@article{Bansal2013,
  author = {Mukul S. Bansal, Eric J. Alm, Manolis Kellis},
  title = {Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {10},
  pages = {738--754},
  year = {2013},
  doi = {10.1089/cmb.2013.0073},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 1-13, Springer, Cham.},
  proceedings_volume = {7821},
  proceedings_pages = {1--13},
  proceedings_doi = {10.1007/978-3-642-37195-0_1}
}

@article{Chen2013,
  author = {Shijian Chen, Anqi Wang, Lei M. Li},
  title = {SEME: A Fast Mapper of Illumina Sequencing Reads with Statistical Evaluation},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {11},
  pages = {847--860},
  year = {2013},
  doi = {10.1089/cmb.2013.0111},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 14-29, Springer, Cham.},
  proceedings_volume = {7821},
  proceedings_pages = {14--29},
  proceedings_doi = {10.1007/978-3-642-37195-0_2}
}

@article{Cho2013,
  author = {Dong-Yeon Cho, Teresa M. Przytycka},
  title = {Dissecting cancer heterogeneity with a probabilistic genotype-phenotype model},
  journal = {Nucleic Acids Research},
  volume = {41},
  number = {17},
  pages = {8011--8020},
  year = {2013},
  doi = {10.1093/nar/gkt577},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 30-31, Springer, Cham.},
  proceedings_volume = {7821},
  proceedings_pages = {30--31},
  proceedings_doi = {10.1007/978-3-642-37195-0_3}
}

@article{Eskin2013,
  author = {Itamar Eskin, Farhad Hormozdiari, Lucía Conde, Jacques Riby, Christine F. Skibola, Eleazar Eskin, Eran Halperin},
  title = {eALPS: Estimating Abundance Levels in Pooled Sequencing Using Available Genotyping Data},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {11},
  pages = {861--877},
  year = {2013},
  doi = {10.1089/cmb.2013.0105},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 32-44, Springer, Cham.},
  proceedings_volume = {7821},
  proceedings_pages = {32--44},
  proceedings_doi = {10.1007/978-3-642-37195-0_4}
}

@article{Bryant2013,
  author = {William A Bryant, Ali A. Faruqi, John W. Pinney},
  title = {Analysis of Metabolic Evolution in Bacteria Using Whole-Genome Metabolic Models},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {10},
  pages = {755--764},
  year = {2013},
  doi = {10.1089/cmb.2013.0079},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 45-57, Springer, Cham.},
  proceedings_volume = {7821},
  proceedings_pages = {45--57},
  proceedings_doi = {10.1007/978-3-642-37195-0_5}
}

@article{Guo2013,
  author = {Fei Guo, Shuai Cheng Li, Wenji Ma, Lusheng Wang},
  title = {Detecting Protein Conformational Changes in Interactions via Scaling Known Structures},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {10},
  pages = {765--779},
  year = {2013},
  doi = {10.1089/cmb.2013.0069},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 58-74, Springer, Cham.},
  proceedings_volume = {7821},
  proceedings_pages = {58--74},
  proceedings_doi = {10.1007/978-3-642-37195-0_6}
}

@article{He2013,
  author = {Dan He, Zhanyong Wang, Buhm Han, Laxmi Parida, Eleazar Eskin},
  title = {IPED: Inheritance Path-based Pedigree Reconstruction Algorithm Using Genotype Data},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {10},
  pages = {780--791},
  year = {2013},
  doi = {10.1089/cmb.2013.0080},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 75-87, Springer, Cham.},
  proceedings_volume = {7821},
  proceedings_pages = {75--87},
  proceedings_doi = {10.1007/978-3-642-37195-0_7}
}

@inproceedings{Jansson2013,
  author = {Jesper Jansson, Chuanqi Shen, Wing-Kin Sung},
  title = {An Optimal Algorithm for Building the Majority Rule Consensus Tree},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 88-99, Springer, Cham.},
  pages = {88--99},
  year = {2013},
  doi = {10.1007/978-3-642-37195-0_8},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 88-99, Springer, Cham.},
  proceedings_volume = {7821},
  proceedings_pages = {88--99},
  proceedings_doi = {10.1007/978-3-642-37195-0_8}
}

