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Results: 1 to 20 of 87

1.

ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation.

Montgomery SB, Griffith OL, Sleumer MC, Bergman CM, Bilenky M, Pleasance ED, Prychyna Y, Zhang X, Jones SJ.

Bioinformatics. 2006 Mar 1;22(5):637-40. Epub 2006 Jan 5.

PMID:
16397004
[PubMed - indexed for MEDLINE]
Free Article
2.

ORegAnno: an open-access community-driven resource for regulatory annotation.

Griffith OL, Montgomery SB, Bernier B, Chu B, Kasaian K, Aerts S, Mahony S, Sleumer MC, Bilenky M, Haeussler M, Griffith M, Gallo SM, Giardine B, Hooghe B, Van Loo P, Blanco E, Ticoll A, Lithwick S, Portales-Casamar E, Donaldson IJ, Robertson G, Wadelius C, De Bleser P, Vlieghe D, Halfon MS, Wasserman W, Hardison R, Bergman CM, Jones SJ; Open Regulatory Annotation Consortium.

Nucleic Acids Res. 2008 Jan;36(Database issue):D107-13. Epub 2007 Nov 15.

PMID:
18006570
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Transcription Regulatory Regions Database (TRRD):its status in 1999.

Kolchanov NA, Ananko EA, Podkolodnaya OA, Ignatieva EV, Stepanenko IL, Kel-Margoulis OV, Kel AE, Merkulova TI, Goryachkovskaya TN, Busygina TV, Kolpakov FA, Podkolodny NL, Naumochkin AN, Romashchenko AG.

Nucleic Acids Res. 1999 Jan 1;27(1):303-6.

PMID:
9847210
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

CardioSignal: a database of transcriptional regulation in cardiac development and hypertrophy.

Zhen Y, Wang Y, Zhang W, Zhou C, Hui R.

Int J Cardiol. 2007 Apr 4;116(3):338-47. Epub 2006 Aug 2.

PMID:
16887212
[PubMed - indexed for MEDLINE]
5.

K-SPMM: a database of murine spermatogenic promoters modules & motifs.

Lu Y, Platts AE, Ostermeier GC, Krawetz SA.

BMC Bioinformatics. 2006 May 3;7:238.

PMID:
16670029
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

PRODORIC (release 2009): a database and tool platform for the analysis of gene regulation in prokaryotes.

Grote A, Klein J, Retter I, Haddad I, Behling S, Bunk B, Biegler I, Yarmolinetz S, Jahn D, Münch R.

Nucleic Acids Res. 2009 Jan;37(Database issue):D61-5. doi: 10.1093/nar/gkn837. Epub 2008 Oct 30.

PMID:
18974177
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes.

Hestand MS, van Galen M, Villerius MP, van Ommen GJ, den Dunnen JT, 't Hoen PA.

BMC Bioinformatics. 2008 Nov 26;9:495. doi: 10.1186/1471-2105-9-495.

PMID:
19036135
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Gene annotation from scientific literature using mappings between keyword systems.

Pérez AJ, Perez-Iratxeta C, Bork P, Thode G, Andrade MA.

Bioinformatics. 2004 Sep 1;20(13):2084-91. Epub 2004 Apr 1.

PMID:
15059832
[PubMed - indexed for MEDLINE]
Free Article
9.

RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation.

Gama-Castro S, Jiménez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Peñaloza-Spinola MI, Contreras-Moreira B, Segura-Salazar J, Muñiz-Rascado L, Martínez-Flores I, Salgado H, Bonavides-Martínez C, Abreu-Goodger C, Rodríguez-Penagos C, Miranda-Ríos J, Morett E, Merino E, Huerta AM, Treviño-Quintanilla L, Collado-Vides J.

Nucleic Acids Res. 2008 Jan;36(Database issue):D120-4. Epub 2007 Dec 23.

