Willie Taylor: Publications

  • Bywater, RP (2017)
    A tensegrity model for hydrogen bond networks in proteins.
    Heliyon 3, e00307 PubMed abstract
  • Godány, M; Khatri, BS and Goldstein, RA (2017)
    Optimal chemotactic responses in stochastic environments.
    PLOS ONE 12, e0179111 PubMed abstract
  • Hargreaves, AD; Zhou, L; Christensen, J; Marlétaz, F; Liu, S; Li, F; Jansen, PG; Spiga, E; Hansen, MT; Pedersen, SVH; Biswas, S; Serikawa, K; Fox, BA; Taylor, WR; Mulley, JF; Zhang, G; Heller, RS and Holland, PWH (2017)
    Genome sequence of a diabetes-prone rodent reveals a mutation hotspot around the ParaHox gene cluster.
    Proceedings of the National Academy of Sciences of the United States of America 114, 7677-7682 PubMed abstract
  • Seddon, GM and Bywater, RP (2017)
    The fate of proteins in outer space.
    International Journal of Astrobiology 16, 19-27
  • Taylor, HB; Khuong, A; Wu, Z; Xu, Q; Morley, R; Gregory, L; Poliakov, A; Taylor, WR and Wilkinson, DG (2017)
    Cell segregation and border sharpening by Eph receptor-ephrin-mediated heterotypic repulsion.
    Journal of the Royal Society Interface 14, 20170338 PubMed abstract
  • Taylor, WR (2017)
    Algorithms for matching partially labelled sequence graphs.
    Algorithms for Molecular Biology 12, 24 PubMed abstract
  • Taylor, WR (2017)
    SimGen: A general simulation method for large systems.
    Journal of Molecular Biology 429, 408-415 PubMed abstract
  • Taylor, WR and Hamilton, RS (2017)
    Exploring RNA conformational space under sparse distance restraints.
    Scientific Reports 7, 44074 PubMed abstract
  • Taylor, WR; Stoye, JP and Taylor, IA (2017)
    A comparative analysis of the foamy and ortho virus capsid structures reveals an ancient domain duplication.
    BMC Structural Biology 17, 3 PubMed abstract
  • Ball, NJ; Nicastro, G; Dutta, M; Pollard, DJ; Goldstone, DC; Sanz-Ramos, M; Ramos, A; Müllers, E; Stirnnagel, K; Stanke, N; Lindemann, D; Stoye, JP; Taylor, WR; Rosenthal, PB and Taylor, IA (2016)
    Structure of a spumaretrovirus gag central domain reveals an ancient retroviral capsid.
    PLOS Pathogens 12, e1005981 PubMed abstract
  • Bywater, RP (2016)
    Comparison of algorithms for prediction of protein structural features from evolutionary data.
    PLOS ONE 11, e0150769 PubMed abstract
  • Bywater, RP and Middleton, JN (2016)
    Melody discrimination and protein fold classification.
    Heliyon 2, e00175 PubMed abstract
  • Khatri, BS (2016)
    Quantifying evolutionary dynamics from variant-frequency time series.
    Scientific Reports 6, 32497 PubMed abstract
  • Pandini, A; Morcos, F and Khan, S (2016)
    The gearbox of the bacterial flagellar motor switch.
    Structure 24, 1209-1220 PubMed abstract
  • Smith, SJ; Towers, N; Saldanha, JW; Shang, CA; Mahmood, SR; Taylor, WR and Mohun, TJ (2016)
    The cardiac-restricted protein ADP-ribosylhydrolase-like 1 is essential for heart chamber outgrowth and acts on muscle actin filament assembly.
    Developmental Biology 416, 373-388 PubMed abstract
  • Taylor, WR (2016)
    An algorithm to parse segment packing in predicted protein contact maps.
    Algorithms for Molecular Biology 11, 17 PubMed abstract
  • Taylor, WR (2016)
    Reduction, alignment and visualisation of large diverse sequence families.
    BMC Bioinformatics 17, 300 PubMed abstract
  • Taylor, WR (2016)
    Steric exclusion and constraint satisfaction in multi-scale coarse-grained simulations.
