{ "title": "28th Annual International Conference on Research in Computational Molecular Biology", "location": "Cambridge, MA, United States", "dates": "April 29 - May 2, 2024", "pc_chair": "Jian Ma", "organization_committee": "Bonnie Berger (co-chair), Lenore Cowen (co-chair), Iman Hajirasouliha, Ezgi Ebren", "keynotes": "Jim Collins, Shafi Goldwasser, Bob Langer, Xihong Lin, Steven Salzberg", "website": "https://recomb.org/recomb2024", "papers": [ { "author": "Kapil Devkota, Anselm Blumer, Xiaozhe Hu, Lenore Cowen", "title": "Fast Approximate IsoRank for Scalable Global Alignment of Biological Networks", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 1-16, Springer, Cham.", "proceedings_volume": "14758", "proceedings_pages": "1-16", "proceedings_doi": "10.1007/978-1-0716-3989-4_1", "preprint_id": "bioRxiv 2023.03.13.532445", "preprint_doi": "10.1101/2023.03.13.532445", "journal": "Journal of Computational Biology", "journal_title": "Approximate IsoRank for Scalable and Functionally Meaningful Cross-Species Alignments of Protein Interaction Networks", "journal_authors": "Kapil Devkota, Anselm Blumer, Xiaozhe Hu, Lenore Cowen", "journal_issue_pages": "31(10):990-1007", "journal_year": "2024", "journal_doi": "10.1089/cmb.2024.0673" }, { "author": "Kexin Huang, Romain Lopez, Jan-Christian Hütter, Takamasa Kudo, Antonio Rios, Aviv Regev", "title": "Sequential Optimal Experimental Design of Perturbation Screens Guided by Multi-modal Priors", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 17-37, Springer, Cham.", "proceedings_volume": "14758", "proceedings_pages": "17-37", "proceedings_doi": "10.1007/978-1-0716-3989-4_2", "preprint_id": "bioRxiv 2023.12.12.571389", "preprint_doi": "10.1101/2023.12.12.571389" }, { "author": "Askar Gafurov, Tomáš Vinař, Paul Medvedev, Broňa Brejová", "title": "Efficient Analysis of Annotation Colocalization Accounting for Genomic Contexts", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 38-53, Springer, Cham.", "proceedings_volume": "14758", "proceedings_pages": "38-53", "proceedings_doi": "10.1007/978-1-0716-3989-4_3", "preprint_id": "bioRxiv 2023.11.22.568259", "preprint_doi": "10.1101/2023.11.22.568259", "journal": "Journal of Computational Biology", "journal_title": "Fast Context-Aware Analysis of Genome Annotation Colocalization", "journal_authors": "Askar Gafurov, Tomáš Vinař, Paul Medvedev, Broňa Brejová", "journal_issue_pages": "31(10):946-964", "journal_year": "2024", "journal_doi": "10.1089/cmb.2024.0667" }, { "author": "Alexander T. Leighton, Yun William Yu", "title": "Secure Federated Boolean Count Queries Using Fully-Homomorphic Cryptography", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 54-67, Springer, Cham.", "proceedings_volume": "14758", "proceedings_pages": "54-67", "proceedings_doi": "10.1007/978-1-0716-3989-4_4", "preprint_id": "bioRxiv 2021.11.10.468090", "preprint_doi": "10.1101/2021.11.10.468090" }, { "author": "Ali Khodabandeh Yalabadi, Mehdi Yazdani-Jahromi, Niloofar Yousefi, Aida Tayebi, Sina Abdidizaji, Ozlem Ozmen Garibay", "title": "FragXsiteDTI: Revealing Responsible Segments in Drug-Target Interaction with Transformer-Driven Interpretation", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 68-85, Springer, Cham.", "proceedings_volume": "14758", "proceedings_pages": "68-85", "proceedings_doi": "10.1007/978-1-0716-3989-4_5", "preprint_id": "arXiv:2311.02326", "preprint_doi": "10.48550/arXiv.2311.02326" }, { "author": "Shani Jacobson, Roded Sharan", "title": "An Integer Programming Framework for Identifying Stable Components in Asynchronous