Publications

BioLayout Express3D Description

 

  1. O’Hara, L. et al. Modelling the Structure and Dynamics of Biological Pathways. PLOS Biol. 14, e1002530 (2016).
  2. Wright D.W., Angus T., Enright A.J. and Freeman T.C.. Visualisation of BioPAX Networks using BioLayout Express3D F1000Research 2014, 3:246 (doi: 10.12688/f1000research.5499.1).
  3. Wright D.W., Angus T. and Freeman T.C. BioLayout Express3D Version 3.2 Biological Pathway Modelling. Poster presented at VIZBI 2014 meeting, EMBL Heidelberg, Germany, March 2014.
  4. Waltemath D. et al. Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE). Stand. Genomic Sci. 9:3 (2014). Details of presentation given at COMBINE 2013 meeting, Institut Curie, Paris, France, September 2013.
  5. Wright D.W., Angus T., Theocharidis A. and Freeman T.C. Conversion of mEPN pathway diagrams to SBGN in BioLayout Express3D. Abstract of presentation given at COMBINE 2013 meeting, Institut Curie, Paris, France, September 2013.
  6. Angus T., Klein K., and Freeman T. Evaluation of graph layout algorithms for the visualization of biological networks in 3D. Abstract submitted to Graph Drawing 2013 meeting, Bordeaux, France, September 2013. See also poster displayed at meeting.
  7. BioLayout Express3D Version 3.0: Network Visualization and Analysis of Complex Data and Biological Pathways. Poster displayed at VIZBI 2013 meeting, Broad Institute, Cambridge, MA, USA, March 2013.
  8. Theocharidis A., Hemani G., Kargas M. and Freeman T.C. A Comparison of CPU and OpenCL Parallelization Methods for Correlation and Graph Layout Algorithms used in the Network Analysis of High Dimensional Data. (2010 Unpublished)
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. Enright A.J., Ouzounis C.A. BioLayout-an automatic graph layout algorithm for similarity visualization. Bioinformatics 2001;17(9):853-4.
  14. Van Dongen S. Graph Clustering by Flow Simulation. PhD thesis, University of Utrecht, May 2000.

BioLayout Express3D Facilitated Research

  1. Safieddine F, Dordevic M, Hamza A.M. Optimization of exam distribution. Eur J Edu Studies 2:1-10 (2016).
  2. Roehe R, Dewhurst RJ, Duthie CA, Rooke JA, McKain N, Ross DW, Hyslop JJ, Waterhouse A, Freeman TC, Watson M, Wallace RJ. Bovine Host Genetic Variation Influences Rumen Microbial Methane Production with Best Selection Criterion for Low Methane Emitting and Efficiently Feed Converting Hosts Based on Metagenomic Gene Abundance. PLoS Genet. 12(2):e1005846 (2016).
  3. Grabert K, Michoel T, Karavolos MH, Clohisey S, Baillie JK, Stevens MP, Freeman TC, Summers KM, McColl BW. Microglial brain region-dependent diversity and selective regional sensitivities to aging. Nat Neurosci. 19(3):504-16 (2016).
  4. Schroyen M, Eisley C, Koltes JE, Fritz-Waters E, Choi I, Plastow GS, Guan L, Stothard P, Bao H, Kommadath A, Reecy JM, Lunney JK, Rowland RR, Dekkers JC, Tuggle CK. Bioinformatic analyses in early host response to Porcine Reproductive and Respiratory Syndrome virus (PRRSV) reveals pathway differences between pigs with alternate genotypes for a major host response QTL. BMC Genomics. 17:196. (2016).
  5. Sharp GC, Hutchinson JL, Hibbert N, Freeman TC, Saunders PT, Norman JE. Transcription Analysis of the Myometrium of Labouring and Non-Labouring Women. PLoS One. 11(5):e0155413 (2016).
  6. Vincenti JE, Murphy L, Grabert K, McColl BW, Cancellotti E, Freeman TC, Manson JC. Defining the Microglia Response during the Time Course of Chronic Neurodegeneration. J Virol. 90(6):3003-17 (2015).
  7. Dobyns AE, Goyal R, Carpenter LG, Freeman TC, Longo LD, Yellon SM. Macrophage gene expression associated with remodeling of the prepartum rat cervix: microarray and pathway analyses. PLoS One. 10(3):e0119782 (2015).
