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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.

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 ,

Patronov, Atanas; Salamanova, Edvokiya; Dimitrov, Ivan; Flower, Darren R. and Doytchinova, Irini (2014). Histidine hydrogen bonding in MHC at pH 5 and pH 7 modeled by molecular docking and molecular dynamics simulations. Current Computer-Aided Drug design, 10 (1), pp. 41-49.

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.),

Flower, Darren R. (2012). Systematic identification of small molecule adjuvants. Expert Opinion on Drug Discovery, 7 (9), pp. 807-817.

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.

Davies, Matthew N; Gloriam, David E; Secker, Andrew; Freitas, Alex A; Timmis, Jon and Flower, Darren R (2011). Present perspectives on the automated classification of the G-protein coupled receptors (GPCRs) at the protein sequence level. Current Topics in Medicinal Chemistry, 11 (15), pp. 1994-2009.

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),

Atanasova, M.; Dimitrov, I.; Flower, D.R. and Doytchinova, I. (2011). MHC class II binding prediction by molecular docking. Molecular Informatics, 30 (4), pp. 368-375.

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.

Secker, A.; Davies, M.N.; Freitas, A A; Clark, E.B.; Timmis, J. and Flower, Darren R. (2010). Hierarchical classification of G-protein-coupled receptors with data-driven selection of attributes and classifiers. International Journal of Data Mining and Bioinformatics, 4 (2), pp. 191-210.

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.

Flower, Darren R. (2009). Advances in predicting and manipulating the immunogenicity of biotherapeutics and vaccines. BioDrugs, 23 (4), pp. 231-240.

Halling-Brown, Mark; Shaban, Raheel; Frampton, Dan; Sansom, Clare E.; Davies, Matthew; Flower, Darren; Duffield, Melanie; Titball, Richard W.; Brusic, Vladimir and Moss, David S. (2009). Proteins accessible to immune surveillance show significant T-cell epitope depletion:implications for vaccine design. Molecular Immunology, 46 (13), pp. 2699-2705.

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),

Mizutori, Y.; Nagayama, Y.; Flower, D.; Misharin, A.; Aliesky, H.A.; Rapoport, B. and McLachlan, S.M. (2008). Role of the transgenic human thyrotropin receptor A-subunit in thyroiditis induced by A-subunit immunization and regulatory T cell depletion. Clinical and Experimental Immunology, 154 (3), pp. 305-315. (Unpublished)

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.

Bayry, Jagadeesh; Tchilian, Elma Z.; Davies, Matthew N.; Forbes, Emily K.; Draper, Simon J.; Kaveri, Srini V.; Hill, Adrian V.S.; Kazatchkine, Michel D.; Beverley, Peter C.L.; Flower, Darren R and Tough, David F. (2008). In silico identified CCR4 antagonists target regulatory T cells and exert adjuvant activity in vaccination. Proceedings of the National Academy of Sciences, 105 (29), pp. 10221-10226.

Vivona, Sandro; Gardy, Jennifer L.; Ramachandran, Srinivasan; Brinkman, Fiona S.L.; Raghava, G.P.S.; Flower, Darren R and Filippini, Francesco (2008). Computer-aided biotechnology:from immuno-informatics to reverse vaccinology. Trends in Biotechnology, 26 (4), pp. 190-200.

Wan, Shunzhou; Flower, Darren R. and Coveney, Peter V. (2008). Toward an atomistic understanding of the immune synapse:large-scale molecular dynamics simulation of a membrane-embedded TCR-pMHC-CD4 complex. Molecular Immunology, 45 (5), pp. 1221-1230.

Davies, Matthew N.; Lamikanra, Abigail; Sansom, Clare E.; Flower, Darren R.; Moss, David S. and Travers, Paul J. (2008). Identification of the HLA-DM/HLA-DR interface. Molecular Immunology, 45 (4), pp. 1063-1070.

