| 2012 | A Practical Approximation Algorithm for Solving Massive Instances of Hybridization Number. Leo van Iersel, Steven Kelk, Nela Lekic, Céline Scornavacca |
| 2012 | A Probabilistic Approach to Accurate Abundance-Based Binning of Metagenomic Reads. Olga Tanaseichuk, James Borneman, Tao Jiang |
| 2012 | A Simplified View of DCJ-Indel Distance. Phillip E. C. Compeau |
| 2012 | Accounting for Gene Tree Uncertainties Improves Gene Trees and Reconciliation Inference. Thi Hau Nguyen, Jean-Philippe Doyon, Stéphanie Pointet, Anne-Muriel Arigon Chifolleau, Vincent Ranwez, Vincent Berry |
| 2012 | Algorithms in Bioinformatics - 12th International Workshop, WABI 2012, Ljubljana, Slovenia, September 10-12, 2012. Proceedings Benjamin J. Raphael, Jijun Tang |
| 2012 | An Optimal Reconciliation Algorithm for Gene Trees with Polytomies. Manuel Lafond, Krister M. Swenson, Nadia El-Mabrouk |
| 2012 | CLIIQ: Accurate Comparative Detection and Quantification of Expressed Isoforms in a Population. Yen-Yi Lin, Phuong Dao, Faraz Hach, Marzieh Bakhshi, Fan Mo, Anna Lapuk, Colin C. Collins, Süleyman Cenk Sahinalp |
| 2012 | Comparing DNA Sequence Collections by Direct Comparison of Compressed Text Indexes. Anthony J. Cox, Tobias Jakobi, Giovanna Rosone, Ole Schulz-Trieglaff |
| 2012 | DCJ-indel Distance with Distinct Operation Costs. Poly H. da Silva, Marília D. V. Braga, Raphael Machado, Simone Dantas |
| 2012 | Distributed String Mining for High-Throughput Sequencing Data. Niko Välimäki, Simon J. Puglisi |
| 2012 | Efficient Computation of Popular Phylogenetic Tree Measures. Constantinos Tsirogiannis, Brody Sandel, Dimitris Cheliotis |
| 2012 | Estimating Population Size via Line Graph Reconstruction. Bjarni V. Halldórsson, Dima Blokh, Roded Sharan |
| 2012 | Extracting Conflict-Free Information from Multi-labeled Trees. Akshay Deepak, David Fernández-Baca, Michelle M. McMahon |
| 2012 | Fast Phylogenetic Tree Reconstruction Using Locality-Sensitive Hashing. Daniel Gregory Brown, Jakub Truszkowski |
| 2012 | FinIS: Improved in silico Finishing Using an Exact Quadratic Programming Formulation. Song Gao, Denis Bertrand, Niranjan Nagarajan |
| 2012 | From de Bruijn Graphs to Rectangle Graphs for Genome Assembly. Nikolay Vyahhi, Alex Pyshkin, Son K. Pham, Pavel A. Pevzner |
| 2012 | Hidden Breakpoints in Genome Alignments. Birte Kehr, Knut Reinert, Aaron E. Darling |
| 2012 | How Accurately Can We Model Protein Structures with Dihedral Angles? Xuefeng Cui, Shuai Cheng Li, Dongbo Bu, Babak Alipanahi Ramandi, Ming Li |
| 2012 | Improved Lower Bounds on the Compatibility of Quartets, Triplets, and Multi-state Characters. Brad Shutters, Sudheer Vakati, David Fernández-Baca |
| 2012 | Lightweight LCP Construction for Next-Generation Sequencing Datasets. Markus J. Bauer, Anthony J. Cox, Giovanna Rosone, Marinella Sciortino |
| 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 | MS-DPR: An Algorithm for Computing Statistical Significance of Spectral Identifications of Non-linear Peptides. Hosein Mohimani, Sangtae Kim, Pavel A. Pevzner |
| 2012 | Preserving Inversion Phylogeny Reconstruction. Matthias Bernt, Kun-Mao Chao, Jyun-Wei Kao, Martin Middendorf, Eric Tannier |
| 2012 | RNA Tree Comparisons via Unrooted Unordered Alignments. Nimrod Milo, Shay Zakov, Erez Katzenelson, Eitan Bachmat, Yefim Dinitz, Michal Ziv-Ukelson |
| 2012 | Reconstructing the Evolution of Molecular Interaction Networks under the DMC and Link Dynamics Models. Yun Zhu, Luay Nakhleh |
| 2012 | Reducing Problems in Unrooted Tree Compatibility to Restricted Triangulations of Intersection Graphs. Rob Gysel, Kristian Stevens, Dan Gusfield |
| 2012 | Resolving Spatial Inconsistencies in Chromosome Conformation Data. Geet Duggal, Rob Patro, Emre Sefer, Hao Wang, Darya Filippova, Samir Khuller, Carl Kingsford |
| 2012 | SibJoin: A Fast Heuristic for Half-Sibling Reconstruction. Daniel Gregory Brown, Daniel Dexter |
| 2012 | Sign Assignment Problems on Protein Networks. Shay Houri, Roded Sharan |
| 2012 | Space-Efficient and Exact de Bruijn Graph Representation Based on a Bloom Filter. Rayan Chikhi, Guillaume Rizk |
| 2012 | Sparse Learning Based Linear Coherent Bi-clustering. Yi Shi, Xiaoping Liao, Xinhua Zhang, Guohui Lin, Dale Schuurmans |
| 2012 | Succinct Multibit Tree: Compact Representation of Multibit Trees by Using Succinct Data Structures in Chemical Fingerprint Searches. Yasuo Tabei |
| 2012 | Succinct de Bruijn Graphs. Alexander Bowe, Taku Onodera, Kunihiko Sadakane, Tetsuo Shibuya |
| 2012 | Tandem Halving Problems by DCJ. Antoine Thomas, Aïda Ouangraoua, Jean-Stéphane Varré |
| 2012 | Tree Decomposition and Parameterized Algorithms for RNA Structure-Sequence Alignment Including Tertiary Interactions and Pseudoknots - (Extended Abstract). Philippe Rinaudo, Yann Ponty, Dominique Barth, Alain Denise |
| 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 |