The genome sequence archive family: toward explosive data growth and diverse data types

T Chen, X Chen, S Zhang, J Zhu, B Tang… - Genomics …, 2021 - academic.oup.com
Abstract The Genome Sequence Archive (GSA) is a data repository for archiving raw
sequence data, which provides data storage and sharing services for worldwide scientific …

Database resources of the national genomics data center, China national center for bioinformation in 2022

Nucleic Acids Research, 2022 - academic.oup.com
Abstract The National Genomics Data Center (NGDC), part of the China National Center for
Bioinformation (CNCB), provides a family of database resources to support global research …

KaKs_Calculator 3.0: calculating selective pressure on coding and non-coding sequences

Z Zhang - Genomics, Proteomics and Bioinformatics, 2022 - academic.oup.com
Abstract KaKs_Calculator 3.0 is an updated toolkit that is capable of calculating selective
pressure on both coding and non-coding sequences. Similar to the nonsynonymous …

Chromosome-level genomes of three key Allium crops and their trait evolution

F Hao, X Liu, B Zhou, Z Tian, L Zhou, H Zong, J Qi… - Nature …, 2023 - nature.com
Allium crop breeding remains severely hindered due to the lack of high-quality reference
genomes. Here we report high-quality chromosome-level genome assemblies for three key …

Mitochondria-ER contact mediated by MFN2-SERCA2 interaction supports CD8+ T cell metabolic fitness and function in tumors

JF Yang, X Xing, L Luo, XW Zhou, JX Feng… - Science …, 2023 - science.org
Metabolic fitness of T cells is essential for their vitality, which is largely dependent on the
behavior of the mitochondria. The nature of mitochondrial behavior in tumor-infiltrating T …

High-Quality Arabidopsis Thaliana Genome Assembly with Nanopore and HiFi Long Reads

B Wang, X Yang, Y Jia, Y Xu, P Jia… - Genomics …, 2022 - academic.oup.com
Arabidopsis thaliana is an important and long-established model species for plant molecular
biology, genetics, epigenetics, and genomics. However, the latest version of reference …

SEdb 2.0: a comprehensive super-enhancer database of human and mouse

Y Wang, C Song, J Zhao, Y Zhang, X Zhao… - Nucleic Acids …, 2023 - academic.oup.com
Super-enhancers (SEs) are cell-specific DNA cis-regulatory elements that can supervise the
transcriptional regulation processes of downstream genes. SEdb 2.0 (http://www. licpathway …

Genome Warehouse: a public repository housing genome-scale data

M Chen, Y Ma, S Wu, X Zheng, H Kang… - Genomics …, 2021 - academic.oup.com
Abstract The Genome Warehouse (GWH) is a public repository housing genome assembly
data for a wide range of species and delivering a series of web services for genome data …

Organochlorine contamination enriches virus-encoded metabolism and pesticide degradation associated auxiliary genes in soil microbiomes

X Zheng, MT Jahn, M Sun, VP Friman… - The ISME …, 2022 - academic.oup.com
Viruses significantly influence local and global biogeochemical cycles and help bacteria to
survive in different environments by encoding various auxiliary metabolic genes (AMGs) …

The 2022 Nucleic Acids Research database issue and the online molecular biology database collection

DJ Rigden, XM Fernández - Nucleic acids research, 2022 - academic.oup.com
Abstract The 2022 Nucleic Acids Research Database Issue contains 185 papers, including
87 papers reporting on new databases and 85 updates from resources previously published …