Laboratorio de Biocomputación y Genómica Aplicada
Publicaciones
Artículos en revistas científicas con comité editorial.
2024
Comparative genomics sheds light on transcription factor-mediated regulation in the extreme acidophilic Acidithiobacillia representatives
Pedro Sepúlveda-Rebolledo, Carolina González-Rosales, Mark Dopson, Ernesto Pérez-Rueda, David S. Holmes, Jorge H. Valdés
Genomic insights into key mechanisms for carbon, nitrogen, and phosphate assimilation by the acidophilic, halotolerant genus Acidihalobacter members, FEMS Microbiology Ecology, Volume 100, Issue 12, December 2024, fiae145
Himel Nahreen Khaleque, Homayoun Fathollahzadeh, Anna H Kaksonen, Jorge Valdés, Eva Vergara, David S Holmes, Elizabeth L J Watkin
Global transcriptome profiles provide insights into muscle cell development and differentiation on microstructured marine biopolymer scaffolds for cultured meat production
Dragica Bezjak, Nicole Orellana, Guillermo Valdivia, Cristian A. Acevedo, Jorge H. Valdes
Towards Understanding the Role of Microstructured Edible Scaffolds for Cultured Meat Production
Dragica Bezjak, Nicole Orellana, Jorge H. Valdés, Tomás Corrales, Cristian A. Acevedo
2023
Draft genome of Pseudomonas sp. RGM 2987 isolated from Stevia philippiana roots reveals its potential as a plant biostimulant and potentially constitutes a novel species, Electronic Journal of Biotechnology, Volume 61, 2023, Pages 9-13, ISSN 0717-3458
Matías Guerra, Jorge Carrasco-Fernández, Jorge H. Valdés, Marcelo Panichini, Jean Franco Castro
Exophiala atacamensis sp. nov. and E. crusticola from the Atacama Desert, northern Chile
Madrid H., Gené J., Quijada L., Cantillo T., Gacitúa R., Valdés J., Sánchez C., Prenafeta-Boldú F., Wijayawardene N., Silva V. &
Mobile genetic elements drive the multidrug resistance and spread of Salmonella serotypes along a poultry meat production line
Krüger GI, Pardo-Esté C, Zepeda P, Olivares-Pacheco J, Galleguillos N, Suarez M, Castro-Severyn J, Alvarez-Thon L, Tello M, Valdes JH, Saavedra CP
2022
Anaerobiosis favors biosynthesis of single and multi-element nanostructures
Mirtha Ríos-Silva, Myriam Pérez, Roberto Luraschi, Esteban Vargas, Claudia Silva-Andrade, Jorge Valdés, Juan Marcelo Sandoval, Claudio Vásquez, Felipe Arenas
Biochemical, genomic and structural characteristics of the Acr3 pump in Exiguobacterium strains isolated from arsenic-rich Salar de Huasco sediments
Castro-Severyn J, Pardo-Esté C, Araya-Durán I, Gariazzo V, Cabezas C, Valdés J, Remonsellez F, Saavedra CP
Draft Genome Sequence of Pseudomonas sp. Strain RGM 3321, a Phyllosphere Endophyte from Fragaria chiloensis subsp. chiloensis f. patagonica
Castro JF, Guerra M, Carrasco-Fernández J, Ortiz-Campos J, Cares-Gatica D, Campos-Quiroz C, Correa F, Beltrán MF, Sagredo B, Valdés JH.
