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Method

Batch correction methods used in single-cell RNA sequencing analyses are often poorly calibrated

Sindri Emmanúel Antonsson
Páll Melsted

First Published July 7, 2025

Research

cis-regulatory elements of target genes" > Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes

Anna Nordin
Chaitali Chakraborty
Mattias Jonasson
Orgena Dano
Gianluca Zambanini
Pierfrancesco Pagella
Silvia Remeseiro
Claudio Cantù

First Published June 23, 2025

Method

QuadST identifies cell–cell interaction–changed genes in spatially resolved transcriptomics data

Xiaoyu Song
Yuqing Shang
Michelle E. Ehrlich
Panos Roussos
Guo-Cheng Yuan
Pei Wang

First Published June 23, 2025

Resource

Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs

Qiuhan Wen
Zhen Wang
Qi Bao
Tianli Ding
Haihan Zhang
Jianbo Li
Zhuang Liu
Jieping Huang
Guoqiang Yi

First Published June 16, 2025

Method

r-index-based pangenome indexing" > Accurate short-read alignment through r-index-based pangenome indexing

Rahul Varki
Massimiliano Rossi
Eddie Ferro
Marco Oliva
Erik Garrison
Ben Langmead
Christina Boucher

First Published June 12, 2025

Research

An iPSC-based model of 47,XYY Jacobs syndrome reveals a DNA methylation-independent transcriptional dysregulation shared with male X aneuploid cells

Veronica Astro
Kelly Yojanna Cardona-Londoño
Lorena Viridiana Cortés-Medina
Rawan Alghamdi
Gustavo Ramírez-Calderón
Fotios Kefalas
Jair Dilmé-Capó
Santiago Radío
Antonio Adamo

First Published June 10, 2025

Research

Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts

Yanis Zekri
Sebastian Gregoricchio
Elif Yapıcı
Chia-Chi Flora Huang
Tunç Morova
Umut Berkay Altıntaş
Gozde Korkmaz
Nathan A. Lack
Wilbert Zwart

First Published June 10, 2025

Research

Pristionchus reveals the environmental responsiveness of a plasticity gene-regulatory network" > Developmental transcriptomics in Pristionchus reveals the environmental responsiveness of a plasticity gene-regulatory network

Shelley Reich
Tobias Loschko
Julie Jung
Samantha Nestel
Ralf J. Sommer
Michael S. Werner

First Published June 9, 2025

Research

Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding

Liangxi Wang
Tiegh Taylor
Kumaragurubaran Rathnakumar
Nadiya Khyzha
Minggao Liang
Azad Alizada Laura F. Campitelli Sara E. Pour Zain M. Patel Lina Antounians Ian C. Tobias Huayun Hou Timothy R. Hughes
... [+8 authors] ...,
Sushmita Roy
Jennifer A. Mitchell
Jason E. Fish
Michael D. Wilson

First Published June 6, 2025

Research

Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation

Marlies E. Oomen
A. Nicole Fox
Inma Gonzalez
Amandine Molliex
Thaleia Papadopoulou
Pablo Navarro
Job Dekker

First Published June 6, 2025

Perspective

Drosophila facilitate classification of variants of uncertain significance associated with rare diseases" > Functional assays in Drosophila facilitate classification of variants of uncertain significance associated with rare diseases

Jung-Wan Mok
Shelley B. Gibson
Haley A. Dostalik
Shinya Yamamoto

First Published June 4, 2025

Corrigendum

Corrigendum: Cre-dependent Cas9-expressing pigs enable efficient in vivo genome editing

Kepin Wang
Qin Jin
Degong Ruan
Yi Yang
Qishuai Liu
Han Wu Zhiwei Zhou Zhen Ouyang Zhaoming Liu Yu Zhao Bentian Zhao Quanjun Zhang Jiangyun Peng Chengdan Lai Nana Fan Yanhui Liang Ting Lan Nan Li Xiaoshan Wang Xinlu Wang Yong Fan Pieter A. Doevendans
... [+17 authors] ...,
Joost P.G. Sluijter
Pentao Liu
Xiaoping Li
Liangxue Lai