  8. Ford CA, Petrova S, Pound JD, Voss JJ, Melville L, Paterson M, Farnworth SL, Gallimore AM, Cuff S, Wheadon H, Dobbin E, Ogden CA, Dumitriu IE, Dunbar DR, Murray PG, Ruckerl D, Allen JE, Hume DA, van Rooijen N, Goodlad JR, Freeman TC, Gregory CD. Oncogenic properties of apoptotic tumor cells in aggressive B cell lymphoma. Curr Biol. 25(5):577-88 (2015).
  9. Joshi A, Pooley C, Freeman TC, Lennartsson A, Babina M, Schmidl C, Geijtenbeek T; the FANTOM Consortium, Michoel T, Severin J, Itoh M, Lassmann T, Kawaji H, Hayashizaki Y, Carninci P, Forrest AR, Rehli M, Hume DA. Transcription factor, promoter, and enhancer utilization in human myeloid cells. J Leukoc Biol. jlb.6TA1014-477RR (2015).
  10. Arner E, et al. (Fantom5 consortium). Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science 347(6225):1010-4 (2015).
  11. Forrest et al. (Fantom5 consortium). A promoter level mammalian expression atlas.  Nature 507, 462–470 (2014).
  12. Andersson R., et al. (Fantom5 consortium). An atlas of active enhancers across human cell types and tissues.  Nature 507, 455–461 (2014).
  13. Polak M.E., Thirdborough S.M., Ung C.Y., Elliott T., Healy E., Freeman T.C. and Ardern-Jones M.R. Distinct molecular signature of human skin Langerhans cells denotes critical differences in cutaneous dendritic cell immune regulation.  J. Invest. Dermatol. 134:695-703 (2014).
  14. Mooney JE, Summers KM, Gongora M, Grimmond SM, Campbell JH, Hume DA, Rolfe BE. Transcriptional switching in macrophages associated with the peritoneal foreign body response. Immunol Cell Biol. 92(6):518-26 (2014).
  15. Nadaf J, Berri C, Dunn I, Godet E, Le Bihan-Duval E, De Koning DJ. An expression QTL of closely linked candidate genes affects pH of meat in chickens. Genetics 196(3):867-74. (2014).
  16. Gordon SB, Jagoe RT, Jarman ER, North JC, Pridmore A, Musaya J, French N, Zijlstra EE, Molyneux ME, Read RC. The alveolar microenvironment of patients infected with human immunodeficiency virus does not modify alveolar macrophage interactions with Streptococcus pneumoniae. Clin Vaccine Immunol. 20(6):882-91 (2013).
  17. Lizio M. et al.  Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biology 16:22 (5 Jan 2014).
  18. Dent J.E., Devescovi V., Li H., Di Lena P., Lu Y., Liu Y., Nardini C. Mechanotransduction map: simulation model, molecular pathway, gene set. Bioinformatics (25 Nov 2014 Epub ahead of print). 
  19. Hume D.A., Freeman T.C. Transcriptomic analysis of mononuclear phagocyte differentiation and activation. Immunol Rev. 262(1):74-84 (Nov 2014).
  20. Mooney JE, Summers KM, Gongora M, Grimmond SM, Campbell JH, Hume DA, Rolfe BE. Transcriptional switching in macrophages associated with the peritoneal foreign body response. Immunol Cell Biol. 92(6):518-26 (Jul 2014).
  21. Raza S., Barnett M.W., Barnett-Itzhaki Z., Amit I., Hume D.A., Freeman T.C. Analysis of the transcriptional networks underpinning the activation of murine macrophages by inflammatory mediators. J. Leukoc Biol. 96(2):167-183 (Epub 10 Apr 2014).
  22. Davis M.R., Andersson R., Severin J., de Hoon M., Bertin N., Baillie J.K., Kawaji H., Sandelin A., Forrest A.R., Summers K.M.; FANTOM Consortium. Transcriptional profiling of the human fibrillin/LTBP gene family, key regulators of mesenchymal cell functions. Mol. Genet Metab. 112(1):73-83 (May 2014, Epub Dec 2013).
  23. The FANTOM Consortium and the RIKEN PMI and CLST (DGT). A promoter-level mammalian expression atlas. Nature 507:462–470 (27 March 2014).
