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Article

Quinzo, Monica J., Lafuente, Esther M., Zuluaga, Pilar, Flower, Darren R. and Reche, Pedro A. (2019). Computational assembly of a human Cytomegalovirus vaccine upon experimental epitope legacy. BMC Bioinformatics, 20 (Suppl ),

Murphy, David, Reche, Pedro and Flower, Darren R (2019). Selection-based design of in silico dengue epitope ensemble vaccines. Chemical Biology and Drug Design, 93 (1), pp. 21-28.

Reche, Pedro, Flower, Darren R., Fridkis-Hareli, Masha and Hoshino, Yoshihiko (2018). Pepti de-Based Immunotherapeutics and Vaccines 2017. Journal of Immunology Research, 2018 ,

Shah, Preksha, Mistry, Jaymisha, Reche, Pedro A., Gatherer, Derek and Flower, Darren R (2018). In silico design of Mycobacterium tuberculosis epitope ensemble vaccines. Molecular Immunology, 97 , pp. 56-62.

Doytchinova, Irini A. and Flower, Darren R. (2018). In silico prediction of cancer immunogens:current state of the art. Immunology, 19 (1),

Damfo, Shymaa Abdullah, Reche, Pedro A., Gatherer, Derek and Flower, Darren R (2017). In silico design of knowledge-based Plasmodium falciparum epitope ensemble vaccines. Journal of Molecular Graphics and Modelling, 78 , pp. 195-205.

Laurie, Jason, Chattopadhyay, Amit K and Flower, Darren R (2017). Protein lipograms. Journal of Theoretical Biology, 430 , pp. 109-116.

Mumtaz, Shahzad, Nabney, Ian T. and Flower, Darren R. (2017). Scrutinizing human MHC polymorphism:supertype analysis using Poisson-Boltzmann electrostatics and clustering. Journal of Molecular Graphics and Modelling, 77 , pp. 130-136.

Mistry, Jaymisha and Flower, Darren R (2017). Designing Epitope Ensemble Vaccines against TB by Selection:Prioritizing Antigens using Predicted Immunogenicity. Bioinformation, 13 (7), pp. 220-223.

Sheikh, Qamar M., Gatherer, Derek, Reche, Pedro A. and Flower, Darren R. (2016). Towards the knowledge-based design of universal influenza epitope ensemble vaccines. Bioinformatics, 32 (21), pp. 3233-3239.

Audain, Enrique, Ramos, Yassel, Hermjakob, Henning, Flower, Darren R. and Perez-Riverol, Yasset (2016). Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences. Bioinformatics, 32 (6), pp. 821-827.

Chattopadhyay, Amit K., Nasiev, Diar and Flower, Darren R. (2015). A statistical physics perspective on alignment-independent protein sequence comparison. Bioinformatics, 31 (15), pp. 2469-2474.

Pappalardo, Francesco, Flower, Darren, Russo, Giulia, Pennisi, Marzio and Motta, Santo (2015). Computational modelling approaches to vaccinology. Pharmacological Research, 92 , pp. 40-45.

Bunkute, Egle, Cummins, Christopher, Crofts, Fraser, Bunce, Gareth, Nabney, Ian T. and Flower, Darren R. (2015). PIP-DB:the protein isoelectric point database. Bioinformatics, 31 (2), pp. 295-296.

Molero-Abraham, Magdalena, Glutting, John-Paul, Flower, Darren R., Lafuente, Esther M. and Reche, Pedro A. (2015). EPIPOX:immunoinformatic characterization of the shared T-cell epitome between variola virus and related pathogenic orthopoxviruses. Journal of Immunology Research, 2015 ,

Reche, Pedro, Flower, Darren R., Fridkis-Hareli, Masha and Hoshino, Yoshihiko (2015). Peptide-based immunotherapeutics and vaccines 2015. Journal of Immunology Research, 2015 ,

Reche, Pedro A., Fernandez-Caldas, Enrique, Flower, Darren R., Fridkis-Hareli, Masha and Hoshino, Yoshihiko (2014). Peptide-based immunotherapeutics and vaccines. Journal of Immunology Research, 2014 ,

Molero-Abraham, Magdalena, Lafuente, Esther M., Flower, Darren R. and Reche, Pedro A. (2013). Selection of conserved epitopes from hepatitis C virus for pan-populational stimulation of T-cell responses. Clinical and Developmental Immunology, 2013 ,

Flower, Darren R. (2013). The immune system as drug target. Immunology and Immunogenetics Insights, 5 ,

Dimitrov, Ivan, Flower, Darren R. and Doytchinova, Irini (2013). AllerTOP - a server for in silico prediction of allergens. BMC Bioinformatics, 14 (Suppl.),

Patronov, Atanas, Dimitrov, Ivan, Flower, Darren R. and Doytchinova, Irini (2012). Peptide binding to HLA-DP proteins at pH 5.0 and pH 7.0:a quantitative molecular docking study. BMC Structural Biology, 12 ,

Flower, Darren R. (2012). On the utility of alternative amino acid scripts. Bioinformation, 8 (12), pp. 539-542.

