journals  

Preprints

    None awaiting formal publication.

 

Journal Publications

 

2024

  • Zareian, N., Eremin, O., Pandha, H., Baird, R., Kwatra, V., Funingana, G., Verma, C., Choy, D., Hargreaves, S., Moghimi, P., Shepherd, A., Lobo, D. N., Eremin, J., Farzaneh, F., Kordasti S., Spicer, J. (2024). A Phase 1 trial of human telomerase reverse transcriptase (hTERT) vaccination combined with therapeutic strategies to control immune-suppressor mechanisms. Experimental Biology and Medicine, accepted for publication.

2022

  • Cantoni, D., Murray, J. M., Kalemera, M. D., Dicken, S. J., Stejskal, L., Brown, G., Lytras, S., Coey, J. D., McKenna, J., Bridgett, S., Simpson, D. Fairley, D., Thorne, L. G., Reuschl, A-K., Forrest, C., Ganeshalingham, M., Muir, L., Palor, M., Jarvis, L., Willett, B., Power, U. F., McCoy, L. E., Jolly, C., Towers, G. J., Doores, K. J., Robertson, D. L., Shepherd, A. J., Reeves, M. B., Bamford, C. G. G., Grove, J. (2022). Evolutionary remodelling of N-terminal domain loops fine-tunes SARS-CoV-2 spike. EMBO Reports, 0:e202154322.
    [article]
  • Stejskal, L., Kalemera, M. D., Lewis, C. B., Palor, M., Walker, L., Daviter, T. Lees, W. D., Moss, D.S., Kremyda-Vlachou, M., Kozlakidis, Z., Gallo, G., Bailey, D., Rosenberg, W., Illingworth, C. J. R., Shepherd, A. J., Grove, J. (2022). An entropic safety catch controls Hepatitis C virus entry and antibody resistance. eLife, e71854.
    [abstract]
    [article]

2021

  • Barbosa, C. R. R., Barton, J., Shepherd, A. J., Mishto, M. (2021). Mechanistic diversity in MHC class I antigen recognition. Biochemical Journal, 478(24):4187-4202.
    [abstract]
    [article]
  • Maitra, A., Nukala, S., Dickman, R., Martin, L. T., Munshi, T., Gupta, A., Shepherd, A. J., Arnvig, K. B., Tabor, A. B., Keep, N. H., Bhakta, S. (2021). Characterization of the MurT/GatD complex in Mycobacterium tuberculosis towards validating a novel anti-tubercular drug target. JAC-Antimicrobial Resistance, 3(1):dlab028.
    [abstract]
    [article]
  • Modi, T., Gervais, D., Smith, S., Miller, J., Subramaniam, S., Thalassinos, K., Shepherd., A. (2021). Characterisation of the UK anthrax vaccine and human immunogenicity. Human Vaccines & Immunotherapeutics, 17:3 747-758.
    [abstract]
    [PDF | EPUB]

2020

  • Collins, A. M., Yaari, G., Shepherd A. J., Lees, W., Watson, C. T. (2020). Germline immunoglobulin genes: disease susceptibility genes hidden in plain sight? Current Opinion in Systems Biology, 24:100-108.
  • Palor, M., Stejskal, L., Mandal, P., Lenman, A., Alberione, M. P., Kirui, J., Moeller, R., Ebner, S., Meissner, F., Gerold, G., Shepherd A. J., Grove, J. (2020). Cholesterol sensing by CD81 is important for hepatitis C virus entry. Journal of Biological Chemistry, 295.50 16931-16948.
    [abstract]
    [PDF]
  • Stejskal, L., Lees, W. D., Moss, D. S., Palor, M., Bingham, R. J., Shepherd, A. J., Grove, J. (2020). Flexibility and intrinsic disorder are conserved features of hepatitis C virus E2 glycoprotein. PLOS Computational Biology 16(2):e1007710.
    [abstract]
    [PDF]
  • Omer, A., Shemesh, O., Peres, A., Polak, P., Shepherd, A. J., Watson, C. T., Boyd, S. D., Collins, A. M., Lees, W. and Yaari, G. (2020). VDJbase: an adaptive immune receptor (AIR) genotype and haplotype database. Nucleic Acids Research gkz872.
    [abstract]
    [article]
  • Lees, W., Busse, C. E., Corcoran, M., Ohlin, M., Scheepers, C., Matsen IV, F. A., Yaari, G., Watson, C. T., The AIRR Community, Collins, A., Shepherd, A. J. (2020). OGRDB: a reference database of inferred immune receptor genes. Nucleic Acids Research gkz822.
    [abstract]
    [article]

