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Method

Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations

Yuwei Cao
Lauren Patel
Lauren Alcoser
Eric Mendenhall
Christopher Benner
Sven Heinz
Alon Goren

First Published December 12, 2025

Research

XIST isoform in male peripheral glia" > Transcription and potential functions of a novel XIST isoform in male peripheral glia

Kevin S. O'Leary
Meng-Yen Li
Kevyn Jackson
Lijie Shi
Elena Ezhkova
Bernice E. Morrow
Deyou Zheng

First Published December 12, 2025

Resource

The PanOryza pangene catalog of Asian cultivated rice

Bruno Contreras-Moreira
Eshan Sharma
Shradha Saraf
Guy Naamati
Parul Gupta
Justin Elser Dmytro Chebotarov Kapeel Chougule Zhenyuan Lu Sharon Wei Andrew Olson Ian Tsang Disha Lodha Yong Zhou Zhichao Yu Wen Zhao Jianwei Zhang Sandeep Amberkar Kawinnat Sue-Ob Zhi Sun Maria Martin Kenneth L. McNally Doreen Ware Eric W. Deutsch Dario Copetti
... [+20 authors] ...,
Rod A. Wing
Pankaj Jaiswal
Sarah Dyer
Andrew R. Jones

First Published December 12, 2025

Method

The oligogenic inheritance test GCOD detects risk genes and their interactions in congenital heart defects

Maureen Pittman
Kihyun Lee
Franco Felix
Yu Huang
Adrienne Lam
Mauro W. Costa
Deepak Srivastava
Katherine S. Pollard

First Published December 12, 2025

Method

6A demethylation in mRNAs" > A versatile type VI CRISPR-based approach for targeted m⁶A demethylation in mRNAs

Panagiotis G. Adamopoulos
Konstantina Athanasopoulou
Andreas Scorilas

First Published December 11, 2025

Research

Drosophila testis tumor stem cell–like cells" > Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells

Jennifer A. Urban
Daniel Ringwalt
John M. Urban
Wingel Xue
Ryan Gleason
Keji Zhao
Xin Chen

First Published December 10, 2025

Review

The superpowers of imprinting control regions

Bertille Montibus
Franck Court
Philippe Arnaud

First Published December 10, 2025

Method

Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates

Marian F. Laughery
Bastian Stark
Benjamin Morledge-Hampton
Steven A. Roberts
John J. Wyrick

First Published December 9, 2025

Research

Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation

Kevin Moyung
Yulong Li
Heather K. MacAlpine
Alexander J. Hartemink
David M. MacAlpine

First Published December 9, 2025

Reviewer Index

List of Reviewers Volume 35, 2025

First Published December 3, 2025

Editorial

RECOMB 2025 Special Issue

Sriram Sankararaman
Bonnie Berger

First Published December 3, 2025

Method

ML-MAGES enables multivariate genetic association analyses with genes and effect size shrinkage

Xiran Liu
Lorin Crawford
Sohini Ramachandran

First Published November 19, 2025

Method

Integration of high-throughput proteomic data and complementary omics layers with PriOmics

Robin Kosch
Katharina Limm
Annette M. Staiger
Nadine S. Kurz
Nicole Seifert
Bence Oláh Stefan Solbrig Viola Poeschel Gerhard Held Marita Ziepert Norbert Schmitz Emil Chteinberg Reiner Siebert Rainer Spang
... [+9 authors] ...,
Helena U. Zacharias
German Ott
Peter J. Oefner
Michael Altenbuchinger

First Published November 18, 2025

Research

Drosophila intestine" > Polycomb misregulation in enterocytes drives tissue decline in the aging Drosophila intestine

Sarah M. Leichter
Kami Ahmad
Steven Henikoff

First Published November 17, 2025

Method

Joint imputation and deconvolution of gene expression across spatial transcriptomics platforms

Hongyu Zheng
Hirak Sarkar
Benjamin J. Raphael

First Published November 17, 2025

Method

OMKar automates genome karyotyping using optical maps to identify constitutional abnormalities

Siavash Raeisi Dehkordi
Zhaoyang Jia
Joey Estabrook
Jen Hauenstein
Neil Miller
Naz Güleray-Lafci Jürgen Neesen Alex Hastie
... [+3 authors] ...,
Alka Chaubey
Andy Wing Chun Pang
Paul Dremsek
Vineet Bafna

First Published November 14, 2025

Method

Graph-based deep reinforcement learning for haplotype assembly with Ralphi

Enzo Battistella
Anant Maheshwari
Barış Ekim
Bonnie Berger
Victoria Popic

First Published November 14, 2025

Research

Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction

Laura Blanco-Berdugo
Alexis Garretson
Beth L. Dumont

First Published November 13, 2025

Method

Unified integration of spatial transcriptomics across platforms with LLOKI

Ellie Haber
Ajinkya Deshpande
Jian Ma
Spencer Krieger

First Published November 13, 2025

Method

Secure phasing of private genomes in a trusted execution environment with TX-Phase

