Publications SIMBIOS Centre

Last updated: February 2012

2012

  1. Falconer, R., Houston, A., Otten, W., and P. Baveye. 2012. Emergent behaviour of fungal dynamics: influence of soil architecture and moisture distribution. Soil Science.Volume 177, Number 2, 111-119
  2. Young, I. M., Feeney, D. S., O'Donnell, A. G., & Goulding, K. W. T. (2012). Fungi in century old managed soils could hold key to the development of soil water repellency. Soil Biology and Biochemistry, 45, 125-127.
  3. T.P. Handford, F.J. Perez-Reche, and S.N. Taraskin, "Exact spin-spin correlation function for the zero-temperature random-field Ising model", J. Stat. Mech. P01001 (2012).

2011

  1. Ludlam, J., Gibson, G., Otten, W., and Gilligan, C.A. 2011. Applications of percolation theory to fungal spread with synergy. Journal Royal Society Interface: doi: 10.1098/rsif.2011.0506.
  2. Perez-Reche, F. J.; Ludlam, J. J.; Taraskin, S. N.; Gilligan, C. A. Synergy in Spreading Processes: From Exploitative to Explorative Foraging Strategies. Physical Review Letters 2011, 106.
  3. De Bartolo, S., Otten, W., Cheng, Q., and A.M. Tarquis. 2011. Modelling soil system: complexity under your feet. Preface. Biogeosciences, 8, 3139 – 3142.
  4. John P. Isaacs, Daniel J. Gilmour, David J. Blackwood, Ruth E. Falconer (2011). Immersive and Non immersive 3D virtual city: Decision support tool for urban sustainability, Journal of Information Technology in Construction (ITcon), Vol. 16, pg. 151-162, http://www.itcon.org/2011/10.
  5. Morales, Veronica L., Sang, Wenjng, Fuka, Daniel R., Lion, Leonard W., Gao, Bin, Steenhuis, Tammo S.2011.Correlation Equation for Predicting Attachment Efficiency (alpha) of Organic Matter-Colloid Complexes in Unsaturated Porous Media. Environmental Science & Technology. Vol. 45. 23. 10096-10101.
  6. Idowu, Michael A. 2011. Cyclin-dependent kinases as drug targets for cell growth and proliferation disorders. A role for systems biology approach in drug development. Part i - cyclin-dependent kinases as drug targets in cancer. Biotechnology & Biotechnological Equipment. Vol. 25. Issue:4. 2583-2586.
  7. Milazzo, L., Bown, J. L., Eberst, A., Phillips, G., Crawford, J. W. 2011. Modelling of Healthcare Associated Infections: A study on the dynamics of pathogen transmission by using an individual-based approach. Computer Methods And Programs In Biomedicine. Vl 104. Is 2. 260-265.
  8. Baveye, Philippe C., Rangel, David, Jacobson, Astrid R., Laba, Magdeline, Darnault, Christophe, Otten, Wilfred, Radulovich, Ricardo, Camargo, Flavio A. O. 2011. From Dust Bowl to Dust Bowl: Soils are Still Very Much a Frontier of Science. Soil Science Society Of America Journal. Vl 75. Is 6. 2037-2048.
  9. Fechtner, Joanna, Koza, Anna, Dello Sterpaio, Patricia, Hapca, Simona M., Spiers, Andrew J. 2011. Surfactants expressed by soil pseudomonads alter local soil-water distribution, suggesting a hydrological role for these compounds. Fems Microbiology Ecology. Vl 78. Is 1. 50-58.
  10. Baveye, Philippe C. 2011. Hydropedology, biohydrology, and the compartmentalization of hydrology into sub-disciplines: Necessary evolution or dispersal of efforts? Journal Of Hydrology. Vl 406. Is 3-4. 137-140.
  11. Neri, Franco M., Bates, Anne, Fuchtbauer, Winnie S., Perez-Reche, Francisco J., Taraskin, Sergei N., Otten, Wilfred, Bailey, Douglas J., Gilligan, Christopher A. 2011. The Effect of Heterogeneity on Invasion in Spatial Epidemics: From Theory to Experimental Evidence in a Model System. Plos Computational Biology. Vl 7. Is 9. E1002174
  12. Gras, Anna, Ginovart, Marta, Valls, Joaquim, Baveye, Philippe C.. 2011. Individual-based modelling of carbon and nitrogen dynamics in soils: Parameterization and sensitivity analysis of microbial components. Ecological Modelling. Vl 222. Is 12. 1998-2010.
  13. Lubbers, I. M.; Brussaard, L.; Otten, W.; van Groenigen, J. W. Earthworm-induced N mineralization in fertilized grassland increases both N(2)O emission and crop-N uptake. European Journal of Soil Science 2011, 62, 152-161.
  14. Krivtsov, V.; Griffiths, B. S.; Liddell, K.; Garside, A.; Salmond, R.; Bezginova, T.; Thompson, J. Soil Nitrogen Availability Is Reflected in the Bacterial Pathway. Pedosphere 2011, 21, 26-30.
  15. Kravchenko, A.; Falconer, R. E.; Grinev, D.; Otten, W. Fungal colonization in soils with different management histories: modeling growth in three-dimensional pore volumes. Ecological Applications 2011, 21, 1202-1210.
  16. Koza, A.; Moshynets, O.; Otten, W.; Spiers, A. J. Environmental modification and niche construction: developing O(2) gradients drive the evolution of the Wrinkly Spreader. Isme Journal 2011, 5, 665-673.
  17. Hapca S.M, Wang, Z.X., Otten, W., Wilson, C, Baveye, P.C. Automated statistical method to align 2D chemical maps with 3D X-ray computed micro-tomographic images of soils. Geoderma. 2011 .doi:10.1016/j.geoderma.2011.05.018.
  18. Griffiths, P.; Baveye, P. C. Peer review-Beyond the call of duty? International Journal of Nursing Studies 2011, 48, 1-2.
  19. Falconer, R. E.; Bown, J.; White, N.; Crawford, J. Linking individual behaviour to community scale patterns in fungi. Fungal Ecology 2011, 4, 76-82.
  20. De Deyn, G. B.; Shiel, R. S.; Ostle, N. J.; McNamara, N. P.; Oakley, S.; Young, I.; Freeman, C.; Fenner, N.; Quirk, H.; Bardgett, R. D. Additional carbon sequestration benefits of grassland diversity restoration. Journal of Applied Ecology 2011, 48, 600-608.
  21. Baveye, P. C.; Trevors, J. T. How Can We Encourage Peer-Reviewing? Water Air and Soil Pollution 2011, 214, 1-3.

