| 2013 | A Fixed-Parameter Algorithm for Minimum Common String Partition with Few Duplications. Laurent Bulteau, Guillaume Fertin, Christian Komusiewicz, Irena Rusu |
| 2013 | A Minimum-Labeling Approach for Reconstructing Protein Networks across Multiple Conditions. Arnon Mazza, Irit Gat-Viks, Hesso Farhan, Roded Sharan |
| 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 Mäkinen |
| 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 | 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 | Algorithms for the Majority Rule (+) Consensus Tree and the Frequency Difference Consensus Tree. Jesper Jansson, Chuanqi Shen, Wing-Kin Sung |
| 2013 | Algorithms in Bioinformatics - 13th International Workshop, WABI 2013, Sophia Antipolis, France, September 2-4, 2013. Proceedings Aaron E. Darling, Jens Stoye |
| 2013 | Cerulean: A Hybrid Assembly Using High Throughput Short and Long Reads. Viraj Deshpande, Eric D. K. Fung, Son Pham, Vineet Bafna |
| 2013 | Characterizing Compatibility and Agreement of Unrooted Trees via Cuts in Graphs. Sudheer Vakati, David Fernández-Baca |
| 2013 | Computing the Skewness of the Phylogenetic Mean Pairwise Distance in Linear Time. Constantinos Tsirogiannis, Brody Sandel |
| 2013 | Detecting Superbubbles in Assembly Graphs. Taku Onodera, Kunihiko Sadakane, Tetsuo Shibuya |
| 2013 | Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures. Rolf Backofen, Markus Fricke, Manja Marz, Jing Qin, Peter F. Stadler |
| 2013 | Extending the Reach of Phylogenetic Inference. Bernard M. E. Moret |
| 2013 | Faster Algorithms for RNA-Folding Using the Four-Russians Method. Balaji Venkatachalam, Dan Gusfield, Yelena Frid |
| 2013 | Faster Mass Decomposition. Kai Dührkop, Marcus Ludwig, Marvin Meusel, Sebastian Böcker |
| 2013 | MSARC: Multiple Sequence Alignment by Residue Clustering. Michal Modzelewski, Norbert Dojer |
| 2013 | Modeling Intratumor Gene Copy Number Heterogeneity Using Fluorescence in Situ Hybridization Data. Charalampos E. Tsourakakis |
| 2013 | Multiscale Identification of Topological Domains in Chromatin. Darya Filippova, Rob Patro, Geet Duggal, Carl Kingsford |
| 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 | On the Matrix Median Problem. João Paulo Pereira Zanetti, Priscila Biller, João Meidanis |
| 2013 | Phylogenetic Analysis of Cell Types Using Histone Modifications. Nishanth Ulhas Nair, Yu Lin, Philipp Bucher, Bernard M. E. Moret |
| 2013 | Probabilistic Approaches to Alignment with Tandem Repeats. Michal Nánási, Tomás Vinar, Brona Brejová |
| 2013 | Protein (Multi-)Location Prediction: Using Location Inter-dependencies in a Probabilistic Framework. Ramanuja Simha, Hagit Shatkay |
| 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 | The Generalized Robinson-Foulds Metric. Sebastian Böcker, Stefan Canzar, Gunnar W. Klau |
| 2013 | Towards Reliable Automatic Protein Structure Alignment. Xuefeng Cui, Shuai Cheng Li, Dongbo Bu, Ming Li |
| 2013 | Unifying Parsimonious Tree Reconciliation. Nicolas Wieseke, Matthias Bernt, Martin Middendorf |
| 2013 | Using Cascading Bloom Filters to Improve the Memory Usage for de Brujin Graphs. Kamil Salikhov, Gustavo Sacomoto, Gregory Kucherov |