- Senior Software Engineer at OneVigor
- San Diego, California, United States
- Marketing and Advertising
- Architectural Lead at Promoboxx
- Software Consultant at Stylux Incorporated
Worcester Polytechnic Institute, BS, Biology
Senior Software Engineer
April 2018 – Present(1 year 6 months)Greater San Diego Area
Worked on node mongoose express stack for the management of media delivery for large broadcasting companies such as PBS. Utilized AWS for Infrastructure as business. Lead development of V2 API.
January 2017 – April 2018(1 year 3 months)Greater Boston Area
Managed dev ops using rightscale, while upgrading to automated CHEF. Built servers for CI with selenium testing. Upgraded front-end infrastructure to componentized VUE 2.X from Angular 1.4. Upgraded serialization middleware to handle complex nested relationships. Improved multi-dimensional search via denormalization. Setup Analytics warehousing ETL pipelines.
June 2012 – November 2017(5 years 5 months)25 Stickney Rd, Atkinson, NH, 03811
Architected multiple SAAS products such as Relaythat.com, Bigwordclub.com, etc.
December 2012 – October 2014(1 year 10 months)Greater Boston Area
Front End Development, Game Design, Market Analysis
Marine Biological Laboratory
2012 – 2013Woods Hole, Massachusetts
September 2010 – June 2012(1 year 9 months)
– Assembled De Novo 454 Transcriptome using Newbler 2.5 (Roche GSassembler) o Extracting sequence and quality data from raw 454 SFF image o Perform quality, and adaptor/vector trimming – Assembled De Novo Illumina Transcriptome using Velvet and Oasis wrapper on the Harvard Odyssey computing cluster o Utilizing high memory nodes (128gb) for tour bus assembly o Utilizing long 454 assembly contigs for rock band algorithm – Design a pipeline to annotate fragmented Transcriptome data using Drosophila melanogaster proteome with Reciprocal BLAST algorithm. – Solely Developed the transcriptome data mining website http://asgard.rc.fas.harvard.edu o Designed the MySQL database schema for asgard backend. This database provides effective queries and storage of De Novo assembly annotation (ORF prediction, Motif prediction, Blast2GO, Ortholog prediction). o Created asgard front end using html5/css3, using jquery to improve the user experience with collapsible items, and auto completion. o Created an xml/rss parser to display most recent related publish articles gathered from pubmed o Developed graphical data display using html5 canvas for transcriptomic fragmentation o Designed the centos VM disk image to host the website using Apache, and support a list of important module/libraries o Created perl scripts for database handling that can be controlled by html form input using AJAX – Compared tissue specific RNA-Seq data by mapping of assembled Transcriptome using bowtie o Perform normalization using RPKM and edgeR package o Determine candidate genes base on differential expression, molecular function annotation, and gene ontology prediction.
May 2010 – September 2010(4 months)
– Managed laboratory Amazon Simple Storage Service (S3) servers – Created Amazon Elastic Computing Cloud (E2) instance for mapping of sequencing data generated by Helicos and Illumina sequencing platform to H. sapiens reference genome – Performed patch assays for genes that have multi genomic variants – Performed sanger sequencing via ABI 3730, including PCR of target gene locus – Operated protedyne 96 well robotic platform
UMass Medical School
May 2009 – May 2010(1 year)
A Bioinfomatics Project focus on discovering novel transcription cofactor genes in C. elegans. This Project’s goal is to create interaction partner for predicted transcription factor in a high throughput yeast two hybrid assay.
National Transportation Safety Board
October 2009 – December 2009(2 months)
Conducting a project that identify and examine marine accident investigation analysis tools used by the NTSB, USCG, and other international marine investigation agencies. The result will be used as a recommendation to improve the investigation effiency of the NTSB’s marine division.
Worcester Polytechnic Institute
2006 – 2010
Activities and Societies
Tau Kappa Epsilon
ASGARD: an open-access database of annotated transcriptomes for emerging model arthropod species.
Web Development/ Bioinformatic Analysis
De novo assembly and characterization of a maternal and developmental transcriptome for the emerging model crustacean Parhyale hawaiensis.
Bioinformatics Analysis on Parhyale hawaiensis
Developmental Gene Discovery in a Hemimetabolous Insect: De Novo Assembly and Annotation of a Transcriptome for the Cricket Gryllus bimaculatus.
