The list below contains a list of most MOAC publications. If you notice one is missing please send the reference preferably in an endnote library to A.rodger@warwick.ac.uk.

MOAC STUDENT PUBLICATIONS

1. Vladimirou E, Harry E, Burroughs N, McAinsh A (2011) Springs, clutches and motors: driving forward kinetochore mechanism by modelling. Chromosome Research: 1-13.

2. Smith B, Chen Z, Reimers L, Doorslaer Kv, Schiffman M, et al. (2011) Sequence Imputation of HPV16 Genomes for Genetic Association Studies. PLoS ONE 6(6): e21375.

3. Silver BR, Fulop V, Unwin PR (2011) Protein crystallization at oil/water interfaces. New Journal of Chemistry.

4. Robin D. Fisher MMM, Michael E. Snowden, Maxim B. Joseph, James A. Covington, Patrick R. Unwin, and Richard I. Walton (2011) Dissolution Kinetics of Polycrystalline Calcium Sulfate-Based Materials: Influence of Chemical Modification. ACS Appl Mater Interfaces 3: 3528-3537.

5. Pacheco-Gómez R, Roper DI, Dafforn TR, Rodger A (2011) The pH Dependence of Polymerization and Bundling by the Essential Bacterial Cytoskeltal Protein FtsZ. PLoS ONE 6(6): e19369.

6. McKelvey K, Snowden ME, Peruffo M, Unwin PR (2011) Quantitative Visualization of Molecular Transport through Porous Membranes: Enhanced Resolution and Contrast Using Intermittent Contact-Scanning Electrochemical Microscopy. Anal Chem 83: 6447-6454.

7. Mbogoro MM, Snowden ME, Edwards MA, Peruffo M, Unwin PR (2011) Intrinsic Kinetics of Gypsum and Calcium Sulfate Anhydrite Dissolution: Surface Selective Studies under Hydrodynamic Control and the Effect of Additives. The Journal of Physical Chemistry C 115: 10147-10154.

8. Kang J, Xu B, Lin W, Yao Y, Hennessy C, et al. (2011) A Dynamical Model Reveals Gene Co-Localizations in Nucleus. PloS Computational Biology 7(7): e1002094.

9. Heal JW, Wells SA, Jimenez-Roldan JE, Freedman RF, Römer RA (2011) Rigidity analysis of HIV-1 protease. J Phys:Conf Ser 286: 012006.

10. Fisher RD, Mbogoro MM, Snowden ME, Joseph MB, Covington JA, et al. (2011) Dissolution Kinetics of Polycrystalline Calcium Sulfate-Based Materials: Influence of Chemical Modification. ACS Appl Mater Interfaces 3: 3528–3537.

11. Edwards MA, Whitworth AL, Unwin PR (2011) Quantitative Analysis and Application of Tip Position Modulation-Scanning Electrochemical Microscopy. Analytical Chemistry 83: 1977-1984.

12. Downey MJ, Vance KW, Bretschneider T (2011) LineageTracker: A statistical scoring method for tracking cell lineages in large cell populations with low temporal resolution. IEEE International Symposium on Biomedical Imaging: 1913-1916.

13. Downey MJ, Jeziorska DM, Ott S, Tamai TK, Koentges G, et al. (2011) Extracting fluorescent reporter time courses of cell lineages from high-throughput microscopy at low temporal resolution. PLoS One.

14. Chen R, Pearce DJG, Fortuna S, Cheung DL, Bon SAF (2011) Polymer Vesicles with a Colloidal Armor of Nanoparticles. Journal of the American Chemical Society 133: 2151-2153.

15. Chan Y-W, Mohr R, Millard AD, Holmes AB, Larkum AW, et al. (2011) Discovery of cyanophage genomes which contain mitochondrial DNA polymerase. Mol Biol Evol.

16. Bolhuis A, Richards AD (2011) Synthesis and Techniques to Probe their Interactions with Biomolecules. Metallointercalators. New York: Springer-Verlag. pp. 427.

