@inproceedings{Alipanahi2012,
  author = {Babak Alipanahi, Nathan Krislock, Ali Ghodsi, Henry Wolkowicz, Logan Donaldson, Ming Li},
  title = {Protein Structure by Semidefinite Facial Reduction},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 1-11, Springer, Cham.},
  pages = {1--11},
  year = {2012},
  doi = {10.1007/978-3-642-29627-7_1},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 1-11, Springer, Cham.},
  proceedings_volume = {7262},
  proceedings_pages = {1--11},
  proceedings_doi = {10.1007/978-3-642-29627-7_1}
}

@article{Rodriguez2013,
  author = {Jesse M. Rodriguez, Sivan Bercovici, Megan Elmore, Serafim Batzoglou},
  title = {Ancestry Inference in Complex Admixtures via Variable-length Markov Chain Linkage Models},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {3},
  pages = {199--211},
  year = {2013},
  doi = {10.1089/cmb.2012.0088},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 12-28, Springer, Cham.},
  proceedings_volume = {7262},
  proceedings_pages = {12--28},
  proceedings_doi = {10.1007/978-3-642-29627-7_2}
}

@article{Canzar2013,
  author = {Stefan Canzar, Mohammed El-Kebir, René Pool, Khaled Elbassioni, Alpeshkumar K. Malde, Alan E. Mark, Daan P. Geerke, Leen Stougie, Gunnar W. Klau},
  title = {Charge Group Partitioning in Biomolecular Simulation},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {3},
  pages = {188--198},
  year = {2013},
  doi = {10.1089/cmb.2012.0239},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 29-43, Springer, Cham.},
  proceedings_volume = {7262},
  proceedings_pages = {29--43},
  proceedings_doi = {10.1007/978-3-642-29627-7_3}
}

@article{Kececioglu2013,
  author = {John Kececioglu, Dan DeBlasio},
  title = {Accuracy Estimation and Parameter Advising for Protein Multiple Sequence Alignment},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {4},
  pages = {259--279},
  year = {2013},
  doi = {10.1089/cmb.2013.0007},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 45-59, Springer, Cham.},
  proceedings_volume = {7262},
  proceedings_pages = {45--59},
  proceedings_doi = {10.1007/978-3-642-29627-7_5}
}

@article{Francis2012,
  author = {Matthew R. Francis, Elana J. Fertig},
  title = {Quantifying the Dynamics of Coupled Networks of Switches and Oscillators},
  journal = {PLoS ONE},
  volume = {7},
  number = {1},
  pages = {e29497},
  year = {2012},
  doi = {10.1371/journal.pone.0029497},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 60-61, Springer, Cham.},
  proceedings_volume = {7262},
  proceedings_pages = {60--61},
  proceedings_doi = {10.1007/978-3-642-29627-7_6},
  preprint_id = {arXiv:1111.7243},
  preprint_doi = {10.48550/arXiv.1111.7243}
}

@article{Gymrek2012,
  author = {Melissa Gymrek, David E. Golan, Saharon Rosset, Yaniv Erlich},
  title = {lobSTR: A short tandem repeat profiler for personal genomes},
  journal = {Genome Research},
  volume = {22},
  number = {6},
  pages = {1154--1162},
  year = {2012},
  doi = {10.1101/gr.135780.111},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 62-63, Springer, Cham.},
  proceedings_volume = {7262},
  proceedings_pages = {62--63},
  proceedings_doi = {10.1007/978-3-642-29627-7_7}
}

@article{He2013,
  author = {Dan He, Buhm Han, Eleazar Eskin},
  title = {Hap-seq: An Optimal Algorithm for Haplotype Phasing with Imputation Using Sequencing Data},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {2},
  pages = {80--92},
  year = {2013},
  doi = {10.1089/cmb.2012.0091},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 64-78, Springer, Cham.},
  proceedings_volume = {7262},
  proceedings_pages = {64--78},
  proceedings_doi = {10.1007/978-3-642-29627-7_8}
}

@article{He2013,
  author = {Lu He, Fabio Vandin, Gopal Pandurangan, Chris Bailey‐Kellogg},
  title = {Ballast : A Ball-based Algorithm for Structural Motifs},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {2},
  pages = {137--151},
  year = {2013},
  doi = {10.1089/cmb.2012.0246},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 79-93, Springer, Cham.},
  proceedings_volume = {7262},
  proceedings_pages = {79--93},
  proceedings_doi = {10.1007/978-3-642-29627-7_9}
}

