Digital Imaging Research Centre | Mobile Information & Network Technologies Centre | Jean-Christophe Nebel

Bioinformatics & Genomic Signal Processing Research Group Group Leader: J.-C. Nebel Official Website

Bioinformatics research training

I am looking for motivated undergraduate and graduate students who would like to contribute to bioinformatics research projects.

• 3-6 month Internship in London, UK
• Masters by Research (MSc by Research) or PhD programmes: applications from self-funded individuals are welcome

Projects

Protein-Protein Interaction Prediction Based on Advanced Mirror Tree Kingston University, poster [PDF]	Pattern Recognition in Protein Sequences - Application of machine learning methods to binding site detection and structure prediction Kingston University and Wroclaw University of Technology (Poland), Master by Research thesis [PDF]
NESTOR3D - Multiple alignment of a set of protein structures containing either ligands, prosthetic groups or PROSITE patterns Kingston University and University of Glasgow, Publications [*]	PROTOPOLO - Generation of protein topology and their analysis Kingston University, poster [PDF]
Genomic Signal Processing for Microarray Data Analysis Kingston University, Publications [*]	Analysis of gene structure - Prediction of the effect of Single Nucleotide Polymorphism (SNP) Kingston University and St George's Medical School, University of London
Structure-based description of binding sites

Current researchers

Reyhaneh Esmaielbeiki, Master by Research student Protein-Protein Interaction Prediction Based on Advanced Mirror Tree Supervision Team: Dr Jean-Christophe Nebel (DoS), Dr Dimitrios Makris

Ala Sungoor, Researcher Genomic Signal Processing Supervision Team: Dr Jean-Christophe Nebel, Prof Robert S. H. Istepanian

Witold Dyrka, PhD student Probabilistic Context-Free Grammar for Protein Structure Prediction Supervision Team: Dr Jean-Christophe Nebel (external advisor), Dr Malgorzata Kotulska (DoS - Wroclaw University of Technology, Poland)

Bogumil Konopka, PhD student De Novo Modelling of the 3D Structure of a Channel Protein Supervision Team: Dr Jean-Christophe Nebel, Dr Malgorzata Kotulska (DoS - Wroclaw University of Technology, Poland)

Completed research students

Ala Sungoor, PhD (2009) Genomic Signal Processing for Microarray Data Analysis Supervision Team: Dr Jean-Christophe Nebel, Prof Robert S. H. Istepanian (DoS)

Witold Dyrka, Master by Research (2006-2007) Probabilistic Context-Free Grammar for Pattern Detection in Protein Sequences Supervision Team: Dr Jean-Christophe Nebel (DoS), Dr Darrel Greenhill, Dr Dimitrios Makris, Dr Ndedi Monekosso, Dr Malgorzata Kotulska (external - Wroclaw University of Technology, Poland), poster [PDF]

Bioinformatics courses

• Bioinformatics, 3rd year module for BSc in Computer Science, BSc in Information Systems and BSc in Forensic Science at Kingston University.
• Introduction to Bioinformatics, 1st year module for BSc in Biomedical Informatics at St George's Medical School, University of London.

Current collaborators

Bioinformatics Research Centre University of Glasgow (Scotland)	Faculty of Fundamental Problems of Technology Wroclaw University of Technology (Poland)
St George's Medical School University of London	Institute of Biomedical & Life Sciences SouthWest London Academic Network
London Bioinformatics Forum

Free resources

Nestor3D - Free software allowing the multiple alignment of a set of protein structures containing either ligands, prosthetic groups or PROSITE patterns. It generates consensus 3D pattern including atom, chemical group and cavity positions.

PROTOPOLO - PROtein complex TOPOLOgy database.

Useful links

Useful databases:

• Sequences & genes
  • Swiss-Prot
  • Gene Ontology TM (GO) Consortium
• 3D Data
  • 3D structures: Protein Database (PDB), MSD
  • PDBsum, PDB-REPRDB
  • Classifications: CATH , SCOP, TOPS
  • Disulphide bonds: AnalyCys, DSDBase
• Ligands & Hetero atoms
  • Ligands: KEGG LIGAND Database, Ligand-Protein Contacts & Contacts of Structural Units
  • Hetero: Het-PDB Navi, The Prosthetic groups & Metal Ions in Protein Active Sites Database
• Motifs
  • Sequence: InterPro, PROSITE
  • 3D: Catalytic Site Atlas (CSA), 3motif
• Phylogenetic trees
  • TreeFam

Useful tools:

• Sequence alignment
  • BLAST, FASTA
  • Multiple sequence alignment: ClustalW, TCoffee, Kalign, MUSCLE
• Secondary structure prediction
  • Jpred
• 3D Structure alignment
  • DALI, CE, VAST
  • NESTOR3D, POSA: Partial Order Structure Alignment
• Cavity and pocket detection
  • PASS, CASTp, Pocket-Finder/Q-SiteFinder

Journals:

• Bioinformatics (Impact Factor: 5.039 [2008])
• BMC Bioinformatics (Impact Factor: 3.493 [2008])
• Proteins: Structure, Function, and Bioinformatics(Impact Factor: 3.354 [2008])

Publications

Copyright notice: This material is presented to ensure timely dissemination of scholarly and technical work. Copyright and all rights therein are retained by authors or by other copyright holders. All persons copying this information are expected to adhere to the terms and constraints invoked by each author's copyright. These works may not be reposted without the explicit permission of the copyright holder.

