Services

Bioinformatics and Comparative Genomics

• Mass spectrometry-based proteomics and bioinformatics analyses to subsequently identify reliable interacting proteins using database search engines, including SEQUEST, STATQUEST, MaxQuant, Xtandem!, MS-GF+, Percolator, and Proteome Discoverer, among others.
• For protein interactions studies, scores are assigned to each interacting protein pair to emphasize the significance and reliability of interactions using algorithms such as Purification enrichment score, Hypergeometric distribution, COMPASS, and SAINT, EPIC, among others.
• Increasing protein identification coverage through integration of search results from various search engines such as MSblender.
• Clustering of predicted protein-protein interactions into complexes using various clustering algorithms such as Markov-Clustering, ClusterOne, and coreMethod, among others
• Further analysis of interaction networks and complexes by incorporating data from various public databases to propose/validate hypothesis via functional enrichment and pathway analysis.
• Genetic and Chemogenomics processing and statistical analysis to generate gene-gene or drug-gene interaction networks through extensive quality control, filtering, normalization using gitter and SGA Tools algorithm to emphasize the significance and reliability of the interactions.
• Single Cell RNA-Seq pipeline includes data pre-processing and visualization, quality control steps, batch correction, data imputation, normalization, feature selection, dimensionality reduction and visualization, PCA, t-SNE, UMAP, clustering and compositional analysis, identification of cell markers, detecting rare cell types, Pseudo time analysis and trajectory inference, differential gene expression analysis, regulatory network analysis, and cell-cell interaction analysis.
• Whole Genome/Exome Sequencing pipeline includes data pre-processing quality control, FastQC, alignment to the genome, removal of PCR products, marking duplicates, identification of germline and somatic variants of interest, single nucleotide polymorphisms, insertions and deletions, copy number variants, variant annotations using ANNOVAR and SnpEff.