Boolean Networks", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 86-98, Springer, Cham.", "proceedings_volume": "14758", "proceedings_pages": "86-98", "proceedings_doi": "10.1007/978-1-0716-3989-4_6" }, { "author": "Yuxuan Du, Wenxuan Zuo, Fengzhu Sun", "title": "ImputeCC Enhances Integrative Hi-C-Based Metagenomic Binning Through Constrained Random-Walk-Based Imputation", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 99-114, Springer, Cham.", "proceedings_volume": "14758", "proceedings_pages": "99-114", "proceedings_doi": "10.1007/978-1-0716-3989-4_7", "preprint_id": "bioRxiv 2023.12.06.570492", "preprint_doi": "10.1101/2023.12.06.570492", "journal": "Journal of Computational Biology", "journal_title": "Imputing Metagenomic Hi-C Contacts Facilitates the Integrative Contig Binning Through Constrained Ra...", "journal_authors": "Yuxuan Du, Wenxuan Zuo, Fengzhu Sun", "journal_issue_pages": "31(10):1008-1021", "journal_year": "2024", "journal_doi": "10.1089/cmb.2024.0663" }, { "author": "Yihang Shen, Lingge Yu, Yutong Qiu, Tianyu Zhang, Carl Kingsford", "title": "Graph-Based Genome Inference from Hi-C Data", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 115-130, Springer, Cham.", "proceedings_volume": "14758", "proceedings_pages": "115-130", "proceedings_doi": "10.1007/978-1-0716-3989-4_8", "preprint_id": "bioRxiv 2023.11.08.566275", "preprint_doi": "10.1101/2023.11.08.566275" }, { "author": "Giulio Ermanno Pibiri, Jason Fan, Rob Patro", "title": "Meta-colored Compacted de Bruijn Graphs", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 131-146, Springer, Cham.", "proceedings_volume": "14758", "proceedings_pages": "131-146", "proceedings_doi": "10.1007/978-1-0716-3989-4_9", "preprint_id": "bioRxiv 2023.07.21.550101", "preprint_doi": "10.1101/2023.07.21.550101", "journal": "Journal of Computational Biology", "journal_title": "Where the Patterns Are: Repetition-Aware Compression for Colored de Bruijn Graphs", "journal_authors": "Alessio Campanelli, Giulio Ermanno Pibiri, Jason Fan, Rob Patro", "journal_issue_pages": "31(10):1022-1044", "journal_year": "2024", "journal_doi": "10.1089/cmb.2024.0714" }, { "author": "Taher Yacoub, Roy González-Alemán, Fabrice Leclerc, Isaure Chauvot de Beauchêne, Yann Ponty", "title": "Color Coding for the Fragment-Based Docking, Design and Equilibrium Statistics of Protein-Binding ssRNAs", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 147-163, Springer, Cham.", "proceedings_volume": "14758", "proceedings_pages": "147-163", "proceedings_doi": "10.1007/978-1-0716-3989-4_10", "preprint_id": "hal-03816423v3", "preprint_url": "https://hal.science/hal-03816423v3" }, { "author": "Luca Renders, Lore Depuydt, Sven Rahmann, Jan Fostier", "title": "Automated Design of Efficient Search Schemes for Lossless Approximate Pattern Matching", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 164-184, Springer, Cham.", "proceedings_volume": "14758", "proceedings_pages": "164-184", "proceedings_doi": "10.1007/978-1-0716-3989-4_11", "journal": "Journal of Computational Biology", "journal_title": "Lossless approximate pattern matching: Automated design of efficient search schemes", "journal_authors": "Luca Renders, Lore Depuydt, Sven Rahmann, Jan Fostier", "journal_issue_pages": "31(10):975-989", "journal_year": "2024", "journal_doi": "10.1089/cmb.2024.0664" }, { "author": "Emaad Khwaja, Yun S. Song, Bo Huang", "title": "CELL-E: A Text-to-Image Transformer for Protein Image Prediction", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 