A

Ashall, Louise, Horton, Caroline A., Nelson, David E., Paszek, Pawel, Harper, Claire V., Sillitoe, Kate, Ryan, Sheila, Spiller, David G., Unitt, John F., Broomhead, D. S. (David S.), Kell, Douglas B., Rand, D. A. (David A.), See, Violaine and White, Michael R. H. (2009) Pulsatile stimulation determines timing and specificity of NF-kappa B-dependent transcription. Science, Vol.324 (No.5924). pp. 242-246. doi:10.1126/science.1164860 ISSN 0036-8075.

B

Berg, Laila, Lale, Rahmi, Bakke, Ingrid, Burroughs, Nigel John and Valla, Svein (2009) The expression of recombinant genes inEscherichia colican be strongly stimulated at the transcript production level by mutating the DNA-region corresponding to the 5′-untranslated part of mRNA. Microbial Biotechnology, Volume 2 (Number 3). pp. 379-389. doi:10.1111/j.1751-7915.2009.00107.x ISSN 1751-7907.

Bosgraaf, Leonard, van Haastert, Peter J. M. and Bretschneider, Till (2009) Analysis of cell movement by simultaneous quantification of local membrane displacement and fluorescent intensities using Quimp2. Cell Motility and the Cytoskeleton, Vol.66 (No.3). pp. 156-165. doi:10.1002/cm.20338 ISSN 0886-1544.

C

Cooke, Emma J., Savage, Richard S. and Wild, David L. (2009) Computational approaches to the integration of gene expression, ChIP-chip and sequence data in the inference of gene regulatory networks. Seminars in Cell and Developmental Biology, Vol.20 (No.7). pp. 863-868. doi:10.1016/j.semcdb.2009.08.004

H

(2009) Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature, Volume 461 (Number 7262). pp. 393-398. doi:10.1038/nature08358

Harkins, Gordon W., Martin, Darren P., Duffy, Siobain, Monjane, Aderito L., Shepherd, Dionne N., Windram, Oliver P., Owor, Betty E., Donaldson, Lara, van Antwerpen, Tania, Sayed, Rizwan A., Flett, Bradley, Ramusi, Moses, Rybicki, Edward P., Peterschmitt, Michel and Varsani, Arvind (2009) Dating the origins of the maize-adapted strain of maize streak virus, MSV-A. Journal of General Virology, Vol.90 (Part 12). pp. 3066-3074. doi:10.1099/vir.0.015537-0 ISSN 0022-1317.

J

Jeziorska, Danuta M., Jordan, Kate W. and Vance, Keith W. (2009) A systems biology approach to understanding cis-regulatory module function. Seminars in Cell and Developmental Biology, Vol.20 (No.7). pp. 856-862. doi:10.1016/j.semcdb.2009.07.007

K

Kiddle, Steven J., Windram, Oliver P., McHattie, Stuart, Mead, A. (Andrew), Beynon, Jim, Buchanan-Wollaston, Vicky, Denby, Katherine J. and Mukherjee, Sach (2009) Temporal clustering by affinity propagation reveals transcriptional modules in Arabidopsis thaliana. Bioinformatics, Vol.26 (No.3). pp. 355-362. doi:10.1093/bioinformatics/btp673 ISSN 1367-4811.

Komorowski, Michal, Finkenstädt, Bärbel, Harper, Claire V. and Rand, D. A. (David A.) (2009) Bayesian inference of biochemical kinetic parameters using the linear noise approximation. BMC Bioinformatics, Vol.10 (No.343). doi:10.1186/1471-2105-10-343 ISSN 1471-2105.

L

Lissina, Anna, Ladell, Kristin, Skowera, Ania, Clement, M., Edwards, Emily, Seggewiss, Ruth, Berg, Hugo van den, Gostick, Emma, Gallagher, K., Jones, Emma, Melenhorst, Jan Joseph, Godkin, Andrew J., Peakman, Mark, Price, D. A., Sewell, Andrew K. and Wooldridge, L. (2009) Protein kinase inhibitors substantially improve the physical detection of T-cells with peptide-MHC tetramers. Journal of Immunological Methods, Volume 340 (Number 1). pp. 11-24. doi:10.1016/j.jim.2008.09.014 ISSN 0022-1759.

Loebel, Alex, Silberberg, Gilad, Helbig, Daniela, Markram, Henry, Tsodyks, Misha and Richardson, Magnus J. E. (2009) Multiquantal release underlies the distribution of synaptic efficacies in the neocortex. Frontiers in Computational Neuroscience, Vol.3 . Article no. 27. doi:10.3389/neuro.10.027.2009 ISSN 1662-5188.

M

Martens, Harald, Veflingstad, Siren R., Plahte, Erik, Martens, M. (Magni), Bertrand, Dominique and Omholt, Stig W. (2009) The genotype-phenotype relationship in multicellular pattern-generating models - the neglected role of pattern descriptors. BMC Systems Biology, Volume 3 . Article number 87. doi:10.1186/1752-0509-3-87 ISSN 1752-0509.

Momiji, Hiroshi and Monk, Nicholas A. M. (2009) Oscillatory Notch-pathway activity in a delay model of neuronal differentiation. Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol.80 (No.2 Part 1). Article no. 021930. doi:10.1103/PhysRevE.80.021930 ISSN 1539-3755.

