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Kelly Vaughan, Ph.D.

Kelly Vaughan, Ph.D. Department of Biostatistics
Ryals Public Health Bldg, 327
University of Alabama at Birmingham
Birmingham, AL 35294
Phone: (205) 975-9272
Fax: (205) 975-2540
E-mail: lkvaughan@uab.edu
Full CV


I received my BS in Biochemistry with a minor in Animal Science from Berry College and a Ph.D. in Biochemistry from Texas A&M University. My thesis focused on understanding the complex genetic relationship of wild, weedy and cultivated rice. I also investigated the underlying mechanism of resistance to the herbicide glufosinate (used for the GMO rice LibertyLink) in a weedy rice variety found in Texas.   This work received national recognition for the application of genetic and statistical methods in the field of Weed Science and was awarded Paper of the Year by the Weed Science Society of America in 2003 (Vaughan et al. 2001). I joined the SSG in the spring of 2005 as a post-doctoral fellow to learn more about the statistical methods used in population genetics research. My work focused on the development, evaluation and application of population stratification, admixture and structured association testing methods.

In 2008 I was awarded a Mentored Career Development Award by the NIDDK entitled Cluster Based Selection of Candidate Genes in Genome Wide Association Studies. I developed this application based on a desire to gain further training in bioinformatics and computational biology. This project was designed to bridge my training in biochemistry, genetics and statistical genetics while strengthening my skills to actively facilitate cross disciplinary research.

Since joining the Department as a Research Assistant Professor in 2008, I have continued to develop my research interest in applying systems biology and bioinformatics approaches in the analysis and interpretation of genomic data. Genes do not act in isolation, although many current statistical analysis methods for high dimensional genomics data make this assumption. My research addresses this by combining biochemical and genetic knowledge with statistical analysis to put the long lists of genes or variants that are produced by genome wide experiments into a biological context. This is accomplished through the application of pathway, network and functional annotation analysis methods to candidate gene, genome wide association, whole genome expression, methylation and other high dimensional genomic data. I am also interested in applying the concepts of reproducible research to genomics and maintain an active interest in admixture and population genetics. Although my current appointment does not focus on teaching, I enjoy opportunities as a guest lecturer in classes at UAB and as an instructor at several short-courses. My broad back ground and diverse research experiences have also given me a unique perspective, and I am privileged to act as a mentor to several graduate students and postdoctoral fellows.

Publications
 

  • 2013
  • 2012
  • 2011
  • 2010
  • 2009
  • 2008
  • 2007
  • Pre 2007
  1. Vaughan LK, Srinivasasainagendra V. Where in the genome are we? A cautionary tale of database use in genomics research. Front Genet. 2013;4:38. Epub 2013 Mar 21. [PMID: 23519237] [doi: 10.3389/fgene.2013.00038]
     
  2. R Reynolds, X. Cui, LK Vaughan, DT Redden, Z Causey, E Perkins, T Shah, LB Hughes, CLEAR Investigators, A Damle, M Kern, PK Gregersen, MR Johnson, SL Bridges, JR. 2013. Gene Expression Patterns in Peripheral Blood cells Associated with Radiographic Severity in African-Americans with Early Rheumatoid Arthritis. Rheumatology International. 33(1):129-137. [PMID: 22238028] [PMCID In process]
  1. Lynch AI, Irvin MR, Boerwinkle E, Davis BR, Vaughan LK, Ford CE, Aissani B, Eckfeldt JH, Arnett DK, Shrestha S. 2012. RYR3 gene polymorphisms and cardiovascular disease outcomes in the context of antihypertensive treatment. Pharmacogenomics J. In press. [PMID: 22664477] [PMCID In process]
     
  2. Duarte, CW, C Willey, D Zhi, X Cui, J Harris, LK Vaughan, T Mehta, R McCubrey, N Khodarev, R Weichselbaum, GY Gillespie. 2012. Expression signature of IFN/STAT1 signaling genes predicts poor survival outcome in Glioblastoma Multiforme in a subtype-specific manner. PLoS ONE. In press. [PMID: 22242177] [PMCID: PMC3252343]
  1. Irvin, MR, S. Shrestha, Y. Chen, HW. Wiener, T Haritunians, LK. Vaughan, HK. Tiwari, KD Taylor, R Scherzer, MS. Saag, C Grunfeld, JI. Rotter and DK. Arnett. 2011. Genes Linked to Energy Metabolism and Immunoregulatory Mechanisms are Associated with Subcutaneous Adipose Tissue Distribution in HIV-infected Men. Pharmacogenetics and Genomics. 21(12)798-807. [PMID: 21897333] [PMCID PMC3210910]
     
  2. Wineinger, NE, NM Pajewski, RE Kennedy, MK Wojczynski, LK Vaughan, SC Hunt, C Gru, DC Rao, U Broeckel, DK Arnett & HK Tiwari. 2011. Characterization of autosomal copy number variation in African Americans: the HyperGEN study. European Journal of Human Genetics. 19(12)1271-5. [PMID: 21673747] [PMCID In process]
     
  3. Divers J, Redden DT, Rice KM, Vaughan LK, Padilla MA, Allison DB, Bluemke DA, Young HJ, Arnett DK. 2011. Comparing self-reported ethnicity to genetic background measures in the context of the Multi-Ethnic Study of Atherosclerosis (MESA). BMC Genetics. 12:28. [PMID: 21375750] [PMCID: PMC3068121]
     
