Aakarsha V. Rao
Graduate Research Assistant at University of Louisville
PhD student | Graduate RA | Bioinformatics | Metagenomics | Gut Microbiome | Metabolomics | Python | Matlab | Cardinal | UofL
Reinventing myself by expanding my skillset to include statistical, computational and analytical components to bolster my research interests in Metagenomics, Metabolomics, Epigenetics, Molecular Biology and Immunology, by pursuing a PhD degree in Bioinformatics. 

Coding skills: Python, C++, MS Excel
Bioinformatics tools: PICRUSt2, QIIME2, LefSe 
Soft Skills: Critical thinking, widely adaptive, quick learner, efficient problem solving abilities

I take pride in being a student of life, always eager to learn and experiment! Nothing keeps me more driven towards my goal than my desire to be versatile and self-sufficient in biomedical research. Looking forward to connecting with the world!
University of Louisville
https://www.linkedin.com/company/university-of-louisville
Louisville, Kentucky, United States
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Graduate Research Assistant
University of Wisconsin-Madison
https://www.linkedin.com/company/uwmadison
-- Examined Bromodomain inhibitions with JQ1 in the context of Head and Neck Squamous Cell Carcinoma. Independently designed, conducted and analyzed experiments to test the differences in response to JQ1 in two primary cell lines. 
--  Well versed in Mammalian Cell Culture, Protein Isolation, Western Blots and Flow Cytometry.
-- Was responsible for lab inventory management and administration of active protocols maintained in the lab.
-- Mentored undergraduate and graduate students to help design and brainstorm ideas for their projects.
Madison, Wisconsin Area
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Research Assistant
University of Louisville
https://www.linkedin.com/company/university-of-louisville
Worked on multiple NIH funded projects on Alcohol and Immune Suppression at The Division of Gastroenterology, Hepatology and Nutrition. My projects revolved around evaluating the effect of alcohol exposure (in vitro and ex-vivo) on various aspects:-
1. Human T-cell proliferation
2. Brain inflammation 
3. Epigenetic changes that dictate the changes in gene expression of certain classes of chemokines

Poster Presentation:
Presented at Research!Louisville 2017, University of Louisville, September 2017.
Title: Role of Promoter Associated Epigenetic Mechanisms In Alcohol- and HIV-Induced Immune Suppression
Authors: S. Ghare, PhD1, P. Peyrani, M.D.2, A. Vijaya Kumar, M.S.1, S. Joshi-Barve, PhD1, C. McClain, M.D.1,3, and S. Barve, PhD1.
1. Division of Gastroenterology, Hepatology and Nutrition, 2. Division of Infectious Diseases, Department of Medicine, University of Louisville; 3. Robley Rex VA Med Center, University of Louisville Alcohol Research Center

