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Review

k-mer approaches for biodiversity genomics" > k-mer approaches for biodiversity genomics

Katharine M. Jenike
Lucía Campos-Domínguez
Marilou Boddé
José Cerca
Christina N. Hodson
Michael C. Schatz
Kamil S. Jaron

First Published January 31, 2025

Method

Enhancing nanopore adaptive sampling for PromethION using readfish at scale

Rory Munro
Alexander Payne
Nadine Holmes
Chris Moore
Inswasti Cahyani
Matthew Loose

First Published January 30, 2025

Method

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
Eva Maria Novoa

First Published January 29, 2025

Review

Artificial intelligence and machine learning in cell-free-DNA-based diagnostics

W.H. Adrian Tsui
Spencer C. Ding
Peiyong Jiang
Y.M. Dennis Lo

First Published January 22, 2025

Resource

Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution

Yujie Chen
Yiran Hou
Qinglin Zeng
Irene Wang
Meiru Shang
Kwangdeok Shin Christopher Hemauer
... [+2 authors] ...,
Xiaoyun Xing
Junsu Kang
Guoyan Zhao
Ting Wang

First Published January 14, 2025

Research

Characterization of the role of spatial proximity of DNA double-strand breaks in the formation of CRISPR-Cas9-induced large structural variations

Mikkel Dahl-Jessen
Thorkild Terkelsen
Rasmus O. Bak
Uffe Birk Jensen

First Published January 13, 2025

Method

Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integration

Zepu Miao
Jia-Xing Yue

First Published January 13, 2025

Method

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

Research

DDX3X and DDX3Y" > Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicases DDX3X and DDX3Y

Shruthi Rengarajan
Jason Derks
Daniel W. Bellott
Nikolai Slavov
David C. Page

First Published January 10, 2025

Research

Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer

Yang Liu
João Botelho
Jaime Iranzo

First Published January 10, 2025

Method

Proxy panels enable privacy-aware outsourcing of genotype imputation

Degui Zhi
Xiaoqian Jiang
Arif Harmanci

First Published January 10, 2025

Method

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

Research

Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths

Fangyuan Yang
Li-Jun Cao
Petr Nguyen
Zhong-Zheng Ma
Jin-Cui Chen
Wei Song
Shu-Jun Wei

First Published January 6, 2025

Research

Drosophila reveal the impact of domain-specific changes in nucleosome repeat length on repair efficiency" > Ultraviolet damage and repair maps in Drosophila reveal the impact of domain-specific changes in nucleosome repeat length on repair efficiency

Benjamin Morledge-Hampton
Kathiresan Selvam
Manish Chauhan
Alan G. Goodman
John J. Wyrick

First Published January 6, 2025

Research

Fusion, fission, and scrambling of the bilaterian genome in Bryozoa

Thomas D. Lewin
Isabel Jiah-Yih Liao
Mu-En Chen
John D.D. Bishop
Peter W.H. Holland
Yi-Jyun Luo

First Published January 6, 2025

Method

Identification of the shortest species-specific oligonucleotide sequences

Ioannis Mouratidis
Maxwell A. Konnaris
Nikol Chantzi
Candace S.Y. Chan
Michail Patsakis
Kimonas Provatas Austin Montgomery Fotis A. Baltoumas Congzhou M. Sha
... [+4 authors] ...,
Manvita Mareboina
Georgios A. Pavlopoulos
Dionysios V. Chartoumpekis
Ilias Georgakopoulos-Soares

First Published January 2, 2025

Method

Combining DNA and protein alignments to improve genome annotation with LiftOn

Kuan-Hao Chao
Jakob M. Heinz
Celine Hoh
Alan Mao
Alaina Shumate
Mihaela Pertea
Steven L. Salzberg

First Published December 27, 2024

Method

Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases

Ming Yan
Thea O. Andersen
Phillip B. Pope
Zhongtang Yu

First Published December 27, 2024

Reviewer Index

Reviewer Index, Volume 34, 2024

First Published December 23, 2024

Research

CRX retinopathy models" > Aberrant homeodomain–DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models

