{ "title": "15th Annual International Conference on Research in Computational Molecular Biology", "location": "Vancouver, BC, Canada", "dates": "March 28 - 31, 2011", "pc_chair": "Vineet Bafna", "organization_committee": "S. Cenk Sahinalp (chair), Cedric Chauve, Martin Ester, Inanc Birol, Fiona Brinkman, Steven Jones, Anne Condon, Jack Chen, Artem Cherkasov, Colin Collins, Tamon Stephen, Stas Volik, Wyeth Wasserman, Kay Wiese", "keynotes": "Evan Eichler, Daphne Koller, Marco Marra, Karen Nelson, Elaine Mardis, Joseph Nadeau", "website": "https://recomb.org/recomb2011/", "papers": [ { "author": "Amnon Amir and Or Zuk", "title": "Bacterial Community Reconstruction Using Compressed Sensing", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 1-15, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "1-15", "proceedings_doi": "10.1007/978-3-642-20036-6_1", "journal": "Journal of Computational Biology", "journal_title": "Bacterial community reconstruction using compressed sensing", "journal_authors": "Amnon Amir, Or Zuk", "journal_issue_pages": "18(11): 1723-1741", "journal_year": "2011", "journal_doi": "10.1089/cmb.2011.0189" }, { "author": "Swapnil Bhatia, Yong J. Kil, Beatrix Ueberheide, Brian Chait, Lemmuel L. Tayo, Lourdes J. Cruz, Bingwen Lu, John R. Yates III, Marshall Bern", "title": "Constrained De Novo Sequencing of Peptides with Application to Conotoxins", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 16-30, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "16-30", "proceedings_doi": "10.1007/978-3-642-20036-6_2" }, { "author": "Leonid Chindelevitch, Aviv Regev, Bonnie Berger", "title": "Metabolic Network Analysis Demystified", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 31-33, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "31-33", "proceedings_doi": "10.1007/978-3-642-20036-6_3" }, { "author": "Leonid Chindelevitch, Daniel Ziemek, Ahmed Enayetallah, Ranjit Randhawa, Ben Sidders, Christoph Brockel, Enoch Huang", "title": "Causal Reasoning on Biological Networks: Interpreting Transcriptional Changes", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 34-37, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "34-37", "proceedings_doi": "10.1007/978-3-642-20036-6_4", "journal": "Bioinformatics", "journal_title": "Causal reasoning on biological networks: interpreting transcriptional changes", "journal_authors": "Leonid Chindelevitch, Daniel Ziemek, Ahmed Enayetallah, Ranjit Randhawa, Ben S. Sidders, Christoph Brockel, Enoch S. Huang", "journal_issue_pages": "28(8): 1114-1121", "journal_year": "2012", "journal_doi": "10.1093/bioinformatics/bts090" }, { "author": "Nilgun Donmez and Michael Brudno", "title": "Hapsembler: An Assembler for Highly Polymorphic Genomes", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 38-52, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "38-52", "proceedings_doi": "10.1007/978-3-642-20036-6_5" }, { "author": "Sinan Erten, Gurkan Bebek, Mehmet Koyutürk", "title": "Disease Gene Prioritization Based on Topological Similarity in Protein-Protein Interaction Networks", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 54-68, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "54-68", "proceedings_doi": "10.1007/978-3-642-20036-6_7", "journal": "Journal of Computational Biology", "journal_title": "Vavien : An Algorithm for Prioritizing Candidate Disease Genes Based on Topological Similarity of Proteins in Interaction Networks", "journal_authors": "Sinan Erten, Gürkan Bebek, Mehmet Koyutürk", "journal_issue_pages": "18(11): 1561-1574", "journal_year": "2011", "journal_doi": "10.1089/cmb.2011.0154" }, { "author": "Allison P. Heath, George N. Bennett, Lydia E. Kavraki", "title": "Identifying Branched Metabolic Pathways by Merging Linear Metabolic Pathways", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 70-84, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "70-84", "proceedings_doi": "10.1007/978-3-642-20036-6_9", "journal": "Journal of Computational Biology", "journal_title": "An