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Article

Hu, Yin, Wang, Su, Ma, N, Hingley-Wilson, Suzie, Rocco, Andrea, McFadden, Johnjoe and Tang, Hongying (2017) Trajectory Energy Minimisation for Cell Growth Tracking and Genealogy Analysis Royal Society Open Science, 4, 170207.

Kanno, AI, Goulart, C, Rofatto, HK, Oliveira, SC, Leite, LC and McFadden, J (2016) New Recombinant Mycobacterium bovis BCG Expression Vectors: Improving Genetic Control over Mycobacterial Promoters. Applied and Environmental Microbiology, 82 (8). pp. 2240-2246.

Wu, H, von Kamp, A, Leoncikas, V, Mori, W, Sahin, N, Gevorgyan, A, Linley, C, Grabowski, M, Mannan, AA, Stoy, N, Stewart, GR, Ward, LT, Lewis, DJM, Sroka, J, Matsuno, H, Klamt, S, Westerhoff, HV, McFadden, J, Plant, NJ and Kierzek, AM (2016) MUFINS: Multi-Formalism Interaction Network Simulator npj Systems Biology and Applications.

Mannan, AA, Toya, T, Shimizu, K, McFadden, J, Kierzek, AM and Rocco, A (2015) Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism PLoS One, 10 (10), e01395.

Karlyshev, AV, Snyder, LAS, McFadden, J and Griffin, R (2015) Insight into proteomic investigations of Neisseria meningitidis serogroup C strain L91543 from analysis of its genome sequence FEMS MICROBIOLOGY LETTERS, 362 (9), ARTN fnv05.

Newcombe, J, Mendum, TA, Ren, CP and McFadden, J (2013) Identification of the immunoproteome of the meningococcus by cell surface immunoprecipitation and mass spectrometry (CSIP-MS). Microbiology.

Lofthouse, EK, Wheeler, PR, Beste, DJV, Khatri, BL, Wu, H, Mendum, TA, Kierzek, AM and McFadden, J (2013) Systems-Based Approaches to Probing Metabolic Variation within the Mycobacterium tuberculosis Complex PLOS ONE, 8 (9), ARTN e7591.

Beste, DJ, Nöh, K, Niedenführ, S, Mendum, TA, Hawkins, ND, Ward, JL, Beale, MH, Wiechert, W and McFadden, J (2013) (13)C-Flux Spectral Analysis of Host-Pathogen Metabolism Reveals a Mixed Diet for Intracellular Mycobacterium tuberculosis. Chem Biol, 20 (8). pp. 1012-1021.

McFadden, J (2013) Making the Quantum Leap. The Biologist, 60 (2). pp. 13-16.

McFadden, J (2013) The CEMI Field Theory Gestalt Information and the Meaning of Meaning JOURNAL OF CONSCIOUSNESS STUDIES, 20 (3-4). pp. 152-182.

Rocco, A, Kierzek, AM and McFadden, J (2013) Slow Protein Fluctuations Explain the Emergence of Growth Phenotypes and Persistence in Clonal Bacterial Populations PLoS One, 8 (1), e54272.

McFadden, J (2013) The CEMI Field Theory Closing the Loop. Journal of Consciousness Studies: controversies in science and the humanities, 20 (1-2). pp. 153-168.

Slayden, RA, Jackson, M, Zucker, J, Ramirez, MV, Dawson, CC, Crew, R, Sampson, NS, Thomas, ST, Jamshidi, N, Sisk, P, Caspi, R, Crick, DC, McNeil, MR, Pavelka, MS, Niederweis, M, Siroy, A, Dona, V, McFadden, J, Boshoff, H and Lew, JM (2013) Updating and curating metabolic pathways of TB TUBERCULOSIS, 93 (1). pp. 47-59.

Golchin, SA, Stratford, J, Curry, RJ and McFadden, J (2012) A microfluidic system for long-term time-lapse microscopy studies of mycobacteria. Tuberculosis (Edinb), 92 (6). pp. 489-496.

Neves, V, Heister, E, Costa, S, Tîlmaciu, C, Flahaut, E, Soula, B, Coley, HM, McFadden, J and Silva, SR (2012) Design of double-walled carbon nanotubes for biomedical applications. Nanotechnology, 23 (36).

