Data Scientist/ Analyst

PRIYA PRAKASH KULKARNI

Master of Technology (Bioinformatics) E-mail: *****.***********@*****.***

Data Science Certificate, UC Irvine Cell: +1-949-***-****

Bachelor of Pharmacy Lake Forest, CA

Post-Master’s Certificate in Sequence Analysis and Genomics (Johns Hopkins University)

(SUMMER 2022)

SUMMARY

Experienced Bioinformatics Professional skilled in Bioinformatics, Systems Biology, Biological network identification, Enrichment Analysis, Skin Systems Biology, Skin cell (Melanocyte, Keratinocyte, Fibroblast) signaling and pathways, Life Sciences, Genomics and NGS data analysis, Data Science, statistical analysis, Spotfire, Tableau, R, Python, Microsoft Excel, SQL, AWS(S3 structure). Proven ability to manage small teams and multiple projects while meeting challenging deadlines. Contributed to establish collaborations with the teams of national and international senior scientists.

WORK EXPERIENCE

Biomedical Data Curator May 2021 – Jan 2023

Genentech, Inc. (Contracting through Experis Manpower group)

●Working on Digital Pathology Project

●Extract, transform and load (ETL) pathological data from multiple sources to AWS (s3) buckets.

●Work closely with stakeholders to support research efforts by managing project data, curating and preparing data for analysis and coordinating data sharing with team members.

●Tools used for ETL process: Python, R, Rclone, AWS, Excel

●Use Jira for task tracking and project management.

Freelance Volunteer Bioinformatics Analyst Jan 2015 – April 2021

●Working with senior neuro-surgeon and scientist affiliated with Loma Linda University, CA

●Provide Support to analyze and find out the various patterns in proteomic/scientific Medulloblastoma Mass spectroscopy data.

●Data Analysis involves understanding the scientific and clinical data followed by data cleaning, preparation, analysis, visualization and interpretation. Used R language, Python and Microsoft Excel for data analysis.

●Perform Pathway enrichment analysis using tools like Reactome and IPA

●Data Visualization dashboards are generated by using Tibco Spotfire, Tableau and Microsoft Excel

●Performed bioinformatics analysis for the poster presentation on ‘Biomarkers for brain tumors: a feasibility study using Proteomic methodologies’.

Domain Lead / Subject Matter Expert (Systems Biology) Aug 2010 - Oct 2013

Persistent Systems Ltd., India

eSkIN

A computational platform that converts large scale high-throughput omics data into biomedical knowledge.

●Involved since the conceptualization of this product and worked on writing the project proposal.

●Worked as a liaison between senior scientists and software development team.

●Development of the Requirement documents and update it on regular basis.

●Data mining: Detail-oriented biological literature mining to find out skin specific genes/proteins. This resulted in identification of curated 2600+ skin specific genes.

●Pathways and processes database: Developed a database of static networks of skin specific 36 processes and pathways. MS SQL is used for database management.

●Data Analysis: Analyzed Proteomic data to find out various patterns in data and to identify biomarkers.

●Coordinated with software development team to provide various requirements, solve domain related queries and functional testing of the software.

Network Analysis of Yeast Stress Response project in collaboration with SBI, Japan

●Comprehensive network building of yeast stress signaling pathways in collaboration with Systems Biology Institute Japan which got published in Nature journal.

Collaborative work for the BM Systems, Paris

●Cytokine and chemokine response in Skin: Identification of pathways and integral mechanism of inflammation in skin cells.

Bio-modeling Scientist Jan 07 – Mar 2010

Cellworks Research India Limited, Bangalore

●As a Project lead conducted biology system integration, development of dynamic biological mathematical models (biological pathways) for various skin cells using biological simulators.

●Worked on Skin hyperpigmentation and Aging.

