email@example.com(408) xxx - xxxxhttp://sha.wncho.com
Bioinformatician, Web Developer, and Linux Hobbyist
Sept. 2014 — May 2016
La Jolla, CA
Sept. 2010 — June 2014
Apr. 2016 — Present
Mar. 2014 — Present
May 2014 — Aug. 2014
May 2012 — June 2013
Aug. 2013 — Aug. 2014
Oct. 2011 — May 2012
Kusenda, M., V. Vacic, D. Malhotra, L. Rodgers, K. Pavon, J. Meth, R. A. Kumar, S. L. Christian, H. Peeters, S. S. Cho, A. Addington, J. L. Rapoport, and J. Sebat. "The Influence of Microdeletions and Microduplications of 16p11.2 on Global Transcription Profiles." Journal of Child Neurology 30.14 (2015): 1947-953.
Copy number variants (CNVs) of a 600 kb region on 16p11.2 are associated with neurodevelopmental disorders and changes in brain volume. The authors hypothesize that abnormal brain development associated with this CNV can be attributed to changes in transcriptional regulation. The authors determined the effects of 16p11.2 dosage on gene expression by transcription profiling of lymphoblast cell lines derived from 6 microdeletion carriers, 15 microduplication carriers and 15 controls. Gene dosage had a significant influence on the transcript abundance of a majority (20/34) of genes within the CNV region. In addition, a limited number of genes were dysregulated in trans. Genes most strongly correlated with patient head circumference included SULT1A, KCTD13, and TMEM242. Given the modest effect of 16p11.2 copy number on global transcriptional regulation in lymphocytes, larger studies utilizing neuronal cell types may be needed in order to elucidate the signaling pathways that influence brain development in this genetic disorder.
Nominated to present at the 2013 UCSD Undergraduate Research Conference.
As geneticists, we are interested in understanding how genes influence complex traits. We have investigated the relationship of genes to neurodevelopment and behavioral phenotypes utilizing Machine Learning Algorithms (MLA) to best predict reciprocating genotypes. This study focuses particularly on the 16p11.2 Copy Number Variant (CNV) of the human genome, which is known to contain the gene Potassium Channel Tetramerization domain 13 (KCTD13) that confers risk to several distinguishing features on brain development and psychiatric features. Deletion is associated with larger head size and BMI, with an increased risk for Intellectual Disability and Autism, while duplication is associated with smaller head size and BMI, and a range of adult psychiatric disorders. We hypothesized that it would be possible to differentiate deletions from duplications at an 80% success rate using the MLA randomForests on phenotypical data.
Nominated to present at the 2012 UCSD Summer Undergraduate Research Conference.
Schizophrenia is a highly heritable neuropsychiatric disorder characterized by social withdrawal, delusions, and hallucinations. Our group has identified a genomic duplication of the neuropeptide receptor gene VIPR2 on chromosome 7 that confers significant risk for schizophrenia. As yet, little is known about the effect of this duplication on brain development and behavior. Here, we investigate this by using an animal model. We analyzed the behavior, and response to various tasks, of mice with none to four copies of the VIPR2 gene. Mice were observed for locomotor and stereotyped behaviors as well as pre-pulse inhibition (PPI), all of which are known to be altered when people start developing schizophrenia. Using this model, we will test the hypothesis that high copy numbers of the VIPR2 gene result in locomotor hyperactivity and a deficit in PPI - comparable behaviors found in people with schizophrenia.
Performed an RNASeq from RNA extraction to cDNA library construction and analyzing with bioinformatics tools.
The purpose of this lab was to use RNAseq and bioinformatics tools in order to find which gene was knocked out of a Saccharomyces cerevisiae yeast strain. Gene expression was quantified and compared to corresponding data of two wild type strains. After thorough pathway analysis using DAVID, Knockout strain #2 was found to be YHL009C, as a number of pathways were being down-regulated, including oxidative phosphorylation (Benjamini = 3.1E-07), intron homing (7.29E-10), and RNA processing (2.11E-02). No pathways were significant up-regulated.