Table of Contents

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

• Daniel Schmitz,
• Adam Ameur,
• and Åsa Johansson

• Abstract
• Full Text
• Full Text (PDF)
• Supplemental Material

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

• Abstract
• Full Text
• Full Text (PDF)
• Supplemental Material

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,
• Kenji Takahashi,
• Yusuke Mizukami,
• Kenzui Taniue,
• and Nobuyoshi Akimitsu

• Abstract
• Full Text
• Full Text (PDF)
• Supplemental Material

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

• Abstract
• Full Text
• Full Text (PDF)
• Supplemental Material

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

• Abstract
• Full Text
• Full Text (PDF)
• Supplemental Material

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

• Abstract
• Full Text
• Full Text (PDF)
• Supplemental Material

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

• Abstract
• Full Text
• Full Text (PDF)
• Supplemental Material

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

• Abstract
• Full Text
• Full Text (PDF)
• Supplemental Material

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

• Abstract
• Full Text
• Full Text (PDF)
• Supplemental Material

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

• Abstract
• Full Text
• Full Text (PDF)
• Supplemental Material

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

• Quanyou Cai,
• Lihui Lin,
• Xin Liu,
• and Jiekai Chen

• Abstract
• Full Text
• Full Text (PDF)
• Supplemental Material

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

• Qunlun Shen,
• Shuqin Zhang,
• and Shihua Zhang

• Abstract
• Full Text
• Full Text (PDF)
• Supplemental Material

Iterative improvement of deep learning models using synthetic regulatory genomics

• André M. Ribeiro-dos-Santos and
• Matthew T. Maurano

• Abstract
• Full Text
• Full Text (PDF)
• Supplemental Material

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

• Haiyue Liu and
• Lea H. Gregersen

• Abstract
• Full Text
• Full Text (PDF)
• Supplemental Material

Deep structural clustering reveals hidden systematic biases in RNA sequencing data

• Qiang Su,
• Yi Long,
• Deming Gou,
• Junmin Quan,
• Xiaoming Zhou,
• and Qizhou Lian

• Abstract
• Full Text
• Full Text (PDF)
• Supplemental Material

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

• Abstract
• Full Text
• Full Text (PDF)
• Supplemental Material

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

• Abstract
• Full Text
• Full Text (PDF)
• Supplemental Material