Genome Res. Table of Contents for May 2024; Vol. 34, No. 5

[Prash]

 

This month Genome Research publishes a reference panel of deeply sequenced diverse human genomes. Researchers harmonized >4,000 whole genomes from 80 populations across the 1000 Genomes Project (1kGP) and Human Genome Diversity Project (HGDP) providing a valuable resource capturing the breadth of genetic variation across diverse geographical regions. This resource has broad applications for studying genomic variation, clinical applications, population genetics, and ancestry. Genome Research May 2024; Vol. 34, No. 5 (NOTE: Depending on your browser settings, you might need to refresh your browser or clear your browser's cache if the Table of Contents that you are viewing does not immediately update to reflect this latest issue.) Mini-Review Toward telomere-to-telomere cat genomes for precision medicine and conservation biology William J. Murphy and Andrew J. Harris Genome Res. 2024; 34: 655-664 https://genome.cshlp.org/content/34/5/655.abstract 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, Zhiqun Tan, Kyoko Yokomori and Xiangmin Xu Genome Res. 2024; 34: 665-679 Open Access https://genome.cshlp.org/content/34/5/665.abstract 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, Patrick Tan, Anders J. Skanderup and Michael A. Beer Genome Res. 2024; 34: 680-695 https://genome.cshlp.org/content/34/5/680.abstract 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 and Hans T. Bjornsson Genome Res. 2024; 34: 696-710 https://genome.cshlp.org/content/34/5/696.abstract Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary Satyam P. Srivastav, Cédric Feschotte and Andrew G. Clark Genome Res. 2024; 34: 711-724 https://genome.cshlp.org/content/34/5/711.abstract 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 and Juan Du Genome Res. 2024; 34: 725-739 https://genome.cshlp.org/content/34/5/725.abstract 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, Jikui Song, Yali Dou, Shan Gao and Yifan Liu Genome Res. 2024; 34: 740-756 https://genome.cshlp.org/content/34/5/740.abstract Methods GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes Tomáš Brůna, Alexandre Lomsadze and Mark Borodovsky Genome Res. 2024; 34: 757-768 Open Access https://genome.cshlp.org/content/34/5/757.abstract 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, Mark Borodovsky and Mario Stanke Genome Res. 2024; 34: 769-777 Open Access https://genome.cshlp.org/content/34/5/769.abstract Simulation of nanopore sequencing signal data with tunable parameters Hasindu Gamaarachchi, James M. Ferguson, Hiruna Samarakoon, Kisaru Liyanage and Ira W. Deveson Genome Res. 2024; 34: 778-783 Open Access https://genome.cshlp.org/content/34/5/778.abstract Identifying genes within pathways in unannotated genomes with PaGeSearch Sohyoung Won, Jaewoong Yu and Heebal Kim Genome Res. 2024; 34: 784-795 Open Access https://genome.cshlp.org/content/34/5/784.abstract 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, gnomAD Project Consortium, Heidi L. Rehm, Benjamin M. Neale, Michael E. Talkowski, Mark J. Daly, Harrison Brand, Konrad J. Karczewski, Elizabeth G. Atkinson and Alicia R. Martin Genome Res. 2024; 34: 796-809 https://genome.cshlp.org/content/34/5/796.abstract 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 and Yun William Yu Genome Res. 2024; 34: 810 Open Access https://genome.cshlp.org/content/34/5/810.extract

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Prashanth N Suravajhala, Ph.D.
Principal Scientist, Systems Genomics
Room # 301, Amrita School of Biotechnology

Amrita University, Amritapuri, Kerala 690525, India. 

Group page: http://www.bioinformatics.org/wiki/Prash 

E mail:  prashATamDOTamritaDOTedu 

Twitter: @prashbio

"One rule is important in science- only courageous people win "   ~ Max Planck