Search | Genome Research

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Review

Building genomic data structures from compressed representations using prefix-free parsing

Rahul Varki
Christina Boucher

First Published May 15, 2026

Method

Cultivation-independent high-quality microbial genome reconstruction from environmental samples with midi-metagenomics

John Vollmers
Maximiano Correa Cassal
Anne-Kristin Kaster

First Published May 15, 2026

Research

N-ethyl-N-nitrosourea" > Evidence for negative selection against somatic mutations induced in normal fibroblasts by N-ethyl-N-nitrosourea

Cutler Ronald
Heid Johanna
Sun Shixiang
Lee Moonsook
Maslov Alex
Zhang Lei
Sidoli Simone
Dong Xiao
Vijg Jan

First Published May 15, 2026

Method

Accurate delineation of cellular niches via integrated spatial transcriptomics and histological imaging with SYMOL

Daoyuan Wang
Fengyi Zhou
Wenlan Chen
Cheng Liang
Fei Guo

First Published May 14, 2026

Research

Allele-specific splicing modulates protein isoforms and Alzheimer's disease risk

Alison J. King
Kofi Amoah
Laixing Zhang
Jae Hoon Bahn
Ryan M. Barney
Giovanni Quinones-Valdez
Xinshu Xiao

First Published May 14, 2026

Research

Characterizing cytosine methylation of polymorphic transposable element insertions using the human pangenome resources

Xiaoyu Zhuo
Chad Tomlinson
Edward A. Belter
Prashant Kumar Kuntala
Wesley N. Saintilnord
Juan Jiang Tina Lindsay Juan F. Macias-Velasco Robert S. Fulton Ting Wang Derek Albracht Ivan A. Alexandrov Jamie Allen Alawi A. Alsheikh-Ali Nicolas Altemose Casey Andrews Dmitry Antipov Lucinda Antonacci-Fulton Mobin Asri Marcelo Ayllon Jennifer R. Balacco Floris P. Barthel Edward A. Belter Halle D. Bender Andrew P. Blair Davide Bolognini Katherine E. Bonini Christina Boucher Guillaume Bourque Silvia Buonaiuto Shuo Cao Andrew Carroll Ann M. Mc Cartney Monika Cechova Mark J.P. Chaisson Pi-Chuan Chang Xian Chang Jitender Cheema Haoyu Cheng Claudio Ciofi Hiram Clawson Sarah Cody Vincenza Colonna Holland C. Conwell Robert Cook-Deegan Mark Diekhans Maria Angela Diroma Daniel Doerr Zheng Dong Danilo Dubocanin 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 E. Garza Margarita Geleta Mohammadmersad Ghorbani Tina A. Graves-Lindsay Richard E. Green Cristian Groza Bida Gu Andrea Guarracino Melissa Gymrek Maximilian Haeussler Leanne Haggerty Ira M. Hall Nancy F. Hansen Yue Hao Mohammad Amiruddin Hashmi David Haussler Prajna Hebbar Peter Heringer Glenn Hickey Todd L. Hillaker S. Nakib Hossain Neng Huang Sarah E. Hunt Toby Hunt Alexander G. Ioannidis Nafiseh Jafarzadeh Nivesh Jain Erich D. Jarvis Maryam Jehangir Juan Jiang Eimear E. Kenny Juhyun Kim Bonhwang Koo Sergey Koren Milinn Kremitzki Charles H. Langley Ben Langmead Heather A. Lawson Daofeng Li Heng Li Wen-Wei Liao Jiadong Lin Tianjie Liu Glennis A. Logsdon Ryan Lorig-Roach Jonathan LoTempio Hailey Loucks Jane E. Loveland Jianguo Lu Shuangjia Lu Julian K. Lucas Walfred Ma Juan F. Macias-Velasco Kateryna D. Makova Maximillian G. Marin Christopher Markovic Tobias Marschall Franco L. Marsico 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 Pilar N. Ossorio Chie Owa Sadye Paez Benedict Paten Clelia Peano Adam M. Phillippy Brandon D. Pickett Laura Pignata Nadia Pisanti David Porubsky Pjotr Prins Anandi Radhakrishnan T. Rhyker Ranallo-Benavidez Brian J. Raney Mikko Rautiainen Alessandro Raveane Luyao Ren Arang Rhie Fedor Ryabov Samuel Sacco Farnaz Salehi 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 Ahmad Abou Tayoun Jack A.S. Tierney Chad Tomlinson Francesca Floriana Tricomi Mohammed Uddin Matteo Tommaso Ungaro Rahul Varki Flavia Villani Ivo Violich 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
... [+208 authors] ...,
Wenjin Zhang
Ying Zhou
Xiaoyu Zhuo
Giulia Zunino

