RECOMB 2013 Proceedings

Beijing, China, April 7-10, 2013

PC Chair: Fengzhu Sun
Organization Committee: Xuegong Zhang (co-chair), Minghua Deng (co-chair), Rui Jiang (co-chair), Jin Gu, Jingdong Han, Ruiqiang Li, Xuan Li, Yixue Li, Jingchu Luo, Geng Tian, Xiujie Wang, Peiheng Zhang
Keynote Speakers: Scott Fraser, Takashi Gojobori, Deborah Nickerson, Nadia A. Rosenthal, Chung-I Wu, Sunny Xie

List of Publications

• Reconciliation Revisited: Handling Multiple Optima When Reconciling with Duplication, Transfer, and Loss. Mukul S. Bansal, Eric J. Alm, Manolis Kellis.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 1-13, Springer, Cham.
    • DOI: 10.1007/978-3-642-37195-0_1
• SEME: A Fast Mapper of Illumina Sequencing Reads with Statistical Evaluation. Shijian Chen, Anqi Wang, Lei M. Li.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 14-29, Springer, Cham.
    • DOI: 10.1007/978-3-642-37195-0_2
• Dissecting Cancer Heterogeneity with a Probabilistic Genotype-Phenotype Model. Dong-Yeon Cho and Teresa M. Przytycka.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 30-31, Springer, Cham.
    • DOI: 10.1007/978-3-642-37195-0_3
• eALPS: Estimating Abundance Levels in Pooled Sequencing Using Available Genotyping Data. Itamar Eskin, Farhad Hormozdiari, Lucia Conde, Jacques Riby, Chris Skibola, Eleazar Eskin, Eran Halperin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 32-44, Springer, Cham.
    • DOI: 10.1007/978-3-642-37195-0_4
• Analysis of Metabolic Evolution in Bacteria Using Whole-Genome Metabolic Models. Ali A. Faruqi, William A. Bryant, John W. Pinney.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 45-57, Springer, Cham.
    • DOI: 10.1007/978-3-642-37195-0_5
• Detecting Protein Conformational Changes in Interactions via Scaling Known Structures. Fei Guo, Shuai Cheng Li, Wenji Ma, Lusheng Wang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 58-74, Springer, Cham.
    • DOI: 10.1007/978-3-642-37195-0_6
• IPED: Inheritance Path Based Pedigree Reconstruction Algorithm Using Genotype Data. Dan He, Zhanyong Wang, Buhm Han, Laxmi Parida, Eleazar Eskin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 75-87, Springer, Cham.
    • DOI: 10.1007/978-3-642-37195-0_7
• An Optimal Algorithm for Building the Majority Rule Consensus Tree. Jesper Jansson, Chuanqi Shen, Wing-Kin Sung.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 88-99, Springer, Cham.
    • DOI: 10.1007/978-3-642-37195-0_8
• UniNovo: A Universal Tool for de Novo Peptide Sequencing. Kyowon Jeong, Sangtae Kim, Pavel A. Pevzner.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 100-117, Springer, Cham.
    • DOI: 10.1007/978-3-642-37195-0_9
• Efficiently Identifying Significant Associations in Genome-Wide Association Studies. Emrah Kostem and Eleazar Eskin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 118-131, Springer, Cham.
    • DOI: 10.1007/978-3-642-37195-0_10
• Identification of Ultramodified Proteins Using Top-Down Spectra. Xiaowen Liu, Shawna Hengel, Si Wu, Nikola Tolić, Ljiljana Pasa-Tolić, Pavel A. Pevzner.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 132-144, Springer, Cham.
    • DOI: 10.1007/978-3-642-37195-0_11
• Distinguishing between Genomic Regions Bound by Paralogous Transcription Factors. Alina Munteanu and Raluca Gordân.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 145-157, Springer, Cham.
    • DOI: 10.1007/978-3-642-37195-0_12
• Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads. Sergey Nurk, Anton Bankevich, Dmitry Antipov, Alexey Gurevich, Anton Korobeynikov, Alla Lapidus, Andrey Prjibelsky, Alexey Pyshkin, Alexander Sirotkin, Yakov Sirotkin, Ramunas Stepanauskas, Jeffrey McLean, Roger Lasken, Scott R. Clingenpeel, Tanja Woyke, Glenn Tesler, Max A. Alekseyev, Pavel A. Pevzner.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 158-170, Springer, Cham.
    • DOI: 10.1007/978-3-642-37195-0_13
• Inferring Intra-tumor Heterogeneity from High-Throughput DNA Sequencing Data. Layla Oesper, Ahmad Mahmoody, Benjamin J. Raphael.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 171-172, Springer, Cham.
    • DOI: 10.1007/978-3-642-37195-0_14
• NP-MuScL: Unsupervised Global Prediction of Interaction Networks from Multiple Data Sources. Kriti Puniyani and Eric P. Xing.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 173-185, Springer, Cham.
    • DOI: 10.1007/978-3-642-37195-0_15
• High Resolution Modeling of Chromatin Interactions. Christopher Reeder and David Gifford.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 186-198, Springer, Cham.
