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Dr. Sanket P. Bapat

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Dr. Sanket P. Bapat

Dr. Sanket P. Bapat

Associate Professor

Overview

Prof. Sanket Bapat received the bachelor’s degree in Biotechnology and the master’s degree in Bioinformatics from the University of Mumbai. He worked as a project fellow in Haffkines Institute of Training, testing and Reseach, Mumbai where he worked on identifying target proteins in Swine Flu.
He later completed his Ph.D. from the premiere CSIR-National Chemical Laboratory and the Biotechnology and Bioinformatics Institute, Pune. The focus of the Ph.D. work was to have a complete study of protein-protein interactions in cancer using machine learning techniques and develop a robust classification and regression model. The pathway modeling approach was used to successfully analyze the conformational changes in the PPI and compute energy-profiles by studying it at a system level. His Ph.D. work won awards in International Conferences.
His research interests include Machine learning, Structural bioinformatics, Molecular dynamics, Cheminformatics, Proteomics, and Genomics studies. Along with knowledge of statistical and biochemical techniques, he has also published several research papers in peer-reviewed journals and written a book chapter to his credit. Apart from research, he has a strong background in academic and institutional teaching experience.

Qualifications
  • Ph.D. in Bioinformatics | Bioinformatics Division, CSIR-NCL & Dr. D.Y. Patil Institute Research, Pune| 2015 – 2019
    Guide: Dr. Renu Vyas
    Topic: Application of Machine Learning based methods for studying protein-protein interaction and pathway modeling of proteins related to cancer.
  • Master’s in Bioinformatics | Mumbai University, Mumbai| 2010 – 2012
  • Bachelor’s in Bioinformatics | Mumbai University, Mumbai| 2007-2010
Teaching: 11 years
Research: 7 years

Management skills and Experience

  • Member Secretary of Central MIT ADTU Alumni Association (2021-Present)
  • Core Member of Bioengineering Admission Cell, (2018 – Present)
  • Alumni Coordinator, Bioengineering Alumni Chapter (2021-Present)
  • Project Mentor for Smart India Hackathon (SIH)
  • Industrial Liasoning officer for MIT-ADT University, Pune.
  • Organized an International Conference on Recent Trends in Bioengineering (ICRTB 2018), Feb 17, 2018 at MIT-ADT University, Pune.
  • Organized the second International Conference on Recent Trends in Bioengineering (ICRTB 2018), Feb 16, 2019 at MIT-ADT University, Pune.
  • Organized a Medical Device Hackathon (MEDHA) August 4, 2018 at MIT- ADT University in collaboration with BETiC Centre IITB and COEP Pune.
  • Organized two days International Conference on Recent Trends in Bioengineering (ICRTB 2018), Jan 31st-1st Feb, 2020.
  • Project Mentor for the Drug Discovery Hackathon (DDH) 2020 which was a joint initiative of AICTE, CSIR and supported by Office of Principal Scientific Advisor, Govt. of India, NIC and MyGov.

Industry Projects

  • Currently a Project Mentor for Machine Learning Project with Bangalore based company, India, 2023 – 2024
  • Project Mentor for a project ‘Analyzing the quality and accuracy of chemical identifiers & product quality assurance’ with Viridis Chem SFO, USA, 2022-23.
  • Project Mentor for a project ‘Collection and curation of global regulatory and hazard-related data, and compilation of reactivity among functional groups’’ on toxicity with Viridis Chem SFO, USA, 2020-21.
  • Project Mentor for a project ‘Comparative study of Predictive models using machine-learning techniques to measure toxicity related endpoints’ with Viridis Chem SFO, USA, 2019-20.
  • Project Mentor for a project on computational toxicity with Viridis Chem SFO, USA.

Awards

  • Young Scientist/Achiever Award, MIT-ADT University, Pune – 8th August 2023
  • Smart Pune Health Hackathon 2023, NITI Aayog National Level Event – 14th February 2023
  • Problem Statement: Application of Machine Learning in Neurodegenerative diseases. Secured Special Recognition Award
  • Secured Second place at State Level in Avishkar Research Convention, Mumbai University on 9th February 2010.
  • Secured Best Paper Award in International Conference on Recent Trends in Bioengineering, MIT ADT University Pune on 1st February 2020.
  • Secured Best Paper Award in International Conference on Recent Trends in Bioengineering, MIT ADT University Pune on 17th February 2019.
  • Secured Best Paper Award in International Conference on Recent Trends in Bioengineering, MIT ADT University Pune on 16th February 2018.