First Published May 14, 2026

Research

DNA conformational flexibility descriptors improve transcription factor binding prediction across diverse transcription factor families

Upalabdha Dey
Venkata Rajesh Yella
Aditya Kumar

First Published May 14, 2026

Method

Tree reconstruction guarantees from CRISPR-Cas9 lineage tracing data using Neighbor-Joining

Kevin An
Sebastian Prillo
Wilson Wu
Ivan Kristanto
Matthew G. Jones
Yun S. Song
Nir Yosef

First Published May 14, 2026

Research

Single-cell transcriptomics reveals rapid divergence of genes guiding meiosis and spermiogenesis in two passerine birds

J. Carolina Segami
Marie Sémon
Catarina Cunha
Claudia Bergin
Carina F. Mugal
Anna Qvarnström

First Published May 14, 2026

Research

Drosophila" > Structural variants are enriched in deleterious visible phenotypes in Drosophila

Alejandra Samano
Matthew Musat
Mihir Junaghare
Asad Ahmad
Mehlum Ali
Sebastian Alves Sreeram Pasupuleti Jelisha Perera Omar Saada
... [+4 authors] ...,
Brady Sabido
Trevor Smith
Sophie Walz
Mahul Chakraborty

First Published May 14, 2026

Research

6A reprogramming unveils vitamin-driven post-transcriptional regulation in mice" > Tissue-specific mRNA m⁶A reprogramming unveils vitamin-driven post-transcriptional regulation in mice

Jia Li
Anrui Liu
Runzhou Liu
Zihe Xu
Meng Yang
Xiaoqi Zheng Ye Tian Shengjun Wen Kaixin Cao
... [+4 authors] ...,
Daoqiang Lu
Chen Huang
Tong-Meng Yan
Xiaoyun Wang

First Published May 11, 2026

Research

Dynamic body size evolution during speciation of predatory cichlid fishes in the Lake Malawi superradiation

Liandong Yang
Holly Scott
Benjamin P. Ngatunga
Asilatu H. Shechonge
George F. Turner
Martin J. Genner

First Published May 4, 2026

Research

Single-cell template strand sequencing reveals culture-induced chromosomal instability in a gibbon cell line

Alessia Daponte
Gerardina Chirico
Annalisa Paparella
Annalaura Montanari
Caterina Manzari
Martina Macino Oliver Dionisi Dyck Francesco De Leonardis Flavia Angela Maria Maggiolini Alberto L'Abbate Francesco Montinaro Sandra Louzada
... [+7 authors] ...,
Mario Ventura
Ashley D. Sanders
Francesca Antonacci
Claudia Rita Catacchio

First Published May 4, 2026

Research

R-loops shape the H2A.Z landscape and promote balanced lineage allocation during differentiation

Chun-Hao Chao
Thomas G. Fazzio

First Published May 4, 2026

Review

Hash functions in nucleotide sequence analysis

Ke Chen
Xiang Li
Qian Shi
Mingfu Shao
Paul Medvedev

First Published May 4, 2026

Method

Using CRISPR barcoding as a molecular clock to capture dynamic processes at single-cell resolution

Yolanda Andres-Lopez
Alice Santambrogio
Ioannis Kafetzopoulos
Christopher D. Todd
Carla El Khouri-Gonzalez
J-Elliot Gonzalez-Alvarez
... [+1 authors] ...,
Celia Alda-Catalinas
Stephen J. Clark
Wolf Reik
Irene Hernando-Herraez

First Published May 1, 2026

Method

Genealogy-based trait association with LOCATER boosts power at loci with allelic heterogeneity

Xinxin Wang
Ryan Christ
Erica Young
Chul Joo Kang
Indraniel Das
Edward A. Belter Markku Laakso
... [+2 authors] ...,
Louis J.M. Aslett
David Steinsaltz
Nathan O. Stitziel
Ira M. Hall

First Published April 16, 2026

Method

Balancing Gene Ontology annotation specificity in protein function prediction based on the protein sequence large graph

Jiangyi Shao
Shutao Chen
Ziwen Wang
Zixu Chen
Bin Liu

First Published April 15, 2026

Research

Age-dependent mutational loads in human tRNA genes are tumor-specific and result in chimeric tRNA sequences that could disrupt the genetic code

Marina Murillo
Marina Salvadores
Aina Vaquer Picó
Lina Tsapanou
Adrian Gabriel Torres
Fran Supek
Lluis Ribas de Pouplana

First Published April 15, 2026

Research

Drosophila innate immune response" > A genome-wide survey reveals that a diverse array of enhancers coordinates the Drosophila innate immune response

