If you use Pathema in your research, we ask that you cite the following publication:
- Pathema: a clade-specific bioinformatics resource center for pathogen research
| Nucleic Acids Res. 2009 Oct 20. [Epub ahead of print] |
| Brinkac, L.M., Davidsen, T., Beck, E., Ganapathy, A., Caler, E., Dodson, R.J., Durkin, A.S., Harkins, D.M., Lorenzi, H., Madupu, R., Sebastian, Y., Shrivastava, S., Thiagarajan, M., Orvis, J., Sundaram, J.P., Crabtree J., Galens, K., Zhao, Y., Inman J.M., Montgomery R., Schobel S., Galinsky K., Tanenbaum D.M., Resnick A., Zafar N., White O., and |
| PubMed Citation |
- Identifying bacterial genes and endosymbiont DNA with Glimmer
| Bioinformatics. 2007 Mar 15; 23(6): 673-9. |
| Delcher, A. L., Bratke, K. A., et al. |
| PubMed Citation |
- Hawkeye: an interactive visual analytics tool for genome assemblies
| Genome Biol. 2007 Mar 09; 8(3): R34. |
| Schatz, M. C., Phillippy, A. M., et al. |
| PubMed Citation |
- Sybil: methods and software for multiple genome comparison and visualization
| Methods Mol Biol. 2007 Jan 01; 408: 93-108. |
| Crabtree, J., Angiuoli, S. V., et al. |
| PubMed Citation |
- TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes
| Nucleic Acids Res. 2006 Dec 06; 35: D260-D264. |
| Selengut, J. D., Haft, D. H., Davidsen, T., Ganapathy, A., Gwinn-Giglio, M., Nelson, W. C., Richter, A. R., White, O. |
| PubMed Citation |
- Use of an EZ-Tn5-based random mutagenesis system to identify a novel toxin regulatory locus in Clostridium perfringens strain 13.
| PLoS One. 2009 Jul 14;4(7):e6232 |
| Vidal JE, Chen J, Li J, McClane BA. |
| PubMed Citation |
- IC50-to-Ki: a web-based tool for converting IC50 to Ki values for inhibitors of enzyme activity and ligand binding
| Nucleic Acids Res. 2009 Apr 24. [Epub ahead of print] |
| Cer RZ, Mudunuri U, Stephens R, Lebeda FJ |
| PubMed Citation |
- Microarray identification of Clostridium difficile core components and divergent regions associated with host origin
| J Bacteriol. 2009 Apr 17. [Epub ahead of print] |
| Janvilisri T, Scaria J, Thompson AD, Nicholson A, Limbago BM, Arroyo LG, Songer JG, Gröhn YT, Chang YF |
| PubMed Citation |
- Development of the Gateway® system for cloning and expressing genes in Entamoeba histolytica Parasitology International
| Parasitol Int. 2009 Mar;58(1):95-7. Epub 2008 Sep 12. |
| Mayuresh M. Abhyankara, Amelia E. Hochreitera, Sarah K. Connella, Carol A. Gilchrista, Barbara J. Manna, b and William A. Petri Jr. |
| PubMed Citation |
- Cloning and identification of a gene coding for a 26-kDa hemoglobin-binding protein from Entamoeba histolytica.
| Biochimie. 2009 Mar;91(3):383-9. Epub 2008 Nov 12. |
| Cruz-Castañeda A, Hernández-Sánchez J, Olivares-Trejo JJ. |
| PubMed Citation |
- The Vacuolar ATPase from Entamoeba histolytica: Molecular cloning of the gene encoding for the B subunit and subcellular localization of the protein.
| BMC Microbiol. 2008 Dec 23;8:235 |
| Melendez-Hernandez MG, Labra Barrios ML, Orozco E, Luna-Arias JP. |
| PubMed Citation |
- Small RNAs with 5'-polyphosphate termini associate with a Piwi-related protein and regulate gene expression in the single-celled eukaryote Entamoeba histolytica.
