{ "title": "26th Annual International Conference on Research in Computational Molecular Biology", "location": "San Diego, CA, United States", "dates": "May 22 - 25, 2022", "pc_chair": "Itsik Pe’er", "organization_committee": "Vineet Bafna (chair), Vikas Bansal, Jocelyn Bernardo, Melissa Gymrek, Siavash Mirarab, Glenn Tesler, Kaiyuan Zhu", "keynotes": "Regina Barzilay, Howard Y. Chang, John Chodera, Lenore Cowen, John Marioni, Bing Ren, Wenyi Wang", "website": "https://recomb.org/recomb2022", "papers": [ { "author": "Pinar Demetci, Rebecca Santorella, Bjorn Sandstede, Ritambhara Singh", "title": "Unsupervised integration of single-cell multi-omics datasets with disparities in cell-type representation", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 3-19, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "3-19", "proceedings_doi": "10.1007/978-3-031-04749-7_1", "preprint_id": "bioRxiv 2021.11.09.467903", "preprint_doi": "10.1101/2021.11.09.467903", "journal": "Journal of Computational Biology", "journal_title": "SCOTv2: Single-Cell Multiomic Alignment with Disproportionate Cell-Type Representation", "journal_authors": "Pinar Demetci, Rebecca Santorella, Manav Chakravarthy, Bjorn Sandstede, Ritambhara Singh", "journal_issue_pages": "29(11): 1213-1228", "journal_year": "2022", "journal_doi": "10.1089/cmb.2022.0270" }, { "author": "Ran Zhang, William Noble, Laetitia Meng-Papaxanthos, Jean-Philippe Vert", "title": "Semi-supervised single-cell cross-modality translation using Polarbear", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 20-35, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "20-35", "proceedings_doi": "10.1007/978-3-031-04749-7_2", "preprint_id": "bioRxiv 2021.11.18.467517", "preprint_doi": "10.1101/2021.11.18.467517", "journal": "Journal of Computational Biology", "journal_title": "Multimodal Single-Cell Translation and Alignment with Semi-Supervised Learning", "journal_authors": "Ran Zhang, Laetitia Meng-papaxanthos, Jean-philippe Vert, William Stafford Noble", "journal_issue_pages": "29(11): 1198-1212", "journal_year": "2022", "journal_doi": "10.1089/cmb.2022.0264" }, { "author": "Jingkang Zhao, Vincentius Martin, Raluca Gordan", "title": "Transcription Factor-Centric Approach to Identify Non-Recurring Putative Regulatory Drivers in Cancer", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 36-51, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "36-51", "proceedings_doi": "10.1007/978-3-031-04749-7_3", "preprint_id": "bioRxiv 2022.01.31.478493", "preprint_doi": "10.1101/2022.01.31.478493" }, { "author": "Quang Minh Hoang, Hongyu Zheng, Carl Kingsford", "title": "DeepMinimizer: A Differentiable Framework for Optimizing Sequence-Specific Minimizer Schemes", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 52-69, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "52-69", "proceedings_doi": "10.1007/978-3-031-04749-7_4", "preprint_id": "bioRxiv 2022.02.17.480870", "preprint_doi": "10.1101/2022.02.17.480870", "journal": "Journal of Computational Biology", "journal_title": "Differentiable Learning of Sequence-Specific Minimizer Schemes with DeepMinimizer", "journal_authors": "Quang Minh Hoang, Hongyu Zheng, Carl Kingsford", "journal_issue_pages": "29(12): 1288-1304", "journal_year": "2022", "journal_doi": "10.1089/cmb.2022.0275" }, { "author": "Vijini Mallawaarachchi, Yu Lin", "title": "MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 70-85, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "70-85", "proceedings_doi": "10.1007/978-3-031-04749-7_5", "preprint_id": "bioRxiv 2021.09.10.459728", "preprint_doi": "10.1101/2021.09.10.459728", "journal": "Journal of Computational Biology", "journal_title": "Accurate Binning of Metagenomic Contigs Using Composition, Coverage, and Assembly Graphs", "journal_authors": "Vijini Mallawaarachchi, Yu Lin", "journal_issue_pages": "29(12): 1357-1376", "journal_year": "2022", "journal_doi": "10.1089/cmb.2022.0262" }, { "author": "Agniva Chowdhury, Aritra Bose, Samson Zhou, David P Woodruff, Petros Drineas", "title": "A Fast, Provably Accurate Approximation Algorithm for Sparse Principal Component Analysis