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Current Issue of Genome Research

Table of Contents — April 2025, 35 (4)

Table of Contents

April 2025; 35 (4)

Editorial

  • Long reads decipher genomes and transcriptomes and offer novel insights into biology and diseases

    • Ana Conesa,
    • Alexander Hoischen,
    • and Fritz J. Sedlazeck
    Genome Res. April 2025 35: xi-xiv; doi:10.1101/gr.280665.125

Mini-Reviews

  • A Hitchhiker's Guide to long-read genomic analysis

    • Medhat Mahmoud,
    • Daniel P. Agustinho,
    • and Fritz J. Sedlazeck
    Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124

  • The additional diagnostic yield of long-read sequencing in undiagnosed rare diseases

    • Giulia F. Del Gobbo and
    • Kym M. Boycott
    Genome Res. April 2025 35: 559-571; Published in Advance February 3, 2025, doi:10.1101/gr.279970.124
    OPEN ACCESS ARTICLE

  • Evolution of genome-wide methylation profiling technologies

    • Carolina Montano and
    • Winston Timp
    Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
    OPEN ACCESS ARTICLE

Perspectives

  • Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation

    • Carolina Monzó,
    • Adam Frankish,
    • and Ana Conesa
    Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
    OPEN ACCESS ARTICLE

  • The impact of long-read sequencing on human population-scale genomics

    • Tobias Rausch,
    • Tobias Marschall,
    • and Jan O. Korbel
    Genome Res. April 2025 35: 593-598; doi:10.1101/gr.280120.124

  • Unraveling the hidden complexity of cancer through long-read sequencing

    • Qiuhui Li,
    • Ayse G. Keskus,
    • Justin Wagner,
    • Michal B. Izydorczyk,
    • Winston Timp,
    • Fritz J. Sedlazeck,
    • Alison P. Klein,
    • Justin M. Zook,
    • Mikhail Kolmogorov,
    • and Michael C. Schatz
    Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
    OPEN ACCESS ARTICLE

Research

  • Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T

    • Luis F. Paulin,
    • Jeremy Fan,
    • Kieran O'Neill,
    • Erin Pleasance,
    • Vanessa L. Porter,
    • Steven J.M. Jones,
    • and Fritz J. Sedlazeck
    Genome Res. April 2025 35: 621-631; Published in Advance March 17, 2025, doi:10.1101/gr.279352.124

  • Assessing DNA methylation detection for primary human tissue using Nanopore sequencing

    • Rylee Genner,
    • Stuart Akeson,
    • Melissa Meredith,
    • Pilar Alvarez Jerez,
    • Laksh Malik,
    • Breeana Baker,
    • Abigail Miano-Burkhardt,
    • CARD-long-read Team,
    • Benedict Paten,
    • Kimberley J. Billingsley,
    • Cornelis Blauwendraat,
    • and Miten Jain
    Genome Res. April 2025 35: 632-643; Published in Advance March 7, 2025, doi:10.1101/gr.279159.124
    OPEN ACCESS ARTICLE

  • Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA

    • Cristian Groza,
    • Bing Ge,
    • Warren A. Cheung,
    • Tomi Pastinen,
    • and Guillaume Bourque
    Genome Res. April 2025 35: 644-652; Published in Advance March 20, 2025, doi:10.1101/gr.279240.124

  • Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation

    • Vanessa L. Porter,
    • Michelle Ng,
    • Kieran O'Neill,
    • Signe MacLennan,
    • Richard D. Corbett,
    • Luka Culibrk,
    • Zeid Hamadeh,
    • Marissa Iden,
    • Rachel Schmidt,
    • Shirng-Wern Tsaih,
    • Carolyn Nakisige,
    • Martin Origa,
    • Jackson Orem,
    • Glenn Chang,
    • Jeremy Fan,
    • Ka Ming Nip,
    • Vahid Akbari,
    • Simon K. Chan,
    • James Hopkins,
    • Richard A. Moore,
    • Eric Chuah,
    • Karen L. Mungall,
    • Andrew J. Mungall,
    • Inanc Birol,
    • Steven J.M. Jones,
    • Janet S. Rader,
    • and Marco A. Marra
    Genome Res. April 2025 35: 653-670; Published in Advance December 5, 2024, doi:10.1101/gr.279041.124
    OPEN ACCESS ARTICLE

  • Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis

    • Tianfu Zeng,
    • Haotian Liao,
    • Lin Xia,
    • Siyao You,
    • Yanqun Huang,
    • Jiaxun Zhang,
    • Yahui Liu,
    • Xuyan Liu,
    • and Dan Xie
    Genome Res. April 2025 35: 671-685; Published in Advance March 4, 2025, doi:10.1101/gr.279617.124
    OPEN ACCESS ARTICLE

  • Long-read single-cell RNA sequencing enables the study of cancer subclone-specific genotypes and phenotypes in chronic lymphocytic leukemia

    • Gage S. Black,
    • Xiaomeng Huang,
    • Yi Qiao,
    • Philip Moos,
    • Deepa Sampath,
    • Deborah M. Stephens,
    • Jennifer A. Woyach,
    • and Gabor T. Marth
    Genome Res. April 2025 35: 686-697; Published in Advance February 18, 2025, doi:10.1101/gr.279049.124

  • Heterogeneous and novel transcript expression in single cells of patient-derived clear cell renal cell carcinoma organoids

    • Tülay Karakulak,
    • Natalia Zajac,
    • Hella Anna Bolck,
    • Anna Bratus-Neuenschwander,
    • Qin Zhang,
    • Weihong Qi,
    • Debleena Basu,
    • Tamara Carrasco Oltra,
    • Hubert Rehrauer,
    • Christian von Mering,
    • Holger Moch,
    • and Abdullah Kahraman
    Genome Res. April 2025 35: 698-711; Published in Advance March 19, 2025, doi:10.1101/gr.279345.124
    OPEN ACCESS ARTICLE

  • Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing

    • Karine Choquet,
    • Louis-Philippe Chaumont,
    • Simon Bache,
    • Autum R. Baxter-Koenigs,
    • and L. Stirling Churchman
    Genome Res. April 2025 35: 712-724; Published in Advance February 14, 2025, doi:10.1101/gr.279203.124

  • Deciphering the largest disease-associated transcript isoforms in the human neural retina with advanced long-read sequencing approaches

    • Merel Stemerdink,
    • Tabea Riepe,
    • Nick Zomer,
    • Renee Salz,
    • Michael Kwint,
    • Jaap Oostrik,
    • Raoul Timmermans,
    • Barbara Ferrari,
    • Stefano Ferrari,
    • Alfredo Dueñas Rey,
    • Emma Delanote,
    • Suzanne E. de Bruijn,
    • Hannie Kremer,
    • Susanne Roosing,
    • Frauke Coppieters,
    • Alexander Hoischen,
    • Frans P.M. Cremers,
    • Peter A.C. ‘t Hoen,
    • Erwin van Wijk,
    • and Erik de Vrieze
    Genome Res. April 2025 35: 725-739; Published in Advance March 4, 2025, doi:10.1101/gr.280060.124

  • Integrating short-read and long-read single-cell RNA sequencing for comprehensive transcriptome profiling in mouse retina

    • Meng Wang,
    • Yumei Li,
    • Jun Wang,
    • Soo Hwan Oh,
    • Yexuan Cao,
    • and Rui Chen
    Genome Res. April 2025 35: 740-754; Published in Advance March 6, 2025, doi:10.1101/gr.279167.124

  • Unraveling undiagnosed rare disease cases by HiFi long-read genome sequencing

    • Wouter Steyaert,
    • Lydia Sagath,
    • German Demidov,
    • Vicente A. Yépez,
    • Anna Esteve-Codina,
    • Julien Gagneur,
    • Kornelia Ellwanger,
    • Ronny Derks,
    • Marjan Weiss,
    • Amber den Ouden,
    • Simone van den Heuvel,
    • Hilde Swinkels,
    • Nick Zomer,
    • Marloes Steehouwer,
    • Luke O'Gorman,
    • Galuh Astuti,
    • Kornelia Neveling,
    • Rebecca Schüle,
    • Jishu Xu,
    • Matthis Synofzik,
    • Danique Beijer,
    • Holger Hengel,
    • Ludger Schöls,
    • Kristl G. Claeys,
    • Jonathan Baets,
    • Liedewei Van de Vondel,
    • Alessandra Ferlini,
    • Rita Selvatici,
    • Heba Morsy,
    • Marwa Saeed Abd Elmaksoud,
    • Volker Straub,
    • Juliane Müller,
    • Veronica Pini,
    • Luke Perry,
    • Anna Sarkozy,
    • Irina Zaharieva,
    • Francesco Muntoni,
    • Enrico Bugiardini,
    • Kiran Polavarapu,
    • Rita Horvath,
    • Evan Reid,
    • Hanns Lochmüller,
    • Marco Spinazzi,
    • Marco Savarese,
    • Solve-RD DITF-ITHACA, Solve-RD DITF-Euro-NMD, Solve-RD DITF-RND, Solve-RD DITF-EpiCARE,
    • Leslie Matalonga,
    • Steven Laurie,
    • Han G. Brunner,
    • Holm Graessner,
    • Sergi Beltran,
    • Stephan Ossowski,
    • Lisenka E.L.M. Vissers,
    • Christian Gilissen,
    • Alexander Hoischen,
    • and on behalf of the Solve-RD consortium
    Genome Res. April 2025 35: 755-768; Published in Advance March 26, 2025, doi:10.1101/gr.279414.124
    OPEN ACCESS ARTICLE

