{ "title": "27th Annual International Conference on Research in Computational Molecular Biology", "location": "İstanbul, Türkiye", "dates": "April 16 - 19, 2023", "pc_chair": "Haixu Tang", "organization_committee": "Can Alkan (co-chair), Attila Gürsoy (co-chair), Zülal Bingöl, A. Ercüment Çiçek, Tunca Doğan, Ezgi Ebren, Arzucan Özgür, Öznur Taştan", "keynotes": "İvet Bahar, Ewan Birney, Richard Durbin, Tuuli Lappalainen, Sohini Ramachandran, Fabian Theis", "website": "https://recomb.org/recomb2023", "papers": [ { "author": "Runpeng Luo, Yu Lin", "title": "VStrains: de novo reconstruction of viral strains via iterative path extraction from assembly graphs", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 3-20, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "3-20", "proceedings_doi": "10.1007/978-3-031-29119-7_1", "preprint_id": "bioRxiv 2022.10.21.513181", "preprint_doi": "10.1101/2022.10.21.513181" }, { "author": "Jason Fan, Jamshed Khan, Giulio Ermanno Pibiri, Robert Patro", "title": "Spectrum preserving tilings enable sparse and modular reference indexing", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 21-40, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "21-40", "proceedings_doi": "10.1007/978-3-031-29119-7_2", "preprint_id": "bioRxiv 2022.10.27.513881", "preprint_doi": "10.1101/2022.10.27.513881" }, { "author": "Yasamin Tabatabaee, Sebastien Roch, Tandy Warnow", "title": "Statistically Consistent Rooting of Species Trees under the Multispecies Coalescent Model", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 41-57, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "41-57", "proceedings_doi": "10.1007/978-3-031-29119-7_3", "preprint_id": "bioRxiv 2022.10.26.513897", "preprint_doi": "10.1101/2022.10.26.513897", "journal": "Journal of Computational Biology", "journal_title": "QR-STAR: A Polynomial-Time Statistically Consistent Method for Rooting Species Trees Under the Coalescent", "journal_authors": "Yasamin Tabatabaee, Sebastien Roch, Tandy Warnow", "journal_issue_pages": "30(11): 1146–1181", "journal_year": "2023", "journal_doi": "10.1089/cmb.2023.0185" }, { "author": "Ghanshyam Chandra, Chirag Jain", "title": "Sequence to graph alignment using gap-sensitive co-linear chaining", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 58-73, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "58-73", "proceedings_doi": "10.1007/978-3-031-29119-7_4", "preprint_id": "bioRxiv 2022.08.29.505691", "preprint_doi": "10.1101/2022.08.29.505691", "journal": "Journal of Computational Biology", "journal_title": "Gap-Sensitive Colinear Chaining Algorithms for Acyclic Pangenome Graphs", "journal_authors": "Ghanshyam Chandra, Chirag Jain", "journal_issue_pages": "30(11): 1182–1197", "journal_year": "2023", "journal_doi": "10.1089/cmb.2023.0186" }, { "author": "Xiaogen Zhou, Zhiqiang Li, Tong Tong", "title": "DM-Net: a dual-model network for automated biomedical image diagnosis", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 74-84, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "74-84", "proceedings_doi": "10.1007/978-3-031-29119-7_5" }, { "author": "Bing-Xue Du, Yi Xu, Siu Ming Yiu, Hui Yu, Jian-Yu Shi", "title": "MTGL-ADMET: A Novel Multi-Task Graph Learning Framework for ADMET Prediction Enhanced by Status-Theory and Maximum Flow", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 85-103, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "85-103", "proceedings_doi": "10.1007/978-3-031-29119-7_6" }, { "author": "Shikha Mallick, Sahely Bhadra", "title": "CDGCN: Conditional de novo Drug generative model using Graph Convolution Networks", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 104-119, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "104-119", "proceedings_doi": "10.1007/978-3-031-29119-7_7" }, { "author": "Soufiane