2010

  1. Wu, C.-Y.; Jacobson, A. R.; Laba, M.; Kim, B.; Baveye, P. C. Surrogate Correlations and Near-Infrared Diffuse Reflectance Sensing of Trace Metal Content in Soils. Water Air and Soil Pollution 2010, 209, 377-390.
  2. Tilston, E.L., Sizmur, T.P., Dixon, G.R., Otten, W., and J.A. Harris. 2010. Chapter 7: The impact of land-use practices on soil microbes. In: Dixon and Tilston (eds.) Soil Microbiology and Sustainable Crop Production, DOI 10.1007/978-90-481-9479-7_7. Springer Science + Business Media B.V.
  3. Siegel, D.; Baveye, P. Battling the Paper Glut. Science 2010, 329, 1466-1466.
  4. Paterson, S.; Vogwill, T.; Buckling, A.; Benmayor, R.; Spiers, A. J.; Thomson, N. R.; Quail, M.; Smith, F.; Walker, D.; Libberton, B.; Fenton, A.; Hall, N.; Brockhurst, M. A. Antagonistic coevolution accelerates molecular evolution. Nature 2010, 464, 275-U154.
  5. Pajor, R; Falconer, R; Hapca, S.; Otten, W. Modelling and quantifying the effect of heterogeneity in soil physical conditions on fungal growth. Biogeosciences 2011, 7, 3731-3740.
  6. Lin, H.; Fluehler, H.; Otten, W.; Vogel, H.-J. Soil architecture and preferential flow across scales. Journal of Hydrology 2010, 393, 1-2.
  7. Lajtha, K.; Baveye, P. C. How should we deal with the growing peer-review problem? Biogeochemistry 2010, 101, 1-3.
  8. Laba, M.; Blair, B.; Downs, R.; Monger, B.; Philpot, W.; Smith, S.; Sullivan, P.; Baveye, P. C. Use of textural measurements to map invasive wetland plants in the Hudson River National Estuarine Research Reserve with IKONOS satellite imagery. Remote Sensing of Environment 2010, 114, 876-886.
  9. Kruitbos, L. M.; Heritage, S.; Hapca, S.; Wilson, M. J. The influence of habitat quality on the foraging strategies of the entomopathogenic nematodes Steinernema carpocapsae and Heterorhabditis megidis. Parasitology 2010, 137, 303-309.
  10. Gregory, A. S.; Bird, N. R. A.; Whalley, W. R.; Matthews, G. P.; Young, I. M. Deformation and Shrinkage Effects on the Soil Water Release Characteristic. Soil Science Society of America Journal 2010, 74, 1104-1112.
  11. Gras, A.; Ginovart, M.; Portell, X.; Baveye, P. C. Individual-Based Modeling of Carbon and Nitrogen Dynamics in Soils: Parameterization and Sensitivity Analysis of Abiotic Components. Soil Science 2010, 175, 363-374.
  12. de Oliveira Camargo, F. A.; Alvarez V, V. H.; Baveye, P. C. Brazilian soil science from its inception to the future, and beyond. Revista Brasileira De Ciencia Do Solo 2010, 34, 589-599.
  13. Baveye, P. C.; Laba, M.; Otten, W.; Bouckaert, L.; Dello Sterpaio, P.; Goswami, R. R.; Grinev, D.; Houston, A.; Hu, Y.; Liu, J.; Mooney, S.; Pajor, R.; Sleutel, S.; Tarquis, A.; Wang, W.; Wei, Q.; Sezgin, M. Observer-dependent variability of the thresholding step in the quantitative analysis of soil images and X-ray microtomography data. Geoderma 2010, 157, 51-63.
  14. Baveye, P. C. Sticker Shock and Looming Tsunami - The High Cost of Academic Serials in Perspective. Journal of Scholarly Publishing 2010, 41, 191-215.
  15. Baveye, P.; Camargo, F. A. O.; Poss, R. The Discipline of Soil Science Is Not Doing Too Badly ... Under Different Skies. Soil Science 2010, 175, 313-314.
  16. Baveye, P. Small things considered: Understanding how spatial micro-heterogeneities affect the response of soils and sediments to environmental change. Geochimica Et Cosmochimica Acta 2010, 74, A61-A61.
  17. Baveye, P. Comment on "The role of scaling laws in upscaling" by BD Wood. Advances in Water Resources 2010, 33, 123-124.
  18. Baveye, P. Comment on "Comparison of bioclogging effects in saturated porous media within one- and two-dimensional flow systems" by Martin Thullner. Ecological Engineering 2010, 36, 835-836.

