Prof Adrian Shepherd
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Overview
Overview
Qualifications
- PhD, UCL, 1995
- PGCert Learning & Teaching in Higher Education, Institute of Education, 2005
- MSc Computer Science , UCL, 1992
- BA (Hons.) History of Art, UEA, 1984
Web profiles
Administrative responsibilities
- Director, MSc Bioinformatics
- Co-Director of the ISMB Wellcome Trust PhD Programme
- Chair of the departmental teaching and student/staff exchange committees
Professional memberships
Member of the AIRR Community of The Antibody Society
Honours and awards
- Fellow of the Higher Education Academy (FHEA), Higher Education Academy (now Advance HE), November 2005
ORCID
0000-0003-0194-8613 -
Research
Research
Research interests
- computational immunology
- computational virology
Research overview
My research focuses on:
- Developing resources to support the analysis of immunoglobulin (IG) genomic information, notably OGRDB and (in collaboration with Gur Yaari's lab at Bar Ilan University) VDJbase
- Using deep learning to analyse adaptive immune receptor repertories, both antibodies and T-cell receptors
- Using molecular dynamics simulations to elucidate antibody binding and the molecular entry mechanisms of viruses (notably hepatitis C virus)
- Understanding antigen presentation and the boundary between self and non-self in the context of protein therapeutics (notably Factor VIII) and cancer.
Research Centres and Institutes
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Supervision and teaching
Supervision and teaching
Supervision
I welcome enquiries from prospective PhD students who are interested in undertaking research in any of my areas of research interest.
Teaching
Teaching modules
- BioComputing I (CRYS001H7)
- The Molecular Basis of Life (CRYS002H7)
- Statistics (CRYS003H7)
- Data Science (CRYS004H7)
- BioComputing II (CRYS006H7)
- Omics (CRYS007H7)
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Publications
Publications
Article
- Maitra, Arundhati and Nukala, Syamasundari and Dickman, R. and Martin, Liam T. and Munshi, Tulika and Gupta, Antima and Shepherd, Adrian J. and Arnvig, K.B. and Tabor, A.B. and Keep, Nicholas H. and Bhakta, Sanjib (2021) Characterization of the MurT/GatD complex in Mycobacterium tuberculosis towards validating a novel anti-tubercular drug target. JAC-Antimicrobial Resistance 3 (1), ISSN 2632-1823.
- Collins, A.M. and Yaari, G. and Shepherd, Adrian J. and Lees, William and Watson, C.T. (2020) Germline immunoglobulin genes: disease susceptibility genes hidden in plain sight?. Current Opinion in Systems Biology ISSN 24523100. (In Press)
- Palor, M. and Stejskal, L. and Mandal, P. and Lenman, A. and Alberione, M.P. and Kirui, J. and Moeller, R. and Ebner, S. and Meissner, F. and Gerold, G. and Shepherd, Adrian and Grove, J. (2020) Cholesterol sensing by CD81 is important for hepatitis C virus entry. Journal of Biological Chemistry ISSN 0021-9258. (In Press)
- Modi, T. and Gervais, D. and Smith, S. and Miller, J. and Subramaniam, S. and Thalassinos, Kostas and Shepherd, Adrian J. (2020) Characterisation of the UK anthrax vaccine and human immunogenicity. Human Vaccines & Immunotherapeutics ISSN 2164-5515. (In Press)
- Stejskal, L. and Lees, William D. and Moss, David S. and Palor, M. and Bingham, R.J. and Shepherd, Adrian J. and Grove, J. (2020) Flexibility and intrinsic disorder are conserved features of hepatitis C virus E2 glycoprotein. PLOS Computational Biology 16 (2), pp. e1007710. ISSN 1553-7358.
- Stejskal, Lenka and Lees, William and Moss, David and Palor, M. and Bingham, R. and Shepherd, Adrian J. and Grove, J. (2020) Flexibility and intrinsic disorder are conserved features of hepatitis C virus E2 glycoprotein. PLoS Computational Biology ISSN 1553-7358.
