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The NCBI BioSystems database

Lewis Y. Geer, Aron Marchler-Bauer, Renata C. Geer, Lianyi Han, Jane He, Siqian He, Chunlei Liu, Wenyao Shi, Stephen H. Bryant
2009 Nucleic Acids Research  
The NCBI BioSystems database, found at http://www.ncbi.nlm.nih.gov/biosystems/, centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating  ...  their pathways and systems into NCBI resources.  ...  ACKNOWLEDGEMENTS We thank the authors of the KEGG, Reactome and BioCyc databases. We also thank the NCBI Information Engineering Branch for continuing assistance with software development.  ... 
doi:10.1093/nar/gkp858 pmid:19854944 pmcid:PMC2808896 fatcat:n37jzpnjivfnjp6aiala5glyte

Fungal genome resources at NCBI

B Robbertse, T Tatusova
2011 Mycology  
The National Center for Biotechnology Information (NCBI) is well known for the nucleotide sequence archive, GenBank and sequence analysis tool BLAST.  ...  Depending on the focus and goal of research projects or the level of interest, a user would select a particular route for accessing genomic databases and resources.  ...  BioSystems The BioSystems database (Table 1) is a recent addition to NCBI and was developed as a complementary project to serve as a centralized repository of data, connecting biosystem records with  ... 
doi:10.1080/21501203.2011.584576 pmid:22737589 pmcid:PMC3379888 fatcat:7rqiu7yzhrc4bekzubkk6rfqde

National Center for Biotechnology Information (NCBI) database search for rubber plant Hevea brasiliensis

M Basyuni, R Hayati, B Pratomo, Lisnawita
2019 IOP Conference Series: Earth and Environment  
The present study describes search National Centre for Biotechnology Information (NCBI) databases (GQuery) on rubber plant Hevea brasiliensis Mull. Arg.  ...  NCBI databases search (https://www.ncbi.nlm.nih.gov/) was employed to generate a number of valuable information. Results found in 26 databases for H. brasiliensis.  ...  Proteins source NCBI database for H. brasiliensis.Nucleotide or FASTA base sequences for genomes can be downloaded on the GFF menu, currently available in 1 genome in GenBank BLAST from NCBI for H. brasiliensis  ... 
doi:10.1088/1755-1315/260/1/012171 fatcat:2pe7lcp2ovam7mkcjebskjxrkm

Database resources of the National Center for Biotechnology Information

D. L. Wheeler, T. Barrett, D. A. Benson, S. H. Bryant, K. Canese, V. Chetvernin, D. M. Church, M. DiCuccio, R. Edgar, S. Federhen, L. Y. Geer, Y. Kapustin (+18 others)
2007 Nucleic Acids Research  
In addition to maintaining the GenBank Õ nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other  ...  biological data made available through the NCBI Web site.  ...  Biosystems NCBI Biosystems (www.ncbi.nlm.nih.gov/biosystems/) collects together molecules that interact in a biological system, such as a biochemical pathway or disease.  ... 
doi:10.1093/nar/gkl1031 pmid:17170002 pmcid:PMC1781113 fatcat:pj7gnwwlpnbmza7c4ae7yatega

Database Resources of the National Center for Biotechnology Information

2016 Nucleic Acids Research  
In addition to maintaining the GenBank Õ nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other  ...  biological data made available through the NCBI Web site.  ...  Biosystems NCBI Biosystems (www.ncbi.nlm.nih.gov/biosystems/) collects together molecules that interact in a biological system, such as a biochemical pathway or disease.  ... 
doi:10.1093/nar/gkw1071 pmid:27899561 pmcid:PMC5210554 fatcat:itaqk5uwv5bv7gm7f55zunbcwq

Signals Enriched For Positive Selection

Vatsiou Alexandra, Bazin Eric, Gaggiotti Oscar
2014 Zenodo  
data downloaded on 5/2014) and the human pathways from the Biosystems database http://www.ncbi.nlm.nih.gov/biosystems (data downloaded on 5/2014).  ...  Methods & Results: We used the HapMap data phase II for genetic data http://hapmap.ncbi.nlm.nih.gov/downloads/phasing/2007-08_rel22/, the human genes from coding regions from the Entrez NCBI database (  ...  Acknowledgements We thank the INTERCROSSING for funding this project and Raquel Tobes for extracting the genes list from Bio4j.  ... 
doi:10.5281/zenodo.35271 fatcat:cu7otnfl7rapnehny27cro2lsu

The insulin-like growth factor-1 pathway mediator genes: SHC1 Met300Val shows a protective effect in breast cancer

K. Wagner
2004 Carcinogenesis  
Acknowledgements The German samples were collected in a project funded by Deutsche Krebshilfe headed by Prof. C.R.Bartram. We are grateful to Michael Wirtenberger for sample preparation.  ...  G Met300Val 22 1 0 NCBI SNP database rs1131397 C!G Arg360Arg 22 1 0 NCBI SNP database rs8191984 C!T Ser367Leu 23 0 0 NCBI SNP database bp1428 G!  ...  G Ala804Ala 19 3 1 NCBI SNP database rs1801120 C!T Ser809Phe 23 0 0 NCBI SNP database rs1801277 A!G Ser892Gly 23 0 0 NCBI SNP database bp 2679 G!  ... 
doi:10.1093/carcin/bgh263 pmid:15308584 fatcat:nuhm7n2hxbbszltdyvh5tzarzq

Page 193 of Cancer Science Vol. 96, Issue 3 [page]

2005 Cancer Science  
The amplified PCR mixture was directly sequenced, and the sequence data were compared with NCBI database (http://www.ncbi.nlm.nih.gov/).  ...  This phe- nomenon, namely the existence of GPR30 with or without 2 bp (CT), was reported to be a deletion/insertion polymorphism in the NCBI website (refSNP ID: rs3840681; NCBI Assay ID: 885027205) by  ... 

