{ "title": "25th Annual International Conference on Research in Computational Molecular Biology", "location": "Padova, Italy (virtual)", "dates": "August 29 - September 1, 2021", "pc_chair": "Jian Peng", "organization_committee": "Fabio Vandin (co-chair), Jian Ma (co-chair), Matteo Comin, Barbara Di Camillo, Leonardo Pellegrina, Cinzia Pizzi", "keynotes": "Trey Ideker, Ming Li, Katie Pollard, Aviv Regev, Marie-France Sagot, Mona Singh", "website": "https://sistemacongressi.wixsite.com/recomb2021", "papers": [ { "author": "Ali Pazokitoroudi, Andy Dahl, Noah Zaitlen, Saharon Rosset, Sriram Sankararaman", "title": "Biobank-scale estimation of the proportion of trait variance explained by gene-environment interactions", "journal": "American Journal of Human Genetics", "journal_title": "A scalable and robust variance components method reveals insights into the architecture of gene-environment interactions underlying complex traits", "journal_authors": "Ali Pazokitoroudi, Zhengtong Liu, Andrew Dahl, Noah Zaitlen, Saharon Rosset, Sriram Sankararaman", "journal_issue_pages": "111(7): 1462-1480", "journal_year": "2024", "journal_doi": "10.1016/j.ajhg.2024.05.015" }, { "author": "Amir Joudaki, Gunnar Ratsch, Andre Kahles", "title": "Fast Alignment-Free Similarity Estimation By Tensor Sketching", "preprint_id": "bioRxiv 2020.11.13.381814", "preprint_doi": "10.1101/2020.11.13.381814" }, { "author": "Anton Bankevich, Andrey Bzikadze, Mikhail Kolmogorov, Pavel Pevzner", "title": "Assembling Long Accurate Reads Using de Bruijn Graphs", "preprint_id": "bioRxiv 2020.12.10.420448", "preprint_doi": "10.1101/2020.12.10.420448", "journal": "Nature Biotechnology", "journal_title": "Multiplex de Bruijn graphs enable genome assembly from long, high-fidelity reads", "journal_authors": "Anton Bankevich, Andrey V. Bzikadze, Mikhail Kolmogorov, Dmitry Antipov, Pavel A. Pevzner", "journal_issue_pages": "40: 1075–1081", "journal_year": "2022", "journal_doi": "10.1038/s41587-022-01220-6" }, { "author": "Baraa Orabi, Brian McConeghy, Cedric Chauve, Faraz Hach", "title": "Freddie: Annotation-independent Detection and Discovery of Transcriptomic Alternative Splicing Isoforms", "preprint_id": "bioRxiv 2021.01.20.427493", "preprint_doi": "10.1101/2021.01.20.427493", "journal": "Nucleic Acids Research", "journal_title": "Freddie: annotation-independent detection and discovery of transcriptomic alternative splicing isoforms using long-read sequencing", "journal_authors": "Baraa Orabi, Ning Xie, Brian McConeghy, Xuesen Dong, Cedric Chauve, Faraz Hach", "journal_issue_pages": "51(2):e11", "journal_year": "2023", "journal_doi": "10.1093/nar/gkac1112" }, { "author": "Barış Ekim, Bonnie Berger, Rayan Chikhi", "title": "Minimizer-space de Bruijn Graphs", "preprint_id": "bioRxiv 2021.06.09.447586", "preprint_doi": "10.1101/2021.06.09.447586", "journal": "Cell Systems", "journal_title": "Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer", "journal_authors": "Barış Ekim, Bonnie Berger, Rayan Chikhi", "journal_issue_pages": "12(10):958-968.e6", "journal_year": "2021", "journal_doi": "10.1016/j.cels.2021.08.009" }, { "author": "Benjamin Chidester, Tianming Zhou, Jian Ma", "title": "SPICEMIX: Integrative single-cell spatial modeling for inferring cell identity", "preprint_id": "bioRxiv 