TY - JOUR AU - Elsik, C. G. AU - Tellam, R. L. AU - Worley, K. C. AU - Gibbs, R. A. AU - Muzny, D. M. AU - Weinstock, G. M. AU - Adelson, D. L. AU - Eichler, E. E. AU - Elnitski, L. AU - Guigo, R. PY - 2009 DA - 2009// TI - The genome sequence of taurine cattle: a window to ruminant biology and evolution JO - Science (New York, NY) VL - 324 UR - https://doi.org/10.1126/science.1169588 DO - 10.1126/science.1169588 ID - Elsik2009 ER - TY - JOUR AU - Donovan, D. M. AU - Kerr, D. E. AU - Wall, R. J. PY - 2005 DA - 2005// TI - Engineering disease resistant cattle JO - Transgenic Res VL - 14 UR - https://doi.org/10.1007/s11248-005-0670-8 DO - 10.1007/s11248-005-0670-8 ID - Donovan2005 ER - TY - JOUR AU - Habing, G. G. AU - Manning, S. AU - Bolin, C. AU - Cui, Y. AU - Rudrik, J. AU - Dietrich, S. AU - Kaneene, J. B. PY - 2015 DA - 2015// TI - Within-farm changes in dairy farm-associated salmonella subtypes and comparison to human clinical isolates in Michigan, 2000-2001 and 2009 JO - Appl Environ Microbiol VL - 81 UR - https://doi.org/10.1128/AEM.00899-15 DO - 10.1128/AEM.00899-15 ID - Habing2015 ER - TY - JOUR AU - Coustou, V. AU - Guegan, F. AU - Plazolles, N. AU - Baltz, T. PY - 2010 DA - 2010// TI - Complete in vitro life cycle of Trypanosoma congolense: development of genetic tools JO - PLoS Negl Trop Dis VL - 4 UR - https://doi.org/10.1371/journal.pntd.0000618 DO - 10.1371/journal.pntd.0000618 ID - Coustou2010 ER - TY - JOUR AU - Courtin, D. AU - Berthier, D. AU - Thevenon, S. AU - Dayo, G. K. AU - Garcia, A. AU - Bucheton, B. PY - 2008 DA - 2008// TI - Host genetics in African trypanosomiasis JO - Infect Genet Evol VL - 8 UR - https://doi.org/10.1016/j.meegid.2008.02.007 DO - 10.1016/j.meegid.2008.02.007 ID - Courtin2008 ER - TY - JOUR AU - Gunther, J. AU - Esch, K. AU - Poschadel, N. AU - Petzl, W. AU - Zerbe, H. AU - Mitterhuemer, S. AU - Blum, H. AU - Seyfert, H. M. PY - 2011 DA - 2011// TI - Comparative kinetics of Escherichia Coli- and Staphylococcus Aureus-specific activation of key immune pathways in mammary epithelial cells demonstrates that S. Aureus elicits a delayed response dominated by interleukin-6 (IL-6) but not by IL-1A or tumor necrosis factor alpha JO - Infect Immun VL - 79 UR - https://doi.org/10.1128/IAI.01071-10 DO - 10.1128/IAI.01071-10 ID - Gunther2011 ER - TY - JOUR AU - Osorio, A. L. AU - Madruga, C. R. AU - Desquesnes, M. AU - Soares, C. O. AU - Ribeiro, L. R. AU - Costa, S. C. PY - 2008 DA - 2008// TI - Trypanosoma (Duttonella) vivax: its biology, epidemiology, pathogenesis, and introduction in the new world--a review JO - Memorias do Instituto Oswaldo Cruz VL - 103 UR - https://doi.org/10.1590/S0074-02762008000100001 DO - 10.1590/S0074-02762008000100001 ID - Osorio2008 ER - TY - JOUR AU - Giamarellos-Bourboulis, E. J. AU - Raftogiannis, M. PY - 2012 DA - 2012// TI - The immune response to severe bacterial infections: consequences for therapy JO - Expert Rev Anti-Infect Ther VL - 10 UR - https://doi.org/10.1586/eri.12.2 DO - 10.1586/eri.12.2 