  4. Shriner, D & LK Vaughan. 2011. Powerful, Flexible, and Efficient Multilocus Genome-wide Association Testing Reveals Pathways Involved in Parkinson Disease. BMC Genomics. 12:89. [PMID: 21281506] [PMCID: PMC3040731]
     
  5. Arnett DK, Meyers KJ, Devereux RB, Tiwari HK, Gu CC, Vaughan LK, Perry RT, Patki A, Claas SA, Sun YV, Broeckel U, Kardia SL. Genetic Variation in NCAM1 Contributes to Left Ventricular Wall Thickness in Hypertensive Families. Circ Res. 2011 Jan 6. [Epub ahead of print] [PMID: 21212386] [DOI: 10.1161/CIRCRESAHA.110.239210]
  1. Shikany JM, Vaughan LK, Baskin ML, Cope MB, Hill JO, Allison DB. Is dietary fat "fattening"? A comprehensive research synthesis. Crit Rev Food Sci Nutr. 2010 Sep;50(8):699-715. [PMID: 20830632]
  1. Vaughan, LK, J Divers, M Padilla, DT Redden, HK Tiwari, D Pomp & DB Allison. 2009. The use of plasmodes as a supplement to simulations: A simple example evaluating individual admixture estimation methodologies. Computational Statistics and Data Analysis. 53(5) 1755-1766 [DOI: 10.1016/j.csda.2008.02.032]
     
  2. Casazza, K, N Natour, J Divers, LK Vaughan, AW Bigham, B A Gower, G Hunter & JR Fernández. 2009. Triglyceride concentration is independently associated with variation in the LPL gene in African American and European American women. The Open Obesity Journal. In Press. [DOI: 10.2174/1876823700901010023]
     
  3. Padilla, MA, J Divers, LK Vaughan, DB Allison, & HK Tiwari. 2009. Multiple Imputation to Correct for Measurement Error in Genetic Structured Association Testing. Human Heredity. 68(1):65-72. [PMID: 19339787]
  1. Kelley, JM, LB Hughes, R Feng, N Liu, MA Padilla, LK Vaughan, SL Bridges. 2008. Evaluating linkage disequilibrium and recombination provides a haplotype-tagging SNP panel of the major histocompatibility complex in African Americans. Genes and Immunity. 9: 271 – 273. [PMID: 8305489]
     
  2. Shriner, D, T Mersha, MPadilla, S Zhang, LK Vaughan, & AE Loraine. 2008. Gene Ontology-Based Prioritization of Candidate Genes from Genome-Wide Linkage Studies. Nucleic Acids Research. 36(4):e26. [PMID: 18263617].
     
  3. Tiwari, HK, J Barnholtz-Sloan, N Wineinger, MA Padilla, LK Vaughan & DB Allison. 2008. Review and evaluation of methods correcting for population stratification with a focus on underlying statistical principles. Human Heredity. 66(2):67-86. [PMID: 18382087]
     
  4. Hughes, LB, D Morrison, JM Kelley, MA Padilla, LK Vaughan, AO Westfall, TR Mikuls, VM Holers, L Parrish, GS Alarcón, DL Conn, B Jonas, LF Callahan, EA Smith, G Gilkeson, G Howard, LW. Moreland, DB Allison, N Patterson, D Reich & SL Bridges, Jr. 2008. The HLA-DRB1 Shared Epitope is Associated with Susceptibility to Rheumatoid Arthritis in African-Americans and Correlates with Degree of Genetic Admixture from Caucasians. Arthritis Research. 58(2):349-58. [PMID: 18240241]
  1. Shriner, D, LK Vaughan, M. Padilla, HK Tiwari. 2007. Letters: Problems with Genome Wide Association Studies. Science. 316(5833):1840 – 1842 [PMID: 17600199]
     
  2. Divers, J, LK Vaughan, M Padilla, DT Redden, JR Fernández & DB Allison. 2007. Correcting for measurement error in individual ancestry estimates in structured association tests. Genetics. 176 (3): 1823. [PMID: 17507670]
     
  3. Redden, DT, J Divers, LK Vaughan, M Padilla, S Musani, HK Tiwari & DB Allison. 2007. Methodologic Challenges in Genetic Studies of Obesity. In Obesity Genomics & Postgenomics. Clément & Sørensen, eds. Informa Healthcare, NY. Pgs 229-246.
  1. Redden D, J Divers, LK Vaughan, HK Tiwari, TM Beasley, J Fernández, RP Kimberly, R Feng, M Padilla, N Lui, M Miller & DB Allison. 2006. Regional admixture mapping and structured association testing: conceptual unification and an extensible general linear model. PLoS Genetics 2: 1254-1264. [PMID: 16934005]
     
  2. Vaughan, LK, BV Ottis, AM Prazak-Havey, CA Bormans, C Sneller, JM Chandler & WD Park. 2001. Is all red rice found in commercial rice fields really Oryza sativa? Weed Science. 49:468-476. [DOI: 10.1614/0043-1745(2001)049[0468:IARRFI]2.0.CO;2]
     

 

Years: 2005 - 2008 (Postdoctoral Fellow)
Mentor(s):  David T. Redden, PhD & David B Allison PhD & Hemant K. Tiwari, PhD
Current Position: Assistant Professor of Biology, Director Bioinformatics Program, King University