2020.11.29.383067", "preprint_doi": "10.1101/2020.11.29.383067", "journal": "Nature Genetics", "journal_title": "SPICEMIX enables integrative single-cell spatial modeling of cell identity", "journal_authors": "Benjamin Chidester, Tianming Zhou, Shahul Alam, Jian Ma", "journal_issue_pages": "55(1):78-88", "journal_year": "2023", "journal_doi": "10.1038/s41588-022-01256-z" }, { "author": "Carlos Oliver, Vincent Mallet, Pericles Philippopoulos, William L Hamilton, Jerome Waldispuhl", "title": "VeRNAl: Mining RNA Structures for Fuzzy Base Pairing Network Motifs", "preprint_id": "arXiv:2009.00664", "preprint_doi": "10.48550/arXiv.2009.00664", "journal": "Bioinformatics", "journal_title": "Vernal: a tool for mining fuzzy network motifs in RNA", "journal_authors": "Carlos Oliver, Vincent Mallet, Pericles Philippopoulos, William L Hamilton, Jerome Waldispuhl", "journal_issue_pages": "38(4): 970-976", "journal_year": "2022", "journal_doi": "10.1093/bioinformatics/btab768" }, { "author": "Damian Wójtowicz, Jan Hoinka, Bayarbaatar Amgalan, Yoo-Ah Kim, Teresa M Przytycka", "title": "RepairSig: Deconvolution of DNA damage and repair contributions to the mutational landscape of cancer", "preprint_id": "bioRxiv 2020.11.21.392878", "preprint_doi": "10.1101/2020.11.21.392878", "journal": "Cell Systems", "journal_title": "RepairSig: Deconvolution of DNA damage and repair contributions to the mutational landscape of cancer", "journal_authors": "Damian Wójtowicz, Jan Hoinka, Bayarbaatar Amgalan, Yoo-Ah Kim, Teresa M Przytycka", "journal_issue_pages": "12(10):994-1003.e4", "journal_year": "2021", "journal_doi": "10.1016/j.cels.2021.07.004" }, { "author": "Diego Santoro, Leonardo Pellegrina, Fabio Vandin", "title": "SPRISS: Approximating Frequent k-mers by Sampling Reads, and Applications", "preprint_id": "arXiv:2101.07117", "preprint_doi": "10.48550/arXiv.2101.07117", "journal": "Bioinformatics", "journal_title": "SPRISS: approximating frequent k-mers by sampling reads, and applications", "journal_authors": "Diego Santoro, Leonardo Pellegrina, Matteo Comin, Fabio Vandin", "journal_issue_pages": "38(13):3343–3350", "journal_year": "2022", "journal_doi": "10.1093/bioinformatics/btac180" }, { "author": "Enrico Seiler, Svenja Mehringer, Mitra Darvish, Etienne Turc, Knut Reinert", "title": "Raptor: A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences", "preprint_id": "bioRxiv 2020.10.08.330985", "preprint_doi": "10.1101/2020.10.08.330985", "journal": "iScience", "journal_title": "Raptor: A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences", "journal_authors": "Enrico Seiler, Svenja Mehringer, Mitra Darvish, Etienne Turc, Knut Reinert", "journal_issue_pages": "24(7):102782", "journal_year": "2021", "journal_doi": "j.isci.2021.102782" }, { "author": "Gryte Satas, Simone Zaccaria, Mohammed El-Kebir, Benjamin J Raphael", "title": "DeCiFering the Elusive Cancer Cell Fraction in Tumor Heterogeneity and Evolution", "preprint_id": "bioRxiv 2021.02.27.429196", "preprint_doi": "10.1101/2021.02.27.429196", "journal": "Cell Systems", "journal_title": "DeCiFering the elusive cancer cell fraction in tumor heterogeneity and evolution", "journal_authors": "Gryte Satas, Simone Zaccaria, Mohammed El-Kebir, Benjamin J Raphael", "journal_issue_pages": "12(10): 