Mourragui, Marco Loog, Mirrelijn van Nee, Mark van de Wiel, Marcel Reinders, Lodewyk Wessels", "title": "Percolate: an exponential family JIVE model to design DNA-based predictors of drug response", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 120-138, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "120-138", "proceedings_doi": "10.1007/978-3-031-29119-7_8", "preprint_id": "bioRxiv 2022.09.11.507473", "preprint_doi": "10.1101/2022.09.11.507473" }, { "author": "Weizhong Zheng, John H.C. Fong, Yuk Kei Wan, Athena H.Y. Chu, Yuanhua Huang, Alan S.L. Wong, Joshua Ho", "title": "Translation rate prediction and regulatory motif discovery with multi-task learning", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 139-154, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "139-154", "proceedings_doi": "10.1007/978-3-031-29119-7_9", "preprint_id": "bioRxiv 2022.05.03.490410", "preprint_doi": "10.1101/2022.05.03.490410" }, { "author": "Spencer Krieger, John Kececioglu", "title": "Computing shortest hyperpaths for pathway inference in cellular reaction networks", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 155-173, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "155-173", "proceedings_doi": "10.1007/978-3-031-29119-7_10", "journal": "Journal of Computational Biology", "journal_title": "Shortest Hyperpaths in Directed Hypergraphs for Reaction Pathway Inference", "journal_authors": "Spencer Krieger, John Kececioglu", "journal_issue_pages": "30(11): 1198–1225", "journal_year": "2023", "journal_doi": "10.1089/cmb.2023.0242" }, { "author": "Ziqi Chen, Martin Min, Hongyu Guo, Chao Cheng, Trevor Clancy, Xia Ning", "title": "T-Cell Receptor Optimization with Reinforcement Learning and Mutation Polices for Precision Immunotherapy", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 174-192, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "174-192", "proceedings_doi": "10.1007/978-3-031-29119-7_11", "preprint_id": "arXiv:2303.02162", "preprint_doi": "10.48550/arXiv.2303.02162" }, { "author": "Yunheng Han, Erin K. Molloy", "title": "TREE-QMC: Improving quartet graph construction for scalable and accurate species tree estimation from gene trees", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 195-196, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "195-196", "proceedings_doi": "10.1007/978-3-031-29119-7", "preprint_id": "bioRxiv 2022.06.25.497608", "preprint_doi": "10.1101/2022.06.25.497608", "journal": "Genome Research", "journal_title": "Improving quartet graph construction for scalable and accurate species tree estimation from gene trees", "journal_authors": "Yunheng Han, Erin K. Molloy", "journal_issue_pages": "33(7):1042-1052", "journal_year": "2023", "journal_doi": "10.1101/gr.277629.122" }, { "author": "Baris Ekim, Kristoffer Sahlin, Paul Medvedev, Bonnie Berger, Rayan Chikhi", "title": "mapquik: Efficient low-divergence mapping of long reads in minimizer space", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 197-199, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "197-199", "proceedings_doi": "10.1007/978-3-031-29119-7", "preprint_id": "bioRxiv 2022.12.23.521809", "preprint_doi": "10.1101/2022.12.23.521809", "journal": "Genome Research", "journal_title": "Efficient mapping of accurate long reads in minimizer space with mapquik", "journal_authors": "Baris Ekim, Kristoffer Sahlin, Paul Medvedev, Bonnie Berger, Rayan Chikhi", "journal_issue_pages": "33(7): 1188-1197", "journal_year": "2023", "journal_doi": "10.1101/gr.277679.123" }, { "author": "Mahmudur Rahman Hera, N. Tessa Pierce-Ward, David Koslicki", "title": "Deriving confidence intervals for mutation rates across a wide range of evolutionary distances using FracMinHash", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 