    Computational Biology and Chemistry 64, 297-312 PubMed abstract
  • Taylor, WR; Matthews-Palmer, TRS and Beeby, M (2016)
    Molecular models for the core components of the flagellar type-III secretion complex.
    PLOS ONE 11, e0164047 PubMed abstract
  • Bywater, RP and Veryazov, V (2015)
    The dipeptide conformations of all twenty amino acid types in the context of biosynthesis.
    SpringerPlus 4, 668 PubMed abstract
  • Collu, F; Spiga, E; Lorenz, CD and Fraternali, F (2015)
    Assembly of influenza hemagglutinin fusion peptides in a phospholipid bilayer by coarse-grained computer simulations.
    Frontiers in Molecular Biosciences 2, 66 PubMed abstract
  • Gregory, LC; Gaston-Massuet, C; Andoniadou, CL; Carreno, G; Webb, EA; Kelberman, D; McCabe, MJ; Panagiotakopoulos, L; Saldanha, JW; Spoudeas, HA; Torpiano, J; Rossi, M; Raine, J; Canham, N; Martinez-Barbera, JP and Dattani, MT (2015)
    The role of the sonic hedgehog signalling pathway in patients with midline defects and congenital hypopituitarism.
    Clinical Endocrinology 82, 728-738 PubMed abstract
  • Herman, JL; Novák, Á; Lyngsø, R; Szabó, A; Miklós, I and Hein, J (2015)
    Efficient representation of uncertainty in multiple sequence alignments using directed acyclic graphs.
    BMC Bioinformatics 16, 108 PubMed abstract
  • Kanabus, M; Shahni, R; Saldanha, JW; Murphy, E; Plagnol, V; Van't Hoff, W; Heales, S and Rahman, S (2015)
    Bi-allelic CLPB mutations cause cataract, renal cysts, nephrocalcinosis and 3-methylglutaconic aciduria, a novel disorder of mitochondrial protein disaggregation.
    Journal of Inherited Metabolic Disease 38, 211-219 PubMed abstract
  • Khatri, BS and Goldstein, RA (2015)
    A coarse-grained biophysical model of sequence evolution and the population size dependence of the speciation rate.
    Journal of Theoretical Biology 378, 56-64 PubMed abstract
  • Khatri, BS and Goldstein, RA (2015)
    Simple biophysical model predicts faster accumulation of hybrid incompatibilities in small populations under stabilising selection.
    Genetics 201, 1525-1537 PubMed abstract
  • Pandini, A; Kleinjung, J; Rasool, S and Khan, S (2015)
    Coevolved mutations reveal distinct architectures for two core proteins in the bacterial flagellar motor.
    PLOS ONE 10, e0142407 PubMed abstract
  • Pandini, A; Kleinjung, J; Taylor, WR; Junge, W and Khan, S (2015)
    The phylogenetic signature underlying ATP synthase c-ring compliance.
    Biophysical Journal 109, 975-987 PubMed abstract
  • Pernigo, S; Fukuzawa, A; Pandini, A; Holt, M; Kleinjung, J; Gautel, M and Steiner, RA (2015)
    The crystal structure of the human titin:obscurin complex reveals a conserved yet specific muscle M-band zipper module.
    Journal of Molecular Biology 427, 718-736 PubMed abstract
  • Riedel, N; Khatri, BS; Lässig, M and Berg, J (2015)
    Multiple-line inference of selection on quantitative traits.
    Genetics 201, 305-322 PubMed abstract
  • Feinberg, H; Saldanha, JW; Diep, L; Goel, A; Widom, A; Veldman, GM; Weis, WI; Schenk, D and Basi, GS (2014)
    Crystal structure reveals conservation of amyloid-β conformation recognized by 3D6 following humanization to bapineuzumab.
    Alzheimer's Research & Therapy 6, 31 PubMed abstract
  • Ferguson, L; Marlétaz, F; Carter, J-M; Taylor, WR; Gibbs, M; Breuker, CJ and Holland, PWH (2014)
    Ancient expansion of the Hox cluster in Lepidoptera generated four homeobox genes implicated in extra-embryonic tissue formation.