2009

  1. Wu, C.-Y.; Jacobson, A. R.; Laba, M.; Baveye, P. C. Alleviating Moisture Content Effects on the Visible Near-Infrared Diffuse-Reflectance Sensing of Soils. Soil Science 2009, 174, 456-465.
  2. Wu, C.-Y.; Jacobson, A. R.; Laba, M.; Baveye, P. C. Accounting for surface roughness effects in the near-infrared reflectance sensing of soils. Geoderma 2009, 152, 171-180.
  3. MacMillan, K.; Haukeland, S.; Rae, R.; Young, I.; Crawford, J.; Hapca, S.; Wilson, M. Dispersal patterns and behaviour of the nematode Phasmarhabditis hermaphrodita in mineral soils and organic media. Soil Biology & Biochemistry 2009, 41, 1483-1490.
  4. Kruitbos, L. M.; Heritage, S.; Hapca, S.; Wilson, M. J. Influence of substrate on the body-waving behaviour of nematodes. Nematology 2009, 11, 917-925.
  5. Koza, A.; Hallett, P. D.; Moon, C. D.; Spiers, A. J. Characterization of a novel air-liquid interface biofilm of Pseudomonas fluorescens SBW25. Microbiology-Sgm 2009, 155, 1397-1406.
  6. Jacobson, A. R.; Militello, R.; Baveye, P. C. Development of computer-assisted virtual field trips to support multidisciplinary learning. Computers & Education 2009, 52, 571-580.
  7. Hapca, S.; Crawford, J. W.; Young, I. M. Anomalous diffusion of heterogeneous populations characterized by normal diffusion at the individual level. Journal of the Royal Society Interface 2009, 6, 111-122.
  8. Hallett, P. D.; Feeney, D. S.; Bengough, A. G.; Rillig, M. C.; Scrimgeour, C. M.; Young, I. M. Disentangling the impact of AM fungi versus roots on soil structure and water transport. Plant and Soil 2009, 314, 183-196.
  9. Gregory, P. J.; Bengough, A. G.; Grinev, D.; Schmidt, S.; Thomas, W. T. B.; Wojciechowski, T.; Young, I. M. Root phenomics of crops: opportunities and challenges. Functional Plant Biology 2009, 36, 922-929.
  10. Gill, A. S.; Bengough, G.; Grinev, D.; Dupuy, L. Imaging the 3D kinematics of circumnutation in maize roots. Comparative Biochemistry and Physiology a-Molecular & Integrative Physiology 2009, 153A, S225-S225.
  11. French, R. A.; Jacobson, A. R.; Kim, B.; Isley, S. L.; Penn, R. L.; Baveye, P. C. Influence of Ionic Strength, pH, and Cation Valence on Aggregation Kinetics of Titanium Dioxide Nanoparticles. Environmental Science & Technology 2009, 43, 1354-1359.
  12. Faratian, D.; Clyde, R. G.; Crawford, J. W.; Harrison, D. J. Systems pathology-taking molecular pathology into a new dimension. Nature Reviews Clinical Oncology 2009, 6, 455-464.
  13. Deurer, M.; Grinev, D.; Young, I.; Clothier, B. E.; Mueller, K. The impact of soil carbon management on soil macropore structure: a comparison of two apple orchard systems in New Zealand. European Journal of Soil Science 2009, 60, 945-955.
  14. Clyde, R. G.; Craig, A. L.; de Breed, L.; Bown, J. L.; Forrester, L.; Vojtesek, B.; Smith, G.; Hupp, T.; Crawford, J. A novel ataxia-telangiectasia mutated autoregulatory feedback mechanism in murine embryonic stem cells. Journal of the Royal Society Interface 2009, 6, 1167-1177.
  15. Baveye, P. C.; Jacobson, A. R. Comment on "A soil science renaissance" by AE Hartemink and A. McBratney. Geoderma 2009, 151, 126-127.
  16. Baveye, P. C. To sequence or not to sequence the whole-soil metagenome? Nature Reviews Microbiology 2009, 7.
  17. Baveye, P. C. Comment on "Conservation of protists: Is it needed at all?" by Cotterill et al. Biodiversity and Conservation 2009, 18, 503-505.
  18. M.W. Silby, A.M. Cerdeño-Tárraga, G. Vernikos, S.R. Giddens, R. Jackson, G. Preston, X-X. Zhang, S. Godfrey, A.J. Spiers, S. Harris, G.L. Challis, A. Morningstar, D. Harris, K. Seeger, L. Murphy, S. Rutter, R. Squares, M.A. Quail, E. Saunders, I. Anderson, K. Mavromat, T.S. Brettin, S. Bentley, C.M. Thomas, J. Parkhill, S.B. Levy, P.B. Rainey & N.R. Thomson (2009). Genomic and functional analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biology 10:R51.