200-202, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "200-202", "proceedings_doi": "10.1007/978-3-031-29119-7", "preprint_id": "bioRxiv 2022.01.11.475870", "preprint_doi": "10.1101/2022.01.11.475870", "journal": "Genome Research", "journal_title": "Deriving confidence intervals for mutation rates across a wide range of evolutionary distances using FracMinHash", "journal_authors": "Mahmudur Rahman Hera, N. Tessa Pierce-Ward, David Koslicki", "journal_issue_pages": "33(7):1061-1068", "journal_year": "2023", "journal_doi": "10.1101/gr.277651.123" }, { "author": "Benjamin Dominik Maier, Kristoffer Sahlin", "title": "Entropy predicts sensitivity of pseudo-random seeds", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 203-204, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "203-204", "proceedings_doi": "10.1007/978-3-031-29119-7", "preprint_id": "bioRxiv 2022.10.13.512198", "preprint_doi": "10.1101/2022.10.13.512198", "journal": "Genome Research", "journal_title": "Entropy predicts sensitivity of pseudorandom seeds", "journal_authors": "Benjamin Dominik Maier, Kristoffer Sahlin", "journal_issue_pages": "33(7): 1162-1174", "journal_year": "2023", "journal_doi": "10.1101/gr.277645.123" }, { "author": "Jim Shaw, Yun William Yu", "title": "Seed-chain-extend alignment is accurate and runs in close to O(m log n) time for similar sequences: a rigorous average-case analysis", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 205-207, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "205-207", "proceedings_doi": "10.1007/978-3-031-29119-7", "preprint_id": "bioRxiv 2022.10.14.512303", "preprint_doi": "10.1101/2022.10.14.512303", "journal": "Genome Research", "journal_title": "Proving sequence aligners can guarantee accuracy in almost O(m log n) time through an average-case analysis of the seed-chain-extend heuristic", "journal_authors": "Jim Shaw, Yun William Yu", "journal_issue_pages": "33(7): 1175-1187", "journal_year": "2023", "journal_doi": "10.1101/gr.277637.122" }, { "author": "Andrea Cracco, Alexandru I. Tomescu", "title": "Extremely-fast construction and querying of compacted and colored de Bruijn graphs with GGCAT", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 208-209, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "208-209", "proceedings_doi": "10.1007/978-3-031-29119-7", "preprint_id": "bioRxiv 2022.10.24.513174", "preprint_doi": "10.1101/2022.10.24.513174", "journal": "Genome Research", "journal_title": "Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCAT", "journal_authors": "Andrea Cracco, Alexandru I. Tomescu", "journal_issue_pages": "33(7): 1198-1207", "journal_year": "2023", "journal_doi": "10.1101/gr.277615.122" }, { "author": "Xinhao Liu, Ron Zeira, Benjamin J. Raphael", "title": "PASTE2: Partial Alignment of Multi-slice Spatially Resolved Transcriptomics Data", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 210-211, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "210-211", "proceedings_doi": "10.1007/978-3-031-29119-7", "preprint_id": "bioRxiv 2023.01.08.523162", "preprint_doi": "10.1101/2023.01.08.523162", "journal": "Genome Research", "journal_title": "Partial alignment of multislice spatially resolved transcriptomics data", "journal_authors": "Xinhao Liu, Ron Zeira, Benjamin J. Raphael", "journal_issue_pages": "33(7): 1124-1132", "journal_year": "2023", "journal_doi": "10.1101/gr.277670.123" }, { "author": "Ardalan Naseri, William Yue, Shaojie Zhang, Degui Zhi", "title": "FastRecomb: Fast Inference of Genetic Recombination Rates in Biobank Scale Data", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 212-213, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "212-213", "proceedings_doi": "10.1007/978-3-031-29119-7", "preprint_id": "bioRxiv 2023.01.09.523304", "preprint_doi": "10.1101/2023.01.09.523304", "journal": "Genome