Integrative Genomics Shed Light on Evolutionary Forces Shaping the Acidithiobacillia Class Acidophilic Lifestyle
Gonzalez Carolina, Vergara Eva, Dopson Mark, Valdes Jorge H. & D.S. Holmes.*
2021
Bacteria Isolated From the Antarctic Sponge Iophon sp. Reveals Mechanisms of Symbiosis in Sporosarcina, Cellulophaga, and Nesterenkonia
Mario Moreno-Pino, Juan Antonio Ugalde, Jorge Hernan Valdes, Susana Rodríguez-Marconi, Génesis Parada-Pozo and Nicole Trefault*
2019
Draft Genome Sequence of Bacillus safensis RP10, Isolated from Soil in the Atacama Desert, Chile
Erwin Strahsburger, Felipe Zapata, Inti Pedroso, Derie Fuentes, Paz Tapia, Raul Ponce, Michael McClelland, Jorge Valdes
Non-lysosomal Activation in Macrophages of Atlantic Salmon (Salmo salar) After Infection with Piscirickettsia salmonis
Pérez-Stuardo D, Morales-Reyes J, Tapia S, Ahumada DE, Espinoza A, Soto-Herrera V, Brianson B, Ibaceta V, Sandino AM, Spencer E, Vallejos-Vidal E, Reyes-López FE, Valdés J, Reyes-Cerpa S*
2018
Draft genomes and reference transcriptomes extend the coding potential of the fish pathogen Piscirickettsia salmonis
Angela D. Millar, Paz Tapia, Fernando A. Gómez, Sergio H. Marshall, Derie E. Fuentes, Jorge H. Valdes
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
Erwin Strahsburger, Felipe Zapata, Inti Pedroso, Derie Fuentes, Paz Tapia, Raul Ponce, Jorge Valdes
2016
A draft genome sequence of Pseudomonas veronii R4: a grapevine (Vitis vinifera L.) root-associated strain with high biocontrol potential
Christian Montes, Fabiola Altimira, Hayron Canchignia, Álvaro Castro, Evelyn Sánchez, María Miccono, Eduardo Tapia, Álvaro Sequeida, Jorge Valdés, Paz Tapia, Carolina González, Humberto Prieto
Bioinformatic analyses of unique (orphan) core genes of the genus Acidithiobacillus: functional inferences and use as molecular probes for genomic and metagenomic/transcriptomic interrogation
González, C., Lazcano, M., Valdés, J.* and Holmes D.S.*
Draft Genome Sequence of a Multi-Metal Resistant Bacterium Pseudomonas putida ATH-43 Isolated from Greenwich Island, Antarctica
Rodríguez-Rojas, F., Tapia, P., Castro-Nallar, E., Undabarrena, A., Muñoz-Díaz, P., Arenas-Salinas, M., Díaz-Vásquez, W., Valdés, J., Vásquez, C.
2015
Metagenomic analysis reveals adaptations to a cold adapted lifestyle in a low temperature acid mine drainage stream
Maria Liljeqvist, Francisco J. Ossandon, Carolina González, Sukithar Rajan, Adam Stell, Jorge Valdes, David S. Holmes, Mark Dopson
2014
Draft genome sequence and transcriptome analysis of the wine spoilage yeast Dekkera bruxellensis lamap2480 provides insights into genetic diversity, metabolism and survival
Jorge Valdes, Paz Tapia, Victoria Cepeda, Javier Varela, Liliana Godoy, Francisco A. Cubillos, Evelyn Silva, Claudio Martinez, Maria Angélica Ganga
Genetic variability of psychrotolerant Acidithiobacillus ferrivorans revealed by (meta)genomic analysis
Carolina González, María Yanquepe, Juan Pablo Cardenas, Jorge Valdes, Raquel Quatrini, David S. Holmes, Mark Dopson
2013
Architecture and gene repertoire of the flexible genome of the extreme acidophile Acidithiobacillus caldus
Lillian G. Acuña, Juan Pablo Cárdenas, Paulo C. Covarrubias, Juan José Haristoy, Rodrigo Flores, Harold Nuñez, Gonzalo Riadi, Amir Shmaryahu, Jorge Valdés, Mark Dopson, Douglas E. Rawlings, Jillian F. Banfield, David S. Holmes, Raquel Quatrini
2011
Draft genome of the psychrotolerant acidophile Acidithiobacillus ferrivorans SS3
Maria Liljeqvist, Jorge Valdes, David S. Holmes, Mark Dopson
Draft genome sequence of the extremely acidophilic biomining bacterium Acidithiobacillus thiooxidans ATCC 19377 provides insights into the evolution of the Acidithiobacillus genus
Jorge Valdes, Francisco Ossandon, Raquel Quatrini, Mark Dopson, David S. Holmes
Sulfur metabolism in the extreme acidophile Acidithiobacillus caldus
Mangold, S., Valdés, J., Holmes DS and Dopson M*
2010
