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Number of items: 77.

Article

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

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.

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 ,

Flower, Darren R. (2013). Designing immunogenic peptides. Nature Chemical Biology, 9 (12), pp. 749-753.

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

Davies, Matthew N.; Secker, Andrew; Freitas, Alex A.; Clark, Edward; Timmis, Jon and Flower, Darren R. (2008). Optimizing amino acid groupings for GPCR classification. BMC Bioinformatics, 24 (18), pp. 1980-1986.

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). 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 ,

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.; 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.; 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.

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.; 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.

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. (2003). Greater CD8+ TCR heterogeneity and functional flexibility in HIV-2 compared to HIV-1 infection. Journal of Immunology, 171 (1), pp. 307-316.

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.

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.

Guan, Pingping; Doytchinova, Irini A.; Zygouri, Christianna and Flower, Darren R. (2003). MHCPred : a server for quantitative prediction of peptide-MHC binding. Nucleic Acids Research, 31 (13), pp. 3621-3624.

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

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

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),

Doytchinova, Irini A. and Flower, Darren R. 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.

Doytchinova, Irini A.; Walshe, Valerie A.; Jones, Nicola A.; Gloster, Simone E.; Borrow, Persephone and Flower, Darren R. 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.

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.

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.

Secker, A.; Davies, M.N.; Freitas, A A; Clark, E.B.; Timmis, J. and Flower, Darren R. 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.

Patronov, Atanas; Salamanova, Edvokiya; Dimitrov, Ivan; Flower, Darren R. and Doytchinova, Irini 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.

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

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

Doytchinova, Irini A. and Flower, Darren R. 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. In silico identification of supertypes for class II MHCs. Journal of Immunology, 174 (11), pp. 7085-7095.

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.

Hattotuwagama, Channa K.; Guan, Pingping; Doytchinova, Irini A. and Flower, Darren R. 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.

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

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

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.

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 ,

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.

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.

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.

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

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

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

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

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

Wan, Shunzhou; Flower, Darren R. and Coveney, Peter V. 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.; 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),

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

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

Guan, Pingping; Doytchinova, Irini A. and Flower, Darren R. 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.

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

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

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

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.

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.

Flower, Darren R. 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. 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.

Liu, Wen; Wan, Ji; Meng, Xiangshan; Flower, Darren R. and Li, Tongbin 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. 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.

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

Davies, Matthew N. and Flower, Darren R. 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.

Guan, Pingping; Doytchinova, Irini A. and Flower, Darren R. 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.

This list was generated on Fri Nov 24 00:55:24 2017 GMT.