Participated in standardizing protocols and preparing SOPs for:
a) Chromatin preparation using micrococcal nuclease from alcohol treated THP-1 cells
b) Multi-color Flow Cytometry (BD FACS Canto II) to characterize human T-cell proliferation patterns, cell death assays (Annexin V and PI) and to characterize various immune cells from a mixed bag of cells from rat liver
Louisville, Kentucky Area
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Research Assistant
University of Texas at Dallas
https://www.linkedin.com/company/university-of-texas-at-dallas
-Worked with ÄKTA pure system to perform protocols for Nickel, Anion Exchange and Gel Filtration chromatography
-Protein expression of FACT (FAcilitates Chromatin Transcription) chaperon and/or its domains Spt16, SSRP1 in bacterial DH5-alpha cells by transformation and in insect SF-21 cells by co-transfection
-Evaluated protein-protein interaction between FACT and histones H2A/H2B and H3/H4 by visualizing using Hi-throughput Interaction by Fluorescence Intensity (Hi-Fi) technique
Richardson, Texas
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Graduate Student Research Volunteer
Indian Institute of Science (IISc)
https://www.linkedin.com/company/indian-institute-of-science
Studied gene expression patterns of novel genes - CALML5, SCRG1 and HORMAD1 in breast cancer tissue obtained from patients' biopsy samples.
-Processed tumor tissue samples by homogenization in liquid nitrogen.
-RNA isolation from samples processed and stored in TRI-zol
-qPCR to evaluate the gene expression patterns. 
-Introduction to data analysis on Graph Pad Prism.
Bengaluru Area, India
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Undergraduate Student Researcher
Biocon
https://www.linkedin.com/company/biocon
-Worked with senior scientists and researchers to design Monoclonal Antibodies (MAbs), novel and biosimilar by purifying protein expressed in CHO cell lines
-Purification techniques followed included High Performance Liquid Chromatography (HPLC), Size Exclusion Chromatography (SEC), Ion Exchange Chromatography (IEX)
-Inculcated the confidence to handle state of the art systems like Waters and Agilent independently, with minimal supervision
-Responsibilities: preparation of chromatography buffers, setting up the systems for running samples, analyzing results, record keeping of experimental protocols and results
Bangalore, India
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Project Trainee
Doctor of Philosophy - PhD
Bioinformatics
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University of Louisville
https://www.linkedin.com/school/university-of-louisville/
Master’s Degree
Cell/Cellular and Molecular Biology
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The University of Texas at Dallas
https://www.linkedin.com/school/university-of-texas-at-dallas/
Bachelor of Engineering (B.E.)
Biotechnology
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PES University
https://www.linkedin.com/school/pesuniversity/
Epigenetic mechanisms underlying HIV-Infection induced susceptibility of CD4+ T cells to enhanced activation-induced FasL expression and cell death
Journal of Acquired Immune Deficiency Syndrome
177Lu-NM600 targeted radionuclide therapy extends survival in syngeneic murine models of triple-negative breast cancer.
Journal of Nuclear Medicine
http://jnm.snmjournals.org/content/61/8/1187.full.pdf+html
Awarded scholarship for 100% funding (tuition + research + Graduate RA)
University of Louisville
Scholarship: fully-funded admission to PhD program, University of Louisville
Distinction Awards and Merit certificates through 8 semesters of engineering in Biotechnology
PES University
Gifted Student Development Program (2010-2014)
Biochemistry
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Cell Biology
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Immunology
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Molecular Biology
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Neuropathology
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Proteomics
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Quantitative Biology
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RNA Biology
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Data Mining
CSE-632
Data Structures
CSE302
Design and Analysis of Algorithms
CSE-619
Introduction to Bioinformatics
CSE660
Probability
PHST-661
Python and Data Analytics
CSE590
Downstream Process Technology
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Genetic Engineering
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Heat and Mass Transfer
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Microbiology
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Upstream Process Technology
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Designed clustering algorithms (K-means, Hierarchical and BIRCH) to group 800+ samples based on the characteristic differential gene expression patterns
Tasks: Data Preprocessing and Descriptive Data Mining 
Packages: SciKit Learn, Pandas DataFrames, NumPy, Matplotlib
RNA-Sequencing: Comparison of Clustering algorithms on RNA-Sequencing Cancer Dataset
Trained 4 machine learning algorithms: Naive Bayes, Logistic Regression, Linear SVC, Decision Trees to predict probability of an applicant to be "at risk" or "at no risk" of delinquency.
Tasks accomplished in a nutshell: Exploratory Data Analysis, Data Preprocessing, Model Training, Analyzing performance of models using F1-score and Area under ROC curve
Packages: Pandas DataFrames, NumPy, SciKit learn, MatplotLib
Machine Learning approach to Prediction of Credit Card Loan Outcomes
Elucidated the influence of social media on perceptions of GameStop controversy. 
Data Preprocessing (Feature Selection, Feature Extraction, Data Normalization) Data Visualization
Packages: Pandas DataFrames, NumPy, MatplotLib
Data Mining: Perceptions of GameStop controversy on Reddit and Twitter
-- Object Oriented Programming design for evaluating pairwise sequence alignment pattern and scores
-- Implementation of the Expectation-Maximization statistical model for Multiple Sequence Alignment in Python 
-- Comparison, Evaluation and Implementation of Distance Matrices in Python
Pairwise Sequence Alignment, Expectation Maximization Algorithm and Implementation of Distance Matrices
Mined social media (Twitter) to collate tweets related to particular topics, preprocessed them, analyzed tweet text for sentiment and tonality, trained and tested unsupervised and supervised machine learning models to predict sentiment of tweets, interpreted and depicted data using graphs and word clouds. 
Packages used:
-- Social media mining: Tweepy library - Twitter API Trends; geopy library - geocoding 
-- Natural Language Processing: TextBlob, StaCy, nltk module
-- Data Interpretation: MatPlotlib, Pandas series and DataFrames, NumPy 
-- Machine Learning: SciKit learn package
Social Media Data Mining and Analysis: Natural Language Processing, Sentiment Analysis and Data Interpretation
Analysis of phenotypic outcomes of BET bromodomain inhibition in the context of Head and Neck Squamous Cell Carcinoma (HNSCC)
Effect of BET bromodomain inhibition by JQ1 on the differences in proliferation and sustenance of HPV-positive Head and Neck Squamous Cell Carcinoma (HNSCC) cell lines.
Poster Presentation:
Presented at Research!Louisville 2017, University of Louisville, September 2017.
Title: Role of Promoter Associated Epigenetic Mechanisms In Alcohol- and HIV-Induced Immune Suppression
Authors: S. Ghare, PhD1, P. Peyrani, M.D.2, A. Vijaya Kumar, M.S.1, S. Joshi-Barve, PhD1, C. McClain, M.D.1,3, and S. Barve, PhD1.
1. Division of Gastroenterology, Hepatology and Nutrition, 2. Division of Infectious Diseases, Department of Medicine, University of Louisville; 3. Robley Rex VA Med Center, University of Louisville Alcohol Research Center
Role of Promoter Associated Epigenetic Mechanisms In Alcohol- and HIV-Induced Immune Suppression
The project carried out at the "Indian Institute of Science" Bangalore, India, mainly centered around evaluating the expression of three novel genes namely CALML5 (Calmodulin Like 5), SCRG1 (Stimulator of Chondrogensis 1) and HORMAD1 (HORMA Domain Containing 1) by comparing their expression with TBP (TATA Box Binding Protein) - a housekeeping gene using quantitative Real Time PCR. The other experiments which were performed include RNA isolation following standard protocol, subsequent conversion of RNA to cDNA by reverse transcription and PCR (Polymerase Chain Reaction) of the cDNA.
Gene Expression Studies in Breast Cancer
CITI Program
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40591784
Human Subjects and HIPAA Research
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CITI Program
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43341490
HIPAA Privacy
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https://www.linkedin.com/in/priyankabhandary
Ames, IA
Priyanka Bhandary
Ph.D. candidate | Bioinformatics and Computational Biology | Machine learning | Bioinformatics Scientist | NGS | RNA-seq |
https://ie.linkedin.com/in/bhairavi-bk-437a60166
Dublin
Bhairavi BK
MSc Diagnostics and Precision Medicine Graduate
https://es.linkedin.com/in/arnau-peris-cuesta-a084781b6
Alcoy
Arnau Peris-Cuesta
Computational Biology / Bioinformatics
https://www.linkedin.com/in/prachikhekare
Santa Clara, CA
Prachi Prakash Khekare
Research Assistant
https://ch.linkedin.com/in/suraj-balakrishna-9aa1b793
Zurich
Suraj Balakrishna
Researcher at University Hospital Zürich
https://www.linkedin.com/in/monica-bautista-8a95526a
Forney, TX
Monica Bautista
Doctoral Student at The University of Texas at Dallas
https://www.linkedin.com/in/shruti-eswar
Cincinnati, OH
Shruti Eswar
Bioinformatician pursuing a doctorate degree | Cincinnati Children's Hospital | Northeastern Alumna
https://www.linkedin.com/in/swethakasetty
White River Junction, VT
Swetha Kasetty
PhD Candidate at Dartmouth College
https://www.linkedin.com/in/keerthananprabhu
Berkeley, CA
Keerthana Nagesh Prabhu
Bioinformatics Associate at Sound Agriculture
https://www.linkedin.com/in/sneha-mohan-7a912117b
Athens, GA
Sneha Mohan
Neuroscience PhD Student at University of Georgia
https://www.linkedin.com/in/sarada-preeta-kalainayakan
Philadelphia, PA
Sarada Preeta Kalainayakan, Ph.D.
Senior Medical Writer at Real Chemistry | Medical Affairs | Oncology | Immunooncology
https://in.linkedin.com/in/natasha-miller-32627a65
Bengaluru
NATASHA miller
Student at sophia college
https://www.linkedin.com/in/priyanarayananbinf
San Francisco Bay Area
Priya Narayanan
Associate Scientist II, Bioinformatics Analyst at AbbVie (Genomics Research Center)
https://in.linkedin.com/in/manasa-m-852489221
Bengaluru
Manasa M
--
https://www.linkedin.com/in/zheng-zhou-tornado
Centreville, VA
Zheng Zhou, Ph.D, PMP
Research Assistant | Biosciences Ph.D. | Seeking jobs in healthcare consulting or life sciences project management
https://www.linkedin.com/in/shobanajayapalan
Greater Houston
Shobana Jayapalan
Research Associate-II| BioAssay Services & PD | Molecular Biologist| Cell & Gene Therapy Enthusiast
https://www.linkedin.com/in/parmithakker
Boston, MA
Parmi Thakker
Senior Research Associate at Ring Therapeutics
https://www.linkedin.com/in/harit7
Madison, WI
Harit Vishwakarma
PhD Student @ UW-Madison
Divya Anantsri
      
