| 2009 | Inferring the Recent Duplication History of a Gene Cluster. | Giltae Song, Louxin Zhang, Toms Vinar, Webb Miller |
| 2009 | Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data. | Suzanne S. Sindi, Benjamin J. Raphael |
| 2009 | Searching Protein 3-D Structures in Linear Time. | Tetsuo Shibuya |
| 2009 | A Statistical Framework for the Functional Analysis of Metagenomes. | Itai Sharon, Amrita Pati, Victor M. Markowitz, Ron Y. Pinter |
| 2009 | Properties of Sequence Conservation in Upstream Regulatory and Protein Coding Sequences among Paralogs in | Dale N. Richardson, Thomas Wiehe |
| 2009 | On the Relationship between DNA Periodicity and Local Chromatin Structure. | Sheila M. Reynolds, Jeff A. Bilmes, William Stafford Noble |
| 2009 | Incorporating Nucleosomes into Thermodynamic Models of Transcription Regulation. | Tali Raveh-Sadka, Michal Levo, Eran Segal |
| 2009 | An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations. | Arvind Ramanathan, Pratul K. Agarwal, Maria G. Kurnikova, Christopher James Langmead |
| 2009 | Overlapping Pools for High Throughput Targeted Resequencing. | Snehit Prabhu, Itsik Pe'er |
| 2009 | Comparative Genomics and Extensive Recombinations in Phage Communities. | Guylaine Poisson, Mahdi Belcaid, Anne Bergeron |
| 2009 | Boosting Protein Threading Accuracy. | Jian Peng, Jinbo Xu |
| 2009 | How Many Bootstrap Replicates Are Necessary? | Nicholas D. Pattengale, Masoud Alipour, Olaf R. P. Bininda-Emonds, Bernard M. E. Moret, Alexandros Stamatakis |
| 2009 | Parking Functions, Labeled Trees and DCJ Sorting Scenarios. | Ada Ouangraoua, Anne Bergeron |
| 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 | Lifting Prediction to Alignment of RNA Pseudoknots. | Mathias Mhl, Sebastian Will, Rolf Backofen |
| 2009 | Rearrangement Models and Single-Cut Operations. | Paul Medvedev, Jens Stoye |
| 2009 | Storage and Retrieval of Individual Genomes. | Veli Mkinen, Gonzalo Navarro, Jouni Sirn, Niko Vlimki |
| 2009 | Cross Species Expression Analysis of Innate Immune Response. | Yong Lu, Roni Rosenfeld, Gerard J. Nau, Ziv Bar-Joseph |
| 2009 | Transcription Factor Binding Probabilities in Orthologous Promoters: An Alignment-Free Approach to the Inference of Functional Regulatory Targets. | Xiao Liu, Neil D. Clarke |
| 2009 | Detection of Locally Over-Represented GO Terms in Protein-Protein Interaction Networks. | Mathieu Lavalle-Adam, Benoit Coulombe, Mathieu Blanchette |
| 2009 | Haplotype Inference in Complex Pedigrees. | Bonnie Kirkpatrick, Javier Rosa, Eran Halperin, Richard M. Karp |
| 2009 | Learning Models for Aligning Protein Sequences with Predicted Secondary Structure. | Eagu Kim, Travis J. Wheeler, John D. Kececioglu |
| 2009 | An Adaptive and Memory Efficient Algorithm for Genotype Imputation. | Hyun Min Kang, Noah Zaitlen, Buhm Han, Eleazar Eskin |
| 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 | Spatial Clustering of Multivariate Genomic and Epigenomic Information. | Rami Jaschek, Amos Tanay |