| 2015 | Sparse RNA Folding Revisited: Space-Efficient Minimum Free Energy Prediction. | Sebastian Will, Hosna Jabbari |
| 2015 | Models and Algorithms for Genome Rearrangement with Positional Constraints. | Krister M. Swenson, Mathieu Blanchette |
| 2015 | Simultaneous Optimization of both Node and Edge Conservation in Network Alignment via WAVE. | Yihan Sun, Joseph Crawford, Jie Tang, Tijana Milenkovic |
| 2015 | Algorithms for Regular Tree Grammar Network Search and Their Application to Mining Human-Viral Infection Patterns. | Ilan Y. Smoly, Amir Carmel, Yonat Shemer-Avni, Esti Yeger Lotem, Michal Ziv-Ukelson |
| 2015 | Graph-Theoretic Modelling of the Domain Chaining Problem. | Poly H. da Silva, Simone Dantas, Chunfang Zheng, David Sankoff |
| 2015 | Optimizing Read Reversals for Sequence Compression - (Extended Abstract). | Zhong Sichen, Lu Zhao, Yan Liang, Mohammadzaman Zamani, Rob Patro, Rezaul Chowdhury, Esther M. Arkin, Joseph S. B. Mitchell, Steven Skiena |
| 2015 | Semi-nonparametric Modeling of Topological Domain Formation from Epigenetic Data. | Emre Sefer, Carl Kingsford |
| 2015 | A Filtering Approach for Alignment-Free Biosequences Comparison with Mismatches. | Cinzia Pizzi |
| 2015 | Higher Classification Accuracy of Short Metagenomic Reads by Discriminative Spaced k-mers. | Rachid Ounit, Stefano Lonardi |
| 2015 | Efficient Design of Compact Unstructured RNA Libraries Covering All k-mers. | Yaron Orenstein, Bonnie Berger |
| 2015 | Jabba: Hybrid Error Correction for Long Sequencing Reads Using Maximal Exact Matches. | Giles Miclotte, Mahdi Heydari, Piet Demeester, Pieter Audenaert, Jan Fostier |
| 2015 | Multiple-Ancestor Localization for Recently Admixed Individuals. | Yaron Margalit, Yael Baran, Eran Halperin |
| 2015 | Orthology Relation and Gene Tree Correction: Complexity Results. | Manuel Lafond, Nadia El-Mabrouk |
| 2015 | Finding a Perfect Phylogeny from Mixed Tumor Samples. | Ademir Hujdurovic, Ursa Kacar, Martin Milanic, Bernard Ries, Alexandru I. Tomescu |
| 2015 | Bloom Filter Trie - A Data Structure for Pan-Genome Storage. | Guillaume Holley, Roland Wittler, Jens Stoye |
| 2015 | BicNET: Efficient Biclustering of Biological Networks to Unravel Non-Trivial Modules. | Rui Henriques, Sara C. Madeira |
| 2015 | Association Mapping for Compound Heterozygous Traits Using Phenotypic Distance and Integer Programming. | Dan Gusfield, Rasmus Nielsen |
| 2015 | Circular Sequence Comparison with q-grams. | Roberto Grossi, Costas S. Iliopoulos, Robert Mercas, Nadia Pisanti, Solon P. Pissis, Ahmad Retha, Fatima Vayani |
| 2015 | The Topological Profile of a Model of Protein Network Evolution Can Direct Model Improvement. | Todd A. Gibson, Debra S. Goldberg |
| 2015 | A Sparsified Four-Russian Algorithm for RNA Folding. | Yelena Frid, Dan Gusfield |
| 2015 | Scrible: Ultra-Accurate Error-Correction of Pooled Sequenced Reads. | Denise Duma, Francesca Cordero, Marco Beccuti, Gianfranco Ciardo, Timothy J. Close, Stefano Lonardi |
| 2015 | A Sub-quadratic Time and Space Complexity Solution for the Dated Tree Reconciliation Problem for Select Tree Topologies. | Benjamin Drinkwater, Michael A. Charleston |
| 2014 | GDNorm: An Improved Poisson Regression Model for Reducing Biases in Hi-C Data. | Ei-Wen Yang, Tao Jiang |
| 2014 | A Common Framework for Linear and Cyclic Multiple Sequence Alignment Problems. | Sebastian Will, Peter F. Stadler |
| 2014 | New Algorithms for Computing Phylogenetic Biodiversity. | Constantinos Tsirogiannis, Brody Sandel, Adrija Kalvisa |