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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  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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