Invited Talks and workshops

  • Invited to give a guest talk by Department of Biological Sciences, SDSOS NMIMS, Mumbai.
  • Invited as a Speaker in National webinar on Drug Design and MD Simulations with Supercomputer, organized by Kathmandu University, Nepal.
  • Invited as a Speaker in National webinar on Molecular Docking organized by Department of Chemistry of Annai college of Arts and Science, Tamil Nadu.
  • Invited as a Panel Member in Seminar conducted at Haffkines Institute of Training, Testing and Research on topic Bioengineering: An EmergingDiscipline.
  • Conducted a workshop on Bioinformatics perspective in Ichthyology at ICAR- Central Institute of Fisheries Education,Mumbai.
  • Invited to give a talk on Exploring the world of Bioinformatics: Molecular Docking for a workshop conducted at Department of Biotechnology in SVKM Mithibai College,Mumbai.
  • Conducted a workshop on ‘Advance Techniques in Bioinformatics’ at Department of Life Science in Sophia College, Mumbai.

Other Notable Activities

  • Invited to give a talk on Research & Development in 2025 for Viksit Bharat Conference.
  • Invited to give a talk on Molecular Modeling in 2022 by IGEM League, Boston.
  • Peer Reviewer for Molecular Diversity journal (Springer Publication)
  • Peer Reviewer for Computers in Biology andMedicine (Elsevier Publication)
  • Board of Studies member for Bioinformatics department of G.N. Khalsa college, Mumbai.
  • Number of Masters students guided:5
  • Reviewer for Manav: A human Atlas initiative by Department of Biotechnology (DBT) and Persistent Labs, Pune.

Technical Skills

Computational Skills Worked on Windows and Linux platforms. Experience of working on cluster systems for High Performance Computing(HPC) and Python. Conversant with major chemoinformatics and bioinformatics techniques related to virtual screening such as Protein-protein interactions, network analysis, Molecular modeling studies, QSAR, Sequence analysis, Homology Modeling, , Text Mining, QM/QC methods, statistical and machine learning models.
Bioinformatics Tools Schrödinger Maestro, MOE, AutoDock Vina, GLIDE, GROMACS, NAMD, CytoScape, VMD, Xmgrace, Inkscape,GIMP.
Chemoinformatics Tools ChemAxon Marvin Suite, ChemDraw, ScreeningAssistant.
MachineLearning Tools RapidMiner, Eureqa Formulize,Weka.
Statistical Tools R Software, SPSS.
Wet Lab Skills Knowledge and trained in wet lab biochemical, molecular biology and biotechnology techniques.

Selected Conferences and Workshops

  • Presented technical paper titled ‘Bioinformatics tool for identification of virulent sequence in viral genome’ at Computer Society of India National conference, Mumbai held on February2014.
  • Attended National Conference ‘Molecular Pathways to Therapeutics: Paradigms and Challenges in Oncology’ held on 11-14th February 2015 at Advanced Centre for Treatment, Researchand Education in Cancer (ACTREC), NaviMumbai.

