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Method

Genotyping of selected germline adaptive immune system loci using short-read sequencing data

  • Michael K.B. Ford
  • Ananth Hari
  • Meredith Yeager
  • Lisa Mirabello
  • Stephen Chanock
  • Ibrahim Numanagić
  • S. Cenk Sahinalp
  • First Published August 5, 2025
Research

Distinct classes of lamina-associated domains are defined by differential patterns of repressive histone methylation

  • Caden J. Martin
  • Elizabeth A. Oser
  • Prabakaran Nagarajan
  • Liudmila V. Popova
  • Benjamin D. Sunkel
  • Benjamin Z. Stanton
  • Mark R. Parthun
  • First Published August 5, 2025
Research

Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations

  • Xiu Fan
  • Qili Qian
  • Wenran Li
  • Tianzi Liu
  • Changqing Zeng
  • Peilin Jia Huandong Lin Xin Gao
  • ... [+3 authors] ...,
  • Li Jin
  • Mingfeng Xia
  • Sijia Wang
  • Fan Liu
  • First Published August 1, 2025
Research

Genotype imputation from low-coverage data for medical and population genetic analyses

  • Simone Andrea Biagini
  • Sara Becelaere
  • Mio Aerden
  • Tatjana Jatsenko
  • Laurens Hannes
  • Philip Van Damme Jeroen Breckpot Koenraad Devriendt
  • ... [+3 authors] ...,
  • Bernard Thienpont
  • Joris Robert Vermeesch
  • Isabelle Cleynen
  • Toomas Kivisild
  • First Published July 22, 2025
Resource

ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data" > The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data

  • Hsin-Yen Larry Wu
  • Isaiah D. Kaufman
  • Polly Yingshan Hsu
  • First Published July 22, 2025
Research

Transcriptional modulation unique to vulnerable motor neurons predicts ALS across species and SOD1 mutations

  • Irene Mei
  • Susanne Nichterwitz
  • Melanie Leboeuf
  • Jik Nijssen
  • Isadora Lenoel
  • Dirk Repsilber
  • Christian S. Lobsiger
  • Eva Hedlund
  • First Published July 17, 2025
Method

Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks

  • Prashanthi Ravichandran
  • Princy Parsana
  • Rebecca Keener
  • Kasper D. Hansen
  • Alexis Battle
  • First Published July 17, 2025
Research

Drosophila melanogaster genome" > Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome

  • Shukla Harsh G.
  • Chakraborty Mahul
  • Emerson J.J.
  • First Published July 16, 2025
Research

Alternative splicing generates HER2 isoform diversity underlying antibody–drug conjugate resistance in breast cancer

  • Gabriela D.A. Guardia
  • Carlos H. dos Anjos
  • Aline Rangel-Pozzo
  • Filipe F. dos Santos
  • Alexander Birbrair
  • Paula F. Asprino
  • Anamaria A. Camargo
  • Pedro A.F. Galante
  • First Published July 15, 2025
Method

A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry

  • Zhang Meilin
  • Du Heng
  • Zhang Yu
  • Zhuo Yue
  • Liu Zhen
  • Xue Yahui
  • ... [+1 authors] ...,
  • Zhou Lei
  • Zhou Sixuan
  • Li Wanying
  • Liu Jian-Feng
  • First Published July 15, 2025
Resource

Caenorhabditis elegans" > CGC1, a new reference genome for Caenorhabditis elegans

  • Kazuki Ichikawa
  • Massa J. Shoura
  • Karen L. Artiles
  • Dae-Eun Jeong
  • Chie Owa
  • Haruka Kobayashi Yoshihiko Suzuki Manami Kanamori Yu Toyoshima Yuichi Iino Ann E. Rougvie
  • ... [+6 authors] ...,
  • Lamia Wahba
  • Andrew Z. Fire
  • Erich M. Schwarz
  • Shinichi Morishita
  • First Published July 15, 2025
Method

Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes

  • Rachel M. Petersen
  • Christopher M. Vockley
  • Amanda J. Lea
  • First Published July 14, 2025
Method

A novel multislice framework for precision 3D spatial domain reconstruction and disease pathology analysis

  • Daijun Zhang
  • Ren Qi
  • Xun Lan
  • Bin Liu
  • First Published July 14, 2025
Resource

A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq

  • Gaynor-Gillett Sophia C.
  • Cheng Lijun
  • Shi Manman
  • Liu Jason
  • Wang Gaoyuan
  • Spector Megan Guo Qiuyu Qi Le Flaherty Mary Wall Martha Hwang Ahyeon Gu Mengting Chen Zhanlin Chen Yuhang Moran Jennifer R. Zhang Jing
  • ... [+11 authors] ...,
  • Lee Donghoon
  • Gerstein Mark
  • Geschwind Daniel
  • White Kevin P.
  • First Published July 11, 2025
Review

De novo gene birth and the conundrum of ORFan genes in bacteria

  • Md. Hassan uz-Zaman
  • Howard Ochman
  • First Published July 10, 2025
Research

Lambdoid phages with abundant Chi recombination hotspots reflect diverse viral strategies for recombination-dependent growth

  • Clarence Zheng
  • Sherwood R. Casjens
  • Alan R. Davidson
  • Susan K. Amundsen
  • Gerald R. Smith
  • First Published July 10, 2025
Research

Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy

  • Hadi Rahmaninejad
  • Yao Xiao
  • Maxime M.C. Tortora
  • Geoffrey Fudenberg
  • First Published July 8, 2025
Method

Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq

  • Yike Xie
  • Abbas Habibalahi
  • Ayad G. Anwer
  • Kanu Wahi
  • Jacqueline Bailey
  • Francis Lin Catherine Gatt Emma M.V. Johansson
  • ... [+3 authors] ...,
  • Tatyana Chtanova
  • Jeff Holst
  • Ewa Goldys
  • Fabio Zanini
  • First Published July 8, 2025
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

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
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
Mini-Review

Revisiting models of enhancer–promoter communication in gene regulation

  • Gilad Barshad
  • Charles G. Danko
  • 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

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

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

Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain

  • Jenna Kalleberg
  • Jacob Rissman
  • Robert D. Schnabel
  • 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
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
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
Research

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

  • Currin Kevin W.
  • Perrin Hannah J.
  • Pandey Gautam K.
  • Alkhawaja Abdalla A.
  • Vadlamudi Swarooparani
  • Musser Annie E. Etheridge Amy S. Broadaway K. Alaine Rosen Jonathan D. Varshney Arushi Chaudhry Amarjit S. Gallins Paul J. Wright Fred A. Zhou Yi-hui Parker Stephen C.J.
  • ... [+10 authors] ...,
  • Raffield Laura M.
  • Schuetz Erin G.
  • Innocenti Federico
  • Mohlke Karen L.
  • First Published May 20, 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

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

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
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
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

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
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