Research Assistant
- Assembled De Novo 454 Transcriptome using Newbler 2.5 (Roche GSassembler)o Extracting sequence and quality data from raw 454 SFF imageo Perform quality, and adaptor/vector trimming- Assembled De Novo Illumina Transcriptome using Velvet and Oasis wrapper on the Harvard Odyssey computing clustero Utilizing high memory nodes (128gb) for tour bus assemblyo 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.eduo 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 pubmedo Developed graphical data display using html5 canvas for transcriptomic fragmentationo Designed the centos VM disk image to host the website using Apache, and support a list of important module/librarieso 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 bowtieo Perform normalization using RPKM and edgeR packageo Determine candidate genes base on differential expression, molecular function annotation, and gene ontology prediction.