Timothy R. Dreszer


I received a Master's in Bioinformatics in 2006, working in David Haussler's lab ,
and have worked with Katie Pollard on biased substitutions in the human genome.
Until recently I was privileged to be a developer on the Human Genome Browser.
        
Dreszer T.R., Wall G.D., Haussler D. and Pollard K.S. Biased clustered substitutions in the human genome: The footprints of male-driven biased gene conversion. Genome Res. 17:1420-1430 Epub: September 4, 2007. ISSN 1088-9051/07.
   Additional material: Supplemental Methods (corrected), Slide Presentation and Plots of UBCS genome wide.

Abstract
We examined fixed substitutions in the human lineage since divergence from the common ancestor with the chimpanzee, and determined what fraction are AT to GC (weak-to-strong). Substitutions that are densely clustered on the chromosomes show a remarkable excess of weak-to-strong "biased" substitutions. These unexpected biased clustered substitutions (UBCS) are common near the telomeres of all autosomes but not the sex chromosomes. Regions of extreme bias are enriched for genes. Human and chimp orthologous regions show a striking similarity in the shape and magnitude of their respective UBCS maps, suggesting a relatively stable force leads to clustered bias. The strong and stable signal near telomeres may have participated in the evolution of isochores. One exception to the UBCS pattern found in all autosomes is chromosome 2, which shows a UBCS peak midchromosome, mapping to the fusion site of two ancestral chromosomes. This provides evidence that the fusion occurred as recently as 740,000 years ago and no more than ~3 million years ago. No biased clustering was found in SNPs, suggesting that clusters of biased substitutions are selected from mutations. UBCS is strongly correlated with male (and not female) recombination rates, which explains the lack of UBCS signal on chromosome X. These observations support the hypothesis that biased gene conversion (BGC), specifically in the male germline, played a significant role in the evolution of the human genome.


Dreszer T.R. Biased Clustered Substitutions in the Human Genome: Sex, Gambling and Non-Darwinian Evolution. masters thesis completed at University of California, Santa Cruz. Dec. 2006. (poster).

Karolchik D, Barber GP, Casper J, Clawson H, Cline MS, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hinrichs AS, Learned K, Lee BT, Li CH, Raney BJ, Rhead B, Rosenbloom KR, Sloan CA, Speir ML, Zweig AS, Haussler D, Kuhn RM, Kent WJ. The UCSC Genome Browser database: 2014 update. Nucleic Acids Res. 2014 Jan 1;42(1):D764-70. Epub 2013 Nov 21. PMID: 24270787; PMC: PMC3964947

Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, Nguyen N, Paten B, Zweig AS, Karolchik D, Kent WJ. Track Data Hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinformatics. 2014 Apr 1;30(7):1003-5. Epub 2013 Nov 13. PMID: 24227676; PMC: PMC3967101

Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, Raney BJ, Pohl A, Malladi VS, Li CH, Lee BT, Learned K, Kirkup V, Hsu F, Heitner S, Harte RA, Haeussler M, Guruvadoo L, Goldman M, Giardine BM, Fujita PA, Dreszer TR, Diekhans M, Cline MS, Clawson H, Barber GP, Haussler D, Kent WJ. The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res. 2013 Jan;41(Database issue):D64-9. PMID: 23155063; PMC: PMC3531082

Rosenbloom KR, Sloan CA, Malladi VS, Dreszer TR, Learned K, Kirkup VM, Wong MC, Maddren M, Fang R, Heitner SG, Lee BT, Barber GP, Harte RA, Diekhans M, Long JC, Wilder SP, Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ. ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic Acids Res. 2013 Jan;41(Database issue):D56-63. PMID: 23193274; PMC: PMC3531152

Dreszer TR, Karolchik D, Zweig AS, Hinrichs AS, Raney BJ, Kuhn RM, Meyer LR, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, Pohl A, Malladi VS, Li CH, Learned K, Kirkup V, Hsu F, Harte RA, Guruvadoo L, Goldman M, Giardine BM, Fujita PA, Diekhans M, Cline MS, Clawson H, Barber GP, Haussler D, Kent WJ The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Res. 2012 Jan;40(Database issue):D918-23. PMID: 22086951; PMC: PMC3245018

