Publications

Below are a list of our published papers. Please contact me directly for PDFs.

  1. Rachakonda V, Gabbert C, Raina A, Bell LN, Cooper S, Malik S, Behari J.Serum metabolomic profiling in acute alcoholic hepatitis identifies multiple dysregulated pathways. PlosOne. December 2 2014 9(12):e113860. PubMed
  2. Skelly DA, Merrihew GE, Riffle M, Connelly CF, Kerr EO, Johansson M, Jaschob D, Graczyk B, Shulman NJ, Wakefield J, Cooper SJ, Fields S, Noble WS, Muller EGD, Davis TN, Dunham MJ, MacCoss MJ, and Akey JM. Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast.Genome Res. September 2013; 23: 1496-1504. PubMed
  3. Fowler DM, Cooper SJ, Stephany JJ, Hendon N, Nelson SK, Fields S. A yeast-based metabolite screen for modulators of statin-mediated growth inhibition. 2010 Molecular Biosystems. Mol Biosys. 2011 Feb 1; 7(2):533-44. PubMed
  4. Cooper SJ, Finney GL,Hesselberth J, Brown SL, Nelson SK, MacCoss MJ, Fields S. High-throughput profiling of amino acids in strains of the S. cerevisiae deletion collection. Genome Research. 2010 Sept 20: 1288-1296. PubMed
  5. The ENCODE Project Consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14; 447(7146):799-816. PubMed
  6. Cooper SJ, Trinklein ND, Nguyen L, Myers RM.  Binding Sites of the Serum Response Factor Differ in Three Human Cell Types. Genome Res. 2007 Feb; 17(2):136-144. PubMed
  7. Cooper SJ, Trinklein ND, Anton ED, Nguyen L, Myers RM. Comprehensive Analysis of Transcriptional Promoter Structure and Function in 1% of the Human Genome. Genome Res. 2006 Jan; 16 (1):1-10. PubMed
  8. Hartman SJ*, Trinklein ND, Anton ED, Marticke SS, Nguyen L, Myers RM. High-Throughput Cloning of Functional Elements in the Human Genome. Clontechniques. 2005 Jul; 20(1): 26-27.
  9. Kim TH, Barrera LO, Qu C, Van Calcar S, Trinklein ND, Cooper SJ, Luna RM, Glass CK, Rosenfeld MG, Myers RM, Ren B. Direct isolation and identification of promoters in the human genome. Genome Res. 2005 Jun; 15(6): 830-839. PubMed
  10. The ENCODE Project Consortium. The ENCODE (Encyclopedia of DNA Elements) Project. Science. 2004 Oct 22;306(5696):636-40.
  11.  Trinklein ND, Murray JI, Hartman SJ*, Botstein D, Myers RM.  The Role of Heat Shock Transcription Factor 1 in the Genome-wide Regulation of the Mammalian Heat Shock Response. Mol Biol Cell. 2004 Mar; 15(3): 1254-1261. PubMed
  12. 10. Trinklein ND, Aldred SF, Hartman SJ*, Schroeder DI, Otillar RP, Myers RM.  An Abundance of Bidirectional Promoters in the Human Genome.  Genome Res. 2004 Jan; 14(1): 62-66. PubMed
  13. 11. Hartman SJ*, Menon I, Haug-Collet K, Colley NJ. Expression of rhodopsin and arrestin during the light-dark cycle in Drosophila. Mol Vis. 2001 Apr 17;7:95-100. PubMed

*Maiden Name