Faraday lecture  

Masters Projects


 

A list of the past Masters projects I have supervised (or co-supervised):

  • "Approaches to visually analysing antibody repertoire datasets", Charles Bird (MRes Bioinformatics with Systems Biology 2015/16)
  • "Probing the boundary between self and non-self: proteomes, somatic mutations and T-cell epitopes", Jacob Househam (MRes Bioinformatics with Systems Biology 2015/16)
  • "Developing a machine learning predictor of cytotoxic T-cell epitope immunodominance", Mark Warren (MSc Bioinformatics with Systems Biology 2015/16)
  • "Chronic hepatitis B: an analysis of viral genotypes, HLA haplotypes and T-cell responses", Sandy MacPherson (MSc Bioinformatics with Systems Biology 2015/16)
  • "In silico evaluation of HIV-1 T-cell epitopes previously predicted by in vitro mapping", Daniel Gugembe-Lule (MSc Bioinformatics with Systems Biology 2015/16)
  • "Computational modelling: predicting the genera and risk associated with fungi in historical properties in the UK", Sam McGreig (MSc Bioinformatics with Systems Biology 2015/16, co-supervised with Dr Jane Nicklin)
  • "Comparison of protein surfaces", Paddy MacMahon (MSc Bioinformatics with Systems Biology 2013-16, co-supervised with Dr Mark Williams)
  • "Antibody CDR3s — diversity and constraints: A large scale analysis of Ig-seq data", Anna Laddach (MRes Bioinformatics with Systems Biology 2014/15, co-supervised with Dr William Lees)
  • "Evaluating antibody modelling and docking methods for the annotation of NGS repertoire data", Zheli Tan (MRes Bioinformatics with Systems Biology 2014/15, co-supervised with Dr William Lees)
  • "Computational analysis of influenza evolution and antigenic pressure from cytotoxic T lymphocytes", Paul Buckley (MSc Bioinformatics with Systems Biology 2014/15, co-supervised with Dr William Lees and Michael Denyer)
  • "The impact of the microbiome on the immune response to selected human pathogens: a computational investigation", Ginny Devonshire (MSc Bioinformatics with Systems Biology 2013-15, co-supervised with Naz Uzun)
  • "Influenza B virus", Siobhan Titre-Johnson (MSc Health and Disease, 2013-15)
  • "Viral surface glycoproteins", Sukhuma Starkings (MSc Microbiology, 2013-15)
  • "The prediction of immunodominant T-cell epitopes and analysis of their conservation", Michael Denyer (MRes Bioinformatics with Systems Biology, 2013/14, co-supervised with William Lees and Charlie Watson)
  • "Neuraminidase — A new look at the influenza A underestimated glycoprotein to improve flu vaccines", Rute Magalhaes (MSc Microbiology, 2012-14)
  • "The importance of researching influenza B", Duldip Sidhu (MSc Health and Disease 2011-14)
  • "Immune responses to protein therapeutics: ethnicity and the stratification of protein risk", Richard Lee (MSc Bioinformatics with Systems Biology, 2012/13)
  • "Identifying novel TCR:pMHC interfaces: taking central tolerance into account by scanning the human proteome", Alison Kakoschke (MSc Bioinformatics with Systems Biology 2011-13, co-supervised with Stuart Skelton)
  • "Towards an improved, chimeric AAV vector for gene therapy: a computational antigenicity prediction method", Nazmiye Uzun (MSc Bioinformatics with Systems Biology, 2011-13)
  • "In-silico risk prediction of Factor VIII inhibitor development in non-severe hemophilia A", Devlatha Naga (MSc Bioinformatics with Systems Biology, 2011-13)
  • "An analysis of CTL mediated immune response on residues in human infleunza A", Charlie Watson (MSc Bioinformatics with Systems Biology, 2010-13)
  • "Investigating the antigenic properties of the dengue virus in relation to vaccine and antiviral development", Lisa Byer (MSc Health and Disease 2011-13)