First Published June 2, 2025

Corrigendum

Arabidopsis thaliana" > Corrigendum: 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 June 2, 2025

Mini-Review

Revisiting models of enhancer–promoter communication in gene regulation

Gilad Barshad
Charles G. Danko

First Published June 2, 2025

Method

Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain

Jenna Kalleberg
Jacob Rissman
Robert D. Schnabel

First Published June 2, 2025

Research

Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing

Nora Zidane
Carla Rodrigues
Valérie Bouchez
Martin Rethoret-Pasty
Virginie Passet
Sylvain Brisse
Chiara Crestani

First Published June 2, 2025

Research

Androgen receptor–mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells

Johannes Hiltunen
Laura Helminen
Niina Aaltonen
Kaisa-Mari Launonen
Hanna Laakso
Marjo Malinen
Einari A. Niskanen
Jorma J. Palvimo
Ville Paakinaho

First Published June 2, 2025

Research

Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids

Benjamin D. Umans
Yoav Gilad

First Published June 2, 2025

Research

cis-regulatory landscape of erythroid precursors" > Regeneration alters open chromatin and cis-regulatory landscape of erythroid precursors

Yichao Zhou
Venkatasai Rahul Dogiparthi
Hannah L. Harris
Suhita Ray
Avik Choudhuri
Song Yang
... [+1 authors] ...,
Yi Zhou
Leonard I. Zon
M. Jordan Rowley
Kyle J. Hewitt

First Published June 2, 2025

Method

Cancer driver topologically associated domains identify oncogenic and tumor-suppressive lncRNAs

Ziyan Rao
Min Zhang
Shaodong Huang
Chenyang Wu
Yuheng Zhou
Weijie Zhang
Xia Lin
Dongyu Zhao

First Published May 27, 2025

Research

Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits

Kevin W. Currin
Hannah J. Perrin
Gautam K. Pandey
Abdalla A. Alkhawaja
Swarooparani Vadlamudi
Annie E. Musser Amy S. Etheridge K. Alaine Broadaway Jonathan D. Rosen Arushi Varshney Amarjit S. Chaudhry Paul J. Gallins Fred A. Wright Yi-hui Zhou Stephen C.J. Parker
... [+10 authors] ...,
Laura M. Raffield
Erin G. Schuetz
Federico Innocenti
Karen L. Mohlke

First Published May 20, 2025

Resource

Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise

Aliza B. Rubenstein
Gregory R. Smith
Zidong Zhang
Xi Chen
Toby L. Chambers
Frederique Ruf-Zamojski Natalia Mendelev Wan Sze Cheng Michel Zamojski Mary Anne S. Amper Venugopalan D. Nair Andrew R. Marderstein Stephen B. Montgomery Olga G. Troyanskaya
... [+9 authors] ...,
Elena Zaslavsky
Todd Trappe
Scott Trappe
Stuart C. Sealfon

First Published May 20, 2025

Method

Spatial domain detection using contrastive self-supervised learning for spatial multi-omics technologies

Jianing Yao
Jinglun Yu
Brian Caffo
Stephanie C. Page
Keri Martinowich
Stephanie C. Hicks

