Filter results by:
Author
Publication date
Article type

Filter by Article type

Your search for returned 6,369 results

Save search
Order by:
Show per page
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
Review

The superpowers of imprinting control regions

  • Bertille Montibus
  • Franck Court
  • Philippe Arnaud
  • 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

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
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
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

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

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

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
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

  • Liubomir Chorbadjiev
  • Murat Cokol
  • Zohar Weinstein
  • Kevin Shi
  • Christopher Fleisch
  • Nikolay Dimitrov Svetlin Mladenov Ivo Todorov Iordan Ivanov Simon Xu Steven Ford Yoon-ha Lee Boris Yamrom Steven Marks
  • ... [+9 authors] ...,
  • Adriana Munoz
  • Alex Lash
  • Natalia Volfovsky
  • Ivan Iossifov
  • First Published September 16, 2025
Show per page