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Understanding the regulation of the immune system from a systems-level perspective

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Authors	Title	Published in
Lynn M.A., Tumes D.J., Choo J.M., Sribnaia A., Blake S.J., Leong L.E.X., Young G.P., Marshall H.S., Wesselingh S.L., Rogers G.B., Lynn D.J. (2018). Early-life antibiotic-driven dysbiosis leads to dysregulated vaccine immune responses in mice. Cell Host & Microbe, 23(5): 653-660. Corresponding Author.	Early-life antibiotic-driven dysbiosis leads to dysregulated vaccine immune responses in mice.	Cell Host & Microbe, 23(5): 653-660. Corresponding Author.
Salamon J., Goenawan I.H., Lynn D.J. (2018). Analysis and visualization of dynamic networks using the DyNet App for Cytoscape. Current Protocols in Bioinformatics, 63(5): e55. Corresponding Author.	Analysis and visualization of dynamic networks using the DyNet App for Cytoscape.	Current Protocols in Bioinformatics, 63(5): e55. Corresponding Author.
MacGregor S., Ong J.S., An J., Han X., Zhou T., Siggs O.M., Law M.H., Souzeau E., Sharma S., Lynn D.J., Beesley J., Sheldrick B., Mills R.A., Landers J., Ruddle J.B., Graham S.L., Healey P.R., White A.J.R., Casson R.J., Best S., Grigg J.R., Goldberg I., Powell J.E., Whiteman D.C., Radford-Smith G.L., Martin N.G., Montgomery G.W., Burdon K.P., Mackey D.A., Gharahkhani P., Craig J.E., Hewitt A.W. (2018). Genome-wide association study of intraocular pressure uncovers new pathways to glaucoma. Nature Genetics, 50(8): 1067-1071.	Genome-wide association study of intraocular pressure uncovers new pathways to glaucoma.	Nature Genetics, 50(8): 1067-1071.
Nguyen E., Centenera M., Moldovan M., Das R., Irani S., Vincent A., Chan H., Horvath L., Lynn D.J., Daly R., Butler L. (2018). Identification of novel response and predictive biomarkers to Hsp90 inhibitors through mass spectrometry-based proteomic profiling of patient-derived prostate tumor explants. Molecular & Cellular Proteomics, 17(8): 1470-1486.	Identification of novel response and predictive biomarkers to Hsp90 inhibitors through mass spectrometry-based proteomic profiling of patient-derived prostate tumor explants.	Molecular & Cellular Proteomics, 17(8): 1470-1486.
Salamon J., Qian X., Nilsson M., Lynn D.J. (2018). Network visualization and analysis of spatially aware gene expression data with InsituNet. Cell Systems, 6(5): 626-630. Corresponding Author.	Network visualization and analysis of spatially aware gene expression data with InsituNet.	Cell Systems, 6(5): 626-630. Corresponding Author.
Dumousseau M., Alonso-López D., Ammari M., Bradley G., Campbell N.H., Ceol A., Cesareni G., Combe C., De Las Rivas .J, Del-Toro N., Heimbach J., Hermjakob H., Jurisica I., Koch M., Licata L., Lovering R.C., Lynn D.J., Meldal B., Micklem G., Panni, S., Porras P., Ricard-Blum S., Roechert B., Salwinski L., Shrivastava A., Sullivan J., Thierry-Mieg N., Yehudi Y., Van Roey K., Orchard S. (2018). Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions. BMC Bioinformatics, 19(1):134.	Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions.	BMC Bioinformatics, 19(1):134.
Gharahkhani P., Burdon K.P., Cooke Bailey J.N., Hewitt A.W., Law M.H., Pasquale L.R., Kang J.H., Haines J.L., Souzeau E., Zhou T., Siggs O.M., Landers J., Awadalla M., Sharma S., Mills R.A., Ridge B., Lynn D.J., NEIGHBORHOOD consortium, Casson R., Graham S.L., Goldberg I., White A., Healey P.R., Grigg J., Lawlor M., Mitchell P., Ruddle J., Coote M., Walland M., Best S., Vincent A, Gale J., Radford Smith G., Whiteman D.C., Montgomery G.W., Martin N.G., Mackey D.A., Wiggs J.L., MacGregor S., Craig J.E. (2018). Analysis combining correlated glaucoma traits identifies five new risk loci for open-angle glaucoma. Scientific Reports, 8(1): 3124.	Analysis combining correlated glaucoma traits identifies five new risk loci for open-angle glaucoma.	Scientific Reports, 8(1): 3124.
