Overview
As data forms the basis of knowledge today, a global race is underway for data acquisition and analytics. Bioinformatics is emerging as a strategic area of knowledge discovery, leveraging advancements in machine learning and artificial intelligence. As a data- and analytics-driven department, we aspire to become a Centre of Excellence in bioinformatics research and education by generating knowledge through data-driven research initiatives and imparting quality education and training to produce competent, skilled personnel in bioinformatics. Some key research areas in the department include computational genomics, computational drug discovery, computational systems and network biology, and biostatistics and data analytics (focusing on statistical modelling, experimental design, and quantitative analysis of biological, biomedical, and health-related data). The department also explores interdisciplinary areas, including biomedical and health data analytics, ecological data analysis, and the applications of machine learning and artificial intelligence. It actively engages in collaborative research and training initiatives with academia and industry. The department also offers an active, research-intensive MSc Bioinformatics program.
Programs
- MSc Bioinformatics
Thrust Areas
- Bioinformatics
- Computational Biology
- Data Analytics
- Computational Drug Discovery
- Computational Systems Biology
- Computational Genomics
- Statistical Modelling in Biomedical Research
- Clinical and Epidemiological Data Analysis
- Health Informatics
- Ecoinformatics
Dr. R Shyama Prasad Rao
- Designation Professor
- Email shyamaprasad.rao@nitte.edu.in
- Joining date
My research interests are in bioinformatics, computational biology, and data analytics.
- Doctor of Philosophy (Biochemistry), University of Mysore, 2007
- Master of Science (Bioscience), Mangalore University 1999
- Nitte (Deemed to be University), Mangaluru, India – 2022 to present
- Yenepoya (Deemed to be University), Mangaluru, India – 2014 to 2022
- University of Missouri-Columbia, USA – 2012 to 2014rn
- Hong Kong Baptist University, Hong Kong – 2011 to 2012
- Aarhus University, Denmark – 2007 to 2010
- Central Food Technological Research Institute, Mysore, India – 2000 to 2005
Bioinformatics, Computational Biology, Data analytics
- Rao RSP*, Pinto L, Suravajhala R, Shenoy BD, Sashindran VK, Ghate SD (2025). Azole resistance: Insights from Y132 substitutions in Candida sterol 14α-demethylase utilizing molecular dynamics simulations. Journal of Biomolecular Structure and Dynamics 43:2479847.
- Rao RSP*, Pinto L, Shastry RP, Dakal TC, Suravajhala PN, Sashindran VK, Ghate SD (2025). Azole resistance: Patterns of amino acid substitutions in Candida sterol 14α-demethylase. Antonie van Leeuwenhoek 118:68.
- Rao RSP*, Ghate SD, Pinto L, Suravajhala P, Patil P, Shetty P, Ahsan N (2024). Extent of virulence and antibiotic resistance genes in Helicobacter pylori and campylobacteria. Current Microbiology 81:154.
- Ghate SD, Pinto L, Alva S, Srinivasa MG, Vangala RK, Naik P, Revanasiddappa BC, Rao RSP* (2024). In silico identification of potential phytochemical inhibitors for mpox virus: Molecular docking, MD simulation, and ADMET studies. Molecular Diversity 28:4067-4086.
- Rao RSP*, Ghate SD, Shastry RP, Kurthkoti K, Suravajhala P, Patil P, Shetty P (2023). Prevalence and heterogeneity of antibiotic-resistant genes in Orientia tsutsugamushi and other rickettsial genomes. Microbial Pathogenesis 174:105953.
Undergraduate
• Bioinformatics
Postgraduate
• Bioinformatics: Programming and Algorithms
• Biostatistics and Data Analytics
• Molecular Evolution
• Bioinformatics
Postgraduate
• Bioinformatics: Programming and Algorithms
• Biostatistics and Data Analytics
• Molecular Evolution
Dr. Gollapalli Pavan
- Designation Assistant Professor Grade II
- Email gollapallipavan@nitte.edu.in
- Joining date 01-07-2025
Dr. Gollapalli Pavan, an accomplished academic and researcher, currently serves as an Assistant Professor Grade-II at the Center for Bioinformatics, Nitte (Deemed to be University). With over 8 years of teaching and 7 years of post-PhD research experience, I have developed a deep expertise in the fields of integrative genomics, computational systems medicine, and computational drug design. Dr. Pavan academic foundation is rooted in excellence, evidenced by my PhD in Bioinformatics from Kuvempu University. During his master's degree in Bioinformatics, he was awarded a Dr. B.R. Abdul Rehman gold medal for securing the first rank. His doctoral research was supported by the prestigious INSPIRE fellowship from the Department of Science and Technology (DST). More recently, he received the Teachers Associateship for Research Excellence (TARE) from SERB, Government of India. His current research is focused on three broad computational challenges of biological network analysis: (1) Recognizing missing edges in a network and extracting key topological modules and pathways hidden inside networks to forecast protein function and disease-causing genes; (2) Pan-genomic based network biology approaches for enhanced prediction of antimicrobial resistance patterns of critical priority pathogens; (3) Understanding the evolutionary and developmental histories of molecular interactions between the gastrointestinal cells and host.
