Kasey Hutt
3822 Sioux Avenue
San Diego, CA 92117
(505)301-0655
USA
krhutt@gmail.com
PERSONAL
I am currently in my second year as a postdoctoral researcher at the University of
California at San Diego. My personal goal is to publish a second first author paper
following the function of TDP-43 as it relates to protein neuropathies, such as FTLD
and ALS.
EDUCATION
2001-2009
1997-2001
1993-1997
Received Ph.D in Bioinformatics in Winter 2009, University of California at San Diego
Received BS in Biochemistry in Spring 2001, University of New Mexico
High School Diploma, Manzano High School
EMPLOYMENT
2010-present
Postdoctoral Research, University of California at San Diego, Yeo Lab
Extended previous sequencing analysis to include CLIP-seq and RNA-seq methods.
Applications to numerous RNA-binding proteins, including numerous hnRNPs and
TDP-43 and TLS. (858)534-9321
2009-2010
Postdoctoral Research, University of California at San Diego, Rosenfeld Lab
Working towards publishing methods for analyzing high-throughput sequencing data.
2003-2009
Thesis Research, University of California at San Diego, Rosenfeld Lab
Investigating microRNA involvement in gene regulation by computational dissection
and prediction of regulatory elements (boundary elements, locus control regions,
insulator elements) of the genome based on evolutionary conservation analysis. Also
involved in statistical analysis of ChIP-DSL microarray data and design of DSL
probes for genome tiling arrays. Responsible for establishing hardware and software
infrastructure for producing and analyzing high-throughput sequencing data
generated by the Illumina Genome Analyzer. (858)534-5858
2001-2003
Graduate Research, University of California at San Diego
Completed three laboratory rotations during graduate career. Worked on highthroughput image analysis of Drosophila heart rate with Dr. Andrew McCulloch. Built
partial metabolic computer model of the organism Mycobacterium Tuberculosis with
Dr. Bernhard Palsson. Learned current, basic wet lab techniques with Dr. Huilin
Zhou.
2000-2001
Undergraduate Research, University of New Mexico Chemistry Department
Worked under Professor Deborah Evans and graduate student Govind Mallick. Used
molecular visualization program, Cerius, to assist in generating viable computer
models of a kerogen molecule.
phone: (505)277-0570
1996-2000
Student Intern, Sandia National Laboratories
Worked under Dr. Brian Stallard. Assisted in numerous presentations and projects by
creating PowerPoint slides and computer programs in IDL and C++. Also learned
how to upgrade computer hardware and software.
phone: (505)844-2631
Basic Techniques
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Proficient in using standard Bioinformatic software and databases, including
NCBI tools, BLAST, Transfac, SMART, Gene Ontology, Vista, UCSC genome
tools and Ensembl, as well as many specific programs for analyzing DNA and
protein motifs, designing primers/oligos for various PCR and FISH techniques,
and clustering microarray results. Also skilled at organizing and analyzing highthroughput sequencing data, from running standard analysis pipeline to
downstream data-mining, including peak-finding and association analysis. Have
analyzed multiple sequencing datasets, including ChIPseq, RNAseq, small
RNAseq, GROseq, CLIPseq, and RIPseq.
Areas of Expertise
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Perl, C++, IDL
Languages
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English, some Spanish
Publications
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Polymenidou M., C. Lagier-Tourenne, K.R. Hutt, S.C. Huelga, J. Moran, T.Y.
Liang, S.C. Ling, E. Sun, E. Wancewicz, C. Mazur, H. Kordasiewicz, Y.
Sedaghat, J.P. Donohue, L. Shiue, C.F. Bennett, G.W. Yeo, D.W. Cleveland,
Long pre-mRNA depletion and RNA missplicing contribute to neuronal
vulnerability from loss of TDP-43. Nat Neurosci, 2011 Apr. 14(4): p. 459-68.
Zisoulis D.G., M.T. Lovci, M.L. Wilbert, K.R. Hutt, Y.L. Liang, A.E. Pasquinelli,
G.W. Yeo, Comprehensive discovery of endogenous Argonaute binding sites in
Caenorhabditis elegans. Nat Struct Mol Biol, 2010. 17(2): p. 173-9.
Hu, Q., Y.S. Kwon, E. Nunez, M.D. Cardamone, K.R. Hutt, K.A. Ohgi, I. GarciaBassets, D.W. Rose, C.K. Glass, M.G. Rosenfeld, and X.D. Fu, Enhancing
nuclear receptor-induced transcription requires nuclear motor and LSD1dependent gene networking in interchromatin granules. Proc Natl Acad Sci U S
A, 2008. 105(49): p. 19199-204.
Lunyak, V.V., G.G. Prefontaine, E. Nunez, T. Cramer, B.G. Ju, K.A. Ohgi, K.
Hutt, R. Roy, A. Garcia-Diaz, X. Zhu, Y. Yung, L. Montoliu, C.K. Glass, and M.G.
Rosenfeld, Developmentally regulated activation of a SINE B2 repeat as a
domain boundary in organogenesis. Science, 2007. 317(5835): p. 248-51.
Garcia-Bassets, I., Y.S. Kwon, F. Telese, G.G. Prefontaine, K.R. Hutt, C.S.
Cheng, B.G. Ju, K.A. Ohgi, J. Wang, L. Escoubet-Lozach, D.W. Rose, C.K.
Glass, X.D. Fu, and M.G. Rosenfeld, Histone methylation-dependent
mechanisms impose ligand dependency for gene activation by nuclear receptors.
Cell, 2007. 128(3): p. 505-18.
Kwon, Y.S., I. Garcia-Bassets, K.R. Hutt, C.S. Cheng, M. Jin, D. Liu, C. Benner,
D. Wang, Z. Ye, M. Bibikova, J.B. Fan, L. Duan, C.K. Glass, M.G. Rosenfeld, and
X.D. Fu, Sensitive ChIP-DSL technology reveals an extensive estrogen receptor
alpha-binding program on human gene promoters. Proc Natl Acad Sci U S A,
2007. 104(12): p. 4852-7