17. Arasaradnam RP, Quraishi N, Kyrou I, Nwokolo CU, Joseph M, et al. (2011) Insights into 'fermentonomics': evaluation of volatile organic compounds (VOCs) in human disease using an electronic 'e-nose'. Med Eng Tech 35: 87-91.

18. Zhang M, Powell HV, Mackenzie SR, Unwin PR (2010) Kinetics of Porphyrin Adsorption and DNA-Assisted Desorption at the Silica−Water Interface. Langmuir 26: 4004-4012.

19. Waldron DE, Marrington R, Grant MC, Hicks MR, Rodger A (2010) Capillary circular dichroism. Chirality.

20. Stegle O, Denby K, Cooke EJ, Wild DL, Ghahramani Z, et al. (2010) A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series. journal of computational molecular cell biology 17: 355-367.

21. Sanchez-Romero MA, Busby SJ, Dyer NP, Ott S, Millard AD, et al. (2010) Dynamic distribution of seqa protein across the chromosome of escherichia coli K-12. mBio 1.

22. Reid J, Evans K, Dyer N, Wernisch L, Ott S (2010) Variable structure motifs for transcription factor binding sites. BMC Genomics 11: 30.

23. McKelvey K, Edwards MA, Unwin PR (2010) Intermittent contact-scanning electrochemical microscopy (IC-SECM): a new approach for tip positioning and simultaneous imaging of interfacial topography and activity. Anal Chem

82: 6334-6337.

24. McGeouch CA, Edwards MA, Mbogoro MM, Parkinson C, Unwin PR (2010) Scanning Electrochemical Microscopy as a Quantitative Probe of Acid-Induced Dissolution: Theory and Application to Dental Enamel. Analytical Chemistry 82: 9322-9328.

25. McGavin WJ, Cock PJA, MacFarlane SA (2010) Partial sequence and RT-PCR diagnostic test for the plant rhabdovirus Raspberry vein chlorosis virus. Plant Pathology.

26. Koohy H, Dyer NP, Reid JE, Koentges G, Ott S (2010) An alignment-free model for comparison of regulatory sequences. Bioinformatics 26: 2391-2397.

27. Jiang H, Wang F, Dyer NP, Wong WH (2010) CisGenome Browser: a flexible tool for genomic data visualization. Bioinformatics 26: 1781-1782.

28. Holmes AB, Kalvala S, Whitworth DE (2010) Spatial Simulations of Myxobacterial Development. PLoS Comput Biol 6: e1000686.

29. Grime JMA, Khan MO, Bohinc K (2010) Interaction between Charged Surfaces Mediated by Rodlike Counterions: The Influence of Discrete Charge Distribution in the Solution and on the Surfaces. Langmuir 26: 6343-6349.

30. Grime JMA, Khan MO (2010) Decreased Osmotic Pressure via Interfacial Charge Clustering. The Journal of Physical Chemistry B 114: 10049-10056.

31. Grime JMA, Khan MO (2010) Effects of Discrete Charge Clustering in Simulations of Charged Interfaces. Journal of Chemical Theory and Computation 6: 3205-3211.

32. Fumagalli L, Gramse G, Esteban-Ferrer D, Edwards MA, Gomila G (2010) Quantifying the dielectric constant of thick insulators using electrostatic force microscopy. Applied Physics Letters 96.

33. Eriksson A, Nilsson Jacobi M, Nyström J, Tunstrøm K (2010) Determining interaction rules in animal swarms. Behavioral Ecology 21: 1106-1111.

34. Ebejer N, Schnippering M, Colburn AW, Edwards MA, Unwin PR (2010) Localized High Resolution Electrochemistry and Multifunctional Imaging: Scanning Electrochemical Cell Microscopy. Analytical Chemistry 82: 9141-9145.

35. Damianoglou A, Rodger A, Pridmore C, Dafforn TR, Mosely JA, et al. (2010) The synergistic action of melittin and phospholipase A2 with lipid membranes: development of linear dichroism for membrane-insertion kinetics. Protein and peptide letters.

