Items where Subject is "MSC 2010, the AMS's Mathematics Subject Classification > 92 Biology and other natural sciences"

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Number of items at this level: 125.

A

Akman, O. E. and Broomhead, D. S. and Abadi, R. V. and Clement, R. A. (2005) Eye movement instabilities and nystagmus can be predicted by a nonlinear dynamics model of the saccadic system. Journal of Mathematical Biology, 51 (6). pp. 661-694. ISSN 1432-1416

Akman, O. E. and Broomhead, D. S. and Clement, R. A. and Abadi, R. V. (2006) Nonlinear time series analysis of jerk congenital nystagmus. [MIMS Preprint]

Akman, Ozgur (2003) Analysis of a nonlinear dynamics model of the saccadic system. Doctoral thesis, University of Manchester Institute of Science and Technology (UMIST).

B

Baker, C. T. H. and Bocharov, G. A. and Ford, J. M. and Lumb, P. M. and Norton, S. J. and Paul, C. A. H. and Junt, T. and Krebs, P. and Ludewig, B. (2005) Computational approahes to parameter estimation and model selection in immunology. Journal of Computational and Applied Mathematics, 184 (1). pp. 50-76. ISSN 0377-0427

Ball, Frank and Neal, Peter (2004) Poisson approximations for epidemics with two levels of mixing. The Annals of Probability, 32 (1B). pp. 1168-1200. ISSN 0091-1798

Baraas, Rigmor C. and Kulikowski, Janus J. and Muldoon, Mark R. (2010) Bar-like S-cone stimuli reveal the importance of an intermediate temporal filter. Journal of the Optical Society of America A, 27 (4). pp. 766-780. ISSN 1749-9097

Baraas, Rigmor C. and Kulikowski, Janus J. and Muldoon, Mark R. (2009) Elongated S-cone stimuli reveal the importance of the intermediate temporal filter. [MIMS Preprint]

Barouch, Dan H. and O'Brien, Kara L. and Simmons, Nathaniel L. and King, Sharon L. and Abbink, Peter and Maxfield, Lori F. and Sun, Ying-Hua and La Porte, Annalena and Riggs, Ambryice M. and Lynch, Diana M. and Clark, Sarah L. and Backus, Katherine and Perry, James R. and Seaman, Michael S. and Carville, Angela and Mansfield, Keith G. and Szinger, James J. and Fischer, Will and Muldoon, Mark and Korber, Bette (2010) Mosaic HIV-1 vaccines expand the breadth and depth of cellular immune responses in rhesus monkeys. Nature Medicine, 16 (3). pp. 319-323. ISSN 1546-170X

Berthelot, K. and Muldoon, M. and Rajkowitsch, L. and Hughes, J. and McCarthy, J. E. G. (2004) Dynamics and processivity of 40S ribosome scanning on mRNA in yeast. Molecular Microbiology, 51 (4). pp. 987-1002. ISSN 0950-382X

Bohl, Erich and Hamilton, Ryan and Lancaster, Peter (2008) Phylogenetic Trees Predicted by an Irreversible Markov Process. [MIMS Preprint]

Broomhead, D. S. and Clement, R. A. and Muldoon, M. R. and Whittle, J. P. and Scallan, C. and Abadi, R. V. (2000) Modelling of congenital nystagmus waveforms produced by saccadic system abnormalities. Biological Cybernetics, 82 (5). pp. 391-399. ISSN 0340-1200

Bull, Simon C. and Muldoon, Mark R. and Doig, Andrew J. (2012) Maximising the Size of Non-Redundant Protein Datasets Using Graph Theory. [MIMS Preprint]

Bull, Simon C. and Muldoon, Mark R. and Doig, Andrew J. (2013) Maximising the Size of Non-Redundant Protein Datasets Using Graph Theory. PLoS ONE, 8 (2012.6). e55484. ISSN 1932-6203

C

Cai, Yu-Dong and Jen, Chi-Hung and Qian, Jiang and Qian, ZiLiang and Muldoon, Mark (2007) Prediction of regulatory networks: identification of transcription factor-target relationship from gene ontology information and gene expression data. [MIMS Preprint]

Cai, Yu-Dong and Muldoon, Mark (2007) Metabolic Pathway Modeling by Using the Nearest Neighbor Algorithm. [MIMS Preprint]

Cañete-Valdeón, José M. and Wieringa, Roel and Smallbone, Kieran (2012) Mechanistic modelling of cancer: some reflections from software engineering and philosophy of science. Naturwissenschaften, 99. pp. 973-983.