Lianne B. Cohen
Tamara Hadzic
Caitlin Sauer
Julia R. Gibbs
Zeba Wunderlich

First Published April 15, 2026

Research

Epigenetic characterization of pseudogenes across human tissues

Yunzhe Jiang
Beatrice Borsari
Mark Gerstein

First Published April 15, 2026

Method

Highly efficient and scarless genome editing via essential-gene-coupled homology-directed repair

Joo Hye Yeo
Hyongbum Henry Kim
Sang Ho Oh
Jinu Lee

First Published April 15, 2026

Method

Dynamics of intronic polyadenylation in the hematopoietic lineage and its regulation by DNA methylation

Richa Rashmi
Abhinaya Muruganandham
Pranita Borkar
Sumana Mallick
Taylor Hubbs
Ari Aviles
Daniel Chung
Irtisha Singh

First Published April 13, 2026

Method

Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie

Krzysztof H. Banecki
Haoxi Chai
Yijun Ruan
Dariusz Plewczynski

First Published April 8, 2026

Resource

Lignature provides a curated resource of ligand-induced transcriptomic signatures for signaling inference

Ying Xin
Md Amanullah
Cheng Qian
Chingmo Zhou
Jiang Qian

First Published April 8, 2026

Method

Nanopore sequencing identifies high-frequency somatic structural variations in laryngeal squamous cell carcinoma genomes

Xuyan Liu
Lin Xia
Yixin Qiao
Yang Li
Yan Huang
Bingyan Yue Xi Liang Xin Yang Honghui Zhang
... [+4 authors] ...,
Jiaxun Zhang
Xiao Chen
Dan Xie
Jifeng Liu

First Published April 8, 2026

Method

Enabling efficient and robust analysis of tandem repeats in genomic data using Wavefront-based String Decomposer

Junhai Qi
Zhidong Yang
Ting Yu
Guojun Li

First Published April 8, 2026

Resource

Whole-genome sequencing of diverse 351 cultured prokaryotes including as-yet-unsequenced type strains

Shingo Kato
Sachiko Masuda
Arisa Shibata
Takashi Itoh
Mitsuo Sakamoto
Ken Shirasu
Moriya Ohkuma

First Published April 7, 2026

Corrigendum

Corrigendum: TP53-inducible putative long noncoding RNAs encode functional polypeptides that suppress cell proliferation

Wenli Xu
Chang Liu
Bing Deng
Penghui Lin
Zhenghua Sun
Anrui Liu Jiajia Xuan Yuying Li Keren Zhou Xiaoqin Zhang Qiaojuan Huang Hui Zhou
... [+7 authors] ...,
Qingyu He
Bin Li
Lianghu Qu
Jianhua Yang

First Published April 7, 2026

Research

Dynamics and consequences of differential RNA isoform production during cardiomyocyte fate determination and early-stage maturation

Joanna Delimata-Raczek
Natalia Koralewska
Bart Krist
Magdalena Rakoczy
Marek Figlerowicz
Ireneusz Stolarek

First Published April 3, 2026

Method

Incorporating valuable prior knowledge to improve deep learning prediction of genetic perturbation responses

Xiuhao Fu
Chao Yang
Chunyan Cui
Aoyun Geng
Yidi Sun
Chao Zha Feifei Cui
... [+2 authors] ...,
Leyi Wei
Quan Zou
Xin Gao
Zilong Zhang

First Published March 26, 2026

Resource

Isoform- and pathway-specific regulation of post-transcriptional RNA processing in human cells

Ishwarya Venkata Narayanan
Karan Bedi
Brian Magnuson
Ariel McShane
Mario Ashaka
Michelle Paulsen
Thomas E Wilson
Mats Ljungman

First Published March 26, 2026

Method

High-fidelity bidirectional translation between single-cell transcriptomes and DNA methylomes with scBOND

Kehan Lang
Chenyang Jia
Siyu Li
Yi Guo
Dingjun Hu
Shengquan Chen

First Published March 26, 2026

Research

Centromeric instability and chromoanasynthesis observed in nine supernumerary marker chromosomes resolved with long-read genome sequencing

Kristine Bilgrav Saether
Angelo Salazar Mantero
Marlene Ek
Maria Pettersson
Elisabeth Syk Lundberg
Christopher M. Grochowski
Claudia M.B. Carvalho
Jesper Eisfeldt
Anna Lindstrand

First Published March 25, 2026

Research

ACTB methylation regulates SMARCA4 genomic occupancy to promote translation and reduce adhesion in colorectal cancer cells

Elina Abaev-Schneiderman
Linh Nguyen
Raz Shalev
Tzofit Elbaz Biton
Anand Chopra
Giritharan Jagadeesan Daniel Sevilla-Sanchez Nili Tickotsky Moskovitz
... [+3 authors] ...,
Liron Levin
Michal Feldman
Capucine Van Rechem
Dan Levy