Algorithm for Efficient Identification of Branched Metabolic Pathways", "journal_authors": "Allison P. Heath, George N. Bennett, Lydia E. Kavraki", "journal_issue_pages": "18(11): 1575-1597", "journal_year": "2011", "journal_doi": "10.1089/cmb.2011.0165" }, { "author": "Glenn Hickey and Mathieu Blanchette", "title": "A Probabilistic Model For Sequence Alignment with Context-Sensitive Indels", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 85-103, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "85-103", "proceedings_doi": "10.1007/978-3-642-20036-6_10", "journal": "Journal of Computational Biology", "journal_title": "A Probabilistic Model for Sequence Alignment with Context-Sensitive Indels", "journal_authors": "Glenn Hickey, Mathieu Blanchette", "journal_issue_pages": "18(11): 1449-1464", "journal_year": "2011", "journal_doi": "10.1089/cmb.2011.0157" }, { "author": "Fereydoun Hormozdiari, Iman Hajirasouliha, Andrew McPherson, Evan E. Eichler, S. Cenk Sahinalp", "title": "Simultaneous Structural Variation Discovery in Multiple Paired-End Sequenced Genomes", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 104-105, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "104-105", "proceedings_doi": "10.1007/978-3-642-20036-6_11", "journal": "Genome Research", "journal_title": "Simultaneous structural variation discovery among multiple paired-end sequenced genomes", "journal_authors": "Fereydoun Hormozdiari, Iman Hajirasouliha, Andrew McPherson, Evan E. Eichler, S. Cenk Sahinalp", "journal_issue_pages": "21(12): 2203-2212", "journal_year": "2011", "journal_doi": "10.1101/gr.120501.111" }, { "author": "Jim C. Huang and Nebojsa Jojic", "title": "Variable Selection through Correlation Sifting", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 106-123, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "106-123", "proceedings_doi": "10.1007/978-3-642-20036-6_12" }, { "author": "Shuai Jiang and Max A. Alekseyev", "title": "Weighted Genomic Distance Can Hardly Impose a Bound on the Proportion of Transpositions", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 124-133, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "124-133", "proceedings_doi": "10.1007/978-3-642-20036-6_13" }, { "author": "Jaebum Kim and Jian Ma", "title": "PSAR: Measuring Multiple Sequence Alignment Reliability by Probabilistic Sampling", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 134-135, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "134-135", "proceedings_doi": "10.1007/978-3-642-20036-6_14", "journal": "Nucleic Acids Research", "journal_title": "PSAR: measuring multiple sequence alignment reliability by probabilistic sampling", "journal_authors": "Jaebum Kim, Jian Ma", "journal_issue_pages": "39(15): 6359-6368", "journal_year": "2011", "journal_doi": "10.1093/nar/gkr334" }, { "author": "Bonnie Kirkpatrick, Shuai Cheng Li, Richard M. Karp, Eran Halperin", "title": "Pedigree Reconstruction Using Identity by Descent", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 136-152, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "136-152", "proceedings_doi": "10.1007/978-3-642-20036-6_15", "journal": "Journal of Computational Biology", "journal_title": "Pedigree Reconstruction Using Identity by Descent", "journal_authors": "Bonnie Kirkpatrick, Shuai Cheng Li, Richard M. Karp, Eran Halperin", "journal_issue_pages": "18(11): 1481-1493", "journal_year": "2011", "journal_doi": "10.1089/cmb.2011.0156" }, { "author": "Mark D.M. Leiserson, Diana Tatar, Lenore J. Cowen, Benjamin J. Hescott", "title": "Inferring Mechanisms of Compensation from E-MAP and SGA Data Using Local Search Algorithms for Max Cut", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 154-167, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "154-167", "proceedings_doi": "10.1007/978-3-642-20036-6_17", "journal": "Journal of Computational Biology", "journal_title": "Inferring Mechanisms of Compensation from E-MAP and SGA Data Using Local Search Algorithms for Max