Comparative genomics begins to unravel the ecophysiology of bioleaching
Jorge Valdés, Juan Pablo Cárdenas, Raquel Quatrini, Mario Esparza, Hector Osorio, Francisco Duarte, Claudia Lefimil, R. Sepulveda, Eugenia Jedlicki, David S. Holmes
Lessons from the genomes of extremely acidophilic eubacteria and archaea with special emphasis on bioleaching microorganisms
Juan Pablo Cárdenas, Jorge Valdés, Raquel Quatrini, Francisco Duarte, David S. Holmes
2009
Draft genome sequence of the extremely acidophilic bacterium Acidithiobacillus caldus ATCC 51756 reveals metabolic versatility in the genus Acidithiobacillus
Jorge Valdes, Raquel Quatrini, Kevin Hallberg, Mark Dopson, Pablo D. T. Valenzuela, David S. Holmes
Genomic Lessons from Biomining Organisms: Case Study of the Acidithiobacillus Genus
Jorge Valdés, David S. Holmes
2008
Acidithiobacillus ferrooxidans Metabolism: From Genome Sequence to Industrial Applications
Jorge Valdés, Inti Pedroso, Raquel Quatrini, Robert J Dodson, Herve Tettelin, Robert Blake II, Jonathan A Eisen, David S Holmes
Comparative Genome Analysis of Acidithiobacillus ferrooxidans, A. thiooxidans and A. caldus: insights into their Metabolism and Ecophysiology
Jorge Valdés, Inti Pedroso, Raquel Quatrini, David S. Holmes
Generation and analysis of an Eucalyptus globulus cDNA library constructed from seedlings under low temperature conditions
Susana Rasmussen-Poblete, Jorge Valdes, Maria Cecilia Gamboa, Pablo D.T. Valenzuela, Erwin Krauskopf
Iron homeostasis strategies in acidophilic iron oxidizers: Studies in Acidithiobacillus and Leptospirillum
Hector Osorio, Verónica Martínez, Felipe A. Veloso, Inti Pedroso, Jorge Valdés, Eugenia Jedlicki, David S. Holmes, Raquel Quatrini
Preparation and Analysis of an Expressed Sequence Tag Library from the Toxic Dinoflagellate Alexandrium catenella
Paulina Uribe, Daniela Fuentes, Jorge Valdés, Amir Shmaryahu, Alicia Zúñiga, David Holmes, Pablo D. T. Valenzuela
2007
Insights into the Metabolism and Ecophysiology of Three Acidithiobacilli Species by Comparative Genome Analysis
Jorge Valdés, Inti Pedroso, Raquel Quatrini, Kevin B. Hallberg, Pablo D.T. Valenzuela, David S. Holmes
Iron Homeostasis Strategies in Acidophilic Iron Oxidizers: Comparative Genomic Analyses
Raquel Quatrini, Verónica Martínez, Hector Osorio, Felipe A. Veloso, Inti Pedroso, Jorge Valdés, Eugenia Jedlicki, David S. Holmes
Regulation of a novel Acidithiobacillus caldus gene cluster involved in metabolism of reduced inorganic sulfur compounds
Olena I. Rzhepishevska, Jorge Valdés, Liucija Marcinkeviciene, Camelia Algora Gallardo, Rolandas Meskys, Violaine Bonnefoy, David S. Holmes, Mark Dopson
2006
Generation and analysis of expressed sequence tags from Botrytis cinerea
Evelyn Silva, Jorge Valdés, David S Holmes, Amir Shmaryahu, Pablo D. T. Valenzuela
Insights into the Iron and Sulfur Energetic Metabolism of Acidthiobacillus ferrooxidans by Microarray Transcriptome Profiling
Raquel Quatrini, Corinne Appia-Ayme, Yann Denis, Jeanine Ratouchniak, Felipe Veloso, Jorge Valdes, Claudia Lefimil, Simon Silver, Frank Roberto, Omar Orellana, François Denizot, Eugenia Jedlicki, David S Holmes, Violaine Bonnefoy
Microarray and Bioinformatic Analyses Suggest Models for Carbon Metabolism in the Autotroph Acidithiobacillus ferrooxidans
Corinne Appia-Ayme, Raquel Quatrini, Yann Denis, François Denizot, Simon Silver, Francisco Roberto, Felipe Veloso, Jorge Valdés, Juan Pablo Cárdenas, Mario Esparza, Omar Orellana, Eugenia Jedlicki, Violaine Bonnefoy, David S. Holmes
2003
Aspects of the Predicted Physiology of Acidithiobacillus ferrooxidans Deduced from an Analysis of its Partial Genome Sequence
Marlen Barreto, Raquel Quatrini, Susan Bueno, Claudia Arriagada, Jorge Valdes, Simon Silver, Eugenia Jedlicki, David S Holmes
Metabolic reconstruction of sulfur assimilation in the extremophile Acidithiobacillus ferrooxidans based on genome analysis
Jorge Valdés, Felipe Veloso, Eugenia Jedlicki, David Holmes