Heister, E, Neves, V, Lamprecht, C, Silva, SRP, Coley, HM and McFadden, J (2012) Drug loading, dispersion stability, and therapeutic efficacy in targeted drug delivery with carbon nanotubes Carbon, 50 (2). pp. 622-632.

Heister, E, Neves, V, Lamprecht, C, Silva, SRP, Coley, HM and McFadden, J (2012) Drug loading, dispersion stability, and therapeutic efficacy in targeted drug delivery with carbon nanotubes Carbon, 50 (2). pp. 622-632.

Borsuk, S, Seixas, FK, Ramos, DF, Mendum, T, McFadden, J and Dellagostin, O (2012) Rational design of diagnostic and vaccination strategies for tuberculosis. Braz J Infect Dis, 16 (1). pp. 68-73.

Neves, V, Gerondopoulos, A, Heister, E, Tîlmaciu, C, Flahaut, E, Soula, B, Silva, SRP, McFadden, J and Coley, HM (2012) Cellular localization, accumulation and trafficking of double-walled carbon nanotubes in human prostate cancer cells Nano Research, 5 (4). pp. 223-234.

Sanz, V, Coley, HM, Silva, SRP and McFadden, J (2012) Modeling the binding of peptides on carbon nanotubes and their use as protein and DNA carriers Journal of Nanoparticle Research, 14 (2).

Sanz, V, Coley, HM, McFadden, J, Sanz, V and Silva, SRP (2012) Protamine and chloroquine enhance gene delivery and expression mediated by RNA-wrapped single walled carbon nanotubes Journal of Nanoscience and Nanotechnology, 12 (3). pp. 1739-1747.

Mendum, TA, Newcombe, J, Mannan, AA, Kierzek, AA and McFadden, J (2011) Interrogation of global mutagenesis data with a genome scale model of Neisseria meningitidis to assess gene fitness in vitro and in sera. Genome Biol, 12 (12).

Sanz, V, Tilmacîu, C, Soula, B, Flahaut, E, Coley, HM, Silva, SRP and McFadden, J (2011) Chloroquine-enhanced gene delivery mediated by carbon nanotubes Carbon, 49 (15). pp. 5348-5358.

Beste, DJ, Bonde, B, Hawkins, N, Ward, JL, Beale, MH, Noack, S, Nöh, K, Kruger, NJ, Ratcliffe, RG and McFadden, J (2011) ¹³C metabolic flux analysis identifies an unusual route for pyruvate dissimilation in mycobacteria which requires isocitrate lyase and carbon dioxide fixation. PLoS Pathog, 7 (7).

Bonde, BK, Beste, DJV, Laing, E, Kierzek, AM and McFadden, J (2011) Differential Producibility Analysis (DPA) of Transcriptomic Data with Metabolic Networks: Deconstructing the Metabolic Response of M. tuberculosis PLOS COMPUTATIONAL BIOLOGY, 7 (6), ARTN e.

Sanz, V, Borowiak, E, Lukanov, P, Galibert, AM, Flahaut, E, Coley, HM, Silva, SRP and McFadden, J (2011) Optimising DNA binding to carbon nanotubes by non-covalent methods Carbon, 49 (5). pp. 1775-1781.

Sroka, J, Bieniasz-Krzywiec, L, Gwóźdź, S, Leniowski, D, Lącki, J, Markowski, M, Avignone-Rossa, C, Bushell, ME, McFadden, J and Kierzek, AM (2011) Acorn: a grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface. BMC Bioinformatics, 12 (196).

Sanz, V, Borowiak, E, Lukanov, P, Galibert, AM, Flahaut, E, Coley, HM, Silva, SRP and McFadden, J (2011) Optimising DNA binding to carbon nanotubes by non-covalent methods Carbon, 49 (5). pp. 1775-1781.

Shi, L, Sohaskey, CD, Pfeiffer, C, Datta, P, Parks, M, McFadden, J, North, RJ and Gennaro, ML (2010) Carbon flux rerouting during Mycobacterium tuberculosis growth arrest MOLECULAR MICROBIOLOGY, 78 (5). pp. 1199-1215.

