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  author = {Tetsuo Shibuya},
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  proceedings_volume = {5541},
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}

@article{He2010,
  author = {Zengyou He, Chao Yang, Can Yang, Robert Z. Qi, Jason Po-Ming Tam, Weichuan Yu},
  title = {Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification},
  journal = {Journal of Computational Biology},
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  year = {2010},
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@inproceedings{Peng2009,
  author = {Jian Peng and Jinbo Xu},
  title = {Boosting Protein Threading Accuracy},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 31-45, Springer, Cham.},
  pages = {31--45},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 31-45, Springer, Cham.},
  proceedings_volume = {5541},
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@inproceedings{Chauve2009,
  author = {Cedric Chauve and Nadia El-Mabrouk},
  title = {New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 46-58, Springer, Cham.},
  pages = {46--58},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 46-58, Springer, Cham.},
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@inproceedings{Zhao2009,
  author = {Feng Zhao, Jian Peng, Joe DeBartolo, Karl F. Freed, Tobin R. Sosnick, Jinbo Xu},
  title = {A Probabilistic Graphical Model for Ab Initio Folding},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 59-73, Springer, Cham.},
  pages = {59--73},
  year = {2009},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 59-73, Springer, Cham.},
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@article{Brückner2009,
  author = {Stefan Brückner, Falk Hüffner, Richard M. Karp, Ron Shamir, Roded Sharan},
  title = {Torque: topology-free querying of protein interaction networks},
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  doi = {10.1093/nar/gkp474},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 74-89, Springer, Cham.},
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@article{Lu2010,
  author = {Yong Lu, Roni Rosenfeld, Gerard J. Nau, Ziv Bar‐Joseph},
  title = {Cross Species Expression Analysis of Innate Immune Response},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 90-107, Springer, Cham.},
  proceedings_volume = {5541},
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@article{Kirkpatrick2010,
  author = {Bonnie Kirkpatrick, Eran Halperin, Richard M. Karp},
  title = {Haplotype Inference in Complex Pedigrees},
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  doi = {10.1089/cmb.2009.0174},
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@article{Mäkinen2008,
  author = {Veli Mäkinen, Gonzalo Navarro, Jouni Sirén, Niko Välimäki},
  title = {Storage and Retrieval of Individual Genomes},
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  volume = {0},
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@article{Ramanathan2010,
  author = {Arvind Ramanathan, Pratul K. Agarwal, Maria G. Kurnikova, Christopher J. Langmead},
  title = {An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations},
  journal = {Journal of Computational Biology},
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@article{Donzé2010,
  author = {Alexandre Donzé, Gilles Clermont, Christopher J. Langmead},
  title = {Parameter Synthesis in Nonlinear Dynamical Systems: Application to Systems Biology},
  journal = {Journal of Computational Biology},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 155-169, Springer, Cham.},
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@inproceedings{Jaschek2009,
  author = {Rami Jaschek and Amos Tanay},
  title = {Spatial Clustering of Multivariate Genomic and Epigenomic Information},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 170-183, Springer, Cham.},
  pages = {170--183},
  year = {2009},
  doi = {10.1007/978-3-642-02008-7_12},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 170-183, Springer, Cham.},
  proceedings_volume = {5541},
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@article{Pattengale2010,
  author = {Nicholas D. Pattengale, Masoud Alipour, Olaf R. P. Bininda‐Emonds, Bernard M. E. Moret, Alexandros Stamatakis},
  title = {How Many Bootstrap Replicates Are Necessary?},
  journal = {Journal of Computational Biology},
  volume = {17},
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  doi = {10.1089/cmb.2009.0179},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 184-200, Springer, Cham.},
  proceedings_volume = {5541},
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@article{Stegle2010,
  author = {Oliver Stegle, Katherine Denby, Emma J. Cooke, David L. Wild, Zoubin Ghahramani, Karsten Borgwardt},
  title = {A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series},
  journal = {Journal of Computational Biology},
  volume = {17},
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  pages = {355--367},
  year = {2010},
  doi = {10.1089/cmb.2009.0175},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 201-216, Springer, Cham.},
  proceedings_volume = {5541},
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@article{Raveh-Sadka2009,
  author = {Tali Raveh-Sadka, Michal Levo, Eran Segal},
