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Advance Online Articles

Last updated July 19, 2024

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.

July 19, 2024

    Graph-based self-supervised learning for repeat detection in metagenomic assembly
    • Ali Azizpour,
    • Advait Balaji,
    • Todd J. Treangen,
    • and Santiago Segarra
    Genome Res. July 19, 2024; Published in Advance July 19, 2024, doi:10.1101/gr.279136.124
    ACCEPTED MANUSCRIPT

July 16, 2024

    High-fidelity, large-scale targeted profiling of microsatellites
    • Caitlin A Loh,
    • Danielle A Shields,
    • Adam Schwing,
    • and Gilad D Evrony
    Genome Res. July 16, 2024; Published in Advance July 16, 2024, doi:10.1101/gr.278785.123
    ACCEPTED MANUSCRIPT
    Haplotype-aware sequence alignment to pangenome graphs
    • Ghanshyam Chandra,
    • Daniel Gibney,
    • and Chirag Jain
    Genome Res. July 16, 2024; Published in Advance July 16, 2024, doi:10.1101/gr.279143.124
    ACCEPTED MANUSCRIPT

July 15, 2024

    Single-cell discovery of m6A RNA modifications in the hippocampus
    • Shuangshuang Feng,
    • Maitena Tellaetxe-Abete,
    • Yujie Zhang,
    • Yan Peng,
    • Han Zhou,
    • Mingjie Dong,
    • Erika Larrea,
    • Liang Xue,
    • Li Zhang,
    • and Magdalena J. Koziol
    Genome Res. July 15, 2024; Published in Advance July 15, 2024, doi:10.1101/gr.278424.123
    OPEN ACCESS ARTICLE

July 11, 2024

    Simultaneous assessment of human genome and methylome data in a single experiment using limited deamination of methylated cytosine
    • Bo Yan,
    • Duan Wang,
    • and Laurence Ettwiller
    Genome Res. June 10, 2024; Published in Advance June 10, 2024, doi:10.1101/gr.278294.123
    OPEN ACCESS ARTICLE

July 10, 2024

    Accurate allocation of multimapped reads enables regulatory element analysis at repeats
    • Alexis Morrissey,
    • Jeffrey Shi,
    • Daniela Q. James,
    • and Shaun Mahony
    Genome Res. July 10, 2024; Published in Advance July 10, 2024, doi:10.1101/gr.278638.123
    DEAD box RNA helicases are pervasive protein kinase interactors and activators
    • Alexander Hirth,
    • Edoardo Fatti,
    • Eugen Netz,
    • Sergio P. Acebron,
    • Dimitris Papageorgiou,
    • Andrea Švorinić,
    • Cristina-Maria Cruciat,
    • Emil Karaulanov,
    • Alexandr Gopanenko,
    • Tianheng Zhu,
    • Irmgard Sinning,
    • Jeroen Krijgsveld,
    • Oliver Kohlbacher,
    • and Christof Niehrs
    Genome Res. July 10, 2024; Published in Advance July 10, 2024, doi:10.1101/gr.278264.123

July 9, 2024

    Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters
    • Jens-Uwe Ulrich and
    • Bernhard Y. Renard
    Genome Res. June 17, 2024; Published in Advance June 17, 2024, doi:10.1101/gr.278623.123
    Accurate estimation of pathway activity in single cells for clustering and differential analysis
    • Daniel Davis,
    • Avishai Wizel,
    • and Yotam Drier
    Genome Res. July 9, 2024; Published in Advance July 9, 2024, doi:10.1101/gr.278431.123
    OPEN ACCESS ARTICLE
    CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing
    • Kaiyuan Zhu,
    • Matthew Gregory Jones,
    • Jens Luebeck,
    • Xinxin Bu,
    • Hyerim Yi,
    • King L. Huang,
    • Ivy Tsz-Lo Wong,
    • Shu Zhang,
    • Paul S. Mischel,
    • Howard Chang,
    • and Vineet Bafna
    Genome Res. July 9, 2024; Published in Advance July 9, 2024, doi:10.1101/gr.279131.124
    OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT

July 8, 2024

    Causes and consequences of a complex recombinational landscape in the ant Cardiocondyla obscurior
    • Mohammed Errbii,
    • Jürgen Gadau,
    • Kerstin Becker,
    • Lukas Schrader,
    • and Jan Oettler
    Genome Res. June 5, 2024; Published in Advance June 5, 2024, doi:10.1101/gr.278392.123
    Comparative genomics of Cryptosporidium parvum reveals the emergence of an outbreak-associated population in Europe and its spread to the United States
    • Greta Bellinzona,
    • Tiago Nardi,
    • Michele Castelli,
    • Gherard Batisti Biffignandi,
    • Karim Adjou,
    • Martha Betson,
    • Yannick Blanchard,
    • Ioana Bujila,
    • Rachel Chalmers,
    • Rebecca Davidson,
    • Nicoletta D'Avino,
    • Tuulia Enbom,
    • Jacinto Gomes,
    • Gregory Karadjian,
    • Christian Klotz,
    • Emma Östlund,
    • Judith Plutzer,
    • Ruska Rimhanen-Finne,
    • Guy Robinson,
    • Anna Rosa Sannella,
    • Jacek Sroka,
    • Christen Rune Stensvold,
    • Karin Troell,
    • Paolo Vatta,
    • Barbora Zalewska,
    • Claudio Bandi,
    • Davide Sassera,
    • and Simone M. Cacciò
    Genome Res. July 8, 2024; Published in Advance July 8, 2024, doi:10.1101/gr.278830.123
    OPEN ACCESS ARTICLE
    Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins
    • Nikolaos Vakirlis and
    • Anne Kupczok
    Genome Res. July 8, 2024; Published in Advance July 8, 2024, doi:10.1101/gr.278977.124
    Single-cell analysis reveals transcriptional dynamics in healthy primary parathyroid tissue
    • Aarthi Venkat,
    • Maximillian J. Carlino,
    • Betty R. Lawton,
    • Manju L. Prasad,
    • Matthew Amodio,
    • Courtney E. Gibson,
    • Caroline J. Zeiss,
    • Scott E. Youlten,
    • Smita Krishnaswamy,
    • and Diane S. Krause
    Genome Res. July 8, 2024; Published in Advance July 8, 2024, doi:10.1101/gr.278215.123

July 2, 2024

    Large-scale genomic analysis of the domestic dog informs biological discovery
    • Reuben M. Buckley and
    • Elaine A. Ostrander
    Genome Res. July 2, 2024; Published in Advance July 2, 2024, doi:10.1101/gr.278569.123
    OPEN ACCESS ARTICLE
    Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles
    • Xuejing Wang and
    • Gerald Heckel
    Genome Res. July 2, 2024; Published in Advance July 2, 2024, doi:10.1101/gr.278487.123

