@article{Thankachan2016,
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@article{Amir2015,
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@article{Ben-Bassat2016,
  author = {Ilan Ben-Bassat, Benny Chor},
  title = {CRISPR Detection From Short Reads Using Partial Overlap Graphs},
  journal = {Journal of Computational Biology},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 16-27, Springer, Cham.},
  proceedings_volume = {9029},
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@article{Berger2020,
  author = {Emily R. Berger, Deniz Yorukoglu, Lillian Zhang, Sarah K. Nyquist, Alex K. Shalek, Manolis Kellis, Ibrahim Numanagić, Bonnie Berger},
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@article{Bishara2015,
  author = {Alex Bishara, Yuling Liu, Ziming Weng, Dorna Kashef-Haghighi, Daniel E. Newburger, Robert West, Arend Sidow, Serafim Batzoglou},
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@article{Biswas2016,
  author = {Surojit Biswas, Meredith McDonald, Derek S. Lundberg, Jeffery L. Dangl, Vladimir Jojic},
  title = {Learning Microbial Interaction Networks from Metagenomic Count Data},
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  doi = {10.1089/cmb.2016.0061},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 32-43, Springer, Cham.},
  proceedings_volume = {9029},
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  preprint_id = {arXiv:1412.0207},
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@article{Bonissone2016,
  author = {Stefano R. Bonissone, Pavel A. Pevzner},
  title = {Immunoglobulin Classification Using the Colored Antibody Graph},
  journal = {Journal of Computational Biology},
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  doi = {10.1089/cmb.2016.0010},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 44-59, Springer, Cham.},
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@article{Canzar2016,
  author = {Stefan Canzar, Sandro Andreotti, David Weese, Knut Reinert, Gunnar W. Klau},
  title = {CIDANE: comprehensive isoform discovery and abundance estimation},
  journal = {Genome Biology},
  volume = {17: 16},
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  doi = {10.1186/s13059-015-0865-0},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 60-61, Springer, Cham.},
  proceedings_volume = {9029},
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@article{Cho2016,
  author = {Hyunghoon Cho, Bonnie Berger, Jian Peng},
  title = {Compact Integration of Multi-Network Topology for Functional Analysis of Genes},
  journal = {Cell Systems},
  volume = {3},
  number = {6},
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  doi = {10.1016/j.cels.2016.10.017},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 62-64, Springer, Cham.},
  proceedings_volume = {9029},
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  preprint_id = {arXiv:1504.02719},
  preprint_doi = {10.48550/arXiv.1504.02719}
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@article{Dührkop2016,
  author = {Kai Dührkop, Sebastian Böcker},
  title = {Fragmentation trees reloaded},
  journal = {Journal of Cheminformatics},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 65-79, Springer, Cham.},
  proceedings_volume = {9029},
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  preprint_id = {arXiv:1412.1929},
  preprint_doi = {10.48550/arXiv.1412.1929}
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@article{Fonseca2016,
  author = {Rasmus Fonseca, Henry van den Bedem, Julie Bernauer},
  title = {Probing RNA Native Conformational Ensembles with Structural Constraints},
  journal = {Journal of Computational Biology},
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  doi = {10.1089/cmb.2015.0201},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 80-95, Springer, Cham.},
  proceedings_volume = {9029},
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@inproceedings{Gambette2015,
  author = {Philippe Gambette, Andreas D.M. Gunawan, Anthony Labarre, Stéphane Vialette, Louxin Zhang},
  title = {Locating a Tree in a Phylogenetic Network in Quadratic Time},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 96-107, Springer, Cham.},
  pages = {96--107},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 96-107, Springer, Cham.},
  proceedings_volume = {9029},
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  proceedings_doi = {10.1007/978-3-319-16706-0_12},
  preprint_id = {arXiv:1502.03379},
  preprint_doi = {10.48550/arXiv.1502.03379}
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@article{Gong2016,
  author = {Huichao Gong, Sai Zhang, Jiangdian Wang, Haipeng Gong, Jianyang Zeng},
  title = {Constructing Structure Ensembles of Intrinsically Disordered Proteins from Chemical Shift Data},
  journal = {Journal of Computational Biology},
  volume = {23},
  number = {5},
  pages = {300--310},
  year = {2016},
  doi = {10.1089/cmb.2015.0184},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 108-121, Springer, Cham.},
  proceedings_volume = {9029},