Cut", "journal_authors": "Mark D.M. Leiserson, Diana Tatar, Lenore Cowen, Benjamin Hescott", "journal_issue_pages": "18(11): 1399-1409", "journal_year": "2011", "journal_doi": "10.1089/cmb.2011.0191" }, { "author": "Wei Li, Jianxing Feng, Tao Jiang", "title": "IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 168-188, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "168-188", "proceedings_doi": "10.1007/978-3-642-20036-6_18", "journal": "Journal of Computational Biology", "journal_title": "IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly", "journal_authors": "Wei Li, Jianxing Feng, Tao Jiang", "journal_issue_pages": "18(11): 1693-1707", "journal_year": "2011", "journal_doi": "10.1089/cmb.2011.0171" }, { "author": "Xin Li and Jing Li", "title": "Haplotype Reconstruction in Large Pedigrees with Many Untyped Individuals", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 189-203, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "189-203", "proceedings_doi": "10.1007/978-3-642-20036-6_19", "journal": "Journal of Computational Biology", "journal_title": "Haplotype Reconstruction in Large Pedigrees with Untyped Individuals through IBD Inference", "journal_authors": "Xin Li, Jing Li", "journal_issue_pages": "18(11): 1411-1421", "journal_year": "2011", "journal_doi": "10.1089/cmb.2011.0167" }, { "author": "Tien-ho Lin, Ziv Bar-Joseph, Robert F. Murphy", "title": "Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 204-221, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "204-221", "proceedings_doi": "10.1007/978-3-642-20036-6_20", "journal": "Journal of Computational Biology", "journal_title": "Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs", "journal_authors": "Tien-ho Lin, Ziv Bar‐Joseph, Robert F. Murphy", "journal_issue_pages": "18(11): 1709-1722", "journal_year": "2011", "journal_doi": "10.1089/cmb.2011.0193" }, { "author": "Jeffrey W. Martin, Anthony K. Yan, Chris Bailey-Kellogg, Pei Zhou, Bruce R. Donald", "title": "A Geometric Arrangement Algorithm for Structure Determination of Symmetric Protein Homo-oligomers from NOEs and RDCs", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 222-237, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "222-237", "proceedings_doi": "10.1007/978-3-642-20036-6_21", "journal": "Journal of Computational Biology", "journal_title": "A Geometric Arrangement Algorithm for Structure Determination of Symmetric Protein Homo-Oligomers from NOEs and RDCs", "journal_authors": "Jeffrey W. Martin, Anthony K. Yan, Chris Bailey‐Kellogg, Pei Zhou, Bruce R. Donald", "journal_issue_pages": "18(11): 1507-1523", "journal_year": "2011", "journal_doi": "10.1089/cmb.2011.0173" }, { "author": "Paul Medvedev, Son Pham, Mark Chaisson, Glenn Tesler, Pavel Pevzner", "title": "Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 238-251, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "238-251", "proceedings_doi": "10.1007/978-3-642-20036-6_22", "journal": "Journal of Computational Biology", "journal_title": "Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers", "journal_authors": "Paul Medvedev, Son Pham, Mark Chaisson, Glenn Tesler, Pavel A. Pevzner", "journal_issue_pages": "18(11): 1625-1634", "journal_year": "2011", "journal_doi": "10.1089/cmb.2011.0151" }, { "author": "Navodit Misra, Guy Blelloch, R. Ravi, Russell Schwartz", "title": "An Optimization-Based Sampling Scheme for Phylogenetic Trees", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 252-266, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "252-266", "proceedings_doi": "10.1007/978-3-642-20036-6_23", "journal": "Journal of Computational Biology", "journal_title": "An Optimization-Based Sampling Scheme for Phylogenetic Trees", "journal_authors": "Navodit Misra, Guy E. Blelloch, R. Ravi, Russell Schwartz", "journal_issue_pages": "18(11): 1599-1609", "journal_year": "2011", "journal_doi": "10.1089/cmb.2011.0164" }, { "author": "Hosein Mohimani, Wei-Ting Liu, Yu-Liang Yang, Susana P. Gaudêncio, William Fenical, Pieter C. Dorrestein, Pavel