Search | Genome Research

Your search for returned 6,440 results

Research

Birth of protein-coding exons by ancient domestication of LINE-1 retrotransposon

Koichi Kitao
Kenji Ichiyanagi
So Nakagawa

First Published May 8, 2025

Method

Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes

Paras Verma
Deeksha Thakur
Deepanshi Awasthi
Shashi Bhushan Pandit

First Published May 7, 2025

Method

Harnessing agent-based frameworks in CellAgentChat to unravel cell–cell interactions from single-cell and spatial transcriptomics

Vishvak Raghavan
Yumin Zheng
Yue Li
Jun Ding

First Published May 2, 2025

Research

Oryza" > Continuous infiltration and evolutionary trajectory of nuclear organelle DNA in Oryza

Chenbo Gong
Yicheng Huang
Mengmeng Liu
Yong Zhou
Yinwei Xu
Nahed Mohammed Xintong Qiao Andrea Zuccolo Weibo Xie
... [+4 authors] ...,
Rod A. Wing
Jianwei Zhang
Fei Zhou
Yongjun Lin

First Published April 25, 2025

Research

Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing

Keegan S. Krick
Marissa Maroni
Erica Korb
Kristen W. Lynch
Elizabeth A. Heller

First Published April 24, 2025

Research

Extreme heterochiasmy and high rates of sex-reversed recombination result in large yet homomorphic sex chromosomes in the Emei moustache toad

Siyu Xie
Jun Li
Wanyan Chen
Lydia J.M. Fong
Chunhua Huang
Yan Feng
... [+1 authors] ...,
Qingbo Ai
Mian Zhao
Judith E. Mank
Hua Wu

First Published April 24, 2025

Research

Blastocystis gut microbiome–associated protists reveal evolutionary diversification to host ecology" > Contiguous and complete assemblies of Blastocystis gut microbiome–associated protists reveal evolutionary diversification to host ecology

Abigail L. Lind
Nathan A. McDonald
Elias R. Gerrick
Ami S. Bhatt
Katherine S. Pollard

First Published April 22, 2025

Method

Dissecting multilayer cell–cell communications with signaling feedback loops from spatial transcriptomics data

Lulu Yan
Jinyu Cheng
Qing Nie
Xiaoqiang Sun

First Published April 22, 2025

Resource

MPRAbase a Massively Parallel Reporter Assay database

Jingjing Zhao
Fotis A Baltoumas
Maxwell A Konnaris
Ioannis Mouratidis
Zhe Liu
Jasmine Sims
... [+1 authors] ...,
Vikram Agarwal
Georgios A Pavlopoulos
Ilias Georgakopoulos-Soares
Nadav Ahituv

First Published April 22, 2025

Research

Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis

Olga M. Sigalova
Mattia Forneris
Frosina Stojanovska
Bingqing Zhao
Rebecca R. Viales
Adam Rabinowitz
... [+1 authors] ...,
Fayrouz Hammal
Benoît Ballester
Judith B. Zaugg
Eileen E.M. Furlong

First Published April 15, 2025

Research

cis-regulatory variation modifies the penetrance of pathogenic SHROOM3 variants in craniofacial microsomia" > Common cis-regulatory variation modifies the penetrance of pathogenic SHROOM3 variants in craniofacial microsomia

Hao Zhu
Jiao Zhang
Soumya Rao
Matthew D. Durbin
Ying Li
Ruirui Lang Jiqiang Liu Baichuan Xiao Hailin Shan Ziqiu Meng Jinmo Wang Xiaokai Tang Zhenni Shi Liza L. Cox Shouqin Zhao Stephanie M. Ware Tiong Y. Tan Michelle de Silva Lyndon Gallacher Ting Liu Jie Mi Changqing Zeng Hou-Feng Zheng
... [+18 authors] ...,
Qingguo Zhang
Stylianos E. Antonarakis
Timothy C. Cox
Yong-Biao Zhang