2008

  1. Zhu, J. J.; Liang, N. G.; Cai, M.; Liew, K. M.; Huang, W. M. Theory of phase transformation and reorientation in single crystalline shape memory alloys. Smart Materials & Structures 2008, 17.
  2. Zhang, X.; Crawford, J. W.; Young, L. M. Does pore water velocity affect the reaction rates of adsorptive solute transport in soils? Demonstration with pore-scale modelling. Advances in Water Resources 2008, 31, 425-437.
  3. Wang, J.; Zhang, X.; Bengough, A. G.; Crawford, J. W. Performance evaluation of the cell-based algorithms for domain decomposition in flow simulation. International Journal of Numerical Methods for Heat & Fluid Flow 2008, 18, 656-672.
  4. Thullner, M.; Baveye, P. Computational pore network modeling of the influence of biofilm permeability on bioclogging in porous media. Biotechnology and Bioengineering 2008, 99, 1337-1351.
  5. Sparks, D. L.; Young, I. M.; Crawford, J. W.; Nunan, N.; Otten, W.; Spiers, A. Microbial Distribution in Soils: Physics and Scaling. In Advances in Agronomy, Vol 100, 2008; Vol. 100, pp 81-121.
  6. Shovman, N.; Scott-Brown, K.; Szymkowiak, A.; Bown, J. Use of 'pop-out' paradigm to test graph comprehension in a three-dimensional scatter plot. Perception 2008, 37, 79-80.
  7. Jeger, M.J.; Lamour, A.; Gilligan, C.A.; Otten, W. A fungal growth model fitted to carbon limited dynamics of Rhizoctonia solani. New Phytologist 2008. 178: 625-633.
  8. French, R. A.; Jacobson, A. R.; Kim, B.; Isley, S. L.; Leepenn, R.; Baveye, P. C. Influence of ionic strength, pH, and cation valence on aggregation kinetics of TiO(2) nanoparticles. Geochimica Et Cosmochimica Acta 2008, 72, A283-A283.
  9. Field, D.; Garrity, G.; Gray, T.; Morrison, N.; Selengut, J.; Sterk, P.; Tatusova, T.; Thomson, N.; Allen, M. J.; Angiuoli, S. V.; Ashburner, M.; Axelrod, N.; Baldauf, S.; Ballard, S.; Boore, J.; Cochrane, G.; Cole, J.; Dawyndt, P.; De Vos, P.; dePamphilis, C.; Edwards, R.; Faruque, N.; Feldman, R.; Gilbert, J.; Gilna, P.; Gloeckner, F. O.; Goldstein, P.; Guralnick, R.; Haft, D.; Hancock, D.; Hermjakob, H.; Hertz-Fowler, C.; Hugenholtz, P.; Joint, I.; Kagan, L.; Kane, M.; Kennedy, J.; Kowalchuk, G.; Kottmann, R.; Kolker, E.; Kravitz, S.; Kyrpides, N.; Leebens-Mack, J.; Lewis, S. E.; Li, K.; Lister, A. L.; Lord, P.; Maltsev, N.; Markowitz, V.; Martiny, J.; Methe, B.; Mizrachi, I.; Moxon, R.; Nelson, K.; Parkhill, J.; Proctor, L.; White, O.; Sansone, S.-A.; Spiers, A.; Stevens, R.; Swift, P.; Taylor, C.; Tateno, Y.; Tett, A.; Turner, S.; Ussery, D.; Vaughan, B.; Ward, N.; Whetzel, T.; Gil, I. S.; Wilson, G.; Wipat, A. The minimum information about a genome sequence (MIGS) specification. Nature Biotechnology 2008, 26, 541-547.
  10. Falconer, R. E.; Bown, J. L.; White, N. A.; Crawford, J. W. Modelling interactions in fungi. Journal of the Royal Society Interface 2008, 5, 603-615.
  11. Deng, J.; Jiang, X.; Zhang, X.; Hu, W.; Crawford, J. W. Continuous time random walk model better describes the tailing of atrazine transport in soil. Chemosphere 2008, 71, 2150-2157.
  12. Deeks, L. K.; Bengough, A. G.; Stutter, M. I.; Young, I. M.; Zhang, X. X. Characterisation of flow paths and saturated conductivity in a soil block in relation to chloride breakthrough. Journal of Hydrology 2008, 348, 431-441.
  13. Deacon, L. J.; Grinev, D. V.; Crawford, J. W.; Harris, J.; Ritz, K.; Young, I. M. Simultaneous preservation of soil structural properties and phospholipid profiles: A comparison of three drying techniques. Pedosphere 2008, 18, 284-287.
  14. Bird, M. I.; Ascough, P. L.; Young, I. M.; Wood, C. V.; Scott, A. C. X-ray microtomographic imaging of charcoal. Journal of Archaeological Science 2008, 35, 2698-2706.
  15. Baveye, P.; Laba, M. Aggregation and toxicology of titanium dioxide nanoparticles. Environmental Health Perspectives 2008, 116, A152-A152.
  16. Abdullahi, Y. A.; Akunna, J. C.; White, N. A.; Hallett, P. D.; Wheatley, R. Investigating the effects of anaerobic and aerobic post-treatment on quality and stability of organic fraction of municipal solid waste as soil amendment. Bioresource Technology 2008, 99, 8631-8636.

