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Erratum

Erratum: Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA

Cristian Groza
Bing Ge
Warren A. Cheung
Tomi Pastinen
Guillaume Bourque

First Published March 2, 2026

Method

Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution

Paul Ashford
Alexander M. Frankell
Zofia Piszka
Camilla S.M. Pang
Mahnaz Abbasian
Maise Al Bakir
... [+1 authors] ...,
Mariam Jamal-Hanjani
Nicholas McGranahan
Charles Swanton
Christine A. Orengo

First Published February 19, 2026

Method

Robust and efficient annotation of cell states through gene signature scoring

Laure Ciernik
Agnieszka Kraft
Florian Barkmann
Josephine Yates
Valentina Boeva

First Published February 18, 2026

Review

A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest

Andrew D. Bates
Dawid Grzela
Maciej Studzian
Louise Brennan
Moli Williams
Conor Fawcett Beth Hammond
... [+2 authors] ...,
Manreen Grewal
Marcin Ratajewski
Lukasz Pulaski
Urszula L. McClurg

First Published February 17, 2026

Method

N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles" > EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles

Shuyu Zhang
Quan Zou
Mengting Niu
Zhibin Lv
Antony Stalin
Ximei Luo

First Published February 17, 2026

Research

Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility

Dongying Xie
Pohao Ye
Yiming Ma
Zhongying Zhao

First Published February 17, 2026

Method

Mapping and quantifying nascent transcript start sites using TT-TSS-seq

Eleanor Elgood Hunt
Claudia Vivori
Richard Mitter
Vedis Agnadottir
Folkert J. van Werven

First Published February 17, 2026

Research

Assessing the readiness of Oxford Nanopore sequencing for clinical genomics applications

Judith Arres
Santosh Elavalli
Shalini Behl
Daniel Matias Sanchez
Ayesha Al Ali
Abdelrahman Ahmed Yehia Abdelaziz Saad Azza Attia Cyla Minas Sharika Pariyachery Shariq Ahmed Fatmah Aldhuhoori Nitu Thulasidharan Gurunath Katagi Omar Soliman Shilp Purohit Vinay Kusuma Raony Cardenas Thyago Cardoso Luis F. Paulin Philippe Sanio Joseph Mafofo Haiguo Wu Val Zvereff Albarah El-Khani
... [+19 authors] ...,
Fahed Al Marzooqi
Tiago R. Magalhães
Fritz J. Sedlazeck
Javier Quilez

First Published February 11, 2026

Research

Drosophila species" > Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species

Daniel Siqueira de Oliveira
Anaïs Larue
William Vilas Boas Nunes
Francois Sabot
Alejandra Bodelón
María Pilar García Guerreiro
Cristina Vieira
Claudia Marcia Aparecida Carareto

First Published February 10, 2026

Method

Analysis of coding gene expression from small RNA sequencing

Aygun Azadova
Anthonia Ekperuoh
Greg N. Brooke
Antonio Marco

First Published February 10, 2026

Method

spRefine denoises and imputes spatial transcriptomic data with a reference-free framework powered by genomic language model

Tianyu Liu
Tinglin Huang
Wengong Jin
Tinyi Chu
Rex Ying
Hongyu Zhao

First Published February 3, 2026

Corrigendum

Corrigendum: Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer

Milad Razavi-Mohseni
Weitai Huang
Yu A. Guo
Dustin Shigaki
Shamaine Wei Ting Ho
Patrick Tan
Anders J. Skanderup
Michael A. Beer

First Published February 3, 2026

Resource

Tetrahymena" > A systems view on DNA damage response kinetics in Tetrahymena

Emily Nischwitz
Vivien A.C. Schoonenberg
Rachel Mullner
Albert Fradera-Sola
Susanne Zimbelmann
Joshua J. Smith
Falk Butter

First Published January 28, 2026

Research

Degrees of convergent evolution in rodent adaptations to arid environments

Domitille Chalopin
Carine Rey
Jeremy Ganofsky
Juliana Blin
Pascale Chevret
Marion Mouginot
... [+1 authors] ...,
Laurent Guéguen
Bastien Boussau
Sophie Pantalacci
Marie Sémon

First Published January 21, 2026

Resource

Cell type–specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease

Yunxiao Ren
Ming Hu
Yang E. Li
Andrew A. Pieper
Jeffrey Cummings
Feixiong Cheng

First Published January 21, 2026

Method

Autoencoders for genomic variation analysis

Margarita Geleta
Daniel Mas Montserrat
Xavier Giro-i-Nieto
Alexander G. Ioannidis