A. Pevzner", "title": "Multiplex De Novo Sequencing of Peptide Antibiotics", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 267-281, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "267-281", "proceedings_doi": "10.1007/978-3-642-20036-6_24", "journal": "Journal of Computational Biology", "journal_title": "Multiplex De Novo Sequencing of Peptide Antibiotics", "journal_authors": "Hosein Mohimani, Wei-Ting Liu, Yuliang Yang, Susana P. Gaudêncio, William Fenical, Pieter C. Dorrestein, Pavel A. Pevzner", "journal_issue_pages": "18(11): 1371-1381", "journal_year": "2011", "journal_doi": "10.1089/cmb.2011.0158" }, { "author": "Daniel Newkirk, Jacob Biesinger, Alvin Chon, Kyoko Yokomori, Xiaohui Xie", "title": "AREM: Aligning Short Reads from ChIP-Sequencing by Expectation Maximization", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 283-297, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "283-297", "proceedings_doi": "10.1007/978-3-642-20036-6_26", "journal": "Journal of Computational Biology", "journal_title": "AREM: Aligning Short Reads from ChIP-Sequencing by Expectation Maximization", "journal_authors": "Daniel A. Newkirk, Jacob Biesinger, Alvin Chon, Kyoko Yokomori, Xiaohui Xie", "journal_issue_pages": "18(11): 1495-1505", "journal_year": "2011", "journal_doi": "10.1089/cmb.2011.0185" }, { "author": "Julio Ng, Amihood Amir, Pavel A. Pevzner", "title": "Blocked Pattern Matching Problem and Its Applications in Proteomics", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 298-319, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "298-319", "proceedings_doi": "10.1007/978-3-642-20036-6_27" }, { "author": "Andrew S. Parker, Karl E. Griswold, Chris Bailey-Kellogg", "title": "Optimization of Combinatorial Mutagenesis", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 321-335, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "321-335", "proceedings_doi": "10.1007/978-3-642-20036-6_29", "journal": "Journal of Computational Biology", "journal_title": "Optimization of Combinatorial Mutagenesis", "journal_authors": "Andrew S. Parker, Karl E. Griswold, Chris Bailey‐Kellogg", "journal_issue_pages": "18(11): 1743-1756", "journal_year": "2011", "journal_doi": "10.1089/cmb.2011.0152" }, { "author": "Yu Peng, Henry C.M. Leung, S.M. Yiu, Francis Y.L. Chin", "title": "T-IDBA: A de novo Iterative de Bruijn Graph Assembler for Transcriptome", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 337-338, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "337-338", "proceedings_doi": "10.1007/978-3-642-20036-6_31" }, { "author": "Tobias Petri, Robert Küffner, Ralf Zimmer", "title": "Experiment Specific Expression Patterns", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 339-354, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "339-354", "proceedings_doi": "10.1007/978-3-642-20036-6_32", "journal": "Journal of Computational Biology", "journal_title": "Experiment Specific Expression Patterns", "journal_authors": "Tobias Petri, Robert Küffner, Ralf Zimmer", "journal_issue_pages": "18(11): 1423-1435", "journal_year": "2011", "journal_doi": "10.1089/cmb.2011.0159" }, { "author": "Yosef Prat, Menachem Fromer, Michal Linial, Nathan Linial", "title": "Geometric Interpretation of Gene Expression by Sparse Reconstruction of Transcript Profiles", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 355-357, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "355-357", "proceedings_doi": "10.1007/978-3-642-20036-6_33" }, { "author": "Shlomi Reuveni, Isaac Meilijson, Martin Kupiec, Eytan Ruppin, Tamir Tuller", "title": "A Ribosome Flow Model for Analyzing Translation Elongation", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 358-360, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "358-360", "proceedings_doi": "10.1007/978-3-642-20036-6_34" }, { "author": "Kyle E. Roberts, Patrick R. Cushing, Prisca Boisguerin, Dean R. Madden, Bruce R. Donald", "title": "Design of Protein-Protein Interactions with a Novel Ensemble-Based