Reveals Human Genetic Variation Across the World", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 86-106, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "86-106", "proceedings_doi": "10.1007/978-3-031-04749-7_6" }, { "author": "Haohan Wang, Oscar Lopez, Wei Wu, Eric Xing", "title": "Gene Set Priorization Guided by Regulatory Networks with p-values through Kernel Mixed Model", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 107-125, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "107-125", "proceedings_doi": "10.1007/978-3-031-04749-7_7", "journal": "Journal of Computational Biology", "journal_title": "Kernel Mixed Model for Transcriptome Association Study", "journal_authors": "Haohan Wang, Oscar Lopez, Eric P. Xing, Wei Wu", "journal_issue_pages": "29(12): 1353-1356", "journal_year": "2022", "journal_doi": "10.1089/cmb.2022.0280" }, { "author": "Seyran Saeedi, Myrna Serrano, Dennis G. Yang, J. Paul Brooks, Gregory A. Buck, Tom Arodz", "title": "Real-valued Group Testing for Quantitative Molecular Assays", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 126-142, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "126-142", "proceedings_doi": "10.1007/978-3-031-04749-7_8", "journal": "Journal of Computational Biology", "journal_title": "Group Testing Matrix Design for PCR Screening with Real-Valued Measurements", "journal_authors": "Seyran Saeedi, Myrna Serrano, Dennis G. Yang, J. Paul Brooks, Gregory A. Buck, Tomasz Arodz", "journal_issue_pages": "29(12): 1397-1411", "journal_year": "2022", "journal_doi": "10.1089/cmb.2022.0413" }, { "author": "Max Hill, Sebastien Roch", "title": "On the Effect of Intralocus Recombination on Triplet-Based Species Tree Estimation", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 143-158, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "143-158", "proceedings_doi": "10.1007/978-3-031-04749-7_9", "preprint_id": "bioRxiv 2021.11.06.467557", "preprint_doi": "10.1101/2021.11.06.467557", "journal": "Journal of Computational Biology", "journal_title": "Inconsistency of Triplet-Based and Quartet-Based Species Tree Estimation under Intralocus Recombination 8", "journal_authors": "Max Hill, Sebastien Roch", "journal_issue_pages": "29(11): 1173-1197", "journal_year": "2022", "journal_doi": "10.1089/cmb.2022.0265" }, { "author": "Sazan Mahbub, Shashata Sawmya, Arpita Saha, Rezwana Reaz, M Sohel Rahman, Md Shamsuzzoha Bayzid", "title": "QT-GILD: Quartet Based Gene Tree Imputation Using Deep Learning Improves Phylogenomic Analyses Despite Missing Data", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 159-176, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "159-176", "proceedings_doi": "10.1007/978-3-031-04749-7_10", "preprint_id": "bioRxiv 2021.11.03.467204", "preprint_doi": "10.1101/2021.11.03.467204", "journal": "Journal of Computational Biology", "journal_title": "Quartet Based Gene Tree Imputation Using Deep Learning Improves Phylogenomic Analyses Despite Missing Data", "journal_authors": "Sazan Mahbub, Shashata Sawmya, Arpita Saha, Rezwana Reaz, M Sohel Rahman, Md Shamsuzzoha Bayzid", "journal_issue_pages": "29(11): 1156-1172", "journal_year": "2022", "journal_doi": "10.1089/cmb.2022.0212" }, { "author": "Shahbaz Khan, Milla Kortelainen, Manuel Caceres, Lucia Williams, Alexandru I Tomescu", "title": "Safe and Complete Flow Decompositions for RNA Assembly", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 177-192, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "177-192", "proceedings_doi": "10.1007/978-3-031-04749-7_11", "preprint_id": "arXiv:2201.10372", "preprint_doi": "10.48550/arXiv.2201.10372", "journal": "Journal of Computational Biology", "journal_title": "Improving RNA Assembly via Safety and Completeness in Flow Decompositions", "journal_authors": "Shahbaz Khan, Milla Kortelainen, Manuel Caceres, Lucia Williams, Alexandru I Tomescu", "journal_issue_pages": "29(12): 1270-1287", "journal_year": "2022", "journal_doi": "10.1089/cmb.2022.0261" }, { "author": "Uthsav Chitra, Tae Yoon Park, Ben Raphael", "title": "NetMix2: Unifying network propagation and altered subnetworks", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 