  title = {Incorporating nucleosomes into thermodynamic models of transcription regulation},
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  year = {2009},
  doi = {10.1101/gr.088260.108},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 217-217, Springer, Cham.},
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@article{Hormozdiari2009,
  author = {Fereydoun Hormozdiari, Can Alkan, Evan E. Eichler, S. Cenk Sahinalp},
  title = {Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes},
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  doi = {10.1101/gr.088633.108},
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  proceedings_volume = {5541},
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@article{Bashir2010,
  author = {Ali Bashir, Qing Lü, Dennis A. Carson, Benjamin J. Raphael, Yu‐Tsueng Liu, Vineet Bafna},
  title = {Optimizing PCR Assays for DNA-Based Cancer Diagnostics},
  journal = {Journal of Computational Biology},
  volume = {17},
  number = {3},
  pages = {369--381},
  year = {2010},
  doi = {10.1089/cmb.2009.0203},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 220-235, Springer, Cham.},
  proceedings_volume = {5541},
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@article{Gusfield2010,
  author = {Dan Gusfield},
  title = {The Multi-State Perfect Phylogeny Problem with Missing and Removable Data: Solutions via Integer-Programming and Chordal Graph Theory},
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  doi = {10.1089/cmb.2009.0200},
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  proceedings_volume = {5541},
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@article{Zhang2010,
  author = {Xiang Zhang, Feng Pan, Yuying Xie, Fei Zou, Wei Wang},
  title = {COE: A General Approach for Efficient Genome-Wide Two-Locus Epistasis Test in Disease Association Study},
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  doi = {10.1089/cmb.2009.0155},
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  proceedings_volume = {5541},
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@article{Prabhu2009,
  author = {Snehit Prabhu, Itsik Pe’er},
  title = {Overlapping pools for high-throughput targeted resequencing},
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  doi = {10.1101/gr.088559.108},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 270-270, Springer, Cham.},
  proceedings_volume = {5541},
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@article{Zagordi2010,
  author = {Osvaldo Zagordi, Lukas Geyrhofer, Volker Röth, Niko Beerenwinkel},
  title = {Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction},
  journal = {Journal of Computational Biology},
  volume = {17},
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  pages = {417--428},
  year = {2010},
  doi = {10.1089/cmb.2009.0164},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 271-284, Springer, Cham.},
  proceedings_volume = {5541},
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@article{Möhl2010,
  author = {Mathias Möhl, Sebastian Will, Rolf Backofen},
  title = {Lifting Prediction to Alignment of RNA Pseudoknots},
  journal = {Journal of Computational Biology},
  volume = {17},
  number = {3},
  pages = {429--442},
  year = {2010},
  doi = {10.1089/cmb.2009.0168},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 285-301, Springer, Cham.},
  proceedings_volume = {5541},
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@article{Lavallée‐Adam2010,
  author = {Mathieu Lavallée‐Adam, Benoit Coulombe, Mathieu Blanchette},
  title = {Detection of Locally Over-Represented GO Terms in Protein-Protein Interaction Networks},
  journal = {Journal of Computational Biology},
  volume = {17},
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  pages = {443--457},
  year = {2010},
  doi = {10.1089/cmb.2009.0165},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 302-320, Springer, Cham.},
  proceedings_volume = {5541},
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@article{Zheng2010,
  author = {Wei Zheng, Karl E. Griswold, Chris Bailey‐Kellogg},
  title = {Protein Fragment Swapping: A Method for Asymmetric, Selective Site-Directed Recombination},
  journal = {Journal of Computational Biology},
  volume = {17},
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  pages = {459--475},
  year = {2010},
  doi = {10.1089/cmb.2009.0189},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 321-338, Springer, Cham.},
  proceedings_volume = {5541},
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@article{Waldispühl2014,
  author = {Jérôme Waldispühl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger},
  title = {Simultaneous Alignment and Folding of Protein Sequences},
  journal = {Journal of Computational Biology},
  volume = {21},
  number = {7},
  pages = {477--491},
  year = {2014},
  doi = {10.1089/cmb.2013.0163},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 339-355, Springer, Cham.},
  proceedings_volume = {5541},
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@article{Dost2012,
  author = {Banu Dost, Nuno Bandeira, Xiangqian Li, Zhouxin Shen, Steven P. Briggs, Vineet Bafna},
  title = {Accurate Mass Spectrometry Based Protein Quantification via Shared Peptides},
  journal = {Journal of Computational Biology},
  volume = {19},
  number = {4},
  pages = {337--348},