    PLOS Genetics 10, e1004698 PubMed abstract
  • Gouti, M; Tsakiridis, A; Wymeersch, FJ; Huang, Y; Kleinjung, J; Wilson, V and Briscoe, J (2014)
    In vitro generation of neuromesodermal progenitors reveals distinct roles for Wnt signalling in the specification of spinal cord and paraxial mesoderm identity.
    PLOS Biology 12, e1001937 PubMed abstract
  • Herman, JL; Challis, CJ; Novák, Á; Hein, J and Schmidler, SC (2014)
    Simultaneous Bayesian estimation of alignment and phylogeny under a joint model of protein sequence and structure.
    Molecular Biology and Evolution 31, 2251-2266 PubMed abstract
  • Kleinjung, J and Fraternali, F (2014)
    Design and application of implicit solvent models in biomolecular simulations.
    Current Opinion in Structural Biology 25, 126-134 PubMed abstract
  • Nikoloudis, D; Pitts, JE and Saldanha, JW (2014)
    A complete, multi-level conformational clustering of antibody complementarity-determining regions.
    PeerJ 2, e456 PubMed abstract
  • Nikoloudis, D; Pitts, JE and Saldanha, JW (2014)
    Disjoint combinations profiling (DCP): a new method for the prediction of antibody CDR conformation from sequence.
    PeerJ 2, e455 PubMed abstract
  • Pennell, S; Déclais, A-C; Li, J; Haire, LF; Berg, W; Saldanha, JW; Taylor, IA; Rouse, J; Lilley, DMJ and Smerdon, SJ (2014)
    FAN1 activity on asymmetric repair intermediates is mediated by an atypical monomeric virus-type replication-repair nuclease domain.
    Cell Reports 8, 84-93 PubMed abstract
  • Baussand, J and Kleinjung, J (2013)
    Specific conformational states of Ras GTPase upon effector binding.
    Journal of Chemical Theory and Computation 9, 738-749 PubMed abstract
  • Chakroun, N; Fornili, A; Prigent, S; Kleinjung, J; Dreiss, CA; Rezaei, H and Fraternali, F (2013)
    Decrypting prion protein conversion into a β-rich conformer by molecular dynamics.
    Journal of Chemical Theory and Computation 9, 2455-2465 PubMed abstract
  • Pandini, A; Fornili, A; Fraternali, F and Kleinjung, J (2013)
    GSATools: analysis of allosteric communication and functional local motions using a Structural Alphabet.
    Bioinformatics 29, 2053-2055 PubMed abstract
  • Pitceathly, RDS; Taanman, J-W; Rahman, S; Meunier, B; Sadowski, M; Cirak, S; Hargreaves, I; Land, JM; Nanji, T; Polke, JM; Woodward, CE; Sweeney, MG; Solanki, S; Foley, AR; Hurles, ME; Stalker, J; Blake, J; Holton, JL; Phadke, R; Muntoni, F; Reilly, MM; Hanna, MG and UK10K Consortium (2013)
    COX10 mutations resulting in complex multisystem mitochondrial disease that remains stable into adulthood.
    JAMA Neurology 70, 1556-1561 PubMed abstract
  • Sadowski, MI and Taylor, WR (2013)
    Prediction of protein contacts from correlated sequence substitutions.
    Science Progress 96, 33-42 PubMed abstract
  • Taylor, WR; Hamilton, RS and Sadowski, MI (2013)
    Prediction of contacts from correlated sequence substitutions.
    Current Opinion in Structural Biology 23, 473-479 PubMed abstract
  • Coluzza, I; Macdonald, JT; Sadowski, MI; Taylor, WR and Goldstein, RA (2012)
    Analytic Markovian rates for generalized protein structure evolution.
    PLOS ONE 7, e34228 PubMed abstract
  • Fraccalvieri, D; Tiberti, M; Pandini, A; Bonati, L and Papaleo, E (2012)
    Functional annotation of the mesophilic-like character of mutants in a cold-adapted enzyme by self-organising map analysis of their molecular dynamics.
    Molecular BioSystems 8, 2680-2691 PubMed abstract
  • Grant, J; Mahadevaiah, SK; Khil, P; Sangrithi, MN; Royo, H; Duckworth, J; McCarrey, JR; VandeBerg, JL; Renfree, MB; Taylor, W; Elgar, G; Camerini-Otero, RD; Gilchrist, MJ and Turner, JM (2012)
    Rsx is a metatherian RNA with Xist-like properties in X-chromosome inactivation.
