Literature DB >> 17237043

FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes.

Evert-Jan Blom1, Dinne W J Bosman, Sacha A F T van Hijum, Rainer Breitling, Lars Tijsma, Remko Silvis, Jos B T M Roerdink, Oscar P Kuipers.   

Abstract

UNLABELLED: FIVA (Function Information Viewer and Analyzer) aids researchers in the prokaryotic community to quickly identify relevant biological processes following transcriptome analysis. Our software assists in functional profiling of large sets of genes and generates a comprehensive overview of affected biological processes. AVAILABILITY: http://bioinformatics.biol.rug.nl/standalone/fiva/

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Year:  2007        PMID： 17237043     DOI： 10.1093/bioinformatics/btl658

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


  16 in total

1.  A Fast and Reliable Pipeline for Bacterial Transcriptome Analysis Case study: Serine-dependent Gene Regulation in Streptococcus pneumoniae.

Authors:  Muhammad Afzal; Irfan Manzoor; Oscar P Kuipers
Journal:  J Vis Exp       Date:  2015-04-25       Impact factor: 1.355

2.  Production and secretion stress caused by overexpression of heterologous alpha-amylase leads to inhibition of sporulation and a prolonged motile phase in Bacillus subtilis.

Authors:  Andrzej T Lulko; Jan-Willem Veening; Girbe Buist; Wiep Klaas Smits; Evert Jan Blom; Aaron C Beekman; Sierd Bron; Oscar P Kuipers
Journal:  Appl Environ Microbiol       Date:  2007-06-22       Impact factor: 4.792

3.  Robust and accurate data enrichment statistics via distribution function of sum of weights.

Authors:  Aleksandar Stojmirović; Yi-Kuo Yu
Journal:  Bioinformatics       Date:  2010-09-08       Impact factor: 6.937

4.  Transcriptional responses of Bacillus cereus towards challenges with the polysaccharide chitosan.

Authors:  Hilde Mellegård; Ákos T Kovács; Toril Lindbäck; Bjørn E Christensen; Oscar P Kuipers; Per E Granum
Journal:  PLoS One       Date:  2011-09-08       Impact factor: 3.240

5.  Time-resolved transcriptomics and bioinformatic analyses reveal intrinsic stress responses during batch culture of Bacillus subtilis.

Authors:  Evert-Jan Blom; Anja N J A Ridder; Andrzej T Lulko; Jos B T M Roerdink; Oscar P Kuipers
Journal:  PLoS One       Date:  2011-11-08       Impact factor: 3.240

6.  DISCLOSE : DISsection of CLusters Obtained by SEries of transcriptome data using functional annotations and putative transcription factor binding sites.

Authors:  Evert-Jan Blom; Sacha A F T van Hijum; Klaas J Hofstede; Remko Silvis; Jos B T M Roerdink; Oscar P Kuipers
Journal:  BMC Bioinformatics       Date:  2008-12-16       Impact factor: 3.169

7.  Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources.

Authors:  Evert Jan Blom; Rainer Breitling; Klaas Jan Hofstede; Jos B T M Roerdink; Sacha A F T van Hijum; Oscar P Kuipers
Journal:  BMC Genomics       Date:  2008-10-21       Impact factor: 3.969

8.  Gene set analyses for interpreting microarray experiments on prokaryotic organisms.

Authors:  Nathan L Tintle; Aaron A Best; Matthew DeJongh; Dirk Van Bruggen; Fred Heffron; Steffen Porwollik; Ronald C Taylor
Journal:  BMC Bioinformatics       Date:  2008-11-05       Impact factor: 3.169

9.  Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.

Authors:  Da Wei Huang; Brad T Sherman; Richard A Lempicki
Journal:  Nucleic Acids Res       Date:  2008-11-25       Impact factor: 16.971

10.  Transient heterogeneity in extracellular protease production by Bacillus subtilis.

Authors:  Jan-Willem Veening; Oleg A Igoshin; Robyn T Eijlander; Reindert Nijland; Leendert W Hamoen; Oscar P Kuipers
Journal:  Mol Syst Biol       Date:  2008-04-15       Impact factor: 11.429
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