2019

  • Olson, B. J., Moghimi, P., Schramm, C., Obraztsova, A., Ralph, D., Vander Heiden, J. A., Shugay, M., Shepherd, A., Lees, W., Matsen IV, F. A. (2019). sumrep: a summary statistic framework for immune receptor repertoire comparison and model validation. Frontiers in Immunology 10:02533.
    [abstract]
    [PDF]
  • Hart, D. P., Uzun, N., Skelton, S., Kakoschke, A., Househam, J., Moss, D. S., Shepherd, A. J. (2019). Factor VIII cross-matches to the human proteome reduce the predicted inhibitor risk in missense mutation hemophilia A. Haematologica 104(3):599-608.
    [abstract]
    [PDF]

2018

  • Pan, R., Qin, Y., Banasik, M., Lees, W., Shepherd, A.J., Cho, M.W., 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 JVI-01894.
    [abstract]
    [PDF]
    JVI Spotlight article

2017

  • Banerjee, S., Shi, H., Banasik, M., Moon, H., Lees, W., Qin, Y., Harley, A., Shepherd, A., 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 505:113-126.
    [abstract]
    [PMC PDF]
  • Lees, W.D., Stejskal, L., Moss, D.S., Shepherd, A.J. (2017). Investigating substitutions in antibody-antigen complexes using molecular dynamics: a case study with broad-spectrum, influenza A antibodies. Frontiers in Immunology 8:143.
    [abstract]
    [PDF]

2016

  • Ashford, A., Hernandez, A., Greco, T.M., Buch, A., Sodeik, B., Cristea, I.M., Grünewald, K., Shepherd, A., Topf, M. (2016). HVint: A strategy for identifying novel protein-protein interactions in herpes simplex virus type 1. Molecular & Cellular Proteomics 15(9):2939-53.
    [abstract]
    [PDF]
  • Denyer, M.P., Pinheiro, D.Y., Garden, O.A., Shepherd, A.J. (2016). Missed, not missing: phylogenomic evidence for the existence of avian FoxP3. PLOS ONE 11(3): e0150988.
    [abstract]
    [PDF]

2015

  • Lees, W.D., Shepherd, A.J. (2015). Utilities for high-throughput analysis of B-cell clonal lineages. Journal of Immunology Research, Article ID 323506, 6 pages.
    [abstract]
    [PDF]
    [tools]
  • Pentiah, K., Lees, W.D., Moss, D.S., Shepherd, A.J. (2015). N-linked glycans on influenza A H3N2 hemagglutinin constrain binding of host antibodies, but shielding is limited. Glycobiology 25(1):124-32.
    [abstract]
    [PDF]
  • Shepherd, A.J., Skelton, S., Sansom, C.E., Gomez, K., Moss, D.S., Hart, D.P. (2015). A large-scale computational study of inhibitor risk in non-severe haemophilia A. British Journal of Haematology 168(3):413-20.
    [abstract]
    [PDF]