Rai, Jade, Lok, Ka In, Mok, Chun Yin, Mann, Harvinder, Noor, Mohammed, Patel, Pritesh and Flower, Darren R (2012). Immunoinformatic evaluation of multiple epitope ensembles as vaccine candidates:E coli 536. Bioinformation, 8 (6), pp. 272-275.

Patronov, Atanas, Dimitrov, Ivan, Flower, Darren R and Doytchinova, Irini (2011). Peptide binding prediction for the human class II MHC allele HLA-DP2:a molecular docking approach. BMC Structural Biology, 11 (32),

Flower, Darren R, Macdonald, Isabel K., Ramakrishnan, Kamna, Davies, Matthew N. and Doytchinova, Irini A. (2010). Computer aided selection of candidate vaccine antigens. Immunome Research, 6 (Suppl.), S1-S16.

Flower, Darren R, Phadwal, Kanchan, Macdonald, Isabel K., Coveney, Peter V., Davies, Matthew N. and Wan, Shunzhou (2010). T-cell epitope prediction and immune complex simulation using molecular dynamics:state of the art and persisting challenges. Immunome Research, 6 (Suppl.), S4.

Macdonald, Isabel K., Harkiolaki, Maria, Hunt, Lawrence, Connelley, Timothy, Carroll, A. Victoria, MacHugh, Niall D., Graham, Simon P., Jones, E. Yvonne, Morrison, W. Ivan, Flower, Darren R and Ellis, Shirley A. (2010). MHC class I bound to an immunodominant Theileria parva epitope demonstrates unconventional presentation to T cell receptors. Plos Pathogens, 6 (10), e1001149.

Dimitrov, Ivan, Garnev, Panayot, Flower, Darren R and Doytchinova, Irini (2010). EpiTOP—a proteochemometric tool for MHC class II binding prediction. Bioinformatics, 26 (16), pp. 2066-8.

Ramakrishnan, Kamna and Flower, Darren R (2010). Discriminating antigen and non-antigen using proteome dissimilarity II:viral and fungal antigens. Bioinformation, 5 (1), pp. 35-38.

Ramakrishnan, Kamna and Flower, Darren R (2010). Discriminating antigen and non-antigen using proteome dissimilarity III:tumour and parasite antigens. Bioinformation, 5 (1), pp. 35-38.

Ramakrishnan, Kamna and Flower, Darren R (2010). Discriminating antigen and non-antigen using proteome dissimilarity:bacterial antigens. Bioinformation, 4 (10), pp. 445-7.

Joosten, Simone A., van Meijgaarden, Krista E., van Weeren, Pascale C., Kazi, Fatima, Geluk, Annemieke, Savage, Nigel D.L., Drijfhout, Jan W., Flower, Darren R, Hanekom, Willem A., Klein, Michèl R. and Ottenhoff, Tom H.M. (2010). Mycobacterium tuberculosis peptides presented by HLA-E molecules are targets for human CD8 T-cells with cytotoxic as well as regulatory activity. Plos Pathogens, 6 (2), e1000782.

Ansari, Hifzur R., Flower, Darren R and Raghava, G.P.S. (2010). AntigenDB:an immunoinformatics database of pathogen antigens. Nucleic Acids Research, 38 (Suppl.), D847-D853.

Dimitrov, Ivan, Garnev, Panayot, Flower, Darren R and Doytchinova, Irini (2010). MHC class II binding prediction:a little help from a friend. Journal of Biomedicine and Biotechnology, 2010 ,

Davies, Matthew N., Bayry, Jagadeesh, Tchilian, Elma Z., Vani, Janakiraman, Shaila, Melkote S., Forbes, Emily K., Draper, Simon J., Beverley, Peter C.L., Tough, David F. and Flower, Darren R. (2009). Toward the discovery of vaccine adjuvants:coupling in silico screening and in vitro analysis of antagonist binding to human and mouse CCR4 receptors. PLoS ONE, 4 (11),

Walshe, Valerie A., Hattotuwagama, Channa K., Doytchinova, Irini A., Wong, MaiLee, Macdonald, Isabel K., Mulder, Arend, Claas, Frans H.J., Pellegrino, Pierre, Turner, Jo, Williams, Ian, Turnbull, Emma L., Borrow, Persephone and Flower, Darren R (2009). Integrating in silico and in vitro analysis of peptide binding affinity to HLA-Cw*0102:a bioinformatic approach to the prediction of new epitopes. PLoS ONE, 4 (11),

O'Brien, Cathal, Flower, Darren R and Feighery, Conleth (2008). Peptide length significantly influences in vitro affinity for MHC class II molecules. Immunome Research, 4 (6),

Davies, Matthew N., Secker, Andrew, Halling-Brown, Mark, Moss, David S., Freitas, Alex A., Timmis, Jon, Clark, Edward and Flower, Darren R (2008). GPCRTree:online hierarchical classification of GPCR function. BMC Research Notes, 1 , p. 67.

