Pranav Khade

People
Graduate Research Assistant, Ph.D., Rotation Student

Interests:

As a young researcher, I am exploring different areas/domains of computational biology to identify my niche. I love the blend of research and software development and I am looking forward towards applications of statistical modeling, machine learning (specially AI and deep learning), parallel computing and optimization algorithms to raise, study and answer the challenging biological questions.

Research:

1. Master's Project: (~12 Months)

Name: Graphically Accelerated CUDA based Systematic Conformer Generation Method.

Guide: Dr. Manali Joshi, University of Pune.

Area: Cheminformatics

Nature: Tool

The tool is written in C++ and also ported on JAVA using SWIG bindings provided by OpenBabel. The tool focuses on systematic conformer generation of small molecules. The serial program is written, but now I attempt to port it on GPU (NVIDIA TESLA K20) using OpenACC and also on HADOOP in order to cater computational intensity. Along with this, my program is being redesigned to use multithreading using OpenMP and GNU Parallel. This project helped me to gain strong background of parallel computing and Object oriented programming using different libraries which can be proved useful even for different fields where parallel computing can be adapted. Along with this, I have built a database using my own text mining Perl LWP scripts to test the tool performance.

2. Model for Identification of Antimicrobial Peptides.

Guide: Dr. Valadi Jayraman

Area: Data Mining and Analysis.

Nature: Analysis

I have also worked on a machine learning project where I was leading a team of eight members. Like any other machine learning project, it involved text mining (I used Perl LWP) followed by feature extraction where I personally tested and used different APIs (such as Discovery studio API and more) followed by Model building using WEKA, LIBSVM and randomForest (R). I also worked on model refinement by doing grid search.

Skills

  •          Operating systems:  UNIX, Linux, Windows.
  •          Development & Scripting: C, C++, Java, Perl, R, Python.
  •          Web Implementation: HTML, PHP, SQL.
  •          GPU/Parallel libraries: OpenMP, OpenACC
  •          Bioinformatics Skills: Data Mining, Optimization Algorithms, Cheminformatics, Machine Learning, High performance computing, Software development, Drug discovery, Data Analysis, Classification Problems, Multiomics study.

Honors and Awards

1. DBT Fellowship: (For Semester 1 & 2)

Awarded by: Department of Biotechnology, Government of India.

For each semester of M.Sc, first fifteen students are awarded with monthly fellowship.

2. IGIB-GNR Scholarship: (For Semester 3 & 4)

Awarded by: IGIB(Institute of Genomics and Integrative Biology), Delhi

For each semester of M.Sc, first five excellent performers are awarded with this scholarship.

3. IIT GeneRations 2014 Gold Medal

Awarded by: Department of Biosciences & Bioengineering , IIT BOMBAY.

A national level quiz competition.

Area of Expertise: 
Machine Learning
High Performance Computing
Bioinformatics
Education: 
B.Sc in Biotechnology from University of Pune
M.Sc in Bioinformatics from University of Pune
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