| PLoS Pathog. 2008 Nov;4(11):e1000219. Epub 2008 Nov 28. |
| Zhang H, Ehrenkaufer GM, Pompey JM, Hackney JA, Singh U. |
| PubMed Citation |
- Putative DEAD and DExH-box RNA helicases families in Entamoeba histolytica.
| Gene. 2008 Nov 15;424(1-2):1-10. Epub 2008 Aug 9. |
| Marchat LA, Orozco E, Guillen N, Weber C, López-Camarillo C. |
| PubMed Citation |
- Characterization of an Entamoeba histolytica high-mobility-group box protein induced during intestinal infection
| Eukaryot Cell. 2008 Sep 01; 7(9): 1565-72. |
| Abhyankar, M. M., Hochreiter, A. E., et al. |
| PubMed Citation |
- Targets of the Entamoeba histolytica Transcription Factor URE3-BP.
| PLoS Negl Trop Dis. 2008;2(8):e282. Epub 2008 Aug 27. |
| Gilchrist CA, Baba DJ, Zhang Y, Crasta O, Evans C,Caler E, Sobral BW, |
| PubMed Citation |
- The Burkholderia mallei BmaR3-BmaI3 quorum-sensing system produces and responds to N-3-hydroxy-octanoyl homoserine lactone
| J Bacteriol. 2008 Jul 01; 190(14): 5137-41. |
| Duerkop, B. A., Herman, J. P., et al. |
| PubMed Citation |
- Entamoeba histolytica encodes unique formins, a subset of which regulates DNA content and cell division
| Infect Immun. 2008 Jun 01; 76(6): 2368-78. |
| Majumder, S., Lohia, A. |
| PubMed Citation |
- Entamoeba histolytica EhDEAD1 is a conserved DEAD-box RNA helicase with ATPase and ATP-dependent RNA unwinding activities.
| Gene. 2008 May 15;414(1-2):19-31. Epub 2008 Feb 16. |
| López-Camarillo C, de la Luz García-Hernández M, Marchat LA, Luna-Arias JP,Hernández de la Cruz O, Mendoza L, Orozco E. |
| PubMed Citation |
- A novel small acid soluble protein variant is important for spore resistance of most Clostridium perfringens food poisoning isolates.
- Transcriptional profile of the homologous recombination machinery and characterization of the EhRAD51 recombinase in response to DNA damage in Entamoeba histolytica
| BMC Mol Biol. 2008 Apr 10; 9: 35. |
| Lopez-Casamichana, M., Orozco, E., et al. |
| PubMed Citation |
- Characterization of the Entamoeba histolytica Ornithine Decarboxylase-Like Enzyme
| PLoS Negl Trop Dis. 2008 Jan 02; 2(1): e115. |
| Jhingran, A., Padmanabhan, P. K., et al. |
| PubMed Citation |
- Glanders: off to the races with Burkholderia mallei
| FEMS Microbiol Lett. 2007 Dec 01; 277(2): 115-22. |
| Whitlock, G. C., Estes, D. M., et al. |
| PubMed Citation |
- Transcriptional regulatory network discovery via multiple method integration: application to e. coli K12
| Algorithms Mol Biol. 2007 Mar 30; 2: 2. |
| Sun, J., Tuncay, K., et al. |
| PubMed Citation |
- Burkholderia Hep_Hap autotransporter (BuHA) proteins elicit a strong antibody response during experimental glanders but not human melioidosis
| BMC Microbiol. 2007 Mar 15; 7(1): 19. |
| Tiyawisutsri, R., Holden, M. T., Tumapa, S., Rengpipat, S., Clarke, S. R., Foster, S. J., Nierman, W. C., Day, N. P., Peacock, S. J. |
| PubMed Citation |
- NIAID Bioinformatics Resource Centers - New Assets for Pathogen Informatics
| Infect Immun. 2007 Apr 09; 75: 3212-3219. |
| Greene, J. M., Collins, F., et al. |
| PubMed Citation |
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