• Why inverse proteins are relatively abundant, J.-C. Nebel and C. Walawage, Protein & Peptide Letters, (Accepted), 2010
• Predicting protein-Protein Interaction Using Mirror Tree, R. Esmaielbeiki and J.-C. Nebel, Third Iranian Conference on Bioinformatics, January 5-6 2010, Tehran, Iran, oral presentation [PDF]

• A Stochastic Context Free Grammar based Framework for Analysis of Protein Sequences, W. Dyrka and J.-C. Nebel, BMC Bioinformatics, 10:323, 2009 [PDF]
• Accuracy in predicting secondary structure of ionic channels, B. Konopka, W. Dyrka, J.-C. Nebel and M. Kotulska, International Conference on Computational Collective Intelligence, 5-7 October, 2009 Wroclaw, Poland, in 'New Challenges in Computational Collective Intelligence', Studies in Computational Intelligence, Springer-Verlag, 315-326, 2009 [PDF]
• Detection and annotation of ligand binding sites based on atomic descriptors, J.-C. Nebel, Protein Sequence, structure and function (Biochemical Society / Wellcome Trust Focused Meeting), January 2009, Hinxton, UK, poster [PDF]

• Structure prediction of a protein channel based on probabilistic formal grammars and the continuous ion flow model, W. Dyrka, M. Kotulska and J.-C. Nebel, ECCB'08: European Conference on Computational Biology, 22-26 September 2008, poster [PDF]
• PROTOPOLO: PROtein complex TOPOLOgy database, I. Weheliye, J. Deivachandran and J.-C. Nebel, ECCB'08: European Conference on Computational Biology, 22-26 September 2008, poster [PDF]
• Fractal Dimension and Wavelet Decomposition for Robust Microarray Data Clustering, R. Istepanian, A. Sungoor and J.-C. Nebel, IEEE Engineering in Medicine and Biology Conference (EMBC08), August 2008, Vancouver, Canada [PDF]

• Evaluation of the usage of probabilistic context-free grammars for the detection of binding sites within protein sequences, W. Dyrka and J.-C. Nebel, GCB'07: German Conference on Bioinformatics, 26-28 September 2007, Potsdam, Germany, poster [PDF]
• Automatic generation of 3D motifs for classification of protein binding sites, J.-C. Nebel, P. Herzyk and D. R. Gilbert, BMC Bioinformatics, 8:32, 2007 [PDF] (Cited by 8)
• Linear Predictive Coding and Wavelet Decomposition for Robust Microarray Data Clustering, R. Istepanian, A. Sungoor and J.-C. Nebel, IEEE International Conference on Engineering in Medicine and Biology Society (EMBC07), 23-26 August 2007, Lyon, France [PDF]
• Linear predictive coding for enhanced microarray data clustering, R. Istepanian, A. Sungoor and J.-C. Nebel, IEEE International Workshop on Genomic Signal Processing and Statistics, 10-12 June 2007, Tuusula, Finland [PDF]
• A probabilistic context-free grammar for the detection of binding sites from a protein sequence, W. Dyrka and J.-C. Nebel, BMC Systems Biology 2007, 1(Suppl 1):P78, BioSysBio 2007, 11-13 January 2007, Manchester, UK, poster [PDF]

• Description and comparison of protein quaternary structures, M. Akbary-Gasany and J.-C. Nebel, GCB'06: German Conference on Bioinformatics, 20-22 September 2006, Tuebingen, Germany, poster [PDF]
• Generation of 3D templates of active sites of proteins with rigid prosthetic groups, J.-C. Nebel, Bioinformatics, 22(10):1183-1189, 2006 [PDF] (Cited by 7)

• Channel Coding Theory for Microarray Data Analysis, A. Sungoor, R. S. H. Istepanian and J.-C. Nebel, Young Bioinformaticians Forum 2005, London, October 2005, poster [PDF]
• Generation of 3D templates of active sites of proteins with rigid prosthetic groups, J.-C. Nebel, GCB'05: German Conference on Bioinformatics, 5-7 October 2005, Hamburg, Germany [PDF]
• Nestor3D: multiple alignment of protein structures based on ligand or prosthetic group position, J.-C. Nebel, BMC Bioinformatics 2005, 6(Suppl 3):S10, Bioinformatics & Systems Biology Conference, Oral presentation, 14-15 July 2005, Edinburgh, Scotland, UK [PDF]
• Modelling of P450 active site based on consensus 3D structures, J.-C. Nebel, International Conference on Biomedical Engineering, BioMed 2005, 16-18 February 2005, Innsbruck, Austria [PDF]