@article{Holloway2013,
  author = {Patrick Holloway, Krister M. Swenson, David H. Ardell, Nadia El-Mabrouk},
  title = {Ancestral Genome Organization: An Alignment Approach},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {4},
  pages = {280--295},
  year = {2013},
  doi = {10.1089/cmb.2012.0292},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 94-112, Springer, Cham.},
  proceedings_volume = {7262},
  proceedings_pages = {94--112},
  proceedings_doi = {10.1007/978-3-642-29627-7_10}
}

@article{Holtby2013,
  author = {Daniel G. Holtby, Shuai Cheng Li, Ming Li},
  title = {LoopWeaver: Loop Modeling by the Weighted Scaling of Verified Proteins},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {3},
  pages = {212--223},
  year = {2013},
  doi = {10.1089/cmb.2012.0078},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 113-126, Springer, Cham.},
  proceedings_volume = {7262},
  proceedings_pages = {113--126},
  proceedings_doi = {10.1007/978-3-642-29627-7_11}
}

@article{Huang2013,
  author = {Yan Huang, Yin Hu, Corbin D. Jones, James N. MacLeod, Derek Y. Chiang, Yufeng Liu, Jan F. Prins, Jinze Liu},
  title = {A Robust Method for Transcript Quantification with RNA-Seq Data},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {3},
  pages = {167--187},
  year = {2013},
  doi = {10.1089/cmb.2012.0230},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 127-147, Springer, Cham.},
  proceedings_volume = {7262},
  proceedings_pages = {127--147},
  proceedings_doi = {10.1007/978-3-642-29627-7_12}
}

@article{Kinsella2012,
  author = {Marcus Kinsella, Vineet Bafna},
  title = {Combinatorics of the Breakage-Fusion-Bridge Mechanism},
  journal = {Journal of Computational Biology},
  volume = {19},
  number = {6},
  pages = {662--678},
  year = {2012},
  doi = {10.1089/cmb.2012.0020},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 148-162, Springer, Cham.},
  proceedings_volume = {7262},
  proceedings_pages = {148--162},
  proceedings_doi = {10.1007/978-3-642-29627-7_13}
}

@article{Li2012,
  author = {Yang Li, Hongmei Li‐Byarlay, Paul Burns, Mark Borodovsky, Gene E. Robinson, Jian Ma},
  title = {TrueSight: a new algorithm for splice junction detection using RNA-seq},
  journal = {Nucleic Acids Research},
  volume = {41},
  number = {4},
  pages = {e51},
  year = {2012},
  doi = {10.1093/nar/gks1311},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 163-164, Springer, Cham.},
  proceedings_volume = {7262},
  proceedings_pages = {163--164},
  proceedings_doi = {10.1007/978-3-642-29627-7_14}
}

@article{Lin2013,
  author = {Yaw-Ling Lin, Charles B. Ward, Steven Skiena},
  title = {Synthetic Sequence Design for Signal Location Search},
  journal = {Algorithmica},
  volume = {67},
  number = {3},
  pages = {368--383},
  year = {2013},
  doi = {10.1007/s00453-013-9760-9},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 165-179, Springer, Cham.},
  proceedings_volume = {7262},
  proceedings_pages = {165--179},
  proceedings_doi = {10.1007/978-3-642-29627-7_15}
}

@article{McPherson2012,
  author = {Andrew McPherson, Chunxiao Wu, Alexander W. Wyatt, Sohrab P. Shah, Colin C. Collins, S. Cenk Sahinalp},
  title = {nFuse: Discovery of complex genomic rearrangements in cancer using high-throughput sequencing},
  journal = {Genome Research},
  volume = {22},
  number = {11},
  pages = {2250--2261},
  year = {2012},
  doi = {10.1101/gr.136572.111},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 181-182, Springer, Cham.},
  proceedings_volume = {7262},
  proceedings_pages = {181--182},
  proceedings_doi = {10.1007/978-3-642-29627-7_17}
}