Kadir, TAA, Mannan, AA, Kierzek, AM, McFadden, J and Shimizu, K (2010) Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification MICROBIAL CELL FACTORIES, 9, ARTN 8.

Neves, V, Heister, E, Costa, S, Tîlmaciu, C, Borowiak-Palen, E, Giusca, CE, Flahaut, E, Soula, B, Coley, HM, McFadden, J and Silva, SRP (2010) Uptake and release of double-walled carbon nanotubes by mammalian cells Advanced Functional Materials, 20 (19). pp. 3272-3279.

Beste, DJV and McFadden, J (2010) Systems biology of the metabolism of Mycobacterium tuberculosis Biochemical Society Transactions, 38 (5). pp. 1286-1289.

Beste, DJV and McFadden, J (2010) Systems biology of the metabolism of Mycobacterium tuberculosis Biochemical Society Transactions, 38 (5). pp. 1286-1289.

McFadden, J (2010) Physics and the mind Comment on 'Natural world physical-, brain operational-, and mind phenomenal-space-time' by Fingelkurts et al. PHYSICS OF LIFE REVIEWS, 7 (2). pp. 250-251.

Heister, E, Lamprecht, C, Neves, V, Tilmaciu, C, Datas, L, Flahaut, E, Soula, B, Hinterdorfer, P, Coley, HM, Silva, SRP and McFadden, J (2010) Higher Dispersion Efficacy of Functionalized Carbon Nanotubes in Chemical and Biological Environments ACS NANO, 4 (5). pp. 2615-2626.

Heister, E, Lamprecht, C, Neves, V, Tilmaciu, C, Datas, L, Flahaut, E, Soula, B, Hinterdorfer, P, Coley, HM, Silva, SRP and McFadden, J (2010) Higher Dispersion Efficacy of Functionalized Carbon Nanotubes in Chemical and Biological Environments ACS NANO, 4 (5). pp. 2615-2626.

Beste, DJV and McFadden, J (2010) System-level strategies for studying the metabolism of Mycobacterium tuberculosis Molecular Biosystems, 6 (12). pp. 2363-2372.

Borsuk, S, Newcombe, J, Mendum, TA, Dellagostin, OA and McFadden, J (2009) Identification of proteins from tuberculin purified protein derivative (PPD) by LC-MS/MS TUBERCULOSIS, 89 (6). pp. 423-430.

Lamprecht, C, Liashkovich, I, Neves, V, Danzberger, J, Heister, E, Rangl, M, Coley, HM, McFadden, J, Flahaut, E, Gruber, HJ, Hinterdorfer, P, Kienberger, F and Ebner, A (2009) AFM imaging of functionalized carbon nanotubes on biological membranes NANOTECHNOLOGY, 20 (43), ARTN 43400.

Heister, E, Neves, V, Tilmaciu, C, Lipert, K, Beltran, VS, Coley, HM, Silva, SRP and McFadden, J (2009) Triple functionalisation of single-walled carbon nanotubes with doxorubicin, a monoclonal antibody, and a fluorescent marker for targeted cancer therapy CARBON, 47 (9). pp. 2152-2160.

Heister, E, Neves, V, Tilmaciu, C, Lipert, K, Beltran, VS, Coley, HM, Silva, SRP and McFadden, J (2009) Triple functionalisation of single-walled carbon nanotubes with doxorubicin, a monoclonal antibody, and a fluorescent marker for targeted cancer therapy CARBON, 47 (9). pp. 2152-2160.

Beste, DJ, Espasa, M, Bonde, B, Kierzek, AM, Stewart, GR and McFadden, J (2009) The genetic requirements for fast and slow growth in mycobacteria. PLoS One, 4 (4), e5349. - - -.

Beste, DJ, Espasa, M, Bonde, B, Kierzek, AM, Stewart, GR and McFadden, J (2009) The genetic requirements for fast and slow growth in mycobacteria. PLoS One, 4 (4), e5349. - - -.

Mendum, TA, Newcombe, J, McNeilly, CL and McFadden, J (2009) Towards the immunoproteome of Neisseria meningitidis. PLoS One, 4 (6).