July 1, 2024

    Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes
    • Guanjue Xiang,
    • Xi He,
    • Belinda M. Giardine,
    • Kathryn J. Isaac,
    • Dylan J. Taylor,
    • Rajiv C. McCoy,
    • Camden Jansen,
    • Cheryl A. Keller,
    • Alexander Q. Wixom,
    • April Cockburn,
    • Amber Miller,
    • Qian Qi,
    • Yanghua He,
    • Yichao Li,
    • Jens Lichtenberg,
    • Elisabeth F. Heuston,
    • Stacie M. Anderson,
    • Jing Luan,
    • Marit W. Vermunt,
    • Feng Yue,
    • Michael E.G. Sauria,
    • Michael C. Schatz,
    • James Taylor,
    • Berthold Göttgens,
    • Jim R. Hughes,
    • Douglas R. Higgs,
    • Mitchell J. Weiss,
    • Yong Cheng,
    • Gerd A. Blobel,
    • David M. Bodine,
    • Yu Zhang,
    • Qunhua Li,
    • Shaun Mahony,
    • and Ross C. Hardison
    Genome Res. July 1, 2024; Published in Advance July 1, 2024, doi:10.1101/gr.277950.123
    OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
    Streamlined spatial and environmental expression signatures characterize the minimalist duckweed Wolffia australiana
    • Tom Denyer,
    • Pin-Jou Wu,
    • Kelly Colt,
    • Bradley Abramson,
    • Zhili Pang,
    • Pavel Solansky,
    • Allen Mamerto,
    • Tatsuya Nobori,
    • Joseph Ecker,
    • Eric Lam,
    • Todd P. Michael,
    • and Marja CP Timmermans
    Genome Res. July 1, 2024; Published in Advance July 1, 2024, doi:10.1101/gr.279091.124
    OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
    CodonBert large language model for mRNA vaccines
    • Sizhen Li,
    • Saeed Moayedpour,
    • Ruijiang Li,
    • Michael Bailey,
    • Saleh Riahi,
    • Lorenzo Kogler-Anele,
    • Milad Miladi,
    • Jacob Miner,
    • Fabien Pertuy,
    • Dinghai Zheng,
    • Jun Wang,
    • Akshay Balsubramani,
    • Khang Tran,
    • Minnie Zacharia,
    • Monica Wu,
    • Xiaobo Gu,
    • Ryan Clinton,
    • Carla Asquith,
    • Joseph Skaleski,
    • Lianne Boeglin,
    • Sudha Chivukula,
    • Anusha Dias,
    • Tod Strugnell,
    • Fernando Ulloa Montoya,
    • Vikram Agarwal,
    • Ziv Bar-Joseph,
    • and Sven Jager
    Genome Res. July 1, 2024; Published in Advance July 1, 2024, doi:10.1101/gr.278870.123
    ACCEPTED MANUSCRIPT

June 24, 2024

    Delineating yeast cleavage and polyadenylation signals using deep learning
    • Emily Stroup and
    • Zhe Ji
    Genome Res. June 24, 2024; Published in Advance June 24, 2024, doi:10.1101/gr.278606.123
    ACCEPTED MANUSCRIPT

June 21, 2024

    Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution
    • Pratibha Jagannatha,
    • Alexandra T Tankka,
    • Daniel A Lorenz,
    • Tao Yu,
    • Brian A Yee,
    • Kristopher W Brannan,
    • Catherine Jiarui Zhou,
    • Jason G Underwood,
    • and Gene W. Yeo
    Genome Res. June 21, 2024; Published in Advance June 21, 2024, doi:10.1101/gr.279176.124
    OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT

June 17, 2024

    Size-based expectation maximization for characterizing nucleosome positions and subtypes
    • Jianyu Yang,
    • Kuangyu Yen,
    • and Shaun Mahony
    Genome Res. June 17, 2024; Published in Advance June 17, 2024, doi:10.1101/gr.279138.124
    ACCEPTED MANUSCRIPT

June 7, 2024

    DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools
    • Anupama Jha,
    • Stephanie C. Bohaczuk,
    • Yizi Mao,
    • Jane Ranchalis,
    • Benjamin J. Mallory,
    • Alan T. Min,
    • Morgan O Hamm,
    • Elliott Swanson,
    • Danilo Dubocanin,
    • Connor Finkbeiner,
    • Tony Li,
    • Dale Whittington,
    • William Stafford Noble,
    • Andrew Ben Stergachis,
    • and Mitchell R Vollger
    Genome Res. June 7, 2024; Published in Advance June 7, 2024, doi:10.1101/gr.279095.124
    ACCEPTED MANUSCRIPT

June 5, 2024

    Long read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation
    • Alexander Ritter,
    • Jolene M Draper,
    • Christopher Vollmers,
    • and Jeremy Sanford
    Genome Res. June 5, 2024; Published in Advance June 5, 2024, doi:10.1101/gr.279170.124
    ACCEPTED MANUSCRIPT
    Full resolution HLA and KIR gene annotations for human genome assemblies
    • Ying Zhou,
    • Li Song,
    • and Heng Li
    Genome Res. June 5, 2024; Published in Advance June 5, 2024, doi:10.1101/gr.278985.124
    ACCEPTED MANUSCRIPT

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