Cao, Yunzhen and Krogstad, Paul and Korber, Bette T. and Koup, Richard A. and Muldoon, Mark and Macken, Catherine and Song, Jia-Li and Jin, Zhanqun and Zhao, Jla-Qi and Clapp, Sheila and Chen, Irvin S. Y. and Ho, David D. and Ammann, Arthur J. and Ariel Project Investigators, the (1997) Maternal HIV-1 viral load and vertical transmission of infection: The Ariel Project for the prevention of HIV transmission from mother to infant. Nature Medicine, 3 (5). pp. 549-552. ISSN 1078-8956

Cehajic-Kapetanovic, Jasmina and Bishop, Paul N. and Liyanage, Sidath and King, Trevor and Muldoon, Mark and Wearne, Ian M. (2010) A novel Ocular Anaesthetic Scoring System, OASS, tool to measure both motor and sensory function following local anaesthesia. British Journal of Ophthalmology, 94 (1). pp. 28-32. ISSN 0007-1161

Chahlaoui, Younes and Korovina, Margarita (2014) CICADA Collection. [MIMS Preprint]

Clement, R. A. and Whittle, J. P. and Muldoon, M. R. and Abadi, R. V. and Broomhead, D. S. and Akman, O. (2002) Characterisation of congenital nystagmus waveforms in terms of periodic orbits. Vision Research, 42 (17). pp. 2123-2130. ISSN 0042-6989

Cotter, Simon (2015) Constrained Approximation of Effective Generators for Multiscale Stochastic Reaction Networks and Application to Conditioned Path Sampling. [MIMS Preprint]

Cotter, Simon and Erban, Radek (2014) Error Analysis of Diffusion Approximation Methods for Multiscale Systems in Reaction Kinetics. [MIMS Preprint]

Cotter, Simon and Vaclav, Klika and Kimpton, Laura and Collins, Sally and Heazell, Alexander (2014) A stochastic model for early placental development. Journal of the Royal Society Interface, 11 (97).

Crabb, Michael (2014) EIT Reconstruction Algorithms for Respiratory Intensive Care. Doctoral thesis, The University of Manchester.

Crabb, Michael and Davidson, John and Little, Ross and Wright, Paul and Morgan, Alexandra and Miller, Chris and Naish, Josephine and Parker, Geoff and Kikinis, Ron and McCann, Hugh and Lionheart, William (2014) Mutual information as a measure of image quality for 3D dynamic lung imaging with EIT. Physiological Measurement, 35 (5). pp. 863-879.

D

Davies, Oluwafemi and Mendes, Pedro and Smallbone, Kieran and Malys, Naglis (2011) Characterisation of multiple substrate-specific (d)ITP/(d)XTPase and modelling of deaminated purine nucleotide metabolism. BMB Reports, 44 (11). (In Press)

Davies, Oluwafemi and Mendes, Pedro and Smallbone, Kieran and Malys, Naglis (2012) Characterisation of multiple substrate-specific (d)ITP/(d)XTPase and modelling of deaminated purine nucleotide metabolism. BMB Reports, 45 (4). pp. 259-264.

Derdeyn, Cynthia A. and Decker, Julie M. and Bibollet-Ruche, Frederic and Mokili, John L. and Muldoon, Mark and Denham, Scott A. and Heil, Marintha L. and Kasolo, Francis and Musonda, Rosemary and Hahn, Beatrice H. and Shaw, George M. and Korber, Bette T. and Allen, Susan and Hunter, Eric (2004) Envelope-Constrained Neutralization-Sensitive HIV-1 After Heterosexual Transmission. Science, 303. pp. 2019-2022. ISSN 0036-8075

Dobson, Paul D. and Smallbone, Kieran and Jameson, Daniel and Simeonidis, Evangelos and Lanthaler, Karin and Pir, Pınar and Lu, Chuan and Swainston, Neil and Dunn, Warwick B. and Fisher, Paul and Hull, Duncan and Brown, Marie and Oshota, Olusegun and Stanford, Natalie J. and Kell, Douglas B. and King, Ross D. and Oliver, Stephen G. and Stevens, Robert D. and Mendes, Pedrp (2010) Further developments towards a genome-scale metabolic model of yeast. BMC Systems Biology, 4 (195).

Dodson, CTJ (2010) An inhomogeneous stochastic rate process for evolution from states in an information geometric neighbourhood of uniform fitness. [MIMS Preprint]

F

Forster, J. E. and Abadi, R. V. and Muldoon, M. and Lloyd, I. C. (2006) Grading infantile cataracts. Ophthalmic and Physiological Optics, 26 (4). pp. 372-379. ISSN 0275-5408

Frahm, Nicole and Kaufmann, Daniel E. and Yusim, Karina and Muldoon, Mark and Kesmir, Can and Linde, Caitlyn H. and Fischer, Will and Allen, Todd M. and Li, Bin and McMahon, Ben H. and Faircloth, Kellie L. and Hewitt, Hannah S. and Mackey, Elizabeth W. and Miura, Toshiyuki and Khatri, Ashok and Wolinsky, Steven and McMichael, Andrew and Funkhouser, Robert K. and Walker, Bruce D. and Brander, Christian and Korber, Bette T. (2007) Increased Sequence Diversity Coverage Improves Detection of HIV-Specific T Cell Responses. Journal of Immunology, 179 (10). pp. 6638-6650. ISSN 0022-1767

