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Projects
Functional Enrichment in Human, Mouse and Termite Gut microbiome: As part of coursework, I am leading a team of 6 on analysis of functional enrichment of protein coding genes in Gut samples from Human, Mouse and Termite to see if there are significant within and between differences. I am also working on phylogenetic analyses of the 16s / 23s rRNA sequences to infer speciation and evolutionary adaptations from its close relatives.
Genome Assembly and Finishing: As part of Lawrence Berkeley National labs’ Genomics division, I am working on assembly and finishing of microbial genomes at the Joint Genome Institute. My work involves assembly and finishing of whole genome shotgun reads and resolving assembly problems including repetitive sequences, gaps and assisting in development of in-house genome analysis software. This is more like a puzzle solving job where attention to details and investigative thinking is critical. I also volunteer in development of various in-house tools for Microbial finishing.
Assembler Comparison: This is one of the biggest projects that we (microbial genomics and informatics group), at JGI undertook to compare various Genome Assemblers' performance. We settled with about 10 parameters based on which we evaulated Arachne, PGA, Phrap, and Phrap4. I actively participated in this evaluation and wrote perl scripts for detecting misassemblies and gaps in assembler output. I also wrote couple of other scripts to calculate various metrices of assembly such as N50 contig length, mate-pair informations, etc. If you are interested in any of these metrics/tools, email me.
GOgroup: GOgroup is a java executable jar program (GOgroup.jar) to group Drosophila melanogaster genes based on GO ids. Given a list of GO ids and FBgn (Flybase) ids, the program will group the genes based on the GO ids. For each GO id, a file is created with a list of FBgns annotated to it or any of its children. If you are interested in this program, you can download it from http://www.oocities.org.vasanthsingan/GOgroup. A brief description is also avaiable from the same link.
Microarray Data Analysis: As part of my master’s thesis, I worked on improving Microarray Data Analysis for statistical significance by integration gene expression profiles with Gene Ontology. Developed algorithm for log-likelihood and rank based permutation test for evaluation of expression profile analysis. I am still extending this project and hoping to get a plublication soon.
MicrosatDesign: I developed a pipeline tool for integrating Phred/Phrap, GCG Findpatterns, EMBOSS etandem and primer3 to extract Microsatellites from DNA trace files and design primers for the amplicon sequences. This automation tool is currently being used by the Daphnia Genomics Consortium. You can download this tool here http://daphnia.cgb.indiana.edu/wfleabase/software/
wFleabase: As leading member of the wFleabase team, GMOD development group and Daphnia Genomics Consortium, currently working on the development of web service infrastructure to curate, archive and share genetic, molecular and functional genomics data and protocols of Daphnia. Worked with various modules including BLAST server setup, Lucegene query, retrieval and Batch downloads. http://wFleaBase.org
Evolution of sex-related genes in Daphnia: Worked with Dr. John Colbourne in understanding the evolution of sex-related genes in Daphnia. Various bioinformatics tools like Phred and BLAST are used for building contigs, identifying genes and studying evolution of these genes.
Unified Gene Page: Worked on the Unified Gene Page (GMOD) to generate Gene Reports for Model Organisms. XML gene reports are indexed and retrieved using Lucegene and stylesheets are developed for various displays. http://www.gmod.org/
Classification and Retrieval: Worked on the Ad-hoc retrieval and Categorization task for TREC (Text Retrieval Conference) Genomics 2004. Applied various Information Extraction and Retrieval techniques. Achieved the highest rank in classification task among 36 submissions from around the world. You can find the paper here, http://trec.nist.gov/pubs/trec13/papers/indianau-seki.geo.pdf
Compositional Spectra analysis:As part of coursework, worked in a team to develop a tool for characterizing genomic sequences. Work involved incorporation of suffix tree algorithm developed by Dan Gusfield for r-mismatch approximate pattern matching.
Enterprise Application Integration using Web Services: As part of my undergraduate project, developed and deployed a Web Services application that integrates two disparate applications at the interface level making them look like a seamless application.
Some of the work here was performed under the auspices of the US DOE of Science, Biological and Environmental Research Program, and by the University of California, LLNL under Contract No. W-7405-Eng-48, LBNL under Contract No. DE-AC02-05CH11231 and LANL under Contract No. W-7405-ENG-36.