K. D. Lafferty, A. P. Dobson, and A. M. Kuris, Parasites dominate food web links, Proc Natl Acad Sci U S A, vol.103, pp.11211-11216, 2006.

P. Schmid-hempel, Evolutionary parasitology???: the integrated study of infections, immunology, ecology, and genetics/by Paul Schmid-Hempel, 2011.

L. D. Sibley, Invasion and intracellular survival by protozoan parasites, Immunol Rev, vol.240, pp.72-91, 2011.

D. G. Biron, D. Nedelkov, D. Missé, and P. Holzmuller, Genetics and evolution of infectious diseases, Proteomics and host pathogen interactions???: bright future???? In: Tibayrenc M, pp.263-303, 2011.

D. G. Biron, H. D. Loxdale, C. Université, U. B. Pascal, and M. Génome, Hostparasite molecular cross-talk during the manipulative process of a host by its parasite, J Exp Biol, pp.148-160, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00834511

S. Capella-gutiérrez, M. Marcet-houben, and T. Gabaldón, Phylogenomics supports microsporidia as the earliest diverging clade of sequenced fungi, BMC Biol, vol.10, p.47, 2012.

J. Vávra and J. Luke?, Microsporidia and the art of living together, Advances in parasitology, vol.82, pp.253-319, 2013.

M. D. Katinka, S. Duprat, E. Cornillot, G. Metenier, and F. Thomarat, Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi, Nature, vol.414, pp.450-453, 2001.
URL : https://hal.archives-ouvertes.fr/hal-00427201

A. Belkorchia, C. Biderre, C. Militon, V. Polonais, and P. Wincker, In vitro propagation of the microsporidian pathogen Brachiola algerae and studies of its chromosome and ribosomal DNA organization in the context of the complete genome sequencing project, Parasitol Int, vol.57, pp.62-71, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00529592

C. Texier, C. Vidau, B. Vigues, H. El-alaoui, and F. Delbac, Microsporidia: a model for minimal parasite-host interactions, Curr Opin Microbiol, vol.13, pp.443-449, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00526579

E. Peyretaillade, O. Gonçalves, S. Terrat, E. Dugat-bony, and P. Wincker, Identification of transcriptional signals in Encephalitozoon cuniculi widespread among Microsporidia phylum: support for accurate structural genome annotation, BMC Genomics, vol.10, p.607, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00461524

E. Peyretaillade, H. El-alaoui, M. Diogon, V. Polonais, and N. Parisot, Extreme reduction and compaction of microsporidian genomes, Res Microbiol, vol.162, pp.598-606, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00814808

G. S. Visvesvara, H. Moura, G. J. Leitch, D. A. Schwartz, and L. X. Xiao, Public health importance of Brachiola algerae (Microsporidia)-an emerging pathogen of humans, Folia Parasitol (Praha), vol.52, pp.83-94, 2005.

G. Margos, W. A. Maier, and H. M. Seitz, The effect of nosematosis on the development of Plasmodium falciparum in Anopheles stephensi, Parasitol Res, vol.78, pp.168-171, 1992.

Z. Kucerova, H. Moura, G. S. Visvesvara, and G. J. Leitch, Differences between Brachiola (Nosema) algerae isolates of human and insect origin when tested using an in vitro spore germination assay and a cultured cell infection assay, J Eukaryot Microbiol, vol.51, pp.339-343

E. Peyretaillade, N. Parisot, V. Polonais, S. Terrat, and J. Denonfoux, Annotation of microsporidian genomes using transcriptional signals, Nat Commun, vol.3, p.1137, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01887975

D. G. Biron, H. Moura, L. Marche, A. L. Hughes, and F. Thomas, Towards a new conceptual approach to ''parasitoproteomics, Trends Parasitol, vol.21, pp.162-168, 2005.

J. M. Wastling, S. D. Armstrong, R. Krishna, and D. Xia, Parasites, proteomes and systems: has Descartes' clock run out of time, Parasitology, vol.139, pp.1103-1118, 2012.

C. Hughes and J. Krijgsveld, Developments in quantitative mass spectrometry for the analysis of proteome dynamics, Trends Biotechnol, vol.30, pp.668-676, 2012.

S. E. Ong, B. Blagoev, I. Kratchmarova, D. B. Kristensen, and H. Steen, Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics, Mol Cell Proteomics, vol.1, pp.376-386, 2002.

D. C. Munday, R. Surtees, E. Emmott, B. K. Dove, and P. Digard, Using SILAC and quantitative proteomics to investigate the interactions between viral and host proteomes, Proteomics, vol.12, pp.666-672, 2012.

J. Petrak, R. Ivanek, O. Toman, R. Cmejla, and J. Cmejlova, Deja vu in proteomics. A hit parade of repeatedly identified differentially expressed proteins, Proteomics, vol.8, pp.1744-1749, 2008.