1004-1018", "journal_year": "2021", "journal_doi": "10.1016/j.cels.2021.07.006" }, { "author": "Han Li, Xinyi Zhao, Shuya Li, Fangping Wan, Jianyang Zeng, Dan Zhao", "title": "MoTSE: an interpretable task similarity estimator for small molecular property prediction tasks", "preprint_id": "bioRxiv 2021.01.13.426608", "preprint_doi": "10.1101/2021.01.13.426608", "journal": "iScience", "journal_title": "Improving molecular property prediction through a task similarity enhanced transfer learning strategy", "journal_authors": "Han Li, Xinyi Zhao, Shuya Li, Fangping Wan, Dan Zhao, Jianyang Zeng", "journal_issue_pages": "25(10): 105231", "journal_year": "2022", "journal_doi": "10.1016/j.isci.2022.105231" }, { "author": "Harsh Shrivastava, Xiuwei Zhang, Srinivas Aluru, Le Song", "title": "An Unrolled Deep Learning Framework for Single Cell Gene Regulatory Networks", "preprint_id": "bioRxiv 2020.04.23.058149", "preprint_doi": "10.1101/2020.04.23.058149", "journal": "Journal of Computational Biology", "journal_title": "GRNUlar: A deep learning framework for recovering single-cell gene regulatory networks", "journal_authors": "Harsh Shrivastava , Xiuwei Zhang, Le Song, Srinivas Aluru", "journal_issue_pages": "29(1):27-44", "journal_year": "2022", "journal_doi": "10.1089/cmb.2021.0437" }, { "author": "Hua-Ting Yao, Jerome Waldispuhl, Yann Ponty, Sebastian Will", "title": "Taming Disruptive Base Pairs to Reconcile Positive and Negative Structural Design of RNA", "preprint_id": "hal-02987566", "preprint_url": "https://hal.science/hal-02987566" }, { "author": "Jin Li, Jinbo Xu", "title": "Study of Real-Valued Distance Prediction For Protein Structure Prediction with Deep Learning", "preprint_id": "bioRxiv 2020.11.26.400523", "preprint_doi": "10.1101/2020.11.26.400523", "journal": "Bioinformatics", "journal_title": "Study of real-valued distance prediction for protein structure prediction with deep learning", "journal_authors": "Jin Li, Jinbo Xu", "journal_issue_pages": "37(19):3197–3203", "journal_year": "2021", "journal_doi": "10.1093/bioinformatics/btab333" }, { "author": "Kaiyuan Zhu, Welles Robinson, Alejandro Schaffer, Junyan Xu, Eytan Ruppin, Funda Ergun, Yuzhen Ye, S Cenk Sahinalp", "title": "Strain Level Microbial Detection and Quantification with Applications to Single Cell Metagenomics", "preprint_id": "bioRxiv 2020.06.12.149245", "preprint_doi": "10.1101/2020.06.12.149245", "journal": "Nature Communications", "journal_title": "Strain level microbial detection and quantification with applications to single cell metagenomics", "journal_authors": "Kaiyuan Zhu, Alejandro A. Schäffer, Welles Robinson, Junyan Xu, Eytan Ruppin, A. Funda Ergun, Yuzhen Ye, S. Cenk Sahinalp", "journal_issue_pages": "13(1):6430", "journal_year": "2022", "journal_doi": "10.1038/s41467-022-33869-7" }, { "author": "Martin Grosshauser, Paul Zaharias, Tandy Warnow", "title": "Re-evaluating deep neural networks for phylogeny estimation: the issue of taxon sampling", "journal": "Journal of Computational Biology", "journal_title": "Re-evaluating deep neural networks for phylogeny estimation: the issue of taxon sampling", "journal_authors": "Paul Zaharias, Martin Grosshauser, Tandy Warnow", "journal_issue_pages": "29(1):74-89", "journal_year": "2022", "journal_doi": "10.1089/cmb.2021.0383" }, { "author": "Natnatee