| 2025 | Fast Pseudoalignment Queries on Compressed Colored de Bruijn Graphs. | Alessio Campanelli, Giulio Ermanno Pibiri, Rob Patro |
| 2025 | Improved Algorithms for Bi-Partition Function Computation. | John D. Bridgers, Jan Hoinka, S. Cenk Sahinalp, Salem Malikic, Teresa M. Przytycka, Funda Ergn |
| 2025 | Haplotype-Aware Long-Read Error Correction. | Parvesh Barak, Daniel Gibney, Chirag Jain |
| 2025 | Approximability of Longest Run Subsequence and Complementary Minimization Problems. | Yuichi Asahiro, Mingyang Gong, Jesper Jansson, Guohui Lin, Sichen Lu, Eiji Miyano, Hirotaka Ono, Toshiki Saitoh, Shunichi Tanaka |
| 2025 | Sequence Similarity Estimation by Random Subsequence Sketching. | Ke Chen, Vinamratha Pattar, Mingfu Shao |
| 2025 | Recursive Parsing and Grammar Compression in the Era of Pangenomics (Invited Talk). | Christina Boucher |
| 2024 | Swiftly Identifying Strongly Unique k-Mers. | Jens Zentgraf, Sven Rahmann |
| 2024 | Anchorage Accurately Assembles Anchor-Flanked Synthetic Long Reads. | Xiaofei Carl Zang, Xiang Li, Kyle Metcalfe, Tuval Ben-Yehezkel, Ryan Kelley, Mingfu Shao |
| 2024 | Front Matter, Table of Contents, Preface, Conference Organization. | |
| 2024 | Bioinformatics of Pathogens (Invited Talk). | Toms Vinar |
| 2024 | Orientability of Undirected Phylogenetic Networks to a Desired Class: Practical Algorithms and Application to Tree-Child Orientation. | Tsuyoshi Urata, Manato Yokoyama, Momoko Hayamizu |
| 2024 | Applying the Safe-And-Complete Framework to Practical Genome Assembly. | Sebastian S. Schmidt, Santeri Toivonen, Paul Medvedev, Alexandru I. Tomescu |
| 2024 | The Path-Label Reconciliation (PLR) Dissimilarity Measure for Gene Trees. | Alitzel Lpez Snchez, Jos Antonio Ramrez-Rafael, Alejandro Flores-Lamas, Maribel Hernndez-Rosales, Manuel Lafond |
| 2024 | Sapling: Inferring and Summarizing Tumor Phylogenies from Bulk Data Using Backbone Trees. | Yuanyuan Qi, Mohammed El-Kebir |
| 2024 | Finding Maximum Common Contractions Between Phylogenetic Networks. | Bertrand Marchand, Nadia Tahiri, Olivier Tremblay-Savard, Manuel Lafond |
| 2024 | The {mod-minimizer}: A Simple and Efficient Sampling Algorithm for Long k-Mers. | Ragnar Groot Koerkamp, Giulio Ermanno Pibiri |
| 2024 | A*PA2: Up to 19 Faster Exact Global Alignment. | Ragnar Groot Koerkamp |
| 2024 | MEM-Based Pangenome Indexing for k-mer Queries. | Stephen Hwang, Nathaniel K. Brown, Omar Y. Ahmed, Katharine M. Jenike, Sam Kovaka, Michael C. Schatz, Ben Langmead |
| 2024 | Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests. | Lukas Hbner, Alexandros Stamatakis |
| 2024 | Cosine Similarity Estimation Using FracMinHash: Theoretical Analysis, Safety Conditions, and Implementation. | Mahmudur Rahman Hera, David Koslicki |
| 2024 | b-move: Faster Bidirectional Character Extensions in a Run-Length Compressed Index. | Lore Depuydt, Luca Renders, Simon Van de Vyver, Lennart Veys, Travis Gagie, Jan Fostier |
| 2024 | On the Complexity of the Median and Closest Permutation Problems. | Lus Cunha, Ignasi Sau, Uverton S. Souza |
| 2024 | AlfaPang: Alignment Free Algorithm for Pangenome Graph Construction. | Adam Cicherski, Anna Lisiecka, Norbert Dojer |
| 2024 | An Efficient Algorithm for the Reconciliation of a Gene Network and Species Tree. | Yao-ban Chan |
| 2024 | McDag: Indexing Maximal Common Subsequences in Practice. | Giovanni Buzzega, Alessio Conte, Roberto Grossi, Giulia Punzi |