First Published April 15, 2025

Resource

Building better genome annotations across the tree of life

Adam H. Freedman
Timothy B. Sackton

First Published April 15, 2025

Mini-Review

Evolution of genome-wide methylation profiling technologies

Carolina Montano
Winston Timp

First Published April 14, 2025

Perspective

The impact of long-read sequencing on human population-scale genomics

Tobias Rausch
Tobias Marschall
Jan O. Korbel

First Published April 14, 2025

Mini-Review

A Hitchhiker's Guide to long-read genomic analysis

Medhat Mahmoud
Daniel P. Agustinho
Fritz J. Sedlazeck

First Published April 14, 2025

Editorial

Long reads decipher genomes and transcriptomes and offer novel insights into biology and diseases

Ana Conesa
Alexander Hoischen
Fritz J. Sedlazeck

First Published April 14, 2025

Research

Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus

Rita Tam
Mareike Möller
Runpeng Luo
Zhenyan Luo
Ashley Jones
Sambasivam Periyannan
John P. Rathjen
Benjamin Schwessinger

First Published April 11, 2025

Method

Analytical validation of germline small variant detection using long-read HiFi genome sequencing

Nathan Hammond
Linda Liao
Pun Wai Tong
Zena Ng
Thuy-Mi P. Nguyen
Chandler Ho
Yao Yang
Stuart A. Scott

First Published April 11, 2025

Method

Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC

Byron J. Smith
Chunyu Zhao
Veronika Dubinkina
Xiaofan Jin
Liron Zahavi
Saar Shoer
Jacqueline Moltzau-Anderson
Eran Segal
Katherine S. Pollard

First Published April 10, 2025

Research

C. elegans" > Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans

Jun Kim
Haoyu Wang
Sevinç Ercan

First Published April 10, 2025

Research

Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements

Fu Xiang Quah
Miguel Vasconcelos Almeida
Moritz Blumer
Chengwei Ulrika Yuan
Bettina Fischer
Kirsten See Ben Jackson Richard Zatha Bosco Rusuwa George F. Turner M. Emília Santos
... [+6 authors] ...,
Hannes Svardal
Martin Hemberg
Richard Durbin
Eric Miska

First Published April 10, 2025

Method

k-mer manifold approximation and projection for visualizing DNA sequences" > k-mer manifold approximation and projection for visualizing DNA sequences

Chengbo Fu
Einari A. Niskanen
Gong-Hong Wei
Zhirong Yang
Marta Sanvicente-García
Marc Güell
Lu Cheng

First Published April 10, 2025

Method

TFcomb identifies transcription factor combinations for cellular reprogramming based on single-cell multiomics data

Chen Li
Sijie Chen
Yixin Chen
Haiyang Bian
Minsheng Hao
Lei Wei
Xuegong Zhang

First Published April 10, 2025

Research

Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes

Yu-Chi Chen
David L.J. Vendrami
Maximilian L. Huber
Luisa E.Y. Handel
Christopher R. Cooney
Joseph I. Hoffman
Toni I. Gossmann

First Published March 31, 2025

Research

Unraveling undiagnosed rare disease cases by HiFi long-read genome sequencing

Wouter Steyaert
Lydia Sagath
German Demidov
Vicente A. Yépez
Anna Esteve-Codina
Julien Gagneur Kornelia Ellwanger Ronny Derks Marjan Weiss Amber den Ouden Simone van den Heuvel Hilde Swinkels Nick Zomer Marloes Steehouwer Luke O'Gorman Galuh Astuti Kornelia Neveling Rebecca Schüle Jishu Xu Matthis Synofzik Danique Beijer Holger Hengel Ludger Schöls Kristl G. Claeys Jonathan Baets Liedewei Van de Vondel Alessandra Ferlini Rita Selvatici Heba Morsy Marwa Saeed Abd Elmaksoud Volker Straub Juliane Müller Veronica Pini Luke Perry Anna Sarkozy Irina Zaharieva Francesco Muntoni Enrico Bugiardini Kiran Polavarapu Rita Horvath Evan Reid Hanns Lochmüller Marco Spinazzi Marco Savarese Leslie Matalonga Steven Laurie Han G. Brunner Holm Graessner Sergi Beltran
... [+44 authors] ...,
Stephan Ossowski
Lisenka E.L.M. Vissers
Christian Gilissen
Alexander Hoischen

First Published March 26, 2025

Research

Analysis of canine gene constraint identifies new variants for orofacial clefts and stature

