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A professor, specialist in bioinformatics with 15+ years of experience in both teaching and research in bioinformatics

Profile Summary

I am Dr. Md Afroz Alam, a certified digital teacher with the ICT Academy. I completed my PhD degree in bioinformatics from the Jaypee University of Information Technology, Solan (Himachal Pradesh) in 2009. I have 11 years of teaching experience at Karunya Institute of Technology and Sciences (KITS), Coimbatore, Tamil Nadu, and 4.5 years of online teaching experience at TeacherOn, Superprof, Teachnook EdTech, and the Nano Science and Technology Consortium (NSTC), as well as 19 years of research experience in bioinformatics. I have 24 research publications in reputed journals, 21 conference proceedings, and 2 book chapters. I have delivered 39 invited lectures at national conferences, seminars, and workshops. I have also participated in 29 programs and also organized 19 programs, such as workshops, seminars, conferences, and add-on courses, at the national and international levels. My area of expertise includes computer-aided drug design, molecular modeling and simulation, QSAR and pharmacophore modeling, biostatistics, R programming, and Unix and Linux. I have supervised 02 Ph.D. students, 23 M.Tech. projects, and 47 B.Tech. projects in the field of bioinformatics. I have also supervised 03 foreign interns who completed their internship project under my able guidance in the IAESTE scheme. My research interest is in the rational designing of lead molecules based upon protein modeling and computational screening of small molecules (drugs) using both structure and free energy calculations of the drug-target docking models. I do this using various algorithms but particularly specialize in Molecular Mechanics-Generalized Born/Surface Area (MM-GB/SA), linear interaction energy models, and Pharmacophore generation) and ligand-based approaches such as, pharmacophore design, 2D-QSAR (quantitative structure activity relationship), 3D-QSAR, similarity searches. Since last 15 years, I have been working on the molecular modeling on the mechanisms of action and biological activity study of podophyllotoxin and Quanizoline based drugs. In this period of time, I have developed various models for the prediction of biological activity of podophyllotoxin and Quanizoline derived drugs. Research work also includes biological sequence analysis, important 3D and 4D protein structure feature extractions for accurate prediction modalities. The use of Machine learning/AI, Artificial Neural Network, Support Vector Machine, Genetic algorithms based on pattern matching were very helpful for functional annotation of raw linear sequences. Prediction of therapeutic targets using comparative genomics and comparative metabolomics and design of candidate drug molecule against therapeutic targets are also an important component of my research area. My project also involved extensive bench-based electrophoretic analyses of DNA fingerprinting. Based on my laboratory data, I performed further computational analyses such as, RAPD, ISSR, SSR, AFLP, phylogenetic analysis. Then I combined chemical profiling of medicinal plants and finally mathematical modeling. Thus, my repertoire of basics is well suited to do extensive experience in successfully discovering new anti-cancer drugs and taking them from bench to bedside.

Subject Matter Expertise

• ★ Molecular Modeling
• ★ Chemoinformatics
• ★ Bioinformatics
• ☆ Molecular Docking
• ☆ Biostatistics
• ☆ Molecular Biology
• ☆ Omics
• ☆ Comparative Genomics
• ☆ Proteomics
• ☆ Genomics
• ☆ Next Generation Sequencing (NGS)
• ☆ Data Analysis
• ☆ Machine Learning
• ☆ Artificial Intelligence
• ☆ Systems Biology
• ☆ Structural Bioinformatics
• ☆ Phylogenetics
• ☆ R

Services

• Writing
• Research
• Data & AI

Writing Medical Writing, Technical Writing, General Proofreading & Editing

Research User Research, Scientific and Technical Research

Data & AI Predictive Modeling, Statistical Analysis, Data Visualization, Big Data Analytics, Data Cleaning, Data Processing

Work Experience

Mentor Bioinformatics

NSTC

August 2023 - Present

Tutor

TeacherOn

October 2020 - Present

Tutor

Superprof

July 2020 - Present

Assistant Professot

Karunya University

June 2009 - July 2020

Education

Ph. D (Bioinformatics)

Jaypee University of Information Technology

May 2005 - November 2009

Certifications

• Certified Digital Teaching Techniques

  ICT Academy

  https://verify.ictacademy.in/badge.aspx?p=DTT&c=0uFzVDv8W4jKFtQyCOwk

  July 2020 - Present

Publications

JOURNAL ARTICLE

Amitha Joy, S. Balaji, Md. Afroz Alam (2021). Interaction network of insulin resistance proteins with organophosphorus and chlorine pesticides . International Journal of Computational Biology and Drug Design.

(2020). Pan-genomic analysis of the species Salmonella enterica: Identification of core essential and putative essential genes . Gene Reports.

Pursuing M. Tech, Department of Biotechnology, Karunya Institute of Technology and Sciences, Coimbatore - Tamil Nadu, India., Neena Elsa Eapen, Md Afroz Alam*, Assistant Professor, Department of Biotechnology, School of Agriculture and Biosciences, Karunya Institute of Technology and Sciences, Coimbatore – 641114, Tamil Nadu, India. (2020). Identifying Structural Features of Sulforaphane Derivatives Based on QM Force Field for Predicting the Anti-Cancer Activity . International Journal of Recent Technology and Engineering (IJRTE).

