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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
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