- Doctor of Philosophy (Bioinformatics), Kuvempu University, 2017
- Master of Science in Bioinformatics
- Assistant Professor Grade II, Nitte University Centre for science education and research, Mangaluru (2025- Till date)rn
- Assistant Professor Grade II, Centre for Bioinformatics, Nitte (Deemed to be University), Mangaluru (2023- 2025)
- Scientist Grade-I, Centre for Bioinformatics and Biostatistics, Nitte (Deemed to be University), Mangalore (2019-2023)
- Assistant Professor Research, Department of Bioinformatics, Vignan’s Foundation for Science, Technology and Research (Deemed to be University), Vadlamudi-522203, Guntur, Andhra Pradesh, India (2018-2019)rn
- Guest Faculty, Department of Biotechnology and Bioinformatics, Jnana Sahyadri Campus, Kuvempu University, Shankaraghatta-577451, Shivamogga, Karnataka, India (2009-2011)rn
- Integrative genomics and computational systems medicine
- Multi-Omics and Genome-Scale Modelling
- Computational Molecular Design, Molecular Dynamics simulations and Computational Drug Design
- Best Research Publication Award for the year 2013-2014 by Nitte (Deemed to be University)
- Awarded Teachers Association for Research Excellence (TARE) fellowship by the Science and Engineering Research Board (SERB), Government of India, October 2022.
- Awarded Inspire fellowship by the Department of Science and Technology (DST) in 2011-2012 to pursue Ph. D. program.
- Awarded a gold medal (Professor B. R. Abdul Rehaman Gold medal) for excellence in performance in M. Sc Bioinformatics, scoring the highest marks and getting the first rank.
- International Society for Computational Biology (ISCB)
- African Society for Bioinformatics and Computational Biology (ASBCB)
- Bioinformatics Club for experimenting scientists (BIOCLUES)
- Kumar, M., Ballamoole, K. K., Shetty, V. A., Rao, R. S. P., & Gollapalli, P. (2025). Perspective on integrated multi-omics approaches and constraint-based modeling to explore metabolic functionality on the evolution of bacterial antibiotic resistance. Microbial pathogenesis, 208, 107999. https://doi.org/10.1016/j.micpath.2025.107999
- Bhat, T., Kumar, M., Ballamoole, K. K., Deekshit, V. K., & Gollapalli, P. (2025). Pangenome-based network analysis of Acinetobacter baumannii reveals the landscape of conserved therapeutic targets. Molecular diversity, 10.1007/s11030-025-11252-0. Advance online publication. https://doi.org/10.1007/s11030-025-11252-0
- Kumar, M., Ashok, A. K., Bhat, T., Ballamoole, K., & Gollapalli, P. (2025). Computational-driven discovery of AI-2 quorum sensing inhibitor targeting the 5'- methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) to combat drug-resistant Helicobacter pylori. Computers in biology and medicine, 184, 109409. https://doi.org/10.1016/j.compbiomed.2024.109409
- Ashok, A. K., Gnanasekaran, T. S., Santosh Kumar, H. S., Srikanth, K., Prakash, N., & Gollapalli, P. (2024). High-throughput screening and molecular dynamics simulations of natural products targeting LuxS/AI-2 system as a novel antibacterial strategy for antibiotic resistance in Helicobacter pylori. Journal of biomolecular structure & dynamics, 42(6), 2913–2928. https://doi.org/10.1080/07391102.2023.2210674
- Prithvisagar, K. S., Gollapalli, P., D'Souza, C., Rai, P., Karunasagar, I., Karunasagar, I., & Ballamoole, K. K. (2023). Genome analysis of clinical genotype Vibrio vulnificus isolated from seafood in Mangaluru Coast, India provides insights into its pathogenicity. The veterinary quarterly, 43(1), 1–17. https://doi.org/10.1080/01652176.2023.2240389
https://scholar.google.com/citations?hl=en&user=lRFSujkAAAAJ&view_op=list_works&sortby=pubdate
Web of Science:
https://www.webofscience.com/wos/author/record/M-2161-2018
Scopus: https://www.scopus.com/authid/detail.uri?authorId=57202726598
PhD students: 03
PG Students: 03
UG Students: 05
PG Students: 03
UG Students: 05
Undergraduate- Bioinformatics
Postgraduate- Biological information and databases,
computational genomics, computer aided-drug discovery,
computational systems biology
Postgraduate- Biological information and databases,
computational genomics, computer aided-drug discovery,
computational systems biology
Extramural Funding-
- Science and Engineering Research Board (SERB) for funding under Teachers Associateship for Research Excellence (TARE) (File Number: TAR/2022/000231) approved project entitled “Estimating differential metabolic functionality in antibiotic-resistant Helicobacter pylori through integrated experimental and computational analysis” dated 06.10.2022 for three years.