36. Damianoglou A, Rodger A (2010) Unpublished work.

37. Cock PJA, Whitworth DE (2010) Evolution of Relative Reading Frame Bias in Unidirectional Prokaryotic Gene Overlaps. Molecular Biology and Evolution 27: 753-756.

38. Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM (2010) The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Research 38: 1767-1771.

39. Bolhuis A, Hand L, Marshall JE, Richards AD, Rodger A, et al. (2010) Antimicrobial activity of ruthenium-based intercalators. European Journal of Pharmaceutical Sciences In Press, Corrected Proof.

40. Armond JW, Turner MS (2010) Force Transduction by the Microtubule-Bound Dam1 Ring. Biophysical journal 98: 1598-1607.

41. Wu J, Sinfield JL, Buchanan-Wollaston V, Feng J (2009) Impact of environmental inputs on reverse-engineering approach to network structures. BMC Systems Biology 3: 113.

42. Wilson RJ (2009) Kinesin's walk: Springy or gated head coordination? Biosystems 96: 121-126.

43. Williams CG, Edwards MA, Colley AL, Macpherson JV, Unwin PR (2009) Scanning micropipet contact method for high-resolution imaging of electrode surface redox activity. Analytical Chemistry 81: 2486-2495.

44. Whitworth D, Cock P (2009) Evolution of prokaryotic two-component systems: insights from comparative genomics. Amino Acids 37: 459-466.

45. Warren G, Oates J, Robinson C, Dixon AM (2009) Contributions of the Transmembrane Domain and a Key Acidic Motif to Assembly and Function of the TatA Complex. Journal of Molecular Biology 388: 122-132.

46. Vladimirou E, Li M, Aldridge CP, Frigerio L, Kirkilionis M, et al. (2009) Diffusion of a membrane protein, Tat subunit Hcf106, is highly restricted within the chloroplast thylakoid network. FEBS letters 583: 3690-3696.

47. Schnippering M, Powell HV, Mackenzie SR, Unwin PR (2009) Real-Time Monitoring of Polyaniline Nanoparticle Formation on Surfaces. The Journal of Physical Chemistry C 113: 20221-20227.

48. Rittman M, Gilroy E, Koohy H, Rodger A, Richards A (2009) Is DNA a worm-like chain in Couette flow? In search of persistence length, a critical review. Science Progress 92: 163-204.

49. Richards AD, Rodger A, Hannon MJ, Bolhuis A (2009) Antimicrobial activity of an iron triple helicate. International journal of antimicrobial agents 33: 469-472.

50. Millard AD, Zwirglmaier K, Downey MJ, Mann NH, Scanlan DJ (2009) Comparative genomics of marine cyanomyoviruses reveals the widespread occurrence of Synechococcus host genes localized to a hyperplastic region: implications for mechanisms of cyanophage evolution. Environmental Microbiology 11: 2370-2387.

51. Li F, Edwards M, Guo J, Unwin PR (2009) Silver Particle Nucleation and Growth at Liquid/Liquid Interfaces: A Scanning Electrochemical Microscopy Approach. The Journal of Physical Chemistry C 113: 3553-3565.

52. Kamei H (2009) The existence and classification of synchrony-breaking bifurcations in regular homogeneous networks using lattice structures. International Journal of Bifurcation and Chaos 19: 3707-3732.

53. Kamei H (2009) Construction of lattices of balanced equivalence relations for regular homogeneous networks using lattice generators and lattice indices. International Journal of Bifurcation and Chaos 19: 3691-3705.

54. Jones JT, Kumar A, Pylypenko LA, Thirugnanasambandam A, Castelli L, et al. (2009) Identification and functional characterization of effectors in expressed sequence tags from various life cycle stages of the potato cyst nematode Globodera pallida. Molecular Plant Pathology 10: 815-828.