  year = {2012},
  doi = {10.1089/cmb.2009.0267},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 356-371, Springer, Cham.},
  proceedings_volume = {5541},
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@article{Hescott2010,
  author = {Benjamin Hescott, Mark D.M. Leiserson, Thuc Duy Le, Donna K. Slonim},
  title = {Evaluating Between-Pathway Models with Expression Data},
  journal = {Journal of Computational Biology},
  volume = {17},
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  year = {2010},
  doi = {10.1089/cmb.2009.0178},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 372-385, Springer, Cham.},
  proceedings_volume = {5541},
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@article{Swenson2010,
  author = {Krister M. Swenson, Vaibhav Rajan, Yu Lin, Bernard M. E. Moret},
  title = {Sorting Signed Permutations by Inversions in O ( n log n ) Time},
  journal = {Journal of Computational Biology},
  volume = {17},
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  year = {2010},
  doi = {10.1089/cmb.2009.0184},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 386-399, Springer, Cham.},
  proceedings_volume = {5541},
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@article{Navlakha2010,
  author = {Saket Navlakha, James R. White, Niranjan Nagarajan, Mihai Pop, Carl Kingsford},
  title = {Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information},
  journal = {Journal of Computational Biology},
  volume = {17},
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  year = {2010},
  doi = {10.1089/cmb.2009.0173},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 400-417, Springer, Cham.},
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@article{Sindi2010,
  author = {Suzanne Sindi, Benjamin J. Raphael},
  title = {Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data},
  journal = {Journal of Computational Biology},
  volume = {17},
  number = {3},
  pages = {517--531},
  year = {2010},
  doi = {10.1089/cmb.2009.0185},
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  proceedings_volume = {5541},
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@inproceedings{Reynolds2009,
  author = {Sheila M. Reynolds, Jeff A. Bilmes, William Stafford Noble},
  title = {On the Relationship between DNA Periodicity and Local Chromatin Structure},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 434-450, Springer, Cham.},
  pages = {434--450},
  year = {2009},
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  proceedings_volume = {5541},
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@inproceedings{Daskalakis2009,
  author = {Constantinos Daskalakis, Elchanan Mossel, Sebastien Roch},
  title = {Phylogenies without Branch Bounds: Contracting the Short, Pruning the Deep},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 451-465, Springer, Cham.},
  pages = {451--465},
  year = {2009},
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  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 451-465, Springer, Cham.},
  proceedings_volume = {5541},
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  preprint_id = {arXiv:0801.4190},
  preprint_doi = {10.48550/arXiv.0801.4190}
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@article{Kang2010,
  author = {Eun Yong Kang, Chun Ye, Ilya Shpitser, Eleazar Eskin},
  title = {Detecting the Presence and Absence of Causal Relationships between Expression of Yeast Genes with Very Few Samples},
  journal = {Journal of Computational Biology},
  volume = {17},
  number = {3},
  pages = {533--546},
  year = {2010},
  doi = {10.1089/cmb.2009.0176},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 466-481, Springer, Cham.},
  proceedings_volume = {5541},
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@article{Kang2010,
  author = {Hyun Min Kang, Noah Zaitlen, Eleazar Eskin},
  title = {EMINIM: An Adaptive and Memory-Efficient Algorithm for Genotype Imputation},
  journal = {Journal of Computational Biology},
  volume = {17},
  number = {3},
  pages = {547--560},
  year = {2010},
  doi = {10.1089/cmb.2009.0199},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 482-495, Springer, Cham.},
  proceedings_volume = {5541},
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@inproceedings{Sharon2009,
  author = {Itai Sharon, Amrita Pati, Victor M. Markowitz, Ron Y. Pinter},
  title = {A Statistical Framework for the Functional Analysis of Metagenomes},
  booktitle = {Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 496-511, Springer, Cham.},
  pages = {496--511},
  year = {2009},
  doi = {10.1007/978-3-642-02008-7_35},
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  proceedings_volume = {5541},
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@article{Kececioglu2010,
  author = {John Kececioglu, Eagu Kim, Travis J. Wheeler},
  title = {Aligning Protein Sequences with Predicted Secondary Structure},
  journal = {Journal of Computational Biology},
  volume = {17},
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  pages = {561--580},
  year = {2010},
  doi = {10.1089/cmb.2009.0222},
  proceedings_name = {Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science, vol 5541, pp 512-532, Springer, Cham.},
  proceedings_volume = {5541},
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