G

Giorgi, Elena E. and Balachandran, Harikrishnan and Muldoon, Mark and Letvin, Norman L. and Haynes, Barton F. and Korber, Bette T. and Santra, Sampa (2014) Cross-reactive potential of human T-lymphocyte responses in HIV-1 infection. Vaccine, 32 (31). pp. 3995-4000. ISSN 0264-410X

Glendinning, Paul (2004) The Mathematics of Motion Camouflage. Proceedings of the Royal Society (London) Series B, 271. pp. 477-481. ISSN 0962-8452

Goodfellow, Marc and Glendinning, Paul (2012) Mechanisms of intermittent state transitions in a coupled heterogeneous oscillator model of epilepsy. [MIMS Preprint]

H

Hazel, Andrew L. and Grzybowski, G.M. and Friedman, M.H. (2003) Modelling the adaptive permeability of porcine iliac arteries to acute changes in mural shear. Annals of Biomedical Engineering, 31 (4). pp. 412-419. ISSN 0090-6964

Hazel, Andrew L. and Heil, Matthias (2003) Steady finite-Reynolds-number flows in three-dimensional collapsible tubes. Journal of Fluid Mechanics, 486. pp. 79-103. ISSN 0022-1120

Hazel, Andrew L. and Heil, Matthias (2005) Surface-tension-induced buckling of liquid-lined elastic tubes: a model pulmonary airway closure. Proceedings of the Royal society A, 461 (2058). pp. 1847-1868. ISSN 1471-2946

Hazel, Andrew L. and Heil, Matthias (2003) Three-dimensional airway reopening: the steady propagation of a semi-indefinite bubble into a buckled elastic tube. Journal of Fluid Mechanics, 478. pp. 47-70. ISSN 0022-1120

Hazel, Andrew L. and Heil, Matthias (2002) The steady propagation of a semi-infinite bubble into a tube of elliptical or rectangular cross-section. Journal of Fluid Mechanics, 470. pp. 91-114. ISSN 0022-1120

Heavner, Benjamin D and Smallbone, Kieran and Barker, Brandon and Mendes, Pedro and Walker, Larry P (2012) Yeast 5 - an Expanded Reconstruction of the Saccharomyces Cerevisiae Metabolic Network. BMC Systems Biology, 6 (55).

Heavner, Benjamin D and Smallbone, Kieran and Barker, Brandon and Mendes, Pedro and Walker, Larry P (2012) Yeast 5 � an Expanded Reconstruction of the Saccharomyces Cerevisiae Metabolic Network. BMC Systems Biology. (In Press)

Heavner, Benjamin D. and Smallbone, Kieran and Price, Nathan D. and Walker, Larry P. (2013) Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance. Database, bat059.

Heil, Matthias and Hazel, Andrew (2003) Mass transfer from a finite strip near an oscillating stagnation point --- implications for atherogenesis. Journal of Engineering Mathematics, 47. pp. 315-334. ISSN 0022-0833

Heil, Matthias and Waters, Sarah L. (2006) Transverse flows in rapidly oscillating elastic cylindrical shells. Journal of Fluid Mechanics, 547. pp. 185-214. ISSN 0022-1120

Herrgård, M.J. and Swainston, N. and Dobson, P. and Dunn, W.B. and Arga, K.Y. and Arvas, M. and Blüthgen, N. and Borger, S. and Costenoble, R. and Heinemann, M. and Hucka, M. and Le Novère, N. and Li, P and Liebermeister, W. and Mo, M.L. and Oliveira, A.P. and Petranovic, D. and Pettifer, S. and Simeonidis, E. and Smallbone, K. and Spasić, I. and Weichart, D. and Brent, R. and Broomhead, D.S. and Westerhoff, H.V. and Kırdar, B.I. and Penttilä, M. and Klipp, E. and Palsson, B.Ø. and Sauer, U. and Oliver, S.G. and Mendes, P. and Nielsen, J. and Kell, D.B. (2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotechnology, 16. pp. 1155-1160. ISSN 1087-0156

Hook, James and Broomhead, Dave (2011) Stochastic production trees as products of i.i.d. componentwise exponential max-plus matrices. [MIMS Preprint]

Huke, Jeremy P. and Muldoon, Mark R. (2015) Embedding and Time Series Analysis. Mathematics Today, 51 (3). pp. 120-123. ISSN 1361-2042

I

Isaac, Andrew D. and Muldoon, Mark and Brown, Keri A. and Brown, Terence A. (2010) Genetic analysis of wheat landraces enables the location of the first agricultural sites in Italy to be identified. Journal of Archaeological Science, 37 (5). pp. 950-956. ISSN 0305-4403 (In Press)

J

Jensen, Oliver E. and Heil, Matthias (2003) High-frequency self-excited oscillations in a collapsible-channel flow. Journal of Fluid Mechanics, 481. pp. 235-268. ISSN 0022-1120

Jin, Xia and Roberts, Caroline G. P. and Nixon, Douglas F. and Cao, Yunzhen and Ho, David D. and Walker, Bruce D. and Muldoon, Mark and Korber, Bette T. M. and Koup, Richard A. and ARIEL Project Investigators, the (1998) Longitudinal and Cross-Sectional Analysis of Cytotoxic T Lymphocyte (CTL) Responses and their Relationship to Vertical HIV Transmission. Journal of Infectious Diseases, 178 (5). pp. 1317-1326. ISSN 0022-1899

K

Kelly, C.J. and Smallbone, K. and Brady, J.M. (2008) Tumour glycolysis: the many faces of HIF. Journal of Theoretical Biology, 254 (2). pp. 508-513. ISSN 0022-5193

Kelly, C.J. and Smallbone, K. and Roose, T. and Brady, J.M. (2007) A model to investigate the feasibility of FDG as a surrogate marker of hypoxia. In: ISBI 2007. 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 12-15 April 2007, Washington DC.

