| 2026 | Towards a Unified Exact Solution of Rearrangement Small Parsimony for Natural Genomes. | Leonard Bohnenkmper, Daria Frolova |
| 2026 | GSI: A New Approach to the Protein Inference Problem. | Aurlien Berthier, Emile Benoist, Guillaume Fertin, Graldine Jean |
| 2026 | CoSTAR: Coarse Stem-Topology Alignment of Pseudoknotted RNA Structures by Relation-Constrained Search. | Finn Archinuk, Hosna Jabbari |
| 2026 | Efficient Algorithms for Pangenome Personalization. | Denys Andrukhovskyi, Martin Madzin, Luca Denti, Toms Vinar, Brona Brejov |
| 2026 | Construction of Distinct k-mer Color Sets via Set Fingerprinting. | Jarno N. Alanko, Simon J. Puglisi |
| 2026 | Fast Set Operations for Compact k-mer Sets. | Jarno N. Alanko, Lore Depuydt, Camille Marchet, Simon J. Puglisi |
| 2026 | Finimap: Fast and Accurate Single-Species Bacterial Pseudoalignment with Finimizers. | Jarno N. Alanko, Elena Biagi, Simon J. Puglisi |
| 2025 | Design of Worst-Case-Optimal Spaced Seeds. | Jens Zentgraf, Sven Rahmann |
| 2025 | Linear-Space Subquadratic-Time String Alignment Algorithm for Arbitrary Scoring Matrices. | Ryosuke Yamano, Tetsuo Shibuya |
| 2025 | Front Matter, Table of Contents, Preface, Conference Organization. | |
| 2025 | A k-mer-Based Estimator of the Substitution Rate Between Repetitive Sequences. | Haonan Wu, Antonio Blanca, Paul Medvedev |
| 2025 | Which Phylogenetic Networks Are Level-k Networks with Additional Arcs? Structure and Algorithms. | Takatora Suzuki, Momoko Hayamizu |
| 2025 | Identifying Breakpoint Median Genomes: A Branching Algorithm Approach. | Poly H. da Silva, Arash Jamshidpey, David Sankoff |
| 2025 | Partitioned Multi-MUM Finding for Scalable Pangenomics (Extended Abstract). | Vikram Shivakumar, Ben Langmead |
| 2025 | An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT. | Ahsan Sanaullah, Degui Zhi, Shaojie Zhang |
| 2025 | We Are What We Index; a Primer for the Wheeler Graph Era (Invited Talk). | Ben Langmead |
| 2025 | Extension of Partial Atom-To-Atom Maps: Uniqueness and Algorithms. | Marcos E. Gonzlez Laffitte, Tieu-Long Phan, Peter F. Stadler |
| 2025 | Average-Tree Phylogenetic Diversity of Networks. | Leo van Iersel, Mark Jones, Jannik Schestag, Cline Scornavacca, Mathias Weller |
| 2025 | Human Readable Compression of GFA Paths Using Grammar-Based Code. | Peter Heringer, Daniel Doerr |
| 2025 | Estimation of Substitution and Indel Rates via k-mer Statistics. | Mahmudur Rahman Hera, Paul Medvedev, David Koslicki, Antonio Blanca |
| 2025 | Spark: Sparsified Hierarchical Energy Minimization of RNA Pseudoknots. | Mateo Gray, Sebastian Will, Hosna Jabbari |
| 2025 | Mutational Signature Refitting on Sparse Pan-Cancer Data. | Gal Gilad, Teresa M. Przytycka, Roded Sharan |
| 2025 | DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs. | Ali Ghaffaari, Alexander Schnhuth, Tobias Marschall |
| 2025 | Dolphyin: A Combinatorial Algorithm for Identifying 1-Dollo Phylogenies in Cancer. | Daniel W. Feng, Mohammed El-Kebir |
| 2025 | Lossless Pangenome Indexing Using Tag Arrays. | Parsa Eskandar, Benedict Paten, Jouni Sirn |