@article{Jeong2013,
  author = {Kyowon Jeong, Sangtae Kim, Pavel A. Pevzner},
  title = {UniNovo: a universal tool for de novo peptide sequencing},
  journal = {Bioinformatics},
  volume = {29},
  number = {16},
  pages = {1953--1962},
  year = {2013},
  doi = {10.1093/bioinformatics/btt338},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 100-117, Springer, Cham.},
  proceedings_volume = {7821},
  proceedings_pages = {100--117},
  proceedings_doi = {10.1007/978-3-642-37195-0_9}
}

@article{Kostem2013,
  author = {Emrah Kostem, Eleazar Eskin},
  title = {Efficiently Identifying Significant Associations in Genome-wide Association Studies},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {10},
  pages = {817--830},
  year = {2013},
  doi = {10.1089/cmb.2013.0087},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 118-131, Springer, Cham.},
  proceedings_volume = {7821},
  proceedings_pages = {118--131},
  proceedings_doi = {10.1007/978-3-642-37195-0_10}
}

@article{Liu2013,
  author = {Xiaowen Liu, Shawna Hengel, Si Wu, Nikola Tolić, Ljiljana Paša‐Tolić, Pavel A. Pevzner},
  title = {Identification of Ultramodified Proteins Using Top-Down Tandem Mass Spectra},
  journal = {Journal of Proteome Research},
  volume = {12},
  number = {12},
  pages = {5830--5838},
  year = {2013},
  doi = {10.1021/pr400849y},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 132-144, Springer, Cham.},
  proceedings_volume = {7821},
  proceedings_pages = {132--144},
  proceedings_doi = {10.1007/978-3-642-37195-0_11}
}

@inproceedings{Munteanu2013,
  author = {Alina Munteanu and Raluca Gordân},
  title = {Distinguishing between Genomic Regions Bound by Paralogous Transcription Factors},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 145-157, Springer, Cham.},
  pages = {145--157},
  year = {2013},
  doi = {10.1007/978-3-642-37195-0_12},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 145-157, Springer, Cham.},
  proceedings_volume = {7821},
  proceedings_pages = {145--157},
  proceedings_doi = {10.1007/978-3-642-37195-0_12}
}

@article{Nurk2013,
  author = {Sergey Nurk, Anton Bankevich, Dmitry Antipov, Alexey Gurevich, Anton Korobeynikov, Alla Lapidus, Andrey D. Prjibelski, Alexey Pyshkin, Alexander Sirotkin, Yakov Sirotkin, Ramūnas Stepanauskas, Scott Clingenpeel, Tanja Woyke, Jeffrey S. McLean, Roger S. Lasken, Glenn Tesler, Max A. Alekseyev, Pavel A. Pevzner},
  title = {Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {10},
  pages = {714--737},
  year = {2013},
  doi = {10.1089/cmb.2013.0084},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 158-170, Springer, Cham.},
  proceedings_volume = {7821},
  proceedings_pages = {158--170},
  proceedings_doi = {10.1007/978-3-642-37195-0_13}
}

@article{Oesper2013,
  author = {Layla Oesper, Ahmad Mahmoody, Benjamin J. Raphael},
  title = {THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data},
  journal = {Genome Biology},
  volume = {14},
  number = {7},
  pages = {R80},
  year = {2013},
  doi = {10.1186/gb-2013-14-7-r80},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 171-172, Springer, Cham.},
  proceedings_volume = {7821},
  proceedings_pages = {171--172},
  proceedings_doi = {10.1007/978-3-642-37195-0_14}
}

@article{Puniyani2013,
  author = {Kriti Puniyani, Eric P. Xing},
  title = {NP-MuScL: Unsupervised Global Prediction of Interaction Networks from Multiple Data Sources},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {11},
  pages = {892--904},
  year = {2013},
  doi = {10.1089/cmb.2013.0093},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 173-185, Springer, Cham.},
  proceedings_volume = {7821},
  proceedings_pages = {173--185},
  proceedings_doi = {10.1007/978-3-642-37195-0_15}
}

@inproceedings{Reeder2013,
  author = {Christopher Reeder and David Gifford},
  title = {High Resolution Modeling of Chromatin Interactions},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 186-198, Springer, Cham.},
  pages = {186--198},
  year = {2013},
  doi = {10.1007/978-3-642-37195-0_16},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 186-198, Springer, Cham.},
  proceedings_volume = {7821},
  proceedings_pages = {186--198},
  proceedings_doi = {10.1007/978-3-642-37195-0_16}
}