Kirchherr, Jennifer L. and Hamilton, Jennifer and Lu, Xiaozhi and Gnanakaran, S. and Muldoon, Mark and Daniels, Marcus and Kasongo, Webster and Chalwe, Victor and Mulenga, Chanda and Mwananyanda, Lawrence and Musonda, Rosemary M. and Yuan, Xing and Montefiori, David C. and Korber, Bette T. and Haynes, Barton F. and Gao, Feng (2011) Identification of amino acid substitutions associated with neutralization phenotype in the human immunodeficiency virus type-1 subtype C gp120. Virology, 409 (2). pp. 163-174.

Korber, B. and Muldoon, M. and Theiler, J. and Gao, F. and Gupta, R. and Lapedes, A. and Hahn, B. H. and Wolinsky, S. and Bhattacharya, T. (2000) Timing the Ancestor of the HIV-1 Pandemic Strains. Science, 288 (5472). pp. 1786-1796. ISSN 0036-8075

Kothe, Denise L. and Decker, Julie M. and Li, Yingying and Weng, Zhiping and Bibollet-Ruche, Frederic and Zammit, Kenneth P. and Slazar, Maraia G. and Chen, Yalu and Salazar-Gonzalez, Jesus F. and Moldoveanu, Zina and Mestecky, Jiri and Gao, Feng and Haynes, Barton F. and Shaw, George M. and Muldoon, Mark and Korber, Bette T. M. and Hahn, Beatrice H. (2007) Antigenicity and immunogenicity of HIV-1 consensus subtype B envelope glycoproteins. Virology, 360 (1). pp. 218-234. ISSN 0042-6822 (In Press)

L

Lee, Dave and Smallbone, Kieran and Dunn, Warwick B. and Murabito, Ettore and Winder, Catherine L. and Kell, Douglas B. and Mendes, Pedro and Swainston, Neil (2012) Constraining flux balance analysis with genome-scale data. [MIMS Preprint]

Lee, Dave and Smallbone, Kieran and Dunn, Warwick B. and Murabito, Ettore and Winder, Catherine L. and Kell, Douglas B. and Mendes, Pedro and Swainston, Neil (2012) Improving metabolic flux predictions using absolute gene expression data. BMC Systems Biology. (In Press)

Lee, Dave and Smallbone, Kieran and Dunn, Warwick B. and Murabito, Ettore and Winder, Catherine L. and Kell, Douglas B. and Mendes, Pedro and Swainston, Neil (2012) Improving metabolic flux predictions using absolute gene expression data. BMC Systems Biology, 6 (73).

Liao, Hua-Xin and Tsao, Chun-Yen and Alam, S. Munir and Muldoon, Mark and Vandergrift, Nathan and Ma, Ben-Jiang and Lu, Xiaozhi and Sutherland, Laura L and Scearce, Richard M. and Bowman, Cindy and Parks, Robert and Chen, Haiyan and Blinn, Julie H and Lapedes, Alan and Watson, Sydeaka and Xia, Shi-Mao and Foulger, Andrew and Hahn, Beatrice H and Shaw, George M and Swanstrom, Ron and Montefiori, David C and Gao, Feng and Haynes, Barton F and Korber, Bette (2013) Antigenicity and Immunogenicity of Transmitted/Founder, Consensus, and Chronic Envelope Glycoproteins of Human Immunodeficiency Virus Type 1. Journal of Virology, 87 (8). pp. 4185-4201. ISSN 0022-538X

Liu, Xuejun (2006) Microarray Data Analysis Using Probabilistic Methods. Doctoral thesis, The University of Manchester.

M

Maini, Philip K and Gatenby, Robert A and Smallbone, Kieran (2010) Modelling Aspects of Tumour Metabolism. In: International Congress of Mathematicians, 19-27 August 2010, Hyderabad, India. (In Press)

Maini, Philip K and Gatenby, Robert A and Smallbone, Kieran (2010) Modelling Aspects of Tumour Metabolism. In: Proceedings. International Congress of Mathematicians, Hyderabad, India, pp. 3091-3104.