ID - Giamarellos-Bourboulis2012 ER - TY - JOUR AU - Haines, L. R. AU - Lehane, S. M. AU - Pearson, T. W. AU - Lehane, M. J. PY - 2010 DA - 2010// TI - Tsetse EP protein protects the fly midgut from trypanosome establishment JO - PLoS Pathog VL - 6 UR - https://doi.org/10.1371/journal.ppat.1000793 DO - 10.1371/journal.ppat.1000793 ID - Haines2010 ER - TY - JOUR AU - Kianmehr, Z. AU - Kaboudanian Ardestani, S. AU - Soleimanjahi, H. AU - Fotouhi, F. AU - Alamian, S. AU - Ahmadian, S. PY - 2015 DA - 2015// TI - Comparison of biological and immunological characterization of Lipopolysaccharides from Brucella abortus RB51 and S19 JO - Jundishapur J Microbiol VL - 8 UR - https://doi.org/10.5812/jjm.24853 DO - 10.5812/jjm.24853 ID - Kianmehr2015 ER - TY - JOUR AU - Amrine, K. C. AU - Blanco-Ulate, B. AU - Cantu, D. PY - 2015 DA - 2015// TI - Discovery of core biotic stress responsive genes in Arabidopsis by weighted gene co-expression network analysis JO - PLoS One VL - 10 UR - https://doi.org/10.1371/journal.pone.0118731 DO - 10.1371/journal.pone.0118731 ID - Amrine2015 ER - TY - JOUR AU - Tully, J. P. AU - Hill, A. E. AU - Ahmed, H. M. AU - Whitley, R. AU - Skjellum, A. AU - Mukhtar, M. S. PY - 2014 DA - 2014// TI - Expression-based network biology identifies immune-related functional modules involved in plant defense JO - BMC Genomics VL - 15 UR - https://doi.org/10.1186/1471-2164-15-421 DO - 10.1186/1471-2164-15-421 ID - Tully2014 ER - TY - JOUR AU - Windram, O. AU - Denby, K. J. PY - 2015 DA - 2015// TI - Modelling signaling networks underlying plant defence JO - Curr Opin Plant Biol VL - 27 UR - https://doi.org/10.1016/j.pbi.2015.07.007 DO - 10.1016/j.pbi.2015.07.007 ID - Windram2015 ER - TY - JOUR AU - Langfelder, P. AU - Horvath, S. PY - 2008 DA - 2008// TI - WGCNA: an R package for weighted correlation network analysis JO - BMC bioinformatics VL - 9 UR - https://doi.org/10.1186/1471-2105-9-559 DO - 10.1186/1471-2105-9-559 ID - Langfelder2008 ER - TY - JOUR AU - Eichmann, R. AU - Schafer, P. PY - 2015 DA - 2015// TI - Growth versus immunity--a redirection of the cell cycle? JO - Curr Opin Plant Biol VL - 26 UR - https://doi.org/10.1016/j.pbi.2015.06.006 DO - 10.1016/j.pbi.2015.06.006 ID - Eichmann2015 ER - TY - JOUR AU - DiAngelo, J. R. AU - Bland, M. L. AU - Bambina, S. AU - Cherry, S. AU - Birnbaum, M. J. PY - 2009 DA - 2009// TI - The immune response attenuates growth and nutrient storage in drosophila by reducing insulin signaling JO - Proc Natl Acad Sci U S A VL - 106 UR - https://doi.org/10.1073/pnas.0906749106 DO - 10.1073/pnas.0906749106 ID - DiAngelo2009 ER - TY - JOUR AU - Huot, B. AU - Yao, J. AU - Montgomery, B. L. AU - He, S. Y. PY - 2014 DA - 2014// TI - Growth-defense tradeoffs in plants: a balancing act to optimize fitness JO - Mol Plant VL - 7 UR - https://doi.org/10.1093/mp/ssu049 DO - 10.1093/mp/ssu049 ID - Huot2014 ER - TY - JOUR AU - Brown, J. K. PY - 2003 DA - 2003// TI - A cost of disease resistance: paradigm or peculiarity? JO - Trends in Genet