Data Clinical Research

Mukta Joshi

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WORK EXPERIENCE:

Beth Israel Deaconess Medical Center - Boston MA Sept 2015 - Present Research Assistant I

The key responsibilities involve analyzing NGS and microarray data.

Write data analysis and pipeline automation using Python and data visualization using R.

RNAseq library preparation, setting up the sequencing run followed by QC and analysis of the data.

Using GATK pipeline for variant calling on whole genome/exome sequencing.

Using tophat-htseq for gene expression analysis from RNAseq data.

Predictor development using algorithms like Randomforest. Georgetown University Medical Centre - Washington D.C Feb 2015 - Sept 2015 Research Intern

The project involved Phylogenomic analysis of GEO expression data to identify dysregulated genes and pathway in Pancreatic cancer and pancreatitis compared to normal pancreases.

Feeding and Handling the Zebra fishes that are used as model organism.

The aim of the job was to maintain and feed these fishes which are used for cancer research. Vlife sciences Technologies Pvt. Ltd - Pune, India May 2012 - June 2012 Intern

This internship was a part of Master of Science in Biotechnology program

The main aim of the project was to find anti-malarial peptides using peptide docking tools like autodock.

Various approaches including molecular modelling and molecular docking were involved.

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ACADEMICS & TRAINING:

Georgetown University – Washington DC Sept 2014 – Sept 2015 Master of Science in Bioinformatics

Symbiosis International University – Pune, India Aug 2011 – May 2013 Master of Science in Biotechnology

University of Mumbai – Mumbai, India Jun 2008 – May 2011 Bachelor of Science in Biotechnology

Haffkine Institute of Training, Research and Testing - Mumbai, India May 2010

This program involved lectures on various topics like Biosafety, a visit to animal house and demonstration of drug dosing and mouse handling techniques. Clinical Research and Management, Mumbai, India Apr 2009 - May 2009

● This course involved learning different phases of clinical trial, understanding and planning each phase. PUBLICATIONS AND BOOK CHAPTER:

Mukta Joshi, Shankar V Kundapura, Thirtha Poovaiah, Kundan Ingle and Pawan K Dhar (2013),

“Discovering Novel Anti-Malarial Peptides from the Not-coding Genome - A Working Hypothesis”, Current Synthetic Systems Biology, 1:1.

Lead author of a chapter “DNA origami: What, How and Where” in the Systems and Synthetic Biology book published by Springer (ISBN 978-94-017-9514-2).

Zeus Antonello, Nancy Hsu, Manoj Bhasin, Giovanni Roti, Mukta Joshi, Paul Van Hummelen, Emily Ye, Agnes Lo, S. Ananth Karumanchi, Christine Bryke, “Vemurafenib-resistance via de novo RBM genes mutations and chromosome 5 aberrations is overcome by combined therapy with palbociclib in thyroid carcinoma with BRAFV600E”, Oncotarget. 2017; 8:847**-*****. SKILLS:

Computational: R, Python, NGS data analysis, GATK, Picard tools, Cytoscape, IPA, BWA, EdgeR, GSEA, LIMMA, TopHat, HTSeq, WGCNA.

Wet lab: RT-PCR, RNAseq prep, NextSeq, ddSeq, molecular biology techniques.

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