Scoring Algorithm", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 361-376, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "361-376", "proceedings_doi": "10.1007/978-3-642-20036-6_35" }, { "author": "Kerstin Scheubert, Franziska Hufsky, Florian Rasche, Sebastian Böcker", "title": "Computing Fragmentation Trees from Metabolite Multiple Mass Spectrometry Data", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 377-391, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "377-391", "proceedings_doi": "10.1007/978-3-642-20036-6_36", "journal": "Journal of Computational Biology", "journal_title": "Computing Fragmentation Trees from Metabolite Multiple Mass Spectrometry Data", "journal_authors": "Kerstin Scheubert, Franziska Hufsky, Florian Rasche, Sebastian Böcker", "journal_issue_pages": "18(11): 1383-1397", "journal_year": "2011", "journal_doi": "10.1089/cmb.2011.0168" }, { "author": "Emre Sefer and Carl Kingsford", "title": "Metric Labeling and Semi-metric Embedding for Protein Annotation Prediction", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 392-407, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "392-407", "proceedings_doi": "10.1007/978-3-642-20036-6_37" }, { "author": "Solomon Shenker, Charles W. O'Donnell, Srinivas Devadas, Bonnie Berger, Jérôme Waldispühl", "title": "Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 408-423, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "408-423", "proceedings_doi": "10.1007/978-3-642-20036-6_38", "journal": "Journal of Computational Biology", "journal_title": "Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models", "journal_authors": "Solomon Shenker, Charles W. O'Donnell, Srinivas Devadas, Bonnie Berger, Jérôme Waldispühl", "journal_issue_pages": "18(11): 1635-1647", "journal_year": "2011", "journal_doi": "10.1089/cmb.2011.0176" }, { "author": "Dana Silverbush, Michael Elberfeld, Roded Sharan", "title": "Optimally Orienting Physical Networks", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 424-436, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "424-436", "proceedings_doi": "10.1007/978-3-642-20036-6_39", "journal": "Journal of Computational Biology", "journal_title": "Optimally Orienting Physical Networks", "journal_authors": "Dana Silverbush, Michael Elberfeld, Roded Sharan", "journal_issue_pages": "18(11): 1437-1448", "journal_year": "2011", "journal_doi": "10.1089/cmb.2011.0163" }, { "author": "Song Gao, Niranjan Nagarajan, Wing-Kin Sung", "title": "Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 437-451, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "437-451", "proceedings_doi": "10.1007/978-3-642-20036-6_40", "journal": "Journal of Computational Biology", "journal_title": "Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences", "journal_authors": "Song Gao, Wing‐Kin Sung, Niranjan Nagarajan", "journal_issue_pages": "18(11): 1681-1691", "journal_year": "2011", "journal_doi": "10.1089/cmb.2011.0170" }, { "author": "Jae Hoon Sul, Buhm Han, Eleazar Eskin", "title": "Increasing Power of Groupwise Association Test with Likelihood Ratio Test", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 452-467, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "452-467", "proceedings_doi": "10.1007/978-3-642-20036-6_41", "journal": "Journal of Computational Biology", "journal_title": "Increasing Power of Groupwise Association Test with Likelihood Ratio Test", "journal_authors": "Jae Hoon Sul, Buhm Han, Eleazar Eskin", "journal_issue_pages": "18(11): 1611-1624", "journal_year": "2011", "journal_doi": "10.1089/cmb.2011.0161" }, { "author": "Ryan Tarpine, Fumei Lam, Sorin Istrail", "title": "Conservative Extensions of Linkage Disequilibrium Measures from Pairwise to Multi-loci and Algorithms for Optimal Tagging SNP Selection", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 468-482, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "468-482", "proceedings_doi": "10.1007/978-3-642-20036-6_42" }, { "author": "Chittaranjan Tripathy, Jianyang