journals  

Journal Publications


 

  • 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.
  • Lees, W.D., Stejskal, L., Moss, D.M., 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.
  • 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.
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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 BMC Highly Accessed
  • Sivalingam, G.N., Shepherd, A.J. (2012). An analysis of B-cell epitope discontinuity. Molecular Immunology 51:304-309
  • 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
  • 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 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
  • 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
  • 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 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
  • 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
  • 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
  • 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
  • Clegg, A.B., Shepherd, A.J. (2007). Benchmarking natural-language parsers for biological applications using dependency graphs. BMC Bioinformatics 8:24 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • Gorse, D., Shepherd, A., Taylor, J.G. (1997). The new ERA in supervised learning. Neural Networks 10(2):343-352
  • 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
  • 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
  • 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
  • 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
  • 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


 

  • 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
  • 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
  • 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
  • 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
  • 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
  • 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