@article{Parker2013,
  author = {Andrew S. Parker, Yoonjoo Choi, Karl E. Griswold, Chris Bailey‐Kellogg},
  title = {Structure-Guided Deimmunization of Therapeutic Proteins},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {2},
  pages = {152--165},
  year = {2013},
  doi = {10.1089/cmb.2012.0251},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 184-198, Springer, Cham.},
  proceedings_volume = {7262},
  proceedings_pages = {184--198},
  proceedings_doi = {10.1007/978-3-642-29627-7_19}
}

@article{Pham2012,
  author = {Son Pham, Dmitry Antipov, Alexander Sirotkin, Glenn Tesler, Pavel A. Pevzner, Max A. Alekseyev},
  title = {Pathset Graphs: A Novel Approach for Comprehensive Utilization of Paired Reads in Genome Assembly},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {4},
  pages = {359--371},
  year = {2012},
  doi = {10.1089/cmb.2012.0098},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 200-212, Springer, Cham.},
  proceedings_volume = {7262},
  proceedings_pages = {200--212},
  proceedings_doi = {10.1007/978-3-642-29627-7_21}
}

@article{Rauf2013,
  author = {Imran Rauf, Florian Rasche, François Nicolas, Sebastian Böcker},
  title = {Finding Maximum Colorful Subtrees in Practice},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {4},
  pages = {311--321},
  year = {2013},
  doi = {10.1089/cmb.2012.0083},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 213-223, Springer, Cham.},
  proceedings_volume = {7262},
  proceedings_pages = {213--223},
  proceedings_doi = {10.1007/978-3-642-29627-7_22}
}

@inproceedings{Roch2012,
  author = {Sebastien Roch and Sagi Snir},
  title = {Recovering the Tree-Like Trend of Evolution Despite Extensive Lateral Genetic Transfer: A Probabilistic Analysis},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 224-238, Springer, Cham.},
  pages = {224--238},
  year = {2012},
  doi = {10.1007/978-3-642-29627-7_23},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 224-238, Springer, Cham.},
  proceedings_volume = {7262},
  proceedings_pages = {224--238},
  proceedings_doi = {10.1007/978-3-642-29627-7_23},
  preprint_id = {arXiv:1206.3520},
  preprint_doi = {10.48550/arXiv.1206.3520}
}

@article{Sahraeian2012,
  author = {Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon},
  title = {RESQUE: Network reduction using semi-Markov random walk scores for efficient querying of biological networks},
  journal = {Bioinformatics},
  volume = {28},
  number = {16},
  pages = {2129--2136},
  year = {2012},
  doi = {10.1093/bioinformatics/bts341},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 239-240, Springer, Cham.},
  proceedings_volume = {7262},
  proceedings_pages = {239--240},
  proceedings_doi = {10.1007/978-3-642-29627-7_24}
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@inproceedings{Salari2012,
  author = {Raheleh Salari, Chava Kimchi-Sarfaty, Michael M. Gottesman, Teresa M. Przytycka},
  title = {Detecting SNP-Induced Structural Changes in RNA: Application to Disease Studies},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 241-243, Springer, Cham.},
  pages = {241--243},
  year = {2012},
  doi = {10.1007/978-3-642-29627-7_25},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 241-243, Springer, Cham.},
  proceedings_volume = {7262},
  proceedings_pages = {241--243},
  proceedings_doi = {10.1007/978-3-642-29627-7_25}
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@inproceedings{Schmiedl2012,
  author = {Christina Schmiedl, Mathias Möhl, Steffen Heyne, Mika Amit, Gad M. Landau, Sebastian Will, Rolf Backofen},
  title = {Exact Pattern Matching for RNA Structure Ensembles},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 245-260, Springer, Cham.},
  pages = {245--260},
  year = {2012},
  doi = {10.1007/978-3-642-29627-7_27},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 245-260, Springer, Cham.},
  proceedings_volume = {7262},
  proceedings_pages = {245--260},
  proceedings_doi = {10.1007/978-3-642-29627-7_27}
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@article{Sharan2013,
  author = {Roded Sharan and Richard M. Karp},
  title = {Reconstructing Boolean models of signaling},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {3},
  pages = {249--57},
  year = {2013},
  doi = {10.1089/cmb.2012.0241},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 261-271, Springer, Cham.},
  proceedings_volume = {7262},
  proceedings_pages = {261--271},
  proceedings_doi = {10.1007/978-3-642-29627-7_28}
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@article{Song2013,
  author = {Kai Song, Jie Ren, Zhiyuan Zhai, Xuemei Liu, Minghua Deng, Fengzhu Sun},
  title = {Alignment-Free Sequence Comparison Based on Next-Generation Sequencing Reads},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {2},
  pages = {64--79},
  year = {2013},
  doi = {10.1089/cmb.2012.0228},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 272-285, Springer, Cham.},
  proceedings_volume = {7262},
  proceedings_pages = {272--285},
  proceedings_doi = {10.1007/978-3-642-29627-7_29}
}