Dokmai, Can Kockan, Kaiyuan Zhu, Xiaofeng Wang, S Cenk Sahinalp, Hyunghoon Cho", "title": "Privacy-Preserving Genotype Imputation in a Trusted Execution Environment", "preprint_id": "bioRxiv 2021.02.02.429428", "preprint_doi": "10.1101/2021.02.02.429428", "journal": "Cell Systems", "journal_title": "Privacy-preserving genotype imputation in a trusted execution environment", "journal_authors": "Natnatee Dokmai, Can Kockan, Kaiyuan Zhu, XiaoFeng Wang, S Cenk Sahinalp, Hyunghoon Cho", "journal_issue_pages": "12(10):983-993.e7", "journal_year": "2021", "journal_doi": "10.1016/j.cels.2021.08.001" }, { "author": "Nicholas Franzese, Jason Fan, Roded Sharan, Mark DM Leiserson", "title": "ScalpelSig: Automated Design of Genomic Panels to Expand Clinical Access to Mutational Signature Analysis", "journal": "Journal of Computational Biology", "journal_title": "ScalpelSig: Automated Design of Genomic Panels to Expand Clinical Access to Mutational Signature Analysis", "journal_authors": "Nicholas Franzese, Jason Fan, Roded Sharan, Mark D M Leiserson", "journal_issue_pages": "29(1): 56-73", "journal_year": "2022", "journal_doi": "10.1089/cmb.2021.0453" }, { "author": "Pinar Demetci, Rebecca Santorella, Bjorn Sandstede, William Stafford Noble, Ritambhara Singh", "title": "Gromov-Wasserstein optimal transport to align single-cell multi-omics data", "preprint_id": "bioRxiv 2020.04.28.066787", "preprint_doi": "10.1101/2020.04.28.066787", "journal": "Journal of Computational Biology", "journal_title": "Gromov-Wasserstein optimal transport to align single-cell multi-omics data", "journal_authors": "Pinar Demetci, Rebecca Santorella, Björn Sandstede, William Stafford Noble, Ritambhara Singh", "journal_issue_pages": "29(1): 3-18", "journal_year": "2021", "journal_doi": "10.1089/cmb.2021.0446" }, { "author": "Rami Nasser, Yonina Eldar, Roded Sharan", "title": "Deep unfolding for non-negative matrix factorization with application to mutational signature analysis", "preprint_id": "arXiv:2108.09138", "preprint_doi": "10.48550/arXiv.2108.09138", "journal": "Journal of Computational Biology", "journal_title": "Deep Unfolding for Non-Negative Matrix Factorization with Application to Mutational Signature Analysis", "journal_authors": "Rami Nasser, Yonina C. Eldar, Roded Sharan", "journal_issue_pages": "29(1):45-55", "journal_year": "2022", "journal_doi": "10.1089/cmb.2021.0438" }, { "author": "Ron Zeira, Max Land, Ben Raphael", "title": "Alignment and Integration of Spatial Transcriptomics Data", "preprint_id": "bioRxiv 2021.03.16.435604", "preprint_doi": "10.1101/2021.03.16.435604", "journal": "Nature Methods", "journal_title": "Alignment and integration of spatial transcriptomics data", "journal_authors": "Ron Zeira, Max Land, Alexander Strzalkowski, Benjamin J Raphael", "journal_issue_pages": "19(5):567-575", "journal_year": "2022", "journal_doi": "10.1038/s41592-022-01459-6" }, { "author": "Ruochi Zhang, Jianzhu Ma, Jian Ma", "title": "Towards the prediction of higher-order genetic interactions", "preprint_id": "bioRxiv 2020.11.26.400739", "preprint_doi": "10.1101/2020.11.26.400739", "journal": "Cell Systems", "journal_title": "Towards the prediction of higher-order genetic interactions", "journal_authors": "Ruochi