ENCODE Project Consortium, Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F, Epstein CB, Frietze S, Harrow J et al. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74. PMID: 22955616; PMC: PMC3439153

Rosenbloom KR, Dreszer TR, Long JC, Malladi VS, Sloan CA, Raney BJ, Cline MS, Karolchik D, Barber GP, Clawson H, Diekhans M, Fujita PA, Goldman M, Gravell RC, Harte RA, Hinrichs AS, Kirkup VM, Kuhn RM, Learned K, Maddren M, Meyer LR, Pohl A, Rhead B, Wong MC, Zweig AS, Haussler D, Kent WJ. ENCODE whole-genome data in the UCSC Genome Browser: update 2012. Nucleic Acids Res. 2012 Jan;40(Database issue):D912-7. PMID: 22075998; PMC: PMC3245183

Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP, Clawson H, Coelho A, Diekhans M, Dreszer TR, Giardine BM, Harte RA, Hillman-Jackson J, Hsu F, Kirkup V, Kuhn RM, Learned K, Li CH, Meyer LR, Pohl A, Raney BJ, Rosenbloom KR, Smith KE, Haussler D, Kent WJ. The UCSC Genome Browser database: update 2011. Nucleic Acids Res. 2011 Jan;39(Database issue):D876-82. PMID: 20959295; PMC: PMC3242726

Raney BJ, Cline MS, Rosenbloom KR, Dreszer TR, Learned K, Barber GP, Meyer LR, Sloan CA, Malladi VS, Roskin KM, Suh BB, Hinrichs AS, Clawson H, Zweig AS, Kirkup V, Fujita PA, Rhead B, Smith KE, Pohl A, Kuhn RM, Karolchik D, Haussler D, Kent WJ. ENCODE whole-genome data in the UCSC genome browser (2011 update). Nucleic Acids Res. 2011 Jan;39(Database issue):D871-5. PMID: 21037257; PMC: PMC3013645

Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA, Diekhans M, Smith KE, Rosenbloom KR, Raney BJ, Pohl A, Pheasant M, Meyer LR, Learned K, Hsu F, Hillman-Jackson J, Harte RA, Giardine B, Dreszer TR, Clawson H, Barber GP, Haussler D, Kent WJ. The UCSC Genome Browser database: update 2010. Nucleic Acids Res. 2010 Jan;38(Database issue):D613-9. PMID: 19906737; PMC: PMC2808870

Rosenbloom KR, Dreszer TR, Pheasant M, Barber GP, Meyer LR, Pohl A, Raney BJ, Wang T, Hinrichs AS, Zweig AS, Fujita PA, Learned K, Rhead B, Smith KE, Kuhn RM, Karolchik D, Haussler D, Kent WJ. ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Res. 2010 Jan;38(Database issue):D620-5. PMID: 19920125; PMC: PMC2808953

Kuhn RM, Karolchik D, Zweig AS, Wang T, Smith KE, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pheasant M, Meyer L, Hsu F, Hinrichs AS, Harte RA, Giardine B, Fujita P, Diekhans M, Dreszer T, Clawson H, Barber GP, Haussler D, Kent WJ. The UCSC Genome Browser Database: update 2009. Nucleic Acids Res. 2009 Jan;37:D755-D761.

Pollard K.S., Salama S.R., King B., Kern A.D., Dreszer T.R., Katzman S., Siepel A., Pedersen J.S., Bejerano G., Baertsch R., Rosenbloom K.R., Kent J. and Haussler D. Forces shaping the fastest evolving regions in the human genome. PLoS Genetics. 2(10):e168. 2006 Oct 13. Epub 2006 Aug 23.


Secrets of my private life can be discovered here.

 
Word Jumble (pdf, ppt): The Search for Protein-DNA recognition sites in the ENCODE region of the human genome.
Contact Lens (pdf, poster): Evaluating Protein Structure by Contacts.
Self-Tuning Memory Manager (patent): A memory manager that I wrote a long time ago.

  It is insulting enough that evolution, which the Christian Right wants to ban from our schools, turns out to be fundamentally conservative.
But now I have to bare witness to genetic conversions?!
      comments?