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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

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

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

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

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

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

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

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

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

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

Research

Molecular and genetic landscapes of retina and brain microglia in neurodegenerative diseases

Khang Ma
Rinki Ratnapriya

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

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

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

Estimating the size of long tandem repeat expansions from short reads with ScatTR

Rashid Al-Abri
Gamze Gürsoy

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

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

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

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

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

Method

Unveiling the functional fate of duplicated genes through expression profiling and structural analysis

Alex Warwick Vesztrocy
Natasha Glover
Paul D. Thomas
Christophe Dessimoz
Irene Julca

First Published August 14, 2025

Method

Multicondition and multimodal temporal profile inference during mouse embryonic development

Ran Zhang
Chengxiang Qiu
Galina N. Filippova
Gang Li
Jay Shendure
Jean-Philippe Vert
Xinxian Deng
William Stafford Noble
Christine M. Disteche

First Published August 14, 2025

Method

FocalSV enables target region–based structural variant assembly and refinement using single-molecule long-read sequencing data

Can Luo
Zimeng Jamie Zhou
Yichen Henry Liu
Xin Maizie Zhou

First Published August 13, 2025

Research

Intergenic accumulation of RNA polymerase II maintains the potential for swift transcriptional restart upon release from quiescence

Manuela Baquero Pérez
Gertjan Laenen
Isabelle Loïodice
Mickaël Garnier
Ugo Szachnowski
Antonin Morillon
Myriam Ruault
Angela Taddei

First Published August 12, 2025

Research

Phylogenetic relatedness rather than aquatic habitat fosters horizontal transfer of transposable elements in animals

Héloïse Muller
Rosina Savisaar
Jean Peccoud
Sylvain Charlat
Clément Gilbert

First Published August 8, 2025

Method

ERC2.0 evolutionary rate covariation update improves inference of functional interactions across large phylogenies

Jordan H. Little
Guillermo Hoffmann Meyer
Aakash Grover
Alex Michael Francette
Raghavendran Partha
Karen M. Arndt
Martin Smith
Nathan Clark
Maria Chikina

First Published August 7, 2025

Method

BRCA1 and BRCA2 splice isoforms" > The SeqSplice multiplexed minigene splicing assay for characterization and quantitation of variant-induced BRCA1 and BRCA2 splice isoforms

Daffodil M. Canson
Michael T. Parsons
Gemma Moir-Meyer
Troy Dumenil
Gemma Montalban
Erica Lin Terri P. McVeigh Aimee L. Davidson
... [+3 authors] ...,
Shaun M. Bouckaert
Matt Trau
Darren Korbie
Amanda B. Spurdle

First Published August 6, 2025

Mini-Review

The paradox of R-loops: guardians of the genome or drivers of disease?

Shachinthaka D. Dissanayaka Mudiyanselage
Phillip Wulfridge
Kavitha Sarma

First Published August 6, 2025

Research

Xist upstream deletion leads to dysregulation of Xist and autosomal gene expression" > Xist upstream deletion leads to dysregulation of Xist and autosomal gene expression

Sudeshna Majumdar
Lakshmi Sowjanya Bammidi
Hemant C. Naik
Avinchal Manhas
Runumi Baro
Akash Kalita Amlan Jyoti Naskar
... [+2 authors] ...,
Sundarraj Nidharshan
Girija S. Bariha
Dimple Notani
Srimonta Gayen

First Published August 6, 2025

Research

Distinct classes of lamina-associated domains are defined by differential patterns of repressive histone methylation

Caden J. Martin
Elizabeth A. Oser
Prabakaran Nagarajan
Liudmila V. Popova
Benjamin D. Sunkel
Benjamin Z. Stanton
Mark R. Parthun

First Published August 5, 2025

Method

3′-end ligation sequencing is a sensitive method to detect DNA nicks at potential sites of off-target activity induced by prime editors

Jacob Stewart-Ornstein
Matthew J. Irby
Marina K. Lilieholm
Dylan Laprise
Maria D. Collier
Thomas Aunins
... [+1 authors] ...,
Dewi Harjanto
Aaron N. Chang
Deepak Reyon
Jeremy S. Duffield

First Published August 5, 2025

Method

Genotyping of selected germline adaptive immune system loci using short-read sequencing data

Michael K.B. Ford
Ananth Hari
Meredith Yeager
Lisa Mirabello
Stephen Chanock
Ibrahim Numanagić
S. Cenk Sahinalp

First Published August 5, 2025

Method

High-resolution spatial transcriptomics in fixed tissue using a cost-effective PCL-seq workflow

Xue Dong
Mengzhu Hu
Xiaonan Cui
Wenjian Zhou
Jingtao Cai
Guangyao Mao
Weiyang Shi

First Published August 5, 2025

Research

H3K27 and H3K9 methylation mask potential CTCF binding sites to maintain 3D genome integrity

Kei Fukuda
Chikako Shimura
Yoichi Shinkai

First Published August 5, 2025

Resource

Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, chemotaxis behavior, and survival

Marina Athanasouli
Tobias Loschko
Christian Rödelsperger

First Published August 5, 2025

Research

Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations

Xiu Fan
Qili Qian
Wenran Li
Tianzi Liu
Changqing Zeng
Peilin Jia Huandong Lin Xin Gao
... [+3 authors] ...,
Li Jin
Mingfeng Xia
Sijia Wang
Fan Liu

First Published August 1, 2025

Resource

ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data" > The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data

Hsin-Yen Larry Wu
Isaiah D. Kaufman
Polly Yingshan Hsu

First Published July 22, 2025

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