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  proceedings_doi = {10.1007/978-3-319-16706-0_13}
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@article{Hallen2016,
  author = {Mark A. Hallen, Bruce R. Donald},
  title = {COMETS (Constrained Optimization of Multistate Energies by Tree Search): A Provable and Efficient Protein Design Algorithm to Optimize Binding Affinity and Specificity with Respect to Sequence},
  journal = {Journal of Computational Biology},
  volume = {23},
  number = {5},
  pages = {311--321},
  year = {2016},
  doi = {10.1089/cmb.2015.0188},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 122-135, Springer, Cham.},
  proceedings_volume = {9029},
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@article{Joo2016,
  author = {Jong Wha J. Joo, Eun Yong Kang, Elin Org, Nick Furlotte, Brian Parks, Farhad Hormozdiari, Aldons J. Lusis, Eleazar Eskin},
  title = {Efficient and Accurate Multiple-Phenotype Regression Method for High Dimensional Data Considering Population Structure},
  journal = {Genetics},
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  year = {2016},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 136-153, Springer, Cham.},
  proceedings_volume = {9029},
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@article{Jou2016,
  author = {Jonathan D. Jou, Swati Jain, Ivelin S. Georgiev, Bruce R. Donald},
  title = {BWM*: A Novel, Provable, Ensemble-Based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design},
  journal = {Journal of Computational Biology},
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  doi = {10.1089/cmb.2015.0194},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 154-166, Springer, Cham.},
  proceedings_volume = {9029},
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@article{Lee2016,
  author = {Seunghak Lee, Aurélie C. Lozano, Prabhanjan Kambadur, Eric P. Xing},
  title = {An Efficient Nonlinear Regression Approach for Genome-wide Detection of Marginal and Interacting Genetic Variations},
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  doi = {10.1089/cmb.2015.0202},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 167-187, Springer, Cham.},
  proceedings_volume = {9029},
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  proceedings_doi = {10.1007/978-3-319-16706-0_17}
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@article{Leelananda2016,
  author = {Sumudu P. Leelananda, Robert L. Jernigan, Andrzej Kloczkowski},
  title = {Predicting Designability of Small Proteins from Graph Features of Contact Maps},
  journal = {Journal of Computational Biology},
  volume = {23},
  number = {5},
  pages = {400--411},
  year = {2016},
  doi = {10.1089/cmb.2015.0209},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 188-201, Springer, Cham.},
  proceedings_volume = {9029},
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@article{Leiserson2015,
  author = {Mark D.M. Leiserson, Hsin-Ta Wu, Fabio Vandin, Benjamin J. Raphael},
  title = {CoMEt: A Statistical Approach to Identify Combinations of Mutually Exclusive Alterations in Cancer},
  journal = {Genome Biology},
  volume = {16: 160},
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  doi = {10.1186/s13059-015-0700-7},
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@article{Li2016,
  author = {Yifeng Li, Chih-Yu Chen, Wyeth W. Wasserman},
  title = {Deep Feature Selection: Theory and Application to Identify Enhancers and Promoters},
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  doi = {10.1089/cmb.2015.0189},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 205-217, Springer, Cham.},
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@article{Ma2015,
  author = {Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu},
  title = {Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning},
  journal = {Bioinformatics},
  volume = {31},
  number = {21},
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  year = {2015},
  doi = {10.1093/bioinformatics/btv472},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 218-221, Springer, Cham.},
  proceedings_volume = {9029},
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  preprint_id = {arXiv:1312.2988},
  preprint_doi = {10.48550/arXiv.1312.2988}
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@article{Mandric2015,
  author = {Igor Mandric, Alex Zelikovsky},
  title = {ScaffMatch: scaffolding algorithm based on maximum weight matching},
  journal = {Bioinformatics},
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  number = {16},
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@article{Manescu2016,
  author = {David Manescu, Uri Keich},
  title = {A Symmetric Length-Aware Enrichment Test},
  journal = {Journal of Computational Biology},
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  doi = {10.1089/cmb.2016.0038},
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@article{Mazza2016,
  author = {Arnon Mazza, Allon Wagner, Eytan Ruppin, Roded Sharan},
  title = {Functional Alignment of Metabolic Networks},
  journal = {Journal of Computational Biology},
  volume = {23},