Armstrong H.K., Gillis J., Johnson I.R.D., Nassar Z.D., Moldovan M., Levrier C., Sadowski M.C., Chin M.Y., Guns E.T., Tarulli G., Lynn D.J., Brooks D.A., Selth L.A., Centenera M.M., Butler L.M. (2018). Dysregulated fibronectin trafficking by Hsp90 inhibition restricts prostate cancer cell invasion. Scientific Reports, 8(1): 2090.	Dysregulated fibronectin trafficking by Hsp90 inhibition restricts prostate cancer cell invasion.	Scientific Reports, 8(1): 2090.
Lynn D.J., Pulendran B. (2018). The potential of the microbiota to influence vaccine responses. Journal of Leukocyte Biology, 103(2): 225-231. Corresponding Author.	The potential of the microbiota to influence vaccine responses.	Journal of Leukocyte Biology, 103(2): 225-231. Corresponding Author.
Smith J.R, Todd S., Ashander L.M., Charitou T., Ma Y., Yeh S., Crozier I., Michael M., Appukuttan B., Lynn D.J., Marsh G.A. (2017). * Joint-senior author. Retinal Pigment Epithelial Cells are a Potential Reservoir for Ebola Virus in the Human Eye. Translational Vision Science & Technology, 6(12): doi :10.1167/tvst.6.4.12.	Retinal Pigment Epithelial Cells are a Potential Reservoir for Ebola Virus in the Human Eye.	Translational Vision Science & Technology, 6(12): doi :10.1167/tvst.6.4.12.
Muetze T., Lynn D.J. (2017). Identification of Contextually Relevant Hubs using the Contextual Hub Analysis Tool (CHAT) in Cytoscape. Current Protocols in Bioinformatics, 59 8.24.1 – 8.24.13 doi : 10.1002/cpbi.35. Corresponding Author.	Identification of Contextually Relevant Hubs using the Contextual Hub Analysis Tool (CHAT) in Cytoscape.	Current Protocols in Bioinformatics, 59 8.24.1 – 8.24.13 doi : 10.1002/cpbi.35. Corresponding Author.
Zhou T., Souzeau E., Sharma S., Landers J., Mills R., Goldberg I., Healey P., Graham S., Hewitt A.W., Mackey D.A., Galanopoulos A., Casson R., Ruddle J., Ellis J., Leo P., Brown M.A., MacGregor S., Lynn D.J., Burdon K.P., Craig J.E. (2017). Whole exome sequencing implicates eye development, the unfolded protein response and plasma membrane homeostasis in primary open-angle glaucoma. PLoS One, 12(3): e0172427.	Whole exome sequencing implicates eye development, the unfolded protein response and plasma membrane homeostasis in primary open-angle glaucoma.	PLoS One, 12(3): e0172427.
Muetze T, Goenawan IH, Wiencko HL, Bernal-Llinares M, Bryan K, Lynn DJ. Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually relevant hubs in biological networks. F1000 Research 2016 (In press).	Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually relevant hubs in biological networks.	F1000 Research 2016 (In press).
Goenawan IH, Bryan K, Lynn DJ. (Corresponding Author) DyNet: visualization and analysis of dynamic molecular interaction networks. Bioinformatics. 2016 Sep 1;32(17):2713-5. doi: 10.1093/bioinformatics/btw187. Epub 2016 May 3.	DyNet: visualization and analysis of dynamic molecular interaction networks.	Bioinformatics. 2016 Sep 1;32(17):2713-5. doi: 10.1093/bioinformatics/btw187. Epub 2016 May 3.
Bryan K, Jarboui MA, Raso C, Bernal-Llinares M, McCann B, Rauch J, Boldt K, Lynn DJ. (Corresponding Author) HiQuant: Rapid Postquantification Analysis of Large-Scale MS-Generated Proteomics Data. J Proteome Res. 2016 Jun 3;15(6):2072-9. doi: 10.1021/acs.jproteome.5b01008. Epub 2016 May 16.	HiQuant: Rapid Postquantification Analysis of Large-Scale MS-Generated Proteomics Data.	J Proteome Res. 2016 Jun 3;15(6):2072-9. doi: 10.1021/acs.jproteome.5b01008. Epub 2016 May 16.