Martin, N. and Koup, R. and Kaslow, R. and Ammann, A. A. and Ammann, A. J. and Asthana, D. and Baur, A. and Bryson, Y. and Clapp, S. and DeLaurentis, S. and Devine, T. and Feinberg, M. and Fitzgibbon, J. E. and Fowler, M. G. and Garratty, E. M. and Geffin, R. and Gonzaga, A. and Gray, M. and Hetherington, S. and Jansen, J. K. and Kaslow, R. A. and Keller, A. and Klotman, M. E. and Korber, B. and Louzao, A. and Luzuriaga, K. and Macken, C. and Mathieson, B. and McSherry, G. and Muldoon, M. and Mullins, J. I. and Nielsen, K. and Oleske, J. and Palumbo, P. and Petru, A. and Plaeger, S. and Riviere, Y. and Rossi, P. and Scott, G. and Sullivan, J. L. and Vermund, S. H. and Wara, D. and Winchester, R. J. and Winkler, C. and Zeegen, S. (1996) Workshop on perinatally acquired human immuno-deficiency virus infection in long-term surviving children: A collaborative study of factors contributing to slow disease progression. Aids Research and Human Retroviruses, 12 (16). pp. 1565-1570. ISSN 0889-2229

Mendes, Pedro and Smallbone, Kieran and Stanford, Natalie (2011) Kinetic modelling of large-scale metabolic networks. In: Proceedings of the 9th International Conference on Computational Methods in Systems Biology. Institut Henri Poincaré, Paris, France. ISBN 978-1-4503-0817-5

Mills, Anna and Marsland, Stephen and Shardlow, Tony (2006) Computing the Geodesic Interpolating Spline. [MIMS Preprint]

Mistry, Hitesh (2007) Stochastic Modeling of Gene Regulatory Networks. Doctoral thesis, The University of Manchester.

Murabito, Ettore and Simeonidis, Evangelos and Smallbone, Kieran and Swinton, Jonathan (2009) Capturing the essence of a metabolic network: A flux balance analysis approach. Journal of Theoretical Biology. (In Press)

Murabito, Ettore and Simeonidis, Evangelos and Smallbone, Kieran and Swinton, Jonathan (2009) Capturing the essence of a metabolic network: A flux balance analysis approach. Journal of Theoretical Biology. ISSN 0022-5193 (In Press)

Murabito, Ettore and Simeonidis, Evangelos and Smallbone, Kieran and Swinton, Jonathan (2009) Capturing the essence of a metabolic network: A flux balance analysis approach. Journal of Theoretical Biology, 260 (3). pp. 445-452. ISSN 0022-5193

Murabito, Ettore and Smallbone, Kieran and Swinton, Jonathan and Westerhoff, Hans V. and Steuer, Ralf (2011) A probabilistic approach to identify putative drug targets in biochemical networks. Journal of the Royal Society Interface, 8 (59). pp. 880-895.

N

Neal, Pete (2006) Stochastic and Deterministic Analysis of SIS Household Epidemics. [MIMS Preprint]

Neal, Peter (2006) Multitype randomised Reed-Frost epidemics and epidemics upon random graphs. [MIMS Preprint]

P

Parrish, Nicholas F and Gao, Feng and Li, Hui and Giorgi, Elena E and Barbian, Hannah J and Parrish, Erica H and Zajic, Lara and Iyer, Shilpa S and Decker, Julie M and Kumar, Amit and Hora, Bhavna and Berg, Anna and Cai, Fangping and Hopper, Jennifer and Denny, Thomas N and Ding, Hairao and Ochsenbauer, Christina and Kappes, John C and Galimidi, Rachel P and West, Anthony P Jr and Bjorkman, Pamela J and Wilen, Craig B and Doms, Robert W and O'Brien, Meagan and Bhardwaj, Nina and Borrow, Persephone and Haynes, Barton F and Muldoon, Mark and Theiler, James P and Korber, Bette and Shaw, George M and Hahn, Beatrice H (2013) Phenotypic properties of transmitted founder HIV-1. PNAS, 110 (17). pp. 6626-6633. ISSN 1091-6490

Platt, Trevor and Broomhead, David S. and Sathyendranath, Shubha and Edwards, Andrew M. and Murphy, Eugene J. (2003) Phytoplankton biomass and residual nitrate in the pelagic ecosystem. Proceedings of the Royal Society of London, Series A, 459 (2033). pp. 1063-1073. ISSN 1471-2946

R

Readman, Mark C. and Kalamatianos, Dimitrios (2012) Cell Death: Linear Control Analysis of Eissing's Model. [MIMS Preprint]

Riley, C.J. and Muldoon, M.R. and Huke, J.P. and Broomhead, D.S. (2007) Does Reaction-diffusion Dynamics on a Fractal Space Imply Power Law Behaviour? [MIMS Preprint]

Riley, Caroline J. (2006) Reaction and Diffusion on the Sierpinski Gasket. Doctoral thesis, The University of Manchester.