Research", "journal_title": "Fast inference of genetic recombination rates in biobank scale data", "journal_authors": "Ardalan Naseri, William Yue, Shaojie Zhang, Degui Zhi", "journal_issue_pages": "33(7): 1015-1022", "journal_year": "2023", "journal_doi": "10.1101/gr.277676.123" }, { "author": "Omar Ahmed, Massimiliano Rossi, Christina Boucher, Ben Langmead", "title": "Efficient Taxa Identification Using a Pangenome Index", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 214-216, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "214-216", "proceedings_doi": "10.1007/978-3-031-29119-7", "journal": "Genome Research", "journal_title": "Efficient taxa identification using a pangenome index", "journal_authors": "Omar Ahmed, Massimiliano Rossi, Christina Boucher, Ben Langmead", "journal_issue_pages": "33(7): 1069-1077", "journal_year": "2023", "journal_doi": "10.1101/gr.277642.123" }, { "author": "Claire McWhite, Mona Singh", "title": "Vector-Clustering Multiple Sequence Alignment: Aligning into the Twilight Zone of Protein Sequence Similarity with Protein Language Models", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 217-218, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "217-218", "proceedings_doi": "10.1007/978-3-031-29119-7", "preprint_id": "bioRxiv 2022.10.21.513099", "preprint_doi": "10.1101/2022.10.21.513099", "journal": "Genome Research", "journal_title": "Leveraging protein language models for accurate multiple sequence alignments", "journal_authors": "Claire McWhite, Isabel Armour-Garb, Mona Singh", "journal_issue_pages": "33(7): 1145-1153", "journal_year": "2023", "journal_doi": "10.1101/gr.277675.123" }, { "author": "Yuelin Liu, Xuan Cindy Li, Farid Rashidi Mehrabadi, Alejandro A. Schäffer, Drew Pratt, David R. Crawford, Salem Malikic, Erin K. Molloy, Vishaka Gopalan, Stephen M. Mount, Eytan Ruppin, Kenneth Aldape, S. Cenk Sahinalp", "title": "Single-Cell Methylation Sequencing Data Reveal Succinct Metastatic Migration Histories and Tumor Progression Models", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 219-221, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "219-221", "proceedings_doi": "10.1007/978-3-031-29119-7", "preprint_id": "bioRxiv 2021.03.22.436475", "preprint_doi": "10.1101/2021.03.22.436475", "journal": "Genome Research", "journal_title": "Single-cell methylation sequencing data reveal succinct metastatic migration histories and tumor progression models", "journal_authors": "Yuelin Liu, Xuan Cindy Li, Farid Rashidi Mehrabadi, Alejandro A. Schäffer, Drew Pratt, David R. Crawford, Salem Malikic, Erin K. Molloy, Vishaka Gopalan, Stephen M. Mount, Eytan Ruppin, Kenneth Aldape, S. Cenk Sahinalp", "journal_issue_pages": "33(7): 1089-1100", "journal_year": "2023", "journal_doi": "10.1101/gr.277608.122" }, { "author": "Chihao Zhang, Yiling Elaine Chen, Shihua Zhang, Jingyi Jessica Li", "title": "Information-Theoretic Classification Accuracy: A Criterion That Guides Data-Driven Combination of Ambiguous Outcome Labels in Multi-class Classification", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 222-223, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "222-223", "proceedings_doi": "10.1007/978-3-031-29119-7", "preprint_id": "arXiv:2109.00582", "preprint_doi": "10.48550/arXiv.2109.00582", "journal": "Journal of Machine Learning Research", "journal_title": "Information-theoretic Classification Accuracy: A Criterion that Guides Data-driven Combination of Ambiguous Outcome Labels in Multi-class Classification", "journal_authors": "Chihao Zhang, Yiling Elaine Chen, Shihua Zhang, Jingyi Jessica Li", "journal_issue_pages": "23(341): 1-65", "journal_year": "2022" }, { "author": "David Pellow, Lianrong Pu, Baris Ekim, Lior Kotlar, Ron Shamir, Yaron Orenstein", "title": "Efficient Minimizer