Program

Program

Program schedule: TBA

Accepted papers to the proceedings track

Dylan Agyemang, Rafael Irizarry and Tavor Baharav Unique molecular identifiers don’t need to be unique: a collision-aware estimator for RNA-seq quantification

Etienne Conchon-Kerjan, Timothé Rouzé, Lucas Robidou, Florian Ingels and Antoine Limasset SuperBloom: Fast and precise filter for streaming queries

Luca Parmigiani and Pierre Peterlongo Interpolating and extrapolating node counts in colored compacted de Bruijn graphs for pangenome diversity

Jonathan Mandl, Marcus Bluestone, Scott Longwell, Polly Fordyce and Yaron Orenstein PrimerDesigner: Designing efficient primers for synthesizing large protein libraries without cross-hybridization

Veronika Hendrychová and Karel Brinda Why phylogenies compress so well: combinatorial guarantees under the infinite sites model

Richard Durbin A run-length-compressed skiplist data structure for dynamic GBWTs supports time and space efficient pangenome operations over syncmers

Josipa Lipovac, Lune Angevin and Krešimir Križanović Using mapping-profiles to refine strain-level metagenomic classification

Ján Plachý, Ondřej Sladký, Karel Břinda and Pavel Veselý Pareto optimization of masked superstrings improves compression of pan-genome k-mer sets

Chandra Sekhar Reddy Edula, Yuxing Sun and Xiuwei Zhang stPularity: Spatial domain identification via purity-constrained Louvain clustering on spatially-smoothed cell type proportions

Accepted papers to the overlay track

Jaebeom Kim and Martin Steinegger Sensitive and scalable metagenomic classification using spaced metamers, reduced alphabets, and syncmers

Francisco Sena, Aleksandr Politov, Corentin Moumard, Manuel Cáceres, Sebastian Schmidt, Juha Harviainen and Alexandru I. Tomescu Identifying all snarls and superbubbles in linear-time, via a unified SPQR-tree framework

Ruben Becker, Davide Cenzato, Travis Gagie, Ragnar Groot Koerkamp, Sung-Hwan Kim, Giovanni Manzini and Nicola Prezza Compressing suffix trees by path decompositions

Rick Beeloo and Ragnar Groot Koerkamp Sassy: Fuzzy searching DNA sequences using SIMD

Jarno N. Alanko, T. Rhyker Ranallo-Benavidez, Floris P. Barthel, Simon J. Puglisi and Camille Marchet Hierarchical genomic feature annotation with variable-length queries

Accepted short talks

Yunwei Zhao, Ankit Bhardwaj, Preetha Balasubramanian and Lakshminarayanan Subramanian BEACON: Bayesian contrastive learning for single-cell gene regulatory inference

Adrian Tkachenko, Sepehr Salem, Zulal Bingol, Nayeem Uddin Mohammed, Ayotomiwa Ezekiel Adeniyi, Akshat Prasanna, Alexander Zelikovsky, Serghei Mangul, Can Alkan and Mohammed Alser FASTR: A computation-native, lossless replacement for FASTQ

Albert Jiménez Blanco Fast and optimal affine-gap sequence-to-graph alignment

Seungmo Lee and Eleazar Eskin TDKC: Ultrafast and memory-efficient sequence classification for target pathogen diagnostics

Askar Gafurov, Kristína Boršová, Boris Klempa, Jozef Nosek, Brona Brejova and Tomas Vinar Blown out of proportion: Effect of PCR artifacts on wastewater surveillance

Ali Osman Berk Şapcı and Siavash Mirarab A likelihood framework for estimating sequence distances and genome-wide (phylogenetic) pattern matching

Davide Cesare Monti, Paola Bonizzoni, Simone Ciccolella, Davide Cozzi, Gianluca Della Vedova, Luca Denti and Fereydoun Hormozdiari Somatic structural variations detection via tumor-specific strings

William O’Brien, Seungmo Lee, Vivek Agarwal and Eleazar Eskin A Bayesian framework for likelihood estimation of pathogenic reads in metagenomic data

Tuna Okçu and Can Alkan FUSOR: Space efficient taxonomic classification using hybrid hierarchical interleaved binary fuse filters with a stash

Stephanie Sammut, Eva Marsalkova, Panagiotis Alexiou and Katarina Gresova GenBenchQC: Automated quality control of genomic sequence benchmarks reveals widespread biases in deep learning datasets

Yunwei Zhao, Preetha Balasubramanian and Lakshminarayanan Subramanian Safe fusion for scRNA-seq trajectory recovery with uncertainty gating and CITE-seq validation

Nikoletta Katsaouni and Marcel H. Schulz RANKOR: Direct drug prioritization from bulk and single-cell transcriptomic signatures