| 2024 | RNA Inverse Folding Can Be Solved in Linear Time for Structures Without Isolated Stacks or Base Pairs. | Tho Boury, Laurent Bulteau, Yann Ponty |
| 2024 | Reconstructing Rearrangement Phylogenies of Natural Genomes. | Leonard Bohnenkmper, Jens Stoye, Daniel Drr |
| 2024 | RNA Triplet Repeats: Improved Algorithms for Structure Prediction and Interactions. | Kimon Boehmer, Sarah J. Berkemer, Sebastian Will, Yann Ponty |
| 2024 | A Unifying Taxonomy of Pattern Matching in Degenerate Strings and Founder Graphs. | Rocco Ascone, Giulia Bernardini, Alessio Conte, Massimo Equi, Estban Gabory, Roberto Grossi, Nadia Pisanti |
| 2024 | PLA-index: A k-mer Index Exploiting Rank Curve Linearity. | Md. Hasin Abrar, Paul Medvedev |
| 2023 | Front Matter, Table of Contents, Preface, Conference Organization. | |
| 2023 | BATCH-SCAMPP: Scaling Phylogenetic Placement Methods to Place Many Sequences (Abstract). | Eleanor Wedell, Chengze Shen, Tandy J. Warnow |
| 2023 | EMMA: Adding Sequences into a Constraint Alignment with High Accuracy and Scalability (Abstract). | Chengze Shen, Baqiao Liu, Kelly P. Williams, Tandy J. Warnow |
| 2023 | Exact Sketch-Based Read Mapping. | Tizian Schulz, Paul Medvedev |
| 2023 | Fractional Hitting Sets for Efficient and Lightweight Genomic Data Sketching. | Timoth Rouz, Igor Martayan, Camille Marchet, Antoine Limasset |
| 2023 | Inferring Temporally Consistent Migration Histories. | Mrinmoy Saha Roddur, Sagi Snir, Mohammed El-Kebir |
| 2023 | Co-Linear Chaining on Pangenome Graphs. | Jyotshna Rajput, Ghanshyam Chandra, Chirag Jain |
| 2023 | Compression Algorithm for Colored de Bruijn Graphs. | Amatur Rahman, Yoann Dufresne, Paul Medvedev |
| 2023 | Revisiting the Complexity of and Algorithms for the Graph Traversal Edit Distance and Its Variants. | Yutong Qiu, Yihang Shen, Carl Kingsford |
| 2023 | Algorithmic Approaches to Study Mutational Processes in Cancer (Invited Talk). | Teresa M. Przytycka |
| 2023 | Fast, Parallel, and Cache-Friendly Suffix Array Construction. | Jamshed Khan, Tobias Rubel, Laxman Dhulipala, Erin K. Molloy, Rob Patro |
| 2023 | Making a Network Orchard by Adding Leaves. | Leo van Iersel, Mark Jones, Esther Julien, Yukihiro Murakami |
| 2023 | Acceleration of FM-Index Queries Through Prefix-Free Parsing. | Aaron Hong, Marco Oliva, Dominik Kppl, Hideo Bannai, Christina Boucher, Travis Gagie |
| 2023 | Quartets Enable Statistically Consistent Estimation of Cell Lineage Trees Under an Unbiased Error and Missingness Model (Abstract). | Yunheng Han, Erin K. Molloy |
| 2023 | Balancing Minimum Free Energy and Codon Adaptation Index for Pareto Optimal RNA Design. | Xinyu Gu, Yuanyuan Qi, Mohammed El-Kebir |
| 2023 | SparseRNAFolD: Sparse RNA Pseudoknot-Free Folding Including Dangles. | Mateo Gray, Sebastian Will, Hosna Jabbari |
| 2023 | Reinforcement Learning for Robotic Liquid Handler Planning. | Mohsen Ferdosi, Yuejun Ge, Carl Kingsford |
| 2023 | Fulgor: A Fast and Compact {k-mer} Index for Large-Scale Matching and Color Queries. | Jason Fan, Noor Pratap Singh, Jamshed Khan, Giulio Ermanno Pibiri, Rob Patro |
| 2023 | Leveraging Constraints Plus Dynamic Programming for the Large Dollo Parsimony Problem. | Junyan Dai, Tobias Rubel, Yunheng Han, Erin K. Molloy |
| 2023 | Automatic Exploration of the Natural Variability of RNA Non-Canonical Geometric Patterns with a Parameterized Sampling Technique. | Tho Boury, Yann Ponty, Vladimir Reinharz |