Pre-2015

  • Lees, W., Moss, D.S., Shepherd, A.J. (2014). Evolution in the influenza A H3 stalk — a challenge for broad-spectrum vaccines? Journal of General Virology 95:317-324.
    [abstract]
    [article]
  • Czarnecki, J., Nobeli, I., Smith, A.M., Shepherd, A.J. (2012). A text-mining system for extracting metabolic reactions from full-text articles. BMC Bioinformatics 13:172.
    [abstract] [PDF]
    BMC Highly Accessed
  • Sivalingam, G.N., Shepherd, A.J. (2012). An analysis of B-cell epitope discontinuity. Molecular Immunology 51:304-309.
    [abstract] [Free PDF]
  • Lees, W.D., Moss, D.S., Shepherd, A.J. (2011). Analysis of antigenically important residues in human influenza A in terms of B-cell epitopes. Journal of Virology 85: 8548-8555.
    [abstract]
  • Garcia-Alcade, F., Blanco, A., Shepherd, A.J. (2010). An intuitionistic approach to scoring DNA sequences against transcription factor binding site motifs. BMC Bioinformatics 11:551.
    [abstract] [PDF]
    BMC Highly Accessed
  • Lees, W., Moss, D.S., Shepherd, A.J. (2010). A computational analysis of the antigenic properties of haemagglutinin in influenza A H3N2. Bioinformatics 26(11):1403-1408.
    [abstract] [PDF]
  • Halling-Brown, M., Pappalardo, F., Rapin, N., Zhang, P., Alemani, D., Emerson, A., Castiglione, F., Duroux, P., Pennisi, M., Miotto, O., Churchill, D., Rossi, E., Moss, D.S., Sansom, C.E., Bernaschi, M., Lefranc, M.P., Brunak, S., Lund, O., Motta, S., Lollini, P.L., Murgo, A., Palladini, A., Basford, K.E., Brusic, V., Shepherd, A.J. (2010). ImmunoGrid: Towards agent-based simulations of the human immune system at a natural scale. Philosophical Transactions of the Royal Society A 368:2799-2815.
    [abstract]
  • Kabiljo, R., Clegg, A.B., Shepherd, A.J. (2009). A realistic assessment of methods for extracting gene/protein interactions from free text. BMC Bioinformatics 10:233.
    [abstract] [PDF]
    BMC Highly Accessed
  • Halling-Brown, M.D., Moss, D.S., Sansom, C.E., Shepherd, A.J. (2009). A computational grid framework for immunological applications. Philosophical Transactions of the Royal Society A 367(1898):2705-2716.
    [abstract]
    [PDF]
  • Pappalardo, F., Halling-Brown, M.D., Rapin, N., Zhang, P., Alemani, D., Emerson, A., Paci, P., Duroux, P., Pennisi, M., Palladini, A., Miotto, O., Churchill, D., Rossi, E., Shepherd, A.J., Moss, D.S., Castiglione, F., Bernaschi, M., Lefranc, M.P., Brunak, S., Motta, S., Lollini, P.L., Basford, K.E., Brusic, V. (2009). ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design, and optimization. Briefings in Bioinformatics 10:330-340.
    [abstract]
    [PDF]
  • Pappalardo, F., Zhang, P., Halling-Brown,M., Basford, K., Scalia, A., Shepherd, A., Moss, D., Motta, S., 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):260-271.
    [abstract]
