhijin Wu, Rafael A. Irizarry},
  title = {Stochastic Models Inspired by Hybridization Theory for Short Oligonucleotide Arrays},
  journal = {Journal of Computational Biology},
  volume = {12},
  number = {6},
  pages = {882--893},
  year = {2005},
  doi = {10.1089/cmb.2005.12.882},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 98–106. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {98--106},
  proceedings_doi = {10.1145/974614.974628}
}

@article{Ledent2005,
  author = {Sabrina Ledent, Stéphane Robin},
  title = {Checking Homogeneity of Motifs' Distribution in Heterogenous Sequences},
  journal = {Journal of Computational Biology},
  volume = {12},
  number = {6},
  pages = {672--685},
  year = {2005},
  doi = {10.1089/cmb.2005.12.672},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 107–114. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {107--114},
  proceedings_doi = {10.1145/974614.974629}
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@inproceedings{Eskin2004,
  author = {Eleazar Eskin},
  title = {From profiles to patterns and back again: a branch and bound algorithm for finding near optimal motif profiles},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2004, pp 115–124. Association for Computing Machinery, New York, NY, USA.},
  pages = {115--124},
  year = {2004},
  doi = {10.1145/974614.974630},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 115–124. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {115--124},
  proceedings_doi = {10.1145/974614.974630}
}

@article{Leung2005,
  author = {Henry C. M. Leung, Francis Y. L. Chin, SM Yiu, Roni Rosenfeld, W.W. Tsang},
  title = {Finding Motifs with Insufficient Number of Strong Binding Sites},
  journal = {Journal of Computational Biology},
  volume = {12},
  number = {6},
  pages = {686--701},
  year = {2005},
  doi = {10.1089/cmb.2005.12.686},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 125–132. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {125--132},
  proceedings_doi = {10.1145/974614.974631}
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@article{Morgante2005,
  author = {Michele Morgante, Alberto Policriti, Nicola Vitacolonna, Andrea Zuccolo},
  title = {Structured Motifs Search},
  journal = {Journal of Computational Biology},
  volume = {12},
  number = {8},
  pages = {1065--1082},
  year = {2005},
  doi = {10.1089/cmb.2005.12.1065},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 133–139. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {133--139},
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@article{Segal2005,
  author = {Eran Segal, Roded Sharan},
  title = {A Discriminative Model for Identifying Spatial cis-Regulatory Modules},
  journal = {Journal of Computational Biology},
  volume = {12},
  number = {6},
  pages = {822--834},
  year = {2005},
  doi = {10.1089/cmb.2005.12.822},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 141–149. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {141--149},
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@inproceedings{Farach-Colton2004,
  author = {Martin Farach-Colton, Yang Huang, John L. L. Woolford},
  title = {Discovering temporal relations in molecular pathways using protein-protein interactions},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2004, pp 150–156. Association for Computing Machinery, New York, NY, USA.},
  pages = {150--156},
  year = {2004},
  doi = {10.1145/974614.974635},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 150–156. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {150--156},
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@inproceedings{Peng2004,
  author = {Hanchuan Peng, Eugene W. Myers},
  title = {Comparing in situ mRNA expression patterns of drosophila embryos},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2004, pp 157–166. Association for Computing Machinery, New York, NY, USA.},
  pages = {157--166},
  year = {2004},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 157–166. Association for Computing Machinery, New York, NY, USA.},
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@article{Battle2005,
  author = {Alexis Battle, Eran Segal, Daphne Koller},
  title = {Probabilistic Discovery of Overlapping Cellular Processes and Their Regulation},
  journal = {Journal of Computational Biology},
  volume = {12},
  number = {7},
  pages = {909--927},
  year = {2005},
  doi = {10.1089/cmb.2005.12.909},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 167–176. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {167--176},
  proceedings_doi = {10.1145/974614.974637}
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@inproceedings{Siepel2004,
  author = {Adam Siepel, David Haussler},