First Published May 20, 2025

Method

Highly accurate assembly polishing with DeepPolisher

Mira Mastoras
Mobin Asri
Lucas Brambrink
Prajna Hebbar
Alexey Kolesnikov
Daniel E. Cook Maria Nattestad Julian Lucas Taylor S. Won Pi-Chuan Chang Andrew Carroll Benedict Paten Kishwar Shafin Ahmad Abou Tayoun Derek Albracht Jamie Allen Alawi A. Alsheikh-Ali Casey Andrews Dmitry Antipov Lucinda Antonacci-Fulton Mobin Asri Marcelo Ayllon Jennifer R. Balacco Edward A. Belter Halle D. Bender Andrew P. Blair Silvia Buonaiuto Davide Bolognini Katherine E. Bonini Christina Boucher Guillaume Bourque Shuo Cao Andrew Carroll Ann M. Mc Cartney Monika Cechova Pi-Chuan Chang Xian Chang Jitender Cheema Haoyu Cheng Claudio Ciofi Sarah Cody Vincenza Colonna Holland C. Conwell Robert Cook-Deegan Mark Diekhans Maria Angela Diroma Daniel Doerr Zheng Dong Richard Durbin Jana Ebler Evan E Eichler Jordan M. Eizenga Parsa Eskandar Eddie Ferro Anna-Sophie Fiston-Lavier Sarah M. Ford Willard W. Ford Giulio Formenti Adam Frankish Mallory A. Freeberg Qichen Fu Stephanie M. Fullerton Robert S. Fulton Yan Gao Gage H. Garcia Obed A. Garcia Joshua M.V. Gardner Shilpa Garg Erik Garrison Nanibaa' A. Garrison John Garza Mohammadmersad Ghorbani Tina Graves-Lindsay Richard E. Green Cristian Groza Andrea Guarracino Melissa Gymrek Leanne Haggerty Ira M. Hall Nancy F. Hansen Mohammad Amiruddin Hashmi Maximilian Haeussler David Haussler Prajna Hebbar Peter Heringer Glenn Hickey Todd L. Hillaker S. Nakib Hossain Neng Huang Sarah E. Hunt Toby Hunt Nafiseh Jafarzadeh Nivesh Jain Erich D. Jarvis Juan Jiang Jonathan LoTempio Eimear E. Kenny Juhyun Kim Bonhwang Koo Sergey Koren Milinn Kremitzki Ben Langmead Xiaoyu Zhuo Heather A. Lawson Daofeng Li Heng Li Wen-Wei Liao Jiadong Lin Tianjie Liu Glennis A. Logsdon Ryan Lorig-Roach Hailey Loucks Jane E. Loveland Jianguo Lu Shuangjia Lu Julian K. Lucas Juan F. Macias-Velasco Maximillian G. Marin Franco L. Marsico Kateryna D. Makova Christopher Markovic Tobias Marschall Fergal J. Martin Mira Mastoras Capucine Mayoud Brandy McNulty Jack A. Medico Julian M. Menendez Karen H. Miga Anna Minkina Matthew W. Mitchell Saswat K. Mohanty Younes Mokrab Jean Monlong Shabir Moosa Avelina Moreno-Ochando Shinichi Morishita Jonathan M. Mudge Katherine M. Munson Njagi Mwaniki Nasna Nassir Chiara Natali Shloka Negi Lingbin Ni Adam M. Novak Chie Owa Sadye Paez Benedict Paten Hiram Clawson Clelia Peano Adam M. Phillippy Brandon D. Pickett Laura Pignata Nadia Pisanti David Porubsky Pjotr Prins Anandi Radhakrishnan Brian J. Raney Mikko Rautiainen Alessandro Raveane Luyao Ren Arang Rhie Farnaz Salehi Samuel Sacco Michael C. Schatz Laura B. Scheinfeldt Aarushi Sehgal William E. Seligmann Mahsa Shabani Kishwar Shafin Shadi Shahatit Ruhollah Shemirani Vikram S. Shivakumar Swati Sinha Jouni Sirén Linnéa Smeds Steven J. Solar Marco Sollitto Nicole Soranzo Andrew B. Stergachis Marie-Marthe Suner Yoshihiko Suzuki Arda Söylev Jack A.S. Tierney Chad Tomlinson Francesca Floriana Tricomi Mohammed Uddin Matteo Tommaso Ungaro Rahul Varki Flavia Villani Mitchell R. Vollger Brian P. Walenz Charles Wang Lisa E. Wang Ting Wang Aaron M. Wenger Conor V. Whelan Zilan Xin Zheng Xu Kai Ye DongAhn Yoo
... [+196 authors] ...,
Wenjin Zhang
Ying Zhou
Ivo Violich
Giulia Zunino

