Research

Our Research

Our research leverages cutting-edge computational tools and AI to tackle pressing challenges in biology and medicine. Key areas include:

• Genomics and Proteomics: Identifying novel drug targets and biomarkers using integrated genomic and proteomic approaches.

• Antimicrobial Resistance: Developing strategies to combat antibiotic-resistant pathogens like Klebsiella pneumoniae and Neisseria gonorrhoeae.

• AI in Biology: Applying machine learning and deep learning for prognostic classification and drug discovery.

• Viral Pathogenesis: Studying SARS-CoV-2 variants (Omicron, Delta) and emerging viruses like monkeypox and HMPV.

• Systems Biology: Network analysis to uncover hub genes in diseases like Alzheimer’s, autism, and cancers.

Current projects include uncovering novel drug targets in antibiotic-resistant Yersinia pestis and computational prediction of COVID-19 severity using imaging and gene expression data.

Key Research Areas

• Computational Drug and Vaccine Discovery

• Antimicrobial Resistance Mechanisms and Target Identification

• Long COVID and Multi-Omics Biomarker Discovery

• Artificial Intelligence and Deep Learning in Healthcare

• Host-Pathogen Interaction & Infectious Disease Modeling

• Machine Learning and Network Biology for Disease Prediction

Current and Recent Research Projects

• AI-Driven Prognostic Classification of COVID-19 – Deep learning applied to chest X-ray data for patient severity prediction.

• Computational Drug Discovery for Klebsiella pneumoniae – Target identification and screening of traditional Chinese medicine compounds.

• GPCR-based Drug Repurposing for Long COVID – In silico screening of phytochemicals and repurposed drugs for persistent post-COVID symptoms.

• Multi-Omics Pathway Analysis for Alzheimer’s Disease and COVID-19 – Comparative transcriptomics and network analysis.

Grants and Funded Research

• Ministry of Higher Education, Malaysia (FRGS): Genome-wide functional annotation of novel proteins from Nepenthes ampullaria (Completed)

• MSU Seed Grant: In silico discovery of drug targets in antibiotic-resistant Yersinia pestis (Ongoing)

Collaborations & Networks

Dr. Suresh Kumar has established extensive international collaborations across Asia, Europe, and North America, actively contributing to global research in bioinformatics, infectious diseases, and computational biology. These collaborations have led to co-authored publications, joint research projects, and invited talks at international platforms. Notable engagements include:

• Austria: Collaborative bioinformatics research during Ph.D. at the University of Vienna and workshops under the Austrian Genome Programme in association with IMP and IMBA.
  
  

• United States: Former Research Assistant Professor at Texas State University; collaborations with M.D. Anderson Cancer Center and Xiphophorus Genetic Stock Center (USA) on RNA-seq, SNP, and triploid medaka projects.

• Taiwan: Ongoing collaboration with Dr. K.J. Senthil Kumar, Associate Professor, Center for General Education, National Chung Hsing University, Taichung, Taiwan, on integrative genomics and drug target research.
  
  

• France and UK: Research roles at INIBAP, Montpellier (France) and University of Leicester (UK) in early-career molecular genomics research.
  
  

• China: Ongoing academic and doctoral supervision collaborations with Henan University of Chinese Medicine and international Ph.D. students from China.
  
  

• Malaysia: Core member of national research consortiums, academic leadership at Management & Science University, and active organizer of international bioinformatics symposiums (INCOBIOM, InBHIs).
  
  

These partnerships strengthen his interdisciplinary contributions to emerging challenges in antimicrobial resistance, vaccine discovery, AI in diagnostics, and host-pathogen interactions.

Publications

Our group has published over 60 peer-reviewed articles in high-impact journals. Selected publications include:

• Kumar, S*., Subramaniam, G., & Senthil Kumar, K. J. (2025). The resurgence of monkeypox clade Ib: a global health emergency and concern. Archives of Virology, 170(4), 84.

• Simbun, A., & Kumar, S*. (2025). Artificial Intelligence-Driven Prognostic Classification of COVID-19 Using Chest X-rays: A Deep Learning Approach. arXiv preprint arXiv:2503.13277.

• Kumar, S*., Subramaniam, G., & Kumar, K. S. (2025). Human Metapneumovirus (HMPV) Outbreak: An Urgent Call for Enhanced Surveillance and Public Health Action. Journal of Medical Virology, 97(2), e70199.

• Kumar, S*., Thambiraja, T. S., Karuppanan, K., & Subramaniam, G. (2022). Omicron and Delta variant of SARS‐CoV‐2: a comparative computational study of spike protein. Journal of Medical Virology, 94(4), 1641-1649. (Highly cited)

• Li, Y., Kumar, S*., & Zhang, L. (2024). Mechanisms of Antibiotic Resistance and Developments in Therapeutic Strategies to Combat Klebsiella pneumoniae Infection. Infection and Drug Resistance, 1107-1119.

For a complete list, visit our Google Scholar profile.

Selected Publications under research themes

🔹 1. Computational Drug Discovery & Vaccine Design

This theme forms the backbone of Dr. Suresh’s scientific inquiry. It involves the in silico identification of drug targets, molecular docking, simulation-based screening of therapeutic compounds, and design of multi-epitope vaccine candidates.