2007

  1. Zhang, X.; Johnson, S. N.; Crawford, J. W.; Gregory, P. J.; Young, I. M. A general random walk model for the leptokurtic distribution of organism movement: Theory and application. Ecological Modelling 2007, 200, 79-88.
  2. Pachepsky, E.; Bown, J. L.; Eberst, A.; Bausenwein, U.; Millard, P.; Squire, G. R.; Crawford, J. W. Consequences of intraspecific variation for the structure and function of ecological communities Part 2: Linking diversity and function. Ecological Modelling 2007, 207, 277-285.
  3. O'Donnell, A. G.; Young, I. M.; Rushton, S. P.; Shirley, M. D.; Crawford, J. W. Visualization, modelling and prediction in soil microbiology. Nature Reviews Microbiology 2007, 5, 689-699.
  4. Krivtsov, V.; Garside, A.; Brendler, A.; Liddell, K.; Griffiths, B. S.; Staines, H. J. A study of population numbers and ecological interactions of soil and forest floor microfauna. Animal Biology 2007, 57, 467-484.
  5. Johnson, S. N.; Zhang, X.; Crawford, J. W.; Gregory, P. J.; Young, I. M. Egg hatching and survival time of soil-dwelling insect larvae: A partial differential equation model and experimental validation. Ecological Modelling 2007, 202, 493-502.
  6. Johnson, S. N.; Crawford, J. W.; Gregory, P. J.; Grinev, D. V.; Mankin, R. W.; Masters, G. J.; Murray, P. J.; Wall, D. H.; Zhang, X. Non-invasive techniques for investigating and modelling root-feeding insects in managed and natural systems. Agricultural and Forest Entomology 2007, 9, 39-46.
  7. Jacobson, A. R.; Dousset, S.; Andreux, F.; Baveye, P. C. Electron microprobe and synchrotron X-ray fluorescence mapping of the heterogeneous distribution of copper in high-copper vineyard soils. Environmental Science & Technology 2007, 41, 6343-6349. (67)
  8. Hapca, S. M.; Budha, P.; Crawford, J. W.; Young, I. M. Movement of the nematode, Phasmarhabditis hermaphrodita, in a structurally heterogeneous environment. Nematology 2007, 9, 731-738.
  9. Hapca, S.; Crawford, J. W.; MacMillan, K.; Wilson, M. J.; Young, L. M. Modelling nematode movement using time-fractional dynamics. Journal of Theoretical Biology 2007, 248, 212-224.
  10. Hapca, S.; Crawford, J.; Rae, R.; Wilson, M.; Young, I. Movement of the parasitic nematode Phasmarhabditis hermaphrodita in the presence of mucus from the host slug Deroceras reticulatum. Biological Control 2007, 41, 223-229.
  11. Falconer, R. E.; Bown, J. L.; White, N. A.; Crawford, J. W. Biomass recycling: a key to efficient foraging by fungal colonies. Oikos 2007, 116, 1558-1568.
  12. Dousset, S.; Jacobson, A. R.; Dessogne, J.-B.; Guichard, N.; Baveye, P. C.; Andreux, F. Facilitated transport of diuron and glyphosate in high copper vineyard soils. Environmental Science & Technology 2007, 41, 8056-8061.
  13. Bown, J. L.; Pachepsky, E.; Eberst, A.; Bausenwein, U.; Millard, P.; Squire, G. R.; Crawford, J. W. Consequences of intraspecific variation for the structure and function of ecological communities Part 1. Model development and predicted patterns of diversity. Ecological Modelling 2007, 207, 264-276.
  14. Blair, J. M.; Falconer, R. E.; Milne, A. C.; Young, I. M.; Crawford, J. W. ModelingThree-dimensional microstructure in heterogeneous media. Soil Science Society of America Journal 2007, 71, 1807-1812.
  15. Benachour, S.; Dabuleanu-Hapca, S.; Laurencot, P. Decay estimates for a viscous Hamilton-Jacobi equation with homogeneous Dirichlet boundary conditions. Asymptotic Analysis 2007, 51, 209-229.

2006

  1. Zhang, X. X.; Johnson, S. N.; Gregory, P. J.; Crawford, J. W.; Young, I. M.; Murray, P. J.; Jarvis, S. C. Modelling the movement and survival of the root-feeding clover weevil, Sitona lepidus, in the root-zone of white clover. Ecological Modelling 2006, 190, 133-146.
  2. Zhang, X.; Qi, X.; Zhou, X.; Pang, H. An in situ method to measure the longitudinal and transverse dispersion coefficients of solute transport in soil. Journal of Hydrology 2006, 328, 614-619.
  3. Young, I. M.; Illian, J.; Harris, J. A.; Ritz, K. Comment on Zhao et al. (2005) "Does ergosterol concentration provide a reliable estimate of soil fungal biomass?" Soil Biology & Biochemistry 2006, 38, 1500-1501.
  4. Wurst, S.; Langel, R.; Rodger, S.; Scheu, S. Effects of belowground biota on primary and secondary metabolites in Brassica oleracea. Chemoecology 2006, 16, 69-73.
  5. Wu, K.; Van Dijke, M. I. J.; Couples, G. D.; Jiang, Z.; Ma, J.; Sorbie, K. S.; Crawford, J.; Young, I.; Zhang, X. 3D stochastic modelling of heterogeneous porous media - Applications to reservoir rocks. Transport in Porous Media 2006, 65, 443-467.
  6. Nunan, N.; Ritz, K.; Rivers, M.; Feeney, D. S.; Young, I. M. Investigating microbial micro-habitat structure using X-ray computed tomography. Geoderma 2006, 133, 398-407.
  7. MacMillan, K.; Blok, V.; Young, I.; Crawford, J.; Wilson, M. J. Quantification of the slug parasitic nematode Phasmarhabditis hermaphrodita from soil samples using real time qPCR. International Journal for Parasitology 2006, 36, 1453-1461.
  8. Krivtsov, V.; Garside, A.; Bezginova, T.; Thompson, J.; Palfreyman, J. W.; Salmond, R.; Liddell, K.; Brendler, A.; Griffiths, B. S.; Watling, R.; Staines, H. J. Ecological study of the forest litter meiofauna of a unique Scottish woodland. Animal Biology 2006, 56, 69-93.
  9. Krivtsov, V.; Bezginova, T.; Salmond, R.; Liddell, K.; Garside, A.; Thompson, J.; Palfreyman, J. W.; Staines, H. J.; Brendler, A.; Griffiths, B.; Watling, R. Ecological interactions between fungi, other biota and forest litter composition in a unique Scottish woodland. Forestry 2006, 79, 201-216.
  10. Johnstone, C.; Day, J. G.; Staines, H.; Benson, E. E. The development of a 2,2 '-azinobis-(3-ethyl-benzothiazoline-6-sulfonic acid) radical cation decolourisation assay for evaluating total antioxidant status in an alga used to monitor environmental impacts in urban aquatic habitats. Ecological Indicators 2006, 6, 280-289.
  11. Johnstone, C.; Day, J. G.; Staines, H.; Benson, E. E. An in vitro oxidative stress test for determining pollutant tolerance in algae. Ecological Indicators 2006, 6, 770-779.
  12. Hallett, P. D.; White, N. A.; Ritz, K. Impact of basidiomycete fungi on the wettability of soil contaminated with a hydrophobic polycyclic aromatic hydrocarbon. Biologia 2006, 61, S334-S338.
  13. Feeney, D. S.; Hallett, P. D.; Rodger, S.; Bengough, A. G.; White, N. A.; Young, L. M. Impact of fungal and bacterial biocides on microbial induced water repellency in arable soil. Geoderma 2006, 135, 72-80.
  14. Feeney, D. S.; Crawford, J. W.; Daniell, T.; Hallett, P. D.; Nunan, N.; Ritz, K.; Rivers, M.; Young, I. M. Three-dimensional microorganization of the soil-root-microbe system. Microbial Ecology 2006, 52, 151-158.
  15. Clyde, R. G.; Bown, J. L.; Hupp, T. R.; Zhelev, N.; Crawford, J. W. The role of modelling in identifying drug targets for diseases of the cell cycle. Journal of the Royal Society Interface 2006, 3, 617-627.