185-200, Springer, Cham.", "proceedings_volume": "14758", "proceedings_pages": "185-200", "proceedings_doi": "10.1007/978-1-0716-3989-4_12", "preprint_id": "bioRxiv 2022.05.27.493774", "preprint_doi": "10.1101/2022.05.27.493774" }, { "author": "C. S. Elder, Minh Hoang, Mohsen Ferdosi, Carl Kingsford", "title": "A Scalable Optimization Algorithm for Solving the Beltway and Turnpike Problems with Uncertain Measurements", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 201-216, Springer, Cham.", "proceedings_volume": "14758", "proceedings_pages": "201-216", "proceedings_doi": "10.1007/978-1-0716-3989-4_13", "preprint_id": "bioRxiv 2024.02.15.580520", "preprint_doi": "10.1101/2024.02.15.580520", "journal": "Journal of Computational Biology", "journal_title": "Approximate and Exact Optimization Algorithms for the Beltway and Turnpike Problems with Duplicated, Missing, Partially Labeled, and Uncertain Measurements", "journal_authors": "C. S. Elder, Minh Hoang, Mohsen Ferdosi, Carl Kingsford", "journal_issue_pages": "31(10):908-926", "journal_year": "2024", "journal_doi": "10.1089/cmb.2024.0661" }, { "author": "Rudolf Schill, Maren Klever, Andreas Lösch, Y. Linda Hu, Stefan Vocht, Kevin Rupp, Lars Grasedyck, Rainer Spang, Niko Beerenwinkel", "title": "Overcoming Observation Bias for Cancer Progression Modeling", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 217-234, Springer, Cham.", "proceedings_volume": "14758", "proceedings_pages": "217-234", "proceedings_doi": "10.1007/978-1-0716-3989-4_14", "preprint_id": "bioRxiv 2023.12.03.569824", "preprint_doi": "10.1101/2023.12.03.569824", "journal": "Journal of Computational Biology", "journal_title": "Correcting for Observation Bias in Cancer Progression Modeling", "journal_authors": "Rudolf Schill, Maren Klever, Andreas Lösch, Y. Linda Hu, Stefan Vocht, Kevin Rupp, Lars Grasedyck, Rainer Spang, Niko Beerenwinkel", "journal_issue_pages": "31(10):927-945", "journal_year": "2024", "journal_doi": "10.1089/cmb.2024.0666" }, { "author": "Holly R. Steach, Siddharth Viswanath, Yixuan He, Xitong Zhang, Natalia Ivanova, Matthew Hirn, Michael Perlmutter, Smita Krishnaswamy", "title": "Inferring Metabolic States from Single Cell Transcriptomic Data via Geometric Deep Learning", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 235-252, Springer, Cham.", "proceedings_volume": "14758", "proceedings_pages": "235-252", "proceedings_doi": "10.1007/978-1-0716-3989-4_15", "preprint_id": "bioRxiv 2023.12.05.570153", "preprint_doi": "10.1101/2023.12.05.570153" }, { "author": "Spencer Krieger, John Kececioglu", "title": "Computing Robust Optimal Factories in Metabolic Reaction Networks", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 253-269, Springer, Cham.", "proceedings_volume": "14758", "proceedings_pages": "253-269", "proceedings_doi": "10.1007/978-1-0716-3989-4_16", "journal": "Journal of Computational Biology", "journal_title": "Robust Optimal Metabolic Factories", "journal_authors": "Spencer Krieger, John Kececioglu", "journal_issue_pages": "31(10):1045-1086", "journal_year": "2024", "journal_doi": "10.1089/cmb.2024.0748" }, { "author": "Tianshuo Zhou, Wei Yu Tang, David H. Mathews, Liang Huang", "title": "Undesignable RNA Structure Identification via Rival Structure Generation and Structure Decomposition", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 270-287, Springer, Cham.", "proceedings_volume": "14758", "proceedings_pages": "270-287", "proceedings_doi": "10.1007/978-1-0716-3989-4_17", "preprint_id": "arXiv:2311.08339", "preprint_doi": "10.48550/arXiv.2311.08339" }, { "author": "Paolo Pellizzoni, Carlos