Shawn Cho

Shawn Cho

Bioinformatician, Web Developer, and Linux Hobbyist

http://sha.wncho.com · La Jolla, CA · sh@wncho.com

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Education

Johns Hopkins University

Baltimore, MD

Bioinformatics MS, GPA: 3.967

Sept. 2014 — May 2016

Relevant Coursework

University of California, San Diego

La Jolla, CA

Bioengineering: Biotech BS, GPA: 3.588

Sept. 2010 — June 2014

Relevant Coursework

Experience

Informatics, Scientist I

Samumed

Samumed

Apr. 2016 — Present

  • Samumed is a leader in medical research and development for tissue-level regeneration. With our platform's origins in small molecule-based Wnt pathway modulation, we develop therapeutics to address a range of degenerative diseases, regenerative medicine and oncology.

Founder, Full-Stack Web Developer & Instructor

Snipcademy.com

Snipcademy

Mar. 2014 — Present

Bioinformatician

Sebat Lab

UCSD Dept. of Psychiatry and Cellular & Molecular Medicine

May 2014 — Aug. 2014

  • Analyzed facial features of 16p11.2 CNV duplication and deletion cohorts using 3dMD software tools.
  • Performed pairwise comparison statistical analysis correcting for false discovery rate in R.

May 2012 — June 2013

  • Utilized Random Forests R package and the "leave-one-out" method to identify 16p11.2 copy number variant genotypes in autistic adolescents using clinical variables.
  • Analyzed locomotor behavior, pre-pulse inhibition, and fear conditioning data using linear regression models on transgenic mice with various copies of theVIPR2 gene.
  • Developed scripts in R to select fixed nucleotide differences between human and chip genomes while masking SNPs, repeats, and DGVs for primer design.
  • Formulated algorithms to calculate silhouette scores for clustering quality control.

Java Application Developer

Bodmer Lab

Sanford-Burnham Medical Research Institute

Aug. 2013 — Aug. 2014

  • Integrated microscope, camera, and a stage controller to develop a Micro-Manager front-end plugin.
  • End product enabled users to easily detect and record 30-second output videos of theDrosophila Melanogaster's heart under hypoxia.
  • Used quantitative image analysis algorithm to elucidate cardiac parameters from output video.

Lab Research Assistant

Creel Lab

UCSD Dept. of Cognitive Science

Oct. 2011 — May 2012

  • Assisted in research consisting of processing complex acoustic information, especially in speech and language.
  • Developed stimuli for experiments involving language and speech recognition.
  • Administered psychological tests to evaluate audible perception capabilities.

Skillset Overview

  • Languages: Python3, Java, JavaScript (JQuery), SQL, HTML, CSS/SASS (Twitter Bootstrap, Bourbon), PHP (Laravel MVC), Bash (Awk/Sed), R.
  • Platforms: Linux (Ubuntu Desktop & Server), OS X, Windows.
  • Software: Git, Eclipse, Sublime, Vim, MySQLWorkBench, Adobe Photoshop, Indesign & Illustrator.
  • Bioinformatics Tools: Galaxy + Linux command line, SAMtools, BEDtools, Tuxedo Suite, IGV, UCSC Genome Browsers, biological databases: dbSNP, NCBI, Ensembl, OMIM.

Awards & Certs

  • Linux+ Certificate and Coursera Genome Data Science Specialization (5/7 courses completed).
  • Ranked in Top 100 worldwide (99.7%) on Rosalind, a site that offers challenging bioinformatics problems. Solved with Python 3.4.3, and placed second in Illumina's 2013 Bioinformatics Code Challenge.
  • Received the Amgen 2012 Scholar's award, a competitive and fully-funded program for undergraduates to conduct a summer's worth of research with a UCSD professor.
  • Nominated for MMW15's Writing Showcase Award in Spring of 2014. "The Human Genome Project - a Work of Collaboration or Competition?"

Publications

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.

Abstract

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.

Projects

Relating Behavioral Clinical Phenotypes to Genotype in Autism Spectrum Disorder

Nominated to present at the 2013 UCSD Undergraduate Research Conference.

Apr. 2013

Abstract

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.

The Mouse and the Viper: Implications of the VIPR2 gene on a mouse's phenotype.

Aug. 2013

Nominated to present at the 2012 UCSD Summer Undergraduate Research Conference.

Abstract

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.

RNASeq Analysis of a Yeast Knockout Strain

Performed an RNASeq from RNA extraction to cDNA library construction and analyzing with bioinformatics tools.

June 2013

Abstract

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.