| 2013 | Efficiently Identifying Significant Associations in Genome-Wide Association Studies. | Emrah Kostem, Eleazar Eskin |
| 2013 | UniNovo: A Universal Tool for de Novo Peptide Sequencing. | Kyowon Jeong, Sangtae Kim, Pavel A. Pevzner |
| 2013 | An Optimal Algorithm for Building the Majority Rule Consensus Tree. | Jesper Jansson, Chuanqi Shen, Wing-Kin Sung |
| 2013 | IPED: Inheritance Path Based Pedigree Reconstruction Algorithm Using Genotype Data. | Dan He, Zhanyong Wang, Buhm Han, Laxmi Parida, Eleazar Eskin |
| 2013 | Detecting Protein Conformational Changes in Interactions via Scaling Known Structures. | Fei Guo, Shuai Cheng Li, Wenji Ma, Lusheng Wang |
| 2013 | Analysis of Metabolic Evolution in Bacteria Using Whole-Genome Metabolic Models. | Ali A. Faruqi, William A. Bryant, John W. Pinney |
| 2013 | eALPS: Estimating Abundance Levels in Pooled Sequencing Using Available Genotyping Data. | Itamar Eskin, Farhad Hormozdiari, Luca Conde, Jacques Riby, Chris Skibola, Eleazar Eskin, Eran Halperin |
| 2013 | Boosting Prediction Performance of Protein-Protein Interaction Hot Spots by Using Structural Neighborhood Properties - (Extended Abstract). | Lei Deng, Jihong Guan, Xiaoming Wei, Yuan Yi, Shuigeng Zhou |
| 2013 | Dissecting Cancer Heterogeneity with a Probabilistic Genotype-Phenotype Model. | Dong-Yeon Cho, Teresa M. Przytycka |
| 2013 | SEME: A Fast Mapper of Illumina Sequencing Reads with Statistical Evaluation. | Shijian Chen, Anqi Wang, Lei M. Li |
| 2013 | Reconciliation Revisited: Handling Multiple Optima When Reconciling with Duplication, Transfer, and Loss. | Mukul S. Bansal, Eric J. Alm, Manolis Kellis |
| 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 | Probabilistic Inference of Viral Quasispecies Subject to Recombination. | Osvaldo Zagordi, Armin Tpfer, Sandhya Prabhakaran, Volker Roth, Eran Halperin, Niko Beerenwinkel |
| 2012 | Structure-Based Whole Genome Realignment Reveals Many Novel Non-coding RNAs. | Sebastian Will, Michael Yu, Bonnie Berger |
| 2012 | CNVeM: Copy Number Variation Detection Using Uncertainty of Read Mapping. | Zhanyong Wang, Farhad Hormozdiari, Wen-Yun Yang, Eran Halperin, Eleazar Eskin |
| 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 | Function-Function Correlated Multi-Label Protein Function Prediction over Interaction Networks. | Hua Wang, Heng Huang, Chris H. Q. Ding |
| 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 | Differential Oestrogen Receptor Binding is Associated with Clinical Outcome in Breast Cancer. | Rory Stark |
| 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 | Reconstructing Boolean Models of Signaling. | Roded Sharan, Richard M. Karp |
| 2012 | Exact Pattern Matching for RNA Structure Ensembles. | Christina Schmiedl, Mathias Mhl, Steffen Heyne, Mika Amit, Gad M. Landau, Sebastian Will, Rolf Backofen |
| 2012 | A Model for Biased Fractionation after Whole Genome Duplication. | David Sankoff, Chunfang Zheng, Baoyong Wang |
| 2012 | Detecting SNP-Induced Structural Changes in RNA: Application to Disease Studies. | Raheleh Salari, Chava Kimchi-Sarfaty, Michael M. Gottesman, Teresa M. Przytycka |
| 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 |