Natnatee Dokmai
Kaiyuan Zhu
S. Cenk Sahinalp
Hyunghoon Cho

First Published November 12, 2025

Method

Statistically rigorous and computationally efficient chromatin stripe detection with Quagga

Fan Feng
Sean Moran
Anders S. Hansen
Xiaotian Zhang
Jie Liu

First Published November 12, 2025

Method

Label-free selection of marker genes in single-cell and spatial transcriptomics with geneCover

An Wang
Stephanie Hicks
Donald Geman
Laurent Younes

First Published November 12, 2025

Method

Partitioned multi-MUM finding for scalable pangenomics with MumemtoM

Vikram S. Shivakumar
Ben Langmead

First Published November 7, 2025

Resource

Epigenomics of embryogenesis in turbot

Oscar Aramburu
Belen G Pardo
Ada Jimenez-Gonzalez
Andrés Blanco-Hortas
Daniel Macqueen
Carmen Bouza
Paulino Martinez

First Published November 4, 2025

Research

Sorex araneus" > Dynamic metabolic and molecular changes during seasonal shrinking in Sorex araneus

William R. Thomas
Cecilia Baldoni
Yuanyuan Zeng
David Carlson
Julie Holm-Jacobsen
Marion Muturi Dominik von Elverfeldt Tue B. Bennike
... [+3 authors] ...,
Dina K.N. Dechmann
John Nieland
Angelique P. Corthals
Liliana M. Dávalos

First Published November 4, 2025

Method

Predicted protein 3D structures provide essential insights into the genetic architecture underlying phenotypic diversity in maize

Shuai Wang
Merritt Khaipho-Burch
Lynn C. Johnson
Zachary R. Miller
Peter J. Bradbury
Doug Speed William J. Allen M. Cinta Romay
... [+3 authors] ...,
Jiquan Xue
Edward S. Buckler
Guillaume P. Ramstein
Baoxing Song

First Published October 31, 2025

Research

3C sites in poly(A) RNA" > Nanopore direct RNA sequencing reveals METTL2A-mediated m³C sites in poly(A) RNA

Shuhei Mitsutomi
Anzu Sugawara
Masahide Seki
Yutaka Suzuki
Sotaro Miyao
Haozhe Du
... [+1 authors] ...,
Kenji Takahashi
Yusuke Mizukami
Kenzui Taniue
Nobuyoshi Akimitsu

First Published October 30, 2025

Method

Real-time analysis and visualization of nanopore metagenomic samples with MARTi

Ned Peel
Samuel Martin
Darren Heavens
Douglas W. Yu
Matthew D. Clark
Richard M. Leggett

First Published October 27, 2025

Method

BayesRVAT enhances rare-variant association testing through Bayesian aggregation of functional annotations

Antonio Nappi
Liubov Shilova
Theofanis Karaletsos
Na Cai
Francesco Paolo Casale

First Published October 24, 2025

Research

A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress

Taylor Anglen
Irene M. Kaplow
Baekgyu Choi
Enya Dewars
Robin M. Perelli
Kevin T. Hagy Duc Tran Megan E. Ramaker Svati H. Shah Inkyung Jung
... [+5 authors] ...,
Andrew P. Landstrom
Ravi Karra
Yarui Diao
Charles A. Gersbach

First Published October 22, 2025

Method

Polyomino reconstructs spatial transcriptomic profiles with single-cell resolution via a region-allocation method

Quanyou Cai
Lihui Lin
Xin Liu
Jiekai Chen

First Published October 22, 2025

Method

Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates

Haiyue Liu
Lea H. Gregersen

First Published October 22, 2025

Research

Epigenetic and evolutionary features of ape subterminal heterochromatin

DongAhn Yoo
Katherine M. Munson
Evan E. Eichler

First Published October 22, 2025

Method

Iterative improvement of deep learning models using synthetic regulatory genomics

André M. Ribeiro-dos-Santos
Matthew T. Maurano

First Published October 22, 2025

Research

Genomic regulatory landscape underlying the antiviral response of Atlantic salmon

Shahmir Naseer
Thomas C Clark
Bertrand Collet
Pooran Dewari
Damir Baranasic
Daniel J Macqueen
Pierre Boudinot
Samuel A.M. Martin

First Published October 22, 2025

Method

Interpretable phenotype decoding from multicondition sequencing data with ALPINE

Wei-Hao Lee
Lechuan Li
Ruth Dannenfelser
Vicky Yao

First Published October 22, 2025

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

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

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

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

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

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

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

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

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

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

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

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

Khang Ma
Rinki Ratnapriya

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

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

Rashid Al-Abri
Gamze Gürsoy

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

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

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

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

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

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

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

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

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

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

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

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

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

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