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Host-specific transcriptomic pattern of Trichoderma virens during interaction with maize or tomato roots.

MorĂ¡n-Diez ME, Trushina N, Lamdan NL, Rosenfelder L, Mukherjee PK, Kenerley CM, Horwitz BA.

BMC Genomics. 2015 Jan 22;16:8. doi: 10.1186/s12864-014-1208-3.


A WNT/p21 circuit directed by the C-clamp, a sequence-specific DNA binding domain in TCFs.

Hoverter NP, Ting JH, Sundaresh S, Baldi P, Waterman ML.

Mol Cell Biol. 2012 Sep;32(18):3648-62. doi: 10.1128/MCB.06769-11. Epub 2012 Jul 9.


A Bayesian approach for decision making on the identification of genes with different expression levels: an application to Escherichia coli bacterium data.

Saraiva EF, Louzada F, Milan LA, Meira S, Cobre J.

Comput Math Methods Med. 2012;2012:953086. doi: 10.1155/2012/953086. Epub 2012 Mar 5.


Differential network biology.

Ideker T, Krogan NJ.

Mol Syst Biol. 2012 Jan 17;8:565. doi: 10.1038/msb.2011.99. Review.


Validation and characterization of DNA microarray gene expression data distribution and associated moments.

Thomas R, de la Torre L, Chang X, Mehrotra S.

BMC Bioinformatics. 2010 Nov 24;11:576. doi: 10.1186/1471-2105-11-576.


Functional analysis: evaluation of response intensities--tailoring ANOVA for lists of expression subsets.

Berger F, De Meulder B, Gaigneaux A, Depiereux S, Bareke E, Pierre M, De Hertogh B, Delorenzi M, Depiereux E.

BMC Bioinformatics. 2010 Oct 13;11:510. doi: 10.1186/1471-2105-11-510.


Internal standard-based analysis of microarray data. Part 1: analysis of differential gene expressions.

Dozmorov I, Lefkovits I.

Nucleic Acids Res. 2009 Oct;37(19):6323-39. doi: 10.1093/nar/gkp706. Epub 2009 Aug 31.


Profiling humoral immune responses to P. falciparum infection with protein microarrays.

Doolan DL, Mu Y, Unal B, Sundaresh S, Hirst S, Valdez C, Randall A, Molina D, Liang X, Freilich DA, Oloo JA, Blair PL, Aguiar JC, Baldi P, Davies DH, Felgner PL.

Proteomics. 2008 Nov;8(22):4680-94. doi: 10.1002/pmic.200800194.


Network-based global inference of human disease genes.

Wu X, Jiang R, Zhang MQ, Li S.

Mol Syst Biol. 2008;4:189. doi: 10.1038/msb.2008.27. Epub 2008 May 6.


Comparative genomic reconstruction of transcriptional regulatory networks in bacteria.

Rodionov DA.

Chem Rev. 2007 Aug;107(8):3467-97. Epub 2007 Jul 18. Review. No abstract available.


A simple method to combine multiple molecular biomarkers for dichotomous diagnostic classification.

Mamtani MR, Thakre TP, Kalkonde MY, Amin MA, Kalkonde YV, Amin AP, Kulkarni H.

BMC Bioinformatics. 2006 Oct 10;7:442.


Survival and growth in the presence of elevated copper: transcriptional profiling of copper-stressed Pseudomonas aeruginosa.

Teitzel GM, Geddie A, De Long SK, Kirisits MJ, Whiteley M, Parsek MR.

J Bacteriol. 2006 Oct;188(20):7242-56.


In vivo dissection of the Helicobacter pylori Fur regulatory circuit by genome-wide location analysis.

Danielli A, Roncarati D, Delany I, Chiarini V, Rappuoli R, Scarlato V.

J Bacteriol. 2006 Jul;188(13):4654-62.


A distinct QscR regulon in the Pseudomonas aeruginosa quorum-sensing circuit.

Lequette Y, Lee JH, Ledgham F, Lazdunski A, Greenberg EP.

J Bacteriol. 2006 May;188(9):3365-70.


Analysis of expressed sequence tag data and gene expression profiles involved in conidial germination of Fusarium oxysporum.

Deng Y, Dong H, Jin Q, Dai C, Fang Y, Liang S, Wang K, Shao J, Lou Y, Shi W, Vakalounakis DJ, Li D.

Appl Environ Microbiol. 2006 Feb;72(2):1667-71.


The H2O2 stress-responsive regulator PerR positively regulates srfA expression in Bacillus subtilis.

Hayashi K, Ohsawa T, Kobayashi K, Ogasawara N, Ogura M.

J Bacteriol. 2005 Oct;187(19):6659-67.


RACE: Remote Analysis Computation for gene Expression data.

Psarros M, Heber S, Sick M, Thoppae G, Harshman K, Sick B.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W638-43.

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