Advance Online Articles

Last updated February 10, 2026

GENOME RESEARCH POSTS ADVANCE ARTICLES, INCLUDING ACCEPTED MANUSCRIPTS, FOR RAPID ACCESS TO THE LATEST RESEARCH.

Advance Articles are published online ahead of print. The online first release date serves as the official date of publication. Upon release of the article's scheduled issue, the advance article (which may not be the final version) will move from this Advance Online Articles index to the issue's full Table of Contents in its final edited form.

Advance Articles also include Accepted Manuscripts, which are PDF versions of manuscripts that have been peer reviewed and accepted for publication but are not yet copyedited or typeset. They are posted as submitted by the authors, subject to the authors' agreement, and do not reflect the changes that will be made before final publication. The Accepted Manuscript remains on the Advance Online Articles page until it is either replaced by a copyedited and typeset version and/or when the final version of the article is published in an issue.

February 10, 2026

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Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species

Daniel Siqueira de Oliveira,
Anaïs Larue,
William Vilas Boas Nunes,
Francois Sabot,
Alejandra Bodelón,
María Pilar García Guerreiro,
Cristina Vieira,
and Claudia Marcia Aparecida Carareto

Genome Res. February 10, 2026; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125

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Analysis of coding gene expression from small RNA sequencing

Aygun Azadova,
Anthonia Ekperuoh,
Greg N. Brooke,
and Antonio Marco

Genome Res. February 10, 2026; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125

February 3, 2026

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spRefine denoises and imputes spatial transcriptomics with a reference-free framework powered by genomic language model

Tianyu Liu,
Tinglin Huang,
Wengong Jin,
Tinyi Chu,
Rex Ying,
and Hongyu Zhao

Genome Res. February 3, 2026; Published in Advance February 3, 2026, doi:10.1101/gr.281001.125

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January 28, 2026

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A systems view on DNA damage response kinetics in Tetrahymena

Emily Nischwitz,
Vivien Schoonenberg,
Rachel Mullner,
Albert Fradera-Sola,
Susanne Zimbelmann,
Joshua J Smith,
and Falk Butter

Genome Res. January 28, 2026; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125

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January 21, 2026

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Cell type-specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease

Yunxiao Ren,
Ming Hu,
Yang E. Li,
Andrew A. Pieper,
Jeffrey Cummings,
and Feixiong Cheng

Genome Res. January 21, 2026; Published in Advance January 21, 2026, doi:10.1101/gr.280436.125

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Degrees of convergent evolution in rodent adaptations to arid environments

Domitille Chalopin,
Carine Rey,
Jeremy Ganofsky,
Juliana Blin,
Pascale Chevret,
Marion Mouginot,
Laurent Gueguen,
Bastien Boussau,
Sophie Pantalacci,
and Marie Semon

Genome Res. January 21, 2026; Published in Advance January 21, 2026, doi:10.1101/gr.280089.124

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January 16, 2026

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Natural diversity of telomere length distributions across 100 Saccharomyces cerevisiae strains

Clotilde Garrido,
Cintia Gómez-Muñoz,
Etienne Kornobis,
Nicolas Agier,
Oana Ilioaia,
Gilles Fischer,
and Zhou Xu

Genome Res. January 16, 2026; Published in Advance January 16, 2026, doi:10.1101/gr.281132.125

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January 15, 2026

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Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit

David R Lougheed,
Tomi Pastinen,
and Guillaume Bourque

Genome Res. January 15, 2026; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125

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January 12, 2026

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Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation

Sophia N. Lee,
Erin C. Banda,
Lu Qiao,
Sarah L. Thompson,
Karan Singh,
Ryan A. Hagenson,
Teresa Davoli,
Stefan F. Pinter,
and Jason M. Sheltzer

Genome Res. January 12, 2026; Published in Advance January 12, 2026, doi:10.1101/gr.280425.125

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Early feature extraction drives model performance in high-resolution chromatin accessibility prediction

Aayush Grover,
Till Muser,
Liine Kasak,
Lin Zhang,
Ekaterina Krymova,
and Valentina Boeva

Genome Res. January 12, 2026; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125

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December 23, 2025

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A spectral component approach leveraging Identity-by-Descent graphs to address recent population structure in genomic analysis

Ruhollah Shemirani,
Gillian M Belbin,
Sinead Cullina,
Christa Caggiano,
Christopher Gignoux,
Noah Zaitlen,
and Eimear Kenny

Genome Res. December 23, 2025; Published in Advance December 23, 2025, doi:10.1101/gr.280659.125

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November 4, 2025

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Epigenomics of embryogenesis in turbot

Oscar Aramburu,
Belen G Pardo,
Ada Jimenez-Gonzalez,
Andrés Blanco-Hortas,
Daniel Macqueen,
Carmen Bouza,
and Paulino Martinez

Genome Res. November 4, 2025; Published in Advance November 4, 2025, doi:10.1101/gr.280355.124

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October 22, 2025

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Genomic regulatory landscape underlying the antiviral response of Atlantic salmon

Shahmir Naseer,
Thomas C Clark,
Bertrand Collet,
Pooran Dewari,
Damir Baranasic,
Daniel J Macqueen,
Pierre Boudinot,
and Samuel A.M. Martin

Genome Res. October 22, 2025; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125

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October 6, 2025

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Integrative chromatin state annotation of 234 human ENCODE4 cell types using Segway

Marjan Farahbod,
Aboud Diab,
Paul Sud,
Meenakshi S. Kagda,
Ian Whaling,
Mehdi Foroozandeh,
Ishan Goel,
Habib Daneshpajouh,
Benjamin Hitz,
J. Michael Cherry,
and Maxwell W. Libbrecht

Genome Res. October 6, 2025; Published in Advance October 6, 2025, doi:10.1101/gr.280633.125

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April 22, 2025

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MPRAbase a Massively Parallel Reporter Assay database

Jingjing Zhao,
Fotis A Baltoumas,
Maxwell A Konnaris,
Ioannis Mouratidis,
Zhe Liu,
Jasmine Sims,
Vikram Agarwal,
Georgios A Pavlopoulos,
Ilias Georgakopoulos-Soares,
and Nadav Ahituv

Genome Res. April 22, 2025; Published in Advance April 22, 2025, doi:10.1101/gr.280387.124

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February 21, 2025

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Exploring the epigenome profiles of repetitive elements with the WashU Repeat Browser

Jiawei Shen,
Siyuan Cheng,
Deepak Purushotham,
Xiaoyu Zhuo,
Alan Y Du,
Wenjin Zhang,
Daofeng Li,
and Ting Wang

Genome Res. February 21, 2025; Published in Advance February 21, 2025, doi:10.1101/gr.279764.124

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February 2026, 36 (2)