193-208, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "193-208", "proceedings_doi": "10.1007/978-3-031-04749-7_12", "preprint_id": "bioRxiv 2022.01.31.478575", "preprint_doi": "10.1101/2022.01.31.478575", "journal": "Journal of Computational Biology", "journal_title": "NetMix2: A Principled Network Propagation Algorithm for Identifying Altered Subnetworks", "journal_authors": "Uthsav Chitra, Tae Yoon Park, Benjamin J. Raphael", "journal_issue_pages": "29(12): 1305-1323", "journal_year": "2022", "journal_doi": "10.1089/cmb.2022.0336" }, { "author": "Alireza Ganjdanesh, Jipeng Zhang, Wei Chen, Heng Huang", "title": "Multi-Modal Genotype and Phenotype Mutual Learning to Single-Modal Input for Longitudinal Outcome Prediction", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 209-229, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "209-229", "proceedings_doi": "10.1007/978-3-031-04749-7_13", "journal": "Journal of Computational Biology", "journal_title": "Multimodal Genotype and Phenotype Data Integration to Improve Partial Data-Based Longitudinal Prediction", "journal_authors": "Alireza Ganjdanesh, Jipeng Zhang, Sarah Yan, Wei Chen, Heng Huang", "journal_issue_pages": "29(12): 1324-1345", "journal_year": "2022", "journal_doi": "10.1089/cmb.2022.0378" }, { "author": "Fernando H C Dias, Lucia Williams, Brendan Mumey, Alexandru I Tomescu", "title": "Fast, Flexible, and Exact Minimum Flow Decompositions via ILP", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 230-245, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "230-245", "proceedings_doi": "10.1007/978-3-031-04749-7_14", "preprint_id": "arXiv:2201.10923", "preprint_doi": "10.48550/arXiv.2201.10923", "journal": "Journal of Computational Biology", "journal_title": "Efficient Minimum Flow Decomposition via Integer Linear Programming", "journal_authors": "Fernando H C Dias, Lucia Williams, Brendan Mumey, Alexandru I Tomescu", "journal_issue_pages": "29(11): 1252-1267", "journal_year": "2022", "journal_doi": "10.1089/cmb.2022.0257" }, { "author": "Chirag Jain, Daniel Gibney, Sharma V Thankachan", "title": "Co-linear chaining with overlaps and gap costs", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 246-262, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "246-262", "proceedings_doi": "10.1007/978-3-031-04749-7_15", "preprint_id": "bioRxiv 2021.02.03.429492", "preprint_doi": "10.1101/2021.02.03.429492", "journal": "Journal of Computational Biology", "journal_title": "Algorithms for Colinear Chaining with Overlaps and Gap Costs", "journal_authors": "Chirag Jain, Daniel Gibney, Sharma V Thankachan", "journal_issue_pages": "29(11): 1237-1251", "journal_year": "2022", "journal_doi": "10.1089/cmb.2022.0266" }, { "author": "Daniel Gibney, Sharma V Thankachan, Srinivas Aluru", "title": "The Complexity of Approximate Pattern Matching on De Bruijn Graphs", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 263-278, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "263-278", "proceedings_doi": "10.1007/978-3-031-04749-7_16", "preprint_id": "arXiv:2201.12454", "preprint_doi": "10.48550/arXiv.2201.12454", "journal": "Journal of Computational Biology", "journal_title": "On the hardness of sequence alignment on de Bruijn graphs", "journal_authors": "Daniel Gibney, Sharma V Thankachan, Srinivas Aluru", "journal_issue_pages": "29(12): 1377-1396", "journal_year": "2022", "journal_doi": "10.1089/cmb.2022.0411" }, { "author": "Hanwen Xu, Sheng Wang", "title": "ProTranslator: zero-shot protein function prediction using textual description", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 279-294, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "279-294", "proceedings_doi": "10.1007/978-3-031-04749-7_17", "preprint_id": "arXiv:2204.10286", "preprint_doi": "10.48550/arXiv.2204.10286" }, { "author": "Chen Li, Maria Virgilio, Kathleen Collins, Joshua Welch", "title": "Single-cell multi-omic velocity infers dynamic and decoupled gene regulation", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 297-299, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "297-299", "proceedings_doi": "10.1007/978-3-031-04749-7_18", "preprint_id": "bioRxiv 