Bioinformatics and Genome Biology


The Center for Bioinformatics and Genome Biology carries out basic research in several areas of genome biology. One research objective is to advance our understanding of the metabolic potential and the ecophysiological interactions between acidophilic microorganisms involved in the industrial recovery of copper (bioleaching). The long term objective is to use this information to suggest improvements for commercial copper recovery. To this end we have sequenced and annotated a number of bioleaching acidophiles. We are also interested in the deep evolution of acidophiles, especially their potential for providing insight into the emergence of life on earth and the potential for life on exoplanets and moons (astrobiology). Other projects currently under investigation include metagenomics of acid environments and the evolution of single exon genes.


Research Head: David Holmes

Doctoral students: René Sepúlveda • Carolina González • Roddy Jorquera


  • Braulio Valdevenito-Maturana, Jose Antonio Reyes-Suarez, Jaime Henriquez, David S. Holmes, Raquel Quatrini, Ehmke Pohl, Mauricio Arenas-Salinas. MUTANTELEC: an In Silico Mutation Simulation Platform for Comparative Electrostatic Potential Profiling of Proteins. J. of Computational Chemistry 38, 467–474 (2017). | | ABSTRACT
  • Mark Dopson, David S Holmes, Marcelo Lazcano, Timothy J McCredden, Kieran T Mulroney, Elizabeth LJ Watkin. Multiple osmotic stress responses in Acidihalobacter prosperous results in a greater tolerance to chloride ions than in Acidithiobacillus ferrooxidans. Front. Microbiol. 05 January, (2017). | | ABSTRACT
  • J-P Cárdenas, R. Quatrini and D. S. Holmes. Genomic and Metagenomic Challenges and Opportunities for Bioleaching: a mini-review. Res Microbiol. Sep;167(7):529-38 (2016). | | ABSTRACT
  • Carolina González, Marcelo Lazcano, Jorge Valdés and David S. Holmes. 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. 7:2035. doi: 10.3389/fmicb.2016.02035 (2016). | | ABSTRACT
  • Jorquera R., Ortiz R., Ossandon F., Cárdenas J.P., Sepúlveda R and Holmes D. S. SinEx DB: A Database for Single Exon Coding Sequences in Mammalian Genomes. DataBase, baw095 doi:10.1093/database/baw095 (2016). | | ABSTRACT
  • Sophie R. Ullrich, Anja Poehlein, Carolina González, Judith S. Tischler, Francisco Ossandon, Rolf Daniel, David S. Holmes, Michael Schlömann, Martin Mühling. Gene loss and horizontal gene transfer contributed to the genome evolution of the extreme acidophile “Ferrovum”. Front. Microbiol. 7:797. doi: 10.3389/fmicb.2016.00797 (2016). | | ABSTRACT
  • Juan Pablo Cardenas, Raquel Quatrini and David S. Holmes. Aerobic lineages of the oxidative stress response protein rubrerythrin emerged in an ancient microaerobic, (hyper)thermophilic environment. Front Microbiol. Nov 18;7:1822 (2016). | | ABSTRACT
  • J-P Cardenas, R. Quatrini and D. S. Holmes. The Genomics of Acidophiles. Chapter 11, pp 179-197 in Acidophiles, eds R. Quatrini and D. B. Johnson, Caister Academic Press, UK (2016) | | ABSTRACT
  • Alberto J.M. Martin, Calixto Dominguez, J. Sebastian Contreras-Riquelme, David S. Holmes, Tomas Perez-Acle. A graphlet-based metric for the comparison of dynamic Gene Regulatory Networks. Plos One. Oct 3;11(10):e0163497 (2016). | | ABSTRACT
  • Francisco Issotta, Pedro Galleguillos, Ana Moya-Beltrán, Carol S. Davis-Belmar, George Rautenbach, Paulo C. Covarrubias, Mauricio Acosta G., Francisco J. Ossandon, Yasna Contador, David S. Holmes, Sabrina Marín-Eliantonio, Raquel Quatrini, Cecilia Demergasso. Draft genome sequence of chloride-tolerant Leptospirillum ferriphilum Sp-Cl from industrial bioleaching operations in northern Chile. Stand Genomic Sci. 2016 Feb 27;11:19. eCollection (2016). | | ABSTRACT
  • Sophie R. Ullrich, Anja Poehlein, Carolina González, Judith S. Tischler, Francisco Ossandon, Rolf Daniel, David S. Holmes, Michael Schlömann, Martin Mühling. Genome Analysis of the Biotechnologically Relevant Acidophilic Iron Oxidising Strain JA12 Indicates Phylogenetic and Metabolic Diversity within the Novel Genus “Ferrovum”. PLoS One. Jan 25;11(1): e0146832. doi: 10.1371 (2016). | | ABSTRACT
  • Mario Esparza, Eugenia Jedlicki, Mark Dopson, and David S. Holmes. Expression and activity of the Calvin-Benson-Bassham cycle transcriptional regulator CbbR from Acidithiobacillus ferrooxidans in Ralstonia eutropha. FEMS Microbiol Lett. Aug;362(15) (2015). | | ABSTRACT
  • Juan Pablo Cárdenas, Rodrigo Ortiz, Paul R. Norris, Elizabeth Watkin and David S. Holmes. Reