Vijaya Parthiban

=Vijaya Parthiban's Page in OpenWetWare=

I am a post doctoral computational biologist in the Wellcome Trust Sanger Institute in Cambridge (UK). I did my Ph.D. and worked as a 'staff scientist' in Colonge University Bioinformatics Center, Germany before moving to Cambridge. I was selected for the Ph.D. program in the International Max Planck Research School in Cologne in 2002. http://www.parthi.net redirects to this page for the time being! I am moving to a new hosting provider soon.

Institutions
In the Sanger Institute, I am in the Genome dynamics and Evolution group, and my work is on genomics of rare diseases. Currently, I am using exome resequencing data to detect CNVs across multiple individuals.

Previously, I was in the proteomic mass spectrometry group. I was associated with several proteomics projects (stem cell biology, pathogen biology, etc.) and developed computational tools for systems biology and mass spectrometry.

I did my PhD in Cologne University Bioinformatics Centre (CUBIC), one of the highly funded bioinformatics facilities in the world and the quality of research there is exceptional in its class. Besides, I was selected for the international Ph.D. program offered by International Max Planck Research School (IMPRS). The scientific, social and career oriented research and training in IMPRS was phenomenal for my research career in bioinformatics.

Research
I am a Computational/Statistical biologist in the Genome Dynamics and Evolution group in the Sanger Institute located at the Wellcome Trust Genome Campus in Cambridge, UK. My current research deals with the genomics of rare diseases using the exome sequencing data, with special focus on detecting CNVs. I'll also be integrating my systems biology expertise to the genomic data.

I was working on computational proteomics and mass spectrometry in the 'Proteomic Mass Spectrometry' group in the Sanger Institute, and my work was on identifying/analysing post-translational modifications (especially phosphorylation) from the MS data using some of the latest algorithms, some of them developed in-house, as well as other algorithms.

As a member of the structural bioinformatics group at CUBIC, the main focus of my work was on computational prediction of protein structural stability. I have analysed and predicted the stability of proteins upon mutations. This study has a huge impact on the industrial applications for engineering thermostable protein mutants, analysing the protein stability upon mutations that cause diseases, etc. The prediction model involves statistical mechanics functions and thorough identification of protein structural factors and has direct implications on protein structure solutions, protein-protein/ligand docking and virtual screening of potential drug targets. The study involves statistical methods, mathematics,  statistical mechanics and empirical approaches to manipulate the experimental data and to develop reliable protein engineering methods. I am familiar with statistical tools and libraries to do cluster analysis, PCA, normilization and various regressions methods.

Research Interests

 * Genomics of rare diseases, cancers, etc.
 * Computational Proteomics / Mass Spectrometry / Systems Biology
 * Protein engineering and stability
 * Protein-protein docking
 * Structural Bioinformatics
 * Drug discovery
 * Protein-Ligand docking
 * Molecular modelling
 * Statistical data mining

Professional Training / Membership

 * Participated in Advanced Workshop on Structural Biology in the Center for Biocrystallographic Research, Poznan.
 * Participated in IMPRS Workshop in Biological Research Center, Hungary.
 * Participated in ISMB/ECCB 04, GCB 04, ISMB 05 and ECCB 05.
 * Member of the ISCB and the President of the ISCB student council.
 * Member of IEEE computer society & engineering in medicine/biology society.
 * Participated in ESF-JSPS workshop (ESF-JSPS fellowships) on functional genomics (From the bench to bioinformatics), Kanagawa, Japan.
 * Chair of the structural bioinformatics session in European Conference on Computational Biology (Madrid): International Student Symposium in Computational Biology.
 * Reviewer for the selection of oral presentation/poster abstracts for the ECCB student symposium (mentioned above).
 * Reviewer: Biopolymers (bi-weekly journal).

Journal Articles

 * Vijaya Parthiban, M. Micheal Gromiha, Dietmar Schomburg. (2006) CUPSAT: prediction of protein stability upon point mutations. Nucleic Acids Research, 34, W239-42.


 * Vijaya Parthiban, M. Michael Gromiha, Christian Hoppe and Dietmar Schomburg. Structural Analysis and Prediction of Protein Mutant Stability using Distance and Torsion Potentials: Role of Secondary Structure and Solvent Accessibility. (2007) Structural analysis and prediction of protein mutant stability using distance and torsion potentials: role of secondary structure and solvent accessibility. 66(1). 41-52.


 * Vijaya Parthiban, M. Micheal Gromiha, Madenhalli Abhinandan, Dietmar Schomburg. (2007) Computational modeling of protein mutant stability: analysis and optimization of statistical potentials and structural features reveal insights into prediction model development. BMC Structural Biology. 7. 54.


 * Devi Mariappan, Johannes Winkler, Vijaya Parthiban, Michael Xavier Doss, Jürgen Hescheler, Agapios Sachinidis. (2006) Dietary small molecules and large-scale gene expression studies: An experimental approach for understanding their beneficial effects on the development of malignant and non-malignant proliferative diseases, Current Medicinal Chemistry, 13, 1481-1489.

Posters/Talks:

 * ISMB / ECCB 2004, Glasgow: Poster Title: Prediction of Factors Determining Changes in Thermostability in Protein Mutants.


 * GCB 2004, Bielefeld: Poster Title: Prediction of Factors Determining Changes in Thermostability in Protein Mutants (with improved results).


 * ISMB 2005, Detroit: Two posters were presented. Poster Title 1: Computational Analysis of RNA Binding Proteins Based On Composition, Sequence And Structural Information. Poster Title 2: http://www.iscbsc.org - A New Professional Web-based ISCB Student Council Framework for Computational Biology Support


 * ECCB 2005, Madrid: Optimisation of Atomic Interaction Models for An Effective Description Of Protein Structure Parameters.


 * ESF-JSPS workshop on Functional Genomics: From the Bench to Bioinformatics. Talk: ‘Structural Analysis and Prediction of Protein Mutant Stability using Distance and Torsion Potentials: Role of Secondary Structure and Solvent Accessibility’