Orders for Large Values of k Using Minimum Decycling Sets", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 224-226, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "224-226", "proceedings_doi": "10.1007/978-3-031-29119-7", "preprint_id": "bioRxiv 2022.10.18.512682", "preprint_doi": "10.1101/2022.10.18.512682", "journal": "Genome Research", "journal_title": "Efficient minimizer orders for large values of k using minimum decycling sets", "journal_authors": "David Pellow, Lianrong Pu, Baris Ekim, Lior Kotlar, Bonnie Berger, Ron Shamir, Yaron Orenstein", "journal_issue_pages": "33(7): 1154-1161", "journal_year": "2023", "journal_doi": "10.1101/gr.277644.123" }, { "author": "Daniel N. Baker, Ben Langmead", "title": "Dashing 2: Genomic Sketching with Multiplicities and Locality-Sensitive Hashing", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 227-228, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "227-228", "proceedings_doi": "10.1007/978-3-031-29119-7", "preprint_id": "bioRxiv 2022.10.16.512384", "preprint_doi": "10.1101/2022.10.16.512384", "journal": "Genome Research", "journal_title": "Genomic sketching with multiplicities and locality-sensitive hashing using Dashing 2", "journal_authors": "Daniel N. Baker, Ben Langmead", "journal_issue_pages": "33(7): 1218-1227", "journal_year": "2023", "journal_doi": "10.1101/gr.277655.123" }, { "author": "Palash Sashittal, Henri Schmidt, Michelle Chan, Benjamin J. Raphael", "title": "Startle: A Star Homoplasy Approach for CRISPR-Cas9 Lineage Tracing", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 229, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "229", "proceedings_doi": "10.1007/978-3-031-29119-7", "preprint_id": "bioRxiv 2022.12.18.520935", "preprint_doi": "10.1101/2022.12.18.520935", "journal": "Cell Systems", "journal_title": "Startle: A star homoplasy approach for CRISPR-Cas9 lineage tracing", "journal_authors": "Palash Sashittal, Henri Schmidt, Michelle Chan, Benjamin J. Raphael", "journal_issue_pages": "14(12): 1113-1121.e9", "journal_year": "2023", "journal_doi": "10.1016/j.cels.2023.11.005" }, { "author": "Louxin Zhang, Niloufar Abhari, Caroline Colijn, Yufeng Wu", "title": "A fast and scalable method for inferring phylogenetic networks from trees by aligning lineage taxon strings", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 230-232, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "230-232", "proceedings_doi": "10.1007/978-3-031-29119-7", "preprint_id": "arXiv:2301.00992", "preprint_doi": "10.48550/arXiv.2301.00992", "journal": "Genome Research", "journal_title": "A fast and scalable method for inferring phylogenetic networks from trees by aligning lineage taxon strings", "journal_authors": "Louxin Zhang, Niloufar Abhari, Caroline Colijn, Yufeng Wu", "journal_issue_pages": "33(7): 1053-1060", "journal_year": "2023", "journal_doi": "10.1101/gr.277669.123" }, { "author": "Amir Joudaki, Alexandru Meterez, Harun Mustafa, Ragnar Groot Koerkamp, André Kahles, Gunnar Rätsch", "title": "Aligning Distant Sequences to Graphs using Long Seed Sketches", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 233-235, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "233-235", "proceedings_doi": "10.1007/978-3-031-29119-7", "preprint_id": "bioRxiv 2022.10.26.513890", "preprint_doi": "10.1101/2022.10.26.513890", "journal": "Genome Research", "journal_title": "Aligning distant sequences to graphs using long seed sketches", "journal_authors": "Amir Joudaki, Alexandru Meterez, Harun Mustafa, Ragnar Groot Koerkamp, André Kahles, Gunnar Rätsch", "journal_issue_pages": "33(7): 1208-1217", "journal_year": "2023", "journal_doi": "10.1101/gr.277659.123" }, { "author": "Uyen Mai, Eduardo Charvel, Siavash Mirarab", "title": "MD-Cat: Phylogenetic Dating under a Flexible Categorical