    • DOI: 10.1007/978-3-642-37195-0_16
• A Linear Inside-Outside Algorithm for Correcting Sequencing Errors in Structured RNAs. Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 199-211, Springer, Cham.
    • DOI: 10.1007/978-3-642-37195-0_17
• An Accurate Method for Inferring Relatedness in Large Datasets of Unphased Genotypes via an Embedded Likelihood-Ratio Test. Jesse M. Rodriguez, Serafim Batzoglou, Sivan Bercovici.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 212-229, Springer, Cham.
    • DOI: 10.1007/978-3-642-37195-0_18
• Learning Natural Selection from the Site Frequency Spectrum. Roy Ronen, Nitin Udpa, Eran Halperin, Vineet Bafna.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 230-233, Springer, Cham.
    • DOI: 10.1007/978-3-642-37195-0_19
• Considering Unknown Unknowns - Reconstruction of Non-confoundable Causal Relations in Biological Networks. Mohammad Javad Sadeh, Giusi Moffa, Rainer Spang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 234-248, Springer, Cham.
    • DOI: 10.1007/978-3-642-37195-0_20
• Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery. Raheleh Salari, Syed Shayon Saleh, Dorna Kashef-Haghighi, David Khavari, Daniel E. Newburger, Robert B. West, Arend Sidow, Serafim Batzoglou.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 249-263, Springer, Cham.
    • DOI: 10.1007/978-3-642-37195-0_21
• Abstract: Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches. Evan Senter, Saad Sheikh, Ivan Dotu, Yann Ponty, Peter Clote.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 264-265, Springer, Cham.
    • DOI: 10.1007/978-3-642-37195-0_22
• MethylCRF, an Algorithm for Estimating Absolute Methylation Levels at Single CpG Resolution from Methylation Enrichment and Restriction Enzyme Sequencing Methods. Michael Stevens, Jeffrey B. Cheng, Mingchao Xie, Joseph F. Costello, Ting Wang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 266-268, Springer, Cham.
    • DOI: 10.1007/978-3-642-37195-0_23
• Counting Motifs in the Entire Biological Network from Noisy and Incomplete Data. Ngoc Hieu Tran, Kwok Pui Choi, Louxin Zhang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 269-270, Springer, Cham.
    • DOI: 10.1007/978-3-642-37195-0_24
• Extracting Structural Information from Residual Chemical Shift Anisotropy: Analytic Solutions for Peptide Plane Orientations and Applications to Determine Protein Structure. Chittaranjan Tripathy, Anthony K. Yan, Pei Zhou, Bruce Randall Donald.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 271-284, Springer, Cham.
    • DOI: 10.1007/978-3-642-37195-0_25
• Genome-Wide Survival Analysis of Somatic Mutations in Cancer. Fabio Vandin, Alexandra Papoutsaki, Benjamin J. Raphael, Eli Upfal.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 285-286, Springer, Cham.
    • DOI: 10.1007/978-3-642-37195-0_26
• Spectral Library Generating Function for Assessing Spectrum-Spectrum Match Significance. Mingxun Wang and Nuno Bandeira.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 287-288, Springer, Cham.
    • DOI: 10.1007/978-3-642-37195-0_27
• SPARSE: Quadratic Time Simultaneous Alignment and Folding of RNAs without Sequence-Based Heuristics. Sebastian Will, Christina Schmiedl, Milad Miladi, Mathias Möhl, Rolf Backofen.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 289-290, Springer, Cham.
    • DOI: 10.1007/978-3-642-37195-0_28
• An Algorithm for Constructing Parsimonious Hybridization Networks with Multiple Phylogenetic Trees. Yufeng Wu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 291-303, Springer, Cham.
    • DOI: 10.1007/978-3-642-37195-0_29
• Fast and Accurate Calculation of Protein Depth by Euclidean Distance Transform. Dong Xu, Hua Li, Yang Zhang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 304-316, Springer, Cham.
    • DOI: 10.1007/978-3-642-37195-0_30
• Inference of Spatial Organizations of Chromosomes Using Semi-definite Embedding Approach and Hi-C Data. ZhiZhuo Zhang, Guoliang Li, Kim-Chuan Toh, Wing-Kin Sung.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 317-332, Springer, Cham.
    • DOI: 10.1007/978-3-642-37195-0_31
• Boosting Prediction Performance of Protein-Protein Interaction Hot Spots by Using Structural Neighborhood Properties. Lei Deng, Jihong Guan, Xiaoming Wei, Yuan Yi, Shuigeng Zhou.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science, vol 7821, pp 333-344, Springer, Cham.
    • DOI: 10.1007/978-3-642-37195-0_32