VL - 19 UR - https://doi.org/10.1016/j.tig.2003.10.008 DO - 10.1016/j.tig.2003.10.008 ID - Brown2003 ER - TY - JOUR AU - Heil, M. AU - Baldwin, I. T. PY - 2002 DA - 2002// TI - Fitness costs of induced resistance: emerging experimental support for a slippery concept JO - Trends Plant Sci VL - 7 UR - https://doi.org/10.1016/S1360-1385(01)02186-0 DO - 10.1016/S1360-1385(01)02186-0 ID - Heil2002 ER - TY - JOUR AU - Bolton, M. D. PY - 2009 DA - 2009// TI - Primary metabolism and plant defense--fuel for the fire JO - Mol Plant Microbe Interact VL - 22 UR - https://doi.org/10.1094/MPMI-22-5-0487 DO - 10.1094/MPMI-22-5-0487 ID - Bolton2009 ER - TY - JOUR AU - Kleessen, S. AU - Laitinen, R. AU - Fusari, C. M. AU - Antonio, C. AU - Sulpice, R. AU - Fernie, A. R. AU - Stitt, M. AU - Nikoloski, Z. PY - 2014 DA - 2014// TI - Metabolic efficiency underpins performance trade-offs in growth of Arabidopsis Thaliana JO - Nat Commun VL - 5 UR - https://doi.org/10.1038/ncomms4537 DO - 10.1038/ncomms4537 ID - Kleessen2014 ER - TY - JOUR AU - Pearce, E. L. AU - Pearce, E. J. PY - 2013 DA - 2013// TI - Metabolic pathways in immune cell activation and quiescence JO - Immunity VL - 38 UR - https://doi.org/10.1016/j.immuni.2013.04.005 DO - 10.1016/j.immuni.2013.04.005 ID - Pearce2013 ER - TY - JOUR AU - Im, S. S. AU - Yousef, L. AU - Blaschitz, C. AU - Liu, J. Z. AU - Edwards, R. A. AU - Young, S. G. AU - Raffatellu, M. AU - Osborne, T. F. PY - 2011 DA - 2011// TI - Linking lipid metabolism to the innate immune response in macrophages through sterol regulatory element binding protein-1a JO - Cell Metab VL - 13 UR - https://doi.org/10.1016/j.cmet.2011.04.001 DO - 10.1016/j.cmet.2011.04.001 ID - Im2011 ER - TY - JOUR AU - Cheon, H. M. AU - Shin, S. W. AU - Bian, G. AU - Park, J. H. AU - Raikhel, A. S. PY - 2006 DA - 2006// TI - Regulation of lipid metabolism genes, lipid carrier protein lipophorin, and its receptor during immune challenge in the mosquito Aedes Aegypti JO - J Biol Chem VL - 281 UR - https://doi.org/10.1074/jbc.M510957200 DO - 10.1074/jbc.M510957200 ID - Cheon2006 ER - TY - JOUR AU - Varga, T. AU - Nagy, L. PY - 2008 DA - 2008// TI - Nuclear receptors, transcription factors linking lipid metabolism and immunity: the case of peroxisome proliferator-activated receptor gamma JO - Eur J Clin Investig VL - 38 UR - https://doi.org/10.1111/j.1365-2362.2008.02022.x DO - 10.1111/j.1365-2362.2008.02022.x ID - Varga2008 ER - TY - JOUR AU - Guo, B. AU - Greenwood, P. L. AU - Cafe, L. M. AU - Zhou, G. AU - Zhang, W. AU - Dalrymple, B. P. PY - 2015 DA - 2015// TI - Transcriptome analysis of cattle muscle identifies potential markers for skeletal muscle growth rate and major cell types JO - BMC Genomics VL - 16 UR - https://doi.org/10.1186/s12864-015-1403-x DO - 10.1186/s12864-015-1403-x ID - Guo2015 ER - TY - JOUR AU - Thompson, C. B. PY - 2011 DA - 2011// TI - Rethinking the regulation of cellular metabolism JO - Cold Spring Harb Symp Quant Biol VL - 76 UR - https://doi.org/10.1101/sqb.2012.76.010496 