Publications

BioLayout Express3D Description

  1. Theocharidis A., van Dongen S., Enright A.J. and Freeman T.C. Network Visualisation and Analysis of Gene Expression Data using BioLayout Express3D. Nature Protocols 2009; Vol.4 No.10:1535-50.
  2. Freeman T.C., Goldovsky L., Brosch M., van Dongen S., Mazière P., Grocock R.J., Freilich S., Thornton J., Enright A.J. Construction, visualisation, and clustering of transcription networks from microarray expression data. PLoS Comput Biol. 2007; 3(10):2032-42.
  3. Goldovsky L., Cases I., Enright A.J., Ouzounis C.A. BioLayout(Java): versatile network visualisation of structural and functional relationships. Appl Bioinformatics. 2005;4(1):71-4.
  4. Enright A.J., Van Dongen S, Ouzounis C.A. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 2002;30(7):1575-84.
  5. Enright A.J., Ouzounis C.A. BioLayout-an automatic graph layout algorithm for similarity visualization. Bioinformatics. 2001;17(9):853-4.
  6. Van Dongen S. Graph Clustering by Flow Simulation. PhD thesis, University of Utrecht, May 2000.

BioLayout Express3D Facilitated Research

  1. Inouye M., Silander K., Hamalainen E., Salomaa V., Harald K., Jousilahti P., Männistö S., Eriksson J.G., Saarela J., Ripatti S., Perola M., van Ommen G.J., Taskinen M.R., Palotie A., Dermitzakis E.T. and Peltonen L. An immune response network associated with blood lipid levels. PLoS Genet. 6(9). pii: e1001113 (2010).
  2. Benítez-Páez A., Villarroya M., Douthwaite S., Gabaldón T., Armengod M.E. YibK is the 2'-O-methyltransferase TrmL that modifies the wobble nucleotide in Escherichia coli tRNA(Leu) isoacceptors. RNA 16(11):2131-43 (2010).
  3. Natividad A., Freeman T.C., Jeffries D., Burton M.J., Mabey D.C.W., Bailey R.L. and Holland M.J. Human conjunctival transcriptome analysis reveals the prominence of innate defence in Chlamydia trachomatis infection. Infection and Immunity 78:4895-911 (2010).
  4. Letek M., González P., MacArthur I., Rodríguez H., Freeman T.C., Valero-Rello A., Blanco M., Buckley T., Cherevach I., Hapeshi A., Holdstock J., Leadon D., Navas J., Quail M.A., Sanders M., Scortti M.M., Prescott J.F., Fogarty U., Meijer W., Parkhill J., Bentley S.D. and Vázquez-Boland J.A. The genome of a pathogenic Rhodococcus: cooptive virulence underpinned by key gene acquisitions. PLoS Genetics 30: e1001145 (2010).
  5. Hume D.A., Summers K.M., Raza S. and Freeman T.C. Functional Clustering and Lineage Makers: Insights into Cellular Differentiation and Gene Function from Large-Scale Microarray Studies of Purified Primary Cell Populations. Genomics 6:328-338 2010.
  6. Freeman T.C., Raza S., Theocharidis A. and Ghazal P. The mEPN Scheme: An Intuitive and Flexible Graphical System for Rendering Biological Pathways. BMC Systems Biology 4:65, 2010.
  7. Raza S., McDerment N., Lacaze P.A., Robertson K., Watterson S., Chen Y., Chisholm M., Eleftheriadis G., Monk S., O'Sullivan M., Turnbull A., Roy D., Theocharidis A., Ghazal P. and Freeman T.C. Construction of a Large Scale Integrated Map of Macrophage Pathogen Recognition and Effector Systems. BMC Systems Biology 4:63, 2010.
  8. Summers K.M., Raza S., van Nimwegen E., Freeman T.C. and Hume D.A. Coexpression clustering of FBN1 with mesenchyme-specific genes in mouse cell lines: implications for phenotypic variability in Marfan syndrome. Eur. J. Human Genetics. In press 2010.
  9. Mabbott N.A., Baillie J.K., Hume D.A. and Freeman T.C. Meta-analysis of Lineage-Specific Gene Expression Signatures in Mouse Leukocyte Populations. Immunobiology. In press 2010.
  10. Edwards K., Bombarely A., Story G.W., Allen F., Mueller L.A., Coates SA. and Jones L. TobEA: an atlas of tobacco gene expression from seed to senescence. BMC Genomics. 2010 Feb 26;11:142.
  11. Fitzpatrick J.M., Peak E., Perally S., Chalmers I.W., Barrett J., Yoshino T.P., Ivens A.C. and Hoffmann K. F. Anti-schistosomal Intervention Targets Identified by Lifecycle Transcriptomic Analyses. PLoS NTD (2009).
  12. Lacaze P., Raza S., Sing G., Page D., Forster T., Storm P., Craigon M., Awad T., Ghazal P. and Freeman T.C. Combined genome-wide expression profiling and targeted RNAi knock-down in mouse primary macrophages reveals perturbation of transcriptional networks associated with interferon signaling. BMC Genomics 10: 372 (2009).
  13. Raza S., Robertson K.A., Lacaze P.A. Page D., Enright A.J., Ghazal P. and Freeman T.C. A logic-based diagram of signalling pathways central to macrophage activation. BMC Systems Biology, v.2; 2008.
  14. Cowley M.J., Cotsapas C.J., Williams R.B., Chan E.K., Pulvers J.N., Liu M.Y., Luo O.J., Nott D.J. and Little PF. Intra- and inter-individual genetic differences in gene expression. Mamm Genome. 2009 May;20(5):281-95. Epub 2009 May 8.
  15. Bossi A. and Lehner B. Tissue specificity and the human protein interaction network. Mol Syst Biol. 2009;5:260. Epub 2009 Apr 7.