Division of Molecular Biosciences Department of Life Sciences Faculty of Natural Sciences

Research Interests

Broadly, my interest lies in the development of computational approaches to help with biological discoveries. Even being specific I find my research interests span a range of topics from Systems Biology to Structure Bioinformatics. My current research focuses on applying machine learning techniques for in-silico generation of experimentally testable hypotheses pertaining to the metabolic regulation of cellular processes of interest. To this end, I am working in collaboration with Prof. Muggleton's lab at the DoC on two projects funded by UIC. In one of the projects the aim is to investigate the perturbed regulation of metabolism in response to a non-genotoxic xenobiolotic that leads to hepatocarcinomas in Rat. Another project takes research objectives to a completely different kingdom of life. The main objective is to explore different metabolic control points regulating the ripening process in the Tomato fruit. The machine Learning technique used in the two project is Inductive Logic Programming (ILP), which has the advantage of suggesting a hypothesis that is human interpretable and experimentally testable. Progol and MC-TopLog are the two ILP systems that are used. In both of these projects, a novel data integration technique combining transcriptomics and metabolomics data with inductive logic programming is implemented for training the ILP systems.

Collaboration

Syngenta UIC, Imperial College London.

Biomathematics and Bioinformatics at Rothamsted Research (Ondex)

Stephen Muggleton's Lab at the Department of Computing, Imperial College London.

Education

PhD., The University of Nottingham. (2009)
THESIS TITLE - Protein structural similarity, classification and prediction.

MSc., Bioinformatics (2005)
Universidade de Lisboa, Portugal.
DISSERTATION - Gene Function Prediction by Mining Biomedical Literature.

MSc., Industrial Microbiology (2000).
Devi Ahilya Vishwavidyalaya, Indore, India.
DISSERTATION - Microbial Production of Biodegradable Polymers.

BSc., Microbiology (1998).
Devi Ahilya Vishwavidyalaya, Indore, India.

Awards

1. Inernational EST Marie-Curie Fellowship under the FP 6 EU Project (February 2006 to January 2009).
2. Research Studentship at INESC-ID from National Research Council of Portugal, FCT.
3. Master Scholarship (January 2003 to September 2004) from Fundacao Oriente, Portugal.

Publications

10. Fernandes P., P. Jain and C. Moita. Training Experimental Biologists in Bioinformatics. Advances in Bioinformatics, Volume 2012, Article ID 672749 (2012).

9. Lin D., J. Chen, H. Watanabe, S. H. Muggleton, P. Jain, M. J. E. Sternberg, C. Baxter, R. Currie, S. Dunbar, M. Earll, and D. Salazar. Does multi-clause learning help in real-world applications? Proceedings of the 21st International Conference on Inductive Logic Programming, LNAI 7207, 221-237, (2012).

8. Jain P. and J. D. Hirst. Automatic structure classification of small proteins using random forest. BMC Bioinformatics, 11, 364 (2010).

7. Jain P. and J. D. Hirst. A geometric approach to protein structural similarity and classification, Jornadas de Bioinformatica (2009).

6. Jain P. and J. D. Hirst. Exploring protein structural dissimilarity to facilitate structure classification, BMC Structural Biology, 9:60 (2009).

5. Jain P., J. M. Garibaldi and J. D. Hirst, Supervised Machine Learning Algorithm for Protein Structure Classification, Computational. Biology and Chemistry, 33, 216-223 (2009).

4. Jain P. and J. D. Hirst, Study of Protein Structural Descriptors: Towards Similarity and Classification. In Proceedings of the NIC Workshop From Computational Biophysics to Systems Biology, 36, 165-167, (2007).

3. Teixeira M. C., P. Monteiro, P. Jain, S. Tenreiro, A. R. Fernandes, N. P. Mira, M. Alenquer, A. T. Freitas, A. L. Oliveira and I. S-Correia The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae Nucleic Acids Research, 34, D446-D451, (2006).

2. Jain P., F. Couto, M. J. Silva, J. D. Becker, Literature based functional annotation of genes. In Proceedings of Bioinformatics: Knowledge Discovery in Biology, 29-33, Lisboa, (2005).

1. Monteiro P., M.C. Teixeira, P. Jain, S. Tenreiro, A.R. Fernandes, N. Mira, M. Alenquer, A.T. Freitas, A.L. Oliveira and I. S-Correia YEASTRACT: a database of transcription regulatory associations in Saccharomyces cerevisiae. In Proceedings of Bioinformatics: Knowledge Discovery in Biology, 34-38, Lisboa, (2005).