RECOMB-Seq 2024 Proceedings

Cambridge, MA, United States, April 27 - 28, 2024.

PC Chairs: Ritambhara Singh, Brown University; and Mingfu Shao, Pennsylvania State University.
Keynote Speakers: Heng Li and Mona Singh.

Full Papers

  • Movi: a fast and cache-efficient full-text pangenome index. Mohsen Zakeri, Nathaniel Brown, Omar Ahmed, Travis Gagie and Ben Langmead. iScience, 27 (12): 111464, (2024)
  • Building a Pangenome Alignment Index via Recursive Prefix-Free Parsing. Eddie Ferro, Marco Oliva, Travis Gagie and Christina Boucher. iScience, 27 (10): 110933, (2024)
  • The Backpack Quotient Filter: a dynamic and space-efficient data structure for querying k-mers with abundance. Victor Levallois, Pierre Peterlongo, Yoann Dufresne, Bertrand Le Gal and Francesco Andreace. iScience, 27 (12): 111435, (2024)
  • Synthetic promoter design in Escherichia coli based on multinomial diffusion model. Qixiu Du, May Nee Poon, Xiaocheng Zeng, Pengcheng Zhang, Zheng Wei, Haochen Wang, Ye Wang, Lei Wei and Xiaowo Wang. iScience, 27 (11): 111207, (2024)
  • Quick and effective approximation of in silico saturation mutagenesis experiments with first-order Taylor expansion. Alexander Sasse, Sara Mostafavi and Maria Chikina. iScience, 27 (9): 110807, (2024)
  • Flowtigs: safety in flow decompositions for assembly graphs. Francisco Sena, Eliel Ingervo, Shahbaz Khan, Andrey Prjibelski, Sebastian Schmidt and Alexandru Tomescu. iScience, 27 (12): 111208, (2024)
  • PLA-complexity of k-mer multisets. Md Hasin Abrar and Paul Medvedev. overlay preprint
  • Phasing Diploid Genome Assembly Graphs with Single-Cell Strand Sequencing. Mir Henglin, Maryam Ghareghani, William Harvey, David Porubsky, Sergey Koren, Evan Eichler, Peter Ebert and Tobias Marschall. overlay preprint
  • CNVeil enables accurate and robust tumor subclone identification and copy number estimation from single cell sequencing data. Weiman Yuan, Can Luo, Yunfei Hu, Liting Zhang, Zihang Wen, Yichen Henry Liu, Xian Mallory and Xin Maizie Zhou. overlay preprint
  • Quality assessment of splice site annotation based on conservation across multiple species. Ilia Minkin and Steven Salzberg. overlay preprint
  • MaskGraphene: Advancing joint embedding, clustering, and batch correction for spatial transcriptomics using graph-based self-supervised learning. Yunfei Hu, Yikang Li, Manfei Xie, Mingxing Rao, Yichen Henry Liu and Xin Maizie Zhou. overlay preprint
  • Investigating the performance of foundation models on human 3’UTR sequences. Sergey Vilov and Matthias Heinig. overlay preprint

Short Talks Selected from Abstracts

  • A whole-genome probe design for massively parallel variant validation using selective circularization. Daniel Newburger, Georges Natsoulis, Hua Xu, Sue Grimes, John Bell and Hanlee Ji.
  • Accurate estimation of gene expression levels from dge sequencing data. Marius Nicolae and Ion Mandoiu.
  • Constrained traversal of repeats with paired sequences. Sébastien Boisvert, Élénie Godzaridis, François Laviolette and Jacques Corbeil.
  • Contig graph mining for duplication breakpoints. Jurgen F. Nijkamp, Jean-Marc Daran, Marcel J.T. Reinders and Dick De Ridder.
  • Counting k-mers with a Bloom Filter. Pall Melsted and Jonathan Pritchard.
  • Finding deletions with exact break points from noisy low coverage paired-end short sequence reads. Jin Zhang and Yufeng Wu.
  • Improved variant discovery and allele frequency estimation from pooled dna resequencing with bayesian latent class analysis and compositional bias models. Shom Paul and Aaron Mackey.
  • Modeling and automation of sequencing-based determination of RNA structure. Sharon Aviran, Cole Trapnell, Julius Lucks, Stefanie Mortimer, Shujun Luo, Gary Schroth, Jennifer Doudna, Adam Arkin and Lior Pachter.
  • mTiM: margin-based transcript mapping from RNA-seq. Georg Zeller, Nico Goernitz, Gunnar Raetsch, Jonas Behr, Andre Kahles, Soeren Sonnenburg and Pramod Mudrakarta.
  • Separating metagenomic data into genomes via clustering. Olga Tanaseichuk and Tao Jiang.
  • TavernaPBS: custom next-generation sequence analysis workflows using high-performance computing resources with Taverna and PBS. Mark Lawson, Paul Shuber and Aaron Mackey.