55. Hicks MR, Dafforn T, Damianoglou A, Wormell P, Rodger A, et al. (2009) Synchrotron radiation linear dichroism spectroscopy of the antibiotic peptide gramicidin in lipid membranes. Analyst 134: 1623–1628.

56. Gilroy E (2009) Second year report. University of Warwick.

57. Eriksson A, Tunstrom K (2009) On the microscopic foundation of dissipative particle dynamics. EPL (Europhysics Letters) 86: 44001.

58. Eriksson A, Jacobi MN, Nystrom J, Tunstrom K (2009) Bottom-up derivation of an effective thermostat for united atoms simulations of water. The Journal of Chemical Physics 130: 164509-164506.

59. Edwards MA, Williams CG, Whitworth AL, Unwin PR (2009) Scanning Ion Conductance Microscopy: a Model for Experimentally Realistic Conditions and Image Interpretation. Analytical Chemistry 81: 4482-4492.

60. Edwards MA, Bertoncello P, Unwin PR (2009) Slow Diffusion Reveals the Intrinsic Electrochemical Activity of Basal Plane Highly Oriented Pyrolytic Graphite Electrodes. The Journal of Physical Chemistry C 113: 9218-9223.

61. Dyer N (2009) Tubulin and its prokaryotic homologue FtsZ: a structural and functional comparison. Science Progress 92: 113-137.

62. Cooke EJ, Savage RS, Wild DL (2009) Computational approaches to the integration of gene expression, ChIP-chip and sequence data in the inference of gene regulatory networks. Seminars in Cell & Developmental Biology 20: 863-868.

63. Cock PJA, Antao T, Chang JT, Chapman BA, Cox CJ, et al. (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25: 1422-1423.

64. Bouchekhima AN, Frigerio L, Kirkilionis, M (2009) Geometric quantification of the plant endoplasmic reticulum. Journal of Microscopy 234: 158-172.

65. Wilson RJ (2008) Towards a cure for dementia: the role of axonal transport in Alzheimer's disease. Sci Prog 91: 65-80.

66. Wilson R (2008) Simulating the Kinesin Walk: A Small Step towards Understanding Dementia. Computer Modeling and Simulation, UKSIM European Symposium on 0: 226-231.

67. Whitworth DE, Holmes AB, Irvine AG, Hodgson DA, Scanlan DJ (2008) Phosphate Acquisition Components of the Myxococcus xanthus Pho Regulon Are Regulated by both Phosphate Availability and Development. J Bacteriol 190: 1997-2003.

68. Whitworth DE, Cock PJA (2008) Two-component systems of the myxobacteria: structure, diversity and evolutionary relationships. Microbiology 154: 360-372.

69. Silver BR, Unwin PR (2008) Protein crystals make it big at electrode surfaces. Chemical Communications: 5179-5181.

70. Schnippering M, Powell HV, Zhang M, Macpherson JV, Unwin PR, et al. (2008) Surface Assembly and Redox Dissolution of Silver Nanoparticles Monitored by Evanescent Wave Cavity Ring-Down Spectroscopy. The Journal of Physical Chemistry C 112: 15274-15280.

71. Qian M, Wilson RJ, Feng JF (2008) Efficiency of Brownian motors in terms of entropy production rate. EPL (Europhysics Letters) 84: 10014.

72. Powell HV, Schnippering M, Mazurenka M, Macpherson JV, Mackenzie SR, et al. (2008) Evanescent Wave Cavity Ring-Down Spectroscopy as a Probe of Interfacial Adsorption: Interaction of Tris(2,2′-bipyridine)ruthenium(II) with Silica Surfaces and Polyelectrolyte Films. Langmuir 25: 248-255.

73. Pattaranit R, van den Berg HA, Spanswick D (2008) The development of insulin resistance in Type 2 diabetes: insights from knockout studies. Science Progress 91: 285-316.

74. Pattaranit R, van den Berg HA (2008) Mathematical models of energy homeostasis. Journal of The Royal Society Interface 5: 1119-1135.

