Volume 34, Issue 5 | May 2024

Mini-Review
- - Toward telomere-to-telomere cat genomes for precision medicine and conservation biology
    William J. Murphy
    Andrew J. Harris
    First Published June 7, 2024
Research
- - Single-cell spatial transcriptomics reveals a dystrophic trajectory following a developmental bifurcation of myoblast cell fates in facioscapulohumeral muscular dystrophy
    Lujia Chen
    Xiangduo Kong
    Kevin G. Johnston
    Ali Mortazavi
    Todd C. Holmes
    First Published May 22, 2024
  - Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer
    Milad Razavi-Mohseni
    Weitai Huang
    Yu A. Guo
    Dustin Shigaki
    Shamaine Wei Ting Ho
    First Published May 22, 2024
  - Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice
    Leandros Boukas
    Teresa Romeo Luperchio
    Afrooz Razi
    Kasper D. Hansen
    Hans T. Bjornsson
    First Published May 3, 2024
  - Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary
    Satyam P. Srivastav
    Cédric Feschotte
    Andrew G. Clark
    First Published May 15, 2024
  - Genome-wide profiles of H3K9me3, H3K27me3 modifications, and DNA methylation during diapause of Asian corn borer (Ostrinia furnacalis)
    Pengfei Lv
    Xingzhuo Yang
    Xianguo Zhao
    Zhangwu Zhao
    Juan Du
    First Published June 12, 2024
  - Semiconservative transmission of DNA N6-adenine methylation in a unicellular eukaryote
    Yalan Sheng
    Yuanyuan Wang
    Wentao Yang
    Xue Qing Wang
    Jiuwei Lu
    Bo Pan Bei Nan Yongqiang Liu Fei Ye Chun Li
    ...[+5 authors]...,
    Jikui Song
    Yali Dou
    Shan Gao
    Yifan Liu
    First Published May 14, 2024
Methods
- - GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes
    Tomáš Brůna
    Alexandre Lomsadze
    Mark Borodovsky
    First Published June 12, 2024
  - BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA
    Lars Gabriel
    Tomáš Brůna
    Katharina J. Hoff
    Matthis Ebel
    Alexandre Lomsadze
    First Published June 12, 2024
  - Simulation of nanopore sequencing signal data with tunable parameters
    Hasindu Gamaarachchi
    James M. Ferguson
    Hiruna Samarakoon
    Kisaru Liyanage
    Ira W. Deveson
    First Published May 1, 2024
  - Identifying genes within pathways in unannotated genomes with PaGeSearch
    Sohyoung Won
    Jaewoong Yu
    Heebal Kim
    First Published June 10, 2024
Resource
- - A harmonized public resource of deeply sequenced diverse human genomes
    Zan Koenig
    Mary T. Yohannes
    Lethukuthula L. Nkambule
    Xuefang Zhao
    Julia K. Goodrich
    Heesu Ally Kim Michael W. Wilson Grace Tiao Stephanie P. Hao Nareh Sahakian Katherine R. Chao Mark A. Walker Yunfei Lyu Heidi L. Rehm Benjamin M. Neale Michael E. Talkowski Mark J. Daly
    ...[+12 authors]...,
    Harrison Brand
    Konrad J. Karczewski
    Elizabeth G. Atkinson
    Alicia R. Martin
    First Published May 15, 2024
Erratum
- - Erratum: Proving sequence aligners can guarantee accuracy in almost O(m log n) time through an average-case analysis of the seed-chain-extend heuristic
    Jim Shaw
    Yun William Yu
    First Published June 25, 2024

Table of Contents

Volume 34, Issue 5 | May 2024

Mini-Review

Toward telomere-to-telomere cat genomes for precision medicine and conservation biology

Research

Single-cell spatial transcriptomics reveals a dystrophic trajectory following a developmental bifurcation of myoblast cell fates in facioscapulohumeral muscular dystrophy

Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer

Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice

Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary

Genome-wide profiles of H3K9me3, H3K27me3 modifications, and DNA methylation during diapause of Asian corn borer (Ostrinia furnacalis)

Semiconservative transmission of DNA N6-adenine methylation in a unicellular eukaryote

Methods

GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes

BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA

Simulation of nanopore sequencing signal data with tunable parameters

Identifying genes within pathways in unannotated genomes with PaGeSearch

Resource

A harmonized public resource of deeply sequenced diverse human genomes

Erratum

Erratum: Proving sequence aligners can guarantee accuracy in almost O(m log n) time through an average-case analysis of the seed-chain-extend heuristic

Table of Contents

Volume 34, Issue 5 | May 2024

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Mini-Review

Research

Methods

Resource

Erratum