Selected References to Kajeka Technology

Thion MS, Low D, Silvin A, Chen J, Grisel P, Schulte-Schrepping J, Blecher R, Ulas T, Squarzoni P, Hoeffel G, Coulpier F, Siopi E, David FS, Scholz C, Shihui F, Lum J, Amoyo AA, Larbi A, Poidinger M, Buttgereit A, Lledo PM, Greter M, Chan JKY, Amit I, Beyer M, Schultze JL, Schlitzer A, Pettersson S, Ginhoux F, Garel S. Microbiome Influences Prenatal and Adult Microglia in a Sex-Specific Manner. Cell 172(3):500-516 (2018).

Regan T., Barnett M.W., Laetsch D.R., Bush S.J., Wragg D., Budge G.E., Highet F., Dainat B., de Miranda J.R., The Bee Microbiome Consortium, Blaxter M. and Freeman T.C. Characterisation of the UK honey bee (Apis mellifera) metagenome. Nature Communications 9(1):4995 (2018).

Bush SJ, Freem L, MacCallum AJ, O’Dell J, Wu C, Afrasiabi C, Psifidi A, Stevens MP, Smith J, Summers KM, Hume DA.  Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken. BMC Genomics. 19(1):594 (2018).

Vallejo AF, Read RC, Arevalo-Herrera M, Herrera S, Elliott T, Polak ME. Malaria systems immunology: Plasmodium vivax induces tolerance during primary infection through dysregulation of neutrophils and dendritic cells. J Infect. 77(5):440-447 (2018).

Livigni A., O’Hara L., Polak, M.E., Angus T., Wright D., Smith L.B., Freeman T.C. A Graphical and Computational Modelling Platform for Biological Pathways. Nature Protocols 13(4):705-722 (2018).

Bush S., Powell-Smith A. and Freeman T.C. Network analysis of the social and demographic influences on name choice within the UK (1838-2016). PloS One 13(10): e0205759.

White RJ, Collins JE, Sealy IM, Wali N, Dooley CM, Digby Z, Stemple DL, Murphy DN, Billis K, Hourlier T, Füllgrabe A, Davis MP, Enright AJ, Busch-Nentwich EM. A high-resolution mRNA expression time course of embryonic development in zebrafish. Elife. 6. pii: e30860 (2017).

Camell CD, Sander J, Spadaro O, Lee A, Nguyen KY, Wing A, Goldberg EL, Youm YH, Brown CW, Elsworth J, Rodeheffer MS, Schultze JL, Dixit VD. Inflammasome-driven catecholamine catabolism in macrophages blunts lipolysis during ageing. Nature 550(7674):119-123 (2017).

Sarnataro S, Chiariello AM, Esposito A, Prisco A, Nicodemi M. Structure of the human chromosome interaction network. PLoS One. 12(11):e0188201 (2017).

Llavero Hurtado M, Fuller HR, Wong AMS, Eaton SL, Gillingwater TH, Pennetta G, Cooper JD, Wishart TM. Proteomic mapping of differentially vulnerable pre-synaptic populations identifies regulators of neuronal stability in vivo. Sci Rep. 7(1):12412 (2017)

Ma S, Ding Z, Li P. Maize network analysis revealed gene modules involved in development, nutrients utilization, metabolism, and stress response. BMC Plant Biol. 17(1):131 (2017).

Ma S, Snyder M, Dinesh-Kumar SP. Discovery of Novel Human Gene Regulators. Modules from Gene Co-expression and Promoter Motif Analysis. Sci Rep. 7(1):5557(2017).

Jackson MD, Xu H, Duran-Nebreda S, Stamm P, Bassel GW. Topological analysis of multicellular complexity in the plant hypocotyl. Elife 6. pii:e26023 (2017).

Suzuki HI, Young RA, Sharp PA. Super-Enhancer-Mediated RNA Processing Revealed by Integrative MicroRNA Network Analysis. Cell. 168(6):1000-1014 (2017).

Clark EL, Bush SJ, McCulloch MEB, Farquhar IL, Young R, Lefevre L, Pridans C, Tsang HG, Wu C, Afrasiabi C, Watson M, Whitelaw CB, Freeman TC, Summers KM, Archibald AL and Hume DA. A high resolution atlas of gene expression in the domestic sheep (Ovis aries). PloS Genetics 13(9):e1006997 (2017).

Polak ME, Ung CY, Masapust J, Freeman TC and Ardern-Jones MR. Petri Net computational modelling of Langerhans cell Interferon Regulatory Factor Network predicts their role in T cell activation. Sci Rep. 7:668 (2017).

Auffret M.D., Dewhurst, R.J., Duthie, C.-A., Rooke, J.A., Wallace R.J., Freeman T.C., Stewart R., Watson M. and Roehe R. The rumen microbiome as a reservoir of antimicrobial resistance and pathogenicity genes is directly affected by diet in beef cattle. Microbiome 5: 159 (2017).