Doytchinova, Irini A. and Flower, Darren R. (2007). VaxiJen:a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics, 8 ,

Salomon, Jesper and Flower, Darren R. (2006). Predicting class II MHC-Peptide binding:a kernel based approach using similarity scores. BMC Bioinformatics, 7 ,

Wan, Ji, Liu, Wen, Xu, Qiqi, Ren, Yongliang, Flower, Darren R. and Li, Tongbin (2006). SVRMHC prediction server for MHC-binding peptides. BMC Bioinformatics, 7 , p. 463.

Taylor, Paul D., Toseland, Christopher P., Attwood, Teresa K. and Flower, Darren R. (2006). TATPred:a Bayesian method for the identification of twin arginine translocation pathway signal sequences. Bioinformation, 1 (5), pp. 184-187.

Liu, Wen, Meng, Xiangshan, Xu, Qiqi, Flower, Darren R. and Li, Tongbin (2006). Quantitative prediction of mouse class I MHC peptide binding affinity using support vector machine regression (SVR) models. BMC Bioinformatics, 7 (3), pp. 182-194.

Davies, Matthew N., Hattotuwagama, Channa K., Moss, David S., Drew, Michael G.B. and Flower, Darren R. (2006). Statistical deconvolution of enthalpic energetic contributions to MHC-peptide binding affinity. BMC Structural Biology, 6 (5),

Doytchinova, Irini A., Guan, Pingping and Flower, Darren R. (2006). EpiJen:a server for multistep T cell epitope prediction. BMC Bioinformatics, 7 (3), pp. 131-141.

Toseland, Christopher P., McSparron, Helen, Davies, Matthew N. and Flower, Darren R. (2006). PPD v1.0 - an integrated, web-accessible database of experimentally determined protein pKa values. Nucleic Acids Research, 34 (Suppl.), D199-D203.

Taylor, Paul D., Toseland, Christopher P., Attwood, Teresa K. and Flower, Darren R. (2006). Alpha helical trans-membrane proteins:enhanced prediction using a Bayesian approach. Bioinformation, 1 (6), pp. 234-236.

Taylor, Paul D., Toseland, Christopher P., Attwood, Teresa K. and Flower, Darren R. (2006). Beta barrel trans-membrane proteins:enhanced prediction using a Bayesian approach. Bioinformation, 1 (6), pp. 231-233.

Taylor, Paul D., Attwood, Teresa K. and Flower, Darren R. (2006). Combining algorithms to predict bacterial protein sub-cellular location:parallel versus concurrent implementations. Bioinformation, 1 (8), pp. 285-289.

Hattotuwagama, Channa K. and Flower, Darren R. (2006). Empirical prediction of peptide octanol-water partition coefficients. Bioinformation, 1 (7), pp. 257-259.

Taylor, Paul D., Toseland, Christopher P., Attwood, Teresa K. and Flower, Darren R. (2006). LIPPRED:a web server for accurate prediction of lipoprotein signal sequences and cleavage sites. Bioinformation, 1 (5), pp. 176-179.

Taylor, Paul D., Attwood, Teresa K. and Flower, Darren R. (2006). Multi-class subcellular location prediction for bacterial proteins. Bioinformation, 1 (7), pp. 260-264.

Thompson, Sarah J., Hattotuwagama, Channa K., Holliday, John D. and Flower, Darren R. (2006). On the hydrophobicity of peptides:comparing empirical predictions of peptide log P values. Bioinformation, 1 (7), pp. 237-241.

Taylor, Paul D., Attwood, Teresa K. and Flower, Darren R. (2006). Toward bacterial protein sub-cellular location prediction:single-class discrimminant models for all gram- and gram+ compartments. Bioinformation, 1 (8), pp. 276-280.

Taylor, Paul D., Toseland, Christopher P., Attwood, Teresa K. and Flower, Darren R. (2006). A predictor of membrane class:discriminating α-helical and β-barrel membrane proteins from non-membranous proteins. Bioinformation, 1 (6), pp. 208-213.

Toseland, Christopher P., McSparron, Helen M. and Flower, Darren R. (2005). DSD - An integrated, web-accessible database of dehydrogenase enzyme stereospecificities. BMC Bioinformatics, 6 ,

Jones, Nicola A., Wei, Xiping, Flower, Darren R., Wong, MaiLee, Michor, Franziska, Saag, Michael S., Hahn, Beatrice H., Nowak, Martin A., Shaw, George M. and Borrow, Persephone (2004). Determinants of human immunodeficiency virus type 1 escape from the primary CD8+ cytotoxic T lymphocyte response. Journal of Experimental Medicine, 200 (10), pp. 1243-1256.

Doytchinova, Irini A., Taylor, Paul and Flower, Darren R. (2003). Proteomics in vaccinology and immunobiology:an informatics perspective of the immunone. Journal of Biomedicine and Biotechnology, 2003 (5), pp. 267-290.

Book Section

Mumtaz, Shahzad, Nabney, Ian and Flower, Darren (2012). Novel visualization methods for protein data. IN: 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). USA: IEEE.