Oliver, Karsten Borgwardt", "title": "Structure- and Function-Aware Substitution Matrices via Learnable Graph Matching", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 288-307, Springer, Cham.", "proceedings_volume": "14758", "proceedings_pages": "288-307", "proceedings_doi": "10.1007/978-1-0716-3989-4_18" }, { "author": "Matthew M. Hong, David Froelicher, Ricky Magner, Victoria Popic, Bonnie Berger, Hyunghoon Cho", "title": "Secure Discovery of Genetic Relatives Across Large-Scale and Distributed Genomic Datasets", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 308-313, Springer, Cham.", "proceedings_volume": "14758", "proceedings_pages": "308-313", "proceedings_doi": "10.1007/978-1-0716-3989-4_19", "preprint_id": "bioRxiv 2024.02.16.580613", "preprint_doi": "10.1101/2024.02.16.580613", "journal": "Genome Research", "journal_title": "Secure discovery of genetic relatives across large-scale and distributed genomic data sets", "journal_authors": "Secure discovery of genetic relatives across large-scale and distributed genomic data sets", "journal_issue_pages": "34(9): 1312–1323", "journal_year": "2024", "journal_doi": "10.1101/gr.279057.124" }, { "author": "Yimin Fan, Yu Li, Jun Ding, Yue Li", "title": "GFETM: Genome Foundation-Based Embedded Topic Model for scATAC-seq Modeling", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 314-319, Springer, Cham.", "proceedings_volume": "14758", "proceedings_pages": "314-319", "proceedings_doi": "10.1007/978-1-0716-3989-4_20", "preprint_id": "bioRxiv 2023.11.09.566403", "preprint_doi": "10.1101/2023.11.09.566403" }, { "author": "Jianyu Yang, Kuangyu Yen, Shaun Mahony", "title": "SEM: Size-Based Expectation Maximization for Characterizing Nucleosome Positions and Subtypes", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 320-323, Springer, Cham.", "proceedings_volume": "14758", "proceedings_pages": "320-323", "proceedings_doi": "10.1007/978-1-0716-3989-4_21", "preprint_id": "bioRxiv 2023.10.17.562727", "preprint_doi": "10.1101/2023.10.17.562727", "journal": "Genome Research", "journal_title": "Size-based expectation maximization for characterizing nucleosome positions and subtypes", "journal_authors": "Jianyu Yang, Kuangyu Yen, Shaun Mahony", "journal_issue_pages": "34(9): 1334–1343", "journal_year": "2024", "journal_doi": "10.1101/gr.279138.124" }, { "author": "Li Song, Ben Langmead", "title": "Centrifuger: Lossless Compression of Microbial Genomes for Efficient and Accurate Metagenomic Sequence Classification", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 324-327, Springer, Cham.", "proceedings_volume": "14758", "proceedings_pages": "324-327", "proceedings_doi": "10.1007/978-1-0716-3989-4_22", "preprint_id": "bioRxiv 2023.11.15.567129", "preprint_doi": "10.1101/2023.11.15.567129", "journal": "Genome Biology", "journal_title": "Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification", "journal_authors": "Li Song, Ben Langmead", "journal_issue_pages": "25(1):106", "journal_year": "2024", "journal_doi": "10.1186/s13059-024-03244-4" }, { "author": "Enakshi Saha, Viola Fanfani, Panagiotis Mandros, Marouen Ben Guebila, Jonas Fischer, Katherine Shutta, Kimberly Glass, Dawn DeMeo, Camila Lopes Ramos, John Quackenbush", "title": "BONOBO: Bayesian Optimized Sample-Specific Networks Obtained by Omics Data", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 328-331, Springer, Cham.", "proceedings_volume": "14758", "proceedings_pages": "328-331", "proceedings_doi": "10.1007/978-1-0716-3989-4_23", "preprint_id": "bioRxiv 