Model using Expectation-Maximization", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 236-238, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "236-238", "proceedings_doi": "10.1007/978-3-031-29119-7", "preprint_id": "bioRxiv 2022.10.06.511147", "preprint_doi": "10.1101/2022.10.06.511147", "journal": "Systematic Biology", "journal_title": "Expectation-Maximization enables Phylogenetic Dating under a Categorical Rate Model", "journal_authors": "Uyen Mai, Eduardo Charvel, Siavash Mirarab", "journal_issue_pages": "73(5): 823-838", "journal_year": "2024", "journal_doi": "10.1093/sysbio/syae034" }, { "author": "Aditya Gorla, Sriram Sankararaman, Esteban Burchard, Jonathan Flint, Noah Zaitlen, Elior Rahmani", "title": "Phenotypic subtyping via contrastive learning", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 239-240, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "239-240", "proceedings_doi": "10.1007/978-3-031-29119-7", "preprint_id": "bioRxiv 2023.01.05.522921", "preprint_doi": "10.1101/2023.01.05.522921" }, { "author": "Sara C. Schulte, Alexander Dilthey, Gunnar W. Klau", "title": "HOGVAX: Exploiting Peptide Overlaps to Maximize Population Coverage in Vaccine Design with Application to SARS-CoV-2", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 241-243, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "241-243", "proceedings_doi": "10.1007/978-3-031-29119-7", "preprint_id": "bioRxiv 2023.01.09.523288", "preprint_doi": "10.1101/2023.01.09.523288", "journal": "Cell Systems", "journal_title": "HOGVAX: Exploiting epitope overlaps to maximize population coverage in vaccine design with application to SARS-CoV-2", "journal_authors": "Sara C. Schulte, Alexander Dilthey, Gunnar W. Klau", "journal_issue_pages": "14(12): 1122-1130", "journal_year": "2023", "journal_doi": "10.1016/j.cels.2023.11.001" }, { "author": "Regev Schweiger, Richard Durbin", "title": "Ultra-fast genome-wide inference of pairwise coalescence times (Final version)", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 244-246, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "244-246", "proceedings_doi": "10.1007/978-3-031-29119-7", "preprint_id": "bioRxiv 2023.01.06.522935", "preprint_doi": "10.1101/2023.01.06.522935", "journal": "Genome Research", "journal_title": "Ultrafast genome-wide inference of pairwise coalescence times", "journal_authors": "Regev Schweiger, Richard Durbin", "journal_issue_pages": "33(7): 1023-1031", "journal_year": "2023", "journal_doi": "10.1101/gr.277665.123" }, { "author": "Nathan LaPierre, Boyang Fu, Steven Turnbull, Eleazar Eskin, Sriram Sankararaman", "title": "Leveraging family data to design Mendelian Randomization that is provably robust to population stratification", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 247-248, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "247-248", "proceedings_doi": "10.1007/978-3-031-29119-7", "preprint_id": "bioRxiv 2023.01.05.522936", "preprint_doi": "10.1101/2023.01.05.522936", "journal": "Genome Research", "journal_title": "Leveraging family data to design Mendelian randomization that is provably robust to population stratification", "journal_authors": "Nathan LaPierre, Boyang Fu, Steven Turnbull, Eleazar Eskin, Sriram Sankararaman", "journal_issue_pages": "33(7): 1032-1041", "journal_year": "2023", "journal_doi": "10.1101/gr.277664.123" }, { "author": "Ahsan Sanaullah, Degui Zhi, Shaojie Zhang", "title": "Minimal Positional Substring Cover: A Haplotype Threading Alternative to Li & Stephens Model", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 249-250, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "249-250", "proceedings_doi": "10.1007/978-3-031-29119-7", "preprint_id": "bioRxiv 2023.01.04.522803", "preprint_doi": "10.1101/2023.01.04.522803", "journal": "Genome