Anisah Ghoorah

From March 2009 to December 2013, I worked in the Orpailleur research team at the Inria Nancy in France. I was an Inria PhD student from Mar 2009 to Sept 2012. I was a research and teaching assistant at the University of Lorraine (ex-Nancy 2) from Oct 2012 to Aug 2013. From Sept 2013 to Dec 2013 I was an Inria research engineer.

As of January 2014, I work as a lecturer in the Department of Computer Science and Engineering at the University of Mauritius.

Research Interests

Knowledge Discovery in Databases (KDD) of Structural Protein-Protein Interactions
Network Analysis of the Human Diseases
Classification of Protein 3D Structures

Research Projects

Ongoing Projects

A systematic identification and analysis of disease-related modules in the human protein-protein interaction network (Funded by MRC under URIGS)

Anisah Ghoorah (Principal Investigator), Shakuntala Baichoo, Oveeyen Moonian, Zahra Mungloo-Dilmohamud, Yasmina Jaufeerally-Fakim

Discovering relationships between diseases and genes using the human structural interactome and biological pathways (Funded by MRC under PGA)

Shivam Oogorah (PhD student at Univeristy of Mauritius), Anisah Ghoorah (Supervisor), Dave Ritchie (Assoc Supervisor)

Completed Projects

To appear...

Research Collaborations

My main collaborator at the Inria Nancy is Dave Ritchie
My collaborators at the University of Mauritius include Shakuntala Baichoo, Yasmina Jaufeerally-Fakim, Oveeyen Moonian, and Zahra Mungloo-Dilmohamud.

Education

PhD Informatics (Bioinformatics), University of Lorraine, France, 2012
MSc Bioinformatics, University of Edinburgh, Scotland, 2008
BSc (Hons) Computing Science, University of Aberdeen, Scotland, 2007

PhD Thesis

Knowledge-based approaches for modelling the 3D structural interactome

Understanding how the protein interactome works at a structural level could provide useful insights into the mechanisms of diseases. Comparative homology modelling and ab initio protein docking are two computational methods for modelling the three-dimensional (3D) structures of protein-protein interactions (PPIs). Previous studies have shown that both methods give significantly better predictions when they incorporate experimental PPI information. However, in general, PPI information is often not available in an easily accessible way, and cannot be re-used by 3D PPI modelling algorithms. Hence, there is currently a need to develop a reliable framework to facilitate the reuse of PPI data. My PhD thesis presents a systematic knowledge-based approach for representing, describing and manipulating 3D interactions to study PPIs on a large scale and to facilitate knowledge-based modelling of protein-protein complexes.

PDF: A copy of my thesis and the presentation slides of my defence (4up).

Supervisors: Marie-Dominique Devignes, Malika Smail-Tabbone and Dave Ritchie.

Funding: Agence Nationale de la Recherche and Orpailleur research project.

Database & Software

Kbdock Server: a database of 3D protein interactions and binding sites.

Documents

Publications

Modeling and Minimising CAPRI Round 30 Symmetrical Protein Complexes from CASP-11 Structural Models. El Houasli, M.^†, Maigret, M., Devignes, M.-D., Ghoorah, A. W., Grudinin, S. and Ritchie, D.W. (2016) PROTEINS: Structure, Function, and Bioinformatics (To appear)
Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment. Lensink, M.^†, ... Ghoorah, A.W. ... and many others (2016). PROTEINS: Structure, Function, and Bioinformatics 2016, 84 (S1):323–348.
Classification and Exploration of 3D Protein Domain Interactions Using Kbdock. Ghoorah, A.W.^†, Devignes, M-D., Smail-Tabbone, M., Ritchie, D.W. (2016). In Methods in Molecular Biology 1415 - Data Mining Techniques for the Life Sciences (Eds. O. Carugo and F. Eisenhaber), 2, 91-105.
Structure-Based Classification and Analysis of Protein Domain Family Binding Sites and Their Interactions. Ghoorah, A.W.^†, Devignes, M-D., Alborzi, S.Z., Smaïl-Tabbone, M., Ritchie, D.W. (2015). Biology 2015; 4: 327-343.
Kbdock 2013: A spatial classification of 3D protein domain family interactions. Ghoorah A.W.^†, Devignes M-D., Smaïl-Tabbone M., and Ritchie D.W. (2014). Nucleic Acids Research 2014; 42(D1): 389-395.
Protein docking using case-based reasoning. Ghoorah A.W.^†, Devignes M-D., Smaïl-Tabbone M., and Ritchie D.W. (2013). PROTEINS: Structure, Function, and Bioinformatics 2013; 81(12): 2150-2158.
Fast Protein Structure Alignment using Gaussian Overlap Scoring of Backbone Peptide Fragment Similarity. Ritchie D.W.^†, Ghoorah A.W., Mavridis L., Venkatraman V. (2012). Bioinformatics 2012; 28 (24): 3274-81 (Supplementary Materials).
Representing and comparing protein folds and fold families using 3D shape-density representations. Mavridis L.^†, Ghoorah A.W., Venkatraman V., and Ritchie D.W. (2012). PROTEINS: Structure, Function, and Bioinformatics 2012; 80(2): 530-545.
Spatial clustering of protein binding sites for template-based protein docking. Ghoorah A.W.^†, Devignes M-D., Smaïl-Tabbone M., and Ritchie D.W. (2011). Bioinformatics 2011; 27(20): 2820-7. [PDF] (see Supplementary Materials for detailed homology docking results).
jMOTU and Taxonerator: Turning DNA Barcode Sequences into Annotated Operational Taxonomic Units. Jones M.^†, Ghoorah A.W.^†, and Blaxter M. (2011). PLoS One. 2011; 6(4): e19259.