Senaratne, RH, Sidders, B, Sequeira, P, Saunders, G, Dunphy, K, Marjanovic, C, Reader, JR, Lima, P, Chan, S, Kendall, S, McFadden, J and Riley, LW (2008) Mycobacterium tuberculosis strains disrupted in mce3 and mce4 operons are attenuated in mice JOURNAL OF MEDICAL MICROBIOLOGY, 57 (2). pp. 164-170.

Casey, R, Newcombe, J, McFadden, J and Bodman-Smith, KB (2008) The acute-phase reactant C-reactive protein binds to phosphorylcholine- expressing Neisseria meningitidis and increases uptake by human phagocytes Infection and Immunity, 76 (3). pp. 1298-1304.

Borsuk, S, Mendum, TA, Fagundes, MQ, Michelon, M, Cunha, CW, McFadden, J and Dellagostin, OA (2007) Auxotrophic complementation as a selectable marker for stable expression of foreign antigens in Mycobacterium bovis BCG TUBERCULOSIS, 87 (6). pp. 474-480.

Beste, DJV, Laing, E, Bonde, B, Avignone-Rossa, C, Bushell, ME and McFadden, JJ (2007) Transcriptomic analysis identifies growth rate modulation as a component of the adaptation of mycobacteria to survival inside the macrophage JOURNAL OF BACTERIOLOGY, 189 (11). pp. 3969-3976.

Beste, DJV, Laing, E, Bonde, B, Avignone-Rossa, C, Bushell, ME and McFadden, JJ (2007) Transcriptomic analysis identifies growth rate modulation as a component of the adaptation of mycobacteria to survival inside the macrophage J BACTERIOL, 189 (11). pp. 3969-3976.

Beste, DJV, Hooper, T, Stewart, G, Bonde, B, Avignone-Rossa, C, Bushell, M, Wheeler, P, Klamt, S, Kierzek, AM and McFadden, J (2007) GSMN-TB: a web-based genome scale network model of Mycobacterium tuberculosis metabolism GENOME BIOLOGY, 8 (5), ARTN r.

Michelon, A, Conceicao, FR, Binsfeld, PC, da Cunha, CW, Moreira, AN, Argondizzo, AP, McIntosh, D, Armoa, GRG, Campos, AS, Farber, M, McFadden, J and Dellagostin, OA (2006) Immunogenicity of Mycobacterium bovis BCG expressing Anaplasma marginale MSP1a antigen VACCINE, 24 (37-39). pp. 6332-6339.

Jeynes, JCG, Mendoza, E, Chow, DCS, Watts, PCR, McFadden, J and Silva, SRP (2006) Generation of chemically unmodified pure single-walled carbon nanotubes by solubilizing with RNA and treatment with ribonuclease A ADVANCED MATERIALS, 18 (12). 1598-+.

Rustam, T, McClean, S, Newcombe, J, McFadden, J and Eales-Reynolds, LJ (2006) Reduced toxicity of lipo-oligosaccharide from a phoP mutant of Neisseria meningitidis: an in vitro demonstration JOURNAL OF ENDOTOXIN RESEARCH, 12 (1). pp. 39-46.

Jeynes, JCG, Mendoza, E, Chow, D, McFadden, J and Silva, SRP (2005) DNA/RNA purified single walled carbon nanotubes on self-assembled networks 2005 NSTI Nanotechnology Conference and Trade Show - NSTI Nanotech 2005 Technical Proceedings. pp. 250-253.

Casey, R, Newcombe, J, McFadden, J and Bodman-Smith, K (2005) The interaction of C-reactive protein with Neisseria meningitidis IMMUNOLOGY, 116. p. 77.

Bigi, F, Gioffre, A, Klepp, L, Santangelo, MP, Velicovsky, CA, Giambartolomei, GH, Fossati, CA, Romano, MI, Mendum, T, McFadden, JJ and Cataldi, A (2005) Mutation in the P36 gene of Mycobacterium bovis provokes attenuation of the bacillus in a mouse model TUBERCULOSIS, 85 (4). pp. 221-226.

Newcombe, J, Jeynes, JC, Mendoza, E, Hinds, J, Marsden, GL, Stabler, RA, Marti, M and McFadden, JJ (2005) Phenotypic and transcriptional characterization of the meningococcal PhoPQ system, a magnesium-sensing two-component regulatory system that controls genes involved in remodeling the meningococcal cell surface JOURNAL OF BACTERIOLOGY, 187 (14). pp. 4967-4975.

