Literature DB >> 12176838

TFBS: Computational framework for transcription factor binding site analysis.

Boris Lenhard1, Wyeth W Wasserman.   

Abstract

MOTIVATION: TFBS is a set of integrated, object-oriented Perl modules for transcription factor binding site detection and analysis. It implements objects representing specificity profile matrices, binding sites and sets thereof, pattern generators, and pattern database interfaces. The modules are interoperable with the BioPerl open source system. AVAILABILITY AND SUPPLEMENTARY INFORMATION: The module package with documentation and example scripts are available at http://forkhead.cgb.ki.se/TFBS/

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Year:  2002        PMID： 12176838     DOI： 10.1093/bioinformatics/18.8.1135

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  96 in total

1.  CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting.

Authors:  Eugene Berezikov; Victor Guryev; Ronald H A Plasterk; Edwin Cuppen
Journal:  Genome Res       Date:  2003-12-12       Impact factor: 9.043

2.  JASPAR: an open-access database for eukaryotic transcription factor binding profiles.

Authors:  Albin Sandelin; Wynand Alkema; Pär Engström; Wyeth W Wasserman; Boris Lenhard
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

3.  Comprehensive quantitative analyses of the effects of promoter sequence elements on mRNA transcription.

Authors:  Michal Lapidot; Yitzhak Pilpel
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

4.  The Bioperl toolkit: Perl modules for the life sciences.

Authors:  Jason E Stajich; David Block; Kris Boulez; Steven E Brenner; Stephen A Chervitz; Chris Dagdigian; Georg Fuellen; James G R Gilbert; Ian Korf; Hilmar Lapp; Heikki Lehväslaiho; Chad Matsalla; Chris J Mungall; Brian I Osborne; Matthew R Pocock; Peter Schattner; Martin Senger; Lincoln D Stein; Elia Stupka; Mark D Wilkinson; Ewan Birney
Journal:  Genome Res       Date:  2002-10       Impact factor: 9.043

5.  ConSite: web-based prediction of regulatory elements using cross-species comparison.

Authors:  Albin Sandelin; Wyeth W Wasserman; Boris Lenhard
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

6.  MSCAN: identification of functional clusters of transcription factor binding sites.

Authors:  Wynand B L Alkema; Ojvind Johansson; Jens Lagergren; Wyeth W Wasserman
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

7.  Regulog analysis: detection of conserved regulatory networks across bacteria: application to Staphylococcus aureus.

Authors:  Wynand B L Alkema; Boris Lenhard; Wyeth W Wasserman
Journal:  Genome Res       Date:  2004-07       Impact factor: 9.043

8.  CisModule: de novo discovery of cis-regulatory modules by hierarchical mixture modeling.

Authors:  Qing Zhou; Wing H Wong
Journal:  Proc Natl Acad Sci U S A       Date:  2004-08-05       Impact factor: 11.205

9.  Statistical analysis of over-represented words in human promoter sequences.

Authors:  Leonardo Mariño-Ramírez; John L Spouge; Gavin C Kanga; David Landsman
Journal:  Nucleic Acids Res       Date:  2004-02-12       Impact factor: 16.971

10.  Myogenic gene expression signature establishes that brown and white adipocytes originate from distinct cell lineages.

Authors:  James A Timmons; Kristian Wennmalm; Ola Larsson; Tomas B Walden; Timo Lassmann; Natasa Petrovic; D Lee Hamilton; Ruth E Gimeno; Claes Wahlestedt; Keith Baar; Jan Nedergaard; Barbara Cannon
Journal:  Proc Natl Acad Sci U S A       Date:  2007-03-05       Impact factor: 11.205
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