| 2009 | A Probabilistic Graphical Model for Ab Initio Folding. Feng Zhao, Jian Peng, Joe DeBartolo, Karl F. Freed, Tobin R. Sosnick, Jinbo Xu |
| 2009 | A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series. Oliver Stegle, Katherine J. Denby, David L. Wild, Zoubin Ghahramani, Karsten M. Borgwardt |
| 2009 | A Statistical Framework for the Functional Analysis of Metagenomes. Itai Sharon, Amrita Pati, Victor M. Markowitz, Ron Y. Pinter |
| 2009 | An Adaptive and Memory Efficient Algorithm for Genotype Imputation. Hyun Min Kang, Noah Zaitlen, Buhm Han, Eleazar Eskin |
| 2009 | An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations. Arvind Ramanathan, Pratul K. Agarwal, Maria G. Kurnikova, Christopher James Langmead |
| 2009 | Boosting Protein Threading Accuracy. Jian Peng, Jinbo Xu |
| 2009 | COE: A General Approach for Efficient Genome-Wide Two-Locus Epistasis Test in Disease Association Study. Xiang Zhang, Feng Pan, Yuying Xie, Fei Zou, Wei Wang |
| 2009 | Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes. Fereydoun Hormozdiari, Can Alkan, Evan E. Eichler, Süleyman Cenk Sahinalp |
| 2009 | Cross Species Expression Analysis of Innate Immune Response. Yong Lu, Roni Rosenfeld, Gerard J. Nau, Ziv Bar-Joseph |
| 2009 | Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction. Osvaldo Zagordi, Lukas Geyrhofer, Volker Roth, Niko Beerenwinkel |
| 2009 | Detecting the Presence and Absence of Causal Relationships between Expression of Yeast Genes with Very Few Samples. Eun Yong Kang, Ilya Shpitser, Chun Ye, Eleazar Eskin |
| 2009 | Detection of Locally Over-Represented GO Terms in Protein-Protein Interaction Networks. Mathieu Lavallée-Adam, Benoit Coulombe, Mathieu Blanchette |
| 2009 | Evaluating Between-Pathway Models with Expression Data. Benjamin J. Hescott, Mark D. M. Leiserson, Lenore Cowen, Donna K. Slonim |
| 2009 | Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information. Saket Navlakha, James Robert White, Niranjan Nagarajan, Mihai Pop, Carl Kingsford |
| 2009 | Haplotype Inference in Complex Pedigrees. Bonnie Kirkpatrick, Javier Rosa, Eran Halperin, Richard M. Karp |
| 2009 | How Many Bootstrap Replicates Are Necessary? Nicholas D. Pattengale, Masoud Alipour, Olaf R. P. Bininda-Emonds, Bernard M. E. Moret, Alexandros Stamatakis |
| 2009 | Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data. Suzanne S. Sindi, Benjamin J. Raphael |
| 2009 | Incorporating Nucleosomes into Thermodynamic Models of Transcription Regulation. Tali Raveh-Sadka, Michal Levo, Eran Segal |
| 2009 | Learning Models for Aligning Protein Sequences with Predicted Secondary Structure. Eagu Kim, Travis J. Wheeler, John D. Kececioglu |
| 2009 | Lifting Prediction to Alignment of RNA Pseudoknots. Mathias Möhl, Sebastian Will, Rolf Backofen |
| 2009 | New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees. Cédric Chauve, Nadia El-Mabrouk |
| 2009 | On the Relationship between DNA Periodicity and Local Chromatin Structure. Sheila M. Reynolds, Jeff A. Bilmes, William Stafford Noble |
| 2009 | Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification. Zengyou He, Chao Yang, Can Yang, Robert Z. Qi, Jason Po-Ming Tam, Weichuan Yu |
| 2009 | Optimizing PCR Assays for DNA Based Cancer Diagnostics. Ali Bashir, Qing Lu, Dennis Carson, Benjamin J. Raphael, Yu-Tsueng Liu, Vineet Bafna |
| 2009 | Overlapping Pools for High Throughput Targeted Resequencing. Snehit Prabhu, Itsik Pe'er |
| 2009 | Parameter Synthesis in Nonlinear Dynamical Systems: Application to Systems Biology. Alexandre Donzé, Gilles Clermont, Axel Legay, Christopher James Langmead |
| 2009 | Phylogenies without Branch Bounds: Contracting the Short, Pruning the Deep. Constantinos Daskalakis, Elchanan Mossel, Sébastien Roch |
| 2009 | Protein Fragment Swapping: A Method for Asymmetric, Selective Site-Directed Recombination. Wei Zheng, Karl E. Griswold, Chris Bailey-Kellogg |
| 2009 | Research in Computational Molecular Biology, 13th Annual International Conference, RECOMB 2009, Tucson, AZ, USA, May 18-21, 2009. Proceedings Serafim Batzoglou |
| 2009 | Searching Protein 3-D Structures in Linear Time. Tetsuo Shibuya |
| 2009 | Shared Peptides in Mass Spectrometry Based Protein Quantification. Banu Dost, Nuno Bandeira, Xiangqian Li, Zhouxin Shen, Steve Briggs, Vineet Bafna |
| 2009 | Simultaneous Alignment and Folding of Protein Sequences. Jérôme Waldispühl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger |
| 2009 | Sorting Signed Permutations by Inversions in O(nlogn) Time. Krister M. Swenson, Vaibhav Rajan, Yu Lin, Bernard M. E. Moret |
| 2009 | Spatial Clustering of Multivariate Genomic and Epigenomic Information. Rami Jaschek, Amos Tanay |
| 2009 | Storage and Retrieval of Individual Genomes. Veli Mäkinen, Gonzalo Navarro, Jouni Sirén, Niko Välimäki |
| 2009 | The Multi-State Perfect Phylogeny Problem with Missing and Removable Data: Solutions via Integer-Programming and Chordal Graph Theory. Dan Gusfield |
| 2009 | Topology-Free Querying of Protein Interaction Networks. Sharon Bruckner, Falk Hüffner, Richard M. Karp, Ron Shamir, Roded Sharan |