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NGS Genomics applications - Whole genome / exome sequencing data analysis - DNA-seq
- NGS QC: Adapter trimming, quality filter, contaminant removal.
- Genome assembly: de novo and reference based assembly; Genome annotations with clinically relevant interpretations.
- Variant Discovery: Mapping to reference genome; Single Nucleotide Polymorphism, Small InDels, copy number variations, structural variation detection; clinical impact of genomic variations.
- Metagenomics: Drafting Pan Genomes; detection of hot and cold spots.
- Genome-wide association studies (GWAS)
NGS Transcriptomics applications - RNA-seq
- Transcriptome assembly: de novo and reference based draft transcriptome; Transcriptome annotation.
- Novel transcripts and gene fusion detection
- Differential Gene expression analysis: Alignment of transcripts and quantification; identifying differentially expressed genes.
- Non-coding RNA expression analysis: lncRNA; micro-RNA; siRNA; TasiRNA.
- Annotation and enrichments: Gene ontology, metabolic pathway and protein-protein interaction network analysis
- Molecular subtyping of diseases: Applying machine learning to gene expression data
Epigenomics – ChIP-seq, Bisulfite-seq, MeDIP-seq
- Methylation: DNA binding peaks across samples, differentially methylated regions, Histone modification
- Transcription factor binding: Genome wide DNA binding sites for transcription factors
- Genome wide metabolic network reconstruction, Flux Based analysis, In-silico gene knockout simulations, Metabolic engineering, Host-pathogen interactions.
Integration of Multi-Omics data - Potential biomarkers and drug target discovery
Immunoinformatics – Subunit vaccine design from pan genome
Rational drug design – Genome to drug
- Structure prediction, molecular docking, virtual screening, e-pharmacophore design, 3D quantitative structure activity relationship, ADEM and toxicity prediction and molecular dynamics simulations.
Data integration, analysis and management
- Data integration and management: Secure storage, database, tools, software, apps and web server development and hosting support
- Statistical analysis: Sample size calculation, hypothesis testing, population based studies, cohort studies, meta-analysis, and statistical model development.
- Disease modelling, machine learning models.
Framing new research proposals and publication support – Bioinformatics and statistics