Most genomic resources available for insects represent the Holometabola, which are insects that undergo complete metamorphosis like beetles and flies. In contrast, the Hemimetabola (direct developing insects), representing the basal branches of the insect tree, have very few genomic resources. We have therefore created a large and publicly available transcriptome for the hemimetabolous insect Gryllus bimaculatus (cricket), a well-developed laboratory model organism whose potential for functional genetic experiments is currently limited by the absence of genomic resources. cDNA was prepared using mRNA obtained from adult ovaries containing all stages of oogenesis, and from embryo samples on each day of embryogenesis. Using 454 Titanium pyrosequencing, we sequenced over four million raw reads, and assembled them into 21,512 isotigs (predicted transcripts) and 120,805 singletons with an average coverage per base pair of 51.3. We annotated the transcriptome manually for over 400 conserved genes involved in embryonic patterning, gametogenesis, and signaling pathways. BLAST comparison of the transcriptome against the NCBI non-redundant protein database (nr) identified significant similarity to nr sequences for 55.5% of transcriptome sequences, and suggested that the transcriptome may contain 19,874 unique transcripts. For predicted transcripts without significant similarity to known sequences, we assessed their similarity to other orthopteran sequences, and determined that these transcripts contain recognizable protein domains, largely of unknown function. We created a searchable, web-based database to allow public access to all raw, assembled and annotated data. This database is to our knowledge the largest de novo assembled and annotated transcriptome resource available for any hemimetabolous insect. We therefore anticipate that these data will contribute significantly to more effective and higher-throughput deployment of molecular analysis tools in Gryllus.
A comprehensive reference transcriptome resource for the common house spider Parasteatoda tepidariorum
Parasteatoda tepidariorum is an increasingly popular model for the study of spider development and the evolution of development more broadly. However, fully understanding the regulation and evolution of P. tepidariorum development in comparison to other animals requires a genomic perspective. Although research on P. tepidariorum has provided major new insights, gene analysis to date has been limited to candidate gene approaches. Furthermore, the few available EST collections are based on embryonic transcripts, which have not been systematically annotated and are unlikely to contain transcripts specific to post-embryonic stages of development. We therefore generated cDNA from pooled embryos representing all described embryonic stages, as well as post-embryonic stages including nymphs, larvae and adults, and using Illumina HiSeq technology obtained a total of 625,076,514 100-bp paired end reads. We combined these data with 24,360 ESTs available in GenBank, and 1,040,006 reads newly generated from 454 pyrosequencing of a mixed-stage embryo cDNA library. The combined sequence data were assembled using a custom de novo assembly strategy designed to optimize assembly product length, number of predicted transcripts, and proportion of raw reads incorporated into the assembly. The de novo assembly generated 446,427 contigs with an N50 of 1,875 bp. These sequences obtained 62,799 unique BLAST hits against the NCBI non-redundant protein data base, including putative orthologs to 8,917 Drosophila melanogaster genes based on best reciprocal BLAST hit identity compared with the D. melanogaster proteome. Finally, we explored the utility of the transcriptome for RNA-Seq studies, and showed that this resource can be used as a mapping scaffold to detect differential gene expression in different cDNA libraries. This resource will therefore provide a platform for future genomic, gene expression and functional approaches using P. tepidariorum.
Front End Development, API Design
Team Members (1):
Web Development, front and back end
Team Members (1):
Skills & Expertise
- Advanced CSS
- Cascading Style Sheets (CSS)
- HTML 5
- Sequence Analysis
- High Throughput Screening
- Database Development
- Ruby on Rails
- Ontology Development
- Gene Expression Profiling
- User Interface Design
- User Experience
- Computational Biology
Honors & Awards
Biogen Idec Hackms
Biogen Idec + Health 2.0
Our second place $10,000 dollar price application helps MS patients to manage stress. The application provides stress management via meditation reminder, step/excise counter, and an algorithm that adjust the suggested excise/relaxation ratio by using local temperature reading for MS patients who has temperature sensitivity.
Volunteer Experience & Causes
September 2012 – April 2013(7 months)Children
Help low income first college bound student succeed in their education and their extracurricular career.
November 2014 – April 2018(3 years 5 months)Children
Working hard with my team Gaming Generation from the Jeremiah E. Burke high school on accomplishing their goal of developing their own business, and become profitable.