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Programmer/Analyst 

Carl E. McIntosh
National Cancer Institute at Frederick 
Building 560:21-23  
Frederick, MD 21702-1201 U.S.A.

Hours: Office Hours
Email: Carl.McIntosh@nih.gov

Biography

Carl McIntosh earned his B.A. degree from the Department of Zoology at the University of Hawaii. He spent the next 14 years at the Smithsonian National Zoological Park's Genetics Laboratory as a research technician and laboratory manager.

In the Fall of 2005, he joined National Cancer Institute in Frederick Maryland as a Bioinformatics Programmer / Analyst. He has participated on 3 Genome-Wide Association Studies (GWAS): HIV, NPC and HBV. Presently, he is assisting with a project to characterize DNA methylation patterns and its role in cancer. He is involved with several next-generation sequencing projects.

This Fall 2013, Carl has completed a M.S degree in Computer Science at Hood College. His coursework and interests are in Bioinformatics, High-preformance computing and advanced programming techniques.

Publications

  1. Tang M, Lautenberger JA, Gao X, Sezgin E, Hendrickson SL, Troyer JL, David VA, Guan L, McIntosh CE, Guo X, Zheng Y, Liao J, Deng H, Malasky M, Kessing B, Winkler CA, Carrington M, Dé The G, Zeng Y, O'Brien SJ. The Principal Genetic Determinants for Nasopharyngeal Carcinoma in China Involve the HLA Class I Antigen Recognition Groove. PLoS Genet. 2012 Nov;8(11):e1003103. doi: 10.1371/journal.pgen.1003103. Epub 2012 Nov 29. PubMed PMID: 23209447.
  2. Yu, W, Briones, V, Lister, R, McIntosh, CE, Lee, E, Ren, J, Han, Y, Terashima, M, Leighty, R, Ecker, J, Muegge, K. H3K4me1 marks at CG hypomethylated sites in Lsh-/- MEFs preserve an epigenetic memory for gene expression (in Preparation).
  3. Troyer JL, Nelson GW, Lautenberger JA, Chinn L, McIntosh C, Johnson RC, Sezgin E, Kessing B, Malasky M, Hendrickson S, Guan L, Minzhong T, An P, Winkler  CA, Limou S Le Clerc S, Delaneau O, Zagury J-F, Schuitemaker H, van Manen D, Bream JH, Gomperts ED, Buchbinder S, Goedert JJ, Kirk GD, O’Brien SJ. Genome-Wide Association Study Implicates PARD3B-Based AIDS Restriction.  J Infect Disease 203: 1491-1502.
  4. Chinn LW, Minzhong T, Kessing BD, Lautenberger JA, Troyer JL, Malasky MJ, McIntosh C, Kirk GD, Wolinsky SW, Buchbinder SP, Gomperts ED, Goedert JJ, and O’Brien SJ. Genetic associations of variants in genes encoding HIV-dependency factors required for HIV-1 infection.  J Infect Disease 202:1833-1845.
  5. Peer, B., McIntosh, C. Birks, S., Rothstein, S. and Fleischer, R. 2010. Complex Biogeographic History of Lanius Spp. Shrikes and its implications for the evolution of host defenses against avian brood parasitism. Condor (accepted Oct 2010).
  6. Sezgin E, Drosdak A, McIntosh C, Kessing B, Lautenberger J, Goedert JJ, Phair JP, Troyer JL, Smith MW, and O’Brien SJ.  Examination of disease based selection, demographic history and population structure in European Y chromosome haplogroup I.  J Hum Genet. 2010 Jun 24. [Epub ahead of print]. PMID: 20574427
  7. Eggert, L. S., Beadell, J. S., McClung, A, McIntosh, C. E., and Fleischer, R. C. 2009. Evolution of Microsatellite Loci in the Adaptive Radiation of Hawaiian Honeycreepers. Journal of Heredity (in press).
