Experiences

Work Experience/s

• Principal Research Engineer (2020/09 onwards)
  Bioinformatics, Core Facility, Faculty of Medicine and Health Sciences, BKV, Linköping University, Sweden

  Key Responsibilities
  

  • Developing bioinformatics pipeline using Python, R for standardization of different DNA, RNA analyses.
    
  • Developing semi/automated Nextflow workflow to analyze the SARS-CoV-2 whole genome data using Illumina and Nanopore sequencing technologies.
    
  • Developing Shiny based graphical user interface to analyze Illumina array-based DNA methylation and downstream analyses.
    
  • Shiny server setup using CentOS.
  • Developing source code on GitHub for general public use.
  • Linux system administration, user group maintenance and setup workstation for development and production.
  • User and project investigator on different HPCs (Tetralith on NSC, Rackham on Uppmax and NGP).
  • Designed course curriculum and carried out course on Bioinformatics for Microbiology at the Medical Microbiology course (8BKG24 2022VT) at Linköping University, Sweden.

  Key Achievements
  

  • Designed and developed own projects.
    
  • Networking with Clinical Genomics, Sweden and Genomic Medicine, Sweden groups.
    
  • Extensive user of contenarized (Docker, Singularity, Conda) VM on different OS architectures.
    
  • Member and owner of Genomic Medicine, Sweden DockerHub organization.
    
  • Active maintainer of Genomic Medcine, Sweden SARS-CoV-2 (GMS-Artic) pipeline group.
    
  • Member of GMS Microbiology group.
    
  • Published 3 peer-reviewed research articles, and another 4 manuscripts under reviewed on reputed journals.

• Postdoctoral Fellow (2017/06 – 2020/08)
  Department of Clinical and Experimental Medicine, Linköping University, Sweden

  Key Responsibilities
  

  • Computational analysis of whole genome (RRBS)/ array based (450K/850K) DNA methylation analysis from different participants in Sweden and Peru.
    
  • Develop analysis pipelines to identify differential methylation patterns in different groups of dataset.
    
  • Develop pipelines with unsupervised analyses like Multi-Dimensional Analysis (MDA), Principal Component Analysis (PCA), Component Analysis (CA), Multiple Factor Analysis (MFA) to reduce the dimensionality of data.
    
  • Pipeline development to use supervised machine learning algorithms (LDA, GLMNET, RandomForest) to identify biosignature from the study.
    
  • Develop analysis pipeline for transcriptome analysis.
    
  • Use of MATLAB image processing to analyze live cell imaging.

  Key Achievements

  • Extensive use of R language.​
    
  • Develop packages in R, notes on R Markdown.
    
  • High performance computing analyses.
    
  • Clustering computing with R and Shell.
    
  • Supervising 2 Ph.D. students
    
  • Supervised (main supervisor) two master degree students.
    
  • Co-supervised 4 bachelor and master degree students.
    
  • Published two first authors, one shared first co-authors and two other co-authored research articles in peer-reviewed journals.

• Senior Research Fellow (2014/01 – 2017/01)
  DST-INSPIRE (Govt. of India), Bioinformatics Centre, Bose Institute, India

  Key Responsibilities​

  • Develop of analysis pipelines to identify different microRNAs (miRNAs) in human diseases and their roles in evolutionary perspective.
    
  • Curation of databases to develop dataset to calculate the evolutionary rates in human and orthologs.
    
  • Linux-based approach to search sequence homology.
    
  • Use of different programming languages like Perl, Python to analyze dataset.

  Key achievements

  • Extensive statistical software analyses with SPSS.​
    
  • Develop algorithm based on shell scripts
    
  • Linux system maintenance

• Junior Research Fellow (2012/01 – 2014/01)
  DST-INSPIRE (Govt. of India), Bioinformatics Centre, Bose Institute, India

• Institute Fellow (2010/09 – 2012/01)
  Bioinformatics Centre, Bose Institute, India

• Research Trainee (2009/07 – 2010/05)
  National Institute of Plant Genome Research, New Delhi, India.

Area of Expertise

Skills