Search | Genome Research

CL_GR_CellEng_728x90

Your search for returned 6,401 results

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

3
4
5