2021.12.13.472472", "preprint_doi": "10.1101/2021.12.13.472472", "journal": "Nature Biotechnology", "journal_title": "Multi-omic single-cell velocity models epigenome-transcriptome interactions and improves cell fate prediction", "journal_authors": "Chen Li, Maria C. Virgilio, Kathleen L. Collins, Joshua D. Welch", "journal_issue_pages": "41(3):387-398", "journal_year": "2023", "journal_doi": "10.1038/s41587-022-01476-y" }, { "author": "Ruochi Zhang, Tianming Zhou, Jian Ma", "title": "Ultrafast and Interpretable Single-cell 3D Genome Analysis with Fast-Higashi", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 300-301, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "300-301", "proceedings_doi": "10.1007/978-3-031-04749-7_19", "preprint_id": "bioRxiv 2022.04.18.488683", "preprint_doi": "10.1101/2022.04.18.488683", "journal": "Cell Systems", "journal_title": "Ultrafast and interpretable single-cell 3D genome analysis with Fast-Higashi", "journal_authors": "Ruochi Zhang, Tianming Zhou, Jian Ma", "journal_issue_pages": "13(10): 798-807.e6", "journal_year": "2022", "journal_doi": "10.1016/j.cels.2022.09.004" }, { "author": "Dunming Hua, Ming Gu, Yanyi Du, Li Qi, Xiangjun Du, Zhidong Bai, Xiaopeng Zhu, Dechao Tian", "title": "DiffDomain enables identification of structurally reorganized topologically associating domains", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 302-303, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "302-303", "proceedings_doi": "10.1007/978-3-031-04749-7_20", "preprint_id": "bioRxiv 2022.12.05.519135", "preprint_doi": "10.1101/2022.12.05.519135", "journal": "Nature Communications", "journal_title": "DiffDomain enables identification of structurally reorganized topologically associating domains", "journal_authors": "Dunming Hua, Ming Gu, Xiao Zhang, Yanyi Du, Hangcheng Xie, Li Qi, Xiangjun Du, Zhidong Bai, Xiaopeng Zhu, Dechao Tian", "journal_issue_pages": "15: 502", "journal_year": "2024", "journal_doi": "10.1038/s41467-024-44782-6" }, { "author": "Xiang Ge Luo, Jack Kuipers, Niko Beerenwinkel", "title": "Joint inference of repeated evolutionary trajectories and patterns of clonal exclusivity or co-occurrence from tumor mutation trees", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 304-305, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "304-305", "proceedings_doi": "10.1007/978-3-031-04749-7_21", "preprint_id": "bioRxiv 2021.11.04.467347", "preprint_doi": "10.1101/2021.11.04.467347", "journal": "Nature Communications", "journal_title": "Joint inference of repeated evolutionary trajectories and patterns of clonal exclusivity or co-occurrence from tumor mutation trees", "journal_authors": "Xiang Ge Luo, Jack Kuipers, Niko Beerenwinkel", "journal_issue_pages": "14: 3676", "journal_year": "2023", "journal_doi": "10.1038/s41467-023-39400-w" }, { "author": "Pesho Ivanov, Benjamin Bichsel, Martin Vechev", "title": "Fast and Optimal Sequence-to-Graph Alignment Guided by Seeds", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 306-325, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "306-325", "proceedings_doi": "10.1007/978-3-031-04749-7_22", "preprint_id": "bioRxiv 2021.11.05.467453", "preprint_doi": "10.1101/2021.11.05.467453" }, { "author": "Pengfei Zhang, Zhengyuan Jiang, Yixuan Wang, Yu Li", "title": "CLMB: deep contrastive learning for robust metagenomic binning", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 326-348, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "326-348", "proceedings_doi": "10.1007/978-3-031-04749-7_23", "preprint_id": "bioRxiv 2021.11.15.468566", "preprint_doi": "10.1101/2021.11.15.468566" }, { "author": "Dongshunyi Li, Jun Ding, Ziv Bar-Joseph", "title": "Unsupervised cell functional annotation for single-cell RNA-Seq", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 349-352, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "349-352", "proceedings_doi": "10.1007/978-3-031-04749-7_24", "preprint_id": "bioRxiv 2021.11.20.469410", "preprint_doi": "10.1101/2021.11.20.469410", "journal": "Genome Research", "journal_title": "Unsupervised