Volume 34, Issue 11 | November 2024

Editorial
- - Revolutionizing genomics and medicine—one long molecule at a time
    Ana Conesa
    Alexander Hoischen
    Fritz J. Sedlazeck
    First Published November 20, 2024
Reviews
- - Leveraging the power of long reads for targeted sequencing
    Shruti V. Iyer
    Sara Goodwin
    William Richard McCombie
    First Published November 20, 2024
  - Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
    Ezequiel Calvo-Roitberg
    Rachel F. Daniels
    Athma A. Pai
    First Published November 20, 2024
  - Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics
    Natan Belchikov
    Justine Hsu
    Xiang Jennie Li
    Julien Jarroux
    Wen Hu
    Anoushka Joglekar
    Hagen U. Tilgner
    First Published November 20, 2024
Research
- - Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders
    Susan M. Hiatt
    James M.J. Lawlor
    Lori H. Handley
    Donald R. Latner
    Zachary T. Bonnstetter
    Candice R. Finnila Michelle L. Thompson Lori Beth Boston Melissa Williams Ivan Rodriguez Nunez Jerry Jenkins Whitley V. Kelley E. Martina Bebin Michael A. Lopez Anna C.E. Hurst
    ...[+10 authors]...,
    Bruce R. Korf
    Jeremy Schmutz
    Jane Grimwood
    Gregory M. Cooper
    First Published September 19, 2024
  - Resolving complex duplication variants in autism spectrum disorder using long-read genome sequencing
    Jesper Eisfeldt
    Edward J. Higginbotham
    Felix Lenner
    Jennifer Howe
    Bridget A. Fernandez
    Anna Lindstrand
    Stephen W. Scherer
    Lars Feuk
    First Published October 29, 2024
  - A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities
    Jesper Eisfeldt
    Adam Ameur
    Felix Lenner
    Esmee Ten Berk de Boer
    Marlene Ek
    Josephine Wincent Raquel Vaz Jesper Ottosson Tord Jonson Sofie Ivarsson Sofia Thunström Alexandra Topa Simon Stenberg Anna Rohlin Anna Sandestig Margareta Nordling Pia Palmebäck Magnus Burstedt Frida Nordin Eva-Lena Stattin Maria Sobol Panagiotis Baliakas Marie-Louise Bondeson Ida Höijer Kristine Bilgrav Saether Lovisa Lovmar
    ...[+21 authors]...,
    Hans Ehrencrona
    Malin Melin
    Lars Feuk
    Anna Lindstrand
    First Published October 29, 2024
  - Leveraging the T2T assembly to resolve rare and pathogenic inversions in reference genome gaps
    Kristine Bilgrav Saether
    Jesper Eisfeldt
    Jesse D. Bengtsson
    Ming Yin Lun
    Christopher M. Grochowski
    Medhat Mahmoud Hsiao-Tuan Chao Jill A. Rosenfeld Pengfei Liu Marlene Ek Jakob Schuy Adam Ameur Hongzheng Dai James Paul Hwang Fritz J. Sedlazeck Weimin Bi Ronit Marom
    ...[+12 authors]...,
    Josephine Wincent
    Ann Nordgren
    Claudia M.B. Carvalho
    Anna Lindstrand
    First Published November 1, 2024
  - Independent expansion, selection, and hypervariability of the TBC1D3 gene family in humans
    Xavi Guitart
    David Porubsky
    DongAhn Yoo
    Max L. Dougherty
    Philip C. Dishuck
    Katherine M. Munson Alexandra P. Lewis Kendra Hoekzema
    ...[+3 authors]...,
    Jordan Knuth
    Stephen Chang
    Tomi Pastinen
    Evan E. Eichler
    First Published August 6, 2024
  - Unraveling the architecture of major histocompatibility complex class II haplotypes in rhesus macaques
    Nanine de Groot
    Marit van der Wiel
    Ngoc Giang Le
    Natasja G. de Groot
    Jesse Bruijnesteijn
    Ronald E. Bontrop
    First Published October 23, 2024
  - Long-read DNA and cDNA sequencing identify cancer-predisposing deep intronic variation in tumor-suppressor genes
    Gulsuner Suleyman
    AbuRayyan Amal
    Mandell Jessica B.
    Lee Ming K.
    Bernier Greta V.
    Norquist Barbara M.
    Pierce Sarah B.
    King Mary-Claire
    Walsh Tom
    First Published September 13, 2024
  - Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations
    Alicja Pacholewska
    Matthias Lienhard
    Mirko Brüggemann
    Heike Hänel
    Lorina Bilalli
    Anja Königs Felix Heß Kerstin Becker Karl Köhrer Jesko Kaiser Holger Gohlke Norbert Gattermann Michael Hallek Carmen D. Herling Julian König
    ...[+10 authors]...,
    Christina Grimm
    Ralf Herwig