Rong, Rong and Gnanakaran, S. and Decker, Julie M. and Bibollet-Ruche, Frederic and Taylor, Jesse and Sfakianos, Jeffrey N. and Mokili, John L. and Muldoon, Mark and Mulenga, Joseph and Allen, Susan and Hahn, Beatrice H. and Shaw, George M. and Blackwell, Jerry L. and Korber, Bette T. and Hunter, Eric and Derdeyn, Cynthia A. (2007) Unique Mutational Patterns in the Envelope α2 Amphipathic Helix and Acquisition of Length in gp120 Hypervariable Domains Are Associated with Resistance to Autologous Neutralization of Subtype C Human Immunodeficiency Virus Type 1. Journal of Virology, 81 (11). pp. 5658-5668. ISSN 0022-538X

Routley, Ben and Muldoon, Mark R. (2007) Llama: an online microarray linear analysis tool. [MIMS Preprint]

Routley, Ben and Muldoon, Mark R. (2007) Review: Practical Design and Analysis of 2-Colour cDNA Microarray Experiments. [MIMS Preprint]

Roy, Shovonlal (2008) Spatial interaction among nontoxic phytoplankton, toxic phytoplankton, and zooplankton:Emergence in space and time. Journal of Biological Physics. ISSN 1573-0689

S

Santra, Sampa and Korber, Bette T. and Muldoon, Mark and Barouch, Dan H. and Nabel, Gary J. and Gao, Feng and Hahn, Beatrice H. and Haynes, Barton F. and Letvin, Norman L. (2008) A centralized gene-based HIV-1 vaccine elicits broad cross-clade cellular immune responses in rhesus monkeys. Proceedings of the National Academy of Sciences of the USA, 105 (30). pp. 10489-10494. ISSN 0027-8424

Santra, Sampa and Liao, Hua-Xin and Zhang, Ruijin and Muldoon, Mark and Watson, Sydeaka and Fischer, Will and Theiler, James and Szinger, James and Balachandran, Harikrishnan and Buzby, Adam and Quinn, David and Parks, Robert J. and Tsao, Chun-Yen and Carville, Angela and Mansfield, Keith G. and Pavlakis, George N. and Felber, Barbara K. and Haynes, Barton F. and Korber, Bette T. and Letvin, Norman L. (2010) Mosaic vaccines elicit CD8+ T lymphocyte responses that confer enhanced immune coverage of diverse HIV strains in monkeys. Nature Medicine, 16 (3). pp. 324-328. ISSN 1546-170X

Santra, Sampa and Muldoon, Mark and Watson, Sydeaka and Buzby, Adam and Balachandran, Harikrishnan and Carlson, Kevin R. and Mach, Linh and Kong, Wing-Pui and McKee, Krishna and Yang, Zhi-Yong and Rao, Srinivas S. and Mascola, John R. and Nabel, Gary J. and Korber, Bette T, and Letvin, Norman L. (2012) Breadth of cellular and humoral immune responses elicited in rhesus monkeys by multi-valent mosaic and consensus immunogens. Virology, 248 (2). pp. 121-127. ISSN 0042-6822

Shaw, Alexander G. and Platt, Robert J. and Withers, Jennifer K. and Blüthgen, Nils and Smallbone, Kieran and Jackson, Dean A. (2009) A stochastic-hybrid Model of DNA replication in mammalian cells. [MIMS Preprint]

Shearer, Tom (2015) A new strain energy function for modelling ligaments and tendons whose fascicles have a helical arrangement of fibrils. Journal of Biomechanics. ISSN 0021-9290 (In Press)

Shearer, Tom (2015) A new strain energy function for modelling ligaments and tendons whose fascicles have a helical arrangement of fibrils. Journal of Biomechanics, 48. pp. 3017-3025. ISSN 0021-9290

Shearer, Tom (2014) A new strain energy function for the hyperelastic modelling of ligaments and tendons based on fascicle microstructure. Journal of Biomechanics. ISSN 0021-9290

Shearer, Tom (2014) A new strain energy function for the hyperelastic modelling of ligaments and tendons based on fascicle microstructure. Journal of Biomechanics, 48. pp. 290-297. ISSN 0021-9290

Simeonidis, Evangelos and Murabito, Ettore and Smallbone, Kieran and Westerhoff, Hans V. (2010) Why does yeast ferment? A flux balance analysis study. Biochemical Society Transactions, 38. pp. 1225-1229. (In Press)

Smallbone, K. and Gatenby, R.A. and Maini, P.K. (2008) Mathematical modelling of tumour acidity. Journal of Theoretical Biology, 255 (1). pp. 106-112. ISSN 0022-5193

Smallbone, K. and Simeonidis, E. and Broomhead, D.S. and Kell, D.B. (2007) Something from nothing: bridging the gap between constraint-based and kinetic modelling. FEBS Journal, 274 (21). pp. 5576-5585. ISSN 0014-2956

Smallbone, Kieran (2009) One lump or two? [MIMS Preprint]

Smallbone, Kieran and Corfe, Bernard M. (2014) A mathematical model of the colon crypt capturing compositional dynamic interactions between cell types. International Journal of Experimental Pathology, 95 (1). pp. 1-7.

