Experimental expertise

Molecular and cell biology

• Single-cell RNA sequencing (10X genomics)

• Next-generation sequencing (Illumina HiSeq-4000, 2500)

• Microarray (Affymetrix)

• NanoString gene expression assays for miRNAs

• ELISpot, Western Blotting, ELISA

• Transfection

• Droplet digital PCR, Quantitative (qRT-PCR), semi-quantitative PCR for gene expression and functional analysis

• Isolation of DNA and RNA (From Blood/Tissue/Saliva), cDNA preparation, PCR-SSP, Multiplex-PCR and PCR-based RFLP, Amplified refractory mutational system (ARMS)-PCR, SSCP (Single-Stranded Conformation Polymorphism), SnapShot-PCR, SDS-PAGE

• Mixed Lymphocyte Reaction, Primary, and secondary cell culture

• Immunohistochemistry, Immunocytochemistry

Histocompatibility

• Serological typing by complement-dependent lymphocytotoxicity

• Panel reactive antibody test using enzyme-linked immunosorbent assay (ELISA)

• Detection of donor-specific antibodies (DSA)

• Molecular HLA typing: Sequence-specific oligonucleotide probe typing (SSOP), Sequence-specific primer-based typing (SSP), DNA sequencing

Experimental animal handling

• Extensive expertise in handling multiple animal models including mice, hamsters, guinea pigs, and rabbits while involved in COVID-19 and Herpes vaccine research

• Highly experienced to work in ABSL3 and ABSL2 laboratories

Bioinformatics and Bio-Statistics

• R and Python Programming Language

• Computer Aided Drug Designing (CADD): Structure based drug design (SBDD) and ligand based drug design (LBDD) 

• Molecular Dynamics Simulation

• Proficient in analyzing DNA and RNA sequencing data

• Proficient in sequence analysis and alignment tools: Sequence analysis software (ABI), DNA Star, Gene Scan, BioEdit, DnaSP etc.

• Copy Number Variation (CNV) data analysis: Chromosome Analysis Suite

• Variant analysis: Alamut visual

• Tools for predicting impacts of variations: Meta-SNP, MutationTaster2, MutPred, Predict-SNP, PROVEAN, DDIG-in, HMMvar, SIFT Indel, DeepSEA, sTRAP, PolyPhen-HCM, POSE etc.

• Protein modeling: Modeller9.11, JMol, Clustal-W etc

• Pathway analysis: GSEA, GOEAST, Gene Ontology, KEGG, WebStalt etc.

• Phylogenetic analysis: MEGA, Phylip, NETWORK, MAFTT

• Statistical packages: SPSS, Arleqin, Popgene, Haploview, Emhapfrequest, Minitab, Instant Graph pad, PRISM, Multifactor Dimensionality Reduction (MDR), Random Forests (RF), Classification and Regression Tree (CART) and Grade of Membership (GoM) analysis etc.  

Software/Tool Development

To obtain the software MASSKIRanalyzer, download the registration form (http://sourceforge.net/projects/masskiranalyzer/files/MASSKIRAnalyzer%20Registration%20Form.pdf/download) fill it and please email to masskiranalyzer@gmail.com