Volume 35, Issue 11 | November 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
  - 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
    First Published September 16, 2025
  - 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
  - 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
  - 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
    First Published October 20, 2025
  - 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
    First Published September 16, 2025
  - Adaptation of centromeres to breakage through local genomic and epigenomic remodeling in wheat
    Jingwei Zhou
    Yuhong Huang
    Huan Ma
    Yiqian Chen
    Chuanye Chen
    First Published September 30, 2025
  - 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
Methods
- - Real-time analysis and visualization of nanopore metagenomic samples with MARTi
    Ned Peel
    Samuel Martin
    Darren Heavens
    Douglas W. Yu
    Matthew D. Clark
    First Published October 27, 2025
  - 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
  - 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
  - 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
  - Iterative improvement of deep learning models using synthetic regulatory genomics
    André M. Ribeiro-dos-Santos
    Matthew T. Maurano
    First Published October 22, 2025
  - Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
    Haiyue Liu
    Lea H. Gregersen
    First Published October 22, 2025
  - Deep structural clustering reveals hidden systematic biases in RNA sequencing data
    Qiang Su
    Yi Long
    Deming Gou
    Junmin Quan
    Xiaoming Zhou
    First Published September 19, 2025
Resources
- - 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
  - 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

Table of Contents

Volume 35, Issue 11 | November 2025

Research

T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population

Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma

Nanopore direct RNA sequencing reveals METTL2A-mediated m3C sites in poly(A) RNA

A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress

Autism spectrum disorder risk genes have convergent effects on transcription and neuronal firing patterns in primary neurons

Dynamic evolution of satellite DNAs drastically differentiates the genomes of Tribolium sibling species

Adaptation of centromeres to breakage through local genomic and epigenomic remodeling in wheat

Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen

Methods

Real-time analysis and visualization of nanopore metagenomic samples with MARTi

PoreMeth2 for decoding the evolution of methylome alterations with nanopore sequencing

Polyomino reconstructs spatial transcriptomic profiles with single-cell resolution via a region-allocation method

Highly accurate reference and method selection for universal cross–data set cell type annotation with CAMUS

Iterative improvement of deep learning models using synthetic regulatory genomics

Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates

Deep structural clustering reveals hidden systematic biases in RNA sequencing data

Resources

Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life

High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae

Table of Contents

Volume 35, Issue 11 | November 2025

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Research

Methods

Resources