Mendez, N., Alam, M.A.(2019). Virtual screening approaches towards the discovery of multi-target drug for Zika virus . Drug Invention Today. 12. (1). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 13-24.

Kaarthik, A., Balamurugan, P., Alam, Md.A.(2018). Quantitative structure activity relationship predictive models for antimitotic agent through machine learning on high-throughput screening of noscapine derivatives . Drug Invention Today. 10. (Special Issue 2). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 3003-3008.

Nixon Mendez, Md. Afroz Alam (2016). Structural Features of Quercetin Derivatives by Using Pharmaco-phore Modeling Approach . Open Pharmaceutical Sciences Journal.

Chand, Y., Alam, M.A., Tejaswini, Y.R.(2015). Performance comparison of artificial neural networks learning algorithms and activation functions in predicting severity of autism . Network Modeling Analysis in Health Informatics and Bioinformatics. 4. (1).

Md Afroz Alam, Department of Bioinformatics, Karunya University, Coimbatore, India, Yamini Chand (2012). Network biology approach for identifying key regulatory genes by expression based study of breast cancer . Bioinformation.

Naik, P. K., Alam, A., Malhotra, A., Rizvi, O.(2010). Molecular modeling and structure-activity relationship of podophyllotoxin and its congeners . Journal of Biomolecular Screening. 15. (5). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 528-540.

Naik, P.K., Alam, M.A., Singh, H., Goyal, V., Parida, S., Kalia, S., Mohapatra, T.(2010). Assessment of genetic diversity through RAPD, ISSR and AFLP markers in Podophyllum hexandrum: A medicinal herb from the Northwestern Himalayan region . Physiology and Molecular Biology of Plants. 16. (2). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 135-148.

Naik, P. K., Alam, M. A., Singh, H., Goyal, V., Parida, S., Kalia, S., Mohapatra, T.(2010). Assessment of genetic diversity through RAPD, ISSR and AFLP markers in Podophyllum hexandrum: A medicinal herb from the Northwestern Himalayan region . Physiology and Molecular Biology of Plants. 16. (2). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 135-148.

Alam, Md A., Gulati, P., Gulati, A. K., Mishra, G. P., Naik, P. K.(2009). Assessment of genetic diversity among Podophyllum hexandrum genotypes of the North-western Himalayan region for podophyllotoxin production . Indian Journal of Biotechnology. 8. (4). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 391-399.

Afroz Alam, Md, Naik, P. K.(2009). Molecular modelling evaluation of the cytotoxic activity of podophyllotoxin analogues . Journal of Computer-Aided Molecular Design. 23. (4). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 209-225.

Alam, Md A., Naik, P. K.(2009). Applying linear interaction energy method for binding affinity calculations of podophyllotoxin analogues with tubulin using continuum solvent model and prediction of cytotoxic activity . Journal of Molecular Graphics and Modelling. 27. (8). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 930-943.

Alam, Md.A., Naik, P.K.(2009). Applying linear interaction energy method for binding affinity calculations of podophyllotoxin analogues with tubulin using continuum solvent model and prediction of cytotoxic activity . Journal of Molecular Graphics and Modelling. 27. (8). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 930-943.

Alam, Md A., Naik, P. K., Mishra, G. P.(2009). Congruence of RAPD and ISSR markers for evaluation of genomic relationship among 28 populations of Podophyllum hexandrum Royle from Himachal Pradesh, India . Turkish Journal of Botany. 33. (1). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1-12.

Alam, Md.A., Gulati, P., Gulati, A.K., Mishra, G.P., Naik, P.K.(2009). Assessment of genetic diversity among Podophyllum hexandrum genotypes of the North-western Himalayan region for podophyllotoxin production . Indian Journal of Biotechnology. 8. (4). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 391-399.

Alam, Md.A., Naik, P.K., Mishra, G.P.(2009). Congruence of RAPD and ISSR markers for evaluation of genomic relationship among 28 populations of Podophyllum hexandrum Royle from Himachal Pradesh, India . Turkish Journal of Botany. 33. (1). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1-12.

Afroz Alam, M., Naik, P. K.(2009). Impact of soil nutrients and environmental factors on podophyllotoxin content among 28 Podophyllum Hexandrum populations of Northwestern Himalayan region using linear and nonlinear approaches . Communications in Soil Science and Plant Analysis. 40. (15-16). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 2485-2504.

Alam, A., Naik, P. K., Gulati, P., Gulati, A. K., Mishra, G. P.(2008). Characterization of genetic structure of Podophyllum hexandrum populations, an endangered medicinal herb of Northwestern Himalaya, using ISSR-PCR markers and its relatedness with podophyllotoxin content . African Journal of Biotechnology. 7. (8). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 1028-1040.

Quantitative structure activity relationship (QSAR) of cardiac glycosides: the development of predictive in vitro cytotoxic activity model.

Virtual screening approaches towards the discovery of multi-target drug for Zika virus.

Quantitative structure activity relationship predictive models for antimitotic agent through machine learning on high-throughput screening of noscapine derivatives.

CONFERENCE PAPER

Exploring Structural Properties of alginate derivatives based on QM/MM approach.