@article{Reinharz2013,
  author = {Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl},
  title = {Using Structural and Evolutionary Information to Detect and Correct Pyrosequencing Errors in Noncoding RNAs},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {11},
  pages = {905--919},
  year = {2013},
  doi = {10.1089/cmb.2013.0085},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 199-211, Springer, Cham.},
  proceedings_volume = {7821},
  proceedings_pages = {199--211},
  proceedings_doi = {10.1007/978-3-642-37195-0_17}
}

@inproceedings{Rodriguez2013,
  author = {Jesse M. Rodriguez, Serafim Batzoglou, Sivan Bercovici},
  title = {An Accurate Method for Inferring Relatedness in Large Datasets of Unphased Genotypes via an Embedded Likelihood-Ratio Test},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 212-229, Springer, Cham.},
  pages = {212--229},
  year = {2013},
  doi = {10.1007/978-3-642-37195-0_18},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 212-229, Springer, Cham.},
  proceedings_volume = {7821},
  proceedings_pages = {212--229},
  proceedings_doi = {10.1007/978-3-642-37195-0_18}
}

@article{Ronen2013,
  author = {Roy Ronen, Nitin Udpa, Eran Halperin, Vineet Bafna},
  title = {Learning Natural Selection from the Site Frequency Spectrum},
  journal = {Genetics},
  volume = {195},
  number = {1},
  pages = {181--193},
  year = {2013},
  doi = {10.1534/genetics.113.152587},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 230-233, Springer, Cham.},
  proceedings_volume = {7821},
  proceedings_pages = {230--233},
  proceedings_doi = {10.1007/978-3-642-37195-0_19}
}

@article{Sadeh2013,
  author = {Mohammad J. Sadeh, Giusi Moffa, Rainer Spang},
  title = {Considering Unknown Unknowns: Reconstruction of Nonconfoundable Causal Relations in Biological Networks},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {11},
  pages = {920--932},
  year = {2013},
  doi = {10.1089/cmb.2013.0119},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 234-248, Springer, Cham.},
  proceedings_volume = {7821},
  proceedings_pages = {234--248},
  proceedings_doi = {10.1007/978-3-642-37195-0_20}
}

@article{Salari2013,
  author = {Raheleh Salari, Syed Shayon Saleh, Dorna Kashef-Haghighi, David Khavari, Daniel E. Newburger, Robert B. West, Arend Sidow, Serafim Batzoglou},
  title = {Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {11},
  pages = {933--944},
  year = {2013},
  doi = {10.1089/cmb.2013.0106},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 249-263, Springer, Cham.},
  proceedings_volume = {7821},
  proceedings_pages = {249--263},
  proceedings_doi = {10.1007/978-3-642-37195-0_21}
}

@article{Senter2012,
  author = {Evan Senter, Saad Sheikh, Iván Dotú, Yann Ponty, Peter Clote},
  title = {Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches},
  journal = {PLoS ONE},
  volume = {7},
  number = {12},
  pages = {e50506},
  year = {2012},
  doi = {10.1371/journal.pone.0050506},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 264-265, Springer, Cham.},
  proceedings_volume = {7821},
  proceedings_pages = {264--265},
  proceedings_doi = {10.1007/978-3-642-37195-0_22}
}

@article{Stevens2013,
  author = {Michael Stevens, Jeffrey B. Cheng, Daofeng Li, Mingchao Xie, Chibo Hong, Cécile L. Maire, Keith L. Ligon, Martin Hirst, Marco A. Marra, J Costello, Ting Wang},
  title = {Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods},
  journal = {Genome Research},
  volume = {23},
  number = {9},
  pages = {1541--1553},
  year = {2013},
  doi = {10.1101/gr.152231.112},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 266-268, Springer, Cham.},
  proceedings_volume = {7821},
  proceedings_pages = {266--268},
  proceedings_doi = {10.1007/978-3-642-37195-0_23}
}

@article{Tran2013,
  author = {Ngoc Hieu Tran, Kwok Pui Choi, Louxin Zhang},
  title = {Counting motifs in the human interactome},
  journal = {Nature Communications},
  volume = {4: 2241},
  year = {2013},
  doi = {10.1038/ncomms3241},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 269-270, Springer, Cham.},
  proceedings_volume = {7821},
  proceedings_pages = {269--270},
  proceedings_doi = {10.1007/978-3-642-37195-0_24}
}

