Selected References to Kajeka Technology

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. 2017 Jul 17;7(1):5557. doi: 10.1038/s41598-017-05705-2. PubMed PMID: 28717181; PubMed Central PMCID: PMC5514134.

Jackson MD, Xu H, Duran-Nebreda S, Stamm P, Bassel GW. Topological analysis of multicellular complexity in the plant hypocotyl. Elife. 2017 Jul 6;6. pii:e26023. doi: 10.7554/eLife.26023. PubMed PMID: 28682235; PubMed Central PMCID: PMC5499946.

Suzuki HI, Young RA, Sharp PA. Super-Enhancer-Mediated RNA Processing Revealed by Integrative MicroRNA Network Analysis. Cell. 2017 Mar 9;168(6):1000-1014.e15. doi: 10.1016/j.cell.2017.02.015. PubMed PMID: 28283057; PubMed Central PMCID: PMC5350633.

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. 2017 Mar 6;13(3):e1006641. doi: 10.1371/journal.pgen.1006641. eCollection 2017 Mar. PubMed PMID: 28263993; PubMed Central PMCID: PMC5358891.

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. 2016 Nov 22;7(6). pii: e01714-16. doi: 10.1128/mBio.01714-16. Erratum in: MBio. 2016 Dec 20;7(6):. PubMed PMID: 27879333; PubMed Central PMCID: PMC5120140.

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. 2016 Sep 13;16(11):2953-2966. doi:10.1016/j.celrep.2016.08.023. PubMed PMID: 27626665; PubMed Central PMCID: PMC5039226.

Charitou T, Bryan K, Lynn DJ. Using biological networks to integrate, visualize and analyze genomics data. Genet Sel Evol. 2016 Mar 31;48:27. doi: 10.1186/s12711-016-0205-1. Review. PubMed PMID: 27036106; PubMed Central PMCID: PMC4818439.

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. 2015 Dec 11;5:18283. doi: 10.1038/srep18283. PubMed PMID: 26655864; PubMed Central PMCID: PMC4675998.

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. 2015 Aug 25;4:38. doi: 10.1186/s13742-015-0077-2. eCollection 2015. Review. PubMed PMID: 26309733; PubMed Central PMCID: PMC4548842.

Clark E.L., Bush S.J., McCulloch M.E.B., Farquhar I.L., Young R., Lefevre L., Pridans C., Tsang H.G., Wu C., Afrasiabi C., Watson M., Whitelaw C.B., Freeman T.C., Summers K.M., Archibald A.L. and Hume D.A. A high resolution atlas of gene expression in the domestic sheep (Ovis aries). PloS Genetics 13(9):e1006997 (2017).

Polak M.E., Ung C.Y., Masapust J., Freeman T.C., Ardern-Jones M.R. Petri Net computational modelling of Langerhans cell Interferon Regulatory Factor Network predicts their role in T cell activation. Sci Rep. 7:668 (2017).

Shih B.B-J., Nirmal A.J., Headon D.J., Akbar A.N., Mabbott N.A. and Freeman T.C.  Derivation of marker gene signatures from human skin and their use in the interpretation trancriptional changes associated with dermatological disorders. J. Pathol. 241(5): 600-613 (2017).

Alibhai J., Blanco R.A., Barria M.A., Piccardo P., Caughey B., Perry V.H., Freeman T.C., 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 M.H., Clohisey S., Baillie J.K., Stevens M.P., Freeman T.C., Summers K.M., McColl B.W. Microglial brain region-dependent diversity and selective regional sensitivities to aging. Nat Neurosci. 19: 504-516 (2016).

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. Leukocyte Biol. 96:167-83 (2014).

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

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

Doig T.N., Theocharidis A., Goodlad J.R, Hume D.A., Gregory C.D. and Freeman T.C. Coexpression analysis of large cancer datasets provides insight into the cellular phenotypes of the tumour microenvironment. BMC Genomics 14:469 (2013).

Freeman T.C., Ivens A., J. Baillie J.K., Beraldi D., Barnett M.W., Dorward D., Downing A., Fairbairn L., Kapetanovic R., Raza S., 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).

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 4:1535 – 1550 (2009).