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

    • Extensive use of statistical tools, like SPSS, MATLAB. Works on MS Excel, NCBI databases.
    • Use of Perl for data analysis.
    • Learn research ethics, use of FAIR data and data sharing.

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

    • Works on MATLAB,
    • Learn R and use of R packages, WGCNA.

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

    • Molecular cloning; primer desinging; bacterial sequencing; Gel electrophoresis;
    • Developed ILP markers using online bioinformatics tools.

Area of Expertise

Teaching & mentoring

  • Teaching (with designing the curriculum, examination) Bioinformatics for Microbiology to the course Medical Microbiology, Linköping University, Sweden (2021, 2022).

  • Mentoring a group of students at NDPIA workshop entitled ‘Live imaging of intracellular infections’ at Department of Clinical and Experimental Medicine in Linköping University (2018/11/12 - 2018/11/16)

  • Mentoring two master’s degree projects (with Maria Lerm) in DNA methylation analysis with R and teaching of fundamental Linux commands. (2018/09 - 2019/01)

  • Expert reviewer for a student’s thesis of International Master’s Program in Medical and Experimental Neuroscience entitled ‘Interactome link between Alzheimer’s disease and diabetes mellitus type II’ (on Bioinformatics analysis) (2018/05/31)

  • Mentoring a master’s degree project report (with Maria Lerm) with image analysis and statistical calculations with live imaging techniques (IncuCyte®) (2018/01 - 2018/11)

  • Design course curriculum, deliver teaching lecture, set question papers and evaluate the answer scripts for M.Sc. students of Bidhannagar Govt. College, West Bengal, India (2015/03 - 2015/07)

Supervision of degree/Ph.D. students

  • Co-supervisor of 2 Ph.D. students at the Faculty of Medicine and Health Sciences, Department of Clinical and Experimental Medicine (BKV), Linköping University, Sweden (2020 - 2024).

  • Main supervisor of 2 master degree students on the final year project at the Faculty of Medicine and Health Sciences, Department of Clinical and Experimental Medicine (BKV), Linköping University, Sweden (2019 - 2020).

Invited Journal Articles Reviewers

1

1 () indicates number of articles reviewed.

  • Bioinformatics; Oxford (2)
  • Frontiers in Genetics; Frontiers (1)
  • Scientific Reports; Nature Portfolio (1)
  • Cancer management and research; MDPI (2)
  • Computational biology and chemistry; Elsevier (3)
  • Genes & genomics; Springer(1)
  • Genomics; Elsevier (2)
  • International journal of environmental research and public health; MDPI (1) International journal of molecular sciences; MDPI (4)
  • Journal of clinical medicine; MDPI(1)
  • Nutrients; MDPI(1)
  • PeerJ; O’Reilly (1)
  • Briefing in Bioinformatics (1),
  • Frontiers in Immunology (1),
  • Clinical Epigenetics (2),
  • Frontiers in Cellular and Infection Microbiology (1),
  • Gene (1),
  • BBA-Cancer (1),
  • BMC Respiratory Research (1)