- Science and Engineering Research Board (SERB) for funding under Core Research Grant (File Number: CRG/2022/000259) approved project entitled “Novel paradigms for the development of antioxidant-based radioprotective agent by targeting Nrf2 for ameliorating radiation-induced damages” dated 1
- NUFR1 project entitled “Uncovering metabolic essentiality of SARS-CoV-2 towards discovering new drug targets and drugs – An approach of systems biology to precision medicine” funded by Nitte (Deemed to be University). Sanction Order No: N/RG/NUFR1/KSHEMA/2020/04 dated 05-11-2020. Status: Completed
Books and Book Chapter
Invited/ guest lecturers delivered
- Gollapalli, P., Prithvisagar, K.S., Kumar, B.K. (2023). Ready Reckoner for Using Bioinformatics Tools in Fish and Shellfish Microbiome Analysis. In: Diwan, A., Harke, S.N., Panche, A. (eds) Microbiome of Finfish and Shellfish. Springer, Singapore. https://doi.org/10.1007/978-981-99-0852-3_5
- Gollapalli Pavan, Manjunath Chavadi, Manjunatha Hanumanthappa and Manjula Ramu. “Next Generation Sequencing for Strain Tracking and Community Profiling of Food Microbes”. In “Microbial Bioinformatics resources for food safety and production” Foodborne pathogens and food related microorganisms. CRC Press, Florida, USA / ISBN: 978-0-367-35118-2, 2023 (1st Edition).
- Hulikal Shivashankara Santosh Kumar, Rachana Shankaraghatta Nagaraj and Gollapalli Pavan. “Frontiers in current aspects of antimicrobial peptides from insects and their therapeutic perspectives”. In “Futuristic Trends in Biotechnology” under IIP Proceedings, Volume 2, Book 26, Part 1, Chapter 10, Nov 2022, ISBN: 978-93-9563283-6.
Invited/ guest lecturers delivered
- Delivered an invited lead lecture on "Integrative Genomics, Computational Drug Design, and Systems Medicine" at the ANRF-PAIR Sponsored Two days National Symposium on “Drug Discovery and Development” held from 14th to 15th October 2025, organized by the Departments of Biochemistry, Biotechnology, Microbiology, Organic Chemistry, Food and Nutrition, and Mathematics at Jnanasiri Campus, Tumkur University, Bidarakatte, Tumakuru.
- Delivered an invited talk at “a workshop on scientific research report writing” as a resource person during Biotech Forum validation organized by the Department of Biotechnology and Bioinformatics, Kuvempu University, Shankaraghatta on 05-10-2023.
- Delivered an invited talk as a key speaker at “International Conference on Emerging Trends in Life Sciences (ICETLS-2020) – Virtual Mode” on 1516 Dec. 2020 organized by the Department of Botany, Telangana University, Dichpally, Nizamabad-503 322, Telangana.
- Invited as a key speaker for the “Technical Hands-on Workshop on Biomarker Discovery” by Bioschoarz Pvt Ltd., Hyderabad and PathGene Healthcare Pvt Ltd. Tirupathi on 18th and 19 October 2019 at Tirupathi, Andhra Pradesh, India.
- Delivered an invited lecture on “Bioinformatics and Genomics”, on 12-102019 at the Department of Biochemistry, K. S. Hegde Medical Academy, Nitte University, Deralakatte, Mangalore-575018, Karnataka.