2005

  1. Zhang, X. X.; Deeks, L. K.; Bengough, A. G.; Crawford, J. W.; Young, L. M. Determination of soil hydraulic conductivity with the lattice Boltzmann method and soil thin-section technique. Journal of Hydrology 2005, 306, 59-70.
  2. Zhang, X. X.; Crawford, J. W.; Deeks, L. K.; Stutter, M. I.; Bengough, A. G.; Young, I. M. A mass balance based numerical method for the fractional advection-dispersion equation: Theory and application. Water Resources Research 2005, 41.
  3. Wang, J. Y.; Zhang, X. X.; Bengough, A. G.; Crawford, J. W. Domain-decomposition method for parallel lattice Boltzmann simulation of incompressible flow in porous media. Physical Review E 2005, 72.
  4. Krivtsov, V.; Liddell, K.; Bezginova, T.; Salmond, R.; Staines, H. J.; Watling, R.; Garside, A.; Thompson, J. A.; Griffiths, B. S.; Brendler, A. Forest litter bacteria: Relationships with fungi, microfauna, and litter composition over a winter-spring period. Polish Journal of Ecology 2005, 53, 383-394.
  5. Johnson, S. N.; Gregory, P. J.; Greenham, J. R.; Zhang, X. X.; Murray, P. J. Attractive properties of an isoflavonoid found in white clover root nodules on the clover root weevil. Journal of Chemical Ecology 2005, 31, 2223-2229.
  6. Jayanthi, M.; Staines, H. J.; Benson, E. E.; Mansor, M.; Krishnapillay, B. Investigating the use of fractional replication and Taguchi techniques in cryopreservation: a case study using orthodox seeds of a tropical rainforest tree species. Biodiversity and Conservation 2005, 14, 3169-3185.
  7. Jarvis, S. C.; Murray, P. J.; Roker, J. A.; Young, I. M.; Ritz, K.; Sturrock, C. S.; Heck, R. Physical constraints in grassland ecosystems, 2005.
  8. Humphris, S. N.; Bengough, A. G.; Griffiths, B. S.; Kilham, K.; Rodger, S.; Stubbs, V.; Valentine, T. A.; Young, I. M. Root cap influences root colonisation by Pseudomonas fluorescens SBW25 on maize. Fems Microbiology Ecology 2005, 54, 123-130.
  9. Falconer, R. E.; Bown, J. L.; White, N. A.; Crawford, J. W. Biomass recycling and the origin of phenotype in fungal mycelia. Proceedings of the Royal Society B-Biological Sciences 2005, 272, 1727-1734.
  10. Crawford, J. W.; Harris, J. A.; Ritz, K.; Young, I. M. Towards an evolutionary ecology of life in soil. Trends in Ecology & Evolution 2005, 20, 81-87.
  11. Bruneau, P. M. C.; Davidson, D. A.; Grieve, I. C.; Young, I. M.; Nunan, N. The effects of soil horizons and faunal excrement on bacterial distribution in an upland grassland soil. Fems Microbiology Ecology 2005, 52, 139-144.
  12. Bardgett, R. D.; Usher, M. B.; Hopkins, D. W.; Young, I. M.; Ritz, K. The habitat of soil microbes, 2005.