Smallbone, Kieran and Malys, Naglis and Messiha, Hanan L. and Wishart, Jill A. and Simeonidis, Evangelos (2011) Building a kinetic model of trehalose biosynthesis in Saccharomyces cerevisiae. In: Methods in Systems Biology. Methods in Enzymology, 500 . Elsevier, pp. 355-370. ISBN 978-0-12-385118-5

Smallbone, Kieran and Mendes, Pedro (2013) Large-Scale Metabolic Models: From Reconstruction to Differential Equations. Industrial Biotechnology, 9 (4). pp. 179-184.

Smallbone, Kieran and Messiha, Hanan L. and Carroll, Kathleen M. and Winder, Catherine L. and Malys, Naglis and Dunn, Warwick B. and Murabito, Ettore and Swainston, Neil and Dada, Joseph O. and Khan, Farid and Pir, Pınar and Simeonidis, Evangelos and Spasić, Irena and Wishart, Jill and Weichart, Dieter and Hayes, Neil W. and Jameson, Daniel and Broomhead, David S. and Oliver, Stephen G. and Gaskell, Simon J. and McCarthy, John E.G. and Paton, Norman W. and Westerhoff, Hans V. and Kell, Douglas B. and Pendes, Pedro (2013) A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes. FEBS Letters, 587 (17). pp. 2832-2841.

Smallbone, Kieran and Simeonidis, Evangelos (2008) Flux balance analysis: A geometric perspective. Journal of Theoretical Biology. ISSN 0022-5193 (In Press)

Smallbone, Kieran and Simeonidis, Evangelos (2009) Flux balance analysis: A geometric perspective. Journal of Theoretical Biology, 258 (2). pp. 311-315. ISSN 0022-5193

Smallbone, Kieran and Simeonidis, Evangelos and Swainston, Neil and Mendes, Pedro (2009) Towards a genome-scale kinetic model of cellular metabolism. BMC Systems Biology. (Submitted)

Smallbone, Kieran and Simeonidis, Evangelos and Swainston, Neil and Mendes, Pedro (2010) Towards a genome-scale kinetic model of cellular metabolism. BMC Systems Biology, 4. p. 6.

Smallbone, Kieran and Stanford, Natalie J. (2012) Kinetic modelling of metabolic pathways: Application to serine biosynthesis. In: Systems Metabolic Engineering: Methods and Protocols. Methods in Molecular Biology . Humana Press. (In Press)

Smallbone, Kieran and Stanford, Natalie J. (2013) Kinetic modelling of metabolic pathways: Application to serine biosynthesis. In: Systems Metabolic Engineering: Methods and Protocols. Methods in Molecular Biology, 985 . Humana Press, pp. 113-121.

Smallbone, Kieran and Wang, Yunjiao (2015) Mathematising biology. [MIMS Preprint]

Smallbone, Kieran D and Maini, Philip K and Gatenby, Robert A (2009) Episodic, transient systemic acidosis delays evolution of the malignant phenotype: Possible mechanism for cancer prevention by increased physical activity. Biology Direct. (Submitted)

Smallbone, Kieran D and Maini, Philip K and Gatenby, Robert A (2010) Episodic, transient systemic acidosis delays evolution of the malignant phenotype: Possible mechanism for cancer prevention by increased physical activity. Biology Direct, 5 (22).

Stanford, Natalie J. and Lubitz, Timo and Smallbone, Kieran and Klipp, Edda and Mendes, Pedro and Liebermeister, Wolfram (2013) Systematic construction of kinetic models from genome-scale metabolic networks. PLoS ONE, 8 (11). e79195.

Stanford, Natalie J. and Smallbone, Kieran (2011) Kinetic modelling of metabolic pathways. The Bioinformatics Knowledgeblog.

Stanford, Natalie J. and Smallbone, Kieran and Mendes, Pedro (2012) Letting the flux define the kinetics: using a single steady state to predict network behaviour under diverse stress conditions. [MIMS Preprint]

Sumpter, D.J.T. and Broomhead, D.S. (2001) Relating Individual Behaviour to Population Dynamics. Proceedings of the Royal Society B: Biological Sciences, 268 (1470). pp. 925-932. ISSN 0962-8452

Swainston, Neil and Golebiewski, Martin and Messiha, Hanan L. and Malys, Naglys and Kania, Renate and Kengne, Sylvestre and Krebs, Olga and Mir, Saqib and Sauer-Danzwith, Heidrun and Smallbone, Kieran and Weidemann, Andreas and Wittig, Ulrike and Kell, Douglas B. and Mendes, Pedro and Müller, Wolfgang and Paton, Norman W. and Rojas, Isabel (2010) Enzyme kinetics informatics: from instrument to browser. FEBS Journal, 277. pp. 3769-3779.

Swainston, Neil and Smallbone, Kieran and Mendes, Pedro and Kell, Douglas B. and Paton, Norman W. (2011) The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks. Journal of Integrative Bioinformatics, 8 (2). p. 186.

T

Tham, Carole (2006) Stochastic Resonance in Vision: Models and Data. Doctoral thesis, The University of Manchester.

