Table of Contents

September 2024; 34 (9)

Editorial

  • Innovations in computational biology: RECOMB 2024 Special Issue

    • Jian Ma and
    • Bonnie Berger
    Genome Res. September 2024 34: vii-viii; doi:10.1101/gr.280036.124

Methods

  • Haplotype-aware sequence alignment to pangenome graphs

    • Ghanshyam Chandra,
    • Daniel Gibney,
    • and Chirag Jain
    Genome Res. September 2024 34: 1265-1275; Published in Advance July 16, 2024, doi:10.1101/gr.279143.124

  • Genetics-driven risk predictions leveraging the Mendelian randomization framework

    • Daniel Sens,
    • Liubov Shilova,
    • Ludwig Gräf,
    • Maria Grebenshchikova,
    • Bjoern M. Eskofier,
    • and Francesco Paolo Casale
    Genome Res. September 2024 34: 1276-1285; Published in Advance September 27, 2024, doi:10.1101/gr.279252.124
    OPEN ACCESS ARTICLE

  • Scalable summary-statistics-based heritability estimation method with individual genotype level accuracy

    • Moonseong Jeong,
    • Ali Pazokitoroudi,
    • Zhengtong Liu,
    • and Sriram Sankararaman
    Genome Res. September 2024 34: 1286-1293; Published in Advance July 22, 2024, doi:10.1101/gr.279207.124
    OPEN ACCESS ARTICLE

  • A scalable adaptive quadratic kernel method for interpretable epistasis analysis in complex traits

    • Boyang Fu,
    • Prateek Anand,
    • Aakarsh Anand,
    • Joel Mefford,
    • and Sriram Sankararaman
    Genome Res. September 2024 34: 1294-1303; Published in Advance August 29, 2024, doi:10.1101/gr.279140.124
    OPEN ACCESS ARTICLE

  • Matrix sketching framework for linear mixed models in association studies

    • Myson Burch,
    • Aritra Bose,
    • Gregory Dexter,
    • Laxmi Parida,
    • and Petros Drineas
    Genome Res. September 2024 34: 1304-1311; Published in Advance September 4, 2024, doi:10.1101/gr.279230.124
    OPEN ACCESS ARTICLE

  • Secure discovery of genetic relatives across large-scale and distributed genomic data sets

    • Matthew M. Hong,
    • David Froelicher,
    • Ricky Magner,
    • Victoria Popic,
    • Bonnie Berger,
    • and Hyunghoon Cho
    Genome Res. September 2024 34: 1312-1323; Published in Advance August 7, 2024, doi:10.1101/gr.279057.124
    OPEN ACCESS ARTICLE

  • Privacy-preserving biological age prediction over federated human methylation data using fully homomorphic encryption

    • Meir Goldenberg,
    • Loay Mualem,
    • Amit Shahar,
    • Sagi Snir,
    • and Adi Akavia
    Genome Res. September 2024 34: 1324-1333; Published in Advance September 5, 2024, doi:10.1101/gr.279071.124
    OPEN ACCESS ARTICLE

  • Size-based expectation maximization for characterizing nucleosome positions and subtypes

    • Jianyu Yang,
    • Kuangyu Yen,
    • and Shaun Mahony
    Genome Res. September 2024 34: 1334-1343; Published in Advance June 17, 2024, doi:10.1101/gr.279138.124

  • CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing

    • Kaiyuan Zhu,
    • Matthew G. Jones,
    • Jens Luebeck,
    • Xinxin Bu,
    • Hyerim Yi,
    • King L. Hung,
    • Ivy Tsz-Lo Wong,
    • Shu Zhang,
    • Paul S. Mischel,
    • Howard Y. Chang,
    • and Vineet Bafna
    Genome Res. September 2024 34: 1344-1354; Published in Advance July 9, 2024, doi:10.1101/gr.279131.124
    OPEN ACCESS ARTICLE

  • Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil

    • Mădălina Giurgiu,
    • Nadine Wittstruck,
    • Elias Rodriguez-Fos,
    • Rocío Chamorro González,
    • Lotte Brückner,
    • Annabell Krienelke-Szymansky,
    • Konstantin Helmsauer,
    • Anne Hartebrodt,
    • Philipp Euskirchen,
    • Richard P. Koche,
    • Kerstin Haase,
    • Knut Reinert,
    • and Anton G. Henssen
    Genome Res. September 2024 34: 1355-1364; Published in Advance August 7, 2024, doi:10.1101/gr.279123.124
    OPEN ACCESS ARTICLE

  • Accurate assembly of circular RNAs with TERRACE

    • Tasfia Zahin,
    • Qian Shi,
    • Xiaofei Carl Zang,
    • and Mingfu Shao
    Genome Res. September 2024 34: 1365-1370; Published in Advance July 26, 2024, doi:10.1101/gr.279106.124

  • Spatial Cellular Networks from omics data with SpaCeNet

    • 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,
    • and Michael Altenbuchinger
    Genome Res. September 2024 34: 1371-1383; Published in Advance September 4, 2024, doi:10.1101/gr.279125.124

  • A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data

    • Cameron Park,
    • Shouvik Mani,
    • Nicolas Beltran-Velez,
    • Katie Maurer,
    • Teddy Huang,
    • Shuqiang Li,
    • Satyen Gohil,
    • Kenneth J. Livak,
    • David A. Knowles,
    • Catherine J. Wu,
    • and Elham Azizi
    Genome Res. September 2024 34: 1384-1396; Published in Advance September 5, 2024, doi:10.1101/gr.279126.124
    OPEN ACCESS ARTICLE

  • Bayesian inference of sample-specific coexpression networks

    • Enakshi Saha,
    • Viola Fanfani,
    • Panagiotis Mandros,
    • Marouen Ben Guebila,
    • Jonas Fischer,
    • Katherine H. Shutta,
    • Dawn L. DeMeo,
    • Camila M. Lopes-Ramos,
    • and John Quackenbush
    Genome Res. September 2024 34: 1397-1410; Published in Advance August 12, 2024, doi:10.1101/gr.279117.124
    OPEN ACCESS ARTICLE

  • Designing realistic regulatory DNA with autoregressive language models

    • Avantika Lal,
    • David Garfield,
    • Tommaso Biancalani,
    • and Gokcen Eraslan
    Genome Res. September 2024 34: 1411-1420; Published in Advance September 25, 2024, doi:10.1101/gr.279142.124
    OPEN ACCESS ARTICLE

  • A best-match approach for gene set analyses in embedding spaces

    • Lechuan Li,
    • Ruth Dannenfelser,
    • Charlie Cruz,
    • and Vicky Yao
    Genome Res. September 2024 34: 1421-1433; Published in Advance September 4, 2024, doi:10.1101/gr.279141.124
    OPEN ACCESS ARTICLE

  • Protein domain embeddings for fast and accurate similarity search

    • Benjamin Giovanni Iovino,
    • Haixu Tang,
    • and Yuzhen Ye
    Genome Res. September 2024 34: 1434-1444; Published in Advance September 5, 2024, doi:10.1101/gr.279127.124
    OPEN ACCESS ARTICLE

  • Parameter-efficient fine-tuning on large protein language models improves signal peptide prediction

    • Shuai Zeng,
    • Duolin Wang,
    • Lei Jiang,
    • and Dong Xu
    Genome Res. September 2024 34: 1445-1454; Published in Advance July 26, 2024, doi:10.1101/gr.279132.124

  • Memory-bound k-mer selection for large and evolutionarily diverse reference libraries

    • Ali Osman Berk Şapcı and
    • Siavash Mirarab
    Genome Res. September 2024 34: 1455-1467; Published in Advance August 29, 2024, doi:10.1101/gr.279339.124
    OPEN ACCESS ARTICLE

  • Graph-based self-supervised learning for repeat detection in metagenomic assembly

    • Ali Azizpour,
    • Advait Balaji,
    • Todd J. Treangen,
    • and Santiago Segarra
    Genome Res. September 2024 34: 1468-1476; Published in Advance July 19, 2024, doi:10.1101/gr.279136.124
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This Issue

September 2024; 34 (9)
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