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Research

Autism spectrum disorder risk genes have convergent effects on transcription and neuronal firing patterns in primary neurons

Alekh Paranjapye
Rili Ahmad
Steven Su
Abraham J. Waldman
Jennifer E. Phillips-Cremins
Shuo Zhang
Erica Korb

First Published October 20, 2025

Method

PoreMeth2 for decoding the evolution of methylome alterations with nanopore sequencing

Gianluca Mattei
Marta Baragli
Barbara Gega
Alessandra Mingrino
Martina Chieca
Tommaso Ducci Gianmaria Frigè Luca Mazzarella Romina D'Aurizio
... [+4 authors] ...,
Francesco De Logu
Romina Nassini
Pier Giuseppe Pelicci
Alberto Magi

First Published October 20, 2025

Research

Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen

Xingmin Han
Chenghui Xu
Yiyi Ren
Meiling Guo
Jiayue Yan
Xuan Wang Chao Liu
... [+2 authors] ...,
Qin Gu
Xing-Xing Shen
Zhonghua Ma
Yun Chen

First Published October 14, 2025

Method

Recovering gene regulatory networks in single-cell multi-omics data with PRISM-GRN

Wenhao Zhang
Lan Cao
Xiaoxuan Gu
Yongyu Long
Ying Wang

First Published October 9, 2025

Research

Loss of multilevel 3D genome organization during breast cancer progression

Roberto Rossini
Saleh Oshaghi
Maxim Nekrasov
Aurélie Bellanger
Renae Domaschenz
Yasmin Dijkwel Mohamed Abdelhalim Rahul Agrawal Marit Ledsaak
... [+4 authors] ...,
Philippe Collas
Ragnhild Eskeland
David Tremethick
Jonas Paulsen

First Published October 9, 2025

Method

c-separated cell types with SepSolve" > Optimal marker genes for c-separated cell types with SepSolve

Bartol Borozan
Tomislav Prusina
Luka Borozan
Domagoj Ševerdija
Francisca Rojas Ringeling
Domagoj Matijević
Stefan Canzar

First Published October 9, 2025

Resource

Integrative chromatin state annotation of 234 human ENCODE4 cell types using Segway

Marjan Farahbod
Aboud Diab
Paul Sud
Meenakshi S. Kagda
Ian Whaling
Mehdi Foroozandeh Ishan Goel
... [+2 authors] ...,
Habib Daneshpajouh
Benjamin Hitz
J. Michael Cherry
Maxwell W. Libbrecht

First Published October 6, 2025

Research

Drosophila melanogaster Y-linked genes" > Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes

A. Bernardo Carvalho
Bernard Y. Kim
Fabiana Uno

First Published October 1, 2025

Method

Highly accurate reference and method selection for universal cross–data set cell type annotation with CAMUS

Qunlun Shen
Shuqin Zhang
Shihua Zhang

First Published October 1, 2025

Corrigendum

Corrigendum: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes

Ran Li
Mian Gong
Xinmiao Zhang
Fei Wang
Zhenyu Liu
Lei Zhang Qimeng Yang Yuan Xu Mengsi Xu Huanhuan Zhang Yunfeng Zhang Xuelei Dai Yuanpeng Gao Zhuangbiao Zhang Wenwen Fang Yuta Yang Weiwei Fu Chunna Cao Peng Yang Zeinab Amiri Ghanatsaman Niloufar Jafarpour Negari Hojjat Asadollahpour Nanaei Xiangpeng Yue Yuxuan Song Xianyong Lan Weidong Deng Xihong Wang Chuanying Pan Ruidong Xiang Eveline M. Ibeagha-Awemu Pat (J.S.) Heslop-Harrison
... [+26 authors] ...,
Benjamin D. Rosen
Johannes A. Lenstra
Shangquan Gan
Yu Jiang

First Published October 1, 2025

Research

Adaptation of centromeres to breakage through local genomic and epigenomic remodeling in wheat

Jingwei Zhou
Yuhong Huang
Huan Ma
Yiqian Chen
Chuanye Chen
Fangpu Han
Handong Su

First Published September 30, 2025

Method

Long-read reconstruction of many diverse haplotypes with devider

Jim Shaw
Christina Boucher
Yun William Yu
Noelle Noyes
Heng Li

First Published September 23, 2025

Method

Deep structural clustering reveals hidden systematic biases in RNA sequencing data

Qiang Su
Yi Long
Deming Gou
Junmin Quan
Xiaoming Zhou
Qizhou Lian

First Published September 19, 2025

Method

Recalibrating differential gene expression by genetic dosage variance prioritizes functionally relevant genes

Philipp Rentzsch
Aaron Kollotzek
Kaushik Ram Ganapathy
Pejman Mohammadi
Tuuli Lappalainen

First Published September 17, 2025

Resource

Analyzing the large and complex SFARI autism cohort data using the Genotypes and Phenotypes in Families (GPF) platform

Liubomir Chorbadjiev
Murat Cokol
Zohar Weinstein
Kevin Shi
Christopher Fleisch
Nikolay Dimitrov Svetlin Mladenov Ivo Todorov Iordan Ivanov Simon Xu Steven Ford Yoon-ha Lee Boris Yamrom Steven Marks
... [+9 authors] ...,
Adriana Munoz
Alex Lash
Natalia Volfovsky
Ivan Iossifov