Reuben M. Buckley
Nüket Bilgen
Alexander C. Harris
Peter Savolainen
Cafer Tepeli
Metin Erdoğan Aitor Serres Armero Dayna L. Dreger Frank G. van Steenbeek Marjo K. Hytönen Heidi G. Parker Jessica Hale
... [+7 authors] ...,
Hannes Lohi
Bengi Çınar Kul
Adam R. Boyko
Elaine A. Ostrander

First Published March 24, 2025

Method

An optimized toolkit for high-molecular-weight DNA extraction and ultra-long-read nanopore sequencing using glass beads and hexamminecobalt(III) chloride

Inswasti Cahyani
John Tyson
Nadine Holmes
Josh Quick
Chris Moore
Nick Loman
Matthew Loose

First Published March 24, 2025

Method

De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies

John Beaulaurier
Lynn Ly
J. Andrew Duty
Carly Tyer
Christian Stevens
Chuan-Tien Hung Akash Sookdeo Alex W. Drong Shreyas Kowdle Axel Guzman-Solis Domenico Tortorella
... [+6 authors] ...,
Daniel J. Turner
Sissel Juul
Scott Hickey
Benhur Lee

First Published March 21, 2025

Research

Optical genome mapping enables accurate testing of large repeat expansions

Bart van der Sanden
Kornelia Neveling
Syukri Shukor
Michael D. Gallagher
Joyce Lee
Stephanie L. Burke Maartje Pennings Ronald van Beek Michiel Oorsprong Ellen Kater-Baats Eveline Kamping Alide A. Tieleman Nicol C. Voermans Ingrid E. Scheffer Jozef Gecz Mark A. Corbett Lisenka E.L.M. Vissers
... [+12 authors] ...,
Andy Wing Chun Pang
Alex Hastie
Erik-Jan Kamsteeg
Alexander Hoischen

First Published March 20, 2025

Method

Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease

Tanner D. Jensen
Bohan Ni
Chloe M. Reuter
John E. Gorzynski
Sarah Fazal
Devon Bonner Rachel A. Ungar Pagé C. Goddard Archana Raja Euan A. Ashley Jonathan A. Bernstein Stephan Zuchner Michael D. Greicius
... [+8 authors] ...,
Stephen B. Montgomery
Michael C. Schatz
Matthew T. Wheeler
Alexis Battle

First Published March 20, 2025

Research

Unexpectedly low recombination rates and presence of hotspots in termite genomes

Turid Everitt
Tilman Rönneburg
Daniel Elsner
Anna Olsson
Yuanzhen Liu
Tuuli Larva
Judith Korb
Matthew T. Webster

First Published March 20, 2025

Method

Examining the dynamics of three-dimensional genome organization with multitask matrix factorization

Da-Inn Lee
Sushmita Roy

First Published March 20, 2025

Research

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 20, 2025

Perspective

Unraveling the hidden complexity of cancer through long-read sequencing

Qiuhui Li
Ayse G. Keskus
Justin Wagner
Michal B. Izydorczyk
Winston Timp
Fritz J. Sedlazeck
... [+1 authors] ...,
Alison P. Klein
Justin M. Zook
Mikhail Kolmogorov
Michael C. Schatz

First Published March 20, 2025

Research

Optical genome mapping identifies rare structural variants in neural tube defects

Nikhil S. Sahajpal
Jane Dean
Benjamin Hilton
Timothy Fee
Cindy Skinner
Alex Hastie
... [+1 authors] ...,
Barbara R. DuPont
Alka Chaubey
Michael J. Friez
Roger E. Stevenson

First Published March 19, 2025

Research

Heterogeneous and novel transcript expression in single cells of patient-derived clear cell renal cell carcinoma organoids

Tülay Karakulak
Natalia Zajac
Hella Anna Bolck
Anna Bratus-Neuenschwander
Qin Zhang
Weihong Qi Debleena Basu Tamara Carrasco Oltra
... [+3 authors] ...,
Hubert Rehrauer
Christian von Mering
Holger Moch
Abdullah Kahraman

