1. MurrayHW, BermanJD, DaviesCR, SaraviaNG (2005) Advances in leishmaniasis. Lancet 366: 1561–1577.
2. MoradinN, DescoteauxA (2012) Leishmania promastigotes: building a safe niche within macrophages. Front Cell Infect Microbiol 2: 121.
3. DograN, WarburtonC, McMasterWR (2007) Leishmania major abrogates gamma interferon-induced gene expression in human macrophages from a global perspective. Infect Immun 75: 3506–3515.
4. LiuD, UzonnaJE (2012) The early interaction of Leishmania with macrophages and dendritic cells and its influence on the host immune response. Front Cell Infect Microbiol 2: 83.
5. BhardwajS, SrivastavaN, SudanR, SahaB (2010) Leishmania interferes with host cell signaling to devise a survival strategy. J Biomed Biotechnol 2010: 109189.
6. GregoryDJ, OlivierM (2005) Subversion of host cell signalling by the protozoan parasite Leishmania. Parasitology 130 Suppl: S27–35.
7. ShioMT, HassaniK, IsnardA, RalphB, ContrerasI, et al. (2012) Host cell signalling and leishmania mechanisms of evasion. J Trop Med 2012: 819512.
8. KhavariDA, SenGL, RinnJL (2010) DNA methylation and epigenetic control of cellular differentiation. Cell Cycle 9: 3880–3883.
9. GhoshS, YatesAJ, FruhwaldMC, MiecznikowskiJC, PlassC, et al. (2010) Tissue specific DNA methylation of CpG islands in normal human adult somatic tissues distinguishes neural from non-neural tissues. Epigenetics 5: 527–538.
10. BirdA (2007) Perceptions of epigenetics. Nature 447: 396–398.
11. IoshikhesIP, ZhangMQ (2000) Large-scale human promoter mapping using CpG islands. Nat Genet 26: 61–63.
12. WeberM, HellmannI, StadlerMB, RamosL, PaaboS, et al. (2007) Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 39: 457–466.
13. JonesMJ, FejesAP, KoborMS (2013) DNA methylation, genotype and gene expression: who is driving and who is along for the ride? Genome Biol 14: 126.
14. JjingoD, ConleyAB, YiSV, LunyakVV, JordanIK (2012) On the presence and role of human gene-body DNA methylation. Oncotarget 3: 462–474.
15. LamLL, EmberlyE, FraserHB, NeumannSM, ChenE, et al. (2012) Factors underlying variable DNA methylation in a human community cohort. Proc Natl Acad Sci U S A 109 Suppl 2: 17253–17260.
16. MinarovitsJ (2009) Microbe-induced epigenetic alterations in host cells: the coming era of patho-epigenetics of microbial infections. A review. Acta Microbiol Immunol Hung 56: 1–19.
17. Gomez-DiazE, JordaM, PeinadoMA, RiveroA (2012) Epigenetics of host-pathogen interactions: the road ahead and the road behind. PLoS Pathog 8: e1003007.
18. LangC, HildebrandtA, BrandF, OpitzL, DihaziH, et al. (2012) Impaired chromatin remodelling at STAT1-regulated promoters leads to global unresponsiveness of Toxoplasma gondii-infected macrophages to IFN-gamma. PLoS Pathog 8: e1002483.
19. Silmon de MonerriNC, KimK (2014) Pathogens Hijack the Epigenome: A New Twist on Host-Pathogen Interactions. Am J Pathol 184: 897–911.
20. BibikovaM, BarnesB, TsanC, HoV, KlotzleB, et al. (2011) High density DNA methylation array with single CpG site resolution. Genomics 98: 288–295.
21. G.K S (2005) Limma: linear models for microarray data. In: Gentleman R. CV, Dudoit S., Irizarry R. and Huber W., editor. Bioinformatics using R and Bioconductor. New York: Springer. pp. 397–420.
22. Huang daW, ShermanBT, LempickiRA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44–57.
23. Huang daW, ShermanBT, LempickiRA (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37: 1–13.
24. MillJ, HeijmansBT (2013) From promises to practical strategies in epigenetic epidemiology. Nat Rev Genet 14: 585–594.
25. OlivierM, BaimbridgeKG, ReinerNE (1992) Stimulus-response coupling in monocytes infected with Leishmania. Attenuation of calcium transients is related to defective agonist-induced accumulation of inositol phosphates. J Immunol 148: 1188–1196.
