Juan A. Ugalde bio photo

Juan A. Ugalde

Research Professor, Centro de Genética y Genómica, Facultad de Medicina, Clinica Alemana-Universidad del Desarrollo

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publications

25. Salgado, A., Sepúlveda, F., Melis, F., Marchandon, G., Quintana, J., Lam, M., García, P., Ugalde, J.A. Whole genome sequencing of chilean CA-MRSA strains: challenges and opportunities. Submitted.

24. Melis, F., Salgado, A., Marchandon, G., Sanchez, C., Garcia, P., Ugalde, J.A. Genomic characterization of a Burkholderia cenocepacia strain isolated from a cystic fibrosis patient. Submitted.

23. Undabarrena, A., Ugalde, J.A., Castro-Nallar, E., Seeger, M., Cámara, B. Nearly-complete genome sequence of Streptomyces sp. strain H-KF8, a marine bacterium exhibiting antibacterial activity, isolated from a northern Chilean Patagonian Fjord. Submitted.

22. Undabarrena, A., Ugalde, J.A., Seeger, M., Cámara, B. Genomic data mining of the marine actinomycete Streptomyces sp. H-KF8 unveils insights into multi-stress related genes and metabolic pathways involved in antimicrobial synthesis. Submitted.

21. Godoy, L., Vera-Wolf, P., Martinez, C., Ugalde, J.A., Ganga, A. Comparative transcriptome assembly and genome-guided profiling for Brettanomyces bruxellensis LAMAP2480 during p-coumaric acid stress. Accepted. Scientific Reports.

20. Garrido, D., Ruiz-Moyano, S., Kirmiz, N., Davis, J.C.C., Totten, S., Lemay, D.G., Ugalde, J.A., German, J.B., Lebrilla, C.B., Mills, D.A. A novel gene cluster allows preferential utilization of fucosylated milk oligosaccharides in Bifidobacterium longum subsp. longum SC596. Accepted. Scientific Reports.

19. Asenjo, F., Olmos, A., Henríquez-Piskulich, P., Aldea, P., Ugalde, J.A.*, Trombert, A.N.* Genome Sequencing and Analysis of the First Complete Genome of Lactobacillus kunkeei Strain MP2, an Apis mellifera Gut Isolate[PeerJ 4:e1950. 2016] (https://peerj.com/articles/1950/)
(*Corresponding authors)

18. Morales, P., Fujio, S., Navarrete, P., Ugalde, J.A., Magne, F., Carrasco-Pozo, C., Tralma, K., Quezada, M.P., Hurtado, C., Covarrubias, N., Brignardello, J., Henriquez, D., Gotteland, M. Impact of Dietary Lipids on Colonic Function and Microbiota: An Experimental Approach Involving Orlistat-Induced Fat Malabsorption in Human Volunteer. Clinical and Translational Gastroenterology 7(4):e161. 2016

17. Tang, X., Li, J., Millán-Aguiñaga, N., Zhang, J.J., O’Neill, E., Ugalde, J.A., Jensen, P., Mantovani, S., Bradley, M. (2015). Identification of Thiotetronic Acid Antibiotic Bisynthetic Pathways by Target-directed Genome Mining. ACS Chemical Biology 10(12):2841-2849. 2015

16. Rojas, R., Miranda, C.D., Romero, J., Asenjo, F., Valderrama, K., Segovia, C., Ugalde, J.A*., Santander, J*. Genome Sequence of Vibrio VPAP30, Isolated from an Episode of Massive Mortality of Reared Larvae of the Scallop Argopecten purpuratus Genome Announcements, 3(4):e00745-15, 2015.
(*Corresponding authors)

15. Martin, L.J., Adams, R., Bateman, A., Bik, H.M., Haws, J., Hird, S.M., Hughes, D., Kembel, S.W., Kinney, K., Kolokotronis, S., Levy, G., McClain, C., Meadow, J.F., Medina, R.F., Mhuireach, G., Moreau, C.S., Munshi-South, J., Nichols, L., Palmer, C., Popova, L., Schal, C., Taeubel, M., Trautwein, M., Ugalde, J.A., Dunn, R.R. Evolution in the Indoor Biome. Trends in Ecology and Evolution, 2015. PDF

14. Plominsky, A.M., Delherbe, N., Ugalde, J.A., Allen, E.E., Blanchet, M., Ikeda, P., Santibañez, Hanselmann, K., Ulloa, O., De La Iglesia, R., von Dassow, P., Astorga, M., Gálvez, M.J., González., M.L., Henríquez-Castillo, C., Vaulot, D., Lopes do Santos, A., van den Engh, G., Gimpel, C., Bertoglio, F., Delgado, Y., Docman, F., Elizondo-Patrone, C., Narváez, S., Sorroche, F., Rojas-Herrera, M., Trefault, N. Metagenome Sequencing of the Microbial Community of a Solar Saltern Crystallizer Pond. Genome Announcements, 2(6): e01172-14, 2014.

