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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
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
Research

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

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

  • Sens Daniel
  • Shilova Liubov
  • Gräf Ludwig
  • Grebenshchikova Maria
  • Eskofier Bjoern M.
  • Casale Francesco Paolo
  • 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
Research

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
Resource

Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize

  • Laura E. Tibbs-Cortes
  • Tingting Guo
  • Carson M. Andorf
  • Xianran Li
  • Jianming Yu
  • First Published September 13, 2024
Research

SF3B1 mutations" > 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
Research

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
Method

A novel approach for in vivo DNA footprinting using short double-stranded cell-free DNA from plasma

  • Jan Müller
  • Christina Hartwig
  • Mirko Sonntag
  • Lisa Bitzer
  • Christopher Adelmann
  • Yevhen Vainshtein Karolina Glanz Sebastian O. Decker
  • ... [+3 authors] ...,
  • Thorsten Brenner
  • Georg F. Weber
  • Arndt von Haeseler
  • Kai Sohn
  • First Published September 13, 2024
Research

Evidence for compensatory evolution within pleiotropic regulatory elements

  • Zane Kliesmete
  • Peter Orchard
  • Victor Yan Kin Lee
  • Johanna Geuder
  • Simon M. Krauß
  • Mari Ohnuki
  • ... [+1 authors] ...,
  • Jessica Jocher
  • Beate Vieth
  • Wolfgang Enard
  • Ines Hellmann
  • First Published September 10, 2024
Method

Genetic complexity of killer-cell immunoglobulin-like receptor genes in human pangenome assemblies

  • Tsung-Kai Hung
  • Wan-Chi Liu
  • Sheng-Kai Lai
  • Hui-Wen Chuang
  • Yi-Che Lee
  • Hong-Ye Lin Chia-Lang Hsu
  • ... [+2 authors] ...,
  • Chien-Yu Chen
  • Ya-Chien Yang
  • Jacob Shujui Hsu
  • Pei-Lung Chen
  • First Published September 9, 2024
Research

Differences in activity and stability drive transposable element variation in tropical and temperate maize

  • Shujun Ou
  • Armin Scheben
  • Tyler Collins
  • Yinjie Qiu
  • Arun S. Seetharam
  • Claire C. Menard Nancy Manchanda Jonathan I. Gent
  • ... [+3 authors] ...,
  • Michael C. Schatz
  • Sarah N. Anderson
  • Matthew B. Hufford
  • Candice N. Hirsch
  • First Published September 9, 2024
Method

Privacy-preserving biological age prediction over federated human methylation data using fully homomorphic encryption

  • Meir Goldenberg
  • Loay Mualem
  • Amit Shahar
  • Sagi Snir
  • Adi Akavia
  • First Published September 5, 2024
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