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Results: 1 to 20 of 127

1.

SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation.

Hu Z, Fu Y, Halees AS, Kielbasa SM, Weng Z.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W235-41.

PMID:
15215387
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

CARRIE web service: automated transcriptional regulatory network inference and interactive analysis.

Haverty PM, Frith MC, Weng Z.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W213-6.

PMID:
15215383
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

SeqVISTA: a graphical tool for sequence feature visualization and comparison.

Hu Z, Frith M, Niu T, Weng Z.

BMC Bioinformatics. 2003 Jan 4;4:1. Epub 2003 Jan 4.

PMID:
12513700
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

A mathematical and computational framework for quantitative comparison and integration of large-scale gene expression data.

Hart CE, Sharenbroich L, Bornstein BJ, Trout D, King B, Mjolsness E, Wold BJ.

Nucleic Acids Res. 2005 May 10;33(8):2580-94. Print 2005.

PMID:
15886390
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

MotifViz: an analysis and visualization tool for motif discovery.

Fu Y, Frith MC, Haverty PM, Weng Z.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W420-3.

PMID:
15215422
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

WordSpy: identifying transcription factor binding motifs by building a dictionary and learning a grammar.

Wang G, Yu T, Zhang W.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W412-6.

PMID:
15980501
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Integrated databases and computer systems for studying eukaryotic gene expression.

Kolchanov NA, Ponomarenko MP, Frolov AS, Ananko EA, Kolpakov FA, Ignatieva EV, Podkolodnaya OA, Goryachkovskaya TN, Stepanenko IL, Merkulova TI, Babenko VV, Ponomarenko YV, Kochetov AV, Podkolodny NL, Vorobiev DV, Lavryushev SV, Grigorovich DA, Kondrakhin YV, Milanesi L, Wingender E, Solovyev V, Overton GC.

Bioinformatics. 1999 Jul-Aug;15(7-8):669-86.

PMID:
10487874
[PubMed - indexed for MEDLINE]
Free Article
8.

A suite of web-based programs to search for transcriptional regulatory motifs.

Liu Y, Wei L, Batzoglou S, Brutlag DL, Liu JS, Liu XS.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W204-7.

PMID:
15215381
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Cluster-Buster: Finding dense clusters of motifs in DNA sequences.

Frith MC, Li MC, Weng Z.

Nucleic Acids Res. 2003 Jul 1;31(13):3666-8.

PMID:
12824389
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

MotifCombinator: a web-based tool to search for combinations of cis-regulatory motifs.

Kato M, Tsunoda T.

BMC Bioinformatics. 2007 Mar 22;8:100.

PMID:
17378935
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Stubb: a program for discovery and analysis of cis-regulatory modules.

Sinha S, Liang Y, Siggia E.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W555-9.

PMID:
16845069
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes.

Pavesi G, Mereghetti P, Mauri G, Pesole G.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W199-203.

PMID:
15215380
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Identifying transcriptional regulatory sites in the human genome using an integrated system.

Huang HD, Horng JT, Sun YM, Tsou AP, Huang SL.

Nucleic Acids Res. 2004 Mar 29;32(6):1948-56. Print 2004.

PMID:
15051813
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

cis-regulatory region analysis using BEARR.

Vega VB.

Methods Mol Biol. 2006;338:119-27.

PMID:
16888354
[PubMed - indexed for MEDLINE]
15.

BOV--a web-based BLAST output visualization tool.

Gollapudi R, Revanna KV, Hemmerich C, Schaack S, Dong Q.

BMC Genomics. 2008 Sep 15;9:414. doi: 10.1186/1471-2164-9-414.

PMID:
18793422
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes.

Pavesi G, Mereghetti P, Zambelli F, Stefani M, Mauri G, Pesole G.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W566-70.

PMID:
16845071
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

The Gaggle: an open-source software system for integrating bioinformatics software and data sources.

Shannon PT, Reiss DJ, Bonneau R, Baliga NS.

BMC Bioinformatics. 2006 Mar 28;7:176.

PMID:
16569235
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Carbon sequestration in Synechococcus Sp.: from molecular machines to hierarchical modeling.

Heffelfinger GS, Martino A, Gorin A, Xu Y, Rintoul MD 3rd, Geist A, Al-Hashimi HM, Davidson GS, Faulon JL, Frink LJ, Haaland DM, Hart WE, Jakobsson E, Lane T, Li M, Locascio P, Olken F, Olman V, Palenik B, Plimpton SJ, Roe DC, Samatova NF, Shah M, Shoshoni A, Strauss CE, Thomas EV, Timlin JA, Xu D.

OMICS. 2002;6(4):305-30.

PMID:
12626091
[PubMed - indexed for MEDLINE]
19.

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
20.

ContDist: a tool for the analysis of quantitative gene and promoter properties.

Hackenberg M, Lasso G, Matthiesen R.

BMC Bioinformatics. 2009 Jan 7;10:7. doi: 10.1186/1471-2105-10-7.

PMID:
19128472
[PubMed - indexed for MEDLINE]
Free PMC Article
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