Zhang, Jianzhu Ma, Jian Ma", "journal_issue_pages": "to appear", "journal_year": "2025", "journal_doi": "10.1016" }, { "author": "Samuel Sledzieski, Rohit Singh, Lenore Cowen, Bonnie Berger", "title": "Sequence-based prediction of protein-protein interactions: a structure-aware interpretable deep learning model", "preprint_id": "bioRxiv 2021.01.22.427866", "preprint_doi": "10.1101/2021.01.22.427866", "journal": "Cell Systems", "journal_title": "D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions", "journal_authors": "Samuel Sledzieski, Rohit Singh, Lenore Cowen, Bonnie Berger", "journal_issue_pages": "12(10):969-982.e6", "journal_year": "2021", "journal_doi": "10.1016/j.cels.2021.08.010" }, { "author": "Serhan Yılmaz, Marzieh Ayati, Daniela Schlatzer, A Ercument Cicek, Mark Chance, Mehmet Koyuturk", "title": "Robust Inference of Kinase Activity Using Functional Networks", "preprint_id": "bioRxiv 2020.05.01.062802", "preprint_doi": "10.1101/2020.05.01.062802", "journal": "Nature Communications", "journal_title": "Robust inference of kinase activity using functional networks", "journal_authors": "Serhan Yılmaz, Marzieh Ayati, Daniela Schlatzer, A Ercument Cicek, Mark Chance, Mehmet Koyuturk", "journal_issue_pages": "12(1):1177", "journal_year": "2021", "journal_doi": "10.1038/s41467-021-21211-6" }, { "author": "Shahab Sarmashghi, Metin Balaban, Eleonora Rachtman, Behrouz Touri, Siavash Mirarab, Vineet Bafna", "title": "Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT", "preprint_id": "bioRxiv 2021.01.28.428636", "preprint_doi": "10.1101/2021.01.28.428636", "journal": "PLOS Computational Biology", "journal_title": "Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT", "journal_authors": "Shahab Sarmashghi, Metin Balaban, Eleonora Rachtman, Behrouz Touri, Siavash Mirarab, Vineet Bafna", "journal_issue_pages": "17(11):e1009449", "journal_year": "2021", "journal_doi": "10.1371/journal.pcbi.1009449" }, { "author": "Siavash Raeisi Dehkordi, Jens Luebeck, Vineet Bafna", "title": "FaNDOM: Fast Nested Distance-based seeding of Optical Maps", "journal": "Patterns", "journal_title": "FaNDOM: Fast nested distance-based seeding of optical maps", "journal_authors": "Siavash Raeisi Dehkordi, Jens Luebeck, Vineet Bafna", "journal_issue_pages": "2(5):100248", "journal_year": "2021", "journal_doi": "10.1016/j.patter.2021.100248" }, { "author": "Tianyi Sun, Dongyuan Song, Wei Vivian Li, Jingyi Jessica Li", "title": "scDesign2: an interpretable simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured", "preprint_id": "bioRxiv 2020.11.17.387795", "preprint_doi": "10.1101/2020.11.17.387795", "journal": "Genome Biology", "journal_title": "scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured", "journal_authors": "Tianyi Sun, Dongyuan Song, Wei Vivian Li, Jingyi Jessica Li", "journal_issue_pages": "22: 163", "journal_year": "2021", "journal_doi": "10.1186/s13059-021-02367-2" }, { "author": "Wei Vivian Li, Yanzeng Li", "title": "scLink: Inferring Sparse Gene Co-expression Networks from Single-cell Expression Data", "preprint_id": "bioRxiv 2020.09.19.304956", "preprint_doi": "10.1101/2020.09.19.304956", "journal": "Genomics, Proteomics & Bioinformatics", "journal_title": "scLink: Inferring Sparse Gene Co-Expression Networks from Single-Cell