  24. Xue J., Schmidt S.V., Sander J., Draffehn A., Krebs W., Quester I., De Nardo D., Gohel T.D., Emde M., Schmidleithner L., Ganesan H., Nino-Castro A., Mallmann M.R., Labzin L., Theis H., Kraut M., Beyer M., Latz E., Freeman T.C., Ulas T., Schultze J.L. Transcriptome-Based Network Analysis Reveals a Spectrum Model of Human Macrophage Activation. Immunity pii: S1074-7613(14)00034-X (Feb 11 2014 Epub ahead of print).
  25. Yamane F., Nishikawa Y., Matsui K., Asakura M., Iwasaki E., Watanabe K., Tanimoto H., Sano H., Fujiwara Y., Stanley E.R., Kanayama N., Mabbott N.A., Magari M., Ohmori H.J. CSF-1 receptor-mediated differentiation of a new type of monocytic cell with B cell-stimulating activity: its selective dependence on IL-34. J Leukoc Biol. 95(1):19-31 (2014).
  26. Hall D.P., Maccormick I.J., Phythian-Adams A.T., Rzechorzek N.M., Hope-Jones D., Cosens S., Jackson S., Bates M.G., Collier D.J., Hume D.A., Freeman T., Thompson A.A. and Baillie J.K. Network Analysis Reveals Distinct Clinical Syndromes Underlying Acute Mountain Sickness. PLoS One. 9(1):e81229 (2014).
  27. Polak M.E., Thirdborough S.M., Ung C.Y., Elliott T., Healy E., Freeman T.C. and Ardern-Jones M.R. Distinct molecular signature of human skin Langerhans cells denotes critical differences in cutaneous dendritic cell immune regulation. J. Invest. Dermatol. (2013 Epub ahead of print).
  28. Mabbott N.A., Baillie J.K., Brown H., Freeman T.C. and Hume D.A.. An expression atlas of human primary cells: inference of gene function from coexpression networks. BMC Genomics 14:632 (2013).
  29. Mabbott N.A. and Gray D. Identification of co-expressed gene signatures in mouse B1, marginal zone and B2 B-cell populations. Immunology (2013 Epub ahead of print).
  30. Kapetanovic R., Fairbairn L., Downing A., Beraldi D., Sester D.P., Freeman T.C., Tuggle C.K., Archibald A.L. and Hume D.A. The impact of breed and tissue compartment on the response of pig macrophages to lipopolysaccharide. BMC Genomics 14:581 (2013 Epub ahead of print).
  31. Dent J.E, Yang X. and Nardini C. SPNConverter: a new link between static and dynamic complex network analysis. Bioinformatics (Aug 1 2013 Epub). 
  32. Dent J.E. and Nardini C. From desk to bed: Computational simulations provide indication for rheumatoid arthritis clinical trials. BMC Systems Biology 7:10 (2013).
  33. Doig T.N., Hume D.A., Theocharidis T., Goodlad J.R., Gregory C.D., Freeman T.C. Coexpression analysis of large cancer datasets provides insight into the cellular phenotypes of the tumour microenvironment. BMC Genomics 14:469 (2013).
  34. Dawson, H.D., Loveland, J.E., Pascal, G., Gilbert, J.G., Uenishi, H., Mann, K.M., Sang, Y., Zhang J., Carvalho-Silva D., Hunt T., Hardy M., Hu, Z., Zhao, S.H., Anselmo, A., Shinkai, H., Chen, C., Badaoui, B., Berman, D., Amid, C., Kay M., Lloyd, D., Snow, C., Morozumi, T., Cheng, R.P., Bystrom, M., Kapetanovic, R., Schwartz, J.C., Kataria, R., Astley, M., Fritz, E., Steward, C., Thomas, M., Wilming, L., Toki, D., Archibald, A.L., Bed’hom, B., Berald,i D., Huang, T.H., Ait-Ali, T., Blecha, F., Botti, S., Freeman, T.C., Giuffra, E., Hume, D.A., Lunney, J.K., Murtaugh, M.P., Reecy, J.M., Harrow, J.L., Rogel-Gaillard, C., Tuggle, C.K. Structural and functional annotation of the porcine immunome. BMC Genomics 14:332 (2013).