First Published May 19, 2025

Method

Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding

Dmitry Antipov
Mikko Rautiainen
Sergey Nurk
Brian P. Walenz
Steven J. Solar
Adam M. Phillippy
Sergey Koren

First Published May 19, 2025

Method

A new compression strategy to reduce the size of nanopore sequencing data

Kavindu Jayasooriya
Sasha P. Jenner
Pasindu Marasinghe
Udith Senanayake
Hassaan Saadat
David Taubman
Roshan Ragel
Hasindu Gamaarachchi
Ira W. Deveson

First Published May 15, 2025

Resource

Charting the regulatory landscape of TP53 on transposable elements in cancer

Xuan Qu
Yonghao Liang
Colin McCornack
Xiaoyun Xing
Heather Schmidt
Chad Tomlinson
... [+1 authors] ...,
Catrina Fronick
Edward A. Belter
Juan F. Macias-Velasco
Ting Wang

First Published May 13, 2025

Method

Tissular chromatin-state cartography based on double-barcoded DNA arrays that capture unloaded PA-Tn5 transposase

Maria Grazia Mendoza-Ferri
Gwendoline Lozachmeur
Maximilien Duvina
Laetitia Perret
Didier Merciris
Anne Gigout
Marco Antonio Mendoza-Parra

First Published May 13, 2025

Method

STCC enhances spatial domain detection through consensus clustering of spatial transcriptomics data

Congcong Hu
Nana Wei
Jiyuan Yang
Hua-Jun Wu
Xiaoqi Zheng

First Published May 12, 2025

Research

C. elegans nonsense-mediated mRNA decay" > Endonucleolytic cleavage is the primary mechanism of decay elicited by C. elegans nonsense-mediated mRNA decay

Marcus J. Viscardi
Enisha Sehgal
Joshua A. Arribere

First Published May 9, 2025

Research

Birth of protein-coding exons by ancient domestication of LINE-1 retrotransposon

Koichi Kitao
Kenji Ichiyanagi
So Nakagawa

First Published May 8, 2025

Method

Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes

Paras Verma
Deeksha Thakur
Deepanshi Awasthi
Shashi Bhushan Pandit

First Published May 7, 2025

Method

Harnessing agent-based frameworks in CellAgentChat to unravel cell–cell interactions from single-cell and spatial transcriptomics

Vishvak Raghavan
Yumin Zheng
Yue Li
Jun Ding

First Published May 2, 2025

Research

Oryza" > Continuous infiltration and evolutionary trajectory of nuclear organelle DNA in Oryza

Chenbo Gong
Yicheng Huang
Mengmeng Liu
Yong Zhou
Yinwei Xu
Nahed Mohammed Xintong Qiao Andrea Zuccolo Weibo Xie
... [+4 authors] ...,
Rod A. Wing
Jianwei Zhang
Fei Zhou
Yongjun Lin

First Published April 25, 2025

Research

Extreme heterochiasmy and high rates of sex-reversed recombination result in large yet homomorphic sex chromosomes in the Emei moustache toad

Siyu Xie
Jun Li
Wanyan Chen
Lydia J.M. Fong
Chunhua Huang
Yan Feng
... [+1 authors] ...,
Qingbo Ai
Mian Zhao
Judith E. Mank
Hua Wu

First Published April 24, 2025

Research

Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing

Keegan S. Krick
Marissa Maroni
Erica Korb
Kristen W. Lynch
Elizabeth A. Heller

First Published April 24, 2025

Research

Blastocystis gut microbiome–associated protists reveal evolutionary diversification to host ecology" > Contiguous and complete assemblies of Blastocystis gut microbiome–associated protists reveal evolutionary diversification to host ecology

Abigail L. Lind
Nathan A. McDonald
Elias R. Gerrick
Ami S. Bhatt
Katherine S. Pollard

