Data Assistant

EDUCATIONAL QUALIFICATIONS:

Master of Science, Bioinformatics December 2014

Indiana University, Indianapolis, IN (IUPUI)

Master of Science, Biotechnology May 2009

G.N Khalsa College, University of Mumbai, India

Bachelor of Science, Biotechnology August 2007

Bhavan’s College, University of Mumbai, India

SKILLS:

BIOINFORMATICS SKILLS

NGS Analysis: SAMTools, Novoalign, VCFtools, Bedtools BWA, GATK, Bowtie & MACS, Pindel, Galaxy, Cufflinks, Edge-R, UCSC genome browser & IGV

Database search: TCGA, RefSeq, GEO, dbSNP, UniProt, Entrez, ENSEMBL, BLAST, BLAT & BFAST

Genome Assemblers: SOAPdenovo, ABySS & Velvet

COMPUTATIONAL SKILLS

Database Applications: MySQL, PostgreSQL

Programming Languages: Perl, Python, Bash scripting i.e UNIX & R programming

WORK & RESEARCH EXPERIENCE:

Bioinformatics Programmer – I, Ambry Genetics, Aliso Viejo – CA Jan 2016 – July 2017

Analyzing NGS data, maintaining the pipeline and validation, supporting the R&D team

Functional testing of the existing pipeline and supporting the pipeline development team

Tested the internal quality control of pipeline while maintaining the data structure of the framework

Participated in 24X7 bioinformatics support to other teams in the company

Bioinformatician, PierianDx, St Louis – MO Mar 2015 – Dec 2015

Supported pipeline operations for analysis of clinical NGS data from sequence alignment to variant calling using data from Illumina (HiSeq, Miseq and Amplicon technology) and Ion Torrent platforms

Analyzed Clinical NGS data, methods and gained exposure with data management in CAP-CLIA environment

Worked on high performance computer clusters like AWS and organized tasks using the Atlassian tool JIRA

Documented pipeline processes and troubleshooting techniques in Confluence

Tested UI design to identify bugs and blockers with the product design and functionalities

Graduate Research Assistant, Indiana University, IN- Supervised Dr. Milan Radovich May 2013 – Dec 2014

Thesis: Detection of Somatic Mutations in Triple Negative Breast Cancer datasets

Developed a Pipeline to detect somatic mutations in TNBC datasets using tumor-normal pairs

Developed a Pipeline to use tools like BLAT/BLAST/LASTZ for alignment, Galaxy, PERL and python scripts for downstream processing.

Validated results using experimental methods like PCR and Sanger sequencing

Handled exome sequencing data from Ion Torrent and Illumina platform. Validated the genes from Cenk’s pipelines using PCR & Sanger sequencing

Graduate Research Assistant, Indiana University, IN – Supervised by Dr. Lang Li Jan 2012 – May 2013 Project Title: Triple negative Breast cancer - INSIGHT project in collaboration with School of Medicine:

Statistically analyzed 222 patient samples that were built on a Mapping algorithm.

Compared eight genotyping methods and ranked the drug to pick the best biomarker for TNBC data.

Independent Study Project, Indiana University, IN – Supervised by Dr. Yunlong Liu May 2012 –Jan 2013

Evaluated transcription factor binding site by ChIP seq analysis.

Analyzed 40+ ChIP seq datasets and compared them to the background model

Graduate Assistantship, Indiana University, IN – Supervised by Dr. Matthew Palakal Jan 2012 – May 2012

Studied Protein-Protein interaction datasets and networks in colo-rectal cancer to test a PPI algorithm

Validated BioMap results by literature mining and cross validating it with UniProt

ACHIEVEMENTS:

Ambry Genetics:

Automated the performance statistics of the pipeline to maintaining its highest efficiency in terms of quality, operation time and utilization of resources.

To minimize delays in processing samples due to errors in the pipeline, part of the team that has automated the troubleshooting process. This has greatly helped the clinical reporting team in preparing correct reports in a timely manner. Part of this tool development and testing process

Developed the novel Alu insertion pipeline to detect Alu insertions in the pipeline

Automated and developed the quality metrics statistics report /process monthly to be send out to every team in the company

Helped R&D team in designing for new assays for carrier screening and long range PCR

Validated new assays and helped clinical team troubleshoot

PierianDx:

Helped in setting up the pipeline and web interface for the new clients required for the demo

Part of the platform development that went through two cycles of development that had WGS data, EXOME data and SNOMED Clinical terms integration along with variant classification improvement

Helped in functional testing of the tool in every release and bug fixing

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