  • Halling-Brown, M.D., Moss, D.S., Shepherd, A.J. (2008). Towards a lightweight generic computational grid framework for biological research. BMC Bioinformatics 9:407.
    [abstract] [PDF]
  • Clegg, A.B., Shepherd, A.J. (2007). Benchmarking natural-language parsers for biological applications using dependency graphs. BMC Bioinformatics 8:24.
    [abstract] [PDF]
    BMC Highly Accessed
  • Shepherd, A.J., Gorse, D., Thornton, J.M. (2003). A novel approach to the recognition of protein architecture from sequence using Fourier analysis and neural networks. Proteins 50(2):290-302.
    [abstract]
  • Pearl, F.M.G., Bennett, C.F., Bray, J.E., Harrison, A.P., Martin, N., Shepherd, A., Sillitoe, I., Thornton, J., Orengo, C.A. (2003). The CATH database: an extended protein family resource for structural and functional genomics. Nucleic Acids Research 31(1):452-455.
    [abstract]
    [PDF]
  • Shepherd, A.J., Martin, N.J., Johnson, R.G., Kellam, P., 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):1666-1672.
    [abstract]
    [PDF]
  • de la Cruz, X., Hutchinson, E.G., Shepherd, A., Thornton, J.M. (2002). Towards predicting protein topology: an approach to identifying beta-hairpins. PNAS 99(17):11157-11162.
    [abstract]
    [PDF]
  • Buchan, D.W.A., Shepherd, A.J., Lee, D., Pearl, F., Rison, S.C.G., Thornton, J.M., Orengo, C.A. (2002). Gene3D: Structural assignment for whole genes and genomes using the CATH domain structure database. Genome Research 12(3):503-514.
    [abstract]
    [PDF]
  • Pearl, F.M.G., Lee, D., Bray, J.E., Buchan, D.W.A., Shepherd, A.J., Orengo, C.A. (2002). The CATH extended protein-family database: Providing structural annotations for genome sequences. Protein Science 11(2):233-244.
    [abstract]
    [PDF]
  • Pearl, F.M.G., Martin, N., Bray, J.E., Buchan, D.W.A., Harrison, A.P., Lee, D., Reeves, G.A., Shepherd, A.J., Sillitoe, I., Todd, A.E., Thornton, J.M., Orengo, C.A. (2001). A rapid classification protocol for the CATH domain database to support structure genomics. Nucleic Acids Research 29(1):223-227.
    [abstract]
    [PDF]
  • Albà, M.M., Lee, D., Pearl, F.M.G., Shepherd, A.J., Martin, N.M., Orengo, C.A., Kellam, P. (2001). VIDA: a virus database system for the organization of virus genome open reading frames. Nucleic Acids Research 29(1):133-136.
    [abstract]
    [PDF]
  • Shepherd, A.J., Gorse, D., Thornton, J.M. (1999). Prediction of the location and type of beta-turns in proteins using neural networks. Protein Science 8(5):1045-1055.
    [abstract]
    [PDF]
  • Gorse, D., Shepherd, A., Taylor, J.G. (1997). The new ERA in supervised learning. Neural Networks 10(2):343-352.
    [abstract]
  • Gorse, D., Shepherd, A., Taylor, J.G. (1993). Avoiding local minima using a range expansion algorithm. Neural Network World 5:503-510.
  • Gorse, D., Shepherd, A. (1992). Adding stochastic search to conjugate gradient algorithms. Neural Network World 2:599-605.