First Published March 19, 2025

Method

De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data

Arthur Dondi
Nico Borgsmüller
Pedro F. Ferreira
Brian J. Haas
Francis Jacob
Viola Heinzelmann-Schwarz
Niko Beerenwinkel

First Published March 19, 2025

Research

Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T

Luis F. Paulin
Jeremy Fan
Kieran O'Neill
Erin Pleasance
Vanessa L. Porter
Steven J.M. Jones
Fritz J. Sedlazeck

First Published March 17, 2025

Method

BINDER achieves accurate identification of hierarchical TADs by comprehensively characterizing consensus TAD boundaries

Yangyang Liu
Bingqiang Liu
Juntao Liu

First Published March 17, 2025

Method

Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution

Qian Qin
Victoria Popic
Kirsty Wienand
Houlin Yu
Emily White
Akanksha Khorgade Asa Shin Christophe Georgescu Catarina D. Campbell Arthur Dondi
... [+5 authors] ...,
Niko Beerenwinkel
Francisca Vazquez
Aziz M. Al'Khafaji
Brian J. Haas

First Published March 14, 2025

Method

Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity

Mayank Murali
Jamie Saquing
Senbao Lu
Ziyang Gao
Emily F. Watts
Ben Jordan Zachary Peters Wakefield Ana Fiszbein
... [+3 authors] ...,
David R. Cooper
Peter J. Castaldi
Dmitry Korkin
Gloria M. Sheynkman

First Published March 14, 2025

Research

KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution

Kai Otsuka
Akihiko Sakashita
So Maezawa
Richard M. Schultz
Satoshi H. Namekawa

First Published March 12, 2025

Research

Assessing DNA methylation detection for primary human tissue using Nanopore sequencing

Rylee Genner
Stuart Akeson
Melissa Meredith
Pilar Alvarez Jerez
Laksh Malik
Breeana Baker Abigail Miano-Burkhardt
... [+2 authors] ...,
Benedict Paten
Kimberley J. Billingsley
Cornelis Blauwendraat
Miten Jain

First Published March 7, 2025

Research

Integrating short-read and long-read single-cell RNA sequencing for comprehensive transcriptome profiling in mouse retina

Meng Wang
Yumei Li
Jun Wang
Soo Hwan Oh
Yexuan Cao
Rui Chen

First Published March 6, 2025

Method

Homozygous editing of multiple genes for accelerated generation of xenotransplantation pigs

Xiaoyue Duan
Chaolei Chen
Chang Du
Liang Guo
Jun Liu
Naipeng Hou Pan Li Xiaolan Qi
... [+3 authors] ...,
Fei Gao
Xuguang Du
Jiangping Song
Sen Wu

First Published March 5, 2025

Research

Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly

Kang Du
Oliver Deusch
Ilja Bezrukov
Christa Lanz
Yann Guiguen
Margarete Hoffmann
... [+1 authors] ...,
Anette Habring
Detlef Weigel
Manfred Schartl
Christine Dreyer

First Published March 5, 2025

Research

Deciphering the largest disease-associated transcript isoforms in the human neural retina with advanced long-read sequencing approaches

Merel Stemerdink
Tabea Riepe
Nick Zomer
Renee Salz
Michael Kwint
Jaap Oostrik Raoul Timmermans Barbara Ferrari Stefano Ferrari Alfredo Dueñas Rey Emma Delanote Suzanne E. de Bruijn Hannie Kremer Susanne Roosing Frauke Coppieters Alexander Hoischen
... [+11 authors] ...,
Frans P.M. Cremers
Peter A.C. ‘t Hoen
Erwin van Wijk
Erik de Vrieze

First Published March 4, 2025

Method

RAmbler resolves complex repeats in human Chromosomes 8, 19, and X

Sakshar Chakravarty
Glennis Logsdon
Stefano Lonardi

First Published March 4, 2025

Research

Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis

Tianfu Zeng
Haotian Liao
Lin Xia
Siyao You
Yanqun Huang
Jiaxun Zhang
Yahui Liu
Xuyan Liu
Dan Xie

First Published March 4, 2025

Method

Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm

Samuel T. Horsfield
Basil C.T. Fok
Yuhan Fu
Paul Turner
John A. Lees
Nicholas J. Croucher

First Published March 4, 2025

6
7
8