    Kathi Zarnack
    Michal R. Schweiger
    First Published September 13, 2024
  - Long-read RNA sequencing of archival tissues reveals novel genes and transcripts associated with clear cell renal cell carcinoma recurrence and immune evasion
    Joshua Lee
    Elizabeth A. Snell
    Joanne Brown
    Charlotte E. Booth
    Rosamonde E. Banks
    Daniel J. Turner
    Naveen S. Vasudev
    Dimitris Lagos
    First Published September 16, 2024
  - Enhanced detection of RNA modifications and read mapping with high-accuracy nanopore RNA basecalling models
    Gregor Diensthuber
    Leszek P. Pryszcz
    Laia Llovera
    Morghan C. Lucas
    Anna Delgado-Tejedor
    Sonia Cruciani
    Jean-Yves Roignant
    Oguzhan Begik
    Eva Maria Novoa
    First Published September 13, 2024
  - Long-read genome assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events
    Marin Volarić
    Evelin Despot-Slade
    Damira Veseljak
    Brankica Mravinac
    Nevenka Meštrović
    First Published October 22, 2024
  - Genomic epidemiology of carbapenem-resistant Enterobacterales at a New York City hospital over a 10-year period reveals complex plasmid-clone dynamics and evidence for frequent horizontal transfer of blaKPC
    Angela Gomez-Simmonds
    Medini K. Annavajhala
    Dwayne Seeram
    Todd W. Hokunson
    Heekuk Park
    Anne-Catrin Uhlemann
    First Published October 4, 2024
Methods
- - Telomere-to-telomere assembly by preserving contained reads
    Sudhanva Shyam Kamath
    Mehak Bindra
    Debnath Pal
    Chirag Jain
    First Published October 15, 2024
  - Gapless assembly of complete human and plant chromosomes using only nanopore sequencing
    Sergey Koren
    Zhigui Bao
    Andrea Guarracino
    Shujun Ou
    Sara Goodwin
    Katharine M. Jenike Julian Lucas Brandy McNulty Jimin Park Mikko Rautiainen Arang Rhie Dick Roelofs Harrie Schneiders Ilse Vrijenhoek Koen Nijbroek Olle Nordesjo Sergey Nurk Mike Vella Katherine R. Lawrence Doreen Ware Michael C. Schatz Erik Garrison Sanwen Huang
    ...[+18 authors]...,
    William Richard McCombie
    Karen H. Miga
    Alexander H.J. Wittenberg
    Adam M. Phillippy
    First Published November 6, 2024
  - Full-resolution HLA and KIR gene annotations for human genome assemblies
    Ying Zhou
    Li Song
    Heng Li
    First Published June 5, 2024
  - Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT and otter
    Niccoló Tesi
    Alex Salazar
    Yaran Zhang
    Sven van der Lee
    Marc Hulsman
    Lydian Knoop Sanduni Wijesekera Jana Krizova Anne-Fleur Schneider Maartje Pennings
    ...[+5 authors]...,
    Kristel Sleegers
    Erik-Jan Kamsteeg
    Marcel Reinders
    Henne Holstege
    First Published October 15, 2024
  - Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing
    Sena A. Gocuk
    James Lancaster
    Shian Su
    Jasleen K. Jolly
    Thomas L. Edwards
    Doron G. Hickey
    ...[+1 authors]...,
    Matthew E. Ritchie
    Marnie E. Blewitt
    Lauren N. Ayton
    Quentin Gouil
    First Published September 16, 2024
  - An optimized protocol for quality control of gene therapy vectors using nanopore direct RNA sequencing
    Kathleen Zeglinski
    Christian Montellese
    Matthew E. Ritchie
    Monther Alhamdoosh
    Cédric Vonarburg
    Rory Bowden
    ...[+1 authors]...,
    Monika Jordi
    Quentin Gouil
    Florian Aeschimann
    Arthur Hsu
    First Published October 28, 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
    ...[+6 authors]...,
    Dale Whittington
    William Stafford Noble
    Andrew B. Stergachis
    Mitchell R. Vollger
    First Published June 7, 2024
  - Detecting m6A RNA modification from nanopore sequencing using a semisupervised learning framework
    Haotian Teng
    Marcus Stoiber
    Ziv Bar-Joseph
    Carl Kingsford
    First Published October 15, 2024
  - Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation
    Alexander J. Ritter
    Jolene M. Draper
    Christopher Vollmers
    Jeremy R. Sanford
    First Published June 5, 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
    Cathy J. Zhou
    Jason G. Underwood