DO - 10.1101/sqb.2012.76.010496 ID - Thompson2011 ER - TY - JOUR AU - van Raam, B. J. AU - Sluiter, W. AU - de Wit, E. AU - Roos, D. AU - Verhoeven, A. J. AU - Kuijpers, T. W. PY - 2008 DA - 2008// TI - Mitochondrial membrane potential in human neutrophils is maintained by complex III activity in the absence of supercomplex organisation JO - PLoS One VL - 3 UR - https://doi.org/10.1371/journal.pone.0002013 DO - 10.1371/journal.pone.0002013 ID - van Raam2008 ER - TY - JOUR AU - Dale, D. C. AU - Boxer, L. AU - Liles, W. C. PY - 2008 DA - 2008// TI - The phagocytes: neutrophils and monocytes JO - Blood VL - 112 UR - https://doi.org/10.1182/blood-2007-12-077917 DO - 10.1182/blood-2007-12-077917 ID - Dale2008 ER - TY - JOUR AU - Koberlin, M. S. AU - Heinz, L. X. AU - Superti-Furga, G. PY - 2016 DA - 2016// TI - Functional crosstalk between membrane lipids and TLR biology JO - Curr Opin Cell Biol VL - 39 UR - https://doi.org/10.1016/j.ceb.2016.01.010 DO - 10.1016/j.ceb.2016.01.010 ID - Koberlin2016 ER - TY - JOUR AU - Guo, J. AU - Liu, Z. AU - Sun, H. AU - Huang, Y. AU - Albrecht, E. AU - Zhao, R. AU - Yang, X. PY - 2015 DA - 2015// TI - Lipopolysaccharide challenge significantly influences lipid metabolism and proteome of white adipose tissue in growing pigs JO - Lipids Health Dis VL - 14 UR - https://doi.org/10.1186/s12944-015-0067-5 DO - 10.1186/s12944-015-0067-5 ID - Guo2015 ER - TY - JOUR AU - Trayhurn, P. AU - Beattie, J. H. PY - 2001 DA - 2001// TI - Physiological role of adipose tissue: white adipose tissue as an endocrine and secretory organ JO - Proc Nutr Soc VL - 60 UR - https://doi.org/10.1079/PNS200194 DO - 10.1079/PNS200194 ID - Trayhurn2001 ER - TY - JOUR AU - Zhang, L. J. AU - Guerrero-Juarez, C. F. AU - Hata, T. AU - Bapat, S. P. AU - Ramos, R. AU - Plikus, M. V. AU - Gallo, R. L. PY - 2015 DA - 2015// TI - Innate immunity. Dermal adipocytes protect against invasive Staphylococcus Aureus skin infection JO - Science (New York, NY) VL - 347 UR - https://doi.org/10.1126/science.1260972 DO - 10.1126/science.1260972 ID - Zhang2015 ER - TY - JOUR AU - Vieira-Potter, V. J. PY - 2014 DA - 2014// TI - Inflammation and macrophage modulation in adipose tissues JO - Cell Microbiol VL - 16 UR - https://doi.org/10.1111/cmi.12336 DO - 10.1111/cmi.12336 ID - Vieira-Potter2014 ER - TY - JOUR AU - Langfelder, P. AU - Horvath, S. PY - 2007 DA - 2007// TI - Eigengene networks for studying the relationships between co-expression modules JO - BMC Syst Biol VL - 1 UR - https://doi.org/10.1186/1752-0509-1-54 DO - 10.1186/1752-0509-1-54 ID - Langfelder2007 ER - TY - JOUR AU - Beiki, H. AU - Nejati-Javaremi, A. AU - Pakdel, A. AU - Masoudi-Nejad, A. AU - Z-L, H. AU - Reecy, J. M. PY - 2016 DA - 2016// TI - Large-scale gene co-expression network as a source of functional annotation for cattle genes JO - BMC Genomics VL - 17 UR - https://doi.org/10.1186/s12864-016-3176-2 DO - 10.1186/s12864-016-3176-2 ID - Beiki2016 ER - TY - JOUR AU - Huntley, R. P. AU - Sawford, T. AU - Mutowo-Meullenet, P. AU - Shypitsyna, A. AU - Bonilla, C. AU - Martin, M. J. AU - O'Donovan, C. PY - 2015 DA - 2015// TI - The GOA database: gene ontology annotation updates for 2015 JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku1113 DO - 10.1093/nar/gku1113 ID - Huntley2015 ER - TY - JOUR AU - Boularan, C. AU - Kehrl, J. H. PY - 2014 DA - 2014// TI - Implications of non-canonical G-protein signaling for the immune system JO - Cell Signal VL - 26 UR - https://doi.org/10.1016/j.cellsig.2014.02.010 DO - 10.1016/j.cellsig.2014.02.010 ID - Boularan2014 ER - TY - JOUR AU - Li, P. AU - Yin, Y. L. AU - Li, D. AU - Kim, S. W. AU - Wu, G. PY - 2007 DA - 2007// TI - Amino acids and immune function JO - Br J Nutr VL - 98 UR - https://doi.org/10.1017/S000711450769936X DO - 10.1017/S000711450769936X ID - Li2007 ER - TY - JOUR AU - Jones, A. L. AU - Hulett, M. D. AU - Parish, C. R. PY - 2005 DA - 2005// TI - Histidine-rich glycoprotein: a novel adaptor protein in plasma that modulates the immune, vascular and coagulation systems JO - Immunol Cell Biol VL - 83 UR - https://doi.org/10.1111/j.1440-1711.2005.01320.x DO - 10.1111/j.1440-1711.2005.01320.x ID - Jones2005 ER - TY - JOUR AU - Wu, G. AU - Meininger, C. J. PY - 2002 DA - 2002// TI - Regulation of nitric oxide synthesis by dietary factors JO - Annu Rev Nutr VL - 22 UR - https://doi.org/10.1146/annurev.nutr.22.110901.145329 DO - 10.1146/annurev.nutr.22.110901.145329 ID - Wu2002 ER - TY - JOUR AU - Ha, E. M. AU - CT, O. AU - Bae, Y. S. AU - Lee, W. J. PY - 2005 DA - 2005// TI - A direct role for dual oxidase in drosophila gut immunity JO - Science (New York, NY) VL - 310 UR - https://doi.org/10.1126/science.1117311 DO - 10.1126/science.1117311 ID - Ha2005 ER - TY - JOUR AU - Platten, M. AU - Ho, P. P. AU - Youssef, S. AU - Fontoura, P. AU - Garren, H. AU - Hur, E. M. AU - Gupta, R. AU - Lee, L. Y. AU - Kidd, B. A. AU - Robinson, W. H. PY - 2005 DA - 2005// TI - Treatment of autoimmune neuroinflammation with a synthetic tryptophan metabolite JO - Science (New York, NY) VL - 310 UR - https://doi.org/10.1126/science.1117634 DO - 10.1126/science.1117634 ID - Platten2005 ER - TY - JOUR AU - Wu, Z. AU - Cui, Q. AU - Yethiraj, A. PY - 2013 DA - 2013// TI - Why do arginine and lysine organize lipids differently? Insights from coarse-grained and atomistic simulations JO - J Phys Chem B VL - 117 UR - https://doi.org/10.1021/jp4068729 DO - 10.1021/jp4068729 ID - Wu2013 ER - TY - JOUR AU - Wang, H. AU - Chen, H. AU - Hao, G. AU - Yang, B. AU - Feng, Y. AU - Wang, Y. AU - Feng, L. AU - Zhao, J. AU - Song, Y. AU - Zhang, H. PY - 2013 DA - 2013// TI - Role of the phenylalanine-hydroxylating system in aromatic substance degradation and lipid metabolism in the oleaginous fungus Mortierella Alpina JO - Appl Environ Microbiol VL - 79 UR - https://doi.org/10.1128/AEM.00238-13 DO - 10.1128/AEM.00238-13 ID - Wang2013 ER - TY - JOUR AU - Shchepin, R. AU - Moller, M. N. AU - Kim, H. Y. AU - Hatch, D. M. AU - Bartesaghi, S. AU - Kalyanaraman, B. AU - Radi, R. AU - Porter, N. A. PY - 2010 DA - 2010// TI - Tyrosine-lipid peroxide adducts from radical termination: para coupling and intramolecular Diels-Alder cyclization JO - J Am Chem Soc VL - 132 UR - https://doi.org/10.1021/ja106503a DO - 10.1021/ja106503a ID - Shchepin2010 ER - TY - JOUR AU - Barrett, T. AU - Wilhite, S. E. AU - Ledoux, P. AU - Evangelista, C. AU - Kim, I. F. AU - Tomashevsky, M. AU - Marshall, K. A. AU - Phillippy, K. H. AU - Sherman, P. M. AU - Holko, M. PY - 2013 DA - 2013// TI - NCBI GEO: archive for functional genomics data sets--update JO - Nucleic Acids Res VL - 41 ID - Barrett2013 ER - TY - JOUR AU - Kolesnikov, N. AU - Hastings, E. AU - Keays, M. AU - Melnichuk, O. AU - Tang, Y. A. AU - Williams, E. AU - Dylag, M. AU - Kurbatova, N. AU - Brandizi, M. AU - Burdett, T. PY - 2015 DA - 2015// TI - ArrayExpress update--simplifying data submissions JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku1057 DO - 10.1093/nar/gku1057 ID - Kolesnikov2015 ER - TY - JOUR AU - Gautier, L. AU - Cope, L. AU - Bolstad, B. M. AU - Irizarry, R. A. PY - 2004 DA - 2004// TI - Affy--analysis of Affymetrix GeneChip data at the probe level JO - Bioinformatics (Oxford, England) VL - 20 UR - https://doi.org/10.1093/bioinformatics/btg405 DO - 10.1093/bioinformatics/btg405 ID - Gautier2004 ER - TY - JOUR AU - Kauffmann, A. AU - Gentleman, R. AU - Huber, W. PY - 2009 DA - 2009// TI - arrayQualityMetrics--a bioconductor package for quality assessment of microarray data JO - Bioinformatics (Oxford, England) VL - 25 UR - https://doi.org/10.1093/bioinformatics/btn647 DO - 10.1093/bioinformatics/btn647 ID - Kauffmann2009 ER - TY - JOUR AU - Liu, H. AU - Zeeberg, B. R. AU - Qu, G. AU - Koru, A. G. AU - Ferrucci, A. AU - Kahn, A. AU - Ryan, M. C. AU - Nuhanovic, A. AU - Munson, P. J. AU - Reinhold, W. C. PY - 2007 DA - 2007// TI - AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets JO - Bioinformatics (Oxford, England) VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm360 DO - 10.1093/bioinformatics/btm360 ID - Liu2007 ER - TY - JOUR AU - Pruitt, K. D. AU - Brown, G. R. AU - Hiatt, S. M. AU - Thibaud-Nissen, F. AU - Astashyn, A. AU - Ermolaeva, O. AU - Farrell, C. M. AU - Hart, J. AU - Landrum, M. J. AU - McGarvey, K. M. PY - 2014 DA - 2014// TI - RefSeq: an update on mammalian reference sequences JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt1114 DO - 10.1093/nar/gkt1114 ID - Pruitt2014 ER - TY - JOUR AU - Johnson, W. E. AU - Li, C. AU - Rabinovic, A. PY - 2007 DA - 2007// TI - Adjusting batch effects in microarray expression data using empirical Bayes methods JO - Biostatistics (Oxford, England) VL - 8 UR - https://doi.org/10.1093/biostatistics/kxj037 DO - 10.1093/biostatistics/kxj037 ID - Johnson2007 ER - TY - JOUR AU - Ritchie, M. E. AU - Phipson, B. AU - Wu, D. AU - Hu, Y. AU - Law, C. W. AU - Shi, W. AU - Smyth, G. K. PY - 2015 DA - 2015// TI - limma powers differential expression analyses for RNA-sequencing and microarray studies JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gkv007 DO - 10.1093/nar/gkv007 ID - Ritchie2015 ER - TY - JOUR AU - Kim, K. I. AU - van de Wiel, M. A. PY - 2008 DA - 2008// TI - Effects of dependence in high-dimensional multiple testing problems JO - BMC bioinformatics VL - 9 UR - https://doi.org/10.1186/1471-2105-9-114 DO - 10.1186/1471-2105-9-114 ID - Kim2008 ER - TY - JOUR AU - Zhao, W. AU - Langfelder, P. AU - Fuller, T. AU - Dong, J. AU - Li, A. AU - Hovarth, S. PY - 2010 DA - 2010// TI - Weighted gene coexpression network analysis: state of the art JO - J Biopharm Stat VL - 20 UR - https://doi.org/10.1080/10543400903572753 DO - 10.1080/10543400903572753 ID - Zhao2010 ER - TY - JOUR AU - Langfelder, P. AU - Zhang, B. AU - Horvath, S. PY - 2008 DA - 2008// TI - Defining clusters from a hierarchical cluster tree: the dynamic tree cut package for R JO - Bioinformatics (Oxford, England) VL - 24 UR - https://doi.org/10.1093/bioinformatics/btm563 DO - 10.1093/bioinformatics/btm563 ID - Langfelder2008 ER - TY - STD TI - Langfelder P, Horvath S, Fast R. Functions for robust correlations and hierarchical clustering. J Stat Softw. 2012;46(11):i11. ID - ref58 ER - TY - JOUR AU - Bindea, G. AU - Mlecnik, B. AU - Hackl, H. AU - Charoentong, P. AU - Tosolini, M. AU - Kirilovsky, A. AU - Fridman, W. H. AU - Pages, F. AU - Trajanoski, Z. AU - Galon, J. PY - 2009 DA - 2009// TI - ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks JO - Bioinformatics (Oxford, England) VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp101 DO - 10.1093/bioinformatics/btp101 ID - Bindea2009 ER - TY - JOUR AU - Croft, D. AU - Mundo, A. F. AU - Haw, R. AU - Milacic, M. AU - Weiser, J. AU - Wu, G. AU - Caudy, M. AU - Garapati, P. AU - Gillespie, M. AU - Kamdar, M. R. PY - 2014 DA - 2014// TI - The Reactome pathway knowledgebase JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt1102 DO - 10.1093/nar/gkt1102 ID - Croft2014 ER - TY - JOUR AU - Benjamini, Y. AU - Hochberg, Y. PY - 1995 DA - 1995// TI - Controlling the false discovery rate: a practical and powerful approach to multiple testing JO - J R Stat Soc Ser B Methodol VL - 57 ID - Benjamini1995 ER - TY - JOUR AU - Huang, D. W. AU - Sherman, B. T. AU - Tan, Q. AU - Collins, J. R. AU - Alvord, W. G. AU - Roayaei, J. AU - Stephens, R. AU - Baseler, M. W. AU - Lane, H. C. AU - Lempicki, R. A. PY - 2007 DA - 2007// TI - The DAVID gene functional classification tool: a novel biological module-centric algorithm to functionally analyze large gene lists JO - Genome Biol VL - 8 UR - https://doi.org/10.1186/gb-2007-8-9-r183 DO - 10.1186/gb-2007-8-9-r183 ID - Huang2007 ER - TY - JOUR AU - Shannon, P. AU - Markiel, A. AU - Ozier, O. AU - Baliga, N. S. AU - Wang, J. T. AU - Ramage, D. AU - Amin, N. AU - Schwikowski, B. AU - Ideker, T. PY - 2003 DA - 2003// TI - Cytoscape: a software environment for integrated models of biomolecular interaction networks JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.1239303 DO - 10.1101/gr.1239303 ID - Shannon2003 ER -