- Delivered an Invited special lecture on “Bioinformatics”, on 06-03-2019 at the P.G. Department of Biotechnology and Microbiology, Karnataka University, Dharwad.
- Delivered a guest lecture on “Nucleic acid analysis and protein sequence analysis” at the Department of Biotechnology, Kuvempu University, Shivamogga, Karnataka for MSc. (Biotechnology) students on 15th to 17th November 2018.
Dr. Caroline DSouza
- Designation Assistant Professor G-1
- Email caroline.dsouza@nitte.edu.in
- Joining date 15-10-2025
My research began with my M.Sc. and Ph.D., studying host immune responses and virulence factors in Vibrio vulnificus infections. Over time, my focus has expanded to analysis of clinical and biomedical data, including predictive modelling of patient outcomes, immune response evaluations, epidemiological studies, and microbial gene expression analyses. I have contributed to study design, data collection, and statistical analysis, applying appropriate methods to draw meaningful insights. My work has supported multiple collaborative research projects and publications, emphasizing the integration of experimental and clinical data for understanding disease mechanisms.
- Assistant Professor, NUCSER, Nitte (DU), since 2025 till date
- Project Associate at Technology Enabling Centre, Nitte (DU), 2020-2025
- PhD Scholar, NUCSER, Nitte (DU), 2016 – 2020rn
- Asst. Lecturer cum Clinical Instructor at NUINS, Nitte (DU), 2013-2014
- Predictive modelling and risk assessment in clinical outcomes
- Biostatistical analysis of clinical and biomedical data
- Epidemiological data analysis and population-based studies
- Statistical evaluation of diagnostic and laboratory data
- Gold Medallist, M.Sc. Biomedical Science, Nitte (Deemed to be University)
- Ph.D. Fellowship Awardee, Directorate of Minorities, Govt. of Karnataka (2017–2020)
- Best Research Paper Award, Nitte (Deemed to be University)
- Karnataka State Eligibility Test (K-SET/2025) for assistant for assistant professor in life sciences
- SAKURA Science Awardee (Japan Science and Technology Agency), University of Miyazaki, 2015
- Scientific illustration featured at a European Congress art gallery and journal of Blood and Thunder
Editorial Committee Member, NUCSER Newsletter
- Anusha Rohit1, Caroline DSouza1, Mala Prasad, Sadanand Dangri Akshay, Dhinakaran Irusan, Angel Jenifer, Suresh Kumar Dorairajan, Collins K. Boahen, Iddya Karunasagar, Vinod Kumar, 2025, Age-Specific Predictive Modelling of Sepsis Mortality: The Diagnostic Utility of CRP and Serum Creatinine, Respiratory Medicine, 250, 108530 DOI: 10.1016/j.rmed.2025.108530
- Anusha Rohit, Caroline DSouza, Suresh Kumar, Meenachi Ct, Vinothini V, Siva Perumal, M Philip, Raju George, Iddya Karunasagar, 2024, IgG responses against SARS-CoV-2 vaccines AZD1222 and BBV-152 and breakthrough infections among health care workers in southern India. Heliyon.
- Kattapuni Suresh Prithvisagar, Pavan Gollapalli, Caroline D’Souza, Praveen Rai, Iddya Karunasagar, Indrani Karunasagar & Krishna Kumar Ballamoole, 2023, Genome analysis of clinical genotype Vibrio vulnificus isolated from seafood in Mangaluru Coast, India provides insights into its pathogenicity. Veterinary Quarterly. DOI: 10.1080/01652176.2023.2240389
- Amita Rao, Caroline DSouza, K Subramanyam, Praveen Rai, Biju Thomas, Mundayat Gopalakrishnan, Indrani Karunasagar, & Ballamoole Krishna Kumar, 2021, Molecular analysis shows the presence of periodontal bacterial DNA in atherosclerotic plaques of patients with coronary artery disease. Indian Heart Journal, volume 73, Page no 218-220 DOI: 10.1016/j.ihj.2021.01.011
- Caroline DSouza, Ballamoole Krishna Kumar, Sachidananda Kapinakadu, Ranjith Shetty, Indrani Karunasagar, Iddya Karunasagar, 2018, PCR-based evidence showing the presence of Vibrio vulnificus in wound infection cases in Mangaluru, India. International Journal of Infectious Disease. Volume 68, Page no 74- 76 DOI: 10.1016/j.ijid.2018.01.018
Undergraduate- Basic research methodology and biostatistics Postgraduate- Research methodology and biostatistics, Biostatistics and data analytics, & Research methodology and publication ethics