First Published September 16, 2025

Research

Tribolium sibling species" > Dynamic evolution of satellite DNAs drastically differentiates the genomes of Tribolium sibling species

Damira Veseljak
Evelin Despot-Slade
Marin Volarić
Lucija Horvat
Tanja Vojvoda Zeljko
Nevenka Meštrović
Brankica Mravinac

First Published September 16, 2025

Research

Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma

Yao Wang
Dong Yu
Yue Mei
ZhiDa Fu
Jian Lin
Di Wu
Yuan Yang
Hongli Yan

First Published September 16, 2025

Research

T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population

Daniel Schmitz
Adam Ameur
Åsa Johansson

First Published September 16, 2025

Research

Mapping multitissue regulatory variants reveals a liver-centric coexpression network associated with duck egg-laying performance

Yang Xi
Jingjing Qi
Zhao Yang
Yutian Zeng
Huicong Zhang
Qiuyu Tao Mengru Xu Anqi Huang Shenqiang Hu Chunchun Han Lili Bai Jiwei Hu
... [+7 authors] ...,
Jiwen Wang
Liang Li
Lingzhao Fang
Hehe Liu

First Published September 10, 2025

Method

ScisTree2 enables large-scale inference of cell lineage trees and genotype calling using efficient local search

Haotian Zhang
Yiming Zhang
Teng Gao
Yufeng Wu

First Published September 3, 2025

Research

Widespread specific intron retention events in nuclear RNA complexes identified by sedimentation analysis of pluripotent cellular extracts

Isabela T. Pereira
Izabela Mamede
Paulo P. Amaral
Gloria R. Franco
John L. Rinn

First Published August 26, 2025

Research

APOBEC3A drives deaminase mutagenesis in human gastric epithelium

Yohan An
Ji-Hyun Lee
Joonoh Lim
Jeonghwan Youk
Seongyeol Park
Ji-Hyung Park Kijong Yi Taewoo Kim Chang Hyun Nam Won Hee Lee Soo A Oh Yoo Jin Bae Thomas M. Klompstra Haeun Lee Jinju Han Junehwak Lee Jung Woo Park Jie-Hyun Kim
... [+13 authors] ...,
Hyunki Kim
Hugo Snippert
Bon-Kyoung Koo
Young Seok Ju

First Published August 26, 2025

Research

Molecular and genetic landscapes of retina and brain microglia in neurodegenerative diseases

Khang Ma
Rinki Ratnapriya

First Published August 26, 2025

Resource

Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life

Nikol Chantzi
Akshatha Nayak
Fotis A. Baltoumas
Eleni Aplakidou
Shiau Wei Liew
Jesslyn Elvaretta Galuh Michail Patsakis Austin Montgomery Camille Moeckel Ioannis Mouratidis Saiful Arefeen Sazed Wilfried Guiblet Panagiotis Karmiris-Obratański Guliang Wang Apostolos Zaravinos
... [+10 authors] ...,
Karen M. Vasquez
Chun Kit Kwok
Georgios A. Pavlopoulos
Ilias Georgakopoulos-Soares

First Published August 26, 2025

Method

Robust 16S rRNA classification based on a compressed LCA index

Omar Ahmed
Christina Boucher
Ben Langmead

First Published August 25, 2025

Resource

High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae

Jacopo Martelossi
Jacopo Vujovic
Yue Huang
Alessia Tatti
Kaiwei Xu
Federico Puliga Yuanxue Chen
... [+2 authors] ...,
Omar Rota Stabelli
Fabrizio Ghiselli
Xiaoping Zhang
Alessandra Zambonelli

First Published August 21, 2025

Method

Pangenome-based genome inference using integer programming

Ghanshyam Chandra
Md Helal Hossen
Stephan Scholz
Alexander T. Dilthey
Daniel Gibney
Chirag Jain

First Published August 21, 2025

Method

Estimating the size of long tandem repeat expansions from short reads with ScatTR

Rashid Al-Abri
Gamze Gürsoy

First Published August 21, 2025

Method

Deciphering context-specific gene programs from single-cell and spatial transcriptomics data with DeCEP

Lin Li
Xianbin Su
Ze-Guang Han

First Published August 21, 2025

Method

Tree-based differential testing using inferential uncertainty for RNA-seq

Noor Pratap Singh
Euphy Y. Wu
Jason Fan
Michael I. Love
Rob Patro

First Published August 21, 2025

Method

Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus

Mari B. Gornitzka
Egil Røsjø
Uddalok Jana
Easton E. Ford
Alan Tourancheau
William D. Lees
... [+1 authors] ...,
Zachary Vanwinkle
Melissa L. Smith
Corey T. Watson
Andreas Lossius

First Published August 21, 2025

Method

Accurate detection of tandem repeats from error-prone sequences with EquiRep

Zhezheng Song
Tasfia Zahin
Xiang Li
Mingfu Shao

First Published August 21, 2025

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

Mini-Review

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

Shachinthaka D. Dissanayaka Mudiyanselage
Phillip Wulfridge
Kavitha Sarma

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

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

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

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

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

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

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

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

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

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

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

Harsh G. Shukla
Mahul Chakraborty
J.J. Emerson

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

Meilin Zhang
Heng Du
Yu Zhang
Yue Zhuo
Zhen Liu
Yahui Xue
... [+1 authors] ...,
Lei Zhou
Sixuan Zhou
Wanying Li
Jian-Feng Liu

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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