First Published April 22, 2025

Method

Dissecting multilayer cell–cell communications with signaling feedback loops from spatial transcriptomics data

Lulu Yan
Jinyu Cheng
Qing Nie
Xiaoqiang Sun

First Published April 22, 2025

Resource

MPRAbase a Massively Parallel Reporter Assay database

Jingjing Zhao
Fotis A Baltoumas
Maxwell A Konnaris
Ioannis Mouratidis
Zhe Liu
Jasmine Sims
... [+1 authors] ...,
Vikram Agarwal
Georgios A Pavlopoulos
Ilias Georgakopoulos-Soares
Nadav Ahituv

First Published April 22, 2025

Research

Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis

Olga M. Sigalova
Mattia Forneris
Frosina Stojanovska
Bingqing Zhao
Rebecca R. Viales
Adam Rabinowitz
... [+1 authors] ...,
Fayrouz Hammal
Benoît Ballester
Judith B. Zaugg
Eileen E.M. Furlong

First Published April 15, 2025

Resource

Building better genome annotations across the tree of life

Adam H. Freedman
Timothy B. Sackton

First Published April 15, 2025

Research

cis-regulatory variation modifies the penetrance of pathogenic SHROOM3 variants in craniofacial microsomia" > Common cis-regulatory variation modifies the penetrance of pathogenic SHROOM3 variants in craniofacial microsomia

Hao Zhu
Jiao Zhang
Soumya Rao
Matthew D. Durbin
Ying Li
Ruirui Lang Jiqiang Liu Baichuan Xiao Hailin Shan Ziqiu Meng Jinmo Wang Xiaokai Tang Zhenni Shi Liza L. Cox Shouqin Zhao Stephanie M. Ware Tiong Y. Tan Michelle de Silva Lyndon Gallacher Ting Liu Jie Mi Changqing Zeng Hou-Feng Zheng
... [+18 authors] ...,
Qingguo Zhang
Stylianos E. Antonarakis
Timothy C. Cox
Yong-Biao Zhang

First Published April 15, 2025

Mini-Review

Evolution of genome-wide methylation profiling technologies

Carolina Montano
Winston Timp

First Published April 14, 2025

Perspective

The impact of long-read sequencing on human population-scale genomics

Tobias Rausch
Tobias Marschall
Jan O. Korbel

First Published April 14, 2025

Mini-Review

A Hitchhiker's Guide to long-read genomic analysis

Medhat Mahmoud
Daniel P. Agustinho
Fritz J. Sedlazeck

First Published April 14, 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

Research

Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus

Rita Tam
Mareike Möller
Runpeng Luo
Zhenyan Luo
Ashley Jones
Sambasivam Periyannan
John P. Rathjen
Benjamin Schwessinger

First Published April 11, 2025

Method

Analytical validation of germline small variant detection using long-read HiFi genome sequencing

Nathan Hammond
Linda Liao
Pun Wai Tong
Zena Ng
Thuy-Mi P. Nguyen
Chandler Ho
Yao Yang
Stuart A. Scott

First Published April 11, 2025

Method

Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC

Byron J. Smith
Chunyu Zhao
Veronika Dubinkina
Xiaofan Jin
Liron Zahavi
Saar Shoer
Jacqueline Moltzau-Anderson
Eran Segal
Katherine S. Pollard

First Published April 10, 2025

Research

C. elegans" > Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans

Jun Kim
Haoyu Wang
Sevinç Ercan

First Published April 10, 2025

Method

TFcomb identifies transcription factor combinations for cellular reprogramming based on single-cell multiomics data

Chen Li
Sijie Chen
Yixin Chen
Haiyang Bian
Minsheng Hao
Lei Wei
Xuegong Zhang

First Published April 10, 2025

Research

Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements

Fu Xiang Quah
Miguel Vasconcelos Almeida
Moritz Blumer
Chengwei Ulrika Yuan
Bettina Fischer
Kirsten See Ben Jackson Richard Zatha Bosco Rusuwa George F. Turner M. Emília Santos
... [+6 authors] ...,
Hannes Svardal
Martin Hemberg
Richard Durbin
Eric Miska

