Vasanth Singan
10 Woodbine Avenue, Blackrock, Co. Dublin, IRELAND
E-mail: Vasanth.Singan@ucdconnect.ie Cell: +353 (0) 86 2414410
OBJECTIVE
Postgraduate study towards PhD in Bioinformatics and Computational Biomedicine.
EDUCATION
Ph.D, (Bioinformatics and Computational Biomedicine) University College Dublin, Ireland (Oct 2012)
(Organelle footprinting through global analysis of Rab protein localization)
M.M.I.B., (International Business) Universitas 21 Global, Singapore (Jul 2009)
M.S., (Bioinformatics) Indiana University - Bloomington, IN, USA (CGPA 3.9 / 4.0) (May 2005)
(Gene Expression meets Gene Ontology: A novel statistical method for microarray analysis)
B.Engg., (Information Technology) Periyar University - Salem, India (top 5%) (May 2003)
(Enterprise Application Integration using Web Services)
Training in Molecular Technology BMERF, Salem, India (May 2003)
WORK EXPERIENCE
1. Rathi Silks / Silken Grace. Tamilnadu, India (Dec '06 `– Sep ‘08)
Managing Partner / Proprietor
Family-run business of women’s garment and traditional saree manufacture, wholesale and exports.
2. Joint Genome Institute, Walnut Creek, CA, USA (Jun '05 – Nov '06)
Research Associate (Microbial Genomics)
With Dr. Alla Lapidus on Assembly and Finishing of microbial genomes. http://www.jgi.doe.gov/
3. Genome Informatics Lab, Indiana University, Bloomington, IN, USA (Aug '03 – May '05)
Graduate Research Assistant
With Dr. Don Gilbert on GMOD (Generic Model Organism Database) www.gmod.org/ and wFleabase
(A genome database for the water-flea, Daphnia). http://wFleaBase.org
4. Center for Genomics and Bioinformatics, Bloomington, IN, USA (May '04 – Aug '04)
Summer Intern
With a team of Bioinformaticians and Programmers on installation, configuration and optimization
of ArrayExpress, MIAMExpress and MAGE-ML Validator for Microarray data. Work involved setting up
Apache and Tomcat servers, Integrating Oracle for database services.
5. The GeneTech, Salem, India (Sep '02 - Jul '03)
Research Assistant
With Dr. R Saravanan at BioMedical Engineering Research Foundation on 'Gene transfer
from hydrocarbon degrading Pseudomonas sp. to E.coli through CSH 57 plasmid Vector'.
PROJECTS
Genome Assembly and Finishing: As part of Lawrence Berkeley National labs’ Genomics division,
worked on assembly and finishing of microbial genomes at the Joint Genome Institute.
Work involved 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. Developed software and scripts for assembler evaluation.
Assembler Complementation Tool: Developed a visualization tool for analyzing genome structures,
rearrangements, comparing related assemblers, identifying gaps, and misassemblies in
computational genome assemblies.
Microarray Data Analysis: As part of my master’s thesis, 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.
MicrosatDesign: 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. http://daphnia.cgb.indiana.edu/wfleabase/software/
wFleabase: As leading member of the wFleabase team, GMOD development group and Daphnia Genomics
Consortium, worked 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
GOgroup: Developed a java executable jar program (GOgroup.jar) to cluster and group Drosophila
melanogaster genes based on Gene Ontology (GO) ids. Given a list of GO ids and FBgn (Flybase) ids,
the program will group the genes based on the GO ids. http://www.geocities.com.vasanthsingan/GOgroup.
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.
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.
TECHNICAL SKILLS
Computer Skills
Bioinformatics: HMMER, ClustalW, GCG, EMBOSS, BLAST servers, phred/phrap/consed, primer3
Languages: C, C++, Java, PHP, Perl, Python, Shell scripting, SQL, HTML, XML
Statistical and Visualization Tools: R, Pajek, SPSS, UCINET
Database: Oracle, PostgreSQL
Web Server: Apache, Tomcat
Operating Systems: Solaris 9 SPARC, Linux, Windows (98, 2000, XP), MS-DOS
Cell and Molecular Biology (Wet Lab) skills
Genomic Technology: Chromosomal/Plasmid DNA isolation, Restriction Fragment length polymorphism (RFLP),
Ligation, Transformation, Conjugation, Transduction
Electrophoresis: SDS-PAGE, Agarose Gel Electrophoresis
Immunotechnology: Propagation of Animal viruses, anti sera production, protein antigen analysis
Kit Standardization: ELISA, Dip-stick dot ELISA (for Leptospirosis)
PUBLICATIONS / POSTERS
1. Udwary, D.W., V.R.Singan, et. al. (2007) Genome Sequencing reveals complex secondary metabolome
in the marine actinomycete Salinospora tropica, Proceedings of the National Academy of
Science of the United States of America (PNAS) 2007, doi:10.1073/pnas.0700962104
2. Chen, F., V.R.Singan, et. al. (2006) 454 Sequencing Is an Effective Method for Gap Closure
in Microbial Whole Genome Shotgun Sequencing, Genomes, Medicine and the Environment Hilton
Head Island, Poster -Hilton Head Island, SC.