    Gene W. Yeo
    First Published June 21, 2024
  - Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications
    Xudong Liu
    Ying Ni
    Lianwei Ye
    Zhihao Guo
    Lu Tan
    Jun Li
    Mengsu Yang
    Sheng Chen
    Runsheng Li
    First Published October 2, 2024
  - Accurate bacterial outbreak tracing with Oxford Nanopore sequencing and reduction of methylation-induced errors
    Mara Lohde
    Gabriel E. Wagner
    Johanna Dabernig-Heinz
    Adrian Viehweger
    Sascha D. Braun
    Stefan Monecke Celia Diezel Claudia Stein
    ...[+3 authors]...,
    Mike Marquet
    Ralf Ehricht
    Mathias W. Pletz
    Christian Brandt
    First Published October 23, 2024
  - Factors impacting target-enriched long-read sequencing of resistomes and mobilomes
    Ilya B. Slizovskiy
    Nathalie Bonin
    Jonathan E. Bravo
    Peter M. Ferm
    Jacob Singer
    Christina Boucher
    Noelle R. Noyes
    First Published November 5, 2024
Resources
- - High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation
    Jonas A. Gustafson
    Sophia B. Gibson
    Nikhita Damaraju
    Miranda P.G. Zalusky
    Kendra Hoekzema
    David Twesigomwe Lei Yang Anthony A. Snead Phillip A. Richmond Wouter De Coster Nathan D. Olson Andrea Guarracino Qiuhui Li Angela L. Miller Joy Goffena Zachary B. Anderson Sophie H.R. Storz Sydney A. Ward Maisha Sinha Claudia Gonzaga-Jauregui Wayne E. Clarke Anna O. Basile André Corvelo Catherine Reeves Adrienne Helland Rajeeva Lochan Musunuri Mahler Revsine Karynne E. Patterson Cate R. Paschal Christina Zakarian Sara Goodwin Tanner D. Jensen Esther Robb William Richard McCombie Fritz J. Sedlazeck Justin M. Zook Stephen B. Montgomery Erik Garrison Mikhail Kolmogorov Michael C. Schatz Richard N. McLaughlin Harriet Dashnow Michael C. Zody
    ...[+38 authors]...,
    Matt Loose
    Miten Jain
    Evan E. Eichler
    Danny E. Miller
    First Published October 2, 2024
  - Visualization and analysis of medically relevant tandem repeats in nanopore sequencing of control cohorts with pathSTR
    Wouter De Coster
    Ida Höijer
    Inge Bruggeman
    Svenn D'Hert
    Malin Melin
    Adam Ameur
    Rosa Rademakers
    First Published August 15, 2024
  - Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding
    Kai Li
    Melissa L. Smith
    J. Chris Blazier
    Kelli J. Kochan
    Jonathan M.D. Wood
    Kerstin Howe Anne E. Kwitek Melinda R. Dwinell Hao Chen Julia L. Ciosek
    ...[+5 authors]...,
    Patrick Masterson
    Terence D. Murphy
    Theodore S. Kalbfleisch
    Peter A. Doris
    First Published November 8, 2024
  - Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe
    Paige A. Byerly
    Alina von Thaden
    Evgeny Leushkin
    Leon Hilgers
    Shenglin Liu
    Sven Winter Tilman Schell Charlotte Gerheim Alexander Ben Hamadou Carola Greve Christian Betz Hanno J. Bolz Sven Büchner Johannes Lang Holger Meinig Evax Marie Famira-Parcsetich Sarah P. Stubbe Alice Mouton Sandro Bertolino Goedele Verbeylen Thomas Briner Lídia Freixas
    ...[+17 authors]...,
    Lorenzo Vinciguerra
    Sarah A. Mueller
    Carsten Nowak
    Michael Hiller
    First Published November 14, 2024
  - Generation and analysis of a mouse multitissue genome annotation atlas
    Matthew Adams
    Christopher Vollmers
    First Published October 23, 2024
  - Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations
    Wenyu Zhang
    Anja Guenther
    Yuanxiao Gao
    Kristian Ullrich
    Bruno Huettel
    Aftab Ahmad
    Lei Duan
    Kaizong Wei
    Diethard Tautz
    First Published September 17, 2024
  - Chromosome-level subgenome-aware de novo assembly provides insight into Saccharomyces bayanus genome divergence after hybridization
    Cory Gardner
    Junhao Chen
    Christina Hadfield
    Zhaolian Lu
    David Debruin
    Yu Zhan
    Maureen J. Donlin
    Tae-Hyuk Ahn
    Zhenguo Lin
    First Published September 17, 2024

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Table of Contents

Volume 34, Issue 11 | November 2024

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Editorial

Reviews

Research

Methods

Resources