P

Palmer, Sarah A., Moore, Jonathan D., Clapham, Alan J., Rose, Pamela and Allaby, Robin G. (2009) Archaeogenetic evidence of ancient Nubian barley evolution from six to two-row indicates local adaptation. PLoS ONE , Vol.4 (No.7). e6301. doi:10.1371/journal.pone.0006301 ISSN 1932-6203.

Podtelezhnikov, Alexei A. and Wild, David L. (2009) Reconstruction and stability of secondary structure elements in the context of protein structure prediction. Biophysical Journal, Vol.96 (No.11). pp. 4399-4408. doi:10.1016/j.bpj.2009.02.057 ISSN 0006-3495.

R

Rasmussen, Carl Edward, De la Cruz, Bernard J., Ghahramani, Zoubin and Wild, David L. (2009) Modeling and visualizing uncertainty in gene expression clusters using Dirichlet process mixtures. IEEE - ACM Transactions on Computational Biology and Bioinformatics, Vol.6 (No.4). pp. 615-628. doi:10.1109/TCBB.2007.70269 ISSN 1545-5963.

Reid, J. E. (John E.), Ott, Sascha and Wernisch, Lorenz (2009) Transcriptional programs : modelling higher order structure in transcriptional control. BMC Bioinformatics, Vol.10 . Article no. 218. doi:10.1186/1471-2105-10-218 ISSN 1471-2105.

Richardson, Magnus J. E. (2009) Dynamics of populations and networks of neurons with voltage-activated and calcium-activated currents. Physical Review E, Vol.80 (No.2 Part 1). Article no. 021928. doi:10.1103/PhysRevE.80.021928 ISSN 1539-3755.

Rossello, M. R., Griffiths, Nathan, Kalvala, Sara, Wellington, E. M. H. and Gaze, William H. (2009) Networking strategies in streptomyces coelicolor. In: 2nd International Conference on Bioinformatics and Systems Biology (BSB 2009), Leipzig, Germany, 23-25 March 2009 (Unpublished)

S

Salazar, Jose Domingo, Saithong, Treenut, Brown, Paul E., Foreman, Julia, Locke, James C. W., Halliday, Karen J., Carré, Isabelle A., Rand, D. A. (David A.) and Millar, A. J. (Andrew J.) (2009) Prediction of photoperiodic regulators from quantitative gene circuit models. Cell, Vol.139 (No.6). pp. 1170-1179. doi:10.1016/j.cell.2009.11.029 ISSN 1097-4172.

Saqi, Mansoor, Dobson, Richard J B, Kraben, Preben, Hodgson, D. A. and Wild, David L. (2009) An approach to pathway reconstruction using whole genome metabolic models and sensitive sequence searching. Journal of Integrative Bioinformatics, Vol.6 (No.1). p. 107. doi:10.2390/biecoll-jib-2009-107 ISSN 1613-4516.

Savage, Richard S., Heller, K. (Katherine), Xu, Yang, Ghahramani, Zoubin, Truman, William M., Grant, Murray, Denby, Katherine J. and Wild, David L. (2009) R/BHC : fast Bayesian hierarchical clustering for microarray data. BMC Bioinformatics, 10 . 242. doi:10.1186/1471-2105-10-242 ISSN 1471-2105.

Spensley, Mark, Kim, Jae-Yean, Picot, Emma, Reid, John, Ott, Sascha, Helliwell, Chris and Carré, Isabelle A. (2009) Evolutionarily conserved regulatory motifs in the promoter of the Arabidopsis clock gene LATE ELONGATED HYPOCOTYL. Plant Cell, Vol.21 (No.9). pp. 2606-2623. doi:10.1105/tpc.109.069898 ISSN 1040-4651.

V

(2009) The role of EUTox in uremic toxin research. Seminars in Dialysis, Vol.22 (No.4). pp. 323-328. doi:10.1111/j.1525-139X.2009.00574.x ISSN 0894-0959.

W

Whitelam, Stephen, Bretschneider, Till and Burroughs, Nigel John (2009) Transformation from spots to waves in a model of actin pattern formation. Physical Review Letters, Vol.102 (No.19). Article: 198103. doi:10.1103/PhysRevLett.102.198103 ISSN 0031-9007.

Whitelam, Stephen, Feng, Edward H., Hagan, Michael F. and Geissler, Phillip L. (2009) The role of collective motion in examples of coarsening and self-assembly. Soft Matter, Vol.5 (No.6). pp. 1251-1262. doi:10.1039/b810031d ISSN 1744-683X.

Whitelam, Stephen, Rogers, Carl, Pasqua, Andrea, Paavola, Chad, Trent, Jonathan and Geissler, Phillip L. (2009) The impact of conformational fluctuations on self-assembly: cooperative aggregation of archaeal chaperonin proteins. Nano Letters, Vol.9 (No.1). pp. 292-297. doi:10.1021/nl8029306 ISSN 1530-6984.

Wooldridge, Linda, Lissina, Anna, Cole, David K., Berg, Hugo van den, Price, David A. and Sewell, Andrew K. (2009) Tricks with tetramers : how to get the most from multimeric peptide-MHC. Immunology, Vol.126 (No.2). pp. 147-164. doi:10.1111/j.1365-2567.2008.02848.x ISSN 0019-2805.