AmoebaDB and MicrosporidiaDB: Functional genomic resources for Amoebozoa and Microsporidia species

Nucleic Acids Research

Volumn 39, Issue SUPPL. 1, 2011, Pages

  Aurrecoechea, Cristina ^a   Barreto, Ana ^b   Brestelli, John ^b   Brunk, Brian P ^b   Caler, Elisabet V ^c   Fischer, Steve ^b   Gajria, Bindu ^b   Gao, Xin ^b   Gingle, Alan ^d   Grant, Greg ^b   Harb, Omar S ^b   Heiges, Mark ^a   Iodice, John ^b   Kissinger, Jessica C ^a,e   Kraemer, Eileen T ^f   Li, Wei ^b   Nayak, Vishal ^b   Pennington, Cary ^a   Pinney, Deborah F ^b   Pitts, Brian ^a   Roos, David S ^b   Srinivasamoorthy, Ganesh ^a   Stoeckert Jr , Christian J ^b   Treatman, Charles ^b   Wang, Haiming ^a   more..

^a UNIVERSITY OF GEORGIA   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

^c J CRAIG VENTER INSTITUTE   (United States)

^d Center for Applied Genetic Technologies   (United States)

^e Institute of Bioinformatics   (United States)

^f Institute of Bioinformatics ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; AMOEBADB; AMOEBOZOA; ARTICLE; BIOINFORMATICS; COMPUTER INTERFACE; ENCEPHALITOZOON CUNICULI; ENCEPHALITOZOON INTESTINALIS; ENTAMOEBA DISPAR; ENTAMOEBA HISTOLYTICA; ENTAMOEBA INVADENS; ENTEROCYTOZOON; EXPRESSED SEQUENCE TAG; FUNCTIONAL GENOMICS; FUNGAL GENOME; GENETIC DATABASE; INFORMATION RETRIEVAL; INTERNET; MICROSPORIDIA; MICROSPORIDIADB; PHYLOGENY; PRIORITY JOURNAL; PROTEIN MOTIF; PROTOZOAL GENETICS;

DATABASES, GENETIC; ENCEPHALITOZOON; ENTAMOEBA; GENOME, FUNGAL; GENOME, PROTOZOAN; GENOMICS;

AMOEBOZOA; ENCEPHALITOZOON CUNICULI; ENTAMOEBA; ENTAMOEBA DISPAR; ENTAMOEBA HISTOLYTICA; ENTAMOEBA INVADENS; MICROSPORIDIA;

EID: 78651323941     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq1006     Document Type: Article

References (26)

