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Table of Contents
November 2025; 35 (11)
Research
Select this article
T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population
Daniel Schmitz
,
Adam Ameur
,
and
Åsa Johansson
Genome Res.
November 2025
35
:
2377
-
2388
;
Published in Advance
September 16, 2025
,
doi:
10.1101/gr.279320.124
Abstract
Full Text
Full Text (PDF)
Supplemental Material
OPEN ACCESS ARTICLE
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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
,
and
Hongli Yan
Genome Res.
November 2025
35
:
2389
-
2405
;
Published in Advance
September 16, 2025
,
doi:
10.1101/gr.279889.124
Abstract
Full Text
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Nanopore direct RNA sequencing reveals METTL2A-mediated m
3
C sites in poly(A) RNA
Shuhei Mitsutomi
,
Anzu Sugawara
,
Masahide Seki
,
Yutaka Suzuki
,
Sotaro Miyao
,
Haozhe Du
,
Kenji Takahashi
,
Yusuke Mizukami
,
Kenzui Taniue
,
and
Nobuyoshi Akimitsu
Genome Res.
November 2025
35
:
2406
-
2417
;
Published in Advance
October 30, 2025
,
doi:
10.1101/gr.280269.124
Abstract
Full Text
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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
,
Andrew P. Landstrom
,
Ravi Karra
,
Yarui Diao
,
and
Charles A. Gersbach
Genome Res.
November 2025
35
:
2418
-
2432
;
Published in Advance
October 22, 2025
,
doi:
10.1101/gr.280825.125
Abstract
Full Text
Full Text (PDF)
Supplemental Material
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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
,
and
Erica Korb
Genome Res.
November 2025
35
:
2433
-
2444
;
Published in Advance
October 20, 2025
,
doi:
10.1101/gr.280698.125
Abstract
Full Text
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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
,
and
Brankica Mravinac
Genome Res.
November 2025
35
:
2445
-
2460
;
Published in Advance
September 16, 2025
,
doi:
10.1101/gr.280516.125
Abstract
Full Text
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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
,
and
Handong Su
Genome Res.
November 2025
35
:
2461
-
2471
;
Published in Advance
September 30, 2025
,
doi:
10.1101/gr.280913.125
Abstract
Full Text
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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
,
Qin Gu
,
Xing-Xing Shen
,
Zhonghua Ma
,
and
Yun Chen
Genome Res.
November 2025
35
:
2472
-
2487
;
Published in Advance
October 14, 2025
,
doi:
10.1101/gr.280560.125
Abstract
Full Text
Full Text (PDF)
Supplemental Material
Methods
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Real-time analysis and visualization of nanopore metagenomic samples with MARTi
Ned Peel
,
Samuel Martin
,
Darren Heavens
,
Douglas W. Yu
,
Matthew D. Clark
,
and
Richard M. Leggett
Genome Res.
November 2025
35
:
2488
-
2500
;
Published in Advance
October 27, 2025
,
doi:
10.1101/gr.280550.125
Abstract
Full Text
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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
,
Francesco De Logu
,
Romina Nassini
,
Pier Giuseppe Pelicci
,
and
Alberto Magi
Genome Res.
November 2025
35
:
2501
-
2512
;
Published in Advance
October 20, 2025
,
doi:
10.1101/gr.280259.124
Abstract
Full Text
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Polyomino reconstructs spatial transcriptomic profiles with single-cell resolution via a region-allocation method
Quanyou Cai
,
Lihui Lin
,
Xin Liu
,
and
Jiekai Chen
Genome Res.
November 2025
35
:
2513
-
2526
;
Published in Advance
October 22, 2025
,
doi:
10.1101/gr.280532.125
Abstract
Full Text
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Highly accurate reference and method selection for universal cross–data set cell type annotation with CAMUS
Qunlun Shen
,
Shuqin Zhang
,
and
Shihua Zhang
Genome Res.
November 2025
35
:
2527
-
2538
;
Published in Advance
October 1, 2025
,
doi:
10.1101/gr.280821.125
Abstract
Full Text
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Iterative improvement of deep learning models using synthetic regulatory genomics
André M. Ribeiro-dos-Santos
and
Matthew T. Maurano
Genome Res.
November 2025
35
:
2539
-
2549
;
Published in Advance
October 22, 2025
,
doi:
10.1101/gr.280540.125
Abstract
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Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
Haiyue Liu
and
Lea H. Gregersen
Genome Res.
November 2025
35
:
2550
-
2562
;
Published in Advance
October 22, 2025
,
doi:
10.1101/gr.280852.125
Abstract
Full Text
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Deep structural clustering reveals hidden systematic biases in RNA sequencing data
Qiang Su
,
Yi Long
,
Deming Gou
,
Junmin Quan
,
Xiaoming Zhou
,
and
Qizhou Lian
Genome Res.
November 2025
35
:
2563
-
2577
;
Published in Advance
September 19, 2025
,
doi:
10.1101/gr.280713.125
Abstract
Full Text
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Resources
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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
,
Karen M. Vasquez
,
Chun Kit Kwok
,
Georgios A. Pavlopoulos
,
and
Ilias Georgakopoulos-Soares
Genome Res.
November 2025
35
:
2578
-
2600
;
Published in Advance
August 26, 2025
,
doi:
10.1101/gr.279790.124
Abstract
Full Text
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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
,
Omar Rota Stabelli
,
Fabrizio Ghiselli
,
Xiaoping Zhang
,
and
Alessandra Zambonelli
Genome Res.
November 2025
35
:
2601
-
2616
;
Published in Advance
August 21, 2025
,
doi:
10.1101/gr.280368.124
Abstract
Full Text
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November 2025;
35
(11)
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November 2025, 35 (11)
In This Issue
Polyomino integrates single-cell and spatial data
Autism spectrum disorder risk genes affect neuronal firing
Myosin expression and cardiomyocyte stress response
Wheat centromere adaptation to breakage
Quadrupia G-quadruplex database
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