Volume 35, Issue 10 | October 2025

Research
- - Molecular and genetic landscapes of retina and brain microglia in neurodegenerative diseases
    Khang Ma
    Rinki Ratnapriya
    First Published August 26, 2025
  - 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
  - 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
  - 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
  - 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
  - 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
  - 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
    First Published August 12, 2025
Methods
- - 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
  - 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
  - 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
  - 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
    First Published August 14, 2025
  - 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
  - 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
  - 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
  - Multicondition and multimodal temporal profile inference during mouse embryonic development
    Ran Zhang
    Chengxiang Qiu
    Galina N. Filippova
    Gang Li
    Jay Shendure
    First Published August 14, 2025
Resources
- - 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
  - 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
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

Table of Contents

Volume 35, Issue 10 | October 2025

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Research

Methods

Resources

Corrigendum