Zeng, Pei Zhou, Bruce Randall Donald", "title": "Protein Loop Closure Using Orientational Restraints from NMR Data", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 483-498, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "483-498", "proceedings_doi": "10.1007/978-3-642-20036-6_43", "journal": "Proteins", "journal_title": "Protein loop closure using orientational restraints from NMR data", "journal_authors": "Chittaranjan Tripathy, Jianyang Zeng, Pei Zhou, Bruce R. Donald", "journal_issue_pages": "80(2): 433-453", "journal_year": "2011", "journal_doi": "10.1002/prot.23207" }, { "author": "Fabio Vandin, Eli Upfal, Benjamin J. Raphael", "title": "De Novo Discovery of Mutated Driver Pathways in Cancer", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 499-500, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "499-500", "proceedings_doi": "10.1007/978-3-642-20036-6_44", "journal": "Genome Research", "journal_title": "De novo discovery of mutated driver pathways in cancer", "journal_authors": "Fabio Vandin, Eli Upfal, Benjamin J. Raphael", "journal_issue_pages": "22(2): 375-385", "journal_year": "2011", "journal_doi": "10.1101/gr.120477.111" }, { "author": "Jérôme Waldispühl and Yann Ponty", "title": "An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes under Evolutionary Pressure", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 501-515, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "501-515", "proceedings_doi": "10.1007/978-3-642-20036-6_45", "journal": "Journal of Computational Biology", "journal_title": "An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes Under Evolutionary Pressure", "journal_authors": "Jérôme Waldispühl, Yann Ponty", "journal_issue_pages": "18(11): 1465-1479", "journal_year": "2011", "journal_doi": "10.1089/cmb.2011.0181" }, { "author": "Fabian L. Wauthier, Michael I. Jordan, Nebojsa Jojic", "title": "Nonparametric Combinatorial Sequence Models", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 516-530, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "516-530", "proceedings_doi": "10.1007/978-3-642-20036-6_46", "journal": "Journal of Computational Biology", "journal_title": "Nonparametric Combinatorial Sequence Models", "journal_authors": "Fabian L. Wauthier, Michael I. Jordan, Nebojša Jojić", "journal_issue_pages": "18(11): 1649-1660", "journal_year": "2011", "journal_doi": "10.1089/cmb.2011.0175" }, { "author": "Yun Yu, Tandy Warnow, Luay Nakhleh", "title": "Algorithms for MDC-Based Multi-locus Phylogeny Inference", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 531-545, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "531-545", "proceedings_doi": "10.1007/978-3-642-20036-6_47", "journal": "Journal of Computational Biology", "journal_title": "Algorithms for MDC-Based Multi-Locus Phylogeny Inference: Beyond Rooted Binary Gene Trees on Single Alleles", "journal_authors": "Yun Yu, Tandy Warnow, Luay Nakhleh", "journal_issue_pages": "18(11): 1543-1559", "journal_year": "2011", "journal_doi": "10.1089/cmb.2011.0174" }, { "author": "Shay Zakov, Yoav Goldberg, Michael Elhadad, Michal Ziv-Ukelson", "title": "Rich Parameterization Improves RNA Structure Prediction", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science, vol 6577, pp 546-562, Springer, Cham.", "proceedings_volume": "6577", "proceedings_pages": "546-562", "proceedings_doi": "10.1007/978-3-642-20036-6_48", "journal": "Journal of Computational Biology", "journal_title": "Rich Parameterization Improves RNA Structure Prediction", "journal_authors": "Shay Zakov, Yoav Goldberg, Michael Elhadad, Michal Ziv-Ukelson", "journal_issue_pages": "18(11): 1525-1542", "journal_year": "2011", "journal_doi": "10.1089/cmb.2011.0184" }, { "author": "Jianyang Zeng, Kyle E. Roberts, Pei Zhou, Bruce R. Donald", "title": "A Bayesian Approach for Determining Protein Side-Chain Rotamer Conformations Using Unassigned NOE Data", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2011. 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