Jibin John
Bioinformatics || Research Scientist
I am Jibin John, a human geneticist and bioinformatician with over eight years of experience. I specialize in analyzing Next Generation Sequencing (NGS) and SNP microarray data to uncover the genetic basis of diseases. My expertise lies in building and managing automated data analysis pipelines, and I use statistical analysis to connect genetic variants and genes to disease biology.
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My Education Journey
Lifelong Learning
XX Winter School on Epigenetics; DNA Methylation Analysis, Madurai Kamaraj University, Tamil Nadu, India
November 2011
Hands-on Training in Embryonic Cells Culture and Maintenance; University of Pittsburgh, Pittsburgh, USA
October 2012
Intro to Linux Shell Scripting; Udemy
September 2018
BASH Programming Course: Master the Linux Command Line; Udemy
February 2020
R Programming A-Z™: R for Data Science with Real Exercises; Udemy
April 2020
Complete Python Bootcamp: From Zero to Hero in Python; Udemy
April 2020
Professional Development Certificate in Data Science and Machine Learning, McGill University
My Career Journey
Feinstein Institutes for Medical Research, New York, USA | Feb 2022 – Present
- Conducted common variant genetic association analyses for cognitive traits (e.g., cognition, reaction time) using Regenie on UK Biobank datasets.
- Performed meta-analyses and pleiotropic analyses of public GWAS summary statistics across imaging-derived phenotypes (IDPs), psychiatric, and cognitive traits.
- Developed a Python-based automated pipeline for harmonizing and processing public GWAS summary statistics into VCF format.
- Estimated heritability and genetic correlations from GWAS summary data.
- Performed post-GWAS analyses including fine mapping, colocalization, gene mapping, gene-based and gene-set enrichment analysis, Mendelian Randomization (MR), SMR & HEIDI, and pleiotropic association testing using UK Biobank and deCODE datasets.
- Calculated polygenic risk scores (PRS) for first-episode psychiatric disorders and schizophrenia.
- Prioritized GWAS genes using multi-layer biological data with tools such as FLAMES, MAGMA, and PoPS.
- Integrated single-cell RNA-seq and ATAC-seq with GWAS data to identify disease-relevant cell types.
- Designed and maintained scalable, reproducible pipelines in Python and R for MR, gene prioritization, and meta-analysis, optimized for HPC and GCP environments.
- Mentored junior scientists and medical residents in statistical genetics and GWAS methodologies.
- Published two peer-reviewed manuscripts based on these research findings.
- Collaborated with interdisciplinary teams to translate genetic discoveries into biological and therapeutic insights.
Semantic Web India Pvt. Ltd., Bengaluru, India | Apr 2022 – Dec 2022
- Developed a cloud-based SaaS platform for exome and genome sequencing data analysis, enabling identification of pathogenic variants in Mendelian disorders and cancers.
- Built an automated pipeline for Copy Number Variation (CNV) detection from exome data, improving analysis efficiency and accuracy.
- Designed an advanced variant filtering and prioritization system integrating patient clinical data with ACMG guidelines for germline variants and AMP/ASCO/CAP guidelines for somatic cancer variants.
Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India | May 2021 – Apr 2022
- Led daily operations of the computational biology lab, managing NGS data analysis projects and ensuring smooth collaboration with wet-lab scientists.
- Supervised, trained, and mentored a team of junior staff, fostering efficient facility operations and high-quality outputs.
- Conducted workshops on clinical exome sequencing and RNA-seq data analysis for clinicians, students, and faculty.
- Delivered NGS data projects for clinicians, agricultural scientists, and microbiologists.
- Designed and implemented custom pipelines for clinical exome analysis, target capture sequencing, de novo genome/transcriptome assembly, ChIP-seq, 16S rRNA and shotgun metagenomics, bacterial genome analysis, RNA-seq, and COVID-19 sequencing.
- Pioneered an Oxford Nanopore sequencing pipeline enabling sensitive detection of SNVs, Indels, and supporting COVID-19 and bacterial genome analyses.