  • A prospective trial comparing programmable targeted long-read sequencing and short-read genome sequencing for genetic diagnosis of cerebellar ataxia

    • Haloom Rafehi,
    • Liam G. Fearnley,
    • Justin Read,
    • Penny Snell,
    • Kayli C. Davies,
    • Liam Scott,
    • Greta Gillies,
    • Genevieve C. Thompson,
    • Tess A. Field,
    • Aleena Eldo,
    • Simon Bodek,
    • Ernest Butler,
    • Luke Chen,
    • John Drago,
    • Himanshu Goel,
    • Anna Hackett,
    • G. Michael Halmagyi,
    • Andrew Hannaford,
    • Katya Kotschet,
    • Kishore R. Kumar,
    • Smitha Kumble,
    • Matthew Lee-Archer,
    • Abhishek Malhotra,
    • Mark Paine,
    • Michael Poon,
    • Kate Pope,
    • Katrina Reardon,
    • Steven Ring,
    • Anne Ronan,
    • Matthew Silsby,
    • Renee Smyth,
    • Chloe Stutterd,
    • Mathew Wallis,
    • John Waterston,
    • Thomas Wellings,
    • Kirsty West,
    • Christine Wools,
    • Kathy H.C. Wu,
    • David J. Szmulewicz,
    • Martin B. Delatycki,
    • Melanie Bahlo,
    • and Paul J. Lockhart
    Genome Res. April 2025 35: 769-785; Published in Advance February 27, 2025, doi:10.1101/gr.279634.124

  • Multiple paralogs and recombination mechanisms contribute to the high incidence of 22q11.2 deletion syndrome

    • Lisanne Vervoort,
    • Nicolas Dierckxsens,
    • Marta Sousa Santos,
    • Senne Meynants,
    • Erika Souche,
    • Ruben Cools,
    • Tracy Heung,
    • Koen Devriendt,
    • Hilde Peeters,
    • Donna M. McDonald-McGinn,
    • Ann Swillen,
    • Jeroen Breckpot,
    • Beverly S. Emanuel,
    • Hilde Van Esch,
    • Anne S. Bassett,
    • and Joris R. Vermeesch
    Genome Res. April 2025 35: 786-797; Published in Advance November 13, 2024, doi:10.1101/gr.279331.124

  • Optical genome mapping identifies rare structural variants in neural tube defects

    • Nikhil S. Sahajpal,
    • Jane Dean,
    • Benjamin Hilton,
    • Timothy Fee,
    • Cindy Skinner,
    • Alex Hastie,
    • Barbara R. DuPont,
    • Alka Chaubey,
    • Michael J. Friez,
    • and Roger E. Stevenson
    Genome Res. April 2025 35: 798-809; Published in Advance March 19, 2025, doi:10.1101/gr.279318.124
    OPEN ACCESS ARTICLE

  • Optical genome mapping enables accurate testing of large repeat expansions

    • Bart van der Sanden,
    • Kornelia Neveling,
    • Syukri Shukor,
    • Michael D. Gallagher,
    • Joyce Lee,
    • Stephanie L. Burke,
    • Maartje Pennings,
    • Ronald van Beek,
    • Michiel Oorsprong,
    • Ellen Kater-Baats,
    • Eveline Kamping,
    • Alide A. Tieleman,
    • Nicol C. Voermans,
    • Ingrid E. Scheffer,
    • Jozef Gecz,
    • Mark A. Corbett,
    • Lisenka E.L.M. Vissers,
    • Andy Wing Chun Pang,
    • Alex Hastie,
    • Erik-Jan Kamsteeg,
    • and Alexander Hoischen
    Genome Res. April 2025 35: 810-823; Published in Advance March 20, 2025, doi:10.1101/gr.279491.124
    OPEN ACCESS ARTICLE

  • Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres

    • Ursula Oggenfuss,
    • Robert T. Todd,
    • Natthapon Soisangwan,
    • Bailey Kemp,
    • Alison Guyer,
    • Annette Beach,
    • and Anna Selmecki
    Genome Res. April 2025 35: 824-838; Published in Advance October 22, 2024, doi:10.1101/gr.279301.124

Methods

  • Geometric deep learning framework for de novo genome assembly

    • Lovro Vrček,
    • Xavier Bresson,
    • Thomas Laurent,
    • Martin Schmitz,
    • Kenji Kawaguchi,
    • and Mile Šikić
    Genome Res. April 2025 35: 839-849; Published in Advance October 29, 2024, doi:10.1101/gr.279307.124

  • Multisample motif discovery and visualization for tandem repeats

    • Yaran Zhang,
    • Marc Hulsman,
    • Alex Salazar,
    • Niccolò Tesi,
    • Lydian Knoop,
    • Sven van der Lee,
    • Sanduni Wijesekera,
    • Jana Krizova,
    • Erik-Jan Kamsteeg,
    • and Henne Holstege
    Genome Res. April 2025 35: 850-862; Published in Advance November 13, 2024, doi:10.1101/gr.279278.124
    OPEN ACCESS ARTICLE

  • RAmbler resolves complex repeats in human Chromosomes 8, 19, and X

    • Sakshar Chakravarty,
    • Glennis Logsdon,
    • and Stefano Lonardi
    Genome Res. April 2025 35: 863-876; Published in Advance March 4, 2025, doi:10.1101/gr.279308.124
    OPEN ACCESS ARTICLE

  • Enhancing nanopore adaptive sampling for PromethION using readfish at scale

    • Rory Munro,
    • Alexander Payne,
    • Nadine Holmes,
    • Chris Moore,
    • Inswasti Cahyani,
    • and Matthew Loose
    Genome Res. April 2025 35: 877-885; Published in Advance January 30, 2025, doi:10.1101/gr.279329.124
    OPEN ACCESS ARTICLE

  • Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling

    • Li-Ting Chen,
    • Myrthe Jager,
    • Dàmi Rebergen,
    • Geertruid J. Brink,
    • Tom van den Ende,
    • Willem Vanderlinden,
    • Pauline Kolbeck,
    • Marc Pagès-Gallego,
    • Ymke van der Pol,
    • Nicolle Besselink,
    • Norbert Moldovan,
    • Nizar Hami,
    • Wigard P. Kloosterman,
    • Hanneke van Laarhoven,
    • Florent Mouliere,
    • Ronald Zweemer,
    • Jan Lipfert,
    • Sarah Derks,
    • Alessio Marcozzi,
    • and Jeroen de Ridder
    Genome Res. April 2025 35: 886-899; Published in Advance January 13, 2025, doi:10.1101/gr.279144.124
    OPEN ACCESS ARTICLE

  • De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data

    • Arthur Dondi,
    • Nico Borgsmüller,
    • Pedro F. Ferreira,
    • Brian J. Haas,
    • Francis Jacob,
    • Viola Heinzelmann-Schwarz,
    • Tumor Profiler Consortium,
    • and Niko Beerenwinkel
    Genome Res. April 2025 35: 900-913; Published in Advance March 19, 2025, doi:10.1101/gr.279281.124
    OPEN ACCESS ARTICLE

  • Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease

    • Tanner D. Jensen,
    • Bohan Ni,
    • Chloe M. Reuter,
    • John E. Gorzynski,
    • Sarah Fazal,
    • Devon Bonner,
    • Rachel A. Ungar,
    • Pagé C. Goddard,
    • Archana Raja,
    • Euan A. Ashley,
    • Jonathan A. Bernstein,
    • Stephan Zuchner,
    • Undiagnosed Diseases Network,
    • Michael D. Greicius,
    • Stephen B. Montgomery,
    • Michael C. Schatz,
    • Matthew T. Wheeler,
    • and Alexis Battle
    Genome Res. April 2025 35: 914-928; Published in Advance March 20, 2025, doi:10.1101/gr.279323.124
    OPEN ACCESS ARTICLE

  • De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies

    • John Beaulaurier,
    • Lynn Ly,
    • J. Andrew Duty,
    • Carly Tyer,
    • Christian Stevens,
    • Chuan-Tien Hung,
    • Akash Sookdeo,
    • Alex W. Drong,
    • Shreyas Kowdle,
    • Axel Guzman-Solis,
    • Domenico Tortorella,
    • Daniel J. Turner,
    • Sissel Juul,
    • Scott Hickey,
    • and Benhur Lee
    Genome Res. April 2025 35: 929-941; Published in Advance March 21, 2025, doi:10.1101/gr.279392.124
    OPEN ACCESS ARTICLE