Yiqiao Zheng
Gary D. Stormo
Shiming Chen

First Published December 23, 2024

Method

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
Ana Conesa

First Published December 23, 2024

Method

KIT associated with depigmentation in white-headed cattle" > 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
Hubert Pausch

First Published December 18, 2024

Method

Diffusion-based generation of gene regulatory networks from scRNA-seq data with DigNet

Chuanyuan Wang
Zhi-Ping Liu

First Published December 18, 2024

Method

Resolving the chromatin impact of mosaic variants with targeted Fiber-seq

Stephanie C. Bohaczuk
Zachary J. Amador
Chang Li
Benjamin J. Mallory
Elliott G. Swanson
Jane Ranchalis Mitchell R. Vollger Katherine M. Munson Tom Walsh
... [+4 authors] ...,
Morgan O. Hamm
Yizi Mao
Andre Lieber
Andrew B. Stergachis

First Published December 9, 2024

Method

MCHelper automatically curates transposable element libraries across eukaryotic species

Simon Orozco-Arias
Pío Sierra
Richard Durbin
Josefa González

First Published December 9, 2024

Research

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

Resource

An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes

Chong Li
Marc Jan Bonder
Sabriya Syed
Matthew Jensen
Mark B. Gerstein
Michael C. Zody Mark J.P. Chaisson Michael E. Talkowski Tobias Marschall
... [+4 authors] ...,
Jan O. Korbel
Evan E. Eichler
Charles Lee
Xinghua Shi

First Published December 5, 2024

Research

Arabidopsis thaliana" > Characterization of DNA methylation reader proteins in Arabidopsis thaliana

Jonathan Cahn
James P.B. Lloyd
Ino D. Karemaker
Pascal W.T.C. Jansen
Jahnvi Pflueger
Owen Duncan Jakob Petereit
... [+2 authors] ...,
Ozren Bogdanovic
A. Harvey Millar
Michiel Vermeulen
Ryan Lister

First Published December 4, 2024

Research

Hydra has mammal-like mutation rates facilitating fast adaptation despite its nonaging phenotype" > Hydra has mammal-like mutation rates facilitating fast adaptation despite its nonaging phenotype

Arne Sahm
Konstantin Riege
Marco Groth
Martin Bens
Johann Kraus
Martin Fischer Hans Kestler
... [+2 authors] ...,
Christoph Englert
Ralf Schaible
Matthias Platzer
Steve Hoffmann

First Published December 4, 2024

Method

Structure-optimized sgRNA selection with PlatinumCRISPr for efficient Cas9 generation of knockouts

Irmgard U. Haussmann
Thomas C. Dix
David W.J. McQuarrie
Veronica Dezi
Abdullah I. Hans
Roland Arnold
Matthias Soller

First Published December 3, 2024

Method

Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression

Howard J. Womersley
Daniel Muliaditan
Ramanuj DasGupta
Lih Feng Cheow

First Published December 2, 2024

Method

Inferring disease progression stages in single-cell transcriptomics using a weakly supervised deep learning approach

Fabien Wehbe
Levi Adams
Jordan Babadoudou
Samantha Yuen
Yoon-Seong Kim
Yoshiaki Tanaka

First Published December 2, 2024

Research

The rate and spectrum of new mutations in mice inferred by long-read sequencing

Eugenio López-Cortegano
Jobran Chebib
Anika Jonas
Anastasia Vock
Sven Künzel
Peter D. Keightley
Diethard Tautz

First Published December 2, 2024

Research

C. elegans" > A low-abundance class of Dicer-dependent siRNAs produced from a variety of features in C. elegans

Thiago L. Knittel
Brooke E. Montgomery
Alex J. Tate
Ennis W. Deihl
Anastasia S. Nawrocki
Frederic J. Hoerndli
Taiowa A. Montgomery