Blohmke CJ, Darton TC, Jones C, Suarez NM, Waddington CS, Angus B, Zhou L, Hill J, Clare S, Kane L, Mukhopadhyay S, Schreiber F,Duque-Correa MA, Wright JC, Roumeliotis TI, Yu L, Choudhary JS, Mejias A, Ramilo O, Shanyinde M, Sztein MB, Kingsley RA, Lockhart S,Levine MM, Lynn DJ, Dougan G, Pollard AJ. Interferon-driven alterations of the host's amino acid metabolism in the pathogenesis of typhoid fever. J Exp Med. 2016 May 30;213(6):1061-77. doi: 10.1084/jem.20151025. Epub 2016 May 23.	Interferon-driven alterations of the host's amino acid metabolism in the pathogenesis of typhoid fever.	J Exp Med. 2016 May 30;213(6):1061-77. doi: 10.1084/jem.20151025. Epub 2016 May 23.
Charitou T, Bryan K, Lynn DJ. (Corresponding Author) 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.	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.
Richardson IW, Berry DP, Wiencko HL, Higgins IM, More SJ, McClure J, Lynn DJ, Bradley DG. A genome-wide association study for genetic susceptibility to Mycobacterium bovis infection in dairy cattle identifies a susceptibility QTL on chromosome 23. Genet Sel Evol. 2016 Mar 9;48:19. doi: 10.1186/s12711-016-0197-x.	A genome-wide association study for genetic susceptibility to Mycobacterium bovis infection in dairy cattle identifies a susceptibility QTL on chromosome 23.	Genet Sel Evol. 2016 Mar 9;48:19. doi: 10.1186/s12711-016-0197-x.
Foley C, Chapwanya A, Callanan JJ, Whiston R, Miranda-CasoLuengo R, Lu J, Meijer WG, Lynn DJ, O’ Farrelly C, Meade KG. Integrated analysis of the local and systemic changes preceding the development of post-partum cytological endometritis. BMC Genomics. 2015 Oct 19;16:811. doi: 10.1186/s12864-015-1967-5.	Integrated analysis of the local and systemic changes preceding the development of post-partum cytological endometritis.	BMC Genomics. 2015 Oct 19;16:811. doi: 10.1186/s12864-015-1967-5.
Frias S, Bryan K, Brinkman FS, Lynn DJ.(Corresponding Author) CerebralWeb: a Cytoscape.js plug-in to visualize networks stratified by subcellular localization. Database (Oxford). 2015 May 7;2015:bav041. doi: 10.1093/database/bav041. Print 2015.	CerebralWeb: a Cytoscape.js plug-in to visualize networks stratified by subcellular localization.	Database (Oxford). 2015 May 7;2015:bav041. doi: 10.1093/database/bav041. Print 2015.
Vegh P, Foroushani ABK, Magee DA, McCabe MS, Browne JA, Nalpas NC, Conlon KM, Gordon SV, Bradley DG, MacHugh DE, Lynn DJ (Corresponding Author). Profiling microRNA expression in bovine alveolar macrophages using a next-generation sequencing based approach. Tuberculosis (Edinb). 2015 Jan;95(1):60-7.	Profiling microRNA expression in bovine alveolar macrophages using a next-generation sequencing based approach.	Tuberculosis (Edinb). 2015 Jan;95(1):60-7.
Lawless N, Reinhardt TA, Bryan K, Baker M, Pesch B, Zimmerman D, Zuelke K, Sonstegard T, O’Farrelly C, Lippolis JD, Lynn DJ (Corresponding Author). MicroRNA regulation of bovine monocyte inflammatory and metabolic networks in an in vivo infection model. G3 (Bethesda). 2014 Jan 27;4(6):957-71. doi: 10.1534/g3.113.009936.	MicroRNA regulation of bovine monocyte inflammatory and metabolic networks in an in vivo infection model.	G3 (Bethesda). 2014 Jan 27;4(6):957-71. doi: 10.1534/g3.113.009936.
Fatima A, Lynn DJ (Corresponding Author), O’Boyle P, Seoighe C, Morris D. The miRNAome of the postpartum dairy cow liver under negative energy balance. BMC Genomics. 2014 Apr 12;15:279. doi: 10.1186/1471-2164-15-279.	The miRNAome of the postpartum dairy cow liver under negative energy balance.	BMC Genomics. 2014 Apr 12;15:279. doi: 10.1186/1471-2164-15-279.