Graph-theoretical comparison of normal and tumor networks in identifying BRCA genes

Joaquin Dopazo, Cesim Erten
2017 BMC Systems Biology  
The AUROC and AUPR values of the gene lists ordered with respect to the measures under study as compared to NCBI BioSystems pathway and the COSMIC database of cancer genes are the largest with the betweenness-based  ...  Finally, we filter the ordered list of the best measure, the betweenness-based differentiation, via a maximum-weight independent set formulation and investigate the top 50 genes in regards to literature  ...  This work is also supported by grants BIO2014-57291-R from the Spanish Ministry of Economy and Competitiveness and "Plataforma de Recursos Biomoleculares y Bioinformáticos" PT13/0001/0007 from the ISCIII  ... 
doi:10.1186/s12918-017-0495-0 pmid:29166896 pmcid:PMC5700672 fatcat:dvzhzvlkprc3fo4cz2d7zoxnwy

Database resources of the National Center for Biotechnology Information

2012 Nucleic Acids Research  
In addition to maintaining the GenBank Õ nucleic acid sequence database, the National Center for Biotechnology Information (NCBI, http://www.ncbi. nlm.nih.gov) provides analysis and retrieval resources  ...  NCBI resources include Entrez, the Entrez  ...  Biosystems The Biosystems database collects together molecules that interact in a biological system, such as a biochemical pathway or disease.  ... 
doi:10.1093/nar/gks1189 pmid:23193264 pmcid:PMC3531099 fatcat:hp2biq76anavbavtbbz4jcvwqm

Information of Cyperus rotundus weed from the national center for information on biotechnology (NCBI)

Wismaroh Sanniwati Saragih, Edison Purba, Lisnawita, Mohammad Basyuni
2019 IOP Conference Series: Earth and Environment  
The present study describes search National Center for Biotechnology Information (NCBI) databases (GQuery) on Cyperus rotundus weed.  ...  NCBI databases search (https://www.ncbi.nlm.nih.gov/) was employed to generate a number of valuable information. Results found in 13 databases for Cyperus rotundus.  ...  Acknowledgment The authors would like to thank the provider of Indonesian Lecturer's Domestic Scholarship (BUDI DN) through Education Fund Management Institution (LPDP) that has supported this research  ... 
doi:10.1088/1755-1315/305/1/012043 fatcat:or7h2z2hz5cirh5pba3itx2p7q

Database resources of the National Center for Biotechnology Information: 2002 update

D. L. Wheeler
2002 Nucleic Acids Research  
Archive, the Taxonomy Browser, Trace Archive and UniGene); and proteins and chemicals (Biosystems, COBALT, the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART),  ...  All of these resources can be accessed through the NCBI home page at http://www.ncbi.nlm.nih.gov.  ...  Biosystems The Biosystems database collects together molecules represented in Gene, Protein and PubChem that interact in a biological system, such as a biochemical pathway or disease.  ... 
doi:10.1093/nar/30.1.13 pmid:11752242 pmcid:PMC99094 fatcat:o3wyt5y72zhzrd7usrrsl57ake

Identification of deer and goat species from skin samples-a DNA barcoding approach

S. Maya, Sanil George, A.R. Sreeranjini, C. Leena, N. S. Sunilkumar, K.B. Sumena
2021 Journal of Veterinary and Animal Sciences  
Acknowledgement The financial assistance extended by the Animal Husbandry Department and the administrative help rendered by the Kerala Veterinary and Animal Sciences University in conducting the research  ...  Present study differentiated the skin samples of sambar deer and goat. It is found that the accuracy of DNA barcoding will be dependent on data quality of database.  ...  . _____________________________________ present in database. Hence, updating the reference datasets (Parson et al. 2004 ) is of utmost importance.  ... 
doi:10.51966/jvas.2021.52.1.85-87 fatcat:a6cqksx6nbcuzpvqacrvm3muia

Database resources of the National Center for Biotechnology Information

E. W. Sayers, T. Barrett, D. A. Benson, E. Bolton, S. H. Bryant, K. Canese, V. Chetvernin, D. M. Church, M. DiCuccio, S. Federhen, M. Feolo, I. M. Fingerman (+31 others)
2011 Nucleic Acids Research  
chemicals (Biosystems and the Pub-Chem suite of small molecule databases).  ...  All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih. gov. † The members of the NCBI Resource Coordinators group are listed in the Appendix.  ...  Biosystems The Biosystems database collects together molecules represented in Gene, Protein and PubChem that interact in a biological system, such as a biochemical pathway or disease.  ... 
doi:10.1093/nar/gkr1184 pmid:22140104 pmcid:PMC3245031 fatcat:zxmwupa435gfzcpusnv7oe3qnm

Bioinformatic analysis of neural stem cell differentiation

Loyal A Goff, Jonathan Davila, Rebecka Jörnsten, Sunduz Keles, Ronald P Hart
2007 Journal of Biomolecular Techniques  
This microarray, while technically advanced, suffers from the difficulty of integrating hybridization results into public databases for systems-level analysis.  ...  of the 27,531 probes from 43% to over 65%.  ...  ACkNowLedgMeNts We thank Robert Genuario of Applied Biosystems for help with obtaining probe sequences and Drs. Qi Wang and Andrew I. Brooks for hybridization and image analysis of the AB1700 arrays.  ... 
pmid:17916793 pmcid:PMC2062565 fatcat:dpqaafazszg5rpg33vwejbehzu
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