  • Single-cell Rapid Capture Hybridization sequencing reliably detects isoform usage and coding mutations in targeted genes

    • Hongke Peng,
    • Jafar S. Jabbari,
    • Luyi Tian,
    • Changqing Wang,
    • Yupei You,
    • Chong Chyn Chua,
    • Natasha S. Anstee,
    • Noorul Amin,
    • Andrew H. Wei,
    • Nadia M. Davidson,
    • Andrew W. Roberts,
    • David C.S. Huang,
    • Matthew E. Ritchie,
    • and Rachel Thijssen
    Genome Res. April 2025 35: 942-955; Published in Advance January 10, 2025, doi:10.1101/gr.279322.124
    OPEN ACCESS ARTICLE

  • Rapid and accurate demultiplexing of direct RNA nanopore sequencing data with SeqTagger

    • Leszek P. Pryszcz,
    • Gregor Diensthuber,
    • Laia Llovera,
    • Rebeca Medina,
    • Anna Delgado-Tejedor,
    • Luca Cozzuto,
    • Julia Ponomarenko,
    • and Eva Maria Novoa
    Genome Res. April 2025 35: 956-966; Published in Advance January 29, 2025, doi:10.1101/gr.279290.124
    OPEN ACCESS ARTICLE

  • Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution

    • Qian Qin,
    • Victoria Popic,
    • Kirsty Wienand,
    • Houlin Yu,
    • Emily White,
    • Akanksha Khorgade,
    • Asa Shin,
    • Christophe Georgescu,
    • Catarina D. Campbell,
    • Arthur Dondi,
    • Niko Beerenwinkel,
    • Francisca Vazquez,
    • Aziz M. Al'Khafaji,
    • and Brian J. Haas
    Genome Res. April 2025 35: 967-986; Published in Advance March 14, 2025, doi:10.1101/gr.279200.124
    OPEN ACCESS ARTICLE

  • Quality assessment of long read data in multisample lrRNA-seq experiments using SQANTI-reads

    • Netanya Keil,
    • Carolina Monzó,
    • Lauren McIntyre,
    • and Ana Conesa
    Genome Res. April 2025 35: 987-998; Published in Advance March 3, 2025, doi:10.1101/gr.280021.124

  • Long-read RNA sequencing reveals allele-specific N6-methyladenosine modifications

    • Dayea Park and
    • Can Cenik
    Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124

  • Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity

    • Mayank Murali,
    • Jamie Saquing,
    • Senbao Lu,
    • Ziyang Gao,
    • Emily F. Watts,
    • Ben Jordan,
    • Zachary Peters Wakefield,
    • Ana Fiszbein,
    • David R. Cooper,
    • Peter J. Castaldi,
    • Dmitry Korkin,
    • and Gloria M. Sheynkman
    Genome Res. April 2025 35: 1012-1024; Published in Advance March 14, 2025, doi:10.1101/gr.279317.124

  • Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm

    • Samuel T. Horsfield,
    • Basil C.T. Fok,
    • Yuhan Fu,
    • Paul Turner,
    • John A. Lees,
    • and Nicholas J. Croucher
    Genome Res. April 2025 35: 1025-1040; Published in Advance March 4, 2025, doi:10.1101/gr.279435.124
    OPEN ACCESS ARTICLE

  • Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle

    • Sotiria Milia,
    • Alexander S. Leonard,
    • Xena Marie Mapel,
    • Sandra Milena Bernal Ulloa,
    • Cord Drögemüller,
    • and Hubert Pausch
    Genome Res. April 2025 35: 1041-1052; Published in Advance December 18, 2024, doi:10.1101/gr.279064.124

  • Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq

    • Alejandro Paniagua,
    • Cristina Agustín-García,
    • Francisco J. Pardo-Palacios,
    • Thomas Brown,
    • Maite De Maria,
    • Nancy D. Denslow,
    • Camila J. Mazzoni,
    • and Ana Conesa
    Genome Res. April 2025 35: 1053-1064; Published in Advance December 23, 2024, doi:10.1101/gr.279864.124
    OPEN ACCESS ARTICLE

This Issue

April 2025; 35 (4)
Cover
  1. Editorial
  2. Mini-Reviews
  3. Perspectives
  4. Research
  5. Methods

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