First Published March 25, 2026

Method

Complete genetic and epigenetic architecture of D4Z4 macrosatellites in FSHD, BAMS, and reference cohorts with D4Z4End2End

Lucinda C. Xiao
Ayush Semwal
Brianna St John
Kathleen Zeglinski
Shian Su
James Lancaster Shifeng Xue Bruno Reversade
... [+3 authors] ...,
Matthew E. Ritchie
Frédérique Magdinier
Marnie E. Blewitt
Quentin Gouil

First Published March 23, 2026

Research

Aphelenchus avenae implicates P5CS in nematode desiccation stress response" > Haplotype-resolved telomere-to-telomere genome of Aphelenchus avenae implicates P5CS in nematode desiccation stress response

Yali Zhang
Yayi Zhou
Yangyang Chen
Xueyu Wang
Boyan Hu
Shahid Siddique Romnick A. Latina Veronica I. Casey Dexin Bo Yucheng Liao
... [+5 authors] ...,
Min Zhang
Ming Sun
Fengjuan Zhang
Dadong Dai

First Published March 23, 2026

Method

k-mer cross-species profiling reveals taxon-specific TE expansions accompanied by KZFP co-option and functional impacts in ruminants" > k-mer cross-species profiling reveals taxon-specific TE expansions accompanied by KZFP co-option and functional impacts in ruminants

Pengju Zhao
Jiayi He
Chen Peng
Yuelang Zhang
Chong Wang
Dongyou Yu
Lingzhao Fang
Zhengguang Wang

First Published March 23, 2026

Method

High-resolution genotype-free mapping of genetic variation with CRI-SPA-Map

Sheila Lutz
Megan Lawler
Samuel Amidon
Frank W. Albert

First Published March 23, 2026

Method

Restoring the potency of a neutralizing antibody via guided hypermutation with hyper-antibody editor HAE1

Yuhong Wang
Yuefeng Guo
Qiuyu Lu
Xinyi Liu
Haoqi Xu
Jiayi Chen Ruiqi Pi Shaopeng Yuan Ziting Yang
... [+4 authors] ...,
Rusen Lu
Fei-Long Meng
Tingting Gan
Jiazhi Hu

First Published March 19, 2026

Method

Parallel analysis of replication timing, gene expression, and copy number with PARTAGE

Lakshana Sruthi Sadu Murari
Quinn Dickinson
Silvia Meyer-Nava
Juan Carlos Rivera-Mulia

First Published March 19, 2026

Research

cis-antisense RNA duplexes" > A transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes

Zohar Rosenwasser
Roni Cohen-Fultheim
Ofir Shliefer
Erez Y. Levanon
Eli Eisenberg

First Published March 12, 2026

Method

Scalable cell-specific coexpression networks for granular regulatory pattern discovery with NeighbourNet

Yidi Deng
Jiadong Mao
Jarny Choi
Kim-Anh Lê Cao

First Published March 5, 2026

Method

Minimizing reference bias with an imputed personalized reference

Kavya Vaddadi
Mao-Jan Lin
Sina Majidian
Taher Mun
Ben Langmead

First Published March 5, 2026

Method

Automated interpretable artificial intelligence genomic prediction with AIGP

Lei Wei
Ziqin Jiang
Baoliang Fan
Yidan Yan
Zhenqiang Xu
Xiaoxiang Hu
Yuzhe Wang

First Published March 5, 2026

Resource

Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease

Kangli Wang
Weikun Xia
Yingli Gu
Songpeng Zu
Qian Yang
Maria Luisa Amaral Yaozhi Wang
... [+2 authors] ...,
Allen Wang
Xiang-Dong Fu
William C. Mobley
Bing Ren

First Published March 4, 2026

Research

Confounding factors in assessing the enriched expression of somatic mutant alleles in bulk tumor samples

Kohei Hagiwara
Andrew Thrasher
Nadezhda V. Terekhanova
Jinghui Zhang

First Published March 4, 2026

Research

cis-regulatory modules acting during vertebrate organogenesis" > Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis

Daniela M. Riley
Randa Elsayed
Mark D. Walsh
Simaran Johal
Ying Lin
Harry Walton
Till Bretschneider
Sascha Ott
Andrew C. Nelson

First Published March 4, 2026

Research

Dynamic A-to-I RNA editing in response to gut microbiome in honey bees

Yuange Duan
Min Huang
Lin Ye
Ling Ma
Yashuai Wu
Yating Du Jiyao Liu Fan Song Li Tian
... [+4 authors] ...,
Wanzhi Cai
Hu Li
Xin Zhou
Shiqi Luo

First Published March 4, 2026

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

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