- Senior Software Engineer at Ambry Genetics
- Bioinformatic Engineer at Memorial Sloan Kettering Cancer Center
University of the Sciences in Philadelphia, MS, Bioinformatics
January 2019 – Present(9 months)San Juan Capistrano, California
– Head developer for API serving bioinformatics results to multiple webapps – Utilize publicly available datasets to generate alteration profiles – Created and Automated testing suite for API endpoints – Developed automated deployment scripts to help increase seamless updates – Maintain and improve data integrity in conjunction with Bioinformatics Department
May 2014 – August 2017(3 years 3 months)Greater New York City Area
– Develop, test, update NGS pipelines with new internal/external software. – Run Whole Exome, RNASeq, Targeted sequencing pipelines – Aid researchers with bioinformatics questions at a weekly clinic – Create, maintain web apps to help non-programmers interact with data and initiate pipeline run – Develop and update validation tools to help automate analysis workflow – Run jobs on LFS (as well as SGE) high performance cluster – Use a variety of version control tools – Write, test, update scripts to pull data from various different resources
August 2010 – May 2014(3 years 9 months)Greater Philadelphia Area
– Analyze next generation sequencing data using bioinformatic programs and web tools – Align RNA-Sequencing data, perform differential expression, alternative splicing, RNA-editing analyses – Compare to previously published data – Validate results in the lab using molecular biology techniques.
Meta-analysis of genome-wide association studies in five cohorts reveals common variants in RBFOX1, a regulator of tissue-specific splicing, associated with refractive error
Human Molecular Genetics
Visual refractive errors (REs) are complex genetic traits with a largely unknown etiology. To date, genome-wide association studies (GWASs) of moderate size have identified several novel risk markers for RE, measured here as mean spherical equivalent (MSE). We performed a GWAS using a total of 7280 samples from five cohorts: the Age-Related Eye Disease Study (AREDS); the KORA study (‘Cooperative Health Research in the Region of Augsburg’); the Framingham Eye Study (FES); the Ogliastra Genetic Park-Talana (OGP-Talana) Study and the Multiethnic Study of Atherosclerosis (MESA). Genotyping was performed on Illumina and Affymetrix platforms with additional markers imputed to the HapMap II reference panel. We identified a new genome-wide significant locus on chromosome 16 (rs10500355, P = 3.9 × 10(-9)) in a combined discovery and replication set (26 953 samples). This single nucleotide polymorphism (SNP) is located within the RBFOX1 gene which is a neuron-specific splicing factor regulating a wide range of alternative splicing events implicated in neuronal development and maturation, including transcription factors, other splicing factors and synaptic proteins.
Comprehensive analysis of gene expression in human retina and supporting tissues
Human Molecular Genetics
Understanding the influence of gene expression on the molecular mechanisms underpinning human phenotypic diversity is fundamental to being able to predict health outcomes and treat disease. We have carried out whole transcriptome expression analysis on a series of eight normal human postmortem eyes by RNA sequencing. Here we present data showing that ∼80% of the transcriptome is expressed in the posterior layers of the eye and that there is significant differential expression not only between the layers of the posterior part of the eye but also between locations of a tissue layer. These differences in expression also extend to alternative splicing and splicing factors. Differentially expressed genes are enriched for genes associated with psychiatric, immune and cardiovascular disorders. Enrichment categories for gene ontology included ion transport, synaptic transmission and visual and sensory perception. Lastly, allele-specific expression was found to be significant for CFH, C3 and CFB, which are known risk genes for age-related macular degeneration. These expression differences should be useful in determining the underlying biology of associations with common diseases of the human retina, retinal pigment epithelium and choroid and in guiding the analysis of the genomic regions involved in the control of normal gene expression.
Skills & Expertise
- RNA-Seq Analysis
- Functional Annotation
- Sequence Alignment
- Data Analysis
- Perl Script
- DNA Sequencing
- Gene Expression
- Molecular Biology
- Shell Scripting
American Society for Microbiology
2008 – 2014
2007 – 2011
Joined club as soon as it started, and was Public Relations officer for 2 years.