  8. Troyer JL, Vandewoude S, Pecon-Slattery J, McIntosh C, Franklin S, Antunes A, Johnson W, O'Brien SJ.  FIV cross-species transmission: An evolutionary prospective. Vet Immunol Immunopathol 123: 159-166. 2008. PMID: 18299153
  9. Fleischer, R. C., Boarman, W. I., Gonzalez, E. G., Godinez, A., Omland, K. E., Young, S., Helgen, L., Syed, G. & McIntosh, C. E. 2007. As the raven flies: using genetic data to infer the history of invasive common raven (Corvus corax). Molecular Ecology 17:464-474.
  10. Fleischer, R. C., B. Slikas, J. Beadell, C. Atkins, C. E. McIntosh, S. Conant. 2007. Genetic Variability and taxonomic status of the Nihoa and Laysan Millerbirds. The Condor: 109 (4): 954-962.
  11. Jarvi, S., C. Tarr, C. McIntosh, C. Atkinson, and R. Fleischer.  2004. Natural Selection of the major histocompatibility complex (Mhc) in Hawaiian Honeycreepers (Drepanidinae).  Molecular Ecology 13:2157-2168.
  12. Chu, M., W. D. Koenig, A. Godinez, C. E. McIntosh, and R. C. Fleischer.  2002.  Social and genetic monogamy in territorial and loosely colonial populations of the Phainopepla (Phainopepla nitens).  Auk 119:770-777.
  13. Fleischer, R. C. and C. E. McIntosh. 2001. Molecular systematics and biogeography of the Hawaiian avifauna. Studies in Avian Biology: 22: 51 - 60.
  14. Fleischer, R. C., C. L. Tarr, H. F. James, B. Slikas and C. E. McIntosh. 2001. Phylogenetic placement of the po`o-uli Melamprosops phaeosoma based on mitochondrial DNA sequence and osteological characters. Studies in Avian Biology: 22: 98 - 103.
  15. Fleischer Robert C. McIntosh Carl E., Tarr Cheryl L. Evolution on a volcanic conveyor belt: Using phylogeographic reconstructions and K-Ar-based ages of the Hawaiian Islands to estimate molecular evolutionary rates. Molecular Ecology 7(4). April, 1998. 533-545.
  16. Paxinos, E., McIntosh, C., Ralls, K., and Fleischer, R. 1997. A non-invasive method for distinguishing among canid species: amplification and enzyme restriction of DNA from dung. Molecular Ecology 6: 483-486.
  17. Cooper, A., Rhymer, J., James, H., Olson, S., McIntosh, C., Sorenson, M. and Fleischer, R. 1996. Ancient DNA and island endemics. Nature 381:484.
  18. Simon, C., Nigro, L., Sullivan, J., Holsinger, K., Martin, A., Grapputo, A., Franke, A., and McIntosh, C., 1996. Large Differences in Substitutional Pattern and Evolutionary Rate of 12S Ribosomal RNA Genes. Molecular Biology & Evolution 13(7) 923-932.
  19. Simon, C., McIntosh, C., Deniega,J. 1993. Standard Restriction Fragment Length Analysis of Mitochondrial Genome is Not Sensitive Enough for Phylogenetic Analysis or Identification of 17-year Periodical Cicada Broods (Hemiptera: Cicadidae): The Potential for a New Technique. Annals of the Entomological Society of America 86(3) 228-238.
  20. Ullman,D. E., German, T. L., McIntosh, C. E., Williams D. D. F., 1991. Effect of heat treatment on closterovirus-like particle associated with mealybug wilt of pineapple. Plant Disease 75 (8): 859-61.

Software

  1. QC Checker - About QC Checker
  2. SNP Edit - About SNP Edit
  3. CocoaGWASNetCDF (Not final name) - About CocoaGWASNetCDF
  4. miRNA Tracks - _A pipeline to generate UCSC Genome Browser Tracks from 100,000s of miRNAs, Piwi-size RNAs and small sequences._
  5. SAS/Intrnet - A pipeline and HTML based graphical-user interface for running SAS analyses.