Program

Program of RECOMB-seq 2025

April 24th, Thursday

Time/Day Event Speaker/Details
8:30-9:30 Registration The Commons, Yonsei University
9:25-9:30 Opening
9:30-10:30 Keynote 1: From Petabytes to Insights: Scaling Sequence Bioinformatics with Logan Rayan Chikhi, Institut Pasteur
10:30-10:45 Coffee break
Session 1: Long talks - Proceedings
10:45-11:10 Tile-X: A vertex reordering approach for scalable long read assembly [Proceedings] Oieswarya Bhowmik, Washington State University
11:10-11:35 Run-length compressed metagenomic read classification with SMEM-finding and tagging [Proceedings] Lore Depuydt, Ghent University
11:35-12:00 Alignment-Free Detection of Differences Between Sequencing Data Sets [Proceedings] Alessia Petescia Comenius, University in Bratislava
12:00-13:30 Lunch / Poster viewing
Session 2: Short talks
13:30-13:40 Metrics Matter: Why We Need to Stop Using Silhouette in Single-Cell Benchmarking Pia Rautenstrauch, MDC Berlin
13:40-13:50 Full length isoform reconstruction in single cell data Marie Van Hecke, Ghent University - imec
13:50-14:00 Masked superstrings as a compact, indexable, and dynamic representation of unconstrained k-mer sets Pavel Veselý, Charles University
14:00-14:10 Automated Annotation of Satellite DNA Alex Sweeten, Johns Hopkins University
14:10-14:30 Break
Session 3: Short talks
14:30-14:40 b-move: Faster Lossless Approximate Pattern Matching in a Run-Length Compressed Index Lore Depuydt, Ghent University
14:40-14:50 strangepg: Toward Pangenome Scale Graph Visualization Konstantinn Bonnet, Heinrich Heine University
14:50-15:00 Improved variant calling via latent breakpoint graphs
15:00-15:10 A Novel K-mer Masking Approach for Improving Specificity in Metagenomic Pathogen Detection Joanne Qiu, UCLA
15:10-16:30 Posters
Session 4: Long talks - Overlay
16:30-16:55 DeepMM: Identify and correct Metagenome Misassemblies with deep learning [Overlay] Ding Yi, Hong Kong Baptist University
16:55-17:20 GPU-accelerated homology search with MMseqs2 [Overlay] Milot Mirdita, Seoul National University
17:20-17:45 On the Coverage Required for Diploid Genome Assembly [Overlay] Chirag Jain, Indian Institute of Science
17:45:00 Satellites reception


April 25th, Friday

Time/Day Event Speaker/Details
8:30-9:30 Registration The Commons, Yonsei University
9:25-9:30 Opening
9:30-10:30 Keynote 2: Single cells and long reads: Transcriptomes at exquisite resolution Alicia Oshlack, Peter MacCallum Cancer Center
10:30-10:45 Coffee break
Session 5: Long talks - Proceedings
10:45-11:10 Decoding the causal drivers of spatial cellular topology [Proceedings] Rohit Singh, Duke
11:10-11:35 Efficient trace reconstruction in DNA storage systems using Bidirectional Beam Search [Proceedings] Gu Zhenhao, National University of Singapore
11:35-12:00 Decoupling Hi-C matrices with non-negative matrix factorization to reveal assorted TADs [Proceedings] Zhao Ling, City university of HongKong
12:00-13:30 Lunch / Poster viewing
Session 6: Short talks
13:30-13:40 Pre-Training Dataset Deduplication Improves Genomic LLMs Mahler Revsine, Johns Hopkins University
13:40-13:50 Edgecopy: Accurate CNV calling in duplicated genes using whole-exome sequencing Sang Yoon Byun, University of California San Diego
13:50-14:00 Vizitig: context-rich exploration of sequencing datasets Camille Marchet, Université de Lille - CNRS
14:00-14:10 Inverted colored de Bruin Graph for practical kmer set storage Timothé Rouzé, Institut Pasteur
14:10-14:30 Break
Session 7: Short talks
14:30-14:40 Reindeer2: practical abundance index at scale Camille Marchet, Université de Lille - CNRS
14:40-14:50 Multi-sample, multi-platform isoform quantification using empirical Bayes Arghamitra Talukder, Columbia University
14:50-15:00 Efficient algorithm for resolving scenarios of Complex Chromosomal Rearrangements Barbara Poszewiecka, University of Warsaw
15:00-15:10 De Bruijn Graphs for Pangenomics: In-depth Performance Benchmarking of de Bruijn Graph-Based Tools for Read Mapping Zülal Bingöl, Bilkent University
15:10-16:30 Posters
Session 8: Long talks - Overlay
16:30-16:55 Pangenome graph augmentation from unassembled long reads [Overlay] Luca Denti, Comenius University in Bratislava
16:55-17:20 De novo clustering of extensive long-read transcriptome datasets with isONclust3 [Overlay] Alexander Petri, Stockholm University
17:20-17:45 Multi-context seeds enable fast and high-accuracy read mapping [Overlay]
17:45:00 RECOMB reception

 

 

 

 

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

  • Accelerating gkm-SVM Training Through GPU Implementation
  • Identifying Potential Therapeutic Targets for Heart Failure through Systematic Transcriptome Analysis, Dongwon Lee, Boston Children’s Hospital
  • Population-specific and universal molecular features of skeletal muscle aging: Comparative transcriptome analysis of Korean and GTEx datasets, Byeong-Don Min, Chungnam National University
  • Unlocking Hidden Protein Functions with a Biochemically Informed Annotation Strategy
  • Unraveling miRNA-seq data: a statistical framework to account for competition for expression towards accurate differential expression analysis
  • Systematic evaluation of dimensionality reduction methods for capturing transcriptomic signatures responding to drug treatments
  • GreedyMini: Generating low-density DNA minimizers, Yaron Orenstein, Bar-Ilan University
  • GPU-accelerated homology search with MMseqs2
  • strangepg: Toward Pangenome Scale Graph Visualization, Konstantinn Bonnet, Heinrich Heine University
  • Vizitig: context-rich exploration of sequencing datasets, Camille Marchet, Université de Lille - CNRS
  • Identifying gene-environment interactions for cancer incidence using epigenomic profiles, Younghoon Kim, KISTI
  • stDyer enables spatial domain clustering with dynamic graph embedding
  • Splicing Junction Classifier for Detecting Abnormal KEAP1-NRF2 System Activation
  • Adapting broad protein language models to viruses
  • b-move: Faster Lossless Approximate Pattern Matching in a Run-Length Compressed Index, Lore Depuydt, Ghent University
  • Full length isoform reconstruction in single cell data, Marie Van Hecke, Ghent University - imec