Jorge Valdés, PhD.

Principal Investigator and Associate Professor

Biocomputing and Applied Genomics Laboratory

PhD. Biotecnology, Universidad Andrés Bello, Chile.

Líneas de Investigación

  • Systems Biotechnology
  • Applied Genetics
  • Comparative, Functional and Evolutionary Genomics
  • Bioinformatics and Computational Biology

Bio-Computing and Applied Genomics Laboratory

The research focus of the Bio-Computing and Applied Genomics Laboratory is the study of genome evolution and its phenotypic consequences in organisms of biotechnological interest using OMICS strategies with a strong emphasis on bioinformatics and experimental approaches. This Laboratory aims to provide expertise and technological tools for the creation of genomics and bioinformatics solutions which will generate innovative technologies for the processing and analysis of massive DNA sequencing projects and other types of OMICS data for their utilization in genetic variation studies at different complexity levels.

The Bio-Computing and Applied Genomics Laboratory is continuously developing research projects in the areas of microbial and eukaryotic genomics, biomarker discovery, applied statistical genetics, proteomic and metabolic profiling in different areas of biotechnological relevance including aquaculture, agriculture, bio-mining and the wine industry. Current research capacities have also been exploited to establish new relationships with environmental and health institutions, national and international universities.


Dr. Jorge Valdes is Director of the Centro de Genómica y Bioinformática and Associate Professor at Universidad Mayor since May 2016. Dr. Valdes has received recognition for his performance since the beginning of his scientific career including i) President of the Republic of Chile Scholarship for outstanding academic performance (1997-2002); ii) Microsoft Sponsored Research Award (2005-2009); iii) Best poster presentation, Global Dialogs on Emerging Science and Technology (GDEST) and iv) The American Society for Microbiology Travel Award (2008). Dr. Valdes has received continuous independent funding from various national and international sources including CORFO (Program of Attraction of Centers of Excellence for InnovaChile-2011-2016); FONDECYT; Millennium Science Initiative (Research Associate); FONDEF; CONICYT-BMBF joint program and several intramural projects. Dr. Valdes is a founding member of the Ibero-American Society of Bioinformatics, member of the Chilean Society for Microbiology and the American Society for Microbiology (ASM). He is also a member of the qualification council at the Faculty of Sciences at the Universidad Mayor, member of the review panel of Frontiers in Bioinformatics and Computational Biology and ad hoc reviewer for Journals including Canadian Journal of Microbiology, Research in Microbiology, Folia Microbiologica, BMC Genomics, among others. Dr. Valdes is a member of the Doctoral Academic Council of the Integrative Genomics PhD program at Universidad Mayor (accredited to the CNA), has directed 3 doctoral, 2 masters and 7 undergraduate theses. Dr. Valdes was director of the Biocomputing and Applied Genetics Division at Fraunhofer Chile Research Foundation from 2011 to 2016, where he was in charge of leading a group of 12 researchers, including 2 postdocs, professionals from the biological, computer sciences, computer engineering, and Bioinformatics. To date Dr. Valdes has published 31 articles in journals with an editorial committee.

Selected publications

Pérez-Stuardo D, Morales-Reyes J, Tapia S, Ahumada DE, Espinoza A, Soto-Herrera V, Brianson B, Ibaceta V, Sandino A, Spencer E, Vallejos-Vidal V, Reyes-López FE, Valdes J, Reyes-Cerpa S (2019). Non-lysosomal activation in macrophages of Atlantic salmon (Salmo salar) after infection with Piscirickettsia salmonis. Frontiers in Immunology. In press.

Angela D. Millar, Paz Tapia, Fernando A. Gómez, Sergio H. Marshall, Derie E. Fuentes and Jorge H. Valdes* (2018). Draft genomes and reference transcriptomes extend the coding potential of the fish pathogen Piscirickettsia salmonis. Electronic Journal of Biotechnology j.ejbt.2018.04.002. doi:10.1016/

Strahsburger E, Zapata F, Pedroso I, Fuentes D, Tapia P, Ponce R, Valdes J* (2017). Draft genome sequence of Exiguobacterium aurantiacum strain PN47 isolate from saline ponds, known as "Salar del Huasco", located in the Altiplano in the North of Chile. Braz J Microbiol 8382(16),31104-2.

González, C., Lazcano, M., Valdés, J.* and Holmes D.S.*. 2016, Bioinformatic analyses of unique (orphan) core genes of the genus Acidithiobacillus: functional inferences and use as molecular probes for genomic and metagenomic/transcriptomic interrogation. Front. Microbiol 27;7:2035. *Both corresponding authors.

Rodríguez-Rojas, F., Tapia, P., Castro-Nallar, E., Undabarrena, A., Muñoz-Díaz, P., Arenas-Salinas, M., Díaz-Vásquez, W., Valdés, J., Vásquez, C., (2016), Draft Genome Sequence of a Multi-Metal Resistant Bacterium Pseudomonas putida ATH-43 Isolated from Greenwich Island, Antarctica. Front Microbiol 8;7:1777.

Montes, C., Altimira, F., Canchignia, H., Castro, Á., Sánchez, E., Miccono, M., Tapia, E., Sequeida, Á., Valdés, J., Tapia, P., González, C., Prieto, H*. (2016), A draft genome sequence of Pseudomonas veronii R4: a grapevine (Vitis vinifera L.) root-associated strain with high biocontrol potential. Stand Genomic Sci. 11:76. Publicado, ISSN: 1944-3277. IF: 1,594

Liljeqvist M, Ossandon FJ, Gonzalez C, Rajan S, Stell A, Valdes J, Holmes DS, Dopson M*. (2015). Metagenomic analysis reveals adaptations to a cold adapted lifestyle in a low temperature acid mine drainage stream. FEMS Microbiol Ecol. 91(4).

González C, Yanquepe M, Cardenas JP, Valdes J, Quatrini R, Holmes DS, Dopson M* (2014). Genetic variability of psychrotolerant Acidithiobacillus ferrivorans revealed by (meta)genomic analysis. Res Microbiol 165(9), 726-34.

Valdés J*, Tapia P, Cepeda V, Varela J, Godoy L, Cubillos F, Silva E, Martinez C, Ganga MA*. (2014). Draft genome sequence and transcriptome analysis of the wine spoilage yeast Dekkera bruxellensis lamap2480 provides insights into genetic diversity, metabolism and survival. FEMS Microbiol Lett 361(2), 104-6.* Both corresponding authors.

Acuña LG, Cárdenas JP, Covarrubias PC, Haristoy JJ, Flores R, Nuñez H, Riadi G, Shmaryahu A, Valdés J, Dopson M, Rawlings DE, Banfield JF, Holmes DS, Quatrini R*. (2013). Architecture and gene repertoire of the flexible genome of the extreme acidophile Acidithiobacillus caldus. PLoS One 8;8(11):e78237.



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