Data Science in Biology:
The Avadis Story
(1995-2010)

Impact: Translational Research to Global Innovation

The Human Genome Project had put out the first complete map of a human reference genome. Genomics had arrived. High throughput proteomics, metabolomics, cellomics,... were just around the corner and the first signs of what is now called the "Fourth Paradigm or Data-Intensive Science" was already evident in research biology.

Professor Chandru and his colleagues in computer science at IISc began an interdisciplinary journey at the interface of computation and biology in the mid-90s. In late 2000, Strand Genomics Pvt Ltd had been launched from IISc as India's first example of sanctioned academic entrepreneurship. The promoters were four professors of computer science and the Society for Innovation and Development (SID) - the commercialization arm of IISc.

 Chandru was a key founder of Strand and he has led the company as executive chairman (CMD) from inception. . He was largely responsible for articulating Strand’s vision, recruiting the founding team, helping the venture graduate from IISc through dialog with the university administration, and developing the first version of Strand’s business plan. Subsequently, Prof Chandru helped raise institutional capital, establish business and technology strategy, and build the R&D, production, and sales teams. Strand now employs over 200 scientists and provides bioinformatics solutions to research labs around the globe and services to Indian healthcare establishment using next generation sequencing based diagnostics.

 

The story of Avadis® over the next ten years has been one of growth of perhaps the only high complexity information technology product conceived and built in India that has achieved large global market share and is a global benchmark even till today  

The Avadis® derived products (distributed globally in partnership with Agilent) have served well over 2000 laboratories around the world and over 20,000 citations in publications.  Strand has undoubtedly been a global trailblazer in bioinformatics.

In 2004, Strand embarked on a research project that would be considered audacious. The scientific team set out to build a “Virtual Liver” that would test the hepato-toxicity of  compounds like drug molecules and other synthetic molecules (ingredients in paints, cosmetics, etc.).

In 2016, after the platform had been validated by industrial partners, this business unit of Strand was sold to Syngene International in Bangalore where it now is part of the offering in contract research services to pharmaceutical and chemical industries.
 

Strand Authors - Scientific Publications

·        Gene regulatory network modeling using literature curated and high throughput data. Systems and synthetic biology

·        Construction of a Global Pain Systems Network Highlights Phospholipid Signaling as a Regulator of Heat Nociception, PLoS Genetics

·        Next Generation Sequencing of Human Mitochondrial Reference Genomes Uncovers High Heteroplasmy Frequency. PLoS Computational Biology

·        COPS: A Sensitive and Accurate Tool for Detecting Somatic Copy Number Alterations Using Short-Read Sequence Data from Paired Samples, PLoS ONE, 7(10): e47812

·        A draft of the genome and four transcriptomes of a medicinal and pesticidal angiosperm Azadirachta indica, BMC Genomics, 13: 464

·        Investigation of serum proteome alterations in human glioblastoma multiforme, Proteomics, 12, 2378–2390

·        Proteomic Investigation of Falciparum and Vivax Malaria for Identification of Surrogate Protein Markers, PLoS ONE, Vol 7(8):e41751

·        Transcriptomic profiling of Medial Temporal Lobe Epilepsy, Journal of Proteomics and Bioinformatics, Vol.5(2); 031-039

·        Customisation of the Exome Data Analysis Pipeline Using a Combinatorial Approach, PLoS ONE, 7(1): e30080

·        De novo sequencing and assembly of Azadirachta indica fruit transcriptome, Curr Sci (India), 101(12): 1553

·        Gene Expression Profiling of Tuberculous Meningitis,  J Proteomics Bioinform 4: 098-105

·        A global in vivo Drosophila RNAi screen identifies NOT3 as a conserved regulator of heart function, Cell, 141(1) p142-153

·        Gene Expression Profiling of Gastric Cancer, Journal of Proteomics and Bioinformatics, Vol.4.4; 074-082

·        MultiMCS: A Fast Algorithm for the Maximum Common Substructure Problem on Multiple Molecules, J. Chem. Inf. Model., 51 (4), pp 788–806

·        Phenotype, Function and Gene Expression Profiles of PD-1hi CD8 T cells in Healthy Human Adults, Journal of Immunology, 186:4200-4212

·        A Genome-wide Drosophila Screen for Heat Nociception Identifies α2δ3 as an Evolutionarily Conserved Pain Gene, Cell, 143(4) p628-638

·        A systems biology based integrative framework to enhance the predictivity of in vitro methods for drug-induced liver injury, Expert Opin Drug Saf, Nov;7(6):647-62

·        B. Mishra, V. Chandru, C. Cantor, R. Hariharan, et al. (27 authors).A sense of life: computational and experimental investigations with models of biochemical and evolutionary processes, OMICS: A Journal of Integrative Biology Volume 7, Number 3, 2003.

·        Vijay Chandru, Abhi Dattasharma, V. S. Anil Kumar: The algorithmics of folding proteins on lattices. Discrete Applied Mathematics 127(1): 145-161 (2003)