Todman, Sarah J.; Halling-Brown, Mark D.; Davies, Matthew N.; Flower, Darren R; Kayikci, Melis and Moss, David S. (2008). Toward the atomistic simulation of T cell epitopes automated construction of MHC:peptide structures for free energy calculations. Journal of Molecular Graphics and Modelling, 26 (6), pp. 957-961.

Bayry, Jagadeesh; Flower, Darren R.; Tough, David F. and Kaveri, Srini V. (2008). From 'perfect mix' to 'potion magique':regulatory T cells and anti-inflammatory cytokines as adjuvant targets. Nature Reviews: Microbiology, 6 (1),

Davies, Matthew N.; Secker, Andrew; Freitas, Alex A.; Mendao, Miguel; Timmis, Jon and Flower, Darren R. (2007). On the hierarchical classification of G protein-coupled receptors. Bioinformatics, 23 (23), pp. 3113-3118.

Davies, Matthew N. and Flower, Darren R. (2007). Harnessing bioinformatics to discover new vaccines. Drug Discovery Today, 12 (9-10), pp. 389-395.

Doytchinova, Irini A. and Flower, Darren R. (2007). Identifying candidate subunit vaccines using an alignment-independent method based on principal amino acid properties. Vaccine, 25 (5), pp. 856-866.

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

Doytchinova, Irini A. and Flower, Darren R. (2007). Predicting class I major histocompatibility complex (MHC) binders using multivariate statistics:comparison of discriminant analysis and multiple linear regression. Journal of Chemical Information and Modeling, 47 (1), pp. 234-238.

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.

Doytchinova, Irini A. and Flower, Darren R. (2006). Class I T-cell epitope prediction:improvements using a combination of proteasome cleavage, TAP affinity, and MHC binding. Molecular Immunology, 43 (13), pp. 2037-2044.

Hattotuwagama, Channa K.; Toseland, Christopher P.; Guan, Pingping; Taylor, Debra J.; Hemsley, Shelley L.; Doytchinova, Irini A. and Flower, Daren R. (2006). Toward prediction of class II mouse major histocompatibility complex peptide binding affinity:in silico bioinformatic evaluation using partial least squares, a robust multivariate statistical technique. Journal of Chemical Information and Modeling, 46 (3), pp. 1491-1502.

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. and Flower, Darren R, (2006). Modeling the peptide-T cell receptor interaction by the comparative molecular similarity indices analysis-soft independent modeling of class analogy technique. Journal of Medicinal Chemistry, 49 (7), pp. 2193-2199.

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.

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.

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.

Doytchinova, Irini; Hemsley, Shelley and Flower, Darren R. (2004). Transporter associated with antigen processing preselection of peptides binding to the MHC:a bioinformatic evaluation. Journal of Immunology, 173 (11), pp. 6813-6819.

Doytchinova, Irini A.; Guan, Pingping and Flower, Darren R. (2004). Quantitative structure-activity relationships and the prediction of MHC supermotifs. Methods, 34 (4), pp. 444-453.

Flower, Darren R. and Attwood, Teresa K. (2004). Integrative bioinformatics for functional genorne annotation:trawling for G protein-coupled receptors. Seminars in Cell and Developmental Biology, 15 (6), pp. 693-701.

Wan, Shunzhou; Coveney, Peter and Flower, Darren R. (2004). Large-scale molecular dynamics simulations of HLA-A*0201 complexed with a tumor-specific antigenic peptide:can the α3 and β2m domains be neglected? Journal of Computational Chemistry, 25 (15), pp. 1803-1813.

Hattotuwagama, Channa K.; Guan, Pingping; Doytchinova, Irini A. and Flower, Darren R. (2004). New horizons in mouse immunoinformatics:reliable in silico prediction of mouse class I histocompatibility major complex peptide binding affinity. Organic and Biomolecular Chemistry, 2 (22), pp. 3274-3283.