Expression Data", "journal_authors": "Wei Vivian Li, Yanzeng Li", "journal_issue_pages": "19(3):475–492", "journal_year": "2021", "journal_doi": "10.1016/j.gpb.2020.11.006" }, { "author": "Xiang Zhou, Hua Chai, Yuansong Zeng, Huiying Zhao, Ching-Hsing Luo, Yuedong Yang", "title": "scAdapt: Virtual adversarial domain adaptation network for single cell RNA-seq data classification across platforms and species", "preprint_id": "bioRxiv 2021.01.18.427083", "preprint_doi": "10.1101/2021.01.18.427083", "journal": "Briefings in Bioinformatics", "journal_title": "scAdapt: Virtual adversarial domain adaptation network for single cell RNA-seq data classification across platforms and species", "journal_authors": "Xiang Zhou, Hua Chai, Yuansong Zeng, Huiying Zhao, Yuedong Yang", "journal_issue_pages": "22(6):bbab281", "journal_year": "2021", "journal_doi": "10.1093/bib/bbab281" }, { "author": "Xinhao Liu, Huw A Ogilvie, Luay Nakhleh", "title": "Variational Inference Using Approximate Likelihood Under the Coalescent With Recombination", "preprint_id": "bioRxiv 2020.08.19.258137", "preprint_doi": "10.1101/2020.08.19.258137", "journal": "Genome Research", "journal_title": "Variational inference using approximate likelihood under the coalescent with recombination", "journal_authors": "Xinhao Liu, Huw A Ogilvie, Luay Nakhleh", "journal_issue_pages": "31(11): 2107-2119", "journal_year": "2021", "journal_doi": "10.1101/gr.273631.120" }, { "author": "Yuepeng Jiang, Stefano Rensi, Sheng Wang, Russ Altman", "title": "DrugOrchestra: Jointly predicting drug response, targets, and side effects via deep multi-task learning", "preprint_id": "bioRxiv 2020.11.17.385757", "preprint_doi": "10.1101/2020.11.17.385757" }, { "author": "Yueyu Jiang, Metin Balaban, Siavash Mirarab", "title": "DEPP: Deep Learning Enables Extending Species Trees using Single Genes", "preprint_id": "bioRxiv 2021.01.22.427808", "preprint_doi": "10.1101/2021.01.22.427808", "journal": "Systematic Biology", "journal_title": "DEPP: Deep Learning Enables Extending Species Trees using Single Genes", "journal_authors": "Yueyu Jiang, Metin Balaban, Qiyun Zhu, Siavash Mirarab", "journal_issue_pages": "72(1):17", "journal_year": "2023", "journal_doi": "10.1093/sysbio/syac031" }, { "author": "Lupeng Kong, Fusong Ju, Wei-mou Zheng, Jianwei Zhu, Shiwei Sun, Jinbo Xu,, Dongbo Bu", "title": "ProALIGN: directly learning alignments for protein structure prediction via exploiting context-specific alignment motifs", "preprint_id": "bioRxiv 2020.12.28.424539", "preprint_doi": "10.1101/2020.12.28.424539", "journal": "Journal of Computational Biology", "journal_title": "ProALIGN: Directly Learning Alignments for Protein Structure Prediction via Exploiting Context-Specific Alignment Motifs", "journal_authors": "Lupeng Kong, Fusong Ju, Wei-mou Zheng, Jianwei Zhu, Shiwei Sun, Jinbo Xu, Dongbo Bu", "journal_issue_pages": "29(2): 92-105", "journal_year": "2022", "journal_doi": "10.1089/cmb.2021.0430" }, { "author": "Yuxuan Du, Sarah M. Laperriere, Jed Fuhrman,, Fengzhu Sun", "title": "HiCzin: Normalizing metagenomic Hi-C data and detecting spurious contacts using zero-inflated negative binomial regression", "preprint_id": "bioRxiv 2021.03.01.433489", "preprint_doi": "10.1101/2021.03.01.433489", "journal": "Journal of