    Nature 487, 254-258 PubMed abstract
  • Kapustin, A; Stepanova, V; Aniol, N; Cines, DB; Poliakov, A; Yarovoi, S; Lebedeva, T; Wait, R; Ryzhakov, G; Parfyonova, Y; Gursky, Y; Yanagisawa, H; Minashkin, M; Beabealashvilli, R; Vorotnikov, A; Bobik, A and Tkachuk, V (2012)
    Fibulin-5 binds urokinase-type plasminogen activator and mediates urokinase-stimulated β1-integrin-dependent cell migration.
    Biochemical Journal 443, 491-503 PubMed abstract
  • Katsimitsoulia, Z and Taylor, WR (2012)
    Coarse-grained simulation of myosin-V movement.
    Computational and Mathematical Methods in Medicine 781456 PubMed abstract
  • Kleinjung, J and Fraternali, F (2012)
    Urea-water solvation forces on prion structures.
    Journal of Chemical Theory and Computation 8, 3977-3984 PubMed abstract
  • Kleinjung, J; Scott, WRP; Allison, JR; van Gunsteren, WF and Fraternali, F (2012)
    Implicit solvation parameters derived from explicit water forces in large-scale molecular dynamics simulations.
    Journal of Chemical Theory and Computation 8, 2391-2403
  • Léger, O and Saldanha, JW (2012)
    Humanization of antibodies.
    In: Antibody drug discovery. Edited by Wood, CR.
    London, Imperial College Press, 2012. 1-23. (Molecular Medicine and Medicinal Chemistry, 4).
  • Pandini, A; Fornili, A; Fraternali, F and Kleinjung, J (2012)
    Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics.
    FASEB Journal 26, 868-881 PubMed abstract
  • Sadowski, MI (2012)
    Prediction of protein domain boundaries from inverse covariances.
    Proteins: Structure, Function, and Bioinformatics 81, 253-260 PubMed abstract
  • Sadowski, MI and Taylor, WR (2012)
    Evolutionary inaccuracy of pairwise structural alignments.
    Bioinformatics 28, 1209-1215
  • Taylor, WR; Jones, DT and Sadowski, MI (2012)
    Protein topology from predicted residue contacts.
    Protein Science 21, 299-305 PubMed abstract
  • Taylor, WR; Morley, R; Krasavin, A; Gregory, L; Wilkinson, DG and Poliakov, A (2012)
    A mechanical model of cell segregation driven by differential adhesion.
    PLOS ONE 7, e43226 PubMed abstract
  • Bordogna, A; Pandini, A and Bonati, L (2011)
    Predicting the accuracy of protein-ligand docking on homology models.
    Journal of Computational Chemistry 32, 81-98
  • Dekker, C; Willison, KR and Taylor, WR (2011)
    On the evolutionary origin of the chaperonins.
    Proteins 79, 1172-1192 PubMed abstract
  • Fraccalvieri, D; Pandini, A; Stella, F and Bonati, L (2011)
    Conformational and functional analysis of molecular dynamics trajectories by Self-Organising Maps.
    BMC Bioinformatics 12, 158
  • Hollup, SM; Fuglebakk, E; Taylor, WR and Reuter, N (2011)
    Exploring the factors determining the dynamics of different protein folds.
    Protein Science 20, 197-209 PubMed abstract
  • Hollup, SM; Sadowski, MI; Jonassen, I and Taylor, WR (2011)
    Exploring the limits of fold discrimination by structural alignment: A large scale benchmark using decoys of known fold.
    Computational Biology and Chemistry 35, 174-188 PubMed abstract
  • Kemena, C; Taly, J-F; Kleinjung, J and Notredame, C (2011)
    STRIKE: evaluation of protein MSAs using a single 3D structure.
    Bioinformatics 27, 3385-3391 PubMed abstract
  • Pitceathly, RDS; Fassone, E; Taanman, J-W; Sadowski, M; Fratter, C; Mudanohwo, EE; Woodward, CE; Sweeney, MG; Holton, JL; Hanna, MG and Rahman, S (2011)
    Kearns-Sayre syndrome caused by defective R1/p53R2 assembly.
