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Engineer, Bioinformatics Scientist, Software development

Location:
Fairfax, Virginia, United States
Posted:
October 31, 2016

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Resume:

C: 205-***-**** Sangeeta Shukla acxbvi@r.postjobfree.com

SANGEETA SHUKLA

**** *** *** *** ***, Fairfax, VA 22031 C: 205-***-**** acxbvi@r.postjobfree.com Professional Overview

Well-qualified Bioinformatics/Computational Scientist and Analyst dedicated to continuous and impactful improvement of tools and infrastructure to maximize scope and speed of data analysis. Expert in algorithm design and parallelization with added skills at mathematical modeling and relational database creation and maintenance facilitating critical analysis of big data to perceive trends that go above and beyond to enable strategic decision-making.

Core Qualifications

Python (with NumPy and SciPy) and C/C++ expert

Fortran, CUDA and OpenMP aficionado

Perl, R and Matlab pro

Proficient in SQL Server

Trained in concepts of Statistics and Probability

Knowledge of supervised and unsupervised machine learning using Hidden Markov Models, Monte- Carlo methods, Decision trees, Neural Networks and Time series analysis among others

Well-versed with fundamentals of software development life cycle

Well-informed of Bioinformatics databases and resources along with basic understanding of Next Generation Sequencing technologies and genome annotation methods

Efficient in using Bioinformatics tools for genomic and proteomic analysis including GATK, BLAST, HMMER, Galaxy and Bowtie among others

Hands-on laboratory experience of molecular biology and immunological techniques such as isolation of nucleic acids, AGE/PAGE, PCR, blotting techniques, cell preparation, protein expression, purification and detection

Education

Ph.D.: Bioinformatics and Computational Biology 2015 George Mason University Fairfax, VA, USA

Master of Science: Bioinformatics 2009

Gujarat University Ahmedabad, Gujarat, India

Bachelor of Science: Bioinformatics 2007

Sardar Patel University Anand, Gujarat, India

Experience

Associate Development Database Engineer 11/2015 - present REI Systems, Inc. Sterling, VA

Create and maintain SQL Server database for patient data to be managed by Bureau of Primary Health Care.

Process health center data to assess annual trends of immensity and spread of diseases on state and national level using SQL Server Integration Service and SQL Server Analysis Services. C: 205-***-**** Sangeeta Shukla acxbvi@r.postjobfree.com

Maintain data repository/warehouse using SQL Server Replication feature enabling availability of real- time information as submitted by user.

Manage version control using SVN Tortoise while also performing query optimization and performance tuning so retrieval of data is accurate and prompt ensuring a robust health care solution tool.

Consistently deliver high quality system analysis, design upgrade, data analysis, IT system architecture road mapping, configuration and implementation support services to client. Graduate Research Assistant 01/2011 - 08/2015

Dept. of Molecular Neuroscience, George Mason University Fairfax, VA

Independently worked as Computational Modeler to model biological systems mathematically.

Drove the planning, designing and development of tools through software lifecycle.

Responsible for version management and documentation of workflows, procedures and overall research.

Used Fortran in Linux based environment for creating, testing and debugging computational tools.

Upgraded existing tools by using parallelization techniques to improve performance using CUDA Fortran and OpenMP.

Prepared modules using CUDA Fortran to customize the architecture of tool for more versatile future use.

Created supplements for visualization and analysis using Matlab and IDL. Graduate Research Assistant 06/2010 - 12/2010

Krasnow Institute for Advanced Study, George Mason University Fairfax, VA

Devised a one-of-a-kind algorithm to apply bioinformatics concepts for genetic/protein analysis to be used for cellular structure comparison.

Designed a scoring matrix to be used by algorithm for comparing structural features of neurons.

Used Python to create a library of regular expressions signifying patterns of digitally reconstructed neuronal morphologies from different regions of the brain based on publicly available data in NeuroMorpho.org.

Created pattern-matching algorithms, using R, for pair-wise multiple sequence alignment based on BLAST fundamentals.

Prepared modules so that could be easily adapted and incorporated in a more comprehensive tool for comparison and analysis.

Independent Project work 06/2010 - 08/2010

George Mason University Fairfax, VA

Devised and designed a Hidden Markov Model based tool, using Python, to predict the secondary structure of a protein sequence.

Linked the results for structure prediction via a SQL Server database with data accessed from online repository for comparison of prediction results with experimental knowledge bank.

Created a web-page displaying contents of database including prediction results from the tool along with references to source organism/tissue and experimentally derived structural specifications, if any. Graduate Research Assistant 08/2009 - 06/2010

School of Systems Biology, George Mason University Fairfax, VA

Planned and designed a unique algorithm as a prototype to predict if and/or when an HIV-positive patient may develop AIDS.

Studied and relied on the trend of mutations in protein sequences of two receptors found on blood cells of patients.

Used an acquired data set to train Hidden Markov Model based algorithm.

Used Python to train the model and simulate stochastic mutations based on Monte Carlo method. Intern 03/2009 - 06/2009

Zydus Research Center Ahmedabad, India

Researched and investigated from variety of literature the cause and effects of inflammatory pathway triggered by cytokine IL6.

Created a flow-chart of inter-connected sequence of events in order to devise and design a Systems Biology based mathematical model to simulate the process of signal transduction.

Used free online tool CellDesigner for generating the model and CoPASi for simulations.



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