75. Koohy H (2008) On finiteness of multiplication modules. Acta Mathematica Hungarica 118: 1-7.

76. Hicks MR, Damianoglou A, Rodger A, Dafforn TR (2008) Folding and membrane insertion of the pore-forming peptide gramicidin occur as a concerted process. J Mol Biol 383: 358-366.

77. Grime JMA, Edwards MA, Unwin PR (2008) Reply to Missner et al.: Timescale for passive diffusion across bilayer lipid membranes. Proceedings of the National Academy of Sciences 105: E124.

78. Grime JMA, Edwards MA, Rudd NC, Unwin PR (2008) Quantitative visualization of passive transport across bilayer lipid membranes. Proceedings of the National Academy of Sciences 105: 14277-14282.

79. Eriksson A, Jacobi MN, Nystrom J, Tunstrom K (2008) Using force covariance to derive effective stochastic interactions in dissipative particle dynamics. Physical Review E 77: 016707.

80. Eriksson A, Jacobi MN, Nystrom J, Tunstrom K (2008) Effective thermostat induced by coarse graining of simple point charge water. The Journal of Chemical Physics 129: 024106-024108.

81. Damianoglou A, Crust EJ, Hicks MJ, Howson SE, Knight AE, et al. (2008) A new reference material for UV-visible circular dichroism spectroscopy. Chirality 20: 1029-1038.

82. Richards AD, Rodger A (2007) Synthetic metallomolecules as agents for the control of DNA structure. Chemical Society Reviews 36: 471-483.

83. Leszczyszyn OI, Evans CD, Keiper SE, Warren GZL, Blindauer CA (2007) Differential reactivity of individual zinc ions in clusters from bacterial metallothioneins. Inorganica Chimica Acta 360: 3-13.

84. Cock PJA, Whitworth DE (2007) Evolution of Prokaryotic Two-Component System Signaling Pathways: Gene Fusions and Fissions. Molecular Biology and Evolution 24: 2355-2357.

85. Cock P, Whitworth D (2007) Evolution of Gene Overlaps: Relative Reading Frame Bias in Prokaryotic Two-Component System Genes. Journal of Molecular Evolution 64: 457-462.

86. Chan Y-W, Nenninger A, Clokie SJH, Mann NH, Scanlan DJ, et al. (2007) Pigment composition and adaptation in free-living and symbiotic strains of Acaryochloris marina. FEMS Microbiology Ecology 61: 65-73.

87. Sinfield JL, Collins DR (2006) Induction of synchronous oscillatory activity in the rat lateral amygdala in vitro is dependent on gap junction activity. The European journal of neuroscience 24: 3091-3095.

88. Rodger A, Marrington R, Geeves MA, Hicks M, de Alwis L, et al. (2006) Looking at long molecules in solution: what happens when they are subjected to Couette flow? Physical Chemistry Chemical Physics 8: 3161-3171.

89. Rajendra J, Damianoglou A, Hicks M, Booth P, Rodger PM, et al. (2006) Quantitation of protein orientation in flow-oriented unilamellar liposomes by linear dichroism. Chem Phys 326: 210-220.

90. Edwards MA, Martin S, Whitworth AL, Macpherson JV, Unwin PR (2006) Scanning electrochemical microscopy: principles and applications to biophysical systems. Physiological measurement 27: R63-108.

91. Bitziou E, Rudd NC, Edwards MA, Unwin PR (2006) Visualization and Modeling of the Hydrodynamics of an Impinging Microjet. Analytical Chemistry 78: 1435-1443.

92. Jacobi MN, Rasmussen S, Tunstrøm K (2005) Modelling the dynamics of a minimal protocell container. International Journal of Astrobiology 4: 81-91.

93. Addinall SG, Johnson KA, Dafforn T, Smith C, Rodger A, et al. (2005) Expression, purification and crystallization of the cell-division protein YgfE from Escherichia coli. Acta Crystallogr Sect F Struct Biol Cryst Communications 61: 305–307.