Service Center Facilities
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Facility Description

Hardware for Bioinformatics Analysis:

Hardware for Highthroughput computation:

Software for Bioinformatics Analysis:

Personnel

Name Position Phone Number Email
Kim M. Gernert
CV		 Facility Director

(404)727-3501
B01A 1462 Clifton Rd.

 gernert@emory.edu
W. Steve Pittard
CV		 Technical Project Manager, Sr.

(404)727-0038
2131A Rollins Research Center

 wsp@emory.edu
Karan Upppal CV Applications Developer / Analyst

(404)727-3501
B28 1462 Clifton Rd.

 kuppal2@emory.edu

 

Sample Writeup for collaborative support:

Bioinformatics Sample Writeup
Sequence Analysis Sample Writeup
Microarray Analysis Sample Writeup
Molecular Modeling Sample Writeup
High-throughput Computation Sample Writeup
Hardware and Equipment Sample Writeup

 

Publications

Sequence Analysis

  1. Flaherty, D.B., Gernert, K.M., Shmeleva, N., Tang, X, Mercer, K.B., Borodovsky, M. and Benian, G.M. (2002) "Titins in C. elegans with Unusual Features: Coiled-Coil Domains, Novel Regulation of Kinase Activity and Two New Possible Elastic Regions", J of Molecular Biology. 323, 533-549.
  2. Small, T.M., Gernert, K.M., Flaherty, D.B., Mercer, K.B., Borodovsky, M., and Benian, G.M. (2004) Three New Isoforms of C. elegans UNC-89 Containing MLCK-like Protein Kinase Domains J. Mol. Biol. 342, 91-108.

High-throughput Sequence Analysis

  1. Tsui, C., Coleman, L.E., Griffith, J.L., Bennett, E.A., Goodson, S.G., Scott, J.D., Pittard, W.S, and Devine, S.E. (2003) Single nucleotide polymorphisms (SNPs) that map to gaps in the human SNP map. Nucleic Acids Res. 31: 4910-4916.
  2. Griffith, J.L., Coleman, L.E., Raymond, A.S., Goodson, S.G., Pittard, W.S., Tsui, C., and Devine, S.E. (2003) Functional genomics reveals relationships between the retrovirus-like Ty1 element and its host Saccharomyces cerevisiae. Genetics 164, 867- 879.
  3. Bennett, E.A., Coleman, L.E., Tsui, C., Pittard, W.S., and Devine, S.E. (2004) Natural genetic variation caused by transposable elements in humans. Genetics 168: 933-951.
  4. Mills, R.E., Bennett, E.A., Iskow, R.C., Luttig, C.T., Tsui, C., Pittard, W.S., and Devine, S.E. (2006) Recently-mobilized transposons in the human and chimpanzee genomes. American Journal of Human Genetics, 78(4): 671-679.
  5. Mills, R.E., Luttig, C.T., Beauchamp, A., Tsui, C., Pittard, W.S., and Devine, S.E. (2006) An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Research. 16(9): 1182-1190.