@inproceedings{Tripathy2013,
  author = {Chittaranjan Tripathy, Anthony K. Yan, Pei Zhou, Bruce Randall Donald},
  title = {Extracting Structural Information from Residual Chemical Shift Anisotropy: Analytic Solutions for Peptide Plane Orientations and Applications to Determine Protein Structure},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 271-284, Springer, Cham.},
  pages = {271--284},
  year = {2013},
  doi = {10.1007/978-3-642-37195-0_25},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 271-284, Springer, Cham.},
  proceedings_volume = {7821},
  proceedings_pages = {271--284},
  proceedings_doi = {10.1007/978-3-642-37195-0_25}
}

@inproceedings{Vandin2013,
  author = {Fabio Vandin, Alexandra Papoutsaki, Benjamin J. Raphael, Eli Upfal},
  title = {Genome-Wide Survival Analysis of Somatic Mutations in Cancer},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 285-286, Springer, Cham.},
  pages = {285--286},
  year = {2013},
  doi = {10.1007/978-3-642-37195-0_26},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 285-286, Springer, Cham.},
  proceedings_volume = {7821},
  proceedings_pages = {285--286},
  proceedings_doi = {10.1007/978-3-642-37195-0_26}
}

@article{Wang2013,
  author = {Mingxun Wang, Nuno Bandeira},
  title = {Spectral Library Generating Function for Assessing Spectrum-Spectrum Match Significance},
  journal = {Journal of Proteome Research},
  volume = {12},
  number = {9},
  pages = {3944--3951},
  year = {2013},
  doi = {10.1021/pr400230p},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 287-288, Springer, Cham.},
  proceedings_volume = {7821},
  proceedings_pages = {287--288},
  proceedings_doi = {10.1007/978-3-642-37195-0_27}
}

@article{Will2015,
  author = {Sebastian Will, Christina Otto, Milad Miladi, Mathias Möhl, Rolf Backofen},
  title = {SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics},
  journal = {Bioinformatics},
  volume = {31},
  number = {15},
  pages = {2489--2496},
  year = {2015},
  doi = {10.1093/bioinformatics/btv185},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 289-290, Springer, Cham.},
  proceedings_volume = {7821},
  proceedings_pages = {289--290},
  proceedings_doi = {10.1007/978-3-642-37195-0_28}
}

@article{Wu2013,
  author = {Yufeng Wu},
  title = {An Algorithm for Constructing Parsimonious Hybridization Networks with Multiple Phylogenetic Trees},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {10},
  pages = {792--804},
  year = {2013},
  doi = {10.1089/cmb.2013.0072},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 291-303, Springer, Cham.},
  proceedings_volume = {7821},
  proceedings_pages = {291--303},
  proceedings_doi = {10.1007/978-3-642-37195-0_29}
}

@article{Xu2013,
  author = {Dong Xu, Hua Li, Yang Zhang},
  title = {Protein Depth Calculation and the Use for Improving Accuracy of Protein Fold Recognition},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {10},
  pages = {805--816},
  year = {2013},
  doi = {10.1089/cmb.2013.0071},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 304-316, Springer, Cham.},
  proceedings_volume = {7821},
  proceedings_pages = {304--316},
  proceedings_doi = {10.1007/978-3-642-37195-0_30}
}

@article{Zhang2013,
  author = {Zhizhuo Zhang, Guoliang Li, Kim-Chuan Toh, Wing‐Kin Sung},
  title = {3D Chromosome Modeling with Semi-Definite Programming and Hi-C Data},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {11},
  pages = {831--846},
  year = {2013},
  doi = {10.1089/cmb.2013.0076},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 317-332, Springer, Cham.},
  proceedings_volume = {7821},
  proceedings_pages = {317--332},
  proceedings_doi = {10.1007/978-3-642-37195-0_31}
}

@article{Deng2013,
  author = {Lei Deng, Jihong Guan, Xiaoming Wei, Yuan Yi, Qiangfeng Cliff Zhang, Shuigeng Zhou},
  title = {Boosting Prediction Performance of Protein–Protein Interaction Hot Spots by Using Structural Neighborhood Properties},
  journal = {Journal of Computational Biology},
  volume = {20},
  number = {11},
  pages = {878--891},
  year = {2013},
  doi = {10.1089/cmb.2013.0083},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 333-344, Springer, Cham.},
  proceedings_volume = {7821},
  proceedings_pages = {333--344},
  proceedings_doi = {10.1007/978-3-642-37195-0_32}
}