13. RECOMB 2009: Tucson, AZ, USA

• Tetsuo Shibuya:
  Searching Protein 3-D Structures in Linear Time. 1-15
  
• Zengyou He, Chao Yang, Can Yang, Robert Z. Qi, Jason Po-Ming Tam, Weichuan Yu:
  Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification. 16-30
  
• Jian Peng, Jinbo Xu:
  Boosting Protein Threading Accuracy. 31-45
  
• Cedric Chauve, Nadia El-Mabrouk:
  New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees. 46-58
  
• Feng Zhao, Jian Peng, Joe DeBartolo, Karl F. Freed, Tobin R. Sosnick, Jinbo Xu:
  A Probabilistic Graphical Model for Ab Initio Folding. 59-73
  
• Sharon Bruckner, Falk Hüffner, Richard M. Karp, Ron Shamir, Roded Sharan:
  Topology-Free Querying of Protein Interaction Networks. 74-89
  
• Yong Lu, Roni Rosenfeld, Gerard J. Nau, Ziv Bar-Joseph:
  Cross Species Expression Analysis of Innate Immune Response. 90-107
  
• Bonnie Kirkpatrick, Javier Rosa, Eran Halperin, Richard M. Karp:
  Haplotype Inference in Complex Pedigrees. 108-120
  
• Veli Mäkinen, Gonzalo Navarro, Jouni Sirén, Niko Välimäki:
  Storage and Retrieval of Individual Genomes. 121-137
  
• Arvind Ramanathan, Pratul K. Agarwal, Maria Kurnikova, Christopher James Langmead:
  An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations. 138-154
  
• Alexandre Donzé, Gilles Clermont, Axel Legay, Christopher James Langmead:
  Parameter Synthesis in Nonlinear Dynamical Systems: Application to Systems Biology. 155-169
  
• Rami Jaschek, Amos Tanay:
  Spatial Clustering of Multivariate Genomic and Epigenomic Information. 170-183
  
• Nicholas D. Pattengale, Masoud Alipour, Olaf R. P. Bininda-Emonds, Bernard M. E. Moret, Alexandros Stamatakis:
  How Many Bootstrap Replicates Are Necessary?. 184-200
  
• Oliver Stegle, Katherine J. Denby, David L. Wild, Zoubin Ghahramani, Karsten M. Borgwardt:
  A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series. 201-216
  
• Tali Raveh-Sadka, Michal Levo, Eran Segal:
  Incorporating Nucleosomes into Thermodynamic Models of Transcription Regulation. 217
  
• Fereydoun Hormozdiari, Can Alkan, Evan E. Eichler, Süleyman Cenk Sahinalp:
  Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes. 218-219
  
• Ali Bashir, Qing Lu, Dennis Carson, Benjamin J. Raphael, Yu-Tsueng Liu, Vineet Bafna:
  Optimizing PCR Assays for DNA Based Cancer Diagnostics. 220-235
  
• Dan Gusfield:
  The Multi-State Perfect Phylogeny Problem with Missing and Removable Data: Solutions via Integer-Programming and Chordal Graph Theory. 236-252
  
• Xiang Zhang, Feng Pan, Yuying Xie, Fei Zou, Wei Wang:
  COE: A General Approach for Efficient Genome-Wide Two-Locus Epistasis Test in Disease Association Study. 253-269
  
• Snehit Prabhu, Itsik Pe'er:
  Overlapping Pools for High Throughput Targeted Resequencing. 270
  
• Osvaldo Zagordi, Lukas Geyrhofer, Volker Roth, Niko Beerenwinkel:
  Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction. 271-284
  
• Mathias Möhl, Sebastian Will, Rolf Backofen:
  Lifting Prediction to Alignment of RNA Pseudoknots. 285-301
  
• Mathieu Lavallée-Adam, Benoit Coulombe, Mathieu Blanchette:
  Detection of Locally Over-Represented GO Terms in Protein-Protein Interaction Networks. 302-320
  
• Wei Zheng, Karl E. Griswold, Chris Bailey-Kellogg:
  Protein Fragment Swapping: A Method for Asymmetric, Selective Site-Directed Recombination. 321-338
  
• Jérôme Waldispühl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger:
  Simultaneous Alignment and Folding of Protein Sequences. 339-355
  
• Banu Dost, Nuno Bandeira, Xiangqian Li, Zhouxin Shen, Steve Briggs, Vineet Bafna:
  Shared Peptides in Mass Spectrometry Based Protein Quantification. 356-371
  
• Benjamin J. Hescott, Mark D. M. Leiserson, Lenore Cowen, Donna K. Slonim:
  Evaluating Between-Pathway Models with Expression Data. 372-385
  
• Krister M. Swenson, Vaibhav Rajan, Yu Lin, Bernard M. E. Moret:
  Sorting Signed Permutations by Inversions in O(nlogn) Time. 386-399
  
• Saket Navlakha, James Robert White, Niranjan Nagarajan, Mihai Pop, Carl Kingsford:
  Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information. 400-417
  
• Suzanne S. Sindi, Benjamin J. Raphael:
  Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data. 418-433
  
• Sheila M. Reynolds, Jeff A. Bilmes, William Stafford Noble:
  On the Relationship between DNA Periodicity and Local Chromatin Structure. 434-450
  
• Constantinos Daskalakis, Elchanan Mossel, Sébastien Roch:
  Phylogenies without Branch Bounds: Contracting the Short, Pruning the Deep. 451-465
  
• Eun Yong Kang, Ilya Shpitser, Chun Ye, Eleazar Eskin:
  Detecting the Presence and Absence of Causal Relationships between Expression of Yeast Genes with Very Few Samples. 466-481
  
• Hyun Min Kang, Noah Zaitlen, Buhm Han, Eleazar Eskin:
  An Adaptive and Memory Efficient Algorithm for Genotype Imputation. 482-495
  
• Itai Sharon, Amrita Pati, Victor M. Markowitz, Ron Y. Pinter:
  A Statistical Framework for the Functional Analysis of Metagenomes. 496-511
  
• Eagu Kim, Travis J. Wheeler, John D. Kececioglu:
  Learning Models for Aligning Protein Sequences with Predicted Secondary Structure. 512-531