●Worked on biological pathway/network building to develop Virtual skin cell system and mechanism for UV induced skin tanning and aging of the skin. Virtual skin cell systems involved development dynamic models of Keratinocyte, Melanocyte and Fibroblast. It is developed by using biological simulators and includes the detailed study of inter and intra cell signaling and the cross talk between signaling. Simulation results are generated and validated against various experimental data. A set of the drugs have been tested on the validated systems and analyzed the results.

●Performed extensive study of melanin biosynthesis. Introduced the genetic variations of 6 different skin types (Skin type I, II, III, IV, V, VI) to virtual skin cell systems and analyzed their response to UV.

PUBLICATIONS

●Eiryo Kawakami1,6, Vivek K Singh2,6, Kazuko Matsubara3, Takashi Ishii1, Yukiko Matsuoka3, Takeshi Hase3, Priya Kulkarni2, Kenaz Siddiqui2, Janhavi Kodilkar2, Nitisha Danve2, Indhupriya Subramanian2, Manami Katoh3, Yuki Shimizu-Yoshida1,4, Samik Ghosh3, Abhay Jere2 and Hiroaki Kitano1,3,4,5. (7 January 2016). Network analyses based on comprehensive molecular interaction maps reveal robust control structures in yeast stress response pathways. npj Systems Biology and Applications.

●Shiva Kumar, Vivek Singh, Vineet Jha, Priya Kulkarni, Abhay jere. (2012). RobExT: a tool to customize microarray data for CellDesigner and Cytoscape ACM, 5.

TECHNICAL SKILLS

AWS cloud platform

●Knowledge of S3 structure

●Knowledge of EC2 instance

●Rclone

Data Science and Computers

●Software Skills: R language, Python

●Database Management Tools: MS SQL Server

●Data Visualization tools: Tableau, Tibco Spotfire

●Statistical analysis: Mean, Median, Variance, Regression analysis, T-test, Naive Bays probability, ANOVA, Excel solver

●MS Office: Excel (macros, charts, pivot tables, formulas), PowerPoint, Access, Word

●Predictive Analysis: STATISTICA, KNIME

Bioinformatics

●Next generation sequencing data analysis (DNA-seq, RNA-seq).

●Database and bioinformatics tools for NGS data analysis: Bedtools, SAMtools, IGV, BWA, Galaxy, HISAT-2, TopHat, UCSC Genome Browser, Ensembl, NCBI Genomes, Map Viewer, Variation Viewer

●Sequence analysis tools: BLAST, FASTA, Splign, BLAT, Multiple sequence analysis tools- CLUSTAW, CLUSTAL Omega, T-COFFEE, MUSCLE.

●Gene Prediction tools: FGENESH, FGENESB, GenScan, HMMGene, Augustus.

●Protein structure prediction tools: GOR based tool, Chou-Fasman based tool (CFSSP), PDBsite, Prosite

●Systems Biology and Network Analysis: Tools like Teranode, Cell Designer, Cell signaling and enzyme kinetics, Pathway Analysis, Ingenuity Pathway Analysis (IPA), Reactome, Cytoscape

●Data Analysis Microarray, Mass Spectroscopy, Statistical Analysis

●Data mining: Entrez, Ensembl, Biomart

●Databases: KEGG, Protein Lounge, Biocarta, Reactome, Enzyme databases: BRENDA

●Familiarity with Unix/Linux

Pharmacy

●Academic courses: Pharmaceutics, Pharmacology, Pharmacognosy, Medicinal Chemistry, Pharmaceutical analytical chemistry

Management Skills

●As a domain lead successfully managed a team

EDUCATION and CERTIFICATION

Post-Master’s Certificate in Sequence Analysis and Genomics (Aug 2022)

Johns Hopkins University

Data Science Certification (June 2017)

University of California, Irvine CA

Master of Technology - Bioinformatics (2007)

Dr. D.Y. Patil Institute for Biotechnology and Bioinformatics, Belapur, Mumbai, India

Bachelor of Pharmacy (2005)

A.B.C.P. Sangli, Shivaji University, India

Contact this candidate