| 2013 | The Generalized Robinson-Foulds Metric. | Sebastian Bcker, Stefan Canzar, Gunnar W. Klau |
| 2013 | Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures. | Rolf Backofen, Markus Fricke, Manja Marz, Jing Qin, Peter F. Stadler |
| 2012 | Reconstructing the Evolution of Molecular Interaction Networks under the DMC and Link Dynamics Models. | Yun Zhu, Luay Nakhleh |
| 2012 | From de Bruijn Graphs to Rectangle Graphs for Genome Assembly. | Nikolay Vyahhi, Alex Pyshkin, Son K. Pham, Pavel A. Pevzner |
| 2012 | Distributed String Mining for High-Throughput Sequencing Data. | Niko Vlimki, Simon J. Puglisi |
| 2012 | Efficient Computation of Popular Phylogenetic Tree Measures. | Constantinos Tsirogiannis, Brody Sandel, Dimitris Cheliotis |
| 2012 | Tandem Halving Problems by DCJ. | Antoine Thomas, Ada Ouangraoua, Jean-Stphane Varr |
| 2012 | A Probabilistic Approach to Accurate Abundance-Based Binning of Metagenomic Reads. | Olga Tanaseichuk, James Borneman, Tao Jiang |
| 2012 | Succinct Multibit Tree: Compact Representation of Multibit Trees by Using Succinct Data Structures in Chemical Fingerprint Searches. | Yasuo Tabei |
| 2012 | DCJ-indel Distance with Distinct Operation Costs. | Poly H. da Silva, Marlia D. V. Braga, Raphael Machado, Simone Dantas |
| 2012 | Improved Lower Bounds on the Compatibility of Quartets, Triplets, and Multi-state Characters. | Brad Shutters, Sudheer Vakati, David Fernndez-Baca |
| 2012 | Sparse Learning Based Linear Coherent Bi-clustering. | Yi Shi, Xiaoping Liao, Xinhua Zhang, Guohui Lin, Dale Schuurmans |
| 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 | Accounting for Gene Tree Uncertainties Improves Gene Trees and Reconciliation Inference. | Thi Hau Nguyen, Jean-Philippe Doyon, Stphanie Pointet, Anne-Muriel Arigon Chifolleau, Vincent Ranwez, Vincent Berry |
| 2012 | MS-DPR: An Algorithm for Computing Statistical Significance of Spectral Identifications of Non-linear Peptides. | Hosein Mohimani, Sangtae Kim, Pavel A. Pevzner |
| 2012 | RNA Tree Comparisons via Unrooted Unordered Alignments. | Nimrod Milo, Shay Zakov, Erez Katzenelson, Eitan Bachmat, Yefim Dinitz, Michal Ziv-Ukelson |
| 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, Sleyman Cenk Sahinalp |
| 2012 | An Optimal Reconciliation Algorithm for Gene Trees with Polytomies. | Manuel Lafond, Krister M. Swenson, Nadia El-Mabrouk |
| 2012 | Hidden Breakpoints in Genome Alignments. | Birte Kehr, Knut Reinert, Aaron E. Darling |
| 2012 | A Practical Approximation Algorithm for Solving Massive Instances of Hybridization Number. | Leo van Iersel, Steven Kelk, Nela Lekic, Cline Scornavacca |
| 2012 | Sign Assignment Problems on Protein Networks. | Shay Houri, Roded Sharan |
| 2012 | Estimating Population Size via Line Graph Reconstruction. | Bjarni V. Halldrsson, Dima Blokh, Roded Sharan |
| 2012 | Reducing Problems in Unrooted Tree Compatibility to Restricted Triangulations of Intersection Graphs. | Rob Gysel, Kristian Stevens, Dan Gusfield |
| 2012 | FinIS: Improved in silico Finishing Using an Exact Quadratic Programming Formulation. | Song Gao, Denis Bertrand, Niranjan Nagarajan |
| 2012 | Resolving Spatial Inconsistencies in Chromosome Conformation Data. | Geet Duggal, Rob Patro, Emre Sefer, Hao Wang, Darya Filippova, Samir Khuller, Carl Kingsford |