 

Articles in Conference Proceedings

 

  • Batty, P.A., Skelton, S., Shepherd, A.J., Hart, D.P. (2014). Amino acid sequence epitope mapping of anti-factor VIII monoclonal antibodies. In British Journal of Haematology 165:8 Special Issue: Abstracts of the 54th Annual Scientific Meeting of the British Society for Haematology, 28-30 April 2014, Birmingham, UK.
  • Batty, P.A., Skelton, S., Shepherd, A.J., Hart, D.P. (2013). Amino acid sequence epitope mapping of four factor VIII monoclonal antibodies. In Journal of Thrombosis and Haemostasis 11(Suppl. 2):579 Abstracts of the XXIV Congress of the International Society on Thrombosis and Haemostasis, 29 June to 4 July 2013, Amsterdam, Netherlands.
  • Skelton, S., Moss, D., Sansom, C., Gomez, K, Shepherd, A.J., Hart, D.P. (2012). Novel MHC-peptide-T cell receptor interfaces are necessary for inhibitor formation in mild/moderate haemophilia A secondary to missense mutation genotypes. In British Journal of Haematology 157:10 Special Issue: Abstracts of the 52nd Annual Scientific Meeting of the British Society for Haematology, 16-18 April 2012, Glasgow, UK.
  • Pappalardo, F., Halling-Brown, M.D., Pennisi, M. Chiacchio, F., Sansom, C., Shepherd, A.J., Moss, D.S., Motta, S., Brusic, V. (2009). The ImmunoGrid simulator: How to use it. In Computational Intelligence Methods for Bioinformatics and Biostatistics, 6th International Meeting, CIBB 2009, Genoa, Italy, October 15-17, 2009, Revised Selected Papers. F. Masulli, L.E. Peterson, R. Tagliaferri (eds.) Lecture Notes in Computer Science, vol. 6160, Springer 2010.
  • Clegg, A.B., Shepherd, A.J. (2008). Syntactic pattern matching with GraphSpider and MPL. In Proceedings of the Third Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland, September 2008, 129-132.
    [PDF]
  • Kabiljo, R., Shepherd, A. (2008). Protein name tagging in the immunological domain. In Proceedings of the Third Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland, September 2008, 141-144.
    [PDF]
  • Mastriani, E., Halling-Brown, M.D., Shepherd A., Motta S. (2008). ImmunoGrid-PI2S2 Integration Architecture. In Proceedings of the Grid Open Days all'Universita di Palermo, Palermo, Sicily, 6-7 December 2007, 111-116.
  • Kabiljo, R., Stoycheva, D., Shepherd, A.J. (2007). ProSpecTome: a new tagged corpus for protein named entity recognition. In Proceedings of the Annual Meeting of the ISMB BioLINK Special Interest Group on Text Data Mining, Vienna, Austria, July 2007, 24-27.
    [PDF]
  • Halling-Brown, M., Moss, D., Sansom, C., Shepherd, A. (2006). Web services, workflow & grid technologies for immunoinformatics. In Proceedings of the International Congress of Immunogenomics and Immunomics (BCII2006) , Budapest, Hungary, 8-12 October 2006, 268.
  • Clegg, A.B., Shepherd, A.J. (2005). Evaluating and integrating treebank parsers on a biomedical corpus. In Proceedings of the Association for Computational Linguistics 43rd Annual Meeting Workshop on Software 2005 , Ann Arbor, US, June 2005.
    [PDF] [supplementary material]
  • Gorse, D., Shepherd, A., Taylor, J.G. (1994). A classical algorithm for avoiding local minima. In Proceedings of WCNN '94, San Diego, June 1994, III-364-369.
  • Gorse, D., Shepherd, A., Taylor, J.G. (1994). Avoiding local minima by a classical range expansion algorithm. In Proceedings of ICANN '94, Sorrento, May 1994, 1:525-528.
  • Gorse, D., Shepherd, A., Taylor, J.G. (1993). Tracking global minima by progressive range expansion. In Proceedings of IJCNN '93, Portland, Oregon, July 1993, IV-350-353.

 

Books and Book Chapters

 

  • Perosanz, M.G., Russo, G., Sanchez-Trincado Lopez, J.L., Pennisi, M., Reche, P.A., Shepherd, A., Pappalardo, F. (2018). Computational Immunogenetics in Reference Module in Life Sciences, Elsevier.
  • Lees, W.D., Shepherd, A.J. (2017). Studying Antibody Repertoires with Next-Generation Sequencing in Bioinformatics Volume II: Structure, Function, and Applications, volume 1526 of the series Methods in Molecular Biology, Springer, 257-279.
    [abstract]
  • Czarnecki, J., Shepherd, A.J. (2017). Metabolic Pathway Mining, in Bioinformatics Volume II: Structure, Function, and Applications, volume 1526 of the series Methods in Molecular Biology, Springer, 139-158.
    [abstract]
  • Czarnecki, J., Shepherd, A.J. (2014). Mining Biological Networks from Full-text Articles, In Biomedical Literature Mining, V.D. Kumar and H.J. Tipney (eds.), Methods in Molecular Biology series, Vol. 1159, Springer, 135-145.
    [abstract]
  • Halling-Brown, M., Shepherd, A.J. (2008). Constructing Computational Pipelines, In Bioinformatics Volume II: Structure, Function and Applications, J.M. Keith (ed.), Methods in Molecular Biology 453, Humana Press, 451-470
    [abstract]
  • Clegg, A.B., Shepherd, A.J. (2008). Text Mining, In Bioinformatics Volume II: Structure, Function and Applications, J.M. Keith (ed.), Methods in Molecular Biology 453, Humana Press, 471-491.
    [abstract]
  • Shepherd, A.J. (1997). Second-Order Methods for Neural Networks: Fast and Reliable Training Methods for Multi-Layer Perceptrons. Perspectives in Neural Computing series, Springer, May 1997 & 2012.