@article{Tunçbağ2013,
  author = {Nurcan Tunçbağ, Alfredo Braunstein, Andrea Pagnani, Shao‐shan Carol Huang, Jennifer Chayes, Christian Borgs, Riccardo Zecchina, Ernest Fraenkel},
  title = {Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {2},
  pages = {124--136},
  year = {2013},
  doi = {10.1089/cmb.2012.0092},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 287-301, Springer, Cham.},
  proceedings_volume = {7262},
  proceedings_pages = {287--301},
  proceedings_doi = {10.1007/978-3-642-29627-7_31}
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@article{Wang2013,
  author = {Hua Wang, Heng Huang, Chris Ding},
  title = {Function–Function Correlated Multi-label Protein Function Prediction over Interaction Networks},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {4},
  pages = {322--343},
  year = {2013},
  doi = {10.1089/cmb.2012.0272},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 302-313, Springer, Cham.},
  proceedings_volume = {7262},
  proceedings_pages = {302--313},
  proceedings_doi = {10.1007/978-3-642-29627-7_32}
}

@article{Wang2013,
  author = {Hua Wang, Heng Huang, Chris Ding, Feiping Nie},
  title = {Predicting Protein–Protein Interactions from Multimodal Biological Data Sources via Nonnegative Matrix Tri-Factorization},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {4},
  pages = {344--358},
  year = {2013},
  doi = {10.1089/cmb.2012.0273},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 314-325, Springer, Cham.},
  proceedings_volume = {7262},
  proceedings_pages = {314--325},
  proceedings_doi = {10.1007/978-3-642-29627-7_33}
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@article{Wang2013,
  author = {Zhanyong Wang, Farhad Hormozdiari, Wen-Yun Yang, Eran Halperin, Eleazar Eskin},
  title = {CNVeM: Copy Number Variation Detection Using Uncertainty of Read Mapping},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {3},
  pages = {224--236},
  year = {2013},
  doi = {10.1089/cmb.2012.0258},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 326-340, Springer, Cham.},
  proceedings_volume = {7262},
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  proceedings_doi = {10.1007/978-3-642-29627-7_34}
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@article{Will2013,
  author = {Sebastian Will, Michael Yu, Bonnie Berger},
  title = {Structure-based whole-genome realignment reveals many novel noncoding RNAs},
  journal = {Genome Research},
  volume = {23},
  number = {6},
  pages = {1018--1027},
  year = {2013},
  doi = {10.1101/gr.137091.111},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 341-341, Springer, Cham.},
  proceedings_volume = {7262},
  proceedings_pages = {341--341},
  proceedings_doi = {10.1007/978-3-642-29627-7_35}
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@article{Töpfer2013,
  author = {Armin Töpfer, Osvaldo Zagordi, Sandhya Prabhakaran, Volker Röth, Eran Halperin, Niko Beerenwinkel},
  title = {Probabilistic Inference of Viral Quasispecies Subject to Recombination},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {2},
  pages = {113--123},
  year = {2013},
  doi = {10.1089/cmb.2012.0232},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 342-354, Springer, Cham.},
  proceedings_volume = {7262},
  proceedings_pages = {342--354},
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@article{Zhang2013,
  author = {Zhizhuo Zhang, Cheng Chang, Willy Hugo, Edwin Cheung, Wing‐Kin Sung},
  title = {Simultaneously Learning DNA Motif Along with Its Position and Sequence Rank Preferences Through Expectation Maximization Algorithm},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {3},
  pages = {237--248},
  year = {2013},
  doi = {10.1089/cmb.2012.0233},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 355-370, Springer, Cham.},
  proceedings_volume = {7262},
  proceedings_pages = {355--370},
  proceedings_doi = {10.1007/978-3-642-29627-7_37}
}