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Taiwan Bioinformatics Institute

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How to cite us
 

The services of The BP Bioinformatics Core is supported by National Core Facility for Biopharmaceuticals (NCFB), National Science and Technology Council (NSTC), since May. 2017. Many of the services had formally been supported ;by MOST Programs, i.e.,National Research Programs for Genomic Medicine (NRPGM), Taiwan, from year 2002. to Apr. 2011 and by NCFPB from May 2011 to April 2017. If these services contributed to your research, we appreciate that you make statements in the Acknowledgements section and cite the publication/URL of the customized data analysis services/tools/databases you used in Material and Methods section when you publish your work.

 

1. Acknowledgement

We welcome your recognition in the acknowledgements of your paper for any services you used, as follows:
We appreciate the support received from ________ Service at the TMBD Bioinformatics Core (http://www.tbi.org.tw), which is funded by the Bioinformatics Core Facility for Biotechnology and Pharmaceuticals.

 

2. Citation in Material and Methods

Please cite the name of the services (customized data analysis services/tools/databases ), our website http//www.tbi.org.tw and the publication of our services. We published most of our in-house methods, tools and databases. You may easily find the citation information within the service page. For some of the services that are not yet published, you are welcome to cite our URL. We hereby provide a list in alphabetical order for you to locate the citation you need.
Databases Reference
After GeneBank Annotated-Feature Extractor from GenBank
BioinfoArchive An online data archive of biological data sets
dbPTM Lee T. Y. et al. dbPTM: an information repository of protein post-translational modification. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D622-7.
FlyDPI Lin C.Y. et al. Fly-DPI: database of protein interactomes for D. melanogaster in the approach of systems biology. BMC Bioinformatics. 2006 Dec 18;7 Suppl 5:S18.
GPDB Genome Profile Database
hp-DPI Lin C.Y. et al. hp-DPI: Helicobacter pylori database of protein interactomes--embracing experimental and inferred interactions. Bioinformatics. 2005 Apr 1;21(7):1288-90. Epub 2004 Oct 28.
HPSG Structural Genomics Databases of Helicobacter pylori
iGenome A database index for the genome summarized information
KPSG Structural Genomics Databases of Klebsiella pneumoniae
RegRNA Huang H. Y. et al. RegRNA: an integrated web server for identifying regulatory RNA motifs and elements. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W429-34
SM Structural Genomics Databases of Stenotrophomonas maltophili
SNP SNP value-added database
SSDB Disulfide Proteins Database
TAG Chan H.H. et. al. TAG: a comprehensive database for cancer research. (2007) Nucleic Acids Research Molecular Biology Database Collection # 922.
The BEST Chen K.F. et. al. Transcriptional repression of human cad gene by hypoxia inducible factor-1. (2005) Nucleic Acids Research 33(16):5190-5198.
TPMD Chang Y.H. et al. TPMD: a database and resources of microsatellite marker genotyped in Taiwanese populations. Nucleic Acids Research, 2005, Vol. 33, Database issue D174-D177.
XCC Structural Genomics Databases of Xanthomonas campestris

 

Tools Reference
3D-BLAST Yang J.M. et al.?Protein structure database search and evolutionary classification. Nucleic Acids Res. 2006 Aug 2;34(13):3646-59.
CELLO Yu C.S. et al.?Prediction of protein subcellular localization. Proteins. 2006 Aug 15;64(3):643-51.
Chameleon Sequence Finder Retrive a small peptide fragment sequence from a collection of PDB sequences
CPSARST Lo W.C. et al.?CPSARST: an efficient circular permutation search tool applied to the detection of novel protein structural relationships. Genome Biol. 2008 Jan 18;9(1):R11.
ENACE System Chen F.C. et al.?Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat. BMC Bioinformatics. In press, 2006.
ESTviewer Chen F.C. et al. "ESTviewer: a Web interface for visualizing mouse, rat, cattle, pig, and chicken conserved ESTs in human genes and human alternatively spliced variants," Bioinformatics, Vol. 21, No.10, pp.2510-2513, 2005.
GEMDOCK Yang J.M. et al. "GEMDOCK: A generic evolutionary method for molecular docking", Proteins: Structure, Function and Bioinformatics, vol. 55, pp. 288-304, 2004.
GenePredict Web-based gene prediction service
GPRM Hu Y.J. et al.?GPRM: A genetic programming approach to finding common RNA secondary structure elements. Nucleic Acids Res. 2003 Jul 1;31(13):3446-9.
Hubba-Hubba Lin C.Y. et al.?Hubba: hub objects analyzer--a framework of interactome hubs identification for network biology.?Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W438-43. Epub 2008
KinasePhos Huang H.D. et al.?KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W226-9.
KPST KEGG Pathway Search Tool
MuSiC Multiple Sequence Alignment with Constraints
PDA Chen S.H. et al. Primer Design Assistant (PDA): A web-based primer design tool. Nucleic Acids Res. 2003 Jul 1;31(13):3751-4.
pKNOT Lai Y.L. et al.?pKNOT: the protein KNOT web server. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W420-4. Epub 2007
POWER Lin C.Y. et al.?POWER: PhylOgenetic WEb Repeater--an integrated and user-optimized framework for biomolecular phylogenetic analysis. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W553-6.
(PS)2 Chen C.C. et al.?(PS)2: protein structure prediction server. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W152-7.
PredictProtein Sequence analysis and structure prediction (mirror at NTHU)
PSEP System Chuang T.J. et al.?"A Comparative Method for Identification of Gene Structures and Alternatively Spliced Variants," Bioinformatics, Vol. 20, No. 17, pp.3064-3079, 2004.
RegRNA Huang H.Y. et al.?RegRNA: an integrated web server for identifying regulatory RNA motifs and elements. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W429-34.
RepeatMasker Screening for low complexity DNA sequences and interspersed repeats (mirror at NCKU)
RMA Reniforced Merging Algorithms
RNAMST Chang T.H. et al. RNAMST: efficient and flexible approach for identifying RNA structural homologs. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W423-8.
SARST Lo W.C. et al. Protein structural similarity search by Ramachandran codes. BMC Bioinformatics. 2007 Aug 23;8:307.
SDSE Sequence Derived Structure Entropy
SpliceInfo Huang H.D. et al.?SpliceInfo: an information repository for mRNA alternative splicing in human genome. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D80-5.
SpliceMotif Identify conserved sequence elements associated to mRNA splicing
StEQ Structural Entropy Query
Tm Predictor Melting Temperature Prediction : Predict thermal stability of proteins
UPS Chen S.H. et al.?The unique probe selector: a comprehensive web service for probe design and oligonucleotide arrays. BMC Bioinformatics. 2008;9 Suppl 1:S8.

 

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