MIT School of Bioengineering Sciences & Research, MIT-ADT University, Pune
- 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
Management skills and Experience
- 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.
- Project Mentor for a project on computational toxicity with Viridis Chem SFO, USA.
- 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
- 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.
|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.
- 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.