cell functional annotation for single-cell RNA-seq", "journal_authors": "Dongshunyi Li, Jun Ding, Ziv Bar-Joseph", "journal_issue_pages": "32(9): 1765-1775", "journal_year": "2022", "journal_doi": "10.1101/gr.276609.122" }, { "author": "Kun Qian, Shiwei Fu, Hongwei Li, Wei Vivian Li", "title": "A novel matrix factorization model for interpreting single-cell gene expression from biologically heterogeneous data", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 353-355, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "353-355", "proceedings_doi": "10.1007/978-3-031-04749-7_25", "preprint_id": "bioRxiv 2021.10.13.464306", "preprint_doi": "10.1101/2021.10.13.464306", "journal": "Genome Biology", "journal_title": "scINSIGHT for interpreting single-cell gene expression from biologically heterogeneous data", "journal_authors": "Kun Qian, Shiwei Fu, Hongwei Li, Wei Vivian Li", "journal_issue_pages": "23(1): 82 20", "journal_year": "2022", "journal_doi": "10.1186/s13059-022-02649-3" }, { "author": "Meihua Dang, Anji Liu, Xinzhu Wei, Sriram Sankararaman, Guy Van den Broeck", "title": "Tractable and expressive generative models of genetic variation data", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 356-357, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "356-357", "proceedings_doi": "10.1007/978-3-031-04749-7_26", "preprint_id": "bioRxiv 2023.05.16.541036", "preprint_doi": "10.1101/2023.05.16.541036" }, { "author": "Yang Yang, Yuchuan Wang, Yang Zhang, Jian Ma", "title": "CONCERT: Genome-wide prediction of sequence elements that modulate DNA replication timing", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 358-359, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "358-359", "proceedings_doi": "10.1007/978-3-031-04749-7_27", "preprint_id": "bioRxiv 2022.04.21.488684", "preprint_doi": "10.1101/2022.04.21.488684" }, { "author": "Chuanyi Zhang, Palash Sashittal, Mohammed El-Kebir", "title": "CORSID enables de novo identification of transcription regulatory sequences and genes in coronaviruses", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 360-362, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "360-362", "proceedings_doi": "10.1007/978-3-031-04749-7_28", "preprint_id": "bioRxiv 2021.11.10.468129", "preprint_doi": "10.1101/2021.11.10.468129", "journal": "Molecular Biology and Evolution", "journal_title": "Accurate Identification of Transcription Regulatory Sequences and Genes in Coronaviruses", "journal_authors": "Chuanyi Zhang, Palash Sashittal, Michael Xiang, Yichi Zhang, Ayesha Kazi, Mohammed El-Kebir", "journal_issue_pages": "39(7): msac133", "journal_year": "2022", "journal_doi": "10.1093/molbev/msac133" }, { "author": "Joshua Wetzel, Kaiqian Zhang, Mona Singh", "title": "Learning probabilistic protein-DNA recognition codes from DNA-binding specificities using structural mappings", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 363-365, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "363-365", "proceedings_doi": "10.1007/978-3-031-04749-7_29", "preprint_id": "bioRxiv 2022.01.31.477772", "preprint_doi": "10.1101/2022.01.31.477772", "journal": "Genome Research", "journal_title": "Learning probabilistic protein-DNA recognition codes from DNA-binding specificities using structural mappings", "journal_authors": "Joshua L Wetzel, Kaiqian Zhang, Mona Singh", "journal_issue_pages": "32(9):1776-1786", "journal_year": "2022", "journal_doi": "10.1101/gr.276606.122" }, { "author": "Eleonora Rachtman, Shahab Sarmashghi, Vineet Bafna, Siavash Mirarab", "title": "Uncertainty quantification using subsampling for assembly-free estimates of genomic distance and phylogenetic relationships", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 366-368, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "366-368", "proceedings_doi": "10.1007/978-3-031-04749-7_30", "journal": "Cell Systems", "journal_title": "Uncertainty Quantification Using Subsampling for Assembly-Free Estimates of Genomic Distance and Phylogenetic Relationships", "journal_authors": "Eleonora Rachtman, Shahab Sarmashghi, Vineet Bafna, Siavash Mirarab", "journal_issue_pages": "13(10): 