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Carlos Araya

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I am a postdoctoral scholar with Michael Snyder, Chair of the Genetics Department, at Stanford University, where I am constructing technologies to control transcriptional networks and am working to build the first spatiotemporally-resolved metazoan TF regulatory network. I completed my PhD. in Genome Sciences with Stanley Fields (HHMI) at the University of Washington in December of 2010, where I designed and constructed various genomic technologies, empowered by next-generation DNA sequencing. My strengths as a scientist lie in my enthusiasm and ability to develop innovative approaches that couple computational and experimental methods. I am most excited about technologies that open novel research areas and opportunities by bringing distinct tools and areas together. My work encompasses research and technological development in: 1) next generation protein directed-evolution for high-resolution sequence-function mapping and protein optimization , 2) analysis of laboratory-evolved genomes, 3) nascent transcript capture and RNA-sequencing for genome-wide RNA polymerase activity tracking, and 4) transcriptional regulatory network analysis in metazoan development integrating >300 ChIP-sequencing experiments and cellular-resolution protein expression tracking in C. elegans.

Position - Company  
Jungla Jun 2011 - Present
Degree - University  
Ph.D., Genome Sciences - University of Washington 2004 - 2010
BS, Molecular Biology and Genetics - Washington State University

Summa cum Laude

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2001 - 2003
BS, Biotechnology - Washington State University

Summa cum Laude

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2001 - 2003
Publication Info
A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function. Araya CL, Fowler DM, Chen W, Muniez I, Kelly JW, Fields S Proc Natl Acad Sci U S A. 109(42):16858-63. doi: 10.1073/pnas.1209751109. October 16, 2012. View on PubMed.
Enrich: software for analysis of protein function by enrichment and depletion of variants. Fowler DM, Araya CL, Gerard W, Fields S Bioinformatics. 27(24):3430-1. doi: 10.1093/bioinformatics/btr577. December 15, 2011. View on PubMed.
Genome-Wide Analysis of Nascent Transcription in Saccharomyces cerevisiae. McKinlay A, Araya CL, Fields S G3 (Bethesda). 1(7):549-58. doi: 10.1534/g3.111.000810. December 2011. View on PubMed.
Deep mutational scanning: assessing protein function on a massive scale. Araya CL, Fowler DM Trends Biotechnol. 29(9):435-42. doi: 10.1016/j.tibtech.2011.04.003. May 10, 2011. View on PubMed.
High-resolution mapping of protein sequence-function relationships. Fowler DM, Araya CL, Fleishman SJ, Kellogg EH, Stephany JJ, Baker D, Fields S Nat Methods. 7(9):741-6. doi: 10.1038/nmeth.1492. August 15, 2010. View on PubMed.
Whole-genome sequencing of a laboratory-evolved yeast strain. Araya CL, Payen C, Dunham MJ, Fields S BMC Genomics. 11:88. doi: 10.1186/1471-2164-11-88. February 3, 2010. View on PubMed.
AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis. Boyle TJ, Bao Z, Murray JI, Araya CL, Waterston RH BMC Bioinformatics. 7:275. doi: 10.1186/1471-2105-7-275. June 1, 2006. View on PubMed.
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