Skills

Computational Genomics

I employ computational tools to understand regulatory aspects of gene expression and the role of chromatin architecture in it. I Find transcription factor targets, their modifications, interactions and accessibility using technology driven data such as Next Generation Sequencing.

Molecular Interactions

Molecular modeling of proteins, peptides and small molecules. Model binding interactions of receptors with their substrates and predict biological function.

Data collection and modelling

Automate and integrate biological data collection from public databases, pre-process, cluster, extract features, apply statistics and model. A data science enthusiast.

Python and Perl

I use Python as language of choice for programming. I am teaching introductory Python and Perl at he university. I am Using Jupyter and iPython extensively for teaching, and have build many applications that are hosted on Github.

R

I use R for Graphics and bioconductor packages. I also teach introductory R to undergrads.

Linux Mint

It is my operating system of choice. I love command line and shell enviromment. Vi is my editor of choice although also I am also exploring Atom currently.

GitHub

Some of my programs are hosted here. This site is also running on GitHub. I am in the process of documenting my code (sphinx) and to host it on hg-pages branch of code repository on GitHub.

Google Cloud

I am running virtual machines complete with essential genomic data processing tools such as Samtools, Bamtools, FastqC, Meme-suite, Bowtie2, Tophat, Cummerbund etc while maintaining static genome builds on separate disk.

Graphics

I use matplotlib in R and Python for data plotting. Exploring tableau currently.

Molecular Dynamics

I do Molecular Dynamics Simulation of biomolecules using Amber suite of programs. I have used it mainly for protein-protein, protein-dna interactions and binding affinities calculations.

Machine-learning

Artificial neural networks and deep learning using scikit-learn library. Support vector mahines.

Photography

Hobbyist. Always learning new tricks and techniques. HDR and long exposure are my favourites.

Experience

 
 
 
 
 

Assistant Professor

Jaypee University of Information Technology

Dec 2017 – Present Waknaghat, Himachal Pradesh, India

Courses Taught:

  • Programming Languages for Bioinformatics
  • Programming Languages for Bioinformatics Lab
  • R-Language Lab
  • Computational Genomics
  • Computational Genomics Lab
  • Structural Bioinformatics
  • Structural Bioinformatics Lab

Research:

  • Genome Mining
 
 
 
 
 

Postdoctoral Fellow (Epigenetics)

Institute of Cancer Sciences, University of Glasgow

Apr 2013 – Dec 2016 Glasgow, UK

Projects:

  • Role of erythroid transcription factors in K562 cells
  • Identifying chromatin boundaries

Responsibilities:

  • Next Generation Sequencing Data Analysis, Storage and Retrieval
  • Genome Mining
  • Tool building
 
 
 
 
 

Postdoctoral Fellow

Center for Study of Systems Biology, Georgia Institute of Technology

Sep 2010 – Jan 2013 Atlanta, Georgia, US

Project:

  • Development of high precision enzyme function prediction algorithms.

Responsibilities:

  • Enzyme function prediction
  • Computational Metabolomics
 
 
 
 
 

Research Associate

National Institute of Immunology

Jan 2010 – Aug 2010 New Delhi, INDIA
Project:

  • Molecular Modelling of Malarial parasite Signalling proteins

Recent Posts

Department of Biotechnology, Government of India recently concluded a very special event – the official Nobel Prize Series, 2019 – at …
2 min read

Tableau is a great tool for data visualisation in an aesthetically pleasing way. It lets you easily create appealing visual …
3 min read

One of the frustrating things bioinformaticians encounter routinely is the incompatibities among packages and their dependencies when …
3 min read

Projects

Past and Present

Projects undertaken at various places and software tools developed while working on them. The code of some of the tools is hosted on the GitHub.

*
All GitHub National Instt of Immunology Georgia Tech University of Glasgow

ChIPseq-Pipeline

ChIP-seq read alignment and processing pipeline

EFICAz2.5

Enzyme Function Inference by a Combined Approach

locStack

Meta-analysis of genomic features

MODPROPEP

MODPROPEP is a structure based program for analysis and prediction of substrates for protein kinases and MHC proteins

PDF Library

A local resource for archiving and retrieval of peer-reviewed research articles

RNAseq-Pipeline

RNA-seq paired end read alignment and processing pipeline

SBSPKS

Structure based sequence analysis of polyketide synthases. (Contributed to Structural Modules)

SUNPRO

A Database of Structure & FUNction Predictions of Proteins from Representative Organisms.

vChIP

SVM based identification of TF binding sites

Teaching

I have developed and taught following B. Tech. courses at Jaypee University of Information Technology, Waknaghat, India.

