| 2012 | A Model for Biased Fractionation after Whole Genome Duplication. David Sankoff, Chunfang Zheng, Baoyong Wang |
| 2012 | A Robust Method for Transcript Quantification with RNA-seq Data. Yan Huang, Yin Hu, Corbin D. Jones, James N. MacLeod, Derek Y. Chiang, Yufeng Liu, Jan F. Prins, Jinze Liu |
| 2012 | Alignment-Free Sequence Comparison Based on Next Generation Sequencing Reads: Extended Abstract. Kai Song, Jie Ren, Zhiyuan Zhai, Xuemei Liu, Minghua Deng, Fengzhu Sun |
| 2012 | Ancestry Inference in Complex Admixtures via Variable-Length Markov Chain Linkage Models. Sivan Bercovici, Jesse M. Rodriguez, Megan Elmore, Serafim Batzoglou |
| 2012 | Ballast: A Ball-Based Algorithm for Structural Motifs. Lu He, Fabio Vandin, Gopal Pandurangan, Chris Bailey-Kellogg |
| 2012 | CNVeM: Copy Number Variation Detection Using Uncertainty of Read Mapping. Zhanyong Wang, Farhad Hormozdiari, Wen-Yun Yang, Eran Halperin, Eleazar Eskin |
| 2012 | Charge Group Partitioning in Biomolecular Simulation. Stefan Canzar, Mohammed El-Kebir, René Pool, Khaled M. Elbassioni, Alpeshkumar K. Malde, Alan E. Mark, Daan P. Geerke, Leen Stougie, Gunnar W. Klau |
| 2012 | Detecting SNP-Induced Structural Changes in RNA: Application to Disease Studies. Raheleh Salari, Chava Kimchi-Sarfaty, Michael M. Gottesman, Teresa M. Przytycka |
| 2012 | Differential Oestrogen Receptor Binding is Associated with Clinical Outcome in Breast Cancer. Rory Stark |
| 2012 | Discovery of Complex Genomic Rearrangements in Cancer Using High-Throughput Sequencing. Andrew W. McPherson, Chunxiao Wu, Alexander Wyatt, Sohrab P. Shah, Colin C. Collins, Süleyman Cenk Sahinalp |
| 2012 | Estimating the Accuracy of Multiple Alignments and its Use in Parameter Advising. Dan F. DeBlasio, Travis J. Wheeler, John D. Kececioglu |
| 2012 | Evidence for Widespread Association of Mammalian Splicing and Conserved Long-Range RNA Structures. Dmitri D. Pervouchine, Ekaterina Khrameeva, Marina Pichugina, Olexii Nikolaienko, Mikhail S. Gelfand, Petr Rubtsov, Andrey A. Mironov |
| 2012 | Evolution of Genome Organization by Duplication and Loss: An Alignment Approach. Patrick Holloway, Krister M. Swenson, David H. Ardell, Nadia El-Mabrouk |
| 2012 | Exact Pattern Matching for RNA Structure Ensembles. Christina Schmiedl, Mathias Möhl, Steffen Heyne, Mika Amit, Gad M. Landau, Sebastian Will, Rolf Backofen |
| 2012 | Finding Maximum Colorful Subtrees in Practice. Imran Rauf, Florian Rasche, François Nicolas, Sebastian Böcker |
| 2012 | Function-Function Correlated Multi-Label Protein Function Prediction over Interaction Networks. Hua Wang, Heng Huang, Chris H. Q. Ding |
| 2012 | Hap-seq: An Optimal Algorithm for Haplotype Phasing with Imputation Using Sequencing Data. Dan He, Buhm Han, Eleazar Eskin |
| 2012 | Increased Methylation Variation in Epigenetic Domains across Cancer Types. Héctor Corrada Bravo |
| 2012 | LoopWeaver - Loop Modeling by the Weighted Scaling of Verified Proteins. Daniel Holtby, Shuai Cheng Li, Ming Li |
| 2012 | Modeling the Breakage-Fusion-Bridge Mechanism: Combinatorics and Cancer Genomics. Marcus Kinsella, Vineet Bafna |
| 2012 | Network-Based Prediction and Analysis of HIV Dependency Factors. T. M. Murali, Matthew D. Dyer, David Badger, Brett M. Tyler, Michael G. Katze |
| 2012 | Pathset Graphs: A Novel Approach for Comprehensive Utilization of Paired Reads in Genome Assembly. Son K. Pham, Dmitry Antipov, Alexander Sirotkin, Glenn Tesler, Pavel A. Pevzner, Max A. Alekseyev |
| 2012 | Predicting Protein-Protein Interactions from Multimodal Biological Data Sources via Nonnegative Matrix Tri-Factorization. Hua Wang, Heng Huang, Chris H. Q. Ding, Feiping Nie |
| 2012 | Probabilistic Inference of Viral Quasispecies Subject to Recombination. Osvaldo Zagordi, Armin Töpfer, Sandhya Prabhakaran, Volker Roth, Eran Halperin, Niko Beerenwinkel |
| 2012 | Protein Structure by Semidefinite Facial Reduction. Babak Alipanahi, Nathan Krislock, Ali Ghodsi, Henry Wolkowicz, Logan Donaldson, Ming Li |
| 2012 | Quantifying the Dynamics of Coupled Networks of Switches and Oscillators. Matthew R. Francis, Elana J. Fertig |
| 2012 | RESQUE: Network Reduction Using Semi-Markov Random Walk Scores for Efficient Querying of Biological Networks (Extended Abstract). Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon |
| 2012 | Reconstructing Boolean Models of Signaling. Roded Sharan, Richard M. Karp |
| 2012 | Recovering the Tree-Like Trend of Evolution Despite Extensive Lateral Genetic Transfer: A Probabilistic Analysis. Sebastien Roch, Sagi Snir |
| 2012 | Research in Computational Molecular Biology - 16th Annual International Conference, RECOMB 2012, Barcelona, Spain, April 21-24, 2012. Proceedings Benny Chor |
| 2012 | Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem. Nurcan Tuncbag, Alfredo Braunstein, Andrea Pagnani, Shao-Shan Carol Huang, Jennifer T. Chayes, Christian Borgs, Riccardo Zecchina, Ernest Fraenkel |
| 2012 | Simultaneously Learning DNA Motif along with Its Position and Sequence Rank Preferences through EM Algorithm. ZhiZhuo Zhang, Cheng Wei Chang, Hugo Willy, Edwin Cheung, Wing-Kin Sung |
| 2012 | Structure-Based Whole Genome Realignment Reveals Many Novel Non-coding RNAs. Sebastian Will, Michael Yu, Bonnie Berger |
| 2012 | Structure-Guided Deimmunization of Therapeutic Proteins. Andrew S. Parker, Karl E. Griswold, Chris Bailey-Kellogg |
| 2012 | Synthetic Sequence Design for Signal Location Search. Yaw-Ling Lin, Charles B. Ward, Steven Skiena |
| 2012 | The Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation. Marc A. Martí-Renom |
| 2012 | TrueSight: Self-training Algorithm for Splice Junction Detection Using RNA-seq. Yang Li, Hong-Mei Li, Paul Burns, Mark Borodovsky, Gene E. Robinson, Jian Ma |
| 2012 | lobSTR: A Short Tandem Repeat Profiler for Personal Genomes. Melissa Gymrek, David Golan, Saharon Rosset, Yaniv Erlich |