Homology Modeling and Structural Analysis

  1. Tobiason, D.M., Buchner, J.M., Thiel, W.H., Gernert, K.M. and Glasgow, A.C. (2001) Conserved amino acid motifs from the novel Piv/MooV family of DNA transposases and site-specific invertases are required for Piv-mediated catalysis of DNA inversion", Molecular Microbiology. 39(3), 641-651.
  2. Ono, S., McGough, A., Pope, B., Tolbert, V., Bui, A., Pohl, J., Benian, G.M., Gernert, K.M. and Weeds, A.G. (2001) "C-Terminal tail of ADF/cofilin (actin depolymerizing factor/cofilin) is critical for maintaining its stable association with F-actin and is implicated in the second actin-binding site", J Biol Chem. 276(8), 5952-5958.
  3. Low, C., Lyuboslavsky, P., French, A., Phong, L., Wyatte, K., Thiel, W.H., Marchan, E., Igarashi, K., Kashiwagi, K., Neyton, J., Paoletti, P., Gernert, K.M., Williams6, K., Traynelis, S.F. and Zheng, F. (2002) "Molecular Determinants of Proton Sensitive NMDA Receptor Gating ", Molecular Pharmacology. 63, 1212-1222.
  4. Von Der Linden, D., Ma, X., Sandberg, E.M., Gernert, K.M., Bernstein, K.E. and Sayeski, P.P. (2002) Mutation of Glutamic Acid Residue 1046 Abolishes Jak2 Tyrosine Kinase Activity, Mol. Cell Biochemistry. 241(1-2), 87-94.
  5. Fulci G., Ishii, N., Maurici, D., Gernert, K.M., Hainaut, P., Kaur, B. and Van Meir, E.G. (2002) Initiation of Human Astrocytoma by Clonal Evolution of Cells with Progressive Loss of p53 Functions in a Patient with a 283H TP53 Germ-line Mutation: Evidence for a Precursor Lesion, Cancer Res. 62(10), 2897-2905.
  6. Spivak-Kroizman T., Friedland, D.E., De Staercke, C., Gernert, K.M., Goss, D.J. and Hagedorn, C.H. (2002) Mutations in the S4-H2 loop of eIF4E which increase the affinity for m7GTP, FEBS Lett. 516(1-3), 9-14.
  7. O'Hern, P. and Gernert, K.M. (2002) Visualizing Molecules. Chime biochemistry companion website. Principles of Biochemistry. 3rd ed. H.R. Horton et al. Prentice Hall Publishers.
  8. Plemper, R.K., Lakdawala, A.S., Gernert, K.M., Synder, J.P and Compans, R.W. (2003) Structural features of paramyxovirus F protein required for fusion initiation, Biochemistry. 42(22), 6645-6655.
  9. Vzorov, A.N., Gernert, K.M., Compans, R.W. (2005) Multiple domains of the SIV Env protein determine virus replication efficiency and neutralization sensitivity. Virology. 5;332(1):89-101.
  10. Berger, A.C., Vanderford, T.H., Gernert, K.M., Nichols, J.W., Faundez, V., Corbett, A.H. (2005) Saccharomyces cerevisiae Npc2p Is a Functionally Conserved Homologue of the Human Niemann-Pick Disease Type C 2 Protein, hNPC2. Eukaryot Cell. 4(11):1851-62.
  11. Seth, S., Skountzou, I., Gernert, KM., Compans RW. (2007) Fusogenic Variants of a Noncytopathic Paramyxovirus. J. Virology. 81(8): 4286-4297.
  12. Lee, W., Weber, DA., Laur, O., Severson, E., McCall, I., Jen, RP., Chin, AC., Wu, T., Gernert, KM., C. Parkos. (2007) Novel Structural Determinants on SIPR alpha that Mediate Binding to CD47 . J. Immunology. 179(11):7741-50.

Microarray Analysis

  1. Peavy, R.D., Hubbard, K.B., Lau, A., Fields, R.B., Xu, K., Lee, C.J., Lee, T.T., Gernert, K.M., Murphy, T.J., Hepler, J.R. (2005) Differential effects of Gq alpha, G14 alpha, and G15 alpha on vascular smooth muscle cell survival and gene expression profiles. Mol Pharmacol. 67(6):2102-14.
  2. Zhang, X., Su, L., Pirani, AA., Wu, H., Zhang, H., Shin, DM., Gernert, K.M., Chen, ZG. (2006) Understanding Metastatic SCCHN cells from Unique Genotypes to Phenotypes with the Aid of an Animal Model and DNA Microarray Studies. Clinical Exp Metastasis. 23(3-4): 209-22.
  3. Pirani, A.A. "Cluster Validation in Microarray gene Expression Data". (2005) Masters Thesis, Computer Science Department, Emory University, mentor James Lu.

Past Fellows:

Gregory H. Doho:  Microarray Specialist II
Emory Biomarker Service Center
Winship Cancer Institute, Emory University
1365B Clifton Rd., Clinic B, Suite B4333
Atlanta, GA 30322
404-778-5123
gdoho@emory.edu
(2006-2008)

Ali Pirani: Infomation Analyst II,
Biomolecular Computing Resource
ali.pirani@emory.edu
(2002 - 2008).

Jesse Miller: Webmaster,
Molecular Modeling Center Biomolecular Computing Resource
Emory University College
Mail: P.O. Box 21202
jsmille@emory.edu

A list of his projects.


Patrick McConnell, Duke Bioinformatics Core
Duke University, Cancer Center, Biostats and Info
DUMC Box 2717, Durham, NC 27710
770-414-8143
patrick.mcconnell@duke.edu

A list of his projects.