  • "An investigation of the antigenic properties of hepatitis C virus", Anthony Folami (MSc Health and Disease 2011-13)
  • "Dissecting drivers for triple-negative breast cancer subtypes through genomics integrated meta-analyses", Johnathan Watkins (MRes Bioinformatics with Systems Biology 2011/12, co-supervised by Dr Anita Grigoriadis, Breakthrough Breast Cancer Research Unit, King's College London)
  • "An assessment of influenza A assays and antibody binding", Olajide Akere (MRes Microbiology, 2011/12, co-supervised with Dr John McCauley, Director of the WHO Influenza Centre, NIMR and William Lees)
  • "Analysing the distribution of antigenically important residues in HIV envelope glycoprotein gp41", Cara Jetten (MSc Bioinformatics, 2010-12, co-supervised with Prof. David Moss and William Lees)
  • "Analysing the distribution of antigenically important residues in HIV envelope glycoprotein gp120", Esther Fearnhill (MSc Bioinformatics, 2010-12, co-supervised with Prof. David Moss and William Lees)
  • "An investigation of the antigenic properties of foot-and-mouth", Patience Tetteh (MSc Health and Disease, 2010-12)
  • "An investigation of the antigenic properties of infectious bronchitis", Christian Search (MSc Health and Disease, 2010-12)
  • "Analysis of PrPd deposition patterns in brains from bovine BSE cases", Sarah Jo Moore (MSc Bioinformatics, 2008-12, co-supervised with the Veterinary Laboratories Agency)
  • "Do virulent influenza strains evade cytotoxic T-cell activity?", Morne Maritz (MSc Bioinformatics, 2009-11, co-supervised with Prof. David Moss)
  • "Towards the prediction of the virulence of influenza virus strains from sequence and structure", Dene Hamer (MSc Bioinformatics, 2008-11, co-supervised with Prof. David Moss)
  • "Developing a generic, configurable informational retrieval system for immunoinformatics using regular expressions", Vijayalakshmi Kona (MSc Bioinformatics, 2008-11)
  • "Metabolic network reconstruction for Malassezia restricta", Rosalind Jack (MSc Bioinformatics, 2009-11, co-supervised with Dr Irilenia Nobeli and Diana Cox, Microbial Biochemist at Unilever)
  • "Prediction of sequence-specific deformations of DNA structure with artificial neural networks", Jana Vandrovcova (MSc Bioinformatics, 2008-10, co-supervised with Dr Alona Sosinsky)
  • "The evolution of the influenza virus: a statistical approach", William Lees (MRes Bioinformatics, 2008/9, co-supervised with Prof. David Moss)
  • "Simulation of the effect of vaccinations against mammary carcinomas", Gordon Haggart (MSc Bioinformatics, 2008/9, co-supervised with Prof. David Moss)
  • "Development and validation of immunoinformatic tools", Stuart Skelton (MSc Bioinformatics, 2008/9, co-supervised with Sari Ward, Senior Scientist at Pfizer)
  • "The molecular cost of highly expressed proteins", John Hurwitz (MSc Bioinformatics, 2007-9, co-supervised with Dr Irilenia Nobeli)
  • "Simulation of the effect of vaccinations against mammary carcinomas", Beatriz Valcarcel (MSc Bioinformatics, 2007/8, co-supervised with Prof. David Moss)
  • "Prediction of sequence-specific deformations of DNA structure with artificial neural networks", Madhu Sukymar (MSc Bioinformatics, 2007/8, co-supervised with Dr Alona Sosinsky)
  • "Molecular mimicry and autoimmune disease", Bracha Erlanger (MSc Bioinformatics, 2006-8, co-supervised with Prof. David Moss and Dr Clare Sansom)
  • "Reconstruction of a genetic network using text mining algorithms", Matthew Grant (MSc Bioinformatics, 2006/7, co-supervised with Dr Christine Slingsby)
  • "Reconstruction of a genetic network using text mining algorithms", Alex Warner (MSc Bioinformatics, 2006/7, co-supervised with Dr Christine Slingsby)