  35. Lopez, F,J., Bernabeu, M., Fernandez-Becerra, C., del Portillo, H.A. A new computational approach redefines the subtelomeric vir superfamily of Plasmodium vivax. BMC Genomics 14:8 (2013).
  36. Gordon, S.B, Jagoe, R.T., Jarman, E.R., North, J.C., Pridmore A., Musaya J., French N., Zijlstra E.E., Molyneux M.E., Read R.C.. The alveolar microenvironment of patients infected with Human Immunodeficiency Virus does not modify alveolar macrophage interactions with Streptococcus pneumoniae. Clin. Vaccine Immunol.  2013 20(6): 882-91 (2013).
  37. Breuer K., Foroushani A.K., Laird M.R., Chen C., Sribnaia A., Lo R., Winsor G.L., Hancock R.E.W., Brinkman F.S.L. and Lynn D.J.  InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation. Nucleic Acids Res. 1;41(D1):D1228-33 (2013).
  38. Freeman T.C., Ivens A., J. Baillie, J.K., Beraldi, D., Barnett, M.W., Dorward, D., Downing A., Fairbairn, L., Kapetanovic, R., Tomoiu, A., Alberio, R., Wu, C., Su, A.I., Summers, K.M., Tuggle, C.K., Archibald, A.L. and Hume D.A.  A gene expression atlas of the domestic pig. BMC Biology 10:90 (2012).
  39. Kobayashi, A., Donaldson, D.S., Kanaya, T., Fukuda, S., Baillie, J.K., Freeman, T.C., Ohno, H., Williams, I.R. and Mabbott, N.A.  Identification of novel genes selectively expressed in the follicle-associated epithelium from the meta-analysis of transcriptomics data from multiple mouse cell and tissue populations.  DNA Res. 19: 407-422 (2012).
  40. McDerment N.A., Wilson P.W., Waddington D., Dunn I.C., Hocking P.M., Identification of novel candidate genes for follicle selection in the broiler breeder ovary. BMC Genomics 13:494 (2012).
  41. Cabrera C.P., Navarro P., Huffman J.E., Wright A.F., Hayward C., Campbell H., Wilson J.F., Rudan I., Hastie N.D., Vitart V., Haley C.S.. Uncovering networks from genome-wide association studies via circular genomic permutation. G3 (Bethesda). 2(9):1067-75 (2012). PubMed PMID: 22973544
  42. Burgess S.T.G., Greer A., Frew D., Wells B., Marr E.J., Nisbet A.J., and Huntley J.F. Transcriptomic Analysis of Circulating Leukocytes Reveals Novel Aspects of the Host Systemic Inflammatory Response to Sheep Scab Mites. PLoS One. 7(8):e42778 (2012).
  43. Thomson, A.J., Pierart, H., Meek, S., Bogerman, A., Sutherland, L., Murray, H., Mountjoy, E., Downing, A., Talbot, R., Sartori, C., Whitelaw, B.A., Freeman, T.C., Archibald, A.L. and Burdon, T.  Reprogramming pig fetal fibroblasts reveals a functional LIF signaling pathway.  Cellular Reprogramming 14:112-122 (2012).
  44. Robert C., Lu X., Law A., Freeman T.C. and Hume D.A. Macrophages.com: an on-line community resource for innate immunity research.  Immunobiology 216: 1203-11, 2011.
  45. Mabbott N.A., Baillie J.K., Kobayashi A., Donaldson D.S. Ohmori H., Yoon S-0., Freedman A.S., Freeman T.C. and Summers K.M. Expression of mesenchyme-specific gene signatures by follicular dendritic cells: insights from the meta-analysis of microarray data from multiple mouse cell populations. Immunology 133 482-98 (2011).
  46. 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).
  47. 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).
  48. 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).
  49. 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).
  50. 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.
  51. 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.
  52. 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.
  53. 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.
  54. 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.
  55. 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.
  56. Janga S.C., Babu M.M. Transcript stability in the protein interaction network of Escherichia coli. Mol. Biosyst. 2009 Feb;5(2):154-62.
  57. 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).
  58. 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).
  59. 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.
  60. 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.
  61. Bossi A. and Lehner B. Tissue specificity and the human protein interaction network. Mol Syst Biol. 2009;5:260. Epub 2009 Apr 7.