RECOMB-Seq 2025 Proceedings

Seoul, South Korea, April 24 - 25, 2025.

PC Chairs: Camille Marchet, University of Lille; and Yoren Orenstein, Bar-Ilan University.
Keynote Speakers: Alicia Oshlack and Rayan Chikhi.

Full Papers

  • Alignment-free detection of differences between sequencing data sets. Alessia Petescia, Luca Denti, Askar Gafurov, Viktória Hodorová, Jozef Nosek, Broňa Brejová and Tomas Vinar. iScience, 113828, (2025)
  • Tile-X: A vertex reordering approach for scalable long read assembly. Oieswarya Bhowmik and Ananth Kalyanaraman. bioRxiv 2025.04.21.649853, (2025)
  • Decoding the causal drivers of spatial cellular topology. Prannav Shankar, Huan Liang, Uthsav Chitra and Rohit Singh. bioRxiv 2025.03.19.644241, (2025)
  • Efficient trace reconstruction in DNA storage systems using Bidirectional Beam Search. Zhenhao Gu, Hongyi Xin, Puru Sharma, Gary Yipeng Goh, Limsoon Wong and Niranjan Nagarajan. bioRxiv 2025.04.16.644694, (2025)
  • Decoupling Hi-C matrices with non-negative matrix factorization to reveal assorted TADs. Zhao Ling, Shi Ying Li, Jingwan Wang, Xikang Feng, Bowen Tan and Shuai Cheng Li.
  • Run-length compressed metagenomic read classification with SMEM-finding and tagging. Lore Depuydt, Omar Y. Ahmed, Jan Fostier, Ben Langmead and Travis Gagie. bioRxiv 2025.02.25.640119, (2025)
  • De novo clustering of extensive long-read transcriptome datasets with isONclust3. Alexander Petri and Kristoffer Sahlin. overlay preprint
  • Multi-context seeds enable fast and high-accuracy read mapping. Ivan Tolstoganov, Marcel Martin and Kristoffer Sahlin. overlay preprint
  • GPU-accelerated homology search with MMseqs2. Felix Kallenborn, Alejandro Chacon, Christian Hundt, Hassan Sirelkhatim, Kieran Didi, Sooyoung Cha, Christian Dallago, Milot Mirdita, Bertil Schmidt and Martin Steinegger. overlay preprint
  • DeepMM: identify and correct metagenome misassemblies with deep learning. Yi Ding, Jin Xiao, Bohao Zou and Lu Zhang. overlay preprint
  • On the coverage required for diploid genome assembly. Daanish Mahajan, Chirag Jain and Navin Kashyap. overlay preprint
  • Pangenome graph augmentation from unassembled long reads. Luca Denti, Paola Bonizzoni, Brona Brejova, Rayan Chikhi, Thomas Krannich, Tomas Vinar and Fereydoun Hormozdiari. overlay preprint

