Volume 35, Issue 4 | April 2025

Editorial
- - Long reads decipher genomes and transcriptomes and offer novel insights into biology and diseases
    Ana Conesa
    Alexander Hoischen
    Fritz J. Sedlazeck
    First Published April 14, 2025
Mini-Reviews
- - A Hitchhiker's Guide to long-read genomic analysis
    Medhat Mahmoud
    Daniel P. Agustinho
    Fritz J. Sedlazeck
    First Published April 14, 2025
  - The additional diagnostic yield of long-read sequencing in undiagnosed rare diseases
    Giulia F. Del Gobbo
    Kym M. Boycott
    First Published February 3, 2025
  - Evolution of genome-wide methylation profiling technologies
    Carolina Montano
    Winston Timp
    First Published April 14, 2025
Perspectives
- - Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
    Carolina Monzó
    Adam Frankish
    Ana Conesa
    First Published March 3, 2025
  - The impact of long-read sequencing on human population-scale genomics
    Tobias Rausch
    Tobias Marschall
    Jan O. Korbel
    First Published April 14, 2025
  - 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
    ...[+1 authors]...,
    Alison P. Klein
    Justin M. Zook
    Mikhail Kolmogorov
    Michael C. Schatz
    First Published March 20, 2025
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
    First Published March 17, 2025
  - 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
    ...[+2 authors]...,
    Benedict Paten
    Kimberley J. Billingsley
    Cornelis Blauwendraat
    Miten Jain
    First Published March 7, 2025
  - Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA
    Cristian Groza
    Bing Ge
    Warren A. Cheung
    Tomi Pastinen
    Guillaume Bourque
    First Published March 20, 2025
  - 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
    ...[+18 authors]...,
    Inanc Birol
    Steven J.M. Jones
    Janet S. Rader
    Marco A. Marra
    First Published December 5, 2024
  - 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
    First Published March 4, 2025
  - 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
    First Published February 18, 2025
  - 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
    ...[+3 authors]...,
    Hubert Rehrauer
    Christian von Mering
    Holger Moch
    Abdullah Kahraman
    First Published March 19, 2025
  - Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing
    Karine Choquet
    Louis-Philippe Chaumont
    Simon Bache
    Autum R. Baxter-Koenigs
    L. Stirling Churchman
    First Published February 14, 2025
  - 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
    ...[+11 authors]...,
    Frans P.M. Cremers
    Peter A.C. ‘t Hoen
    Erwin van Wijk
    Erik de Vrieze
    First Published March 4, 2025
  - 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
    First Published March 6, 2025
  - 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 Leslie Matalonga Steven Laurie Han G. Brunner Holm Graessner Sergi Beltran
    ...[+44 authors]...,
    Stephan Ossowski
    Lisenka E.L.M. Vissers
    Christian Gilissen
    Alexander Hoischen
    First Published March 26, 2025
  - 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
    ...[+33 authors]...,
    David J. Szmulewicz
    Martin B. Delatycki
    Melanie Bahlo
    Paul J. Lockhart
    First Published February 27, 2025
  - 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
    ...[+7 authors]...,
    Beverly S. Emanuel
    Hilde Van Esch
    Anne S. Bassett
    Joris R. Vermeesch
    First Published November 13, 2024
  - Optical genome mapping identifies rare structural variants in neural tube defects
    Nikhil S. Sahajpal
    Jane Dean
    Benjamin Hilton
    Timothy Fee
    Cindy Skinner
    Alex Hastie
    ...[+1 authors]...,
    Barbara R. DuPont
    Alka Chaubey
    Michael J. Friez
    Roger E. Stevenson
    First Published March 19, 2025
  - 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
    ...[+12 authors]...,
    Andy Wing Chun Pang
    Alex Hastie
    Erik-Jan Kamsteeg
    Alexander Hoischen
    First Published March 20, 2025
  - 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
    First Published October 22, 2024
Methods
- - Geometric deep learning framework for de novo genome assembly
    Lovro Vrček
    Xavier Bresson
    Thomas Laurent
    Martin Schmitz
    Kenji Kawaguchi
    First Published October 29, 2024
  - Multisample motif discovery and visualization for tandem repeats
    Yaran Zhang
    Marc Hulsman
    Alex Salazar
    Niccolò Tesi
    Lydian Knoop
    Sven van der Lee
    ...[+1 authors]...,
    Sanduni Wijesekera
    Jana Krizova
    Erik-Jan Kamsteeg
    Henne Holstege
    First Published November 13, 2024
  - RAmbler resolves complex repeats in human Chromosomes 8, 19, and X
    Sakshar Chakravarty
    Glennis Logsdon
    Stefano Lonardi
    First Published March 4, 2025
  - Enhancing nanopore adaptive sampling for PromethION using readfish at scale
    Rory Munro
    Alexander Payne
    Nadine Holmes
    Chris Moore
    Inswasti Cahyani
    First Published January 30, 2025
  - 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
    ...[+11 authors]...,
    Jan Lipfert
    Sarah Derks
    Alessio Marcozzi
    Jeroen de Ridder
    First Published January 13, 2025
  - 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
    First Published March 19, 2025
  - 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 Michael D. Greicius
    ...[+8 authors]...,
    Stephen B. Montgomery
    Michael C. Schatz
    Matthew T. Wheeler
    Alexis Battle
    First Published March 20, 2025
  - 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
    ...[+6 authors]...,
    Daniel J. Turner
    Sissel Juul
    Scott Hickey
    Benhur Lee
    First Published March 21, 2025
  - 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
    ...[+5 authors]...,
    Andrew W. Roberts
    David C.S. Huang
    Matthew E. Ritchie
    Rachel Thijssen
    First Published January 10, 2025
  - Rapid and accurate demultiplexing of direct RNA nanopore sequencing data with SeqTagger
    Leszek P. Pryszcz
    Gregor Diensthuber
    Laia Llovera
    Rebeca Medina
    Anna Delgado-Tejedor
    First Published January 29, 2025
  - 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
    ...[+5 authors]...,
    Niko Beerenwinkel
    Francisca Vazquez
    Aziz M. Al'Khafaji
    Brian J. Haas
    First Published March 14, 2025
  - Quality assessment of long read data in multisample lrRNA-seq experiments using SQANTI-reads
    Netanya Keil
    Carolina Monzó
    Lauren McIntyre
    Ana Conesa
    First Published March 3, 2025
  - Long-read RNA sequencing reveals allele-specific N6-methyladenosine modifications
    Dayea Park
    Can Cenik
    First Published October 29, 2024
  - 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
    ...[+3 authors]...,
    David R. Cooper
    Peter J. Castaldi
    Dmitry Korkin
    Gloria M. Sheynkman
    First Published March 14, 2025
  - 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
    First Published March 4, 2025
  - 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
    First Published December 18, 2024
  - 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
    First Published December 23, 2024

Table of Contents

Volume 35, Issue 4 | April 2025

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Editorial

Mini-Reviews

Perspectives

Research

Methods