Foroushani A, Brinkman FSL, Lynn DJ (Corresponding Author). Pathway-GPS and SIGORA: Identifying relevant pathways based on the over-representation of their gene-pair signatures. PeerJ. 2013 Dec 19;1:e229. doi: 10.7717/peerj.229. eCollection 2013.	Pathway-GPS and SIGORA: Identifying relevant pathways based on the over-representation of their gene-pair signatures.	PeerJ. 2013 Dec 19;1:e229. doi: 10.7717/peerj.229. eCollection 2013.
Meredith BK, Berry DP, Kearney JF, Finlay EK, Fahey AG, Bradley DG, Lynn DJ (Corresponding Author). A Genome-wide association study for somatic cell score using the illumina high-density bovine BeadChip identifies several novel QTL potentially related to mastitis susceptibility. Front Genet. 2013 Nov 6;4:229. doi: 10.3389/fgene.2013.00229. eCollection 2013.	A Genome-wide association study for somatic cell score using the illumina high-density bovine BeadChip identifies several novel QTL potentially related to mastitis susceptibility.	Front Genet. 2013 Nov 6;4:229. doi: 10.3389/fgene.2013.00229. eCollection 2013.
Lawless N, Foroushani AK, McCabe M, O’Farrelly C, Lynn DJ (Corresponding Author). Next generation sequencing reveals the expression of a unique miRNA profile in response to a Gram-positive bacterial infection. PLoS One. 2013;8(3):e57543. doi: 10.1371/journal.pone.0057543. Epub 2013 Mar 5.	Next generation sequencing reveals the expression of a unique miRNA profile in response to a Gram-positive bacterial infection.	PLoS One. 2013;8(3):e57543. doi: 10.1371/journal.pone.0057543. Epub 2013 Mar 5.
Achtman AH, Pilat S, Law CW, Lynn DJ, Janot L, Mayer ML, Ma S, Kindrachuk J, Finlay BB, Brinkman FSL, Smyth GK, Hancock REW, Schofield L. Effective adjunctive therapy by an innate defense regulatory Peptide in a preclinical model of severe malaria. Sci Transl Med. 2012 May 23;4(135):135ra64. doi: 10.1126/scitranslmed.3003515.	Effective adjunctive therapy by an innate defense regulatory Peptide in a preclinical model of severe malaria.	Sci Transl Med. 2012 May 23;4(135):135ra64. doi: 10.1126/scitranslmed.3003515.
Orchard S, Kerrien S, Abbani S, Aranda B, Bhate J, Bidwell S, Bridge A, Briganti L, Brinkman FS, Cesareni G, Chatr-aryamontri A, Chautard E, Chen C, Dumousseau M, Goll J, Hancock RE, Hannick LI, Jurisica I, Khadake J, Lynn DJ, Mahadevan U, Perfetto L, Raghunath A, Ricard-Blum S, Roechert B, Salwinski L, Stümpflen V, Tyers M, Uetz P, Xenarios I, Hermjakob H. Protein Interaction Data Curation - The International Molecular Exchange Consortium (IMEx). Nat Methods. 2012 Apr;9(4):345-50. doi: 10.1038/nmeth.1931.	Protein Interaction Data Curation - The International Molecular Exchange Consortium (IMEx).	Nat Methods. 2012 Apr;9(4):345-50. doi: 10.1038/nmeth.1931.
Aranda B, Blankenburg H, Kerrien S, Brinkman FS, Ceol A, Chautard E, Dana JM, De Las Rivas J, Dumousseau M, Galeota E, Gaulton A, Goll J, Hancock RE, Isserlin R, Jimenez RC, Kerssemakers J, Khadake J, Lynn DJ, Michaut M, O’Kelly G, Ono K, Orchard S, Prieto C, Razick S, Rigina O, Salwinski L, Simonovic M, Velankar S, Winter A, Wu G, Bader GD, Cesareni G, Donaldson IM, Eisenberg D, Kleywegt GJ, Overington J, Ricard-Blum S, Tyers M, Albrecht M, Hermjakob H. PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat Methods. 2011 Jun 29;8(7):528-9. doi: 10.1038/nmeth.1637.	PSICQUIC and PSISCORE: accessing and scoring molecular interactions.	Nat Methods. 2011 Jun 29;8(7):528-9. doi: 10.1038/nmeth.1637.
