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Research

Cyanophora paradoxa reveals unique repair signature" > Elevated DNA insertion rate in Cyanophora paradoxa reveals unique repair signature

Marc Krasovec
Anna Lipzen
Nigel Grimsley
Gilles Mirambeau
Kerrie Barry
Igor V Grigoriev
Gwenael Piganeau

First Published June 12, 2026

Method

A comparison of ancient DNA yields across ossicles and the petrous bone reveals the best preservation in the stapes and incus

Ekin Sağlıcan
Arda Sevkar
Duygu Deniz Kazancı
Gonzalo Oteo García
Sevgi Yorulmaz
Kıvılcım Başak Vural Gökhan Çakan Gökçen Adiloğlu Duru Buldak Güneş Duru Aliye Öztan Brenna Hassett Nurcan Kayacan Aslı Erim Özdoğan Anders Götherström
... [+10 authors] ...,
Füsun Özer
Ömür Dilek Erdal
Yılmaz Selim Erdal
Mehmet Somel

First Published June 11, 2026

Research

Evolution of an adaptive, inducible defensive trait in a model crustacean

Zhixiong Deng
Sen Xu
Dengqing Li
Guo Yu
Swatantra Neupane
Li Wang
... [+1 authors] ...,
David Blair
Wei Hu
Adam Petrusek
Mingbo Yin

First Published June 5, 2026

Method

Reference-informed spatial domain detection using weak supervision for spatial transcriptomics

Xin Ma
Weijia Jin
Qing Lu
Ramon C. Sun
Li Chen

First Published June 3, 2026

Method

Transfer learning enhances clinical utility of polygenic scores with small, phenotypically refined cohorts

YuChung Lin
Christoph Patrick Beier
Zuzana Sobiskova
Hamandi Khalid
Tommy Stodberg
Ching Ching Ng Danielle Andrade Marte Roa Syvertsen Elena Gardella Alessandro Orsini Choong Yi Fong Jana Zarubova Michaela Kajsov Kheng Seang Lim Kaja Kristine Selmer Emanuele Cerulli Irelli
... [+11 authors] ...,
Guido Rubboli
Pasquale Striano
Deb K. Pal
Lisa J Strug

First Published June 2, 2026

Research

Genome evolution in parthenogenetic nematodes shaped by chromosome rearrangements and introgression

George Chung
Lewis Stevens
Xiaoguang Dai
Scott Hickey
Karin Kiontke
Priyesh Rughani Manuela R. Kieninger Joanna C. Collins Sissel Juul
... [+4 authors] ...,
Fabio Piano
David H. A. Fitch
Mark Blaxter
Kristin C. Gunsalus

First Published May 29, 2026

Method

Augmenting transcriptome annotations through the lens of splicing evolution

Xiaofei Carl Zang
Ke Chen
Irtesam Mahmud Khan
Mingfu Shao

First Published May 29, 2026

Research

Transposable element small RNAs and large RNAs in aging brains and implications in Huntington's and Parkinson's disease

Gargi Dayama
Jou-Hsuan Roxie Lee
Shruti Gupta
Christian Brion
Brianne K. Connizzo
Adam T. Labadorf
Richard H. Myers
Nelson C. Lau

First Published May 28, 2026

Resource

A comprehensive single-cell atlas of monoallelic expression across various tissues in zebrafish

Hui Zeng
Zhan Liu
Huimin Xiang
Boliang Liu
Di Zhang
Xionglei He
Shanjun Deng
Li Liu

First Published May 28, 2026

Research

Whole-genome variant detection in long-read sequencing data from ultralow input patient samples

Katherine Wang
Cera J. Aex
Hayan Lee
Lucas Finot
Kevin Zhu
Julianna R. Chang Aaron M. Horning William J. Rowell
... [+3 authors] ...,
Philip Li
Sarah B. Kingan
Michael P. Snyder
Graham S. Erwin

First Published May 28, 2026

Method

RECOMBINE identifies recurrent composite markers of cell types and states

Xubin Li
Justin Nguyen
Anil Korkut

First Published May 20, 2026

Research

Interplay between purging and admixture shapes genetic load in an invasive guppy population

Katarzyna Burda
Mary J Janecka
Ryan S Mohammed
David R Clark
Rachael Kramp
Jessica F Stephenson
Jacek Radwan
Mateusz Konczal

First Published May 20, 2026

Research

Herbaria provide a valuable resource for obtaining informative mRNA

Alexa S. Tyszka
Khong-Sam Chia
Eric C. Bretz
Linda Mansour
Drew A. Larson
Nathanael Walker-Hale
Philip Carella
Joseph F. Walker

First Published May 19, 2026

Method

Deep learning the TF regulatory code for gene expression

Yuanyuan Li
Xiaohui Huang
Yixuan Qi
Zheng Zhang
Hui Ding
Quan Zou
Li Liu

First Published May 15, 2026

Review

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

Rahul Varki
Christina Boucher

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

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

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

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 Macias 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

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

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

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

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

J. Carolina Segami Marzal
Marie Semon
Catarina Cunha
Claudia Bergin
Carina Mugal
Anna Qvarnstrom

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

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

Research

Epigenetic characterization of pseudogenes across human tissues

Yunzhe Jiang
Beatrice Borsari
Mark Gerstein

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

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

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

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

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

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

Method

Autoencoders for genomic variation analysis

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

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

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

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

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

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

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

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