Posters

  • Compressed Indexing for Pangenome Substring Queries . Stephen Hwang, Nathaniel K. Brown, Omar Y. Ahmed, Katharine Jenike, Sam Kovaka, Michael C. Schatz and Ben Langmead.
  • Pan-genome de Bruijn Graph using the Bidirectional FM-index. Lore Depuydt, Luca Renders, Thomas Abeel and Jan Fostier.
  • Mumemto: efficient maximal matching across multiple genomes. Vikram Shivakumar and Ben Langmead.
  • A*PA & A*PA2: Up to 20 times faster exact global pairwise alignment. Ragnar Groot Koerkamp and Pesho Ivanov.
  • Accelerating whole-genome alignment using parallel chaining algorithm. Ghanshyam Chandra and Chirag Jain.
  • Full resolution HLA and KIR genes annotation for human genome assemblies. Ying Zhou, Li Song and Heng Li.
  • Combining DNA and protein alignments to improve genome annotation with LiftOn. Kuan-Hao Chao, Jakob M Heinz, Celine Hoh, Alan Mao, Alaina Shumate, Mihaela Pertea and Steven L Salzberg.
  • DupCaller enables robust detection of somatic mutations from Error-Corrected Sequencing. Yuhe Cheng and Ludmil B Alexandrov.
  • Comprehensive Tissue-Specific Somatic Mutation Profiling via RNA-seq in Diverse Mice. Alexis Garretson and Beth L Dumont.
  • VISTA: An integrated framework for structural variant discovery. Varuni Sarwal, Seungmo Lee, Jianzhi Yang, Sriram Sankararaman, Mark Chaisson, Eleazar Eskin and Serghei Mangul.
  • An efficient and accurate germline SNP caller for long-read RNA sequencing data. Neng Huang and Heng Li.
  • Analyzing the relatedness of genomic variation in malaria parasites using a reference-free approach. Cecile P G Meier-Scherling, Tavor Baharav, Karamoko Niaré, Julia Salzman, Lorin Crawford and Jeffrey A Bailey.
  • Identification of B cell subsets based on antigen receptor sequences using deep learning. Hyunho Lee, Kyoungseob Shin, Yongju Lee, Soobin Lee, Seungyoun Lee, Eunjae Lee, Seung Woo Kim, Ha Young Shin, Jong Hoon Kim, Junho Chung and Sunghoon Kwon.
  • Optimizing Design of Genomics Studies for Clonal Evolution Analysis. Arjun Srivatsa and Russell Schwartz.
  • Comprehensive benchmarking of methods to infer from TCR-Seq data. Mohammad Vahed, Yu Ning Huang, Jiaqi Fu, Kerui Peng and Serghei Mangul.
  • PA-Bench: A framework for benchmarking pairwise aligners. Ragnar Groot Koerkamp and Daniel Liu.
  • Block Aligner: an adaptive SIMD-accelerated aligner for sequences and position-specific scoring matrices. Daniel Liu and Martin Steinegger.
  • Gut derived Extracellular Vesicles Reaching Kupffer Cells: An alternative route for lipid transport out of the gut. Estefania Torrejón, Akiko Teshima, Inês Ferreira, Ana Sofia Carvalho, Hans Christian Beck, Rune Matthiesen, Fabrizia Carli, Amalia Gastaldelli, Maria Paula Macedo and Rita Machado de Oliveira.
  • A Unitig-Centered Pan-Genome Approach for Predicting Antibiotic Resistance and Discovering Novel Resistance Genes in Bacterial Strains. Thi Duyen Do, Ming-Ren Yang and Yu-Wei Wu.
  • Assessing Microbial Genome Representation Across Various Reference Databases: A Comprehensive Evaluation. Grigore Boldirev, Nitesh Sharma, Alex Zelikovsky and Serghei Mangul.
  • Validating a liquid soil model to explore soil microbial community dynamics. Siqin Li, Nicole Genesis Nicole Carpio Paucar and Natalie Farny.
  • Genetic Architecture of the Germline Mutation Rate and Reproductive Success in the Collaborative Cross. Alexis Garretson and Beth L Dumont.
  • WGTDA: A Topological Framework for Biomarker Discovery in Gene Expression Data. Ndivhuwo Nyase, Lebohang Mashatola, Stephanie Muller, Aviwe Kohlakala and Kahn Rhrissorrakrai.
  • QDSWorkflow: An Elastic Net-Based Tool for Modeling Cellular Dormancy. Michelle Wei and Guang Yao.
  • Comprehensive characterization of pseudogenes across 26 human tissues. Yunzhe Jiang, Beatrice Borsari and Mark Gerstein.
  • Partial gene predictions on unassembled reads: evaluating the Good, the Bad and the slightly ORF. Amanda Clare, Wayne Aubrey, Mike Surette and Nicholas Dimonaco.
  • A unified hypothesis-free feature extraction framework for diverse epigenomic data. Maria Chikina and Tugrul Balci.
  • Benchmarking of machine learning algorithms to predict mortality in sepsis from transcriptomic data. Karishma Chhugani, Serghei Mangul, Oleg Arnaut, Nitesh Sharma and Belin Korukoğlu.
  • Comparative Evaluation of T-Cell Receptor Repertoire Sequencing Methods. Dhrithi Deshpande and Serghei Mangul.
  • Statistical assessment of gene functional annotation clustering in graph models of chromosome conformation capture data. Dallas Nygard, Julie St-Pierre and Mathieu Lavallée-Adam.
  • Community: A Novel R-Tool for Enhanced Differential Communication Analysis in scRNAseq Data. Muhammet Celik, Felix Roman Salcher, Frank Ziemann, Maria Solovey and Maria Colome-Tatche.
  • Recovering approximate single cell distribution from aggregate measurements. Pratik Worah.
  • scFedVI: A Privacy-Preserving Approach to Mitigating Batch Effects in Single-Cell RNA-Sequencing Data. Parishad Mokhber, Alireza Gargoorimotlagh and Babak Khalaj.
  • sceptre: statistically rigorous, computationally efficient, and user-friendly single-cell CRISPR screen data analysis. Timothy Barry, Joseph Deutch, Xihong Lin and Eugene Katsevich.