Computational Biology", "journal_title": "Normalizing Metagenomic Hi-C Data and Detecting Spurious Contacts Using Zero-Inflated Negative Binomial Regression", "journal_authors": "Yuxuan Du, Sarah M. Laperriere, Jed Fuhrman, Fengzhu Sun", "journal_issue_pages": "29(2): 106-120", "journal_year": "2022", "journal_doi": "10.1089/cmb.2021.0439" }, { "author": "Hongyu Zheng, Cong Ma,, Carl Kingsford", "title": "Deriving Ranges of Optimal Estimated Transcript Expression due to Non-identifiability", "preprint_id": "bioRxiv 2019.12.13.875625", "preprint_doi": "10.1101/2019.12.13.875625", "journal": "Journal of Computational Biology", "journal_title": "Deriving Ranges of Optimal Estimated Transcript Expression due to Nonidentifiability", "journal_authors": "Hongyu Zheng, Cong Ma, Carl Kingsford", "journal_issue_pages": "29(2): 121-139", "journal_year": "2022", "journal_doi": "10.1089/cmb.2021.0444" }, { "author": "Yoshihiro Shibuya, Djamal Belazzougui,, Gregory Kucherov", "title": "Set-Min sketch: a probabilistic map for power-law distributions with application to k-mer annotation", "preprint_id": "bioRxiv 2020.11.14.382713", "preprint_doi": "10.1101/2020.11.14.382713", "journal": "Journal of Computational Biology", "journal_title": "Set-Min Sketch: A Probabilistic Map for Power-Law Distributions with Application to k-Mer Annotation", "journal_authors": "Yoshihiro Shibuya, Djamal Belazzougui, Gregory Kucherov", "journal_issue_pages": "29(2): 140-154", "journal_year": "2022", "journal_doi": "10.1089/cmb.2021.0429" }, { "author": "Antonio Blanca, Robert S. Harris, David Koslicki,, Paul Medvedev", "title": "The statistics of k-mers from a sequence undergoing a simple mutation process without spurious matches", "preprint_id": "bioRxiv 2021.01.15.426881", "preprint_doi": "10.1101/2021.01.15.426881", "journal": "Journal of Computational Biology", "journal_title": "The Statistics of k-mers from a Sequence Undergoing a Simple Mutation Process Without Spurious Matches", "journal_authors": "Antonio Blanca, Robert S. Harris, David Koslicki, Paul Medvedev", "journal_issue_pages": "29(2): 155-168", "journal_year": "2022", "journal_doi": "10.1089/cmb.2021.0431" }, { "author": "Massimiliano Rossi, Marco Oliva, Ben Langmead, Travis Gagie,, Christina Boucher", "title": "MONI: A Pangenomics Index for Finding MEMs", "preprint_id": "bioRxiv 2021.07.06.451246", "preprint_doi": "10.1101/2021.07.06.451246", "journal": "Journal of Computational Biology", "journal_title": "MONI: A Pangenomic Index for Finding Maximal Exact Matches", "journal_authors": "Massimiliano Rossi, Marco Oliva, Ben Langmead, Travis Gagie, Christina Boucher", "journal_issue_pages": "29(2): 169-187", "journal_year": "2022", "journal_doi": "10.1089/cmb.2021.0290" }, { "author": "Jim Shaw, Yun William Yu", "title": "Practical probabilistic and graphical formulations of long-read polyploid haplotype phasing", "preprint_id": "bioRxiv 2020.11.06.371799", "preprint_doi": "10.1101/2020.11.06.371799", "journal": "Journal of Computational Biology", "journal_title": "flopp: Extremely Fast Long-Read Polyploid Haplotype Phasing by Uniform Tree Partitioning", "journal_authors": "Jim Shaw, Yun William Yu", "journal_issue_pages": "29(2): 195-211", "journal_year": "2022", "journal_doi": "10.1089/cmb.2021.0436" } ] }