Volume 35, Issue 9 | September 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
- - Genotype imputation from low-coverage data for medical and population genetic analyses
    Simone Andrea Biagini
    Sara Becelaere
    Mio Aerden
    Tatjana Jatsenko
    Laurens Hannes
    Philip Van Damme Jeroen Breckpot Koenraad Devriendt
    ...[+3 authors]...,
    Bernard Thienpont
    Joris Robert Vermeesch
    Isabelle Cleynen
    Toomas Kivisild
    First Published July 22, 2025
  - Alternative splicing generates HER2 isoform diversity underlying antibody–drug conjugate resistance in breast cancer
    Gabriela D.A. Guardia
    Carlos H. dos Anjos
    Aline Rangel-Pozzo
    Filipe F. dos Santos
    Alexander Birbrair
    First Published July 15, 2025
  - 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
    First Published August 5, 2025
  - Transcriptional modulation unique to vulnerable motor neurons predicts ALS across species and SOD1 mutations
    Irene Mei
    Susanne Nichterwitz
    Melanie Leboeuf
    Jik Nijssen
    Isadora Lenoel
    First Published July 17, 2025
  - 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
  - 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
  - Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
    Harsh G. Shukla
    Mahul Chakraborty
    J.J. Emerson
    First Published July 16, 2025
Methods
- - 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
    First Published August 7, 2025
  - High-resolution spatial transcriptomics in fixed tissue using a cost-effective PCL-seq workflow
    Xue Dong
    Mengzhu Hu
    Xiaonan Cui
    Wenjian Zhou
    Jingtao Cai
    First Published August 5, 2025
  - 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
  - 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
    First Published August 5, 2025
  - Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
    Prashanthi Ravichandran
    Princy Parsana
    Rebecca Keener
    Kasper D. Hansen
    Alexis Battle
    First Published July 17, 2025
  - 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
Resources
- - Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
    Qiuhan Wen
    Zhen Wang
    Qi Bao
    Tianli Ding
    Haihan Zhang
    First Published June 16, 2025
  - 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

Table of Contents

Volume 35, Issue 9 | September 2025

Mini-Review

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

Research

Genotype imputation from low-coverage data for medical and population genetic analyses

Alternative splicing generates HER2 isoform diversity underlying antibody–drug conjugate resistance in breast cancer

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

Transcriptional modulation unique to vulnerable motor neurons predicts ALS across species and SOD1 mutations

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

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

Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome

Methods

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

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

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

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

Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks

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

Resources

Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs

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

Table of Contents

Volume 35, Issue 9 | September 2025

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Mini-Review

Research

Methods

Resources