Table of Contents

July 2023; 33 (7)

Methods

  • Minimal positional substring cover is a haplotype threading alternative to Li and Stephens model

    • Ahsan Sanaullah,
    • Degui Zhi,
    • and Shaojie Zhang
    Genome Res. July 2023 33: 1007-1014; Published in Advance June 14, 2023, doi:10.1101/gr.277673.123

  • Fast inference of genetic recombination rates in biobank scale data

    • Ardalan Naseri,
    • William Yue,
    • Shaojie Zhang,
    • and Degui Zhi
    Genome Res. July 2023 33: 1015-1022; Published in Advance June 22, 2023, doi:10.1101/gr.277676.123

  • Ultrafast genome-wide inference of pairwise coalescence times

    • Regev Schweiger and
    • Richard Durbin
    Genome Res. July 2023 33: 1023-1031; Published in Advance August 10, 2023, doi:10.1101/gr.277665.123
    OPEN ACCESS ARTICLE

  • Leveraging family data to design Mendelian randomization that is provably robust to population stratification

    • Nathan LaPierre,
    • Boyang Fu,
    • Steven Turnbull,
    • Eleazar Eskin,
    • and Sriram Sankararaman
    Genome Res. July 2023 33: 1032-1041; Published in Advance May 17, 2023, doi:10.1101/gr.277664.123

  • Improving quartet graph construction for scalable and accurate species tree estimation from gene trees

    • Yunheng Han and
    • Erin K. Molloy
    Genome Res. July 2023 33: 1042-1052; Published in Advance May 17, 2023, doi:10.1101/gr.277629.122

  • A fast and scalable method for inferring phylogenetic networks from trees by aligning lineage taxon strings

    • Louxin Zhang,
    • Niloufar Abhari,
    • Caroline Colijn,
    • and Yufeng Wu
    Genome Res. July 2023 33: 1053-1060; Published in Advance May 22, 2023, doi:10.1101/gr.277669.123
    OPEN ACCESS ARTICLE

  • Deriving confidence intervals for mutation rates across a wide range of evolutionary distances using FracMinHash

    • Mahmudur Rahman Hera,
    • N. Tessa Pierce-Ward,
    • and David Koslicki
    Genome Res. July 2023 33: 1061-1068; Published in Advance June 21, 2023, doi:10.1101/gr.277651.123
    OPEN ACCESS ARTICLE

  • Efficient taxa identification using a pangenome index

    • Omar Ahmed,
    • Massimiliano Rossi,
    • Christina Boucher,
    • and Ben Langmead
    Genome Res. July 2023 33: 1069-1077; Published in Advance May 31, 2023, doi:10.1101/gr.277642.123
    OPEN ACCESS ARTICLE

  • Modeling and predicting cancer clonal evolution with reinforcement learning

    • Stefan Ivanovic and
    • Mohammed El-Kebir
    Genome Res. July 2023 33: 1078-1088; Published in Advance June 21, 2023, doi:10.1101/gr.277672.123

  • Single-cell methylation sequencing data reveal succinct metastatic migration histories and tumor progression models

    • Yuelin Liu,
    • Xuan Cindy Li,
    • Farid Rashidi Mehrabadi,
    • Alejandro A. Schäffer,
    • Drew Pratt,
    • David R. Crawford,
    • Salem Malikić,
    • Erin K. Molloy,
    • Vishaka Gopalan,
    • Stephen M. Mount,
    • Eytan Ruppin,
    • Kenneth D. Aldape,
    • and S. Cenk Sahinalp
    Genome Res. July 2023 33: 1089-1100; Published in Advance June 14, 2023, doi:10.1101/gr.277608.122

  • Assessing transcriptomic reidentification risks using discriminative sequence models

    • Shuvom Sadhuka,
    • Daniel Fridman,
    • Bonnie Berger,
    • and Hyunghoon Cho
    Genome Res. July 2023 33: 1101-1112; Published in Advance August 4, 2023, doi:10.1101/gr.277699.123
    OPEN ACCESS ARTICLE

