Assistant Development

HRISHIKESH LOKHANDE

****, **** ******, ***-*, Los Alamos, New Mexico Ph-219-***-**** ******@****.***

CAREER OBJECTIVE

Seeking a bioinformatics position where I get an opportunity to utilize my technical expertise and

bioinformatics skills for developing new tools and for performing effective data research.

EDUCATION

Master of Science in Bioinformatics May 2013

Indiana University, School of Informatics, Indianapolis, IN GPA-3.3/4.0

Advanced Diploma in Bioinformatics May 2010

Bharti Vidyapeeth University, India GPA-3.5/4.0

Bachelors of Biotechnology M ay 2009

Pune University, India GPA-3.2/4.0

COMPUTATIONAL PROFICIENCY

Languages & Scripts: R, PERL, PHP, Python, XML, SAS.

Platforms: UNIX, Windows, Linux, Centos, Mac OS X.

Databases: MySQL, MySQL workbench, SQL Server, PostgreSQL.

Web Development: HTML, CSS, Drupal, Mason, Mod_perl.

Other Tools: Git, Aqua Data Studio, Toad (MySQL).

BIOINFORMATICS PROFICIENCY

Database search: Influenza Sequence Database, GEO, Drugbank, Entrez, BLAST, GenBank.

Visualization tools: Cytoscape, Metacore, GeneGo, Pathway studio,i-GSEA, Archaeopteryx.

Ontologies: Disease ontology, Gene ontology, Cell ontology, Cell line ontology.

Enrichment tools: DAVID, GeneMAPP, Gene Ontology tools like Protégé and OBO-EDIT2.

Sequence Analysis: BLAST, BLAST+, CLUSTAL W.

Phylogenetic Analysis: PhyML, RAxML, FastTree, Taxit, Pplacer, Guppy.

Next generation seq: SAMtools, BWA, Bowtie, IGV.

EXPERIENCE

Software developer Feb 2013- Present

Los Alamos National Laboratory, Los Alamos, New Mexico

Responsibilities:

Administration, maintenance, management and timely upgrade of the Influenza Sequence Database (ISD).

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Migrating the ISD from FreeBSD operation system to UNIX based Centos 6.

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Creating Object Oriented Perl scripts for database communication and other analysis.

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Developing Perl based command line tools using core modules like Getopt::Long and Getopt::Std.

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Developing custom Perl scripts that incorporate public tools like BLAST, FastTree,PhyML, RAxML etc.

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Developing a common Perl tool for classification of virus segment like H1N1, H5N1 etc.

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Utilize the R ‘Ape’ package to perform phylogenetic and evolutionary analysis of the Influenza viruses.

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Utilize R to perform basic statistical analysis and plotting.

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Setting cron jobs for automated upload, curation and classification of FLU data into ISD.

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Improving existing upload and curation Perl scripts by upgrading to newest available modules.

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Adding new functionalities to Mason and mod_perl2 based ISD website.

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Writing documentations providing usage information of various scripts.

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Graduate research assistant Sept 2011-Jan 2013

Center for Computational Biology and Bioinformatics (CCBB), Indianapolis, IN

Thesis- “Development of an ontology based information retrieval system, semantic corpus and tagger for

Pharmacodynamics literature.”

Responsibilities:

Develop pharmacodynamics ontology, classifying drug interaction into synergistic, additive and

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antagonistic categories.

Mine literature using Perl scripts to find drug interaction following pharmacodynamics ontology.

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Determine cell based phenotypes involved in in-vitro pharmacodynamics experiments,

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Develop a semantic corpus and a keyword based information retrieval system with high precision and recall

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using a python scripts.

Develop drug dictionary and organ specific cell line ontology to enhance and improve keyword and

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category based searches (combination of Python and Perl).

Develop a web tool to provide access to the Ontology, keyword search, corpus etc.

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Graduate research assistant Jan 2011- May 2011

Indiana center for Systems Biology and Personalized medicine, Indianapolis, IN

Performed database development, web development and data analysis for “HOMER: a human organ-

specific molecular electronic repository” BMC bioinformatics 2011.

CLASS PROJECTS

SNP Based pathway analysis of Alzheimer’s genome-wide association study.

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Hierarchical access control system for patient privacy in a social health network.

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Development of leukemia database using Drupal.

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