Facilities and Services: Bioinformatics

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Mission/Aims

The five central goals of the Bioinformatics Core Facility are to:

Develop and maintain a bioinformatic hardware and software infrastructure that is functional for the campus research community and has a manageable size with regard to the available resources.
Organize tutorials and workshops on bioinformatic and related topics with extensive manuals and present lectures in relevant student courses.
Provide consulting services for students and researchers on a wide variety of bioinformatic and cheminformatic topics.
Collaborate with experimental and theoretical scientists in publishable, multidisciplinary research projects, which will allow the bioinformatics core to grow by creating a competitive research environment that is attractive to talented students and researchers.

Maintain an extensive web portal that provides efficient access to the available hardware resources, online tools, databases, software and training opportunities.

Research/Publications

Key Publications
The following are selected publications of research utilizing the expertise of the Bioinformatics Core.

Jin H, Vacic V, Girke T, Lonardi S, Zhu JK (2008) Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis. BMC Mol Biol 14;9:6. HubMed

Gollery M, Harper J, Cushman J, Mittler T, Girke T, Zhu JK, Bailey-Serres J, Mittler
R (2006) What makes species unique? The contribution of proteins with obscure features. Genome Biol 7 (7): R57. HubMed

Katiyar-Agarwal S, Morgan R, Dahlbeck D, Borsani O, Villegas A, Zhu JK, Staskawicz BJ, Jin H (2006) A pathogen-inducible endogenous siRNA in plant immunity. Proc Natl Acad Sci U S A 103(47): 18002-7. HubMed

Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu JK (2005) Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 123 (7): 1279–1291. HubMed

Horan K, Lauricha J, Bailey-Serres J, Raikhel N, Girke T (2005) Genome cluster
database. A sequence family analysis platform for Arabidopsis and rice. Plant Physiol 138 (1): 47–54. HubMed

Sunkar R, Girke T, Jain PK, Zhu JK, (2005a) Cloning and characterization of microRNAs from rice. Plant Cell 17 (5): 1397–1411. HubMed

Sunkar R, Girke T, Zhu J.K (2005b) Identification and characterization of endogenous small interfering RNAs from rice. Nucleic Acids Res 33 (14): 4443–4454. HubMed

Surpin M, Rojas-Pierce M, Carter, C, Hicks GR, Vasquez J, Raikhel NV (2005) The power of chemical genomics to study the link between endomembrane system components and the gravitropic response. Proc Natl Acad Sci U S A 102 (13): 4902– 4907. HubMed

Girke T, Cheng LC, Raikhel NV (2005) ChemMine. A compound mining database for chemical genomics. Plant Physiol 138 (2), 573–577. HubMed

Girke T, Lauricha J, Tran H, Keegstra K, Raikhel N (2004) The Cell Wall Navigator database. A systems-based approach to organism-unrestricted mining of protein families involved in cell wall metabolism. Plant Physiol 136 (2): 3003–3008. HubMed

Carter C, Pan S, Zouhar J, Avila EL, Girke T, Raikhel NV (2004) The vegetative vacuole proteome of Arabidopsis thaliana reveals predicted and unexpected proteins. Plant Cell 16 (12): 3285–3303. HubMed

Gibbons R, Dugaiczyk LJ, Girke T, Duistermars B, Zielinski R, Dugaiczyk A (2004) Distinguishing humans from great apes with AluYb8 repeats. J Mol Biol 339 (4): 721–729. HubMed

Heilmann I, Pidkowich MS, Girke T, Shanklin J (2004) Switching desaturase enzyme
specificity by alternate subcellular targeting. Proc Natl Acad Sci U S A 101 (28): 10266–10271. HubMed

Kawaguchi R, Girke T, Bray EA, Bailey-Serres J (2004) Differential mRNA translation contributes to gene regulation under non-stress and dehydration stress conditions in Arabidopsis thaliana. Plant J 38 (5): 823–839. HubMed

Zouhar J, Hicks GR, Raikhel NV (2004) Sorting inhibitors (Sortins): Chemical compounds to study vacuolar sorting in Arabidopsis. Proc Natl Acad Sci U S A 101 (25): 9497–9501. HubMed

Girke T, Ozkan M, Carter D, Raikhel NV (2003) Towards a modeling infrastructure for studying plant cells. Plant Physiol 132 (2): 410–414. HubMed

Morrell PL, Lundy KE, Clegg MT (2003) Distinct geographic patterns of genetic diversity are maintained in wild barley (Hordeum vulgare ssp. spontaneum) despite migration. Proc Natl Acad Sci U S A 100 (19): 10812–10817. HubMed

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