          



            
              
        
              
  

    
        Aakarsha is a very hardworking and talented molecular biologist. I had the privilege of collaborating with her on various class projects and practical classes in immunology and molecular biology and found her enthusiasm for science to be very inspiring. She is definitely a team player and has an inquisitive mind. I strongly believe that her drive for scientific research strong technical skills will make her a great fit for a biotechnology industry position. 
Liked by Aakarsha V. Rao
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Congratulations to Mengwei Jiang for receiving the AASLD Early Career Investigator Award in Basic Science! 👏🎉
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Chantal Vidal, Ph.D., a post-doc in Dr. Prasanna Alluri's lab, has been selected as a UT Southwestern Provost’s Initiative for Diverse Emerging…
Liked by Aakarsha V. Rao
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Our new study is rolling-out!!#MiaGB Study, #aging, #geriatrics #brainhealth, #dementia, #alzheimer #diet, #microbiome#probiotics, #postbiotics…
MCB/MCO Alumni
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Changing FDA Regulatory landscape in the United States
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Society for Industrial Microbiology and Biotechnology  (SIMB)
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MD Anderson Cancer Center
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Pharmaceutical, Biotech, Medical & Healthcare Network: Business, Jobs, Events & News
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Genomics Jobs
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Bioconductor R Packages
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UT Dallas JSOM Career Management Center
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UT Dallas - UTD - University of Texas at Dallas
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Cell and Molecular Biology
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