Doytchinova, Irini A.; Walshe, Valerie A.; Jones, Nicola A.; Gloster, Simone E.; Borrow, Persephone and Flower, Darren R. (2004). Coupling in silico and in vitro analysis of peptide-MHC binding:a bioinformatic approach enabling prediction of superbinding peptides and anchorless epitopes. Journal of Immunological Methods, 172 (12), pp. 7495-7502.

Doytchinova, Irini A.; Guan, Pingping and Flower, Darren R. (2004). Identifiying human MHC supertypes using bioinformatic methods. Journal of Immunology, 172 (7), pp. 4314-4323.

Hattotuwagama, Channa K.; Guan, Pingping; Doytchinova, Irini A.; Zygouri, Christianna and Flower, Darren R. (2004). Quantitative online prediction of peptide binding to the major histocompatibility complex. Journal of Molecular Graphics and Modelling, 22 (3), pp. 195-207.

Flower, Darren R. (2003). Towards in silico prediction of immunogenic epitopes. Trends in Immunology, 24 (12), pp. 667-674.

McSparron, Helen; Blythe, Martin J.; Zygouri, Christianna; Doytchinova, Irini A. and Flower, Darren R. (2003). JenPep : a novel computational information resource for immunobiology and vaccinology. Journal of Chemical Information and Modeling, 43 (4), pp. 1276-1287.

Taylor, Paul D.; Attwood, Teresa K. and Flower, Darren R. (2003). BPROMPT:a consensus server for membrane protein prediction. Nucleic Acids Research, 31 (13), pp. 3698-3700.

Guan, Pingping; Doytchinova, Irini A. and Flower, Darren R. (2003). A comparative molecular similarity indices (CoMSIA) study of peptide binding to the HLA-A3 superfamily. Bioorganic and Medicinal Chemistry Letters, 11 (10), pp. 2307-2311.

Doytchinova, Irini and Flower, Darren (2003). The HLA-A2-supermotif:a QSAR definition. Organic and Biomolecular Chemistry, 1 (15), pp. 2648-2654.

Atanasova, Mariyana; Patronov, Atanas; Dimitrov, Ivan; Flower, Darren R. and Doytchinova, Irini EpiDOCK:a molecular docking-based tool for MHC class II binding prediction. Protein Engineering, Design and Selection, 26 (10), pp. 631-634.

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

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. 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),

Davies, Matthew N.; Gloriam, David E.; Secker, Andrew; Freitas, Alex A.; Mendao, Miguel; Timmis, Jon and Flower, Darren R. Proteomic applications of automated GPCR classification. Proteomics, 7 (16), pp. 2800-2814.

Davies, Matthew N.; Secker, Andrew; Freitas, Alex A.; Clark, Edward; Timmis, Jon and Flower, Darren R. Optimizing amino acid groupings for GPCR classification. BMC Bioinformatics, 24 (18), pp. 1980-1986.

Dimitrov, Ivan; Bangov, Ivan; Flower, Darren R. and Doytchinova, Irini AllerTOP v.2 - a server for in silico prediction of allergens. Journal of Molecular Modeling, 20 (6),

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

Dimitrov, Ivan; Garnev, Panayot; Flower, Darren R. and Doytchinova, Irini Peptide binding to the HLA-DRB1 supertype:a proteochemometrics analysis. European Journal of Medicinal Chemistry, 45 (1), pp. 236-243.

Doytchinova, I.A. and Flower, D.R. Towards the in silico identification of class II restricted T-cell epitopes:a partial least squares iterative self-consistent algorithm for affinity prediction. Bioinformatics, 19 (17), pp. 2263-2270.

Doytchinova, Irini; Petkov, Peicho; Dimitrov, Ivan; Atanasova, Mariyana and Flower, Darren R HLA-DP2 binding prediction by molecular dynamics simulations. Protein Science, 20 (11), pp. 1918-28.

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

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

Flower, Darren R. Designing immunogenic peptides. Nature Chemical Biology, 9 (12), pp. 749-753.

