Search | Genome Research

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Method

Efficient integration of spatial omics data for joint domain detection, matching, and alignment with stMSA

Han Shu
Jing Chen
Chang Xu
Jialu Hu
Yongtian Wang
Jiajie Peng
Qinghua Jiang
Xuequn Shang
Tao Wang

First Published August 14, 2025

Method

Unveiling the functional fate of duplicated genes through expression profiling and structural analysis

Alex Warwick Vesztrocy
Natasha Glover
Paul D. Thomas
Christophe Dessimoz
Irene Julca

First Published August 14, 2025

Method

Multicondition and multimodal temporal profile inference during mouse embryonic development

Ran Zhang
Chengxiang Qiu
Galina N. Filippova
Gang Li
Jay Shendure
Jean-Philippe Vert
Xinxian Deng
William Stafford Noble
Christine M. Disteche

First Published August 14, 2025

Method

FocalSV enables target region–based structural variant assembly and refinement using single-molecule long-read sequencing data

Can Luo
Zimeng Jamie Zhou
Yichen Henry Liu
Xin Maizie Zhou

First Published August 13, 2025

Research

Intergenic accumulation of RNA polymerase II maintains the potential for swift transcriptional restart upon release from quiescence

Manuela Baquero Pérez
Gertjan Laenen
Isabelle Loïodice
Mickaël Garnier
Ugo Szachnowski
Antonin Morillon
Myriam Ruault
Angela Taddei

First Published August 12, 2025

Research

Phylogenetic relatedness rather than aquatic habitat fosters horizontal transfer of transposable elements in animals

Héloïse Muller
Rosina Savisaar
Jean Peccoud
Sylvain Charlat
Clément Gilbert

First Published August 8, 2025

Method

ERC2.0 evolutionary rate covariation update improves inference of functional interactions across large phylogenies

Jordan H. Little
Guillermo Hoffmann Meyer
Aakash Grover
Alex Michael Francette
Raghavendran Partha
Karen M. Arndt
Martin Smith
Nathan Clark
Maria Chikina

First Published August 7, 2025

Method

BRCA1 and BRCA2 splice isoforms" > The SeqSplice multiplexed minigene splicing assay for characterization and quantitation of variant-induced BRCA1 and BRCA2 splice isoforms

Daffodil M. Canson
Michael T. Parsons
Gemma Moir-Meyer
Troy Dumenil
Gemma Montalban
Erica Lin Terri P. McVeigh Aimee L. Davidson
... [+3 authors] ...,
Shaun M. Bouckaert
Matt Trau
Darren Korbie
Amanda B. Spurdle

First Published August 6, 2025

Research

Xist upstream deletion leads to dysregulation of Xist and autosomal gene expression" > Xist upstream deletion leads to dysregulation of Xist and autosomal gene expression

Sudeshna Majumdar
Lakshmi Sowjanya Bammidi
Hemant C. Naik
Avinchal Manhas
Runumi Baro
Akash Kalita Amlan Jyoti Naskar
... [+2 authors] ...,
Sundarraj Nidharshan
Girija S. Bariha
Dimple Notani
Srimonta Gayen

First Published August 6, 2025

Mini-Review

The paradox of R-loops: guardians of the genome or drivers of disease?

Mudiyanselage Shachinthaka D. Dissanayaka
Wulfridge Phillip
Sarma Kavitha

First Published August 6, 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

Resource

Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, chemotaxis behavior, and survival

Marina Athanasouli
Tobias Loschko
Christian Rödelsperger

First Published August 5, 2025

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

Method

3′-end ligation sequencing is a sensitive method to detect DNA nicks at potential sites of off-target activity induced by prime editors

Jacob Stewart-Ornstein
Matthew J. Irby
Marina K. Lilieholm
Dylan Laprise
Maria D. Collier
Thomas Aunins
... [+1 authors] ...,
Dewi Harjanto
Aaron N. Chang
Deepak Reyon
Jeremy S. Duffield

First Published August 5, 2025

Research

H3K27 and H3K9 methylation mask potential CTCF binding sites to maintain 3D genome integrity

Kei Fukuda
Chikako Shimura
Yoichi Shinkai

First Published August 5, 2025

Method

High-resolution spatial transcriptomics in fixed tissue using a cost-effective PCL-seq workflow

Xue Dong
Mengzhu Hu
Xiaonan Cui
Wenjian Zhou
Jingtao Cai
Guangyao Mao
Weiyang Shi

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

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

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

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

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

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

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