Shih BB-J, Nirmal AJ, Headon DJ, Akbar AN, Mabbott NA. and Freeman TC. Derivation of marker gene signatures from human skin and their use in the interpretation transcriptional changes associated with dermatological disorders. J. Pathol. 241(5): 600-613 (2017).

Baillie JK, Arner E, Daub C, De Hoon M, Itoh M, Kawaji H, Lassmann T, Carninci P, Forrest AR, Hayashizaki Y; FANTOM Consortium, Faulkner GJ, Wells CA, Rehli M, Pavli P, Summers KM, Hume DA Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease. PLoS Genet. 13(3):e1006641(2017).

Côté JP, French S, Gehrke SS, MacNair CR, Mangat CS, Bharat A, Brown ED. The Genome-Wide Interaction Network of Nutrient Stress Genes in Escherichia coli. MBio. 7(6). pii: e01714-16 (2016).

O’Hara L., Livigni A., Theo T., Boyer B., Angus T., Wright D., Chen S-H., Raza S., Barnett M.W., Digard P., Smith L.B. and Freeman T.C. Modelling the Structure and Dynamics of Biological Pathways. PLoS Biol. 14(8):e1002530 (2016).

Alibhai J, Blanco RA, Barria MA, Piccardo P, Caughey B, Perry VH, Freeman TC and Manson, J.  Distribution of misfolded prion protein seeding activity alone does not predict regions of neurodegeneration. PLoS Biol. 14(11): e1002579 (2016).

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: 504-516 (2016).

Roehe R., Dewhurst R.J., Duthie C.-A., Rooke J.A., McKain N., Ross D.W., Hyslop J.J., Waterhouse A., Freeman T.C., Watson M., Wallace, R.J. 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: e1005846 (2016).

Worah K, Mathan TSM, Vu Manh TP, Keerthikumar S, Schreibelt G, Tel J, Duiveman-de Boer T, Sköld AE, van Spriel AB, de Vries IJM, Huynen MA, Wessels HJ, Gloerich J, Dalod M, Lasonder E, Figdor CG, Buschow SI. Proteomics of Human Dendritic Cell Subsets Reveals Subset-Specific Surface Markers and Differential Inflammasome Function. Cell Rep. 16(11):2953-2966. (2016).

Charitou T, Bryan K, Lynn DJ. Using biological networks to integrate, visualize and analyze genomics data. Genet Sel Evol. 48:27. (2016).

Wang K, Jiang S, Sun C, Lin Y, Yin R, Wang Y, Zhang M. The Spatial and Temporal Transcriptomic Landscapes of Ginseng, Panax ginseng C. A. Meyer. Sci Rep. 5:18283. (2015).

Pavlopoulos GA, Malliarakis D, Papanikolaou N, Theodosiou T, Enright AJ, Iliopoulos I. Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future. Gigascience. 4:38. (2015).

Raza S, Barnett MW, Barnett-Itzhaki Z, Amit I, Hume DA, Freeman TC. Analysis of the transcriptional networks underpinning the activation of murine macrophages by inflammatory mediators.  J. Leukocyte Biol. 96:167-83 (2014).

Forrest et al. A promoter level mammalian expression atlas. Nature. 507, 462–470 (2014).

Xue J, Schmidt SV, Sander J, Draffehn A, Krebs W, Quester I, de  Nardo D , Gohel TD, Ganesan H, Nino-Castro A, Mallmann M, Labzin L, Theis H, Kraut M, Beyer M, Latz E, Freeman TC, Ulas T, Schultze JL. Network engineering on transcriptional level reveals a multi-strata model of human macrophage activation.  Immunity 40: 274-288 (2014).

Doig TN, Theocharidis A, Goodlad JR, Hume DA, Gregory CD and Freeman TC Coexpression analysis of large cancer datasets provides insight into the cellular phenotypes of the tumour microenvironment. BMC Genomics 14:469 (2013).

Freeman TC, Ivens A, J Baillie JK, Beraldi D, Barnett MW, Dorward D, Downing A, Fairbairn L, Kapetanovic R, Raza S, Tomoiu A, Alberio R, Wu C, Su AI, Summers KM, Tuggle CK, Archibald AL and Hume DA. A gene expression atlas of the domestic pig. BMC Biology 10:90 (2012).

Theocharidis A, van Dongen S, Enright AJ and Freeman TC. Network visualisation and analysis of gene expression data using BioLayout Express3D. Nature Protocols 4:1535 – 1550 (2009).

Freeman TC, Goldovsky L, Brosch M, van Dongen S, Mazière P, Grocock RJ, Freilich S, Thornton J, Enright AJ. Construction, visualisation, and clustering of transcription networks from microarray expression data. PLoS Comput Biol. 3(10):2032-42 (2007).