| 2013 | Unifying Parsimonious Tree Reconciliation. | Nicolas Wieseke, Matthias Bernt, Martin Middendorf |
| 2013 | Faster Algorithms for RNA-Folding Using the Four-Russians Method. | Balaji Venkatachalam, Dan Gusfield, Yelena Frid |
| 2013 | Characterizing Compatibility and Agreement of Unrooted Trees via Cuts in Graphs. | Sudheer Vakati, David Fernndez-Baca |
| 2013 | Modeling Intratumor Gene Copy Number Heterogeneity Using Fluorescence in Situ Hybridization Data. | Charalampos E. Tsourakakis |
| 2013 | Computing the Skewness of the Phylogenetic Mean Pairwise Distance in Linear Time. | Constantinos Tsirogiannis, Brody Sandel |
| 2013 | A Novel Combinatorial Method for Estimating Transcript Expression with RNA-Seq: Bounding the Number of Paths. | Alexandru I. Tomescu, Anna Kuosmanen, Romeo Rizzi, Veli Mkinen |
| 2013 | Protein (Multi-)Location Prediction: Using Location Inter-dependencies in a Probabilistic Framework. | Ramanuja Simha, Hagit Shatkay |
| 2013 | Using Cascading Bloom Filters to Improve the Memory Usage for de Brujin Graphs. | Kamil Salikhov, Gustavo Sacomoto, Gregory Kucherov |
| 2013 | A Polynomial Delay Algorithm for the Enumeration of Bubbles with Length Constraints in Directed Graphs and Its Application to the Detection of Alternative Splicing in RNA-seq Data. | Gustavo Sacomoto, Vincent Lacroix, Marie-France Sagot |
| 2013 | Detecting Superbubbles in Assembly Graphs. | Taku Onodera, Kunihiko Sadakane, Tetsuo Shibuya |
| 2013 | Probabilistic Approaches to Alignment with Tandem Repeats. | Michal Nnsi, Toms Vinar, Brona Brejov |
| 2013 | Phylogenetic Analysis of Cell Types Using Histone Modifications. | Nishanth Ulhas Nair, Yu Lin, Philipp Bucher, Bernard M. E. Moret |
| 2013 | Extending the Reach of Phylogenetic Inference. | Bernard M. E. Moret |
| 2013 | MSARC: Multiple Sequence Alignment by Residue Clustering. | Michal Modzelewski, Norbert Dojer |
| 2013 | Sibelia: A Scalable and Comprehensive Synteny Block Generation Tool for Closely Related Microbial Genomes. | Ilya Minkin, Anand Patel, Mikhail Kolmogorov, Nikolay Vyahhi, Son K. Pham |
| 2013 | A Minimum-Labeling Approach for Reconstructing Protein Networks across Multiple Conditions. | Arnon Mazza, Irit Gat-Viks, Hesso Farhan, Roded Sharan |
| 2013 | Mutual Enrichment in Ranked Lists and the Statistical Assessment of Position Weight Matrix Motifs. | Limor Leibovich, Zohar Yakhini |
| 2013 | On NP-Hardness of the Paired de Bruijn Sound Cycle Problem. | Evgeny Kapun, Fedor Tsarev |
| 2013 | Algorithms for the Majority Rule (+) Consensus Tree and the Frequency Difference Consensus Tree. | Jesper Jansson, Chuanqi Shen, Wing-Kin Sung |
| 2013 | Multiscale Identification of Topological Domains in Chromatin. | Darya Filippova, Rob Patro, Geet Duggal, Carl Kingsford |
| 2013 | Accurate Decoding of Pooled Sequenced Data Using Compressed Sensing. | Denisa Duma, Mary Wootters, Anna C. Gilbert, Hung Q. Ngo, Atri Rudra, Matthew Alpert, Timothy J. Close, Gianfranco Ciardo, Stefano Lonardi |
| 2013 | Faster Mass Decomposition. | Kai Dhrkop, Marcus Ludwig, Marvin Meusel, Sebastian Bcker |
| 2013 | Cerulean: A Hybrid Assembly Using High Throughput Short and Long Reads. | Viraj Deshpande, Eric D. K. Fung, Son Pham, Vineet Bafna |
| 2013 | Towards Reliable Automatic Protein Structure Alignment. | Xuefeng Cui, Shuai Cheng Li, Dongbo Bu, Ming Li |
| 2013 | A Fixed-Parameter Algorithm for Minimum Common String Partition with Few Duplications. | Laurent Bulteau, Guillaume Fertin, Christian Komusiewicz, Irena Rusu |