Guan, Pingping; Doytchinova, Irini A.; Zygouri, Christianna and Flower, Darren R. MHCPred : a server for quantitative prediction of peptide-MHC binding. Nucleic Acids Research, 31 (13), pp. 3621-3624.

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

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 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.

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

Lopes, A. Ross; Jaye, Assan; Dorrell, Lucy; Sabally, Sehu; Alabi, Abraham; Jones, Nicola A.; Flower, Darren R.; de Groot, Anne; Newton, Phillipa; Lascar, R. Monica; Williams, Ian; Whittle, Hilton; Bertoletti, Antonio; Borrow, Persephone and Maini, Mala K. Greater CD8+ TCR heterogeneity and functional flexibility in HIV-2 compared to HIV-1 infection. Journal of Immunology, 171 (1), pp. 307-316.

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

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

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

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

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

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

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

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

Book Section

Davies, Matthew N.; Pere, Helene; Bosschem, Iris; Haesebrouck, Freddy; Flahou, Bram; Tartour, Eric; Flower, Darren R.; Tough, David F. and Bayry, Jagadeesh (2016). In silico adjuvant design and validation. IN: Vaccine adjuvants. Fox, Christopher B. (ed.) Methods in Molecular Biology . New York (US): Springer.

Mumtaz, Shahzad; Flower, Darren R. and Nabney, Ian (2014). Multi-level visualisation using Gaussian process latent variable models. IN: IVAPP 2014. Laramee, Robert S.; Kerren, Andreas and Braz, José (eds) Lisbon (PT): SciTePress.

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). IEEE.

Flower, Darren R. (2011). Immunological protein-protein interactions:a critical reflection. IN: Protein-protein interactions. Kangueane, Pandjassarame (ed.) Biochemistry Research Trends . Nova science.

Davies, Matthew N. and Flower, Darren R. (2009). In silico identification of novel G protein coupled receptors. IN: Membrane proteomics. Peirce, Matthew J. and Wait, Robin (eds) Methods in molecular biology . Humana Press.

Davies, Matthew N. and Flower, Darren R. (2007). Static energy analysis of MHC class I and class II peptide-binding affinity. IN: Immunoinformatics. Flowers, Darren R. (ed.) Methods in molecular biology™ . Totowa, NJ (US): Humana Press.

Flower, Darren R. (2007). Immunoinformatics and the in silico prediction of immunogenicity:an introduction. IN: Immunoinformatics. Flower, Darren R. (ed.) Methods in molecular biology™ . Totowa, NJ (US): Humana Press.

Flower, Darren R. (2007). Preface. IN: Immunoinformatics. Flower, Darren R. (ed.) Methods in molecular miology™ . Totowa, NJ (US): Humana Press.

Guan, Pingping; Doytchinova, Irini A. and Flower, Darren R. (2007). The classification of HLA supertypes by GRID/CPCA and hierarchical clustering methods. IN: Immunoioformatics. Flower, Darren R. (ed.) Methods in molecular biology™ . Totowa, NJ (US): Humana Press.

Hattotuwagama, Channa K.; Doytchinova, Irini A. and Flower, Darren R (2007). Toward the prediction of class I and II mouse major histocompatibility complex-peptide-binding affinity:in silico bioinformatic step-by-step guide using quantitative structure-activity relationships. IN: Immunoinformatics. Flowers, Darren R. (ed.) Methods in molecular biology™ . Totowa, NJ (US): Humana Press.

Liu, Wen; Wan, Ji; Meng, Xiangshan; Flower, Darren R. and Li, Tongbin (2007). In silico prediction of peptide-MHC binding affinity using SVRMHC. IN: Immunoinformatics. Flowers, Darren R. (ed.) Methods in molecular biology™ . Totowa, NJ (US): Humana Press.

Wan, Shunzhou; Coveney, Peter V. and Flower, Darren R. (2007). Molecular dynamics simulations:bring biomolecular structures alive on a computer. IN: Immunoinformatics. Flowers, Darren R. (ed.) Methods in molecular biology™ . Totowa, NJ (US): Humana Press.