Key Publications:

• Li Y., Kumar S.*, Zhang L. (2024). Shikimate Kinase 1 from Klebsiella pneumoniae as a New Drug Target. IJPER, 58(3), 1110-1120.
  
  

• Kumar S.* (2020). Broad-Spectrum Drug Targets Against Vibrio Cholerae by Integrated Genomics and Proteomics. MJMHS, 16(2).
  
  

• Kumar S.* (2020). Drug and Vaccine Design against SARS-CoV-2 Spike Protein. Preprints.org.
  
  

• Kumar S.*, Omeershffudin U.N.M. (2020). Functional and Toxicity Prediction of Shigella Dysenteriae Proteins. IJMTLM, 23.
  
  

🔹 2. Antimicrobial Resistance (AMR) and Pathogen Genomics

Dr. Suresh has published extensively on antibiotic resistance mechanisms, highlighting both resistance gene characterization and target identification in multidrug-resistant pathogens.

Key Publications:

• Li Y., Kumar S.*, Zhang L. (2024). Mechanisms of Antibiotic Resistance in Klebsiella pneumoniae. IDR, 1107–1119.
  
  

• Omeershffudin U.N.M., Kumar S.* (2023). AMR in Neisseria gonorrhoeae. Arch Microbiol, 205(10), 330.
  
  

• Chen L., Kumar S.*, Wu H. (2023). Review on Antibiotic Resistance and Promising Antibiotics. Arch Microbiol, 205(11), 356.
  
  

• Kumar S.*, Omeershffudin U.N.M. (2022). DNA Adenine Methyltransferase as a Drug Target in K. pneumoniae. Genomics & Informatics, 20(4).
  
  

🔹 3. AI and Machine Learning in Genomics & Health Informatics

Dr. Suresh integrates AI, deep learning, and support vector machines (SVMs) into diagnostic modeling and genomic data mining, often in the context of pandemic response.

Key Publications:

• Simbun A., Kumar S.* (2025). AI-Driven Prognostic Classification of COVID-19 Using Chest X-rays. arXiv:2503.13277.
  
  

• Kumar S.* (2024). Prediction of Oligomeric Status by Sequential Minimal Optimization for SVM. bioRxiv.
  
  

• Kumar S., et al. (2023). Deep Learning in Computational Biology: Advances and Challenges. arXiv:2310.03086.
  
  

🔹 4. Long COVID, Host-Pathogen Interactions & Multi-Omics Integration

Dr. Suresh explores the molecular mechanisms underlying Long COVID, including immune modulation, GPCR signaling, and bioinformatics-based drug repurposing.

Key Publications:

• Das S., Kumar S.* (2023). Gene Expression and Symptoms in Long COVID. J Med Virol, 95(9), e29077.
  
  

• Guruparan D., Kumar S.* (2024). GPCR Genes and Pathways in Long COVID. Preprints.
  
  

• Davagandhi D., Kumar S.* (2024). Natural Compounds for Long COVID Based on Hub Gene Biomarkers. Preprints.
  
  

• Aaron P., Kumar S.* (2024). Docking Study of Phytochemicals for Long COVID. Preprints.
  
  

🔹 5. Structural Bioinformatics and Protein Modeling

A long-standing area of strength, Dr. Suresh has developed 3D models of novel proteins, identified druggable sites, and studied protein disorder and interaction networks.

Key Publications:

• Kumar S.* (2015). Binding Analysis of Orphan Human CYP4X1. BMC Research Notes, 8.
  
  

• Kumar S.* (2011). Comparative Modeling of CYP4V2 Protein. Bioinformation, 7(7), 360.
  
  

• Kumar S.* (2017). Metal Ion Binding Sites Using Random Forest Model. Genomics & Informatics, 15(4), 162.
  
  

🔹 6. Systems Biology & Network-Based Approaches

Dr. Suresh has applied PPI networks, enrichment analysis, and pathway exploration for cancer, infection, and neurological conditions.

Key Publications:

• Shajahan S.R., Kumar S.* (2024). COVID-19 and Alzheimer’s Disease: A Network-Based Review. Front Aging Neurosci, 15.
  
  

• Mathavan S., Kue C.S., Kumar S.* (2021). Hub Genes in Lip and Oral Cavity Cancer. Genomics & Informatics, 19(1).
  
  

• Wee J.J., Kumar S.* (2020). PPI Network in Alzheimer’s Disease. Genomics & Informatics, 18(4).
  
  

🔹 7. NGS, Transcriptomics, and Gene Expression

This theme highlights applications of next-generation sequencing in gene discovery, differential expression, and comparative genomics.

Key Publications:

• Kumar S.* et al. (2022). Structural-based Computational Assessment of Omicron Variants. J Med Virol, 94(10).
  
  

• Bakar S.A., Kumar S., et al. (2016). DNA-seq Analysis of Garcinia mangostana. Genomics Data, 7, 62.
  
  

• Pabuwal V., Kumar S., et al. (2013). Transcriptomic Response to Cr(VI) Exposure in Whale Skin Cells. Aquatic Toxicology, 134.
  
  

🔹 8. Supervision and Capacity Building

Dr. Suresh has:

• Supervised 4 Ph.D., 2 M.Sc., and 100+ B.Sc. projects in bioinformatics and computational biology.
  
  

• Served as a mentor and examiner for research across Malaysia, India, and China.
  
  

• Organized international symposia like InBHiS, INCOBIOM, and IMPaCHS.