First Published April 10, 2025

Method

k-mer manifold approximation and projection for visualizing DNA sequences" > k-mer manifold approximation and projection for visualizing DNA sequences

Chengbo Fu
Einari A. Niskanen
Gong-Hong Wei
Zhirong Yang
Marta Sanvicente-García
Marc Güell
Lu Cheng

First Published April 10, 2025

Research

Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes

Yu-Chi Chen
David L.J. Vendrami
Maximilian L. Huber
Luisa E.Y. Handel
Christopher R. Cooney
Joseph I. Hoffman
Toni I. Gossmann

First Published March 31, 2025

Research

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

Research

Analysis of canine gene constraint identifies new variants for orofacial clefts and stature

Reuben M. Buckley
Nüket Bilgen
Alexander C. Harris
Peter Savolainen
Cafer Tepeli
Metin Erdoğan Aitor Serres Armero Dayna L. Dreger Frank G. van Steenbeek Marjo K. Hytönen Heidi G. Parker Jessica Hale
... [+7 authors] ...,
Hannes Lohi
Bengi Çınar Kul
Adam R. Boyko
Elaine A. Ostrander

First Published March 24, 2025

Method

An optimized toolkit for high-molecular-weight DNA extraction and ultra-long-read nanopore sequencing using glass beads and hexamminecobalt(III) chloride

Inswasti Cahyani
John Tyson
Nadine Holmes
Josh Quick
Chris Moore
Nick Loman
Matthew Loose

First Published March 24, 2025

Method

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

Method

Examining the dynamics of three-dimensional genome organization with multitask matrix factorization

Da-Inn Lee
Sushmita Roy

First Published March 20, 2025

Research

Unexpectedly low recombination rates and presence of hotspots in termite genomes

Turid Everitt
Tilman Rönneburg
Daniel Elsner
Anna Olsson
Yuanzhen Liu
Tuuli Larva
Judith Korb
Matthew T. Webster

First Published March 20, 2025

Research

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

Research

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

Method

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

Perspective

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

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

Research

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

Method

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
Viola Heinzelmann-Schwarz
Niko Beerenwinkel

First Published March 19, 2025

Method

BINDER achieves accurate identification of hierarchical TADs by comprehensively characterizing consensus TAD boundaries

Yangyang Liu
Bingqiang Liu
Juntao Liu

First Published March 17, 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
Steven J.M. Jones
Fritz J. Sedlazeck

First Published March 17, 2025

Method

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

Method

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

Research

KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution

Kai Otsuka
Akihiko Sakashita
So Maezawa
Richard M. Schultz
Satoshi H. Namekawa

First Published March 12, 2025

Research

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

Research

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
Rui Chen

First Published March 6, 2025

Method

Homozygous editing of multiple genes for accelerated generation of xenotransplantation pigs

Xiaoyue Duan
Chaolei Chen
Chang Du
Liang Guo
Jun Liu
Naipeng Hou Pan Li Xiaolan Qi
... [+3 authors] ...,
Fei Gao
Xuguang Du
Jiangping Song
Sen Wu

First Published March 5, 2025

Research

Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly

Kang Du
Oliver Deusch
Ilja Bezrukov
Christa Lanz
Yann Guiguen
Margarete Hoffmann
... [+1 authors] ...,
Anette Habring
Detlef Weigel
Manfred Schartl
Christine Dreyer

First Published March 5, 2025

Research

Vertebrates show coordinated elevated expression of mitochondrial and nuclear genes after birth

Hadar Medini
Dan Mishmar

First Published March 4, 2025

Research

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

Method

RAmbler resolves complex repeats in human Chromosomes 8, 19, and X

Sakshar Chakravarty
Glennis Logsdon
Stefano Lonardi

First Published March 4, 2025

Research

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
Jiaxun Zhang
Yahui Liu
Xuyan Liu
Dan Xie

