Professor Bhushan Bonde (DFI)

Professor Bhushan’s research interests are primarily focused on application of artificial intelligence (AI) and machine learning (ML) for developing better disease treatments and using novel methods like Quantum Computing (QC) for application to Drug Discovery and AI Deep Learning methods.

His work involves performing meta and advanced data analytics using Machine and AI/Deep Learning techniques for drug discovery, Systems Biology modelling (E.coli, Yeast, M.TB, CHO cell line Genome Scale models), Genetics (GWAS/PheWAS) based Patient stratification, NGS data analysis (DNA-Seq, ChIP-Seq, RNA-Seq, and various NGS Seq data analysis), omics scale meta-analysis (Gene Set Enrichment/Causal Reasoning), Integrative -omics data analysis (-omics Integrome).

• Over 15 years of Python programming experience in Systems Biology, Bioinformatics and Computational Biology and modelling, with 12 publications, 10 international conference presentation and 10 industrial high impact projects
• HPC lead and administration of Linux (UNIX) Servers, Maintenance, High Performance Cluster (HPC) computing (CPU/GPU) for Scientific, Bioinformatics/mathematical computing applications and programming.
• Hybrid infrastructure management (Cloud/on-premise): Google, Azure and Amazon (AWS) cloud deployment, Azure-DevOps, Git and Agile project management. Container engineering for Scientific applications.

Student Supervision:

• Simulation of Small molecules on Quantum Computers, Oxford Uni. DPhil Project, Maranga Mokaya, DPhil candidate in Sustainable Approaches to Biomedical Science, Supervised by: Prof. Philip Biggin and Industry Supervisors Dr. Bhushan Bonde and Jiye She, UCB, September 2020
• Application of Causal Reasoning to Yeast Molecular Interaction Networks,
  Thesis: Effrosyni Karakitsou, Surrey Uni. MSc Systems Biology, Supervisors: Dr Emma Laing, Professor Andre Gerber, Industry Supervisor: Dr Bhushan Bonde, Sept 2015.

Selected Publications:

• GSMN-ML- a genome scale metabolic network reconstruction of the obligate human pathogen Mycobacterium leprae, PLoS Negl Trop Dis (2020), Borah K, Kearney J-L, Banerjee R, Vats P, Wu H, Dahale S, Bonde B et.al. 14(7): e0007871. https://doi.org/10.1371/journal.pntd.0007871
• RNASeq_similarity_matrix: visually identify sample mix-ups in RNASeq data using a ‘genomic’ sequence similarity matrix, Bioinformatics (2020) Nicolaas C Kist, Robert A Power, Andrew Skelton, Seth D Seegobin, Moira Verbelen, Bhushan Bonde, Karim Malki, Vol-36(6),P-1940-1941, https://doi.org/10.1093/bioinformatics/btz821
• Network analysis plays diverse roles in drug discovery,  Samiul Hasan, Bhushan K Bonde, Natalie S Buchan, Matthew D Hall, Drug Discov Today. 2012 Aug;17(15-16):869-74.
• ¹³C metabolic flux analysis identifies an unusual route for pyruvate dissimilation in mycobacteria which requires isocitrate lyase and carbon dioxide fixation. Beste DJ, Bonde B, Hawkins N, Ward JL, Beale MH, Noack S, Nöh K, Kruger NJ, Ratcliffe RG, McFadden J. PLoS Pathog. 2011 Jul;7(7).
• The application of next-generation sequencing technologies to drug discovery and development. Woollard PM, Mehta NA, Vamathevan JJ, Van Horn S, Bonde BK, Dow DJ. Drug Discov Today. 2011 Jun;16(11-12):512-9.
• Differential Producibility Analysis (DPA) of transcriptomic data in the context of genome scale metabolic reaction networks: Deconstructing the metabolic response of M. tuberculosis to the host environment. Bhushan Bonde, Dany Beste , Emma Laing, Andrzej Kierzek, Johnjoe McFadden. Bonde BK, Beste DJ, Laing E, Kierzek AM, McFadden J. PLoS Comput Biol. 2011 Jun;7(6):e1002060. Epub 2011 Jun 30.
• Selection of objective function in genome scale flux balance analysis for process feed development in antibiotic production. Chiraphan Khannapho, Hongjuan Zhao, Bhushan K Bonde, Andrzej M Kierzek, Claudio A Avignone-Rossa, Michael E Bushell, Metab Eng. 2008 Sep;10(5):227-33.
• The Genetic Requirements for Fast and Slow Growth in Mycobacteria. Dany J. V. Beste, Mateus Espasa, Bhushan Bonde, Andrzej M. Kierzek, Graham R. Stewart, and Johnjoe McFadden, PLoS ONE. 2009; 4(4): e5349.

• GSMN-TB: a web-based genome scale network model of Mycobacterium tuberculosis metabolism. Dany Beste, Tracy Hooper, UBhushan BondeU, Graham Stewart, Claudio Avignone-Rossa, Michael Bushell, Paul Wheeler, Steffen Klamt, Andrzej Kierzek and Johnjoe McFadden, Genome Biology, 2007, 8:R89
• Transcriptomic analysis identifies growth rate modulation as a component of the adaptation of mycobacteria to survival inside the macrophage, Dany Beste, Emma Laing, Bhushan Bonde, Claudio Avignone-Rossa, Michael Bushell and Johnjoe McFadden J. Bacteriology, 2007, 189(11), 3969-3976.
• Challenges to Be Faced in the Reconstruction of Metabolic Networks from Public Databases, Poolman, M. G., Bonde, B. K., Gevorgyan, A., Patel, H. H. and Fell, D. A. (2006), IEE Proc. Syst. Biol. 153, 379-384
• Patents in Pharmacy: The Indian Scenario, Bhushan K. Bonde and V. M. Aurangabadkar. The Eastern Pharmacists, 1999, Vol. XLII (501), 21-27