    Journal of Medical Genetics 48, 610-617 PubMed abstract
  • Sadowski, MI; Maksimiak, K and Taylor, WR (2011)
    Direct correlation analysis improves fold recognition.
    Computational Biology and Chemistry 35, 323-332 PubMed abstract
  • Taylor, W; Katsimitsoulia, Z and Poliakov, A (2011)
    Simulation of cell movement and interaction.
    Journal of Bioinformatics and Computational Biology 9, 91-110 PubMed abstract
  • Taylor, WR and Sadowski, MI (2011)
    Structural constraints on the covariance matrix derived from multiple aligned protein sequences.
    PLOS ONE 6, e28265
  • Fassone, E; Duncan, AJ; Taanman, J-W; Pagnamenta, AT; Sadowski, MI; Holand, T; Qasim, W; Rutland, P; Calvo, SE; Mootha, VK; Bitner-Glindzicz, M and Rahman, S (2010)
    FOXRED1, encoding a FAD-dependent oxidoreductase complex-I specific molecular chaperone, is mutated in infantile-onset mitochondrial encephalopathy.
    Human Molecular Genetics 19, 4837-4847 PubMed abstract
  • Fernandes, LP; Annibale, A; Kleinjung, J; Coolen, ACC and Fraternali, F (2010)
    Protein networks reveal detection bias and species consistency when analysed by information-theoretic methods.
    PLOS ONE 5, e12083 PubMed abstract
  • Goldstone, DC; Yap, MW; Robertson, LE; Haire, LF; Taylor, WR; Katzourakis, A; Stoye, JP and Taylor, IA (2010)
    Structural and functional analysis of prehistoric lentiviruses uncovers an ancient molecular interface.
    Cell Host & Microbe 8, 248-259 PubMed abstract
  • Grainger, B; Sadowski, MI and Taylor, WR (2010)
    Re-evaluating the "rules" of protein topology.
    Journal of Computational Biology 17, 1253-1266 PubMed abstract
  • Grant, J; Saldanha, JW and Gould, AP (2010)
    A Drosophila model for primary coenzyme Q deficiency and dietary rescue in the developing nervous system.
    Disease Models & Mechanisms 3, 799-806 PubMed abstract
  • Katsimitsoulia, Z and Taylor, WR (2010)
    A hierarchic collision detection algorithm for simple Brownian dynamics.
    Computational Biology and Chemistry 34, 71-79 PubMed abstract
  • Macdonald, JT; Maksimiak, K; Sadowski, MI and Taylor, WR (2010)
    De novo backbone scaffolds for protein design.
    Proteins 78, 1311-1325 PubMed abstract
  • Pandini, A; Fornili, A and Kleinjung, J (2010)
    Structural alphabets derived from attractors in conformational space.
    BMC Bioinformatics 11, 97 PubMed abstract
  • Sadowski, MI and Taylor, WR (2010)
    On the evolutionary origins of "Fold Space Continuity": A study of topological convergence and divergence in mixed alpha-beta domains.
    Journal of Structural Biology 172, 244-252 PubMed abstract
  • Sadowski, MI and Taylor, WR (2010)
    Protein structures, folds and fold spaces.
    Journal of Physics. Condensed Matter 22, 033103 PubMed abstract
  • Schmitz, S; Schaap, IAT; Kleinjung, J; Harder, S; Grainger, M; Calder, L; Rosenthal, PB; Holder, AA and Veigel, C (2010)
    Malaria parasite actin polymerisation and filament structure.
    Journal of Biological Chemistry 285, 36577-36585 PubMed abstract
  • Taylor, WR and Katsimitsoulia, Z (2010)
    A coarse-grained molecular model for actin-myosin simulation.
    Journal of Molecular Graphics & Modelling 29, 266-279 PubMed abstract
  • Taylor, WR and Katsimitsoulia, Z (2010)
    A soft collision detection algorithm for simple Brownian dynamics.
    Computational Biology and Chemistry 34, 1-10 PubMed abstract

[Page last updated 1 Nov 2017]