  title = {Computational identification of evolutionarily conserved exons},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2004, pp 177–186. Association for Computing Machinery, New York, NY, USA.},
  pages = {177--186},
  year = {2004},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 177–186. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {177--186},
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@article{Chatterji2005,
  author = {Sourav Chatterji, Lior Pachter},
  title = {Large Multiple Organism Gene Finding by Collapsed Gibbs Sampling},
  journal = {Journal of Computational Biology},
  volume = {12},
  number = {6},
  pages = {599--608},
  year = {2005},
  doi = {10.1089/cmb.2005.12.599},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 187–193. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {187--193},
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@article{Erdmann2005,
  author = {Michael Erdmann},
  title = {Protein Similarity from Knot Theory: Geometric Convolution and Line Weavings},
  journal = {Journal of Computational Biology},
  volume = {12},
  number = {6},
  pages = {609--637},
  year = {2005},
  doi = {10.1089/cmb.2005.12.609},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 195–204. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {195--204},
  proceedings_doi = {10.1145/974614.974641}
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@inproceedings{Ban2004,
  author = {Yih-En Andrew Ban, Herbert Edelsbrunner, Johannes Rudolph},
  title = {Interface surfaces for protein-protein complexes},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2004, pp 205–212. Association for Computing Machinery, New York, NY, USA.},
  pages = {205--212},
  year = {2004},
  doi = {10.1145/974614.974642},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 205–212. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {205--212},
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@article{Pevzner2004,
  author = {Paul A. Pevzner, Haixu Tang, Glenn Tesler},
  title = {De Novo Repeat Classification and Fragment Assembly},
  journal = {Genome Research},
  volume = {14},
  number = {9},
  pages = {1786--1796},
  year = {2004},
  doi = {10.1101/gr.2395204},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 213–222. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {213--222},
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@article{Wexler2005,
  author = {Ydo Wexler, Zohar Yakhini, Yechezkel Kashi, Dan Geiger},
  title = {Finding Approximate Tandem Repeats in Genomic Sequences},
  journal = {Journal of Computational Biology},
  volume = {12},
  number = {7},
  pages = {928--942},
  year = {2005},
  doi = {10.1089/cmb.2005.12.928},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 223–232. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {223--232},
  proceedings_doi = {10.1145/974614.974644}
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@article{Lippert2005,
  author = {Ross A. Lippert, Xiaoyue Zhao, Liliana Florea, Clark Mobarry, Sorin Istrail},
  title = {Finding Anchors for Genomic Sequence Comparison},
  journal = {Journal of Computational Biology},
  volume = {12},
  number = {6},
  pages = {762--776},
  year = {2005},
  doi = {10.1089/cmb.2005.12.762},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 233–241. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {233--241},
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@article{Weinberg2004,
  author = {Zasha Weinberg, Walter L. Ruzzo},
  title = {Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy},
  journal = {Bioinformatics},
  volume = {20},
  number = {suppl_1},
  pages = {i334--i341},
  year = {2004},
  doi = {10.1093/bioinformatics/bth925},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 243–251. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {243--251},
  proceedings_doi = {10.1145/974614.974647}
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@article{Tang2005,
  author = {Xinyu Tang, Bonnie Kirkpatrick, Shawna Thomas, Guang Song, Nancy M. Amato},
  title = {Using Motion Planning to Study RNA Folding Kinetics},
  journal = {Journal of Computational Biology},
  volume = {12},
  number = {6},
  pages = {862--881},
  year = {2005},
  doi = {10.1089/cmb.2005.12.862},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 252–261. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {252--261},
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@article{Li2005,
  author = {Haifeng Li, Tao Jiang},
  title = {A Class of Edit Kernels for SVMs to Predict Translation Initiation Sites in Eukaryotic mRNAs},
  journal = {Journal of Computational Biology},
  volume = {12},
  number = {6},
  pages = {702--718},
  year = {2005},
  doi = {10.1089/cmb.2005.12.702},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 262–271. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {262--271},