The Bovine HapMap Consortium. Genome wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science. 2009 Apr 24;324(5926):528-32. doi: 10.1126/science.1167936.	Genome wide survey of SNP variation uncovers the genetic structure of cattle breeds.	Science. 2009 Apr 24;324(5926):528-32. doi: 10.1126/science.1167936.
Shkoporov, A.N., Ryan, F.J., Draper, L.A., Forde, A., Stockdale, S.R., Daly, K.M., McDonnell, S.A., Nolan, J.A., Sutton, T.D., Dalmasso, M. and McCann, A. (2018) Reproducible protocols for metagenomic analysis of human faecal phageomes. Microbiome, 6(1), p.68.	Reproducible protocols for metagenomic analysis of human faecal phageomes.	Microbiome, 6(1), p.68.
Stilling, R.M., Moloney, G.M., Ryan, F.J., Hoban, A.E., Bastiaanssen, T., Shanahan, F., Clarke, G., Claesson, M.J., Dinan, T.G. and Cryan, J.F. (2018) Social interaction-induced activation of RNA splicing in the amygdala of microbiome-deficient mice. eLife, 7, p.e33070.	Social interaction-induced activation of RNA splicing in the amygdala of microbiome-deficient mice.	eLife, 7, p.e33070.
McCann, A., Ryan, F.J., Stockdale, S.R., Dalmasso, M., Blake, T., Ryan, C.A., Stanton, C., Mills, S., Ross, P.R. and Hill, C. (2018) Viromes of one-year-old infants reveal the impact of birth mode on microbiome diversity. PeerJ, 6, p.e4694.	Viromes of one-year-old infants reveal the impact of birth mode on microbiome diversity.	PeerJ, 6, p.e4694.
Flemer, B., Lynch, D.B., Brown, J.M., Jeffery, I.B., Ryan, F.J., Claesson, M.J., O’riordain, M., Shanahan, F. and O’toole, P.W. (2017) Tumour-associated and non-tumour-associated microbiota in colorectal cancer. Gut, 66(4), pp.633-643.	Tumour-associated and non-tumour-associated microbiota in colorectal cancer.	Gut, 66(4), pp.633-643.
Hoban, A.E., Stilling, R.M., Ryan, F.J., Shanahan, F., Dinan, T.G., Claesson, M.J., Clarke, G. and Cryan, J.F. (2016) Regulation of prefrontal cortex myelination by the microbiota. Translational Psychiatry, 6(4), p.e774.	Regulation of prefrontal cortex myelination by the microbiota.	Translational Psychiatry, 6(4), p.e774.
Allard, G., Ryan, F.J., Jeffery, I.B. and Claesson, M.J. (2015) SPINGO: a rapid species-classifier for microbial amplicon sequences. BMC Bioinformatics,16(1), p.324.	SPINGO: a rapid species-classifier for microbial amplicon sequences.	BMC Bioinformatics,16(1), p.324.
Murray J, +4, Eden GL, +14, Fletcher JI. Suppression of the ATP-binding cassette transporter ABCC4 impairs neuroblastoma growth and sensitises to irinotecan in vivo. Eur J Cancer, 2017 Sep; 83:132-141.	Suppression of the ATP-binding cassette transporter ABCC4 impairs neuroblastoma growth and sensitises to irinotecan in vivo.	Eur J Cancer, 2017 Sep; 83:132-141.
Bajic JE, Eden GL, Lampton LS, Cheah KY, Lymn KA, Pei JV, Yool AJ and Howarth GS. Rhubarb extract partially improves mucosal integrity in chemotherapy-induced mucositis. World J Gastroenterol, 2016 Oct 7; 22(37):8322-8333.	Rhubarb extract partially improves mucosal integrity in chemotherapy-induced mucositis.	World J Gastroenterol, 2016 Oct 7; 22(37):8322-8333.
Mashtoub S, Lampton LS, Eden GL, Cheah KY, Lymn KA, Bajic JE and Howarth GS. Emu oil combined with Lyprinol™ reduces small intestinal damage in a rat model of chemotherapy-induced mucositis. Nutr Cancer, 2016 Oct; 68(7);1171.	Emu oil combined with Lyprinol™ reduces small intestinal damage in a rat model of chemotherapy-induced mucositis.	Nutr Cancer, 2016 Oct; 68(7);1171.