First Published January 20, 2026

Method

scSHEFT enables multiomics label transfer from scRNA-seq to scATAC-seq through dual alignment

Zhitao Huang
Ruiqing Zheng
Pengzhen Jia
Xuhua Yan
Jinmiao Chen
Min Li

First Published January 20, 2026

Review

Recent advances in methods to characterize archaic introgression in modern humans

David Peede
Mayra M. Bañuelos
Jazeps Medina Tretmanis
Miriam Miyagi
Emilia Huerta-Sánchez

First Published January 16, 2026

Method

cis-regulatory elements" > A scalable computational framework for predicting gene expression from candidate cis-regulatory elements

Qinhu Zhang
Siguo Wang
Zhipeng Li
Wenzheng Bao
Wenjian Liu
De-Shuang Huang

First Published January 16, 2026

Research

Saccharomyces cerevisiae strains" > Natural diversity of telomere length distributions across 100 Saccharomyces cerevisiae strains

Clotilde Garrido
Cintia Gómez-Muñoz
Etienne Kornobis
Nicolas Agier
Oana Ilioaia
Gilles Fischer
Zhou Xu

First Published January 16, 2026

Method

Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit

David R. Lougheed
Tomi Pastinen
Guillaume Bourque

First Published January 15, 2026

Method

Quantifying pathological progression from single-cell transcriptomic data with scPSS

Samin Rahman Khan
M Saifur Rahman
M. Sohel Rahman
Md Abul Hassan Samee

First Published January 14, 2026

Method

Strain-level metagenomic profiling using pangenome graphs with PanTax

Wenhai Zhang
Yuansheng Liu
Guangyi Li
Jialu Xu
Enlian Chen
Alexander Schönhuth
Xiao Luo

First Published January 14, 2026

Research

Stable genome structures in living fossil fishes

Cheng Wang
Chase D. Brownstein
Wenjun Chen
Zufa Ding
Dan Yu
Yu Deng
... [+1 authors] ...,
Chenguang Feng
Thomas J. Near
Shunping He
Liandong Yang

First Published January 13, 2026

Method

Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation

Sophia N. Lee
Erin C. Banda
Lu Qiao
Sarah L. Thompson
Karan Singh
Ryan A. Hagenson
Teresa Davoli
Stefan F. Pinter
Jason M. Sheltzer

First Published January 12, 2026

Research

MHC in newts illuminates the evolutionary dynamics of complex regions in giant genomes

Wiesław Babik
Katarzyna Dudek
Gemma Palomar
Marzena Marszałek
Grzegorz Dubin
Maximina H. Yun
Magdalena Migalska

First Published January 12, 2026

Research

Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells

Marcel Tarbier
Sebastian D. Mackowiak
Vaishnovi Sekar
Franziska Bonath
Etka Yapar
Bastian Fromm
Omid R. Faridani
Inna Biryukova
Marc R. Friedländer

First Published January 12, 2026

Method

Early feature extraction drives model performance in high-resolution chromatin accessibility prediction

Aayush Grover
Till Muser
Liine Kasak
Lin Zhang
Ekaterina Krymova
Valentina Boeva

First Published January 12, 2026

Research

LTR7-PLAAT4 as a potential oncogene and therapeutic target in pancreatic adenocarcinoma" > Transcriptomic landscape of transposable elements reveals LTR7-PLAAT4 as a potential oncogene and therapeutic target in pancreatic adenocarcinoma

Meilong Shi
Chuanqi Teng
Shan Zhang
Xiaobo He
Lingyun Xu
Fengxian Han Rongqi Wen Ganjun Yu Jingwen Liu Yang Feng
... [+5 authors] ...,
Yanfeng Wu
Yan Ren
Gang Jin
Jing Li

First Published January 8, 2026

Method

A spectral component approach leveraging identity-by-descent graphs to address recent population structure in genomic analysis

Ruhollah Shemirani
Gillian M. Belbin
Sinead Cullina
Christa Caggiano
Christopher R. Gignoux
Noah Zaitlen
Eimear E. Kenny

First Published December 23, 2025

Resource

The SynMall resource for characterizing the functional impact of synonymous variation

Chen Ye
Xiaoyan Li
Na Cheng
Yansen Su
Junfeng Xia

First Published December 17, 2025

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

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

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

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

Zheng Hongyu
Sarkar Hirak
Raphael Benjamin J.

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

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

Statistically rigorous and computationally efficient chromatin stripe detection with Quagga

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

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

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

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

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