McGill University, Montreal, Canada | 2018 – 2021
- Led genomic studies to identify common and rare variants (gene- and pathway-based) associated with psychiatric disorders by analyzing SNP microarray and whole-exome data from multigenerational families (10 families; 230 samples) and unrelated individuals.
- Interpreted the biological relevance of associated loci using systems genomics approaches.
- Conducted polygenic risk score analyses to understand genetic risk architecture.
- Performed both family-based and population-based rare/common variant association analyses.
- Managed and mentored graduate students, undergraduate researchers, and lab technicians, fostering collaboration and productivity.
University of Delhi, New Delhi, India | 2017 – 2018
- Developed and maintained automated pipelines for WES and RNA-seq data analysis.
- Identified genes and variants associated with psychiatric disorders, tardive dyskinesia, and strabismus through analysis of familial and sporadic WES datasets.
- Contributed to RNA-seq analysis of fibroblasts from rheumatoid arthritis patients.
- Trained junior researchers in WES and genotyping data analysis.
- Served as the lab’s technical expert on NGS data analysis.
- Authored and published seven manuscripts, including several as first author.
University of Pittsburgh, Pittsburgh, USA | 2012
- Awarded a prestigious training fellowship from the Fogarty International Center, NIH.
- Cultured and maintained induced pluripotent stem cells (iPSCs) and differentiated them into neurons.
- Performed quality control assays to ensure accuracy and validity of experimental results.
Awards And Fellowships
Council for Scientific and Industrial Research (CSIR), New Delhi, India, 2011
University Grants Commission (UGC), New Delhi, India, 2011
Fogarty International Center, National Institutes of Health (NIH), USA, 2012
Council for Scientific and Industrial Research (CSIR), New Delhi, India, 2012–2014
International Conference of Human Genetics & 39th Annual Meeting of the Indian Society of Human Genetics, Ahmedabad, India, 2014
Indian Council of Medical Research (ICMR), New Delhi, India, to attend the World Congress of Psychiatric Genetics (WCPG), Toronto, Canada, 2015
Council for Scientific and Industrial Research (CSIR), Delhi, India, 2015
Healthy Brains for Healthy Lives (HBHL) initiative, McGill University, Montreal, Canada, 2019; CAD 125,000
My Specializations
Advanced bioinformatics and data analyses across genomics, transcriptomics, and population-level studies.
Exome Sequencing Data Analysis
Somatic and germline variant Interpretation based on ACMG/AMP/ASCO/CAP Guidelines
Genome-Wide Association Studies (GWAS).
Post-GWAS Analysis
Single-Cell RNA Sequencing
Multi-Omics Integration
RNA-seq Data Analysis
Conferences & Meetings
- Indian society of human genetics meeting 2016
- Indian society of human genetics meeting 2017
- Indian society of human genetics meeting 2018
- Indian society of human genetics meeting 2019
- American society of human genetics
Professional Memberships
- Life time member of Indian society of human genetics
- American society of human genetics
- International society of psychiatry genetics
Awards And Fellowships
Council for Scientific and Industrial Research (CSIR), New Delhi, India, 2011
University Grants Commission (UGC), New Delhi, India, 2011
Fogarty International Center, National Institutes of Health (NIH), USA, 2012
Council for Scientific and Industrial Research (CSIR), New Delhi, India, 2012–2014
International Conference of Human Genetics & 39th Annual Meeting of the Indian Society of Human Genetics, Ahmedabad, India, 2014
Indian Council of Medical Research (ICMR), New Delhi, India, to attend the World Congress of Psychiatric Genetics (WCPG), Toronto, Canada, 2015
Council for Scientific and Industrial Research (CSIR), Delhi, India, 2015
Healthy Brains for Healthy Lives (HBHL) initiative, McGill University, Montreal, Canada, 2019; CAD 125,000
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Feel Free To Consult Me
Have a question or want to collaborate? I'm available to discuss my expertise in bioinformatics and human genetics. You can reach me directly using the contact information provided below.