First Published December 2, 2024

Research

Analysis of a cell-free DNA–based cancer screening cohort links fragmentomic profiles, nuclease levels, and plasma DNA concentrations

Yasine Malki
Guannan Kang
W.K. Jacky Lam
Qing Zhou
Suk Hang Cheng
Peter P.H. Cheung Jinyue Bai Ming Lok Chan Chui Ting Lee Wenlei Peng Yiqiong Zhang Wanxia Gai Winsome W.S. Wong Mary-Jane L. Ma Wenshuo Li Xinzhou Xu Zhuoran Gao Irene O.L. Tse Huimin Shang
... [+14 authors] ...,
L.Y. Lois Choy
Peiyong Jiang
K.C. Allen Chan
Y.M. Dennis Lo

First Published November 27, 2024

Research

Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging

Amy R. Vandiver
Allen Herbst
Paul Stothard
Jonathan Wanagat

First Published November 27, 2024

Method

A deconvolution framework that uses single-cell sequencing plus a small benchmark data set for accurate analysis of cell type ratios in complex tissue samples

Shuai Guo
Xiaoqian Liu
Xuesen Cheng
Yujie Jiang
Shuangxi Ji
Qingnan Liang Andrew Koval Yumei Li Leah A. Owen Ivana K. Kim Ana Aparicio Sanghoon Lee Anil K. Sood Scott Kopetz John Paul Shen
... [+10 authors] ...,
John N. Weinstein
Margaret M. DeAngelis
Rui Chen
Wenyi Wang

First Published November 25, 2024

Research

Convergent relaxation of molecular constraint in herbivores reveals the changing role of liver and kidney functions across mammalian diets

Matthew D. Pollard
Wynn K. Meyer
Emily E. Puckett

First Published November 22, 2024

Research

Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay

Bertille Montibus
James A. Cain
Rocio T. Martinez-Nunez
Rebecca J. Oakey

First Published November 22, 2024

Research

Bacteriovorax bacteria" > The chromatin landscape of the histone-possessing Bacteriovorax bacteria

Georgi K. Marinov
Benjamin Doughty
Anshul Kundaje
William J. Greenleaf

First Published November 21, 2024

Method

KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome

Samuel H. Kim
Georgi K. Marinov
William J. Greenleaf

First Published November 21, 2024

Review

Advancements in prospective single-cell lineage barcoding and their applications in research

Xiaoli Zhang
Yirui Huang
Yajing Yang
Qi-En Wang
Lang Li

First Published November 21, 2024

Editorial

Revolutionizing genomics and medicine—one long molecule at a time

Ana Conesa
Alexander Hoischen
Fritz J. Sedlazeck

First Published November 20, 2024

Review

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

Review

Leveraging the power of long reads for targeted sequencing

Shruti V. Iyer
Sara Goodwin
William Richard McCombie

First Published November 20, 2024

Perspective

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

Method

Modeling gene interactions in polygenic prediction via geometric deep learning

Han Li
Jianyang Zeng
Michael P. Snyder
Sai Zhang

First Published November 19, 2024

Resource

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

Resource

High-quality sika deer omics data and integrative analysis reveal genic and cellular regulation of antler regeneration

Zihe Li
Ziyu Xu
Lei Zhu
Tao Qin
Jinrui Ma
Zhanying Feng Huishan Yue Qing Guan Botong Zhou Ge Han Guokun Zhang Chunyi Li Shuaijun Jia
... [+8 authors] ...,
Qiang Qiu
Dingjun Hao
Yong Wang
Wen Wang

First Published November 14, 2024

Research

Paramecium" > ISWI1 complex proteins facilitate developmental genome editing in Paramecium

Aditi Singh
Lilia Häußermann
Christiane Emmerich
Emily Nischwitz
Brandon K.B. Seah
Falk Butter
Mariusz Nowacki
Estienne C. Swart

First Published November 14, 2024

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

bla_KPC" > 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 bla_KPC

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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