V. and U. Ah, Nosema algerae n. sp. (Cnidospora, Microsporida) a Pathogen in a Laboratory Colony of Anopheles stephensi Liston (Diptera, Culicidae), J Protozool, vol.17, pp.240-249, 1970.

S. Ong and M. Mann, A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC), Nat Protoc, vol.1, pp.2650-2660, 2006.
DOI : 10.1038/nprot.2006.427

J. Cox and M. Mann, MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification, Nat Biotechnol, vol.26, pp.1367-1372, 2008.
DOI : 10.1038/nbt.1511

J. Cox, N. Neuhauser, A. Michalski, and J. Scheltema-r-a,-olsen, Andromeda: a peptide search engine integrated into the MaxQuant environment, J Proteome Res, vol.10, pp.1794-1805, 2011.
DOI : 10.1021/pr101065j
URL : https://doi.org/10.1021/pr101065j

C. B. Dean and J. D. Nielsen, Generalized linear mixed models: a review and some extensions, Lifetime Data Anal, vol.13, pp.497-512, 2007.
DOI : 10.1007/s10985-007-9065-x

E. C. Dimmer, R. P. Huntley, Y. Alam-faruque, T. Sawford, and C. O'donovan, The UniProt-GO Annotation database in 2011, Nucleic Acids Res, vol.40, pp.565-70, 2012.
DOI : 10.1093/nar/gkr1048
URL : https://academic.oup.com/nar/article-pdf/40/D1/D565/9475879/gkr1048.pdf

A. Conesa, S. Götz, J. M. García-gómez, J. Terol, and M. Talón, Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research, Bioinformatics, vol.21, pp.3674-3676, 2005.
DOI : 10.1093/bioinformatics/bti610
URL : https://academic.oup.com/bioinformatics/article-pdf/21/18/3674/521920/bti610.pdf

T. N. Petersen, S. Brunak, G. Von-heijne, and H. Nielsen, SignalP 4.0: discriminating signal peptides from transmembrane regions, Nat Methods, vol.8, pp.785-786, 2011.

K. D. Pruitt, T. Tatusova, and D. R. Maglott, NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins, Nucleic Acids Res, vol.35, pp.61-66, 2007.
DOI : 10.1093/nar/gkl842
URL : https://academic.oup.com/nar/article-pdf/35/suppl_1/D61/3841232/gkl842.pdf

A. Mehta, A. Brasileiro, D. Souza, E. Romano, and M. A. Campos, Plant-pathogen interactions: what is proteomics telling us?, FEBS J, vol.275, pp.3731-3746, 2008.
DOI : 10.1111/j.1742-4658.2008.06528.x
URL : http://onlinelibrary.wiley.com/doi/10.1111/j.1742-4658.2008.06528.x/pdf

S. Patramool, V. Choumet, P. Surasombatpattana, L. Sabatier, and F. Thomas, Update on the proteomics of major arthropod vectors of human and animal pathogens, Proteomics, vol.12, pp.3510-3523, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-01054612

D. G. Biron, P. Agnew, L. Marche, R. L. Sidobre, and C. , Proteome of Aedes aegypti larvae in response to infection by the intracellular parasite Vavraia culicis, Int J Parasitol, vol.35, pp.1385-1397, 2005.

A. B. Duncan, P. Agnew, V. Noel, E. Demettre, and M. Seveno, Proteome of Aedes aegypti in response to infection and coinfection with microsporidian parasites, Ecol Evol, vol.2, pp.681-694, 2012.

P. Vincendeau, A. P. Gobert, S. Daulouède, D. Moynet, and M. D. Mossalayi, Arginases in parasitic diseases, Trends Parasitol, vol.19, pp.9-12, 2003.
DOI : 10.1016/s1471-4922(02)00010-7

V. Kostourou, S. P. Robinson, J. E. Cartwright, and G. Whitley, Dimethylarginine dimethylaminohydrolase I enhances tumour growth and angiogenesis, Br J Cancer, vol.87, pp.673-680, 2002.
DOI : 10.1038/sj.bjc.6600518
URL : https://www.nature.com/articles/6600518.pdf

B. Weber, C. Schaper, Y. Wang, J. Scholz, and B. Bein, Interaction of the ubiquitin carboxyl terminal esterase L1 with alpha(2)-adrenergic receptors inhibits agonist-mediated p44/42 MAP kinase activation, Cell Signal, vol.21, pp.1513-1521, 2009.