Beste, DJV, Peters, J, Hooper, T, Avignone Rossa, CA, Bushell, ME and McFadden, JJ (2005) Compiling a molecular inventory for Mycobacterium bovis BCG at two growth rates: Evidence for growth rate-mediated regulation of ribosome biosynthesis and lipid metabolism Journal of Bacteriology, 187 (5). pp. 1677-1684.

Newcombe, J, Eales-Reynolds, L, Wootton, L, Gorringe, AR, Funnell, SGP, Taylor, SC and McFadden, JJ (2004) Infection with an avirulent phoP mutant of Neisseria meningitidis confers broad cross-reactive immunity INFECTION AND IMMUNITY, 72 (1). pp. 338-344.

Johnson, CR, Newcombe, J, Thorne, S, Borde, HA, Eales-Reynolds, LJ, Gorringe, AR, Funnell, SGP and McFadden, JJ (2001) Generation and characterization of a PhoP homologue mutant of Neisseria meningitidis MOLECULAR MICROBIOLOGY, 39 (5). pp. 1345-1355.

Stewart, GR, Ehrt, S, Riley, LW, Dale, JW and McFadden, J (2000) Deletion of the putative antioxidant noxR1 does not alter the virulence of Mycobacterium tuberculosis H37Rv TUBERCLE AND LUNG DISEASE, 80 (4-5). pp. 237-242.

Newcombe, J, Cartwright, K, Dyer, S and McFadden, J (1998) Naturally occurring insertional inactivation of the porA gene of Neisseria meningitidis by integration of IS 1301 MOLECULAR MICROBIOLOGY, 30 (2). pp. 453-454.

Newcombe, J, Dyer, S, Blackwell, L, Cartwright, K, Palmer, WH and McFadden, J (1997) PCR-single-stranded confirmational polymorphism analysis for non-culture-based subtyping of meningococcal strains in clinical specimens JOURNAL OF CLINICAL MICROBIOLOGY, 35 (7). pp. 1809-1812.

Newcombe, J, Cartwright, K, Palmer, WH and McFadden, J (1996) PCR of peripheral blood for diagnosis of meningococcal disease JOURNAL OF CLINICAL MICROBIOLOGY, 34 (7). pp. 1637-1640.

Book Section

Beste, DJV and McFadden, J (2013) Metabolism of Mycobacterium tuberculosis In: Systems biology of tuberculosis. UNSPECIFIED. ISBN 1461449650

Rocco, A, Kierzek, AM and McFadden, J (2013) Stochastic gene expression in bacterial pathogens: A mechanism for persistence? In: Systems Biology of Tuberculosis. Springer, pp. 157-177. ISBN 1461449650

Beste, DJV and McFadden, J (2012) System-level Strategies for Studying the Metabolism of Mycobacterium tuberculosis In: Systems Microbiology: Current Topics and Applications. UNSPECIFIED. ISBN 1908230029

Conference or Workshop Item

Jenson, JS, Casey, R, Newcombe, J, Smith, M, McFadden, JJ and Bodman-Smith, K (2008) Dendritic cell responses to C-reactive protein-opsonised Neisseria meningitidis In: Annual Congress of the British-Society-of-Immunology, 2008-11-17 - 2008-11-21, Glasgow, SCOTLAND.

Casey, R, McFadden, J, Newcombe, J, Bodman-Smith, M and Bodman-Smith, K (2007) C-reactive protein binds to Neisseria meningitidis and affects macrophage responses to infection In: Annual Congress of the British-Society-of-Immunology, 2007-02-20 - 2007-02-23, Glasgow, SCOTLAND.

Rustam, TP, McClean, S, Newcombe, J, McFadden, J and Eales-Reynolds, LJ (2005) Reduced toxicity of lipooligosaccharide from a phoP mutant of Neisseria meningitidis: an in vitro demonstration. In: 38th Annual Meeting of the Society-for-Leukocyte-Biology, 2005-09-21 - 2005-09-24, Sir William Dunn Sch Pathol, Oxford, ENGLAND.

Book

McFadden, J, Beste, DJV and Kierzek, AM (2012) Systems Biology of Tuberculosis Springer. ISBN 1461449669

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