| 2019 | Faster Pan-Genome Construction for Efficient Differentiation of Naturally Occurring and Engineered Plasmids with Plaster. | Qi Wang, Ryan A. Leo Elworth, Tian Rui Liu, Todd J. Treangen |
| 2019 | Rapidly Computing the Phylogenetic Transfer Index. | Jakub Truszkowski, Olivier Gascuel, Krister M. Swenson |
| 2019 | Bounded-Length Smith-Waterman Alignment. | Alexander Tiskin |
| 2019 | Weighted Minimum-Length Rearrangement Scenarios. | Pijus Simonaitis, Annie Chateau, Krister M. Swenson |
| 2019 | Topological Data Analysis Reveals Principles of Chromosome Structure in Cellular Differentiation. | Natalie Sauerwald, Yihang Shen, Carl Kingsford |
| 2019 | Detecting Transcriptomic Structural Variants in Heterogeneous Contexts via the Multiple Compatible Arrangements Problem. | Yutong Qiu, Cong Ma, Han Xie, Carl Kingsford |
| 2019 | Synteny Paths for Assembly Graphs Comparison. | Evgeny Polevikov, Mikhail Kolmogorov |
| 2019 | Fast and Accurate Structure Probability Estimation for Simultaneous Alignment and Folding of RNAs. | Milad Miladi, Martin Raden, Sebastian Will, Rolf Backofen |
| 2019 | Consensus Clusters in Robinson-Foulds Reticulation Networks. | Alexey Markin, Oliver Eulenstein |
| 2019 | Jointly Embedding Multiple Single-Cell Omics Measurements. | Jie Liu, Yuanhao Huang, Ritambhara Singh, Jean-Philippe Vert, William Stafford Noble |
| 2019 | Read Mapping on Genome Variation Graphs. | Naga Sai Kavya Vaddadi, Rajgopal Srinivasan, Naveen Sivadasan |
| 2019 | Building a Small and Informative Phylogenetic Supertree. | Jesper Jansson, Konstantinos Mampentzidis, Sandhya T. P. |
| 2019 | Validating Paired-End Read Alignments in Sequence Graphs. | Chirag Jain, Haowen Zhang, Alexander T. Dilthey, Srinivas Aluru |
| 2019 | pClay: A Precise Parallel Algorithm for Comparing Molecular Surfaces. | Georgi D. Georgiev, Kevin F. Dodd, Brian Y. Chen |
| 2019 | A Combinatorial Approach for Single-cell Variant Detection via Phylogenetic Inference. | Mohammad Amin Edrisi, Hamim Zafar, Luay Nakhleh |
| 2019 | Quantified Uncertainty of Flexible Protein-Protein Docking Algorithms. | Nathan L. Clement |
| 2019 | TRACTION: Fast Non-Parametric Improvement of Estimated Gene Trees. | Sarah A. Christensen, Erin K. Molloy, Pranjal Vachaspati, Tandy J. Warnow |
| 2019 | Inferring Diploid 3D Chromatin Structures from Hi-C Data. | Alexandra Gesine Cauer, Grkan Yardimci, Jean-Philippe Vert, Nelle Varoquaux, William Stafford Noble |
| 2019 | Empirical Performance of Tree-Based Inference of Phylogenetic Networks. | Zhen Cao, Jiafan Zhu, Luay Nakhleh |
| 2019 | Finding All Maximal Perfect Haplotype Blocks in Linear Time. | Jarno Alanko, Hideo Bannai, Bastien Cazaux, Pierre Peterlongo, Jens Stoye |
| 2018 | New Absolute Fast Converging Phylogeny Estimation Methods with Improved Scalability and Accuracy. | Qiuyi (Richard) Zhang, Satish Rao, Tandy J. Warnow |
| 2018 | A Duality-Based Method for Identifying Elemental Balance Violations in Metabolic Network Models. | Hooman Zabeti, Tamon Stephen, Bonnie Berger, Leonid Chindelevitch |
| 2018 | Front Matter, Table of Contents, Preface, Conference Organization. | |
| 2018 | Kermit: Guided Long Read Assembly using Coloured Overlap Graphs. | Riku Walve, Pasi Rastas, Leena Salmela |
| 2018 | A Dynamic Algorithm for Network Propagation. | Barak Sternberg, Roded Sharan |