817-829.e3", "journal_year": "2022", "journal_doi": "10.1016/j.cels.2022.06.007" }, { "author": "Pavel Skums, Fatemeh Mohebbi, Viachaslau Tsyvina, Pelin Burcak Icer, Yury Khudyakov", "title": "SOPHIE: viral outbreak investigation and transmission history reconstruction in a joint phylogenetic and network theory framework", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 369-370, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "369-370", "proceedings_doi": "10.1007/978-3-031-04749-7_31", "preprint_id": "bioRxiv 2022.05.05.490757", "preprint_doi": "10.1101/2022.05.05.490757", "journal": "Cell Systems", "journal_title": "SOPHIE: Viral outbreak investigation and transmission history reconstruction in a joint phylogenetic and network theory framework", "journal_authors": "Pavel Skums, Fatemeh Mohebbi, Vyacheslav Tsyvina, Pelin Icer Baykal, Alina Nemira, Sumathi Ramachandran, Yury Khudyakov", "journal_issue_pages": "13(10):844-856.e4", "journal_year": "2022", "journal_doi": "10.1016/j.cels.2022.07.005" }, { "author": "Elior Rahmani, Michael Jordan, Nir Yosef", "title": "Identifying systematic variation at the single-cell level by leveraging low-resolution population-level data", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 371-371, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "371-371", "proceedings_doi": "10.1007/978-3-031-04749-7_32", "preprint_id": "bioRxiv 2022.01.27.478115", "preprint_doi": "10.1101/2022.01.27.478115" }, { "author": "Cong Ma, Uthsav Chitra, Shirley Zhang, Benjamin Raphael", "title": "Belayer: Modeling distinct cell type clusters and continuous variation of expression in spatial transcriptomics from layered tissues", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 372-373, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "372-373", "proceedings_doi": "10.1007/978-3-031-04749-7_33", "preprint_id": "bioRxiv 2022.02.05.479261", "preprint_doi": "10.1101/2022.02.05.479261", "journal": "Cell Systems", "journal_title": "Belayer: Modeling discrete and continuous spatial variation in gene expression from spatially resolved transcriptomics", "journal_authors": "Cong Ma, Uthsav Chitra, Shirley Zhang, Benjamin J Raphael", "journal_issue_pages": "13(10): 786-797.e13", "journal_year": "2022", "journal_doi": "10.1016/j.cels.2022.09.002" }, { "author": "Mikhail Karasikov, Harun Mustafa, Gunnar Ratsch, Andre Kahles", "title": "Lossless Indexing with Counting de Bruijn Graphs", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 374-376, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "374-376", "proceedings_doi": "10.1007/978-3-031-04749-7_34", "preprint_id": "bioRxiv 2021.11.09.467907", "preprint_doi": "10.1101/2021.11.09.467907", "journal": "Genome Research", "journal_title": "Lossless indexing with counting de Bruijn graphs", "journal_authors": "Mikhail Karasikov, Harun Mustafa, Gunnar Ratsch, Andre Kahles", "journal_issue_pages": "32(9):1754-1764", "journal_year": "2022", "journal_doi": "10.1101/gr.276607.122" }, { "author": "Amatur Rahman, Paul Medvedev", "title": "Uncovering hidden assembly artifacts: when unitigs are not safe and bidirected graphs are not helpful", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 377-379, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "377-379", "proceedings_doi": "10.1007/978-3-031-04749-7_35", "preprint_id": "bioRxiv 2022.01.20.477068", "preprint_doi": "10.1101/2022.01.20.477068", "journal": "Genome Research", "journal_title": "Assembler artifacts include misassembly because of unsafe unitigs and underassembly because of bidirected graphs", "journal_authors": "Amatur Rahman, Paul Medvedev", "journal_issue_pages": "32(9): 1746-1753", "journal_year": "2022", "journal_doi": "10.1101/gr.276601.122" }, { "author": "Pedro F Ferreira, Jack Kuipers, Niko Beerenwinkel", "title": "Mapping single-cell transcriptomes to copy number evolutionary trees", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 380-381, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "380-381", "proceedings_doi": "10.1007/978-3-031-04749-7_36", "preprint_id": "bioRxiv 2021.11.04.467244", "preprint_doi": "10.1101/2021.11.04.467244" }, { "author": "Michael