PMID:
18158297
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

A new advance in alternative splicing databases: from catalogue to detailed analysis of regulation of expression and function of human alternative splicing variants.

de la Grange P, Dutertre M, Correa M, Auboeuf D.

BMC Bioinformatics. 2007 Jun 4;8:180.

PMID:
17547750
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Text-mining of PubMed abstracts by natural language processing to create a public knowledge base on molecular mechanisms of bacterial enteropathogens.

Zaremba S, Ramos-Santacruz M, Hampton T, Shetty P, Fedorko J, Whitmore J, Greene JM, Perna NT, Glasner JD, Plunkett G 3rd, Shaker M, Pot D.

BMC Bioinformatics. 2009 Jun 10;10:177. doi: 10.1186/1471-2105-10-177.

PMID:
19515247
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Identification of key mechanisms controlling gene expression in Leishmania infected macrophages using genome-wide promoter analysis.

Ghedira K, Hornischer K, Konovalova T, Jenhani AZ, Benkahla A, Kel A.

Infect Genet Evol. 2011 Jun;11(4):769-77. doi: 10.1016/j.meegid.2010.10.015. Epub 2010 Nov 18.

PMID:
21093613
[PubMed - indexed for MEDLINE]
13.

CoryneRegNet 4.0 - A reference database for corynebacterial gene regulatory networks.

Baumbach J.

BMC Bioinformatics. 2007 Nov 6;8:429.

PMID:
17986320
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

BacTregulators: a database of transcriptional regulators in bacteria and archaea.

Martínez-Bueno M, Molina-Henares AJ, Pareja E, Ramos JL, Tobes R.

Bioinformatics. 2004 Nov 1;20(16):2787-91. Epub 2004 May 27.

PMID:
15166024
[PubMed - indexed for MEDLINE]
Free Article
15.

SNP@Promoter: a database of human SNPs (single nucleotide polymorphisms) within the putative promoter regions.

Kim BC, Kim WY, Park D, Chung WH, Shin KS, Bhak J.

BMC Bioinformatics. 2008;9 Suppl 1:S2. doi: 10.1186/1471-2105-9-S1-S2.

PMID:
18315851
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Transcription Regulatory Regions Database (TRRD): its status in 2002.

Kolchanov NA, Ignatieva EV, Ananko EA, Podkolodnaya OA, Stepanenko IL, Merkulova TI, Pozdnyakov MA, Podkolodny NL, Naumochkin AN, Romashchenko AG.

Nucleic Acids Res. 2002 Jan 1;30(1):312-7.

PMID:
11752324
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation.

Panitz F, Stengaard H, Hornshøj H, Gorodkin J, Hedegaard J, Cirera S, Thomsen B, Madsen LB, Høj A, Vingborg RK, Zahn B, Wang X, Wang X, Wernersson R, Jørgensen CB, Scheibye-Knudsen K, Arvin T, Lumholdt S, Sawera M, Green T, Nielsen BJ, Havgaard JH, Brunak S, Fredholm M, Bendixen C.

Bioinformatics. 2007 Jul 1;23(13):i387-91.

PMID:
17646321
[PubMed - indexed for MEDLINE]
Free Article
18.

ExtraTrain: a database of Extragenic regions and Transcriptional information in prokaryotic organisms.

Pareja E, Pareja-Tobes P, Manrique M, Pareja-Tobes E, Bonal J, Tobes R.

BMC Microbiol. 2006 Mar 15;6:29.

PMID:
16539733
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

PlnTFDB: an integrative plant transcription factor database.

Riaño-Pachón DM, Ruzicic S, Dreyer I, Mueller-Roeber B.

BMC Bioinformatics. 2007 Feb 7;8:42.

PMID:
17286856
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

ABS: a database of Annotated regulatory Binding Sites from orthologous promoters.

Blanco E, Farré D, Albà MM, Messeguer X, Guigó R.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D63-7.

PMID:
16381947
[PubMed - indexed for MEDLINE]
Free PMC Article

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