Accepted Papers to the Proceedings Track
- Alessia Petescia, Luca Denti, Askar Gafurov, Viktória Hodorová, Jozef Nosek, Broňa Brejová and Tomas Vinar Alignment-Free Detection of Differences Between Sequencing Data Sets
- Oieswarya Bhowmik and Ananth Kalyanaraman Tile-X: A vertex reordering approach for scalable long read assembly
- Prannav Shankar, Huan Liang, Uthsav Chitra and Rohit Singh Decoding the causal drivers of spatial cellular topology
- Zhenhao Gu, Hongyi Xin, Puru Sharma, Gary Yipeng Goh, Limsoon Wong and Niranjan Nagarajan Efficient trace reconstruction in DNA storage systems using Bidirectional Beam Search
- Zhao Ling, Shi Ying Li, Jingwan Wang, Xikang Feng, Bowen Tan and Shuai Cheng Li Decoupling Hi-C matrices with non-negative matrix factorization to reveal assorted TADs
- Lore Depuydt, Omar Y. Ahmed, Jan Fostier, Ben Langmead and Travis Gagie Run-length compressed metagenomic read classification with SMEM-finding and tagging
Accepted Papers to the Overlay Track
- Alexander Petri and Kristoffer Sahlin De novo clustering of extensive long-read transcriptome datasets with isONclust3
- Ivan Tolstoganov, Marcel Martin and Kristoffer Sahlin Multi-context seeds enable fast and high-accuracy read mapping
- Felix Kallenborn, Alejandro Chacon, Christian Hundt, Hassan Sirelkhatim, Kieran Didi, Sooyoung Cha, Christian Dallago, Milot Mirdita, Bertil Schmidt and Martin Steinegger GPU-accelerated homology search with MMseqs2
- Yi Ding, Jin Xiao, Bohao Zou and Lu Zhang DeepMM: Identify and correct Metagenome Misassemblies with deep learning
- Daanish Mahajan, Chirag Jain and Navin Kashyap On the Coverage Required for Diploid Genome Assembly
- Luca Denti, Paola Bonizzoni, Brona Brejova, Rayan Chikhi, Thomas Krannich, Tomas Vinar and Fereydoun Hormozdiari Pangenome graph augmentation from unassembled long reads
Accepted Short Talks
- Pia Rautenstrauch and Uwe Ohler Metrics Matter: Why We Need to Stop Using Silhouette in Single-Cell Benchmarking
- Marie Van Hecke, Koen Deserranno, Elise Callens, Filip Van Nieuwerburgh and Kathleen Marchal Full length isoform reconstruction in single cell data
- Ondřej Sladký, Pavel Veselý and Karel Brinda Masked superstrings as a compact, indexable, and dynamic representation of unconstrained k-mer sets
- Alexander Sweeten, Adam Phillippy and Michael Schatz Automated Annotation of Satellite DNA
- Lore Depuydt, Luca Renders, Simon Van de Vyver, Lennart Veys, Travis Gagie and Jan Fostier b-move: Faster Lossless Approximate Pattern Matching in a Run-Length Compressed Index
- Konstantinn Bonnet and Tobias Marschall strangepg: Toward Pangenome Scale Graph Visualization
- Megan Le, Lillian Zhang, Can Koçkan, Barış Ekim, Houlin Yu, Brian Haas, Aziz Al'Khafaji, Bonnie Berger and Victoria Popic Improved variant calling via latent breakpoint graphs
- Junqiong Qiu, Seungmo Lee, Vivek Agarwal and William O'Brien A Novel K-mer Masking Approach for Improving Specificity in Metagenomic Pathogen Detection
- Mahler Revsine, Daniel Khashabi and Michael Schatz Pre-Training Dataset Deduplication Improves Genomic LLMs
- Sang Yoon Byun and Vikas Bansal Edgecopy: Accurate CNV calling in duplicated genes using whole-exome sequencing
- Bastien Degardins, Charles Paperman and Camille Marchet Vizitig: context-rich exploration of sequencing datasets
- Timothé Rouzé, Rayan Chikhi and Antoine Limasset Inverted colored de Bruin Graph for practical kmer set storage
- Yohan Hernandez Courbevoie, Mikaël Salson, Chloé Bessière, Haoliang Xue, Daniel Gautheret, Camille Marchet and Antoine Limasset Reindeer2: practical abundance index at scale
- Arghamitra Talukder, Shree Thavarekere, Madison Mehlferber, Gloria M Sheynkman and David A. Knowles Multi-sample, multi-platform isoform quantification using empirical Bayes
- Zülal Bingöl, Berkan Şahin, Konstantina Koliogeorgi, Ricardo Roman-Brenes, Klea Zambaku, Can Firtina, Onur Mutlu and Can Alkan De Bruijn Graphs for Pangenomics: In-depth Performance Benchmarking of de Bruijn Graph-Based Tools for Read Mapping
- Barbara Poszewiecka, Krzysztof Gogolewski and Anna Gambin Efficient algorithm for resolving scenarios of Complex Chromosomal Rearrangements
Accepted Posters
- 101. Accelerating gkm-SVM Training Through GPU Implementation
- 102. Identifying Potential Therapeutic Targets for Heart Failure through Systematic Transcriptome Analysis, Hello, Kim Min-Ju, Department of Pharmacy, Pusan National University
- 103. Population-specific and universal molecular features of skeletal muscle aging: Comparative transcriptome analysis of Korean and GTEx datasets, Byeong-Don Min, Chungnam National University
- 104. Unlocking Hidden Protein Functions with a Biochemically Informed Annotation Strategy
- 105. Unraveling miRNA-seq data: a statistical framework to account for competition for expression towards accurate differential expression analysis
- 106. Systematic evaluation of dimensionality reduction methods for capturing transcriptomic signatures responding to drug treatments
- 107. GreedyMini: Generating low-density DNA minimizers, Yaron Orenstein, Bar-Ilan University
- 108. GPU-accelerated homology search with MMseqs2
- 109. strangepg: Toward Pangenome Scale Graph Visualization, Konstantinn Bonnet, Heinrich Heine University
- 110. Vizitig: context-rich exploration of sequencing datasets, Camille Marchet, Université de Lille - CNRS
- 111. Identifying gene-environment interactions for cancer incidence using epigenomic profiles, Younghoon Kim, KISTI
- 112. stDyer enables spatial domain clustering with dynamic graph embedding
- 113. Splicing Junction Classifier for Detecting Abnormal KEAP1-NRF2 System Activation
- 114. Adapting broad protein language models to viruses
- 115. b-move: Faster Lossless Approximate Pattern Matching in a Run-Length Compressed Index, Lore Depuydt, Ghent University
- 116. Full length isoform reconstruction in single cell data, Marie Van Hecke, Ghent University - imec
- 117. A Novel Computational Pipeline for the Functional Characterization and Deorphanization of G-Protein Coupled Receptors; Catherine Zhou, Stanford University
- 118. Parallel and space efficient exact local alignment, Evelin Aasna, Max Planck Institute for Molecular Genetics
- 119. Pre-Training Dataset Deduplication Improves Genomic LLMs, Mahler Revsine, John Hopkins University