Ford, Ananth Hari, Oscar Rodriguez, Junyan Xu, Justin Lack, Cihan Oguz, Yu Zhang, Sarah Weber, Mary Magliocco, Jason Barnett, Sandhya Xirasagar, Smilee Samuel, Luisa Imberti, Paolo Bonfanti, Andrea Biondi, Clifton Dalgard, Stephen Chanock, Lindsey Rosen, Steven Holland, Helen Su, Luigi Notarangelo, Uzi Vishkin, Corey Watson, S Cenk Sahinalp", "title": "ImmunoTyper-SR: A Novel Computational Approach for Genotyping Immunoglobulin Heavy Chain Variable Genes using Short Read Data", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 382-384, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "382-384", "proceedings_doi": "10.1007/978-3-031-04749-7_37", "preprint_id": "bioRxiv 2022.01.31.478564", "preprint_doi": "10.1101/2022.01.31.478564", "journal": "Cell Systems", "journal_title": "ImmunoTyper-SR: A computational approach for genotyping immunoglobulin heavy chain variable genes using short-read data", "journal_authors": "Michael K. B. Ford, Ananth Hari, Oscar Rodriguez, Junyan Xu, Justin Lack, Cihan Oguz, Yu Zhang, Sarah Weber, Mary Magliocco, Jason Barnett, Sandhya Xirasagar, Smilee Samuel, Luisa Imberti, Paolo Bonfanti, Andrea Biondi, Clifton L. Dalgard, Stephen Chanock, Lindsey Rosen, Steven Holland, Helen Su, Luigi Notarangelo, NIAID COVID Consortium; Uzi Vishkin, Corey T. Watson, S. Cenk Sahinalp", "journal_issue_pages": "13(10): 808-816.e5", "journal_year": "2022", "journal_doi": "10.1016/j.cels.2022.08.008" }, { "author": "Ulzee An, Na Cai, Andy Dahl, Sriram Sankararaman", "title": "AutoComplete: Deep Learning-based Phenotype Imputation for Large-scale Biomedical Data", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 385-386, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "385-386", "proceedings_doi": "10.1007/978-3-031-04749-7_38", "preprint_id": "bioRxiv 2022.08.15.503991", "preprint_doi": "10.1101/2022.08.15.503991", "journal": "Nature Genetics", "journal_title": "Deep learning-based phenotype imputation on population-scale biobank data increases genetic discoveries", "journal_authors": "Ulzee An, Ali Pazokitoroudi, Marcus Alvarez, Lianyun Huang, Silviu Bacanu, Andrew J. Schork, Kenneth Kendler, Päivi Pajukanta, Jonathan Flint, Noah Zaitlen, Na Cai, Andy Dahl. Sriram Sankararaman", "journal_issue_pages": "55(12):2269-2276", "journal_year": "2023", "journal_doi": "10.1038/s41588-023-01558-w" }, { "author": "Nathan Guerin, Teresa Kaserer, Bruce Donald", "title": "Resistor: an algorithm for predicting resistance mutations using Pareto optimization over multistate protein design and mutational signatures", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 387-389, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "387-389", "proceedings_doi": "10.1007/978-3-031-04749-7_39", "preprint_id": "bioRxiv 2022.01.18.476733", "preprint_doi": "10.1101/2022.01.18.476733", "journal": "Cell Systems", "journal_title": "Resistor: An algorithm for predicting resistance mutations via Pareto optimization over multistate protein design and mutational signatures", "journal_authors": "Nathan Guerin, Andreas Feichtner, Eduard Stefan, Teresa Kaserer, Bruce Donald", "journal_issue_pages": "3(10):830-843.e3", "journal_year": "2022", "journal_doi": "10.1016/j.cels.2022.09.003" }, { "author": "Zheng Dai, Sachit Saksena, Geraldine Horny, Christine Banholzer, Stefan Ewert, David Gifford", "title": "Ultra high diversity factorizable libraries for efficient therapeutic discovery", "proceedings_name": "Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science, vol 13278, pp 390-392, Springer, Cham.", "proceedings_volume": "13278", "proceedings_pages": "390-392", "proceedings_doi": "10.1007/978-3-031-04749-7_40", "preprint_id": "bioRxiv 2022.01.17.476670", "preprint_doi": "10.1101/2022.01.17.476670", "journal": "Genome Research", "journal_title": "Ultra-high-diversity factorizable libraries for efficient therapeutic discovery", "journal_authors": "Zheng Dai, Sachit D Saksena, Geraldine Horny, Christine Banholzer, Stefan Ewert, David K Gifford", "journal_issue_pages": "32(9):1787-1794", "journal_year": "2022", "journal_doi": "10.1101/gr.276593.122" } ] }