First Published March 4, 2025

Method

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
Nicholas J. Croucher

First Published March 4, 2025

Research

Spirodela polyrhiza" > Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza

Rodolphe Dombey
Daniel Buendía-Ávila
Verónica Barragán-Borrero
Laura Diezma-Navas
Arturo Ponce-Mañe
José Mario Vargas-Guerrero
Rana Elias
Arturo Marí-Ordóñez

First Published March 4, 2025

Research

Estrogen-induced chromatin looping changes identify a subset of functional regulatory elements

Hosiana Abewe
Alexandra Richey
Jeffery M. Vahrenkamp
Matthew Ginley-Hidinger
Craig M. Rush
Noel Kitchen
Xiaoyang Zhang
Jason Gertz

First Published March 3, 2025

Method

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

Perspective

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

Research

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

Resource

Exploring the epigenome profiles of repetitive elements with the WashU Repeat Browser

Jiawei Shen
Siyuan Cheng
Deepak Purushotham
Xiaoyu Zhuo
Alan Y Du
Wenjin Zhang
Daofeng Li
Ting Wang

First Published February 21, 2025

Research

The genomic consequences and persistence of sociality in spiders

Jilong Ma
Jesper Bechsgaard
Anne Aagaard
Palle Villesen
Trine Bilde
Mikkel Heide Schierup

First Published February 20, 2025

Method

A unified analysis of atlas single-cell data

Hao Chen
Nam D. Nguyen
Matthew Ruffalo
Ziv Bar-Joseph

First Published February 18, 2025

Research

Transcriptomic and proteomic effects of gene deletion are not evolutionarily conserved

Yang Li
Jianzhi Zhang

First Published February 18, 2025

Research

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
Deborah M. Stephens
Jennifer A. Woyach
Gabor T. Marth

First Published February 18, 2025

Research

Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection

Jian-Hai Chen
Patrick Landback
Deanna Arsala
Alexander Guzzetta
Shengqian Xia
Jared Atlas Dylan Sosa
... [+2 authors] ...,
Yong E. Zhang
Jingqiu Cheng
Bairong Shen
Manyuan Long

First Published February 14, 2025

Research

Ancient dog introgression into the Iberian wolf genome may have facilitated adaptation to human-dominated landscapes

Diana Lobo
Hernán E. Morales
Cock Van Oosterhout
José Vicente López-Bao
Pedro Silva
Luis Llaneza Carolina Pacheco Diana Castro Germán Hernández-Alonso George Pacheco
... [+5 authors] ...,
John Archer
M. Thomas P. Gilbert
Nuno Ferrand
Raquel Godinho

First Published February 14, 2025

Research

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

Research

cis-regulatory element evolution after whole-genome duplication" > The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication

Øystein Monsen
Lars Grønvold
Alex Datsomor
Thomas Harvey
James Kijas
Alexander Suh
Torgeir R. Hvidsten
Simen Rød Sandve

First Published February 12, 2025

Method

Fast sequence alignment for centromeres with RaMA

Pinglu Zhang
Yanming Wei
Qinzhong Tian
Quan Zou
Yansu Wang

First Published February 12, 2025

Research

Nucleosome binding by TP53, TP63, and TP73 is determined by the composition, accessibility, and helical orientation of their binding sites

Patrick D. Wilson
Xinyang Yu
Christopher R. Handelmann
Michael J. Buck

First Published February 10, 2025

Research

Variation in the fitness impact of translationally optimal codons among animals

Florian Bénitière
Tristan Lefébure
Laurent Duret

First Published February 10, 2025

Method

Kernel-bounded clustering for spatial transcriptomics enables scalable discovery of complex spatial domains

Hang Zhang
Yi Zhang
Kai Ming Ting
Jie Zhang
Qiuran Zhao

First Published February 5, 2025

Mini-Review

The additional diagnostic yield of long-read sequencing in undiagnosed rare diseases

Giulia F. Del Gobbo
Kym M. Boycott

First Published February 3, 2025

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