† First-author

Presentations

Kbdock - a case-based reasoning approach to model 3D protein complexes, 5th CAPRI Evaluation Meeting, Utrecht, 2013. [PDF] (This talk was given by Dave Ritchie)
Knowledge-based approaches for modelling the 3D structural interactome, PhD Defence, Ecole Doctorale IAEM, Université de Lorraine, LORIA, INRIA, Nancy, 2012. [PDF]
Spatial Clustering of Protein Binding Sites for Template-Based Protein Docking, BeNeLux Bioinformatics Conference (BBC 2011), Luxembourg, 2011.
Extracting and visualising protein-protein interfaces for knowledge-based docking, Journées Scientifiques de la Fédération Charles Hermite, Nancy, 2010.

Posters

Representing and comparing protein folds and families using 3D shape-density representations. ISMB-3DSIG, Vienna, 2011. [PDF]
Extracting and visualizing protein-protein complexes for knowledge-based docking. LIX Bioinformatics Colloquium 2010, Paris, 2010. [PDF]
Extracting and visualizing protein-protein complexes for knowledge-based docking. 9th ECCB, Ghent, 2010. [PDF]
Using Human Expertise in Protein-Protein Docking: From Biological Knowledge to Interactive Simulations. 4th CAPRI Evaluation Meeting, Barcelona, 2009. [PDF]
Developing a Knowledge-Based Approach to Protein-Protein Docking. 4th CAPRI Evaluation Meeting, Barcelona, 2009. [PDF]

Other

Knowledge-based approaches for modelling the 3D structural interactome, PhD Thesis, University of Lorraine, 2012. [PDF]
MOTU_define: A tool for DNA barcode analyses, MSc Thesis, University of Edinburgh, 2008.
Aligning protein 3D structures, Undergraduate Project Report, University of Aberdeen, 2007.

Teaching

Lecture and Practical/Tutorial

Data Structures and Algortithms (BSc Software Engineering), University of Mauritius, Aug-May 2016.
Algorithms and Complexities (BSc Computer Science), University of Mauritius, Aug-May 2016.
Software Programming (BSc Software Engineering), University of Mauritius, Aug-May 2015, Aug-May 2016.
Database and Information Systems (BSc Electronics with Computer Science / BSc Information and Communication Technologies), University of Mauritius, Aug-May 2015, Aug-May 2016.
Basic Computer Applications (Misc BSc programmes from Faculty of Law and Management), University of Mauritius, Jan-May 2014, Jan-May 2015, Jan-May 2016.
Applied Data Structures and Algorithms (BSc Computer Applications / BSc Information Systems), University of Mauritius, Jan-May 2015.
Communications and Business Skills for IT (BSc Information Systems), University of Mauritius, Aug-May 2015.
Introduction to Information Technology (Misc BSc programmes from Faculty of Law and Management), University of Mauritius, Jan-May 2015.
Data Structures and Algortithms (BSc Computer Science), University of Mauritius, Jan-May 2014.
Database Systems I (BSc Computer Applications), University of Mauritius, Jan-May 2014.
Initiation à la programmation avec Python (Licence Informatique 1ère année), Dept. Math-Info, Université de Lorraine, Jan-May 2013.
Traitement du Web (Licence Informatique 2ème année), Dept. Math-Info, Université de Lorraine, Jan-May 2013.
Conception Systèmes Information (Formation Continue), Dept. Math-Info, Université de Lorraine, Apr-Jun 2013.
Certificat Informatique et Internet Partie 2 (Licence Economie 1ère année), Université de Lorraine, Jan-May 2013.
Certificat Informatique et Internet Partie 1 (Licence Langues et Lettres 1ère année), Université de Lorraine, Sept-Jan 2013.
Certificat Informatique et Internet Partie 1 (Licence Droit et Economie 1ère année), Université Nancy 2, Sept-Jan 2012.

Practical/Tutorial Only

Bases de Données (Licence Informatique 2ème année), Dept. Math-Info, Université de Lorraine, Jan-May 2013.
Algorithmique (Licence Informatique 1ère année), Dept. Math-Info, Université de Lorraine, Mar-May 2013.
Projet Bibliographie et Application (Master Informatique), Dept. Math-Info, Université de Lorraine, Sept-Feb 2013.
Bases de Données (Licence Informatique 3ème année), ESIAL, Université Henri Poincaré, Apr-May 2012.
Technologies de l'information et de la communication (Licence Sciences du Vivant 1ère année), Université Henri Poincaré, Jan-Apr 2012.

Contact

Room 2.17, Phase 2
Faculty of Engineering
University of Mauritius
Reduit
E-mail: a.ghoorah AT uom.ac.mu