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Research

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
Method

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
Resource

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
Method

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
Method

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
Research

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
Research

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
Research

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
Method

N6-methyladenosine modifications" > Long-read RNA sequencing reveals allele-specific N6-methyladenosine modifications

  • Dayea Park
  • Can Cenik
  • First Published October 29, 2024
Method

Geometric deep learning framework for de novo genome assembly

  • Lovro Vrček
  • Xavier Bresson
  • Thomas Laurent
  • Martin Schmitz
  • Kenji Kawaguchi
  • Mile Šikić
  • First Published October 29, 2024
Mini-Review

The chromatin tapestry as a framework for neurodevelopment

  • Ben Nolan
  • Timothy E. Reznicek
  • Christopher T. Cummings
  • M. Jordan Rowley
  • First Published October 29, 2024
Method

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
Resource

Generation and analysis of a mouse multitissue genome annotation atlas

  • Matthew Adams
  • Christopher Vollmers
  • First Published October 23, 2024
Method

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
Research

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
Research

Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events" > 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
Resource

Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships" > Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships

  • Michelle Kudron
  • Louis Gevirtzman
  • Alec Victorsen
  • Bridget C. Lear
  • Jiahao Gao
  • Jinrui Xu Swapna Samanta Emily Frink Adri Tran-Pearson Chau Huynh Dionne Vafeados Ann Hammonds William Fisher Martha Wall Greg Wesseling Vanessa Hernandez Zhichun Lin Mary Kasparian Kevin White Ravi Allada Mark Gerstein
  • ... [+16 authors] ...,
  • LaDeana Hillier
  • Susan E. Celniker
  • Valerie Reinke
  • Robert H. Waterston
  • First Published October 22, 2024
Research

Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres" > 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
  • Anna Selmecki
  • First Published October 22, 2024
Method

Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR

  • Artem Mikelov
  • George Nefediev
  • Alexander Tashkeev
  • Oscar L. Rodriguez
  • Diego Aguilar Ortmans
  • Valeriia Skatova Mark Izraelson Alexey N. Davydov Stanislav Poslavsky Souad Rahmouni
  • ... [+5 authors] ...,
  • Corey T. Watson
  • Dmitriy Chudakov
  • Scott D. Boyd
  • Dmitry Bolotin
  • First Published October 21, 2024
Method

Inferring ancestry with the hierarchical soft clustering approach tangleGen

  • Klara Elisabeth Burger
  • Solveig Klepper
  • Ulrike von Luxburg
  • Franz Baumdicker
  • First Published October 21, 2024
Research

Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development

  • Song Zhang
  • Chao Wang
  • Shenghua Qin
  • Choulin Chen
  • Yongzhou Bao
  • Yuanyuan Zhang Lingna Xu Qingyou Liu
  • ... [+3 authors] ...,
  • Yunxiang Zhao
  • Kui Li
  • Zhonglin Tang
  • Yuwen Liu
  • First Published October 21, 2024
Research

Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer

  • Yueqiang Song
  • Fuyuan Li
  • Shangzi Wang
  • Yuntong Wang
  • Cong Lai
  • Lian Chen Ning Jiang
  • ... [+2 authors] ...,
  • Jin Li
  • Xingdong Chen
  • Swneke D. Bailey
  • Xiaoyang Zhang
  • First Published October 18, 2024
Resource

Dynamic dysregulation of retrotransposons in neurodegenerative diseases at the single-cell level

  • Wankun Deng
  • Citu Citu
  • Andi Liu
  • Zhongming Zhao
  • First Published October 18, 2024
Research

De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes

  • Basanta Bista
  • Laura González-Rodelas
  • Lucía Álvarez-González
  • Zhi-qiang Wu
  • Eugenia E. Montiel
  • Ling Sze Lee Daleen B. Badenhorst Srihari Radhakrishnan Robert Literman Beatriz Navarro-Dominguez John B. Iverson
  • ... [+6 authors] ...,
  • Simon Orozco-Arias
  • Josefa González
  • Aurora Ruiz-Herrera
  • Nicole Valenzuela
  • First Published October 16, 2024
Method

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
Method

Telomere-to-telomere assembly by preserving contained reads

  • Sudhanva Shyam Kamath
  • Mehak Bindra
  • Debnath Pal
  • Chirag Jain
  • First Published October 15, 2024
Research

Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements

  • Luis E. Valentin-Alvarado
  • Ling-Dong Shi
  • Kathryn E. Appler
  • Alexander Crits-Christoph
  • Valerie De Anda
  • Benjamin A. Adler Michael L. Cui Lynn Ly Pedro Leão Richard J. Roberts
  • ... [+5 authors] ...,
  • Rohan Sachdeva
  • Brett J. Baker
  • David F. Savage
  • Jillian F. Banfield
  • First Published October 15, 2024
Method

Theoretical framework for the difference of two negative binomial distributions and its application in comparative analysis of sequencing data

  • Alicia Petrany
  • Ruoyu Chen
  • Shaoqiang Zhang
  • Yong Chen
  • First Published October 15, 2024
Research

Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries

  • Shaoqiang Hu
  • Xiangguo Zeng
  • Yuguo Liu
  • Yongping Li
  • Minghao Qu
  • Wen-Biao Jiao
  • Yongchao Han
  • Chunying Kang
  • First Published October 15, 2024
Resource

PWAS Hub for exploring gene-based associations of common complex diseases

  • Guy Kelman
  • Roei Zucker
  • Nadav Brandes
  • Michal Linial
  • First Published October 15, 2024
Method

otter" > 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
Method

k-mer analysis" > Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis

  • Romain Derelle
  • Johanna von Wachsmann
  • Tommi Mäklin
  • Joel Hellewell
  • Timothy Russell
  • Ajit Lalvani
  • ... [+1 authors] ...,
  • Leonid Chindelevitch
  • Nicholas J. Croucher
  • Simon R. Harris
  • John A. Lees
  • First Published October 15, 2024
Editorial

Innovations in computational biology: RECOMB 2024 Special Issue

  • Jian Ma
  • Bonnie Berger
  • First Published October 11, 2024
Research

blaKPC" > 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
Method

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
Resource

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
Method

Genetics-driven risk predictions leveraging the Mendelian randomization framework

  • Daniel Sens
  • Liubov Shilova
  • Ludwig Gräf
  • Maria Grebenshchikova
  • Bjoern M. Eskofier
  • Francesco Paolo Casale
  • First Published September 27, 2024
Research

Targeted and complete genomic sequencing of the major histocompatibility complex in haplotypic form of individual heterozygous samples

  • Taishan Hu
  • Timothy L. Mosbruger
  • Nikolaos G. Tairis
  • Amalia Dinou
  • Pushkala Jayaraman
  • Mahdi Sarmady Kingham Brewster
  • ... [+2 authors] ...,
  • Yang Li
  • Tristan J. Hayeck
  • Jamie L. Duke
  • Dimitri S. Monos
  • First Published September 26, 2024
Research

Evolutionary dynamics of polyadenylation signals and their recognition strategies in protists

  • Marcin P. Sajek
  • Danielle Y. Bilodeau
  • Michael A. Beer
  • Emma Horton
  • Yukiko Miyamoto
  • Katrina B. Velle
  • ... [+1 authors] ...,
  • Lars Eckmann
  • Lillian Fritz-Laylin
  • Olivia S. Rissland
  • Neelanjan Mukherjee
  • First Published September 26, 2024
Method

Designing realistic regulatory DNA with autoregressive language models

  • Avantika Lal
  • David Garfield
  • Tommaso Biancalani
  • Gokcen Eraslan
  • First Published September 25, 2024
Research

AGAP duplicons associate with structural diversity at Chromosome 10q11.22" > AGAP duplicons associate with structural diversity at Chromosome 10q11.22

  • Stefania Fornezza
  • Vincenza Simona Delvecchio
  • William T. Harvey
  • Philip C. Dishuck
  • Evan E. Eichler
  • Giuliana Giannuzzi
  • First Published September 25, 2024
Method

Contrasting and combining transcriptome complexity captured by short and long RNA sequencing reads

  • Seong Woo Han
  • San Jewell
  • Andrei Thomas-Tikhonenko
  • Yoseph Barash
  • First Published September 25, 2024
Method

Rapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change

  • Apurva Narechania
  • Dean Bobo
  • Kevin Deitz
  • Rob DeSalle
  • Paul J. Planet
  • Barun Mathema
  • First Published September 25, 2024
Method

Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories

  • Borislav Hrisimirov Hristov
  • William Stafford Noble
  • Alessandro Bertero
  • First Published September 25, 2024
Research

CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain" > Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain

  • James L. Shepherdson
  • David M. Granas
  • Jie Li
  • Zara Shariff
  • Stephen P. Plassmeyer
  • Alex S. Holehouse
  • Michael A. White
  • Barak A. Cohen
  • First Published September 25, 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
Resource

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
Resource

Saccharomyces bayanus genome divergence after hybridization" > 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
Research

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
Method

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
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