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The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform

2019 Nucleic Acids Research  
Formed in late 1999, the Rat Genome Database (RGD, https://rgd.mcw.edu) will be 20 in 2020, the Year of the Rat.  ...  At its inception, before the sequencing of the rat genome, RGD started with only a few data types localized on genetic and radiation hybrid (RH) maps and offered only a few tools for querying and consolidating  ...  SUPPLEMENTARY DATA Supplementary Data are available at NAR Online.  ... 
doi:10.1093/nar/gkz1041 pmid:31713623 pmcid:PMC7145519 fatcat:4a6ja3vobncmtbp7m2hivrebr4

Computational resources associating diseases with genotypes, phenotypes and exposures

Wenliang Zhang, Haiyue Zhang, Huan Yang, Miaoxin Li, Zhi Xie, Weizhong Li
2018 Briefings in Bioinformatics  
He is interested in understanding transcriptional and translational regulation through the integrative analysis of multi-omics data.  ...  Huan Yang is a PhD student in Zhongshan School of Medicine at Sun Yat-sen University. Her research is focused on the integrative analysis of multiomics data.  ...  Five years later, the Human Gene Mutation Database (HGMD) was published to handle the data of human gene mutations [18, 19] , followed by the construction of dbSNP [20] and Orphanet [21] in the late  ... 
doi:10.1093/bib/bby071 pmid:30102366 fatcat:63ijmbhgxbf6pousquyuhl3s3a

Workshop report: 1st INCF Workshop on Mouse and Rat Brain Digital Atlasing Systems

Jyl Boline, Michael Hawrylycz, Robert Williams
2007 Nature Precedings  
A first step has been completed with the recent completion of the rat genome sequencing project. Other techniques such as RNAi knock-down may make species such as the rat genetically tractable.  ...  Researcher goals and platforms differ, and all participants at this workshop accept, and even encourage, a wide variety of approaches to brain atlasing.  ... 
doi:10.1038/npre.2007.1046.1 fatcat:5mxnau7o4ngfjdjr2s6c6wo6um

Workshop report: 1st INCF Workshop on Mouse and Rat Brain Digital Atlasing Systems

Jyl Boline, Jyl Boline, Michael Hawrylycz, Robert Williams
2007 Nature Precedings  
A first step has been completed with the recent completion of the rat genome sequencing project. Other techniques such as RNAi knock-down may make species such as the rat genetically tractable.  ...  Researcher goals and platforms differ, and all participants at this workshop accept, and even encourage, a wide variety of approaches to brain atlasing.  ... 
doi:10.1038/npre.2007.1046 fatcat:z24zvfjejbev5ntlyb3sbzds54

Database Resources of the National Genomics Data Center in 2020

2019 Nucleic Acids Research  
The National Genomics Data Center (NGDC) provides a suite of database resources to support worldwide research activities in both academia and industry.  ...  With the rapid advancements in higher-throughput and lower-cost sequencing technologies and accordingly the huge volume of multi-omics data generated at exponential scales and rates, NGDC is continually  ...  The National Genomics Data Center is indebted to its funders, including the Ministry of Science & Technology and the Ministry of Finance of the People's Republic of China as well as Chinese Academy of  ... 
doi:10.1093/nar/gkz913 pmid:31702008 pmcid:PMC7145560 fatcat:rx2p2whldnh5zpg2pyjs3mtaba

Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

Yingyao Zhou, Bin Zhou, Lars Pache, Max Chang, Alireza Hadj Khodabakhshi, Olga Tanaseichuk, Christopher Benner, Sumit K. Chanda
2019 Nature Communications  
Successful analysis requires the integration of a broad set of current biological databases and the application of a robust analytical pipeline to produce readily interpretable results.  ...  A critical component in the interpretation of systems-level studies is the inference of enriched biological pathways and protein complexes contained within OMICs datasets.  ...  ., C.B. and S.C. acknowledge support by NIH grants U19 AI106754, U19 AI135972, and R01 DA033773.  ... 
doi:10.1038/s41467-019-09234-6 pmid:30944313 pmcid:PMC6447622 fatcat:vofkc6cfvva2rhvbl73lh44f3a

Exploring the Ferroptosis Mechanism of Zhilong Huoxue Tongyu Capsule for the Treatment of Intracerebral Hemorrhage Based on Network Pharmacology and In Vivo Validation

Lixia Wang, Wei Ren, Li Wang, Linshen Mao, Maryam Mazhar, Chen Zhou, Houping Xu, Sijin Yang, Youhua Wang
2022 Evidence-Based Complementary and Alternative Medicine  
The active ingredients and related key targets of the ZL capsule were screened using the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP).  ...  The gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were also performed.  ...  Acknowledgments e authors acknowledge the support by the supervisor, Prof. Sijin Yang, and appreciate the efforts of all the lab members who helped in conducting this research study.  ... 
doi:10.1155/2022/5033135 fatcat:panmuclls5cyfgfru6d52r435i

The Gene Ontology resource: enriching a GOld mine

Gene Ontology Consortium
2020 Nucleic Acids Research  
To maintain an accurate resource and support traceability and reproducibility, we have made available a historical archive covering the past 15 years of GO data with a consistent format and file structure  ...  Here, we report the advances of the consortium over the past two years.  ...  ACKNOWLEDGEMENTS We want to thank all the contributors to the GO resource over the last 20 years (http://geneontology.org/ page/acknowledgments-contributors), and all the authors  ... 
doi:10.1093/nar/gkaa1113 pmid:33290552 pmcid:PMC7779012 fatcat:socxl3x5svamfoc2sobzyvjjoy