1. Aurrecoechea, C., Brestelli, J., Brunk, B.P., Fischer, S., Gajria, B., Gao, X., Gingle, A., Grant, G., Harb, O.S., Heiges, M. et al. (2010) EuPathDB: A portal to eukaryotic pathogen databases. Nucleic Acids Res., 38, D415-D419.
2. Aslett, M., Aurrecoechea, C., Berriman, M., Brestelli, J., Brunk, B.P., Carrington, M., Depledge, D.P., Fischer, S., Gajria, B., Gao, X. et al. (2010) TriTrypDB: A functional genomic resource for the Trypanosomatidae. Nucleic Acids Res., 38, D457-D462.
3. Aurrecoechea, C., Brestelli, J., Brunk, B.P., Carlton, J.M., Dommer, J., Fischer, S., Gajria, B., Gao, X., Gingle, A., Grant, G. et al. (2009) GiardiaDB and TrichDB: Integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis. Nucleic Acids Res., 37, D526-D530.
4. Aurrecoechea, C., Brestelli, J., Brunk, B.P., Dommer, J., Fischer, S., Gajria, B., Gao, X., Gingle, A., Grant, G., Harb, O.S. et al. (2009) PlasmoDB: A functional genomic database for malaria parasites. Nucleic Acids Res., 37, D539-D543.
5. Gajria, B., Bahl, A., Brestelli, J., Dommer, J., Fischer, S., Gao, X., Heiges, M., Iodice, J., Kissinger, J.C., Mackey, A.J. et al. (2008) ToxoDB: An integrated Toxoplasma gondii database resource. Nucleic Acids Res., 36, D553-D556.
6. Heiges, M., Wang, H., Robinson, E., Aurrecoechea, C., Gao, X., Kaluskar, N., Rhodes, P., Wang, S., He, C.Z., Su, Y. et al. (2006) CryptoDB: A Cryptosporidium bioinformatics resource update. Nucleic Acids Res., 34, D419-D422.
7. Brinkac, L.M., Davidsen, T., Beck, E., Ganapathy, A., Caler, E., Dodson, R.J., Durkin, A.S., Harkins, D.M., Lorenzi, H., Madupu, R. et al. Pathema: A clade-specific bioinformatics resource center for pathogen research. Nucleic Acids Res., 38, D408-D414.
8. Squires, B., Macken, C., Garcia-Sastre, A., Godbole, S., Noronha, J., Hunt, V., Chang, R., Larsen, C.N., Klem, E., Biersack, K. et al. (2008) BioHealthBase: Informatics support in the elucidation of influenza virus host pathogen interactions and virulence. Nucleic Acids Res., 36, D497-D503.
9. Visvesvara, G.S., Moura, H. and Schuster, F.L. (2007) Pathogenic and opportunistic free-living amoebae: Acanthamoeba spp., Balamuthia mandrillaris, Naegleria fowleri, and Sappinia diploidea. FEMS Immunol. Med. Microbiol., 50, 1-26.
10. Harb, O.S., Gao, L.Y. and Abu Kwaik, Y. (2000) From protozoa to mammalian cells: A new paradigm in the life cycle of intracellular bacterial pathogens. Environ. Microbiol., 2, 251-265.
11. Ximenez, C., Moran, P., Rojas, L., Valadez, A. and Gomez, A. (2009) Reassessment of the epidemiology of amebiasis: State of the art. Infect. Genet. Evol., 9, 1023-1032.
12. Silberman, J.D., Clark, C.G., Diamond, L.S. and Sogin, M.L. (1999) Phylogeny of the genera Entamoeba and Endolimax as deduced from small-subunit ribosomal RNA sequences. Mol. Biol. Evol., 16, 1740-1751.
13. Fotedar, R., Stark, D., Beebe, N., Marriott, D., Ellis, J. and Harkness, J. (2007) Laboratory diagnostic techniques for Entamoeba species. Clin. Microbiol. Rev., 20, 511-532.
14. Diamond, L.S. and Clark, C.G. (1993) A redescription of Entamoeba histolytica Schaudinn, 1903 (Emended Walker, 1911) separating it from Entamoeba dispar Brumpt, 1925. J. Eukaryot. Microbiol., 40, 340-344.
15. Haque, R. and Petri, W.A. Jr (2006) Diagnosis of amebiasis in Bangladesh. Arch. Med. Res., 37, 273-276.
16. Haque, R., Huston, C.D., Hughes, M., Houpt, E. and Petri, W.A. Jr (2003) Amebiasis. N. Engl. J. Med., 348, 1565-1573.
17. Vazquezdelara-Cisneros, L.G. and Arroyo-Begovich, A. (1984) Induction of encystation of Entamoeba invadens by removal of glucose from the culture medium. J. Parasitol., 70, 629-633.
18. Loftus, B., Anderson, I., Davies, R., Alsmark, U.C., Samuelson, J., Amedeo, P., Roncaglia, P., Berriman, M., Hirt, R.P., Mann, B.J. et al. (2005) The genome of the protist parasite Entamoeba histolytica. Nature, 433, 865-868.
19. Lorenzi, H.A., Puiu, D., Miller, J.R., Brinkac, L.M., Amedeo, P., Hall, N. and Caler, E.V. New assembly, reannotation and analysis of the Entamoeba histolytica genome reveal new genomic features and protein content information. PLoS Negl. Trop. Dis., 4, e716.
20. Ehrenkaufer, G.M., Haque, R., Hackney, J.A., Eichinger, D.J. and Singh, U. (2007) Identification of developmentally regulated genes in Entamoeba histolytica: Insights into mechanisms of stage conversion in a protozoan parasite. Cell Microbiol., 9, 1426-1444.
21. Gilchrist, C.A., Houpt, E., Trapaidze, N., Fei, Z., Crasta, O., Asgharpour, A., Evans, C., Martino-Catt, S., Baba, D.J., Stroup, S. et al. (2006) Impact of intestinal colonization and invasion on the Entamoeba histolytica transcriptome. Mol. Biochem. Parasitol., 147, 163-176.
22. Keeling, P.J. and Fast, N.M. (2002) Microsporidia: Biology and evolution of highly reduced intracellular parasites. Annu. Rev. Microbiol., 56, 93-116.
23. Didier, E.S. and Weiss, L.M. (2006) Microsporidiosis: Current status. Curr. Opin. Infect. Dis., 19, 485-492.
24. Katinka, M.D., Duprat, S., Cornillot, E., Metenier, G., Thomarat, F., Prensier, G., Barbe, V., Peyretaillade, E., Brottier, P., Wincker, P. et al. (2001) Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature, 414, 450-453.
25. Akiyoshi, D.E., Morrison, H.G., Lei, S., Feng, X., Zhang, Q., Corradi, N., Mayanja, H., Tumwine, J.K., Keeling, P.J., Weiss, L.M. et al. (2009) Genomic survey of the non-cultivatable opportunistic human pathogen, Enterocytozoon bieneusi. PLoS Pathog., 5, e1000261.
26. Corradi, N., Akiyoshi, D.E., Morrison, H.G., Feng, X., Weiss, L.M., Tzipori, S. and Keeling, P.J. (2007) Patterns of genome evolution among the microsporidian parasites Encephalitozoon cuniculi, Antonospora locustae and Enterocytozoon bieneusi. PLoS ONE, 2, e1277.