Summary
Overview
Work History
Education
Skills
Certification
Publications
AREA OF EXPERTISE
Timeline
Generic

SHAKTIPRASAD MISHRA

Bhubaneswar

Summary

Innovative and detail-driven Bioinformatician with 3+ years of hands-on experience in high-throughput sequencing, NGS data analysis, and multi-omics interpretation in translational immunology and infectious disease research. Adept at designing and optimizing scalable bioinformatics pipelines using Python, R, and Shell scripting, with deep proficiency in RNA-seq (bulk, single-cell and spatial), variant analysis and pathway enrichment. Proven ability to translate complex biological data into actionable insights using industry-standard tools (e.g., Seurat, Scanpy, Slingshot, SCENIC, GATK, HISAT2), while operating Illumina platforms (NovaSeq 6000,NextSeq 550) to deliver high-quality,reproducible data. Experienced in cross-functional collaboration, mentoring, and scientific communication.

Overview

4
4
years of professional experience
1
1
Certification

Work History

Project Associate-I

BRIC-Institute of Life Sciences
07.2022 - Current
  • Lead Bioinformatics Researcher: Translational & Single-cell Genomics: Led integrative lncRNA–mRNA–miRNA network analysis to reveal novel immune regulatory circuits using bulk RNA-seq. Conducted single-cell RNA-seq analysis of TLR-stimulated models to map immune subpopulations and pathways with Seurat, Slingshot, and SCENIC. Directed mTB host-response scRNA-seq project to chart dynamic immune cell trajectories and transcriptional reprogramming.
  • Collaborative Projects: Multi-Institutional Transcriptomics: Contributed to CDRI-led transcriptomics study in Leukemia, providing analysis, visualization, and interpretation for a published work. Supported gene expression profiling and pathway enrichment analysis in AIIMS and IBSD projects, including treatment-responsive plant transcriptomes.
  • NGS Instrumentation & Workflow Oversight: Operated and maintained Illumina NovaSeq 6000 & NextSeq 550 for high-throughput sequencing; managed plate design, sample sheet prep (IEM, LRM), and end-to-end run execution. Supervised library QC and loading, ensured compliance with Illumina QA protocols, and resolved issues via routine maintenance and engineer coordination. Handled demultiplexing (bcl2fastq, BCL Convert) for in-house and client data. Developed an rsync-based secure data pipeline for DNBSEQ-G400, optimizing data transfer and downstream integration.
  • Training, Mentorship & Scientific Outreach: Co-led hands-on workshops on single-cell RNA-seq and exome analysis, training researchers in key tools (Cell Ranger, Seurat,GATK, BWA, ANNOVAR) with a focus on data wrangling, visualization, and reproducible workflows.
  • Developed a machine learning model to classify systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) patients using clinical and flow cytometry data; applied feature engineering, model selection, and cross-validation to achieve high classification accuracy.
  • Implemented algorithms in Python (scikit-learn, XGBoost), performed data preprocessing, normalization, and feature selection, and evaluated performance with ROC-AUC, precision-recall, and confusion matrix.

Student Trainee

ICAR-National Rice Research Institute
12.2021 - 05.2022
  • CRISPR-Cas9 Assisted Functional Genomics in Rice (Sponsored by DST & DBT-Odisha)
  • Designed and executed CRISPR-Cas9 mediated gene editing targeting the TPS gene in Oryza spp., with the goal of enhancing stress resilience and metabolic efficiency in rice.
  • Engineered and cloned gRNA constructs using DH5αand Top10 E. coli strains, optimizing vector assembly and transformation efficiency.
  • Applied molecular biology techniques such as PCR screening, plasmid extraction, restriction digestion, and sequencing validation to confirm gene edits.

Dissertation Trainee

ICMR- Regional Medical Research Center
06.2021 - 12.2021
  • Mapped viral evolution of Dengue virus (DENV) isolates from Bhubaneswar by performing phylogenetic analysis using MEGA and BEAST, identifying region-specific mutation patterns from historic to contemporary outbreaks.
  • Inferred transmission dynamics by comparing local isolates with nationally circulating DENV lineages, uncovering potential introductions and divergence points.
  • Worked hands-on in BSL-2 environment with clinical viral samples, ensuring biosafety compliance during nucleic acid extractions, serotyping, and PCR- based molecular diagnostics.
  • Conducted comprehensive serological and molecular assays, including ELISA, RNA/DNA extraction, RT-PCR, and serotyping, contributing to viral surveillance and public health insight.