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@article{He2005,
  author = {Xin He, Michael H. Goldwasser},
  title = {Identifying Conserved Gene Clusters in the Presence of Homology Families},
  journal = {Journal of Computational Biology},
  volume = {12},
  number = {6},
  pages = {638--656},
  year = {2005},
  doi = {10.1089/cmb.2005.12.638},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 272–280. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {272--280},
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@article{Sharan2005,
  author = {Roded Sharan, Trey Ideker, Brian Kelley, Ron Shamir, Richard M. Karp},
  title = {Identification of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein Interaction Data},
  journal = {Journal of Computational Biology},
  volume = {12},
  number = {6},
  pages = {835--846},
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  doi = {10.1089/cmb.2005.12.835},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 282–289. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {282--289},
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@inproceedings{Meyerguz2004,
  author = {Leonid Meyerguz, David Kempe, Jon Kleinberg, Ron Elber},
  title = {The evolutionary capacity of protein structures},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2004, pp 290–297. Association for Computing Machinery, New York, NY, USA.},
  pages = {290--297},
  year = {2004},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 290–297. Association for Computing Machinery, New York, NY, USA.},
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@article{Menke2005,
  author = {Matthew Menke, Jonathan King, Bonnie Berger, Lenore Cowen},
  title = {Wrap-and-Pack: A New Paradigm for Beta Structural Motif Recognition with Application to Recognizing Beta Trefoils},
  journal = {Journal of Computational Biology},
  volume = {12},
  number = {6},
  pages = {777--795},
  year = {2005},
  doi = {10.1089/cmb.2005.12.777},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 298–307. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {298--307},
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@inproceedings{Huan2004,
  author = {Jun Huan, Wei Wang, Deepak Bandyopadhyay, Jack Snoeyink, Jan Prins, Alexander Tropsha},
  title = {Mining protein family specific residue packing patterns from protein structure graphs},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2004, pp 308–315. Association for Computing Machinery, New York, NY, USA.},
  pages = {308--315},
  year = {2004},
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@inproceedings{Górecki2004,
  author = {Pawel Górecki},
  title = {Reconciliation problems for duplication, loss and horizontal gene transfer},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2004, pp 316–325. Association for Computing Machinery, New York, NY, USA.},
  pages = {316--325},
  year = {2004},
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  proceedings_pages = {316--325},
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@inproceedings{Arvestad2004,
  author = {Lars Arvestad, Ann-Charlotte Berglund, Jens Lagergren, Bengt Sennblad},
  title = {Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2004, pp 326–335. Association for Computing Machinery, New York, NY, USA.},
  pages = {326--335},
  year = {2004},
  doi = {10.1145/974614.974657},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 326–335. Association for Computing Machinery, New York, NY, USA.},
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  proceedings_doi = {10.1145/974614.974657}
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@article{Nakhleh2005,
  author = {Luay Nakhleh, Tandy Warnow, C. Randal Linder, Katherine St. John},
  title = {Reconstructing Reticulate Evolution in Species—Theory and Practice},
  journal = {Journal of Computational Biology},
  volume = {12},
  number = {6},
  pages = {796--811},
  year = {2005},
  doi = {10.1089/cmb.2005.12.796},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 337–346. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {337--346},
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@article{Tofigh2011,
  author = {Ali Asghar Tofigh, Michael Hallett, Jens Lagergren},
  title = {Simultaneous Identification of Duplications and Lateral Gene Transfers},
  journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics},
  volume = {8},
  number = {2},
  pages = {517--535},
  year = {2011},
  doi = {10.1109/tcbb.2010.14},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2004, pp 347–356. Association for Computing Machinery, New York, NY, USA.},
  proceedings_pages = {347--356},
  proceedings_doi = {10.1145/974614.974660}
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