The 27th annual Nucleic Acids Research database issue and molecular biology database collection

Daniel J Rigden, Xosé M Fernández
2019 Nucleic Acids Research  
hierarchical structure; while the new Alliance of Genome Resources brings together a number of Model Organism databases to pool knowledge and tools.  ...  It is available at http://www.oxfordjournals.org/nar/database/c/.  ...  ACKNOWLEDGEMENTS We thank Dr Martine Bernardes-Silva, especially, and the rest of the Oxford University Press team led by Joanna Ventikos for their help in compiling this issue.  ... 
doi:10.1093/nar/gkz1161 pmid:31906604 pmcid:PMC6943072 fatcat:2dx37pg3krcs5hamrlmgyb4h5e

IP4M: an integrated platform for mass spectrometry-based metabolomics data mining

Dandan Liang, Quan Liu, Kejun Zhou, Wei Jia, Guoxiang Xie, Tianlu Chen
2020 BMC Bioinformatics  
Additionally, a KEGG-derived metabolic reaction database was embedded and a series of ratio variables (product/substrate) can be generated with enlarged information on enzyme activity.  ...  The performance of IP4M was evaluated and compared with existing computational platforms using 2 data sets derived from standards mixture and 2 data sets derived from serum samples, from GC–MS and LC–MS  ...  Many thanks to Zequn Zheng and Fan Yang of InfinityBio and BIOZERON Ltd., Co. for their support on software development.  ... 
doi:10.1186/s12859-020-03786-x pmid:33028191 fatcat:xvxp33njmnbl7piiq65sprb6ai

Remodeling Cildb, a popular database for cilia and links for ciliopathies

Olivier Arnaiz, Jean Cohen, Anne-Marie Tassin, France Koll
2014 Cilia  
Cildb is a multi-species knowledgebase gathering high throughput studies, which allows advanced searches to identify proteins involved in centrosome, basal body or cilia biogenesis, composition and function  ...  Results: Due to constant evolution of the ciliary and centrosomal field, Cildb has been recently upgraded twice, with new species whole proteomes and new ciliary studies, and the latter version displays  ...  This work was carried out in the context of the CNRS-supported European Research Group "Paramecium Genome Dynamics and Evolution".  ... 
doi:10.1186/2046-2530-3-9 pmid:25422781 pmcid:PMC4242763 fatcat:v262gj6ypndizeinpb354bualm

Remodeling Cildb, a popular database for cilia and links for ciliopathies

O Arnaiz, J Cohen, AM Tassin, F Koll
2015 Cilia  
Cildb is a multi-species knowledgebase gathering high throughput studies, which allows advanced searches to identify proteins involved in centrosome, basal body or cilia biogenesis, composition and function  ...  Results: Due to constant evolution of the ciliary and centrosomal field, Cildb has been recently upgraded twice, with new species whole proteomes and new ciliary studies, and the latter version displays  ...  This work was carried out in the context of the CNRS-supported European Research Group "Paramecium Genome Dynamics and Evolution".  ... 
doi:10.1186/2046-2530-4-s1-p21 pmcid:PMC4518628 fatcat:e6xtruhonfd3pbakh52yezjcum

Follicle Online: an integrated database of follicle assembly, development and ovulation

J. Hua, B. Xu, Y. Yang, R. Ban, F. Iqbal, H. J. Cooke, Y. Zhang, Q. Shi
2015 Database: The Journal of Biological Databases and Curation  
Here, we are reporting a database 'Follicle Online' that provides the experimentally validated gene/protein map of the folliculogenesis in a number of species.  ...  A large number of genes/proteins associated with folliculogenesis have been identified from different species.  ...  Supplementary Data Supplementary data are available at Database Online. Conflict of interest. None declared.  ... 
doi:10.1093/database/bav036 pmid:25931457 pmcid:PMC4414955 fatcat:xcvdtsp6kjhohb25l7dltxzzee

Invertebrate Model Organisms as a Platform to Investigate Rare Human Neurological Diseases

Ji-Hye Lee
2022 Experimental Neurobiology  
Recent efforts in building large-scale genomic databases and in silico prediction platforms have facilitated identification of potentially pathogenic variants causative of rare human diseases of a Mendelian  ...  However, the functional significance of individual variants remains elusive in many cases, thus requiring incorporation of versatile and rapid model organism (MO)-based platforms for functional analyses  ...  ACKNOWLEDGEMENTS This work was supported by the Financial Supporting Project of Long-term Overseas Dispatch of PNU's Tenure-track Faculty, 2019 to Ji-Hye Lee.  ... 
doi:10.5607/en22003 pmid:35256540 pmcid:PMC8907251 fatcat:r2fcfwmddjbxfpew37siqcgxfq

Identification of the Active Constituents and Significant Pathways of Cangfu Daotan Decoction for the Treatment of PCOS Based on Network Pharmacology

Wenting Xu, Mengyu Tang, Jiahui Wang, Lihong Wang
2020 Evidence-Based Complementary and Alternative Medicine  
The active ingredients of CDD and their potential targets were obtained from the TCM system pharmacology analysis platform.  ...  To explore the active ingredients and related pathways of CDD for treating PCOS, a network pharmacology-based analysis was carried out.  ...  knowledgebase of human genes and genetic disorders in the human genome.  ... 
doi:10.1155/2020/4086864 pmid:32148541 pmcid:PMC7057008 fatcat:yyvew6scdbd2deo356zln6d4oq
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