X. Zhou, J. J. Michal, L. Zhang, B. Ding, and J. K. Lunney, Interferon induced IFIT family genes in host antiviral defense, Int J Biol Sci, vol.9, pp.200-208, 2013.
DOI : 10.7150/ijbs.5613
URL : http://www.ijbs.com/v09p0200.pdf

S. Pichyangkul, K. Yongvanitchit, U. Kum-arb, H. Hemmi, and S. Akira, Malaria blood stage parasites activate human plasmacytoid dendritic cells and murine dendritic cells through a Toll-like receptor 9-dependent pathway, J Immunol, vol.172, pp.4926-4933, 2004.
DOI : 10.4049/jimmunol.172.8.4926
URL : http://www.jimmunol.org/content/jimmunol/172/8/4926.full.pdf

D. B. Stetson and R. Medzhitov, Recognition of cytosolic DNA activates an IRF3-dependent innate immune response, Immunity, vol.24, pp.93-103, 2006.

D. J. Hui, F. Terenzi, W. C. Merrick, and G. C. Sen, Mouse p56 blocks a distinct function of eukaryotic initiation factor 3 in translation initiation, J Biol Chem, vol.280, pp.3433-3440, 2005.

S. K. Prajapati and O. P. Singh, Remodeling of human red cells infected with Plasmodium falciparum and the impact of PHIST proteins, Blood Cells Mol Dis, vol.51, pp.195-202, 2013.

M. Scanlon, G. J. Leitch, G. S. Visvesvara, and A. P. Shaw, Relationship between the host cell mitochondria and the parasitophorous vacuole in cells infected with Encephalitozoon microsporidia, J Eukaryot Microbiol, vol.51, pp.81-87, 2004.

J. González-billault, C. Dawson, H. N. Vitek, M. P. Avila, and J. , Role of MAP1B in axonal retrograde transport of mitochondria, Biochem J, vol.397, pp.53-59, 2006.

S. Saha, P. Sugumar, P. Bhandari, and P. N. Rangarajan, Identification of Japanese encephalitis virus-inducible genes in mouse brain and characterization of GARG39/IFIT2 as a microtubule-associated protein, J Gen Virol, vol.87, pp.3285-3289, 2006.

E. Motylewska, H. Lawnicka, M. Kowalewicz-kulbat, P. Sicinska, and A. Niedziela, Interferon alpha and rapamycin inhibit the growth of pheochromocytoma PC12 line in vitro Interferon alfa i rapamycyna hamuja ? wzrost linii komórkowej, Endokrynol Pol, vol.64, pp.368-374, 2013.

M. Stawowczyk, S. Van-scoy, K. P. Kumar, and N. C. Reich, The interferon stimulated gene 54 promotes apoptosis, J Biol Chem, vol.286, pp.7257-7266, 2011.

D. Gomez and N. C. Reich, Stimulation of primary human endothelial cell proliferation by IFN, J Immunol, vol.170, pp.5373-5381, 2003.

J. Weiske and O. Huber, The histidine triad protein Hint1 triggers apoptosis independent of its enzymatic activity, J Biol Chem, vol.281, pp.27356-27366, 2006.

R. K. Slotkin and R. Martienssen, Transposable elements and the epigenetic regulation of the genome, Nat Rev Genet, vol.8, pp.272-285, 2007.

J. Volff, Turning junk into gold: domestication of transposable elements and the creation of new genes in eukaryotes, Bioessays, vol.28, pp.913-922, 2006.

C. , A brief history of the status of transposable elements: from junk DNA to major players in evolution, Genetics, vol.186, pp.1085-1093, 2010.

M. Pardue and P. G. Debaryshe, Retrotransposons provide an evolutionarily robust non-telomerase mechanism to maintain telomeres, Annu Rev Genet, vol.37, pp.485-511, 2003.

C. Baudry, S. Malinsky, M. Restituito, A. Kapusta, and S. Rosa, PiggyMac, a domesticated piggyBac transposase involved in programmed genome rearrangements in the ciliate Paramecium tetraurelia, Genes Dev, vol.23, pp.2478-2483, 2009.

S. Mi, X. Lee, X. Li, G. M. Veldman, and H. Finnerty, Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis, Nature, vol.403, pp.785-789, 2000.

V. Kapitonov and J. Jurka, RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons, PLoS Biol, vol.3, p.181, 2005.

A. Streit, A. J. Berliner, C. Papanayotou, A. Sirulnik, and C. D. Stern, Initiation of neural induction by FGF signalling before gastrulation, Nature, vol.406, pp.74-78, 2000.

E. Lerat, A. Birot, J. Samarut, and A. Mey, Maintenance in the chicken genome of the retroviral-like cENS gene family specifically expressed in early embryos, J Mol Evol, vol.65, pp.215-227, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00434619

J. González, K. Lenkov, M. Lipatov, J. M. Macpherson, and D. A. Petrov, High rate of recent transposable element-induced adaptation in Drosophila melanogaster, PLoS Biol, vol.6, p.251, 2008.

J. A. Carrero, Confounding roles for type I interferons during bacterial and viral pathogenesis, Int Immunol, 2013.