Program

Program of RECOMB-seq 2025

April 24th, Thursday

Time/Day Event Speaker/Details
8:30-9:30 am Registration The Commons, Yonsei University
9:25-9:30 am Opening B125 Grand Ballroom
9:30-10:30 am Keynote 1: From Petabytes to Insights: Scaling Sequence Bioinformatics with Logan Rayan Chikhi, Institut Pasteur
10:30-10:45 am Coffee break
Session 1: Long talks - Proceedings Session chair: Rayan Chikhi
10:45-11:10 am Tile-X: A vertex reordering approach for scalable long read assembly [Proceedings, remote] Oieswarya Bhowmik, Washington State University
11:10-11:35 am Run-length compressed metagenomic read classification with SMEM-finding and tagging [Proceedings] Lore Depuydt, Ghent University
11:35-12:00 am Alignment-Free Detection of Differences Between Sequencing Data Sets [Proceedings] Alessia Petescia Comenius, University in Bratislava
12:00-1:30 pm Lunch / Poster viewing (odd numbers)
Session 2: Short talks Session chair: Milot Mirdita
1:30-1:42 pm Metrics Matter: Why We Need to Stop Using Silhouette in Single-Cell Benchmarking Pia Rautenstrauch, MDC Berlin
1:42-1:54 pm Full length isoform reconstruction in single cell data Marie Van Hecke, Ghent University - imec
1:55-2:07 pm Masked superstrings as a compact, indexable, and dynamic representation of unconstrained k-mer sets Pavel Veselý, Charles University
2:07-2:19 pm Automated Annotation of Satellite DNA Alex Sweeten, Johns Hopkins University
2:20-2:40 pm Break
Session 3: Short talks Session chair: Chirag Jain
2:40-2:52 pm b-move: Faster Lossless Approximate Pattern Matching in a Run-Length Compressed Index Lore Depuydt, Ghent University
2:52-3:04 pm strangepg: Toward Pangenome Scale Graph Visualization Konstantinn Bonnet, Heinrich Heine University
3:05-3:17 pm Improved variant calling via latent breakpoint graphs Megan Le, Broad Institute
3:17-3:29 pm A Novel K-mer Masking Approach for Improving Specificity in Metagenomic Pathogen Detection Joanne Qiu, UCLA
3:30-3:45 pm Break
Session 4: Long talks - Overlay Session chair: Pavel Veselý
3:45-4:10 pm DeepMM: Identify and correct Metagenome Misassemblies with deep learning [Overlay] Ding Yi, Hong Kong Baptist University
4:10-4:35 pm GPU-accelerated homology search with MMseqs2 [Overlay] Milot Mirdita, Seoul National University
4:35-5:00 pm On the Coverage Required for Diploid Genome Assembly [Overlay] Chirag Jain, Indian Institute of Science
5:00-5:15 pm Poster highlights (odd numbers)
5:15 pm Poster viewing (odd numbers) Slots 101 to 120


April 25th, Friday

Time/Day Event Speaker/Details
8:30-9:30 am Registration The Commons, Yonsei University
9:25-9:30 am Opening B125 Grand Ballroom
9:30-10:30 am Keynote 2: Single cells and long reads: Transcriptomes at exquisite resolution Alicia Oshlack, Peter MacCallum Cancer Center
10:30-10:45 am Coffee break
Session 5: Long talks - Proceedings Session chair: Alicia Oshlack
10:45-11:10 am Decoding the causal drivers of spatial cellular topology [Proceedings] Rohit Singh, Duke
11:10-11:35 am Efficient trace reconstruction in DNA storage systems using Bidirectional Beam Search [Proceedings] Gu Zhenhao, National University of Singapore
11:35-12:00 am Decoupling Hi-C matrices with non-negative matrix factorization to reveal assorted TADs [Proceedings] Zhao Ling, City university of HongKong
12:00-1:30 pm Lunch / Poster viewing (even numbers)
Session 6: Short talks Session chair: Rohit Singh
1:30-1:42 pm Pre-Training Dataset Deduplication Improves Genomic LLMs Mahler Revsine, Johns Hopkins University
1:42-1:54 pm Edgecopy: Accurate CNV calling in duplicated genes using whole-exome sequencing Sang Yoon Byun, University of California San Diego
1:55-2:07 pm Reindeer2: practical abundance index at scale Camille Marchet, Université de Lille - CNRS
2:07-2:19 pm Inverted colored de Bruin Graph for practical kmer set storage Timothé Rouzé, Institut Pasteur
2:20-2:40 pm Coffee break
Session 7: Short talks Session chair: Luca Denti
2:40-2:52 pm Vizitig: context-rich exploration of sequencing datasets Camille Marchet, Université de Lille - CNRS
2:52-3:04 pm Multi-sample, multi-platform isoform quantification using empirical Bayes Arghamitra Talukder, Columbia University
3:05-3:17 pm Efficient algorithm for resolving scenarios of Complex Chromosomal Rearrangements Barbara Poszewiecka, University of Warsaw
3:17-3:29 pm De Bruijn Graphs for Pangenomics: In-depth Performance Benchmarking of de Bruijn Graph-Based Tools for Read Mapping Zülal Bingöl, Bilkent University
3:30-3:45 pm Coffee break
Session 8: Long talks - Overlay Session chair: Yaron Orenstein
3:45-4:10 pm Pangenome graph augmentation from unassembled long reads [Overlay] Luca Denti, Comenius University in Bratislava
4:10-4:35 pm De novo clustering of extensive long-read transcriptome datasets with isONclust3 [Overlay] Alexander Petri, Stockholm University
4:35-5:00 pm Multi-context seeds enable fast and high-accuracy read mapping [Overlay] Ivan Tolstoganov, Stockholm University
5:00-5:15 pm Poster highlights (even numbers)
5:15 pm Poster viewing (even numbers) Slots 101 to 120

 

 

 

 

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