26. ShadabM, AliN (2011) Evasion of Host Defence by Leishmania donovani: Subversion of Signaling Pathways. Mol Biol Int 2011: 343961.
27. AudersetF, SchusterS, CoutazM, KochU, DesgrangesF, et al. (2012) Redundant Notch1 and Notch2 signaling is necessary for IFNgamma secretion by T helper 1 cells during infection with Leishmania major. PLoS Pathog 8: e1002560.
28. JaramilloM, GomezMA, LarssonO, ShioMT, TopisirovicI, et al. (2011) Leishmania repression of host translation through mTOR cleavage is required for parasite survival and infection. Cell Host Microbe 9: 331–341.
29. PinheiroNFJr, HermidaMD, MacedoMP, MengelJ, BaficaA, et al. (2006) Leishmania infection impairs beta 1-integrin function and chemokine receptor expression in mononuclear phagocytes. Infect Immun 74: 3912–3921.
30. RabhiI, RabhiS, Ben-OthmanR, RascheA, DaskalakiA, et al. (2012) Transcriptomic signature of Leishmania infected mice macrophages: a metabolic point of view. PLoS Negl Trop Dis 6: e1763.
31. Garcia-GarciaJC, BaratNC, TrembleySJ, DumlerJS (2009) Epigenetic silencing of host cell defense genes enhances intracellular survival of the rickettsial pathogen Anaplasma phagocytophilum. PLoS Pathog 5: e1000488.
32. PaschosK, AlldayMJ (2010) Epigenetic reprogramming of host genes in viral and microbial pathogenesis. Trends Microbiol 18: 439–447.
33. Koch-NolteF, KernstockS, Mueller-DieckmannC, WeissMS, HaagF (2008) Mammalian ADP-ribosyltransferases and ADP-ribosylhydrolases. Front Biosci 13: 6716–6729.
34. PriveC, DescoteauxA (2000) Leishmania donovani promastigotes evade the activation of mitogen-activated protein kinases p38, c-Jun N-terminal kinase, and extracellular signal-regulated kinase-1/2 during infection of naive macrophages. Eur J Immunol 30: 2235–2244.
35. GhoshS, BhattacharyyaS, SirkarM, SaGS, DasT, et al. (2002) Leishmania donovani suppresses activated protein 1 and NF-kappaB activation in host macrophages via ceramide generation: involvement of extracellular signal-regulated kinase. Infect Immun 70: 6828–6838.
36. RogerT, LugrinJ, Le RoyD, GoyG, MombelliM, et al. (2011) Histone deacetylase inhibitors impair innate immune responses to Toll-like receptor agonists and to infection. Blood 117: 1205–1217.
37. HirschDS, PironeDM, BurbeloPD (2001) A new family of Cdc42 effector proteins, CEPs, function in fibroblast and epithelial cell shape changes. J Biol Chem 276: 875–883.
38. LermM, HolmA, SeironA, SarndahlE, MagnussonKE, et al. (2006) Leishmania donovani requires functional Cdc42 and Rac1 to prevent phagosomal maturation. Infect Immun 74: 2613–2618.
39. LieblD, GriffithsG (2009) Transient assembly of F-actin by phagosomes delays phagosome fusion with lysosomes in cargo-overloaded macrophages. J Cell Sci 122: 2935–2945.
40. RodriguezNE, Gaur DixitU, AllenLA, WilsonME (2011) Stage-specific pathways of Leishmania infantum chagasi entry and phagosome maturation in macrophages. PLoS One 6: e19000.
41. (2008) R Development Core Team. R: A language and environment for statistical computing.
42. DuP, KibbeWA, LinSM (2008) lumi: a pipeline for processing Illumina microarray. Bioinformatics 24: 1547–1548.
43. DuP, ZhangX, HuangCC, JafariN, KibbeWA, et al. (2010) Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. BMC Bioinformatics 11: 587.
44. SmythGK (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3: Article3.
45. PriceME, CottonAM, LamLL, FarreP, EmberlyE, et al. (2013) Additional annotation enhances potential for biologically-relevant analysis of the Illumina Infinium HumanMethylation450 BeadChip array. Epigenetics Chromatin 6: 4.
46. SchmittgenTD, LivakKJ (2008) Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc 3: 1101–1108.