- Olson, B.J. and Moghimi, P. and Schramm, C.A. and Obraztsova, A. and Ralph, D. and Vander Heiden, J.A. and Shugay, M. and Shepherd, Adrian J. and Lees, William and Matsen IV, F.A. (2019) sumrep: a summary statistic framework for immune receptor repertoire comparison and model validation. Frontiers In Immunology 10 (2533), ISSN 1664-3224.
- Aviv, O. and Shemesh, O. and Peres, A. and Polak, P. and Shepherd, Adrian J. and Watson, C.T. and Boyd, S.D. and Collins, A.M. and Lees, William and Yaari, G. (2019) VDJbase: an adaptive immune receptor genotype and haplotype database. Nucleic Acids Research ISSN 0305-1048.
- Lees, William and Busse, C.E. and Corcoran, M. and Ohlin, M. and Scheepers, C. and Matsen, F.A. and Yaari, G. and Watson, C.T. and Community, A. and Collins, A. and Shepherd, Adrian J. (2019) OGRDB: a reference database of inferred immune receptor genes. Nucleic Acids Research ISSN 0305-1048. (In Press)
- Hart, D.P. and Uzun, Nazmiye and Skelton, S. and Kakoschke, A. and Househam, J. and Moss, David S. and Shepherd, Adrian J. (2018) Factor VIII cross-matches to the human proteome reduce the predicted inhibitor risk in missense mutation hemophilia A. Haematologica 103 (10), ISSN 0390-6078.
- Pan, R. and Qin, Y. and Banasik, M. and Lees, William and Shepherd, Adrian J. and Cho, M. and Kong, X.-P. (2018) Increased epitope complexity correlated with antibody affinity maturation and a novel binding mode revealed by structures of rabbit antibodies against the third variable loop (V3) of HIV-1 gp120.. Journal of Virology ISSN 0022-538X. (In Press)
- Lees, W.D. and Stejskal, L. and Moss, D.S. and Shepherd, Adrian J. (2017) Investigating substitutions in antibody–antigen complexes using molecular dynamics: a case study with broad-spectrum, Influenza A antibodies. Frontiers In Immunology ISSN 1664-3224.
- Banerjee, S. and Shi, H. and Banasik, M. and Moon, H. and Lees, W. and Qin, Y. and Harley, A. and Shepherd, Adrian J. and Cho, M.W. (2017) Evaluation of a novel multi-immunogen vaccine strategy for targeting 4E10/10E8 neutralizing epitopes on HIV-1 gp41 membrane proximal external region. Virology 505, pp. 113-126. ISSN 0042-6822.
- Ashford, Paul and Hernandez duran, Anna and Greco, T.M. and Buch, A. and Sodeik, B. and Cristea, I.M. and Grünewald, K. and Shepherd, Adrian J. and Topf, Maya (2016) HVint: a strategy for identifying novel protein-protein interactions in Herpes Simplex Virus Type 1. Molecular & Cellular Proteomics 15 (9), pp. 2939-2953. ISSN 1535-9476.
- Denyer, Michael P. and Pinheiro, D.Y. and Garden, O.A. and Shepherd, Adrian J. (2016) Missed, not missing: Phylogenomic evidence for the existence of Avian FoxP3. PLoS One 11 (3), pp. e0150988. ISSN 1932-6203.
Book Section
- Czarnecki, Jan and Shepherd, Adrian J. (2016) Metabolic pathway mining. In: Keith, J.M. (ed.) Bioinformatics Volume II: Structure, Function, and Applications. Methods in Molecular Biology. New York, U.S.: Humana Press. pp. 139-158. ISSN 1064-3745. ISBN 9781493966110.
- Lees, William and Shepherd, Adrian J. (2016) Studying antibody repertoires with next-generation sequencing. In: Keith, J.M. (ed.) Bioinformatics. Methods in Molecular Biology. New York, U.S.: Humana Press. pp. 257-270. ISSN 1064-3745. ISBN 9781493966110.