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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

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

Drosophila innate immune response" > A genome-wide survey reveals 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

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

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

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

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

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

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 neutralizing antibody via guided hypermutation with hyper-antibody editor

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Review

The superpowers of imprinting control regions

Bertille Montibus
Franck Court
Philippe Arnaud

First Published December 10, 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

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

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

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

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

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

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

Partitioned multi-MUM finding for scalable pangenomics with MumemtoM

Vikram S. Shivakumar
Ben Langmead

First Published November 7, 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

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

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

Epigenetic and evolutionary features of ape subterminal heterochromatin

DongAhn Yoo
Katherine M. Munson
Evan E. Eichler

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

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

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

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