3. Singan, V.R., Trong, S. et al. Assembler Complementation Tool. First Annual Finishing
in the Future meeting, Poster- Santa Fe, NM.
4. Goltsman, E., V.R.Singan, et. al. (2006) Statistical Methods for Troubleshooting of
Genomic Shotgun Data, First Annual Finishing in the Future - Santa Fe, Poster - Santa Fe, NM
5. Trong, S., V.R. Singan, et. al. Comparison of Whole Genome Shotgun Assemblers.
CAR Showcase, Lawrence Livermore National Laboratory, Poster-Livermore.
6. Chen, F., V.R.Singan, et. al. Comparison of 454 Sequencing Platform with Traditional Sanger
Sequencing: a Case Study with de novo Sequencing of Prochlorococcus marinus NATL2A Genome.
Plant and Animal Genome (PAG) Conference – 2006.
7. Gilbert, D., V.R. Singan and J.K. Colbourne. wFleaBase: the Daphnia genomics information system.
Available online via: http://wFleaBase.org:7182/, BMC Bioinformatics 2005, 6:45 doi: 10.1186/1471-2105/6/45.
8. Singan, V.R., and J.K. Colbourne (2005). MicrosatDesign: a pipeline tool for transforming sequencer
trace files into DNA markers, CGB Technical Report 2005-01.
9. Seki, K., J. Costello, V.R. Singan, J. Mostafa (2004). TREC 2004 Genomics track experiments
at IUB. In the proceedings of the thirteenth Text REtrieval Conference (TREC 2004).
10. Gilbert, D., V.R. Singan, et. al., Argos, a replicable genome information system for Flybase,
euGenes and other databases. in preparation.
11. Singan, V.R., H.A. Sheth, et. al., (2004) Literature Based Gene Disease Relationship Discovery
Tool, First Annual Indiana Bioinformaticians Conference, Poster-Indianapolis
12. Gilbert, D., Singan, V.R., et. al., (2004) ARGOS: A Replicable Genome infOrmation System
for Flybase and wFleaBase, First Annual Indiana Bioinformaticians Conference, Poster-Indianapolis.
AWARDS/HONORS
2008-2012 - Irish Research Council for Science, Engineering and Technology (IRCSET) GREP grant – PhD.
2007-2009 - Universitas 21 Global student study grant US$2000.
2005-2006 - SPOT recognition award by Ernest Orlando Lawrence Berkeley National Laboratory.
2004-2005 - Graduate Research Assistantship, Indiana University, Bloomington. (US$ 21,500+ fee waiver)
2003-2004 - Graduate Research Assistantship, Indiana University, Bloomington. (US$ 21,500+ fee waiver)
2002-2003 - Academic Year's Best Project Award for “EAI using Web Services” at Cyberminds 2003.
2001-2002 - Academic Excellence award by Sona College of Technology.
2001-2002 - Award of Merit for securing 2nd Rank in University Exam.
2001 - First Prize in SoftGlow Software contest conducted by Sona College of Technology, Salem.
REFERENCES
1. Prof. Jeremy Charles Simpson
Professor of Cell Biology
School of Biology and Environmental Science
University College Dublin
Dublin 4
IRELAND
Email: Jeremy.Simpson@ucd.ie
Ph: +353 (0)1 716 2345
2. Dr. Kathleen Curran
Biological Imaging Group
School of Medicine and Medical Science
University College Dublin (UCD)
Dublin 4
IRELAND
Email: Kathleen.Curran@ucd.ie
Ph: +353 (0)1 716 6541
3. Dr. Alla Lapidus
Group Leader – Microbial Genomics
DOE - Joint Genome Institute
2800 Mitchell Dr
Walnut Creek, CA – 94598
USA
Email: ALapidus@lbl.gov
Ph: +1 (925) 296-5778