13. Valenzuela, C., Ugalde, J.A., Mora, G.C., Alvarez, S., Contrerars, I., Santiviago, C.A. Draft genome sequence of Salmonella enterica serovar Typhi strain STH23270. Genome Announcements, 2(1):e00104-14, 2014.

12. Ugalde, J.A., Narasingarao, P., Kuo, S., Podell, S., Allen E.E. Draft Genome Sequence of “Candidatus Halobonum tyrrellensis” Strain G22 Isolated from the Hypersaline Waters of Lake Tyrrell, Australia. Genome Announcements, 1(6):e01001-13, 2013. PDF.

11. Podell, S, Emerson, J., Jones, C.M., Ugalde, J.A., Welch, S., Heidelberg, K.B., Banfield, J.F., Allen, E.E. Seasonal Fluctuations In Ionic Concentrations Drive Microbial Succession in a Hypersaline Lake Community. ISME Journal., Advance Online Publication, December 12 2013. PDF

10. Malfatti, F, Turk, V., Tinta, T., Mozetic, P., Manganelli, M., Samo, T., Ugalde J.A., Kovac, N., Stefanelli, M., Antonioli, M., Fonda-Umani, S., Del Negro, P., Cataletto, B., Hozic Zimmermann, A., Ivošević Denardi, N., Žutić, V., Svetličić, V., Mišic Radić,T., Radić, T., Fuchs D., Azam, F. Microbial mechanisms coupling carbon and phosphorus cycles in phosphorous-limited northern Adriatic Sea, and response to phosphorus enrichment. Science of the Total Environment., 470-471:1173-1183. 2014. PDF

9. Kharbush, J., Ugalde, J.A., Hogle, S. Allen, E.E., Aluwihare, L. Diversity of composite bacterial hopanoids and their microbial producers across oxygen gradients in the water column of the California Current. Applied and Environmental Microbiology, Published ahead of print. PDF

8. Ugalde, J.A*, Gallardo, M.J., Belmar, C., Muñoz, P., Ruiz-Tagle, N., Ferrada-Fuentes, S., Espinoza, C., Allen, E.E., Gallardo, V.A.** Microbial life in a Fjord: Metagenomic analysis of a microbial mat in Chilean Patagonia.** PLoS One, 8 (8):e71952. 2013.. PDF.
(*Corresponding author)

7. Podell, S., Ugalde, J.A., Narasingarao, P., Banfield, J.F., Heidelberg, K.B., Allen, E.E. Assembly-driven Community Genomics of a Hypersaline Microbial Ecosystem. Plos One, 8 (4):e61692. 2013.. PDF

6. Narasingarao, P., Podell, S., Ugalde, J.A., Brochier-Armanet, C., Emerson, J.B., Brocks, J.J., Heidelberg, K.B., Banfield, J.F., Allen, E.E. ** De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities.** ISME Journal, 6, 81-93. 2012.PDF

5. Ugalde, J.A., Podell, S., Narasingarao P., Allen, E.E. Xenorhodopsins, an enigmatic new class of microbial rhodopsins horizontally transferred between archaea and bacteria. Biology Direct, 6:52. 2011.PDF

4. Levican, G*., Ugalde, J.A*., Ehrenfeld N., Maass, A., Parada, P. Comparative genomic analysis of carbon and nitrogen assimilation mechanisms in three indigenous bioleaching bacteria: predictions and validations. BMC Genomics, 9:581. 2008..PDF.
(*First authors)

3. Chang, B.S., Matz, M.V., Ugalde, J.A. Applications of ancestral protein reconstruction in understanding protein function: GFP-like proteins. Methods in Enzynmology, 395: 652-670. 2005. PDF

2. Ugalde, J.A., Chang, B.S., Matz, M.V. Evolution of coral colors recreated. Science, 305:1433. 2004.. PDF.

1. Shagin, D.A., Barsova, E.V., Yanushevich, Y.G., Fradkov, A.F., Lukyanov, K.A., Labas, Y.A., Semenova, T.N., Ugalde, J.A., Meyer, A., Nunes, J.M., Widder, E.A., Lukyanov, S.A., Matz, M.V. GFP-like proteins as ubiquitous Metazoan superfamily: evolution of functional features and structural complexity. Molecular Biology and Evolution, 21:841-850. 2004. PDF.