Experiences
Work Experience/s
Principal Research Engineer (2020/09 onwards)
Bioinformatics, Core Facility, Faculty of Medicine and Health Sciences, BKV, Linköping University, SwedenKey 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.
- Developing bioinformatics pipeline using Python, R for standardization of different DNA, RNA analyses.
Postdoctoral Fellow (2017/06 – 2020/08)
Department of Clinical and Experimental Medicine, Linköping University, SwedenKey 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.
- Computational analysis of whole genome (RRBS)/ array based (450K/850K) DNA methylation analysis from different participants in Sweden and Peru.
Senior Research Fellow (2014/01 – 2017/01)
DST-INSPIRE (Govt. of India), Bioinformatics Centre, Bose Institute, IndiaKey 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
- Develop of analysis pipelines to identify different microRNAs (miRNAs) in human diseases and their roles in evolutionary perspective.
Junior Research Fellow (2012/01 – 2014/01)
DST-INSPIRE (Govt. of India), Bioinformatics Centre, Bose Institute, IndiaInstitute Fellow (2010/09 – 2012/01)
Bioinformatics Centre, Bose Institute, IndiaResearch Trainee (2009/07 – 2010/05)
National Institute of Plant Genome Research, New Delhi, India.