Education

Master Of Science - Bioinformatics

Odisha University of Agriculture And Technology
Bhubaneswar
01.2021

Bachelor Of Science (Honours) - Bioscience

Sri Sathya Sai Institute of Higher Learning
Bangalore
01.2018

Skills

  • RNA-seq, Single-Cell & Spatial Transcriptomics Data Analysis,
  • Machine Learning: Supervised classification (Random Forest, SVM, Logistic Regression, XGBoost), Feature Selection, Cross-validation, Model Evaluation (ROC-AUC, Precision, Recall, Confusion Matrix)
  • Exome data analysis using GATK pipeline,
  • 16s and microbial WGS analysis,
  • Multi-Omics Data Integration & Network Biology,
  • Bioinformatics Pipeline Development (Python, Shell, Nextflow),
  • Illumina Sequencing Workflow & Quality Assurance,
  • Data Visualization (ggplot2, Plotly, Matplotlib, Seaborn),
  • Translational Immunology & Host– Pathogen Interaction Analysis,
  • Data Harmonization & Public Dataset Integration (GEO, ENA),
  • HPC Based Bioinformatics Computing,
  • Scientific Writing & Peer-Reviewed Publication Support,
  • Mentorship & Bioinformatics Training Delivery

Certification

  • Network Addressing and Basic Troubleshooting, Cisco
  • Networking Basics, Cisco

Publications

  • Https://doi.org/10.1038/s41375-024-02344-1 Uncovering Therapeutic Vulnerabilities in Lymphoma Microenvironment Targeting CERS6-AS1/FGFR1 axis as synthetic vulnerability to constrain stromal cell-supported proliferation in Mantle Cell Lymphoma. Leukemia 38, 2196–2209 (2024)
  • Https://doi.org/10.1038/s43432-024-00034-1 Metabolic Rewiring in Dendritic Cells During Chronic Inflammation SMRT-depleted conventional DCs maintain inflammation despite lower glycolysis via mTOR signalling and succinate oxidation. npj Metabolism & Health Disease 2, 35 (2024)

AREA OF EXPERTISE

  • Sequencing Operations & Quality Assurance: Hands-on experience with Illumina sequencing platforms (NovaSeq 6000, NextSeq 550), including run monitoring, demultiplexing (bcl2fastq, BCL Convert), and troubleshooting to ensure data integrity.
  • Data Harmonization & Regulatory Readiness: Adept at integrating in-house and public datasets (GEO, ENA), aligning with best practices for validation, reproducibility, and clinical relevance in translational research.
  • High-Performance Computing (HPC): Experience running compute-intensive bioinformatics workflows in Linux-based HPC environments, using resource-optimized and scalable solutions.
  • Collaborative Research & Multi-Omics Projects: Effective contributor to cross-institutional studies (AIIMS, CDRI, IBSD), applying transcriptomics and systems biology approaches to uncover disease mechanisms and therapeutic targets.
  • Technical Leadership & Mentorship: Led training workshops and mentored junior researchers in bioinformatics tools and scripting (FastQC, BWA, Cell Ranger, ANNOVAR), fostering a culture of technical excellence and continuous learning.
  • Genomic Data Visualization & Reporting: Strong ability to present findings via high-impact visualizations (ggplot2, plotly, clusterProfiler), translating multidimensional datasets into digestible formats for both technical and non-technical audiences.

Timeline

Project Associate-I

BRIC-Institute of Life Sciences
07.2022 - Current

Student Trainee

ICAR-National Rice Research Institute
12.2021 - 05.2022

Dissertation Trainee

ICMR- Regional Medical Research Center
06.2021 - 12.2021

Master Of Science - Bioinformatics

Odisha University of Agriculture And Technology

Bachelor Of Science (Honours) - Bioscience

Sri Sathya Sai Institute of Higher Learning

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