Research", "journal_title": "Minimal positional substring cover is a haplotype threading alternative to Li and Stephens model", "journal_authors": "Ahsan Sanaullah, Degui Zhi, Shaojie Zhang", "journal_issue_pages": "33(7): 1007-1014", "journal_year": "2023", "journal_doi": "10.1101/gr.277673.123" }, { "author": "Hao Chen, Dongshunyi Li, Ziv Bar-Joseph", "title": "Cell segmentation for high-resolution spatial transcriptomics", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 251-253, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "251-253", "proceedings_doi": "10.1007/978-3-031-29119-7", "preprint_id": "bioRxiv 2023.01.11.523658", "preprint_doi": "10.1101/2023.01.11.523658", "journal": "Nature Methods", "journal_title": "SCS: cell segmentation for high-resolution spatial transcriptomics", "journal_authors": "Hao Chen, Dongshunyi Li, Ziv Bar-Joseph", "journal_issue_pages": "20(8): 1237-1243", "journal_year": "2023", "journal_doi": "10.1038/s41592-023-01939-3" }, { "author": "Yudi Zhang, Ha Vu, Geetu Tuteja, Karin Dorman", "title": "Unsupervised Deep Peak Caller for ATAC-seq", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 254-256, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "254-256", "proceedings_doi": "10.1007/978-3-031-29119-7", "preprint_id": "bioRxiv 2023.01.07.523108", "preprint_doi": "10.1101/2023.01.07.523108", "journal": "Genome Research", "journal_title": "Unsupervised contrastive peak caller for ATAC-seq", "journal_authors": "Ha T.H. Vu, Yudi Zhang, Geetu Tuteja, Karin Dorman", "journal_issue_pages": "33(7): 1133-1144", "journal_year": "2023", "journal_doi": "10.1101/gr.277677.123" }, { "author": "Rohit Singh, Alexander Wu, Anish Mudide, Bonnie Berger", "title": "Unraveling causal gene regulation from the RNA velocity graph using Velorama", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 257-258, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "257-258", "proceedings_doi": "10.1007/978-3-031-29119-7", "preprint_id": "bioRxiv 2022.10.18.512766", "preprint_doi": "10.1101/2022.10.18.512766", "journal": "Cell Systems", "journal_title": "Causal gene regulatory analysis with RNA velocity reveals an interplay between slow and fast transcription factors", "journal_authors": "Rohit Singh, Alexander Wu, Anish Mudide, Bonnie Berger", "journal_issue_pages": "15(5):462-474", "journal_year": "2024", "journal_doi": "10.1016/j.cels.2024.04.005" }, { "author": "Vitalii Stebliankin, Azam Shirali, Prabin Baral, Prem Chapagain, Giri Narasimhan", "title": "PIsToN: Evaluating Protein Binding Interfaces with Transformer Networks", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 259-261, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "259-261", "proceedings_doi": "10.1007/978-3-031-29119-7", "preprint_id": "bioRxiv 2023.01.03.522623", "preprint_doi": "10.1101/2023.01.03.522623", "journal": "Nature Machine Intelligence", "journal_title": "Evaluating protein binding interfaces with transformer networks", "journal_authors": "Vitalii Stebliankin, Azam Shirali, Prabin Baral, Jimeng Shi, Prem Chapagain, Kalai Mathee, Giri Narasimhan", "journal_issue_pages": "5: 1042–1053", "journal_year": "2023", "journal_doi": "10.1038/s42256-023-00715-4" }, { "author": "Rıza Özçelik, Alperen Bağ, Berk Atıl, Melih Barsbey, Arzucan Özgür, Elif Ozkirimli", "title": "DebiasedDTA: A Framework for Improving the Generalizability of Drug-Target Affinity Prediction Models", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 262-264, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "262-264", "proceedings_doi": "10.1007/978-3-031-29119-7", "preprint_id": "arXiv:2107.05556", "preprint_doi": "10.48550/arXiv.2107.05556", "journal": "Journal of Computational Biology", "journal_title": "A Framework for Improving the Generalizability of Drug–Target Affinity