| 2012 | Extracting Conflict-Free Information from Multi-labeled Trees. | Akshay Deepak, David Fernndez-Baca, Michelle M. McMahon |
| 2012 | How Accurately Can We Model Protein Structures with Dihedral Angles? | Xuefeng Cui, Shuai Cheng Li, Dongbo Bu, Babak Alipanahi Ramandi, Ming Li |
| 2012 | Comparing DNA Sequence Collections by Direct Comparison of Compressed Text Indexes. | Anthony J. Cox, Tobias Jakobi, Giovanna Rosone, Ole Schulz-Trieglaff |
| 2012 | A Simplified View of DCJ-Indel Distance. | Phillip E. C. Compeau |
| 2012 | Space-Efficient and Exact de Bruijn Graph Representation Based on a Bloom Filter. | Rayan Chikhi, Guillaume Rizk |
| 2012 | MORPH-PRO: A Novel Algorithm and Web Server for Protein Morphing. | Natalie Castellana, Andrey Lushnikov, Piotr Rotkiewicz, Natasha Sefcovic, Pavel A. Pevzner, Adam Godzik, Kira Vyatkina |
| 2012 | Fast Phylogenetic Tree Reconstruction Using Locality-Sensitive Hashing. | Daniel Gregory Brown, Jakub Truszkowski |
| 2012 | SibJoin: A Fast Heuristic for Half-Sibling Reconstruction. | Daniel Gregory Brown, Daniel Dexter |
| 2012 | Succinct de Bruijn Graphs. | Alexander Bowe, Taku Onodera, Kunihiko Sadakane, Tetsuo Shibuya |
| 2012 | δ-TRIMAX: Extracting Triclusters and Analysing Coregulation in Time Series Gene Expression Data. | Anirban Bhar, Martin Haubrock, Anirban Mukhopadhyay, Ujjwal Maulik, Sanghamitra Bandyopadhyay, Edgar Wingender |
| 2012 | Preserving Inversion Phylogeny Reconstruction. | Matthias Bernt, Kun-Mao Chao, Jyun-Wei Kao, Martin Middendorf, Eric Tannier |
| 2012 | Lightweight LCP Construction for Next-Generation Sequencing Datasets. | Markus J. Bauer, Anthony J. Cox, Giovanna Rosone, Marinella Sciortino |
| 2011 | OMG! Orthologs in Multiple Genomes - Competing Graph-Theoretical Formulations. | Chunfang Zheng, Krister M. Swenson, Eric Lyons, David Sankoff |
| 2011 | GASTS: Parsimony Scoring under Rearrangements. | Andrew Wei Xu, Bernard M. E. Moret |
| 2011 | Dynamic Programming Algorithms for Efficiently Computing Cosegmentations between Biological Images. | Hang Xiao, Melvin Zhang, Axel Mosig, Hon Wai Leong |
| 2011 | Clustering with Overlap for Genetic Interaction Networks via Local Search Optimization. | Joseph Andrew Whitney, Judice L. Y. Koh, Michael Costanzo, Grant Brown, Charles Boone, Michael Brudno |
| 2011 | Finding Driver Pathways in Cancer: Models and Algorithms. | Fabio Vandin, Eli Upfal, Benjamin J. Raphael |
| 2011 | Separating Metagenomic Short Reads into Genomes via Clustering - (Extended Abstract). | Olga Tanaseichuk, James Borneman, Tao Jiang |
| 2011 | Efficiently Solvable Perfect Phylogeny Problems on Binary and k-State Data with Missing Values. | Kristian Stevens, Bonnie Kirkpatrick |
| 2011 | Indexing Finite Language Representation of Population Genotypes. | Jouni Sirn, Niko Vlimki, Veli Mkinen |
| 2011 | A Combinatorial Framework for Designing (Pseudoknotted) RNA Algorithms. | Yann Ponty, Cdric Saule |
| 2011 | Parsimonious Reconstruction of Network Evolution. | Rob Patro, Emre Sefer, Justin Malin, Guillaume Marais, Saket Navlakha, Carl Kingsford |
| 2011 | Algorithm for Identification of Piecewise Smooth Hybrid Systems: Application to Eukaryotic Cell Cycle Regulation. | Vincent Noel, Sergei Vakulenko, Ovidiu Radulescu |
| 2011 | Maximum Likelihood Estimation of Incomplete Genomic Spectrum from HTS Data. | Serghei Mangul, Irina Astrovskaya, Marius Nicolae, Bassam Tork, Ion I. Mandoiu, Alexander Zelikovsky |
| 2011 | Using Dominances for Solving the Protein Family Identification Problem. | Nol Malod-Dognin, Mathilde Le Boudic-Jamin, Pritish Kamath, Rumen Andonov |