Publications

  • Bapat, S. “Modeling of protein complexes involved in signaling pathway for Non-Small Cell Lung Cancer” (2019) In. Vyas, R. (Eds.) Advances in Bioengineering, Springer, ISBN: 978-981-15-2062-4
  • Bapat, S., Vyas, R., Karthikeyan, M., “Exploring energy profiles of protein-protein interactions (PPIs) using DFT method.” (2019) Letters in Drug Design & Discovery 16 (6), 670-677
  • Bapat, S., Vyas, R., Karthikeyan, M. , Muthukrishnan, M., “Synthesis, Biological Evaluation and Molecular Modeling Studies of Novel Chromone/Aza-Chromone Fused α- Aminophosphonates as Src Kinase Inhibitors” (2019) Journal of Scientific and Industrial Research- NISCAIR 78 (02), 111-117
  • Bapat, S., et al. “2018 Index IEEE/ACM Transactions on Computational Biology and Bioinformatics Vol. 15.” IEEE/ACM Transactions on Computational Biology and Bioinformatics 16.1 (2019): 1.
  • Nalla, V., Shaikh, A., Bapat, S., Vyas, R., Karthikeyan, M., Yogeeswari, P., Sriram, D. & Muthukrishnan, M., (2018). Identification of potent chromone embedded [1, 2, 3]-triazoles as novel anti-tubercular agents. Royal Society Open Science, 5(4),p.171750.
  • Tiwary, S., Naniwadekar, M., Sonolikar, R., Bapat, S., Yerudkar, A., Kamble, S. P., & Tambe, S. S. (2018). Prediction of Rate Constants of Photocatalytic Degradation of Pharmaceutical Pollutants by Artificial Intelligence based Genetic Programming Formalism. Current Environmental Engineering, 5(1),58-67.
  • Vyas, R., Bapat, S., Karthikeyan, M., Tambe, S., & Kulkarni, B. D. (2016) Application of Genetic Programming (GP) formalism for building disease predictive models from protein- protein interactions (PPI) data. Transactions on computational biology andBioinformatics.
  • Vyas,R.,Bapat,S.,Jain,E.,Karthikeyan,M.,Tambe,S.,&Kulkarni,B.D.(2016).Buildingand analysis of protein-protein interactions related to diabetes mellitus using support vector machine, biomedical text mining and network analysis. Computational Biology and Chemistry, 65, 37-44.
  • Goel, P., Bapat, S., Vyas, R., Tambe, A., & Tambe, S. S. (2015). Genetic programming based quantitative structure–retention relationships for the prediction of Kovats retention indices. Journal of Chromatography A, 1420,98-109.
  • Vyas, R., Bapat, S., Jain, E., S Tambe, S., Karthikeyan, M., & D Kulkarni, B. (2015). A Study of Applications of Machine Learning Based Classification Methods for Virtual Screening of Lead Molecules. Combinatorial chemistry & high throughput screening, 18(7),658-672.
  • Karthikeyan, M., Nimje, D., Pahujani, R., Tyagi, K., Bapat, S., Vyas, R., & Pillai Padmakumar, K. (2015). Chemoinformatics Approach for Building Molecular Networks from Marine Organisms. Combinatorial chemistry & high throughput screening, 18(7), 673-684.
  • Chavan,R.,Bapat,S.,PatilV.&Chowdhary,A.(2015). Computationalanalysisininfluenzavirus.Receptor: Clinical Investigation ; 4: e1574. doi: 10.14800/rci.1574, 2017.
  • Chavan, R., Samant, L., Bapat, S., & Chowdhary, A. (2015). Protein Modeling and Docking of Curcurin Against Neuraminidase, Hemagglutinin Proteins of Pandemic InfluenzaH1N1/2009. Journal of Pharmaceutical Sciences and Research, 7(2), 70
  • Chatterjee, P., Samant, L., Bapat, S., Mukherjee, S. & Chowdhary, A. (2014). Computational 3D Modelling and In Silico Characterization of Human Interferon Induced Transmembrane Proteins,Research Journal of Pharmaceutical, Biological and Chemical Sciences. 5(2), 1142-1154
  • Bapat, S., Ghanashyam, M., Shalmali, P., & Ankita, I. (2014). Bioinformatics Tool for Identification of Virulent Sequence in ViralGenome.

Additional Academic Information

  • Qualified Ph.D. Entrance Test (PET), 2013 in Life Sciences from Mumbai University.
  • Currently pursuing Science Journalism course by Indian Science Communication Society, Lucknow.

Selected Peer Reviewed Papers

  • Saha, S., Bapat, S., Vijayasarathi, D. et al. Exploring potential biomarkers and lead molecules in gastric cancer by network biology, drug repurposing and virtual screening strategies. Mol Divers (2024).https://doi.org/10.1007/s11030-024-10995-6
  • Kotharkar N., Bapat S., Vyas R., Pathak Pranav, A Comparative Chemoinformatics Analysis of compounds extracted from Nyctanthes arbor-tristis, Combinatorial Chemistry & High Throughput Screening (2023); 26
  • Wadapurkar, R., Bapat, S., Mahajan, R., & Vyas, R.. Machine learning approaches for prediction of ovarian cancer driver genes from mutational and network analysis. Data Technologies and Applications, (2023)
  • Shaikh N, Bapat S, Karthikeyan M, Vyas R. A Review on Computational Analysis of Big Data in Breast Cancer for Predicting Potential Biomarkers. Current Topics in Medicinal Chemistry.(2022);22 (21):1793-1810.
  • Panchal R, Bapat S, Mukherjee S, Chowdhary A. In silico binding analysis of lutein and rosmarinic acid against envelope domain III protein of dengue virus. Indian J Pharmacol. (2021) Nov-Dec;53(6):471-479
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