Pradeep Varathan

PhD Student in Bioinformatics

Indiana University Indianapolis

Biography

‘It is not uncommon for people to spend their whole life waiting to start living.' -Eckhart Tolle

Pradeep Varathan is a doctoral student in Bioinformatics at Indiana University. He is also the current president of Bioinformatics Club at IUPUI while also beinga graduate ambassador for SOIC. Being born in Chennai, India and graduating with the bachelors degree in Biotechnology, he had his eyes set on exploring the connection between biology and computer science, and the very essence of medicine in the future, precision medicine. He spends his days working on multiple approaches to build tools and analyze data for precision diagnosis and identification of genetic factors for neurodegenerative disorders while following the words of Tolle to its truest sense.

Interests

Deep Learning
Neuroscience
Systems Biology
Network Analysis

Education

Bachelors in Biotechnology, 2015-2019
National Institute of Technology Calicut

Curriculum Vitae

PhD Student

Indiana University

Aug 2019 – Present Indianapolis

Working under the guidance of Dr. Jingwen Yan, Pradeep’s research revolves around diagnosis and identification of the specific genes and variants that are responsible for Alzheimer’s disease. Dr Jingwen’s Lab being a part of the Alzheimer’s Disease Neuroimaging Initiative (ADNI), he also works under mutiple other sub projects from this initiative. He is a part of the Ambassador’s Program at School of Informatics and Computing helping new incoming students in the process of accomodating to the courses. He also holds the position as the President of Bioinformatics Club, which conducts multiple events all year round with workshops and lecture series.

Skills

R

PRS packages/ Built ImmuneSpect

Python

C-SHAL and Deep Learning pipeline

Cytoscape

Complete Network analysis

Research Internships

Sage Bionetworks

Data Analyst Intern May 2021 – Nov 2021

Worked on developing the metanetwork package with multiple network building algorithms, module construction algorithms and finally building a consensus network over different methods in R while collaborating over git and confluence, using the AWS cluster and MUNNIN supercomputer. Also, worked on creating a new pipeline using YML config files and created terminal-R based wrappers for the entire process and created a new package to process metanetwork and connect with Synapse. Built a CentOS-based docker container to run the whole pipeline in R and include Singularity for HPC work.

Research Intern

Basal Ganglia Explorers, Indian Institute of Technology Madras Jul 2018 – Sep 2018

Created a model network of neurons depending on the subject conditions to characterize various energy requirements of a particular disease.

Rajiv Gandhi Centre for Biotechnology

Research Intern Nov 2017 – Dec 2017

Placed on circulation to learn various techniques, study signaling pathways unique for neuronal stem cells and witness animal experiments.Worked on Cytoscape to analyze gene microarray networks from the experimental microarray data of neuronal stem cells.

Recent & Upcoming Talks

Bioinformatics Bio-Python Lecture Series

A bioinformatics workshop series in biopython.

Nov 6, 2020 1:00 PM IUPUI SOIC IT Building

Bioinformatics Bio-Python Lecture Series

Featured Publications

Linhui Xie, Pradeep Varathan, Kwangsik Nho, Andrew J Saykin, Pual Salama, Jingwen Yan

June 2020 PLoS ONE 15(6)

Identification of functionally connected multi-omic biomarkers for Alzheimer’s disease using modularity-constrained Lasso

Network analysis of multi-omic data using modularity constrained Lasso and identifying the biomarkers from the subnetworks which relates to the cognitive performance deterioration in AD.

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