2004

  1. Zhang, X. S.; Zhang, X. X. Exact integrations of two-dimensional high-order discontinuous boundary elements of elastostatics problems. Engineering Analysis with Boundary Elements 2004, 28, 725-732.
  2. Wu, K. J.; Nunan, N.; Crawford, J. W.; Young, I. M.; Ritz, K. An efficient Markov chain model for the simulation of heterogeneous soil structure. Soil Science Society of America Journal 2004, 68, 346-351.
  3. Rodger, S.; Griffiths, B. S.; McNicol, J. W.; Wheatley, R. W.; Young, I. M. The impact of bacterial diet on the migration and navigation of Caenorhabditis elegans. Microbial Ecology 2004, 48, 358-365.
  4. Krivtsov, V.; Walker, S. J. J.; Staines, H. J.; Watling, R.; Burt-Smith, G.; Garside, A. Integrative analysis of ecological patterns in an untended temperate woodland utilising standard and customised software. Environmental Modelling & Software 2004, 19, 325-335.
  5. Krivtsov, V.; Griffiths, B. S.; Salmond, R.; Liddell, K.; Garside, A.; Bezginova, T.; Thompson, J. A.; Staines, H. J.; Watling, R.; Palfreyman, J. W. Some aspects of interrelations between fungi and other biota in forest soil. Mycological Research 2004, 108, 933-946.
  6. Deeks, L. K.; Bengough, A. G.; Low, D.; Billett, M. F.; Zhang, X.; Crawford, J. W.; Chessell, J. M.; Young, I. M. Spatial variation of effective porosity and its implications for discharge in an upland headwater catchment in Scotland. Journal of Hydrology 2004, 290, 217-228.

2003

  1. Zhang, X. X.; Ren, L. Lattice Boltzmann model for agrochemical transport in soils. Journal of Contaminant Hydrology 2003, 67, 27-42.
  2. Zhang, X. X. Comment on "A three-dimensional spatial model for plant competition in an heterogeneous soil environment" by Biondini. Ecological Modelling 2003, 166, 185-186.
  3. Zhang, X. S.; Zhang, X. X. Exact integration in the boundary element method for two-dimensional elastostatic problems. Engineering Analysis with Boundary Elements 2003, 27, 987-997.
  4. Rodger, S.; Bengough, A. G.; Griffiths, B. S.; Stubbs, V.; Young, I. M. Does the presence of detached root border cells of Zea mays alter the activity of the pathogenic nematode Meloidogyne incognita? Phytopathology 2003, 93, 1111-1114.
  5. Read, D. B.; Bengough, A. G.; Gregory, P. J.; Crawford, J. W.; Robinson, D.; Scrimgeour, C. M.; Young, I. M.; Zhang, K.; Zhang, X. Plant roots release phospholipid surfactants that modify the physical and chemical properties of soil. New Phytologist 2003, 157, 315-326.
  6. Palfreyman, J. W.; Gartland, J. S.; Sturrock, C. J.; Lester, D.; White, N. A.; Low, G. A.; Bech-Andersen, J.; Cooke, D. E. L. The relationship between 'wild' and 'building' isolates of the dry rot fungus Serpula lacrymans. Fems Microbiology Letters 2003, 228, 281-286.
  7. Nunan, N.; Wu, K. J.; Young, I. M.; Crawford, J. W.; Ritz, K. Spatial distribution of bacterial communities and their relationships with the micro-architecture of soil. Fems Microbiology Ecology 2003, 44, 203-215.
  8. Krivtsov, V.; Watling, R.; Walker, S.; Knott, D.; Palfreyman, J.; Staines, H. Analysis of fungal fruiting patterns at the Dawyck Botanic Garden. Ecological Modelling 2003, 170, 393-406.
  9. Krivtsov, V.; Liddell, K.; Bezginova, T.; Salmond, R.; Garside, A.; Thompson, J.; Palfreyman, J. W.; Staines, H. J.; Watling, R.; Brendler, A.; Griffiths, B. Ecological interactions of heterotrophic flagellates, ciliates and naked amoebae in forest litter of the Dawyck Cryptogamic Sanctuary (Scotland, UK). European Journal of Protistology 2003, 39, 183-198.
  10. Krivtsov, V.; Illian, J. B.; Liddell, K.; Garside, A.; Bezginova, T.; Salmond, R.; Thompson, J.; Griffiths, B.; Staines, H. J.; Watling, R.; Brendler, A.; Palfreyman, J. W. Some aspects of complex interactions involving soil mesofauna: analysis of the results from a Scottish woodland. Ecological Modelling 2003, 170, 441-452.
  11. Harris, K.; Young, I. M.; Gilligan, C. A.; Otten, W.; Ritz, K. Effect of bulk density on the spatial organisation of the fungus Rhizoctonia solani in soil. Fems Microbiology Ecology 2003, 44, 45-56.
  12. Corlett, J.; Palfreyman, J. W.; Staines, H. J.; Marr, H. Factors influencing theoretical knowledge and practical skill acquisition in student nurses: an empirical experiment. Nurse Education Today 2003, 23, 183-190.

