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bioinfosourabh/README.md

Sourabh Kumar

Bioinformatics Scientist | Metropolis Healthcare | AIIMS Delhi
📧 [email protected]
🌐 LinkedIn • ORCID
📸 Outside of research, I also pursue photography/filmaking .

My tech tools 💻

Python R Shell Script GNU-Bash MySQL Linux Anaconda PyTorch Keras SciPy GitHub Actions

WES WGS CNV/SV Variant Calling

Nextflow Docker Singularity AWS HPC XGBoost GNN Deep Learning AI-Scoring

Molecular Docking scRNA-Seq RNA-Seq 16S Metagenomics ChIP-Seq

Research Focus

I specialize in high-throughput genomic analysis, precision diagnostics, and cloud-native bioinformatics. My work spans the development of scalable pipelines for whole exome/genome sequencing, machine learning models for variant prioritization, and integrative multi-omics frameworks for pediatric tumors and rare genetic disorders.

Areas of Expertise

  • Computational Genomics: WES, WGS, CNV/SV detection, somatic/germline variant calling
  • NGS Pipeline Development: Nextflow, Docker/Singularity, AWS, HPC environments
  • Machine Learning in Genomics: XGBoost, GNNs, Deep Learning, AI-based variant scoring
  • Structural Bioinformatics: Molecular dynamics (GROMACS), mutational modeling, docking
  • Multi-Omics Integration: scRNA-Seq, RNA-Seq, 16S metagenomics, ChIP-Seq

Projects

  • TrioExome-Analysis:
    Clinical pipeline for trio-based whole exome sequencing with automated annotation and priortization.

  • Variant-Prioritizer:
    Framework for deleterious variant classification integrating CADD, SIFT, and dbNSFP.

  • WGS-AMR:
    Whole genome sequencing pipeline for identifying antimicrobial resistance markers.

  • Single-Cell-Analysis:
    Single Cell Data Analysis Workflow using the Seurat package

Publications

• Kumar, Sourabh, et al. "Exploring Familial Hypospadias: Genetic Insights from Copy Number Variants in a Quad Family." (2024). [https://doi.org/10.21203/rs.3.rs-4843906/v1]

• Phugat, S., Sharma, J., Kumar, S., Jain, V., Dhua, A. K., Yadav, D. K., ... & Goel, P. (2024). Genetic landscape of congenital pouch colon: systematic review and functional enrichment study. Pediatric Surgery International, 40(1), 314.

• Goel, P., Sharma, M., Kaushik, H., Kumar, S., Singh, H., Jain, V., ... & Agarwala, S. (2024). Genetic Markers of Spina Bifida in an Indian Cohort. Journal of Indian Association of Pediatric Surgeons, 29(5), 529-535.

• Sharma, J., Sharma, M., Kumar, S., Kaushik, H., Pandey, H., Lal, D., ... & Goel, P. (2025). Genetic Markers of Spina Bifida: Enrichment of Pathogenic Variants and Variants of Uncertain Significance. Journal of Indian Association of Pediatric Surgeons, 30(2), 163-169.

• Kumar, S., Sharma, J., Sardar, R., Jain, V., Dhua, A. K., Yadav, D. K., ... & Goel, P. (2025). KMT2C Polymorphism in Familial Hypospadias. Indian Journal of Pediatrics, 1-3

• Goel, Prabudh, et al. "Chromosomal Microarray Analysis in Spina Bifida: Genetic Heterogeneity and Its Clinical Implications". Journal of Indian Association of Pediatric Surgeons

• Kumar, Sourabh, et al. "Novel CTNNB1 Gene Mutations Reveal Critical Pathogenic Mechanisms in Pediatric Hepatoblastoma". Pediatric Surgery International

• Book Chapter: "Deep-genomics: Deep Learning Based Analysis of Genome Sequenced Data for Identification of Gene Alternation" for a book entitled “Artificial Intelligence (AI) in Cell and Genetic Engineering” (https://www.springer.com/series/7651), published by Springer Protocols.

Contact

Feel free to connect .
📬 [email protected]

Pinned Loading

  1. Single-Cell-Analysis Single-Cell-Analysis Public

    Single Cell Data Analysis Workflow using the Seurat package in R, covering essential steps, such as quality control, clustering, cell type identification, differential gene expression analysis, and…

    R 6 1

  2. Somatic-Variant-Calling-Pipeline Somatic-Variant-Calling-Pipeline Public

    This repository provides an automated somatic variant calling pipeline using BWA-MEM, GATK Mutect2, and bcftools. The pipeline processes paired-end FASTQ files, performs alignment, duplicate markin…

    Shell

  3. Trio-Exome-Analysis-Pipeline Trio-Exome-Analysis-Pipeline Public

    A pipeline for Trio Exome Analysis to identify de novo, inherited (AR, AD, X-linked), and mosaic variants

    Shell

  4. Germline-Variant-Calling-Pipeline Germline-Variant-Calling-Pipeline Public

    This repository provides a fully automated and modular Germline Variant Calling Pipeline using BWA, GATK, Samtools, Fastp, and bcftools. The pipeline supports end-to-end processing starting from ra…

    Shell 1

  5. Protein-Simulation-Pipeline Protein-Simulation-Pipeline Public

    A structured pipeline for performing all major steps of protein molecular dynamics simulations using GROMACS—starting from structure preparation to energy minimization, equilibration, production ru…

    1

  6. ngs-automation-nextflow ngs-automation-nextflow Public

    A modular and reproducible workflow built with Nextflow for processing short-read sequencing data. The pipeline integrates standard bioinformatics tools and follows best practices for scalable and …

    Nextflow