  • "Antigen discovery using dissimilarity versus the human genome", Masayo Mochizuki (MSc Bioinformatics, 2006/7, co-supervised with Dr Darren Flower at the Edward Jenner Institute for Vaccine Research)
  • "A comparison of plant and human metabolites using QSAR and artificial neural networks", Michael Fox (MRes Bioinformatics, 2006/7, co-supervised with Dr Irilenia Nobeli at Kings College London)
  • "Computational study of the dissociation of protein dimers", Jonathan Mowatt (MRes Bioinformatics, 2006/7, co-supervised with Prof. David Moss)
  • "Comparison of gene expression across bacterial species using microarray data stored in BuG@SBase, a bacterial microarray database", Lucy Brooks (MSc Bioinformatics 2005-7, co-supervised with Adam Witney)
  • "Developing an information retrieval system to support simulations of the human immune system", Richard Tyler (MRes Bioinformatics, 2005/6, co-supervised with Prof. David Moss)
  • "Developing immunology-related text mining applications using web services and scientific workflow software", Dr Mike Jarman (MSc Bioinformatics, 2005/6)
  • "Developing an information retrieval system to support research into the functional promiscuity of proteins", Ola Ogunlayi (MSc Bioinformatics, 2005/6, co-supervised with Dr Irilenia Nobeli at Kings College London)
  • "Metabolome 3D: structures and properties of biologically important small molecules", Dimitrios Mekras (MSc Bioinformatics, 2005/6, co-supervised with Dr Irilenia Nobeli at Kings College London)
  • "The development of Bayesian approaches to modelling uncertainty in antigen processing", Sam Adams (MRes Bioinformatics, 2004/5, co-supervised with Prof. David Moss)
  • "Evaluating the reliability of automatically assigned GO terms", Vimarsh Mehta (MSc Bioinformatics, 2004/5)
  • "Analysis and prediction of Cathepsin specificity and peptide cleavage patterns", Maria Barcelos (MSc Bioinformatics, 2004/5, co-supervised with Dr Darren Flower at the Edward Jenner Institute for Vaccine Research)
  • "The automated extraction of data collection temperature information from crystallographic texts", Richard Thompson (MSc Bioinformatics, 2003-5, co-supervised with Dr Nick Keep)
  • "The discovery and ranking of oncology-related texts in Medline using the Gene Ontology and Information Retrieval techniques", Jonathan Welti (MSc Bioinformatics, 2003/4)
  • "Refining neural network predictions of the location and type of beta-turns", Eleni Rapsomaniki (MSc Bioinformatics, 2003/4)
  • "An enhanced vector cosine model for biological text retrieval" with relevance feedback implemented in Perl, Dr Simon Cowen (MSc Bioinformatics, 2002/3)
  • "An enhanced vector cosine model for biological text retrieval" with query expansion implemented in Java, Renata Kabiljo (MSc Bioinformatics, 2002/3)
  • "Reclustering protein families in the CATH database", Stephen Ho (MRes Bioinformatics, 2002/3)
  • "Developing and evaluating an automated retraining system for BTPRED", Dharmesh Krishnamoorthy (MSc Bioinformatics, 2002/3)

Undergraduate Projects


 

A list of the past undergraduate projects I have supervised:

  • "A computational analysis of the potential for heterologous cytotoxic T cell immunity in human herpesviruses", Aaron Yi Long Lam (final year project student, BSc Biochemistry, UCL, 2014/15)
  • "A computational analysis of T cell epitope immunodominance in viruses", Jake Saklatvala (final year project student, BSc Biochemistry, UCL, 2013/14)
  • "A bioinformatics investigation into the distribution of class I T-cell epitopes in viral proteins", Mike Doyle (final year project student, BSc Chemical and Molecular Biology 2013/14)
  • "Computational analysis of B-cell epitopes", William Otterburn (final year project student, BSc Biochemistry, UCL, 2012/13)