Prediction Models", "journal_authors": "Rıza Özçelik, Alperen Bağ, Berk Atıl, Melih Barsbey, Arzucan Özgür, Elif Ozkirimli", "journal_issue_pages": "30(11): 1226–1239", "journal_year": "2023", "journal_doi": "10.1089/cmb.2023.0208" }, { "author": "Zhihang Hu, Qinze Yu, Yucheng Guo, Taifeng Wang, Irwin King, Xin Gao, Le Song, Yu Li", "title": "Drug Synergistic Combinations Predictions via Large-Scale Pre-Training and Graph Structure Learning", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 265-267, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "265-267", "proceedings_doi": "10.1007/978-3-031-29119-7", "preprint_id": "arXiv:2301.05931", "preprint_doi": "10.48550/arXiv.2301.05931" }, { "author": "Jiacheng Lin, Hanwen Xu, Addie Woicik, Jianzhu Ma, Sheng Wang", "title": "Pisces: a cross-modal contrastive learning approach to synergistic drug combination prediction", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 268-270, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "268-270", "proceedings_doi": "10.1007/978-3-031-29119-7", "preprint_id": "bioRxiv 2022.11.21.517439", "preprint_doi": "10.1101/2022.11.21.517439", "journal": "Cell Genomics", "journal_title": "Pisces: A multi-modal data augmentation approach for drug combination synergy prediction", "journal_authors": "Hanwen Xu, Jiacheng Lin, Addie Woicik, Zixuan Liu, Jianzhu Ma, Sheng Zhang, Hoifung Poon, Liewei Wang, Sheng Wang", "journal_issue_pages": "5(7): 100892", "journal_year": "2025", "journal_doi": "10.1016/j.xgen.2025.100892" }, { "author": "Stefan Ivanovic, Mohammed El-Kebir", "title": "Modeling and Predicting Cancer Clonal Evolution with Reinforcement Learning", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 271-273, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "271-273", "proceedings_doi": "10.1007/978-3-031-29119-7", "preprint_id": "bioRxiv 2022.12.11.519917", "preprint_doi": "10.1101/2022.12.11.519917", "journal": "Genome Research", "journal_title": "Modeling and predicting cancer clonal evolution with reinforcement learning", "journal_authors": "Stefan Ivanovic, Mohammed El-Kebir", "journal_issue_pages": "33(7): 1078-1088", "journal_year": "2023", "journal_doi": "10.1101/gr.277672.123" }, { "author": "Rajagopal Venkatesaramani, Zhiyu Wan, Brad Malin, Yevgeniy Vorobeychik", "title": "Enabling Trade-offs in Privacy and Utility in Genomic Data Beacons and Summary Statistics", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 274-276, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "274-276", "proceedings_doi": "10.1007/978-3-031-29119-7", "preprint_id": "arXiv:2302.01763", "preprint_doi": "10.48550/arXiv.2302.01763", "journal": "Genome Research", "journal_title": "Enabling tradeoffs in privacy and utility in genomic data Beacons and summary statistics", "journal_authors": "Rajagopal Venkatesaramani, Zhiyu Wan, Brad Malin, Yevgeniy Vorobeychik", "journal_issue_pages": "33(7): 1113-1123", "journal_year": "2023", "journal_doi": "10.1101/gr.277674.123" }, { "author": "Shuvom Sadhuka, Daniel Fridman, Bonnie Berger, Hyunghoon Cho", "title": "Accurate evaluation of transcriptomic re-identification risks using discriminative sequence models", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science, vol 13976, pp 277-279, Springer, Cham.", "proceedings_volume": "13976", "proceedings_pages": "277-279", "proceedings_doi": "10.1007/978-3-031-29119-7", "preprint_id": "bioRxiv 2023.04.13.536784", "preprint_doi": "10.1101/2023.04.13.536784", "journal": "Genome Research", "journal_title": "Assessing transcriptomic reidentification risks using discriminative sequence models", "journal_authors": "Shuvom Sadhuka, Daniel Fridman, Bonnie Berger, Hyunghoon Cho", "journal_issue_pages": "33(7):1101–1112", "journal_year": "2023", "journal_doi": "10.1101/gr.277699.123" } ] }