Thiele, Ines and Swainston, Neil and Fleming, Ronan M.T. and Hoppe, Andreas and Sahoo, Swagatika and Aurich, Maike K. and Haraldsdottir, Hulda and Mo, Monica L. and Rolfsson, Ottar and Stobbe, Miranda D. and Thorleifsson, Stefan G. and Agren, Rasmus and Bölling, Christian and Bordel, Sergio and Chavali, Arvind K. and Dobson, Paul D. and Dunn, Warwick B. and Endler, Lukas and Hala, David and Hucka, Michael and Jameson, Daniel and Jamshidi, Neema and Jonsson, Jon J. and Juty, Nick and Keating, Sarah and Nookaew, Intawat and Le Novère, Nicolas and Malys, Naglis and Mazein, Alexander and Papin, Jason A. and Price, Nathan D. and Selkov, Sr., Evgeni and Sigurdsson, Martin I. and Simeonidis, Evangelos and Sonnenschein, Nikolaus and Smallbone, Kieran and Sorokin, Antony and van Beek, Johannes H.G.M. and Weichart, Dieter and Goryanin, Igor and Neilsen, Jens and Westerhoff, Hans V. and Kell, Douglas B, and Mendes, Pedro M. and Palsson, Bernhard Ø. (2013) A community-driven global reconstruction of human metabolism. Nature Biotechnology, 31 (5). pp. 419-425.

Tindall, Marcus J. and Dyson, Louise and Smallbone, Kieran and Maini, Philip K. (2009) Modelling acidosis and the cell cycle in multicellular tumour spheroids. [MIMS Preprint]

Tindall, Marcus J. and Dyson, Louise and Smallbone, Kieran and Maini, Philip K. (2011) Modelling acidosis and the cell cycle in multicellular tumour spheroids. Journal of Theoretical Biology. (In Press)

Tindall, Marcus J. and Dyson, Louise and Smallbone, Kieran and Maini, Philip K. (2012) Modelling acidosis and the cell cycle in multicellular tumour spheroids. Journal of Theoretical Biology, 298. pp. 107-115.

V

Van Dyke, R. B. and Korber, B. T. and Popek, E. and Macken, C. and Widmayer, S. M. and Bardeguez, A. and Hanson, I. C. and Wiznia, A. and Luzuriaga, K. and Viscarello, R. R. and Wolinsky, S. and Ariel Core Investigators, the (1999) The Ariel Project: A prospective cohort study of maternal-child transmission of human immunodeficiency virus type 1 in the era of maternal antiretroviral therapy. Journal of Infectious Diseases, 179 (2). pp. 319-328. ISSN 0022-1899

Villaverde, Alejandro F. and Henriques, David and Smallbone, Kieran and Bongard, Sophia and Schmid, Joachim and Cicin-Sain, Damjan and Crombach, Anton and Saez-Rodriguez, Julio and Mauch, Klaus and Balsa-Canto, Eva and Mendes, Pedro and Jaeger, Johannes and Banga, Julio (2015) BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology. BMC Systems Biology, 9 (8).

W

Wang, Yunjiao and Broomhead, David S. and Horton, Caroline A. and Kell, Douglas B. and White, Michael R. H. (2009) Oscillations in the NF-κB Signaling Pathway. [MIMS Preprint]

Wang, Yunjiao and Paszek, Pawel and Horton, Caroline A. and Hong, Yue and White, Michael R. H. and Kell, Douglas B. and Muldoon, Mark R. and Broomhead, David S. (2012) A systematic survey of the response of a model NF-κB signalling pathway to TNFα stimulation. Journal of Theoretical Biology, 297. pp. 137-147. ISSN 0022-5193

Wang, Yunjiao and Paszek, Pawel and Horton, Caroline A. and Kell, Douglas B. and White, Michael R. H. and Broomhead, David S. and Muldoon, Mark R. (2011) Interactions among oscillatory pathways in NF-κB signalling. BMC Systems Biology, 5 (1). pp. 1-23. ISSN 1752-0509

Weaver, Eric A. and Lu, Zhongjing and Camacho, Zenadio T. and Moukdar, Fatiha and Liao, Hua-Xin and Ma, Ben-Jiang and Muldoon, Mark and Theiler, James and Nabel, Gary J. and Letvin, Norman L. and Korber, Bette T. and Hahn, Beatrice H. and Haynes, Barton F. and Gao, Feng (2006) Cross-Subtype T-Cell Immune Responses Induced by a Human Immunodeficiency Virus Type 1 Group M Consensus Env Immunogen. Journal of Virology, 80 (14). pp. 6745-6756. ISSN 0022-538X

Y

Yusim, Karina and Peters, Martine and Pybus, Oliver and Bhattacharya, Tanmoy and Delaporte, Eric and Mulanaga, Claire and Muldoon, Mark and Theiler, James and Korber, Bette (2001) Using human immunodeficiency virus type 1 sequences to infer historical features of the acquired immune deficiency syndrome epidemic and human immunodeficiency virus evolution. Philosophical Transactions of the Royal Society of London, B, 356 (1410). pp. 855-866. ISSN 0962-8436

This list was generated on Sat Nov 25 01:00:24 2017 GMT.