Even Semester, 2019

  • Programming Languages for Bioinformatics
  • Programming Languages for Bioinformatics Lab
  • R Languages Lab

Odd Semester, 2018

  • Computational Genomics
  • Computational Genomics Lab
  • Biological Computation
  • Biological Computation Lab
  • Structural Bioinformatics
  • Structural Bioinformatics Lab

Even Semester, 2018

  • Programming Languages for Bioinformatics
  • Programming Languages for Bioinformatics Lab
  • Molecular Modeling Lab

Condensed Semester, 2018

  • Immunoinformatics ( Selected topics)

People

Principal Investigators

Researchers

Avatar

Narendra Kumar, PhD

Assistant Professor, Computational Biology and Bioinformatics

Computational Genomics, Chromatin Remodelling, Gene Regulation, Genome Mining, Next-Gen Sequencing Data, Data Sciences, Structural Biology, Protein-protein Interaction, Intramolecular Interaction, Data Visualization, Computational tool development, Machine Learning

Grad Students

Administration

Visitors

Avatar

Narendra Kumar, PhD

Assistant Professor, Computational Biology and Bioinformatics

Computational Genomics, Chromatin Remodelling, Gene Regulation, Genome Mining, Next-Gen Sequencing Data, Data Sciences, Structural Biology, Protein-protein Interaction, Intramolecular Interaction, Data Visualization, Computational tool development, Machine Learning

Alumni

Publications

A novel glyA gene was screened from a marine bacterium, Idiomarina loihiensis encoding a thermo-stable serine hydroxymethyl transferase …
DOI

Genome guided discovery of novel natural products has been a promising approach for identification of new bioactive compounds. SBSPKS …
PDF Source Document DOI

The solvent accessibility of the Ser/Thr/Tyr containing peptide stretches in the substrate proteins of various kinases are likely to …
PDF Source Document DOI

Summary: High-quality enzyme function annotation is essential for understanding the biochemistry, metabolism and disease processes of …
PDF Source Document DOI

Calcium-dependent protein kinases (CDPKs) are major effectors of calcium signaling in apicomplexan parasites like Toxoplasma and …
DOI

Protein structures and functions are essential for understanding all biological processes in living systems. Threedimensional protein …
PDF Dataset

Identification of MHC binding peptides is essential for understanding the molecular mechanism of immune response. However, most of the …
DOI

Polyketide synthases (PKSs) catalyze biosynthesis of a diverse family of pharmaceutically important secondary metabolites. …
PDF DOI

Motivation: In silico methods are being widely used for identifying substrates for various kinases and deciphering cell signaling …
PDF DOI

MODPROPEP is a web server for knowledge-based modeling of protein–peptide complexes, specifically peptides in complex with major …
PDF DOI

Tags

Anaconda Binding Energy Calculation Biosynthetic Pathways BowTie2 Combined Approach Computational Immunology conda Cummerbund Curvy Timeline Data Analysis Data Visualization Database DNA-protein interaction Enzyme Design Enzyme Function Characterization Enzyme function prediction Enzyme Substrate Prediction Epitope Prediction FastqC Function Prediction Gene Clusters Gene Regulation Genome Genome Analysis Georgia Tech GitHub Indian Nobel Laureates Ligand Binding Malaria Parasite Meta Analysis Metabolite Biosynthesis Metabolomics MHC-peptide Interaction Molecular Dynamics Simulations Molecular Interaction Molecular Modelling National Instt of Immunology networkx Next Generation Sequencing NIRF Rankings Nobel Prize NRPS Paired End Reads PKS Plasmodium falciparum Protein Kinases Protein-peptide Interaction Protein Phosphorylation Protein-protein Interaction Proteome Proteome Analysis Python Python Environments RNA-seq Secondary Metabolite Single End Reads Site Directed Mutagenesis Structural Analysis Structural Modelling Structure Prediction Structure Visualization Surface Accessibility T-cell Epitope Tableau Desktop Tableau Public Thermostability TopHat2 Transcription factor binding TrimGallore University of Glasgow Vaccine Design Virtual Screening Web-server

Contact

  • +91 179-223-9522 (work)
  • Opposite Gut Simulation Lab, Third floor, Vivekanand Bhawan, Department of Biotechology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, HP 173234, INDIA
  • Monday to Friday 09:00AM to 05:00PM Saturday 09:00AM to 01:00PM
  • Email for appointment
  • DM Me
  • Skype Me