2002

  1. Zhang, X. X.; Bengough, A. G.; Deeks, L. K.; Crawford, J. W.; Young, I. M. A novel three-dimensional lattice Boltzmann model for solute transport in variably saturated porous media. Water Resources Research 2002, 38.
  2. Zhang, X. X.; Bengough, A. G.; Crawford, J. W.; Young, I. M. Efficient methods for solving water flow in variably saturated soils under prescribed flux infiltration. Journal of Hydrology 2002, 260, 75-87.
  3. Zhang, X. X.; Bengough, A. G.; Crawford, J. W.; Young, I. M. A lattice BGK model for advection and anisotropic dispersion equation. Advances in Water Resources 2002, 25, 1-8.
  4. Zhang, X. S.; Zhang, X. X. Coupling FEM and discontinuous BEM for elastostatics and fluid-structure interaction. Engineering Analysis with Boundary Elements 2002, 26, 719-725.
  5. Sturrock, C. J.; Ritz, K.; Samson, W. B.; Bown, J. L.; Staines, H. J.; Palfreyman, J. W.; Crawford, J. W.; White, N. A. The effects of fungal inoculum arrangement (scale and context) on emergent community development in an agar model system. Fems Microbiology Ecology 2002, 39, 9-16.
  6. Pachepsky, E.; Taylor, T.; Jones, S. Mutualism promotes diversity and stability in a simple artificial ecosystem. Artificial Life 2002, 8, 5-24.
  7. Nunan, N.; Wu, K.; Young, I. M.; Crawford, J. W.; Ritz, K. In situ spatial patterns of soil bacterial populations, mapped at multiple scales, in an arable soil. Microbial Ecology 2002, 44, 296-305.
  8. Krivtsov, V.; Sigee, D.; Bellinger, E. Elemental concentrations and correlations in winter micropopulations of Stephanodiscus rotula: an autecological study over a period of cell size reduction and restoration. European Journal of Phycology 2002, 37, 27-35.
  9. Harris, K.; Crabb, D.; Young, I. M.; Weaver, H.; Gilligan, C. A.; Otten, W.; Ritz, K. In situ visualisation of fungi in soil thin sections: problems with crystallisation of the fluorochrome FB 28 (Calcofluor M2R) and improved staining by SCRI Renaissance 2200. Mycological Research 2002, 106, 293-297.
  10. Feltham, D. L.; Chaplain, M. A. J.; Young, I. M.; Crawford, J. W. A mathematical analysis of a minimal model of nematode migration in soil. Journal of Biological Systems 2002, 10, 15-32.
  11. Davidson, D. A.; Bruneau, P. M. C.; Grieve, I. C.; Young, I. M. Impacts of fauna on an upland grassland soil as determined by micromorphological analysis. Applied Soil Ecology 2002, 20, 133-143.

2001

  1. Young, L. M.; Crawford, J. W. Protozoan life in a fractal world. Protist 2001, 152, 123-126.
  2. Young, I. M.; Crawford, J. W. Protozoan life in a fractal world. Protist 2001, 152, 123-126.
  3. Ronn, R. M.; Griffiths, B. S.; Young, I. M. Protozoa, nematodes and N-mineralization across a prescribed soil textural gradient. Pedobiologia 2001, 45, 481-495.
  4. Preston, S.; Wirth, S.; Ritz, K.; Griffiths, B. S.; Young, L. M. The role played by microorganisms in the biogenesis of soil cracks: importance of substrate quantity and quality. Soil Biology & Biochemistry 2001, 33, 1851-1858.
  5. Pachepsky, E.; Crawford, J. W.; Bown, J. L.; Squire, G. Towards a general theory of biodiversity. Nature 2001, 410, 923-926.
  6. Nunan, N.; Ritz, K.; Crabb, D.; Harris, K.; Wu, K. J.; Crawford, J. W.; Young, I. M. Quantification of the in situ distribution of soil bacteria by large-scale imaging of thin sections of undisturbed soil. Fems Microbiology Ecology 2001, 37, 67-77.
  7. McGovern, H. J.; Deeks, L. K.; Hallett, P. D.; Ritz, K.; Young, I. M. A sterile environment for growing, and monitoring, micro-organisms under a range of soil matric potentials. Soil Biology & Biochemistry 2001, 33, 689-691.
  8. Krivtsov, V.; Sigee, D. C.; Bellinger, E. G.; Porteous, G. Determination of P release from Rostherne Mere sediment cores. Acta Hydrochimica Et Hydrobiologica 2001, 29, 111-117.
  9. Krivtsov, V.; Sigee, D.; Bellinger, E. A one-year study of the Rostherne Mere ecosystem: seasonal dynamics of water chemistry, plankton, internal nutrient release, and implications for long-term trophic status and overall functioning of the lake. Hydrological Processes 2001, 15, 1489-1506.
  10. Krivtsov, V.; Goldspink, C.; Sigee, D. C.; Bellinger, E. G. Expansion of the model 'Rostherne' for fish and zooplankton: role of top-down effects in modifying the prevailing pattern of ecosystem functioning. Ecological Modelling 2001, 138, 153-171.
  11. Krivtsov, V.; Bellinger, E. G.; Sigee, D. C. A note on the factors limiting Anabaena bloom in a temperate eutrophic lake. Archiv fuer Hydrobiologie Supplement 2001, 63-73. (152)
  12. Gadd, G. M.; Ramsay, L.; Crawford, J. W.; Ritz, K. Nutritional influence on fungal colony growth and biomass distribution in response to toxic metals. Fems Microbiology Letters 2001, 204, 311-316.

2000

  1. Krivtsov, V.; Corliss, J.; Bellinger, E.; Sigee, D. Indirect regulation rule for consecutive stages of ecological succession. Ecological Modelling 2000, 133, 73-82.
  2. White, N. A., Hallet, P. D., Feeney, D., Palfreyman, J. W., Ritz, K. 2000. Changes to water repellence of soil caused by the growth of white-rot fungi: studies using a novel microcosm system. FEMS Microbiology Letters 2000, 184, 73-77.

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