  • Enabling tradeoffs in privacy and utility in genomic data Beacons and summary statistics

    • Rajagopal Venkatesaramani,
    • Zhiyu Wan,
    • Bradley A. Malin,
    • and Yevgeniy Vorobeychik
    Genome Res. July 2023 33: 1113-1123; Published in Advance May 22, 2023, doi:10.1101/gr.277674.123
    OPEN ACCESS ARTICLE

  • Partial alignment of multislice spatially resolved transcriptomics data

    • Xinhao Liu,
    • Ron Zeira,
    • and Benjamin J. Raphael
    Genome Res. July 2023 33: 1124-1132; Published in Advance August 8, 2023, doi:10.1101/gr.277670.123

  • Unsupervised contrastive peak caller for ATAC-seq

    • Ha T.H. Vu,
    • Yudi Zhang,
    • Geetu Tuteja,
    • and Karin S. Dorman
    Genome Res. July 2023 33: 1133-1144; Published in Advance May 22, 2023, doi:10.1101/gr.277677.123
    OPEN ACCESS ARTICLE

  • Leveraging protein language models for accurate multiple sequence alignments

    • Claire D. McWhite,
    • Isabel Armour-Garb,
    • and Mona Singh
    Genome Res. July 2023 33: 1145-1153; Published in Advance July 6, 2023, doi:10.1101/gr.277675.123
    OPEN ACCESS ARTICLE

  • Efficient minimizer orders for large values of k using minimum decycling sets

    • David Pellow,
    • Lianrong Pu,
    • Bariş Ekim,
    • Lior Kotlar,
    • Bonnie Berger,
    • Ron Shamir,
    • and Yaron Orenstein
    Genome Res. July 2023 33: 1154-1161; Published in Advance August 9, 2023, doi:10.1101/gr.277644.123
    OPEN ACCESS ARTICLE

  • Entropy predicts sensitivity of pseudorandom seeds

    • Benjamin Dominik Maier and
    • Kristoffer Sahlin
    Genome Res. July 2023 33: 1162-1174; Published in Advance May 22, 2023, doi:10.1101/gr.277645.123
    OPEN ACCESS ARTICLE

  • Proving sequence aligners can guarantee accuracy in almost O(m log n) time through an average-case analysis of the seed-chain-extend heuristic

    • Jim Shaw and
    • Yun William Yu
    Genome Res. July 2023 33: 1175-1187; Published in Advance March 29, 2023, doi:10.1101/gr.277637.122
    OPEN ACCESS ARTICLE

  • Efficient mapping of accurate long reads in minimizer space with mapquik

    • Bariş Ekim,
    • Kristoffer Sahlin,
    • Paul Medvedev,
    • Bonnie Berger,
    • and Rayan Chikhi
    Genome Res. July 2023 33: 1188-1197; Published in Advance June 30, 2023, doi:10.1101/gr.277679.123
    OPEN ACCESS ARTICLE

  • Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCAT

    • Andrea Cracco and
    • Alexandru I. Tomescu
    Genome Res. July 2023 33: 1198-1207; Published in Advance May 30, 2023, doi:10.1101/gr.277615.122
    OPEN ACCESS ARTICLE

  • Aligning distant sequences to graphs using long seed sketches

    • Amir Joudaki,
    • Alexandru Meterez,
    • Harun Mustafa,
    • Ragnar Groot Koerkamp,
    • André Kahles,
    • and Gunnar Rätsch
    Genome Res. July 2023 33: 1208-1217; Published in Advance April 18, 2023, doi:10.1101/gr.277659.123

  • Genomic sketching with multiplicities and locality-sensitive hashing using Dashing 2

    • Daniel N. Baker and
    • Ben Langmead
    Genome Res. July 2023 33: 1218-1227; Published in Advance July 6, 2023, doi:10.1101/gr.277655.123
    OPEN ACCESS ARTICLE
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July 2023; 33 (7)
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