2023.11.16.567119", "preprint_doi": "10.1101/2023.11.16.567119", "journal": "Genome Research", "journal_title": "Bayesian Inference of Sample-Specific Coexpression Networks", "journal_authors": "Enakshi Saha, Viola Fanfani, Panagiotis Mandros, Marouen Ben Guebila, Jonas Fischer, Katherine H. Shutta, Dawn L. DeMeo, Camila M. Lopes-Ramos, John Quackenbush", "journal_issue_pages": "34:1397–1410", "journal_year": "2024", "journal_doi": "10.1101/gr.279117.124" }, { "author": "Avantika Lal, David Garfield, Tommaso Biancalani, Gokcen Eraslan", "title": "regLM: Designing Realistic Regulatory DNA with Autoregressive Language Models", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 332-335, Springer, Cham.", "proceedings_volume": "14758", "proceedings_pages": "332-335", "proceedings_doi": "10.1007/978-1-0716-3989-4_24", "preprint_id": "bioRxiv 2024.02.14.580373", "preprint_doi": "10.1101/2024.02.14.580373", "journal": "Genome Research", "journal_title": "Designing realistic regulatory DNA with autoregressive language models", "journal_authors": "Avantika Lal, David Garfield, Tommaso Biancalani, Gokcen Eraslan", "journal_issue_pages": "34(9): 1411–1420", "journal_year": "2024", "journal_doi": "10.1101/gr.279142.124" }, { "author": "Nathan Guerin, Henry Childs, Pei Zhou, Bruce R. Donald", "title": "DexDesign: A New OSPREY-Based Algorithm for Designing de novo D-peptide Inhibitors", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 336-339, Springer, Cham.", "proceedings_volume": "14758", "proceedings_pages": "336-339", "proceedings_doi": "10.1007/978-1-0716-3989-4_25", "preprint_id": "bioRxiv 2024.02.12.579944", "preprint_doi": "10.1101/2024.02.12.579944", "journal": "Journal of Computational Biology", "journal_title": "Protocol for Designing De Novo Noncanonical Peptide Binders in OSPREY", "journal_authors": "Henry Childs, Nathan Guerin, Pei Zhou, Bruce R. Donald", "journal_issue_pages": "31(10):965-974", "journal_year": "2024", "journal_doi": "10.1089/cmb.2024.0669" }, { "author": "Ali Osman Berk Şapcı, Siavash Mirarab", "title": "Memory-Bound and Taxonomy-Aware K-Mer Selection for Ultra-Large Reference Libraries", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 340-343, Springer, Cham.", "proceedings_volume": "14758", "proceedings_pages": "340-343", "proceedings_doi": "10.1007/978-1-0716-3989-4_26", "preprint_id": "bioRxiv 2024.02.12.580015", "preprint_doi": "10.1101/2024.02.12.580015", "journal": "Genome Research", "journal_title": "Memory-Bound k-Mer Selection for Large and Evolutionary Diverse Reference Libraries", "journal_authors": "Ali Osman Berk Şapcı and Siavash Mirarab", "journal_issue_pages": "34(9): 1455–1467", "journal_year": "2024", "journal_doi": "10.1101/gr.279339.124" }, { "author": "Stefan Schrod, Niklas Lück, Robert Lohmayer, Stefan Solbrig, Tina Wipfler, Katherine H. Shutta, Marouen Ben Guebila, Andreas Schäfer, Tim Beißbarth, Helena U. Zacharias, Peter J. Oefner, John Quackenbush, Michael Altenbuchinger", "title": "SpaCeNet: Spatial Cellular Networks from Omics Data", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 344-347, Springer, Cham.", "proceedings_volume": "14758", "proceedings_pages": "344-347", "proceedings_doi": "10.1007/978-1-0716-3989-4_27", "preprint_id": "bioRxiv 2022.09.01.506219", "preprint_doi": "10.1101/2022.09.01.506219", "journal": "Genome Research", "journal_title": "Spatial Cellular Networks from omics data with SpaCeNet", "journal_authors": "Stefan Schrod, Niklas Lück, Robert Lohmayer, Stefan Solbrig, Dennis Völkl, Tina Wipfler, Katherine H. Shutta, Marouen Ben Guebila, Andreas Schäfer, Tim Beißbarth, Helena