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.

Modi, T. and Gervais, D. and Smith, S. and Miller, J. and Subramaniam, S. and Thalassinos, Kostas and Shepherd, Adrian J. (2021) Characterisation of the UK anthrax vaccine and human immunogenicity. Human Vaccines & Immunotherapeutics 17 (3), pp. 747-758. ISSN 2164-5515.

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 24 , pp. 100-108. ISSN 24523100.

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.

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), e1007710. ISSN 1553-7358.

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. (2020) OGRDB: a reference database of inferred immune receptor genes. Nucleic Acids Research 48 (D1), D1051-D1056. ISSN 0305-1048.

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 (02533), 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.

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 92 (7), e01894. ISSN 0022-538X.

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), e0150988. ISSN 1932-6203.

Shepherd, Adrian J. and Skelton, Stuart and Sansom, Clare E. and Gomez, K. and Moss, David S. and Hart, D.P. (2015) A large-scale computational study of inhibitor risk in non-severe haemophilia A. British Journal of Haematology 168 (3), pp. 413-420. ISSN 0007-1048.

Pentiah, Kevin and Lees, William D. and Moss, David S. and Shepherd, Adrian J. (2015) N-linked glycans on influenza A H3N2 hemagglutinin constrain binding of host antibodies, but shielding is limited. Glycobiology 25 (1), pp. 124-132. ISSN 0959-6658.

Lees, William D. and Shepherd, Adrian J. (2015) Utilities for high-throughput analysis of B-cell clonal lineages. Journal of Immunology Research , p. 323506. ISSN 2314-8861.

Lees, William D. and Moss, David S. and Shepherd, Adrian J. (2014) Evolution in the influenza A H3 stalk - a challenge for broad-spectrum vaccines? Journal of General Virology 95 (2), pp. 317-324. ISSN 0022-1317.

Czarnecki, J. and Shepherd, Adrian J. (2014) Mining biological networks from full-text articles. Methods in Molecular Biology 1159 , pp. 135-145. ISSN 1064-3745.

Czarnecki, Jan M. and Nobeli, Irene and Smith, Adrian M.L. and Shepherd, Adrian J. (2012) A text-mining system for extracting metabolic reactions from full-text articles. BMC Bioinformatics 13 (172), ISSN 1471-2105.

Sivalingam, G.N. and Shepherd, Adrian J. (2012) An analysis of B-cell epitope discontinuity. Molecular Immunology 51 (3-4), pp. 304-309. ISSN 0161-5890.

Lees, William D. and Moss, David S. and Shepherd, Adrian J. (2011) Analysis of antigenically important residues in human influenza A virus in terms of B-cell epitopes. Journal of Virology 85 (17), pp. 8548-8555. ISSN 0022-538X.

Garcia-Alcalde, F. and Blanco, A. and Shepherd, Adrian J. (2010) An intuitionistic approach to scoring DNA sequences against transcription factor binding site motifs. BMC Bioinformatics 11 (1), p. 551. ISSN 1471-2105.

Halling-Brown, Mark D. and Pappalardo, F. and Rapin, N. and Zhang, P. and Alemani, D. and Emerson, A. and Castiglione, F. and Duroux, P. and Pennisi, M. and Miotto, O. and Churchill, D. and Rossi, E. and Moss, David S. and Sansom, Clare E. and Bernaschi, M. and Lefranc, M.P. and Brunak, S. and Lund, O. and Motta, S. and Lollini, P.L. and Murgo, A. and Palladini, A. and Basford, K.E. and Brusic, V. and Shepherd, Adrian J. (2010) ImmunoGrid: towards agent-based simulations of the human immune system at a natural scale. Philosophical Transactions of the Royal Society A 368 (1920), pp. 1799-1815. ISSN 0080-4614.

Lees, William D. and Moss, David S. and Shepherd, Adrian J. (2010) A computational analysis of the antigenic properties of Haemagglutinin in Influenza A H3N2. Bioinformatics 26 (11), pp. 1403-1408. ISSN 1367-4803.

Halling-Brown, Mark D. and Moss, David S. and Sansom, Clare E. and Shepherd, Adrian J. (2009) A computational grid framework for immunological applications. Philosophical Transactions of the Royal Society A 367 (1898), pp. 2705-2716. ISSN 1364-503X.

Kabiljo, R. and Clegg, A.B. and Shepherd, Adrian J. (2009) A realistic assessment of methods for extracting gene/protein interactions from free text. BMC Bioinformatics 10 , p. 233. ISSN 1471-2105.

Pappalardo, F. and Halling-Brown, Mark D. and Rapin, N. and Zhang, P. and Alemani, D. and Emerson, A. and Paci, P. and Duroux, P. and Pennisi, M. and Palladini, A. and Miotto, O. and Churchill, D. and Rossi, E. and Shepherd, Adrian J. and Moss, David S. and Castiglione, F. and Bernaschi, M. and Lefranc, M.P. and Brunak, S. and Motta, S. and Lollini, P.L. and Basford, K.E. and Brusic, V. (2009) ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization. Briefings in Bioinformatics 10 (3), pp. 330-340. ISSN 1467-5463.

Pappalardo, F. and Zhang, P. and Halling-Brown, Mark D. and Basford, K.E. and Scalia, A. and Shepherd, Adrian J. and Moss, David S. and Motta, S. and Brusic, V. (2008) Computational simulations of the immune system for personalized medicine: state of the art and challenges. Current Pharmacogenomics and Personalized Medicine 6 (4), pp. 260-271. ISSN 1875-6921.

Halling-Brown, Mark D. and Moss, David S. and Shepherd, Adrian J. (2008) Towards a lightweight generic computational grid framework for biological research. BMC Bioninformatics 9 , ISSN 1471-2105.

Halling-Brown, Mark D. and Shepherd, Adrian J. (2008) Constructing computational pipelines. Methods in Molecular Biology 453 (4), pp. 451-470. ISSN 1064-3745.

Clegg, A.B. and Shepherd, Adrian J. (2008) Text Mining. Methods in Molecular Biology 453 (4), pp. 471-491. ISSN 1064-3745.

Pearl, F.M.G. and Bennett, C.F. and Bray, J.E. and Harrison, A.P. and Martin, Nigel and Shepherd, Adrian J. and Sillitoe, I. and Thornton, Janet M. and Orengo, C.A. (2003) The CATH database: an extended protein family resource for structural and functional genomics. Nucleic Acids Research 31 (1), pp. 452-455. ISSN 0305-1048.

Shepherd, Adrian J. and Martin, Nigel and Johnson, Roger and Kellam, P. and Orengo, C.A. (2002) PFDB: a generic protein family database integrating the CATH domain structure database with sequence based protein family resources. Bioinformatics 18 (12), pp. 1666-1672. ISSN 1367-4803.

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 1526. New York, U.S.: Humana Press, pp. 139-158. 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 1526. New York, U.S.: Humana Press, pp. 257-270. ISBN 9781493966110.

Conference or Workshop Item

Shepherd, Adrian J. and Kabiljo, R. (2008) Protein name tagging in the immunological domain. In: Proceedings of the Third Symposium on Semantic Mining in Biomedicine, September 1-3 2008, Turku, Finland.

Shepherd, Adrian J. and Clegg, A.B. (2008) Syntactic pattern matching with GraphSpider and MPL. In: Proceedings of the Third Symposium on Semantic Mining in Biomedicine, September 1-3 2008, Turku, Finland.