Short Talks Selected from Abstracts

  • Metrics Matter: why we need to stop using silhouette in single-cell benchmarking. Pia Rautenstrauch and Uwe Ohler .
  • Full length isoform reconstruction in single cell data. Marie Van Hecke, Koen Deserranno, Elise Callens, Filip Van Nieuwerburgh and Kathleen Marchal .
  • Masked superstrings as a compact, indexable, and dynamic representation of unconstrained k-mer sets. Ondřej Sladký, Pavel Veselý and Karel Brinda .
  • Automated annotation of satellite DNA. Alexander Sweeten, Adam Phillippy and Michael Schatz .
  • b-move: faster lossless approximate pattern matching in a run-length compressed index. Lore Depuydt, Luca Renders, Simon Van de Vyver, Lennart Veys, Travis Gagie and Jan Fostier .
  • strangepg: toward pangenome scale graph visualization. Konstantinn Bonnet and Tobias Marschall .
  • Improved variant calling via latent breakpoint graphs. Megan Le, Lillian Zhang, Can Koçkan, Barış Ekim, Houlin Yu, Brian Haas, Aziz Al’Khafaji, Bonnie Berger and Victoria Popic .
  • A novel k-mer masking approach for improving specificity in metagenomic pathogen detection. Junqiong Qiu, Seungmo Lee, Vivek Agarwal and William O’Brien .
  • Pre-training dataset deduplication improves genomic LLMs. Mahler Revsine, Daniel Khashabi and Michael Schatz .
  • Edgecopy: accurate CNV calling in duplicated genes using whole-exome sequencing. Sang Yoon Byun and Vikas Bansal .
  • Vizitig: context-rich exploration of sequencing datasets. Bastien Degardins, Charles Paperman and Camille Marchet .
  • Inverted colored de Bruin graph for practical kmer set storage. Timothé Rouzé, Rayan Chikhi and Antoine Limasset .
  • Reindeer2: practical abundance index at scale. Yohan Hernandez Courbevoie, Mikaël Salson, Chloé Bessière, Haoliang Xue, Daniel Gautheret, Camille Marchet and Antoine Limasset .
  • Multi-sample, multi-platform isoform quantification using empirical Bayes. Arghamitra Talukder, Shree Thavarekere, Madison Mehlferber, Gloria M Sheynkman and David A. Knowles .
  • De Bruijn graphs for pangenomics: in-depth performance benchmarking of de Bruijn graph-based tools for read mapping. Zülal Bingöl, Berkan Şahin, Konstantina Koliogeorgi, Ricardo Roman-Brenes, Klea Zambaku, Can Firtina, Onur Mutlu and Can Alkan .
  • Efficient algorithm for resolving scenarios of complex chromosomal rearrangements. Barbara Poszewiecka, Krzysztof Gogolewski and Anna Gambin .

Posters

  • Accelerating gkm-SVM training through GPU implementation. Dongwon Lee.
  • Identifying potential therapeutic targets for heart failure through systematic transcriptome analysis. Min-Ju Kim and Haeseung Lee.
  • Population-specific and universal molecular features of skeletal muscle aging: Comparative transcriptome analysis of Korean and GTEx datasets. Byeong-Don Min and Sang-Min Park.
  • Unlocking hidden protein functions with a biochemically informed annotation strategy. Olga Botvinnik.
  • Unraveling miRNA-seq data: a statistical framework to account for competition for expression towards accurate differential expression analysis. Seong-Hwan Jun.
  • Systematic evaluation of dimensionality reduction methods for capturing transcriptomic signatures responding to drug treatments. Yuseong Kwon, Sojeong Park, Soyoung Park and Haeseung Lee.
  • GreedyMini: generating low-density DNA minimizers. Shay Golan, Ido Tziony, Matan Kraus, Yaron Orenstein and Arseny Shur.
  • GPU-accelerated homology search with MMseqs2. Felix Kallenborn, Alejandro Chacon, Christian Hundt, Hassan Sirelkhatim, Kieran Didi, Sooyoung Cha, Christian Dallago, Milot Mirdita, Bertil Schmidt and Martin Steinegger .
  • strangepg: toward pangenome scale graph visualization. Konstantinn Bonnet and Tobias Marschall.
  • Vizitig: context-rich exploration of sequencing datasets. Bastien Degardins, Charles Paperman and Camille Marchet.
  • Identifying gene-environment interactions for cancer incidence using epigenomic profiles. Younghoon Kim.
  • stDyer enables spatial domain clustering with dynamic graph embedding. Ke Xu, Yu Xu, Zirui Wang, Xin Zhou and Lu Zhang.
  • Splicing junction classifier for detecting abnormal KEAP1-NRF2 system activation. Raul Mateos, Wira Winardi, Kenichi Chiba, Ai Okada, Ayako Suzuki, Yoichiro Mitsuishi and Yuichi Shiraishi.
  • Adapting broad protein language models to viruses. Spyros Lytras, Adam Strange, Jumpei Ito and Kei Sato.
  • b-move: faster lossless approximate pattern matching in a run-length compressed index. Lore Depuydt, Luca Renders, Simon Van de Vyver, Lennart Veys, Travis Gagie and Jan Fostier.
  • Full length isoform reconstruction in single cell data. Marie Van Hecke, Koen Deserranno, Elise Callens, Filip Van Nieuwerburgh and Kathleen Marchal.
  • A novel computational pipeline for the functional characterization and deorphanization of G-protein coupled receptors. Catherine Zhou.
  • Parallel and space efficient exact local alignment. Evelin Aasna.
  • Pre-training dataset deduplication improves genomic LLMs. Mahler Revsine, Daniel Khashabi and Michael Schatz.