U. Zacharias, Peter J. Oefner, John Quackenbush, Michael Altenbuchinger", "journal_issue_pages": "34(9): 1371–1383", "journal_year": "2024", "journal_doi": "10.1101/gr.279125.124" }, { "author": "Ziting Zhang, Wenxu Wu, Lei Wei, Xiaowo Wang", "title": "Discovering and Overcoming the Bias in Neoantigen Identification by Unified Machine Learning Models", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 348-351, Springer, Cham.", "proceedings_volume": "14758", "proceedings_pages": "348-351", "proceedings_doi": "10.1007/978-1-0716-3989-4_28", "preprint_id": "bioRxiv 2024.02.07.579420", "preprint_doi": "10.1101/2024.02.07.579420" }, { "author": "Myson Burch, Aritra Bose, Gregory Dexter, Laxmi Parida, Petros Drineas", "title": "MaSk-LMM: A Matrix Sketching Framework for Linear Mixed Models in Association Studies", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 352-355, Springer, Cham.", "proceedings_volume": "14758", "proceedings_pages": "352-355", "proceedings_doi": "10.1007/978-1-0716-3989-4_29", "preprint_id": "bioRxiv 2023.11.13.23298469", "preprint_doi": "10.1101/2023.11.13.23298469", "journal": "Genome Research", "journal_title": "Matrix sketching framework for linear mixed models in association studies", "journal_authors": "Myson Burch, Aritra Bose, Gregory Dexter, Laxmi Parida, Petros Drineas", "journal_issue_pages": "34(9): 1304–1311", "journal_year": "2024", "journal_doi": "10.1101/gr.279230.124" }, { "author": "Fatemeh Mohebbi, Alexander Zelikovsky, Serghei Mangul, Gerardo Chowell, Pavel Skums", "title": "Community Structure and Temporal Dynamics of Viral Epistatic Networks Allow for Early Detection of Emerging Variants with Altered Phenotypes", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 356-359, Springer, Cham.", "proceedings_volume": "14758", "proceedings_pages": "356-359", "proceedings_doi": "10.1007/978-1-0716-3989-4_30", "preprint_id": "bioRxiv 2023.04.02.535277", "preprint_doi": "10.1101/2023.04.02.535277" }, { "author": "Uyen Mai, Gillian Chu, Benjamin J. Raphael", "title": "Maximum Likelihood Inference of Time-Scaled Cell Lineage Trees with Mixed-Type Missing Data", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 360-363, Springer, Cham.", "proceedings_volume": "14758", "proceedings_pages": "360-363", "proceedings_doi": "10.1007/978-1-0716-3989-4_31", "preprint_id": "bioRxiv 2024.03.05.583638", "preprint_doi": "10.1101/2024.03.05.583638", "journal": "Genome Biology", "journal_title": "Maximum likelihood inference of time-scaled cell lineage trees with mixed-type missing data using LAML", "journal_authors": "Gillian Chu, Uyen Mai, Henri Schmidt, Benjamin J. Raphael", "journal_issue_pages": "26: 189", "journal_year": "2025", "journal_doi": "10.1186/s13059-025-03649-9" }, { "author": "Leah L. Weber, Derek Reiman, Mrinmoy S. Roddur, Yuanyuan Qi, Mohammed El-Kebir, Aly A. Khan", "title": "TRIBAL: Tree Inference of B Cell Clonal Lineages", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. Lecture Notes in Computer Science, vol 14758, pp 364-367, Springer, Cham.", "proceedings_volume": "14758", "proceedings_pages": "364-367", "proceedings_doi": "10.1007/978-1-0716-3989-4_32", "preprint_id": "bioRxiv 2023.11.27.568874", "preprint_doi": "10.1101/2023.11.27.568874" }, { "author": "Uthsav Chitra, Brian Arnold, Hirak Sarkar, Cong Ma, Sereno Lopez-Darwin, Kohei Sanno, Ben Raphael", "title": "Mapping the Topography of Spatial Gene Expression with Interpretable Deep Learning", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2024. 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