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  pages = {390--399},
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  doi = {10.1089/cmb.2015.0203},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 243-255, Springer, Cham.},
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@article{McPherson2017,
  author = {Andrew W. McPherson, Andrew Roth, Gavin Ha, Cedric Chauve, Adi Steif, Camila P. E. de Souza, Peter Eirew, Alexandre Bouchard-Côté, Sam Aparicio, S. Cenk Sahinalp, Sohrab P. Shah},
  title = {ReMixT: clone-specific genomic structure estimation in cancer},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 256-258, Springer, Cham.},
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@article{Nguyen2015,
  author = {Nam-Phuong D. Nguyen, Siavash Mirarab, Keerthana Kumar, Tandy Warnow},
  title = {Ultra-large alignments using Phylogeny-aware Profiles},
  journal = {Genome Biology},
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@inproceedings{Parida2015,
  author = {Laxmi Parida, Filippo Utro, Deniz Yorukoglu, Anna Paola Carrieri, David Kuhn, Saugata Basu},
  title = {Topological Signatures for Population Admixture},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 261-275, Springer, Cham.},
  pages = {261--275},
  year = {2015},
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@article{Ronen2015,
  author = {Roy Ronen, Glenn Tesler, Ali Akbari, Shay Zakov, Noah A. Rosenberg, Vineet Bafna},
  title = {Predicting Carriers of Ongoing Selective Sweeps without Knowledge of the Favored Allele},
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@article{Salmela2016,
  author = {Leena Salmela, Kristoffer Sahlin, Veli Mäkinen, Alexandru I. Tomescu},
  title = {Gap Filling as Exact Path Length Problem},
  journal = {Journal of Computational Biology},
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  doi = {10.1089/cmb.2015.0197},
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  proceedings_volume = {9029},
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@article{Sefer2016,
  author = {Emre Sefer, Geet Duggal, Carl Kingsford},
  title = {Deconvolution of Ensemble Chromatin Interaction Data Reveals the Latent Mixing Structures in Cell Subpopulations},
  journal = {Journal of Computational Biology},
  volume = {23},
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  proceedings_volume = {9029},
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@article{Shao2016,
  author = {Mingfu Shao, Bernard M.E. Moret},
  title = {A Fast and Exact Algorithm for the Exemplar Breakpoint Distance},
  journal = {Journal of Computational Biology},
  volume = {23},
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  doi = {10.1089/cmb.2015.0193},
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@article{Temerinac-Ott2015,
  author = {Maja Temerinac-Ott, Armaghan W. Naik, Robert F. Murphy},
  title = {Deciding when to stop: Efficient experimentation to learn to predict drug-target interactions},
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  proceedings_volume = {9029},
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  preprint_id = {arXiv:1504.02406},
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@article{Vandin2016,
  author = {Fabio Vandin, Benjamin J. Raphael, Eli Upfal},
  title = {On the Sample Complexity of Cancer Pathways Identification},
  journal = {Journal of Computational Biology},
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  year = {2016},
  doi = {10.1089/cmb.2015.0100},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 326-337, Springer, Cham.},
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@article{Wilentzik2015,
  author = {Roni Wilentzik, Irit Gat-Viks},
  title = {A statistical framework for revealing signaling pathways perturbed by DNA variants},
  journal = {Nucleic Acids Research},
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  doi = {10.1093/nar/gkv203},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 338-339, Springer, Cham.},
  proceedings_volume = {9029},
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@article{Yang2016,
  author = {Shuo Yang, Shai Carmi, Itsik Pe'er},
  title = {Rapidly Registering Identity-by-Descent Across Ancestral Recombination Graphs},
  journal = {Journal of Computational Biology},
  volume = {23},
  number = {6},
  pages = {495--507},
  year = {2016},
  doi = {10.1089/cmb.2016.0016},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 340-353, Springer, Cham.},
  proceedings_volume = {9029},
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@article{Zhou2016,
  author = {Yichao Zhou, Yuexin Wu, Jianyang Zeng},
  title = {Computational Protein Design Using AND/OR Branch-and-Bound Search},
  journal = {Journal of Computational Biology},
  volume = {23},
  number = {6},
  pages = {439--451},
  year = {2016},
  doi = {10.1089/cmb.2015.0212},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science, vol 9029, pp 354-366, Springer, Cham.},
  proceedings_volume = {9029},
  proceedings_pages = {354--366},
  proceedings_doi = {10.1007/978-3-319-16706-0_36}
}