Key areas of services offered
Data Analysis Services
- NGS: RNA-Seq, De-novo and Reference assembly, Metagenomics, SNP analysis, Exome-Seq, ChIP-Seq etc.
- Microarray: mRNA, Exon, Non-coding RNAs, ChIP-chip, etc.
- Functional analysis: Gene Ontology, Pathways, protein interactions, molecular network generation and visualizations, transcription factors and binding sites, miRNA-mRNA interactions, etc.
- Integrated gene expression data analysis
- Molecular docking and structural analysis
- Mass-spectrometry data analysis
General Bioinformatics analysis Gene and protein information (e.g., expression, location, function), Primer designing, RAPD analysis, Sequence analysis (e.g., BLAST, MSA, Phylogenetics), etc.
Sequencing: DNA, RNA and Amplicon sequencing using NGS sequencers (we work with partnering companies for experimental work).
Creation of custom designed databases and software
Data mining and biocuration
Clinical data analysis
Advanced literature review and meta-analysis
Biomarker discovery by in silico approaches
1We can also carry out some of the initial wet-lab work (purifications, quality checks etc) or any other molecular biology laboratory work, in some cases, with the help of our collaborating companies.
- Developing databases and performing gene expression1 analysis using microarray1 and RNA sequencing1 data [multiple projects and collaborations; 3 of the collaborative work published]
- Metagenomics1 analysis of sequencing data from NGS & Sanger's method in the context of human gut microbiome [completed for a medical research group in India]
- Reference and de novo genome sequence1 assembly, gene annotations (miRNA included), phylogenetic analysis of raw genome sequence reads [multiple projects]
- miRNA (microarray)1 data analysis [completed for a research group at CCMB, Hyderabad, India]
- Exon-array (Affymetrix)1 data analysis for brain tissue [completed for a research group at CCMB, Hyderbad, India]
- CHiP-seq1 data analysis [completed for a research group at KMIO, Bengaluru, India]
- Primer and mutation1 analysis in the context of oral cancer [completed for a company, Malaysia]
- Protein interaction and pathway analysis applied to mass spec and microarray data in the context of a human disease [completed for an academic research group, Mumbai, India]
- Development of a novel meta-analysis algorithm to make use of different types of gene expression data [in-house]
- Development of a new computational platform for protein-interaction analysis [in-house]
- Development of new RNA-protein interaction database by biocuration [in-house]
- Development of online test system for screening candidates for course/job-suitability in the area of life sciences [in-house]
- Development of a software for compiling hits obtained by literature search across multiple important resources [in-house]
- Development of a portal for majority of bioinformatics resources as a guide for biologists [in-house: please visit www.startbioinfo.com for more details]
- Computational structural analysis to screen and dock ligands [collaboration with VIT, Tamilnadu, India; published]
- Roy D et al. Probing the Binding of Syzygium-Derived α-Glucosidase Inhibitors with N- and C-Terminal Human Maltase Glucoamylase by Docking and Molecular Dynamics Simulation. Applied biochemistry and biotechnology,  172(1):102-14
- Bhagwat S et al. Acetylated alpha tubulin is reduced in individuals with poor sperm motility. Fertility & Sterility, 101(1):95-104.e3
- Chitturi N et al. TIPMaP: a web server to establish transcript isoform profiles from reliable microarray probes. BMC Genomics,  14: 922
- Bhagwat SR et al. Endometrial receptivity: a revisit to functional genomics studies on human endometrium and creation of HGEx-ERdb. PLOS One,  8(3), e58419
- Bajpai et al. MGEx-Udb: A Mammalian Uterus Database for Expression-Based Cataloguing of Genes across Conditions, Including Endometriosis and Cervical Cancer PLOS One, , 7(5), e36776
- Bajpai et al. In search of the right literature search engine(s) Nature Precedings, 
- Acharya, KK et al. A novel tissue-specific meta-analysis approach for gene-expression predictions, initiated with a mammalian gene expression testis database. BMC Genomics, , 11: 467
- Kshitish Acharya K: Capacities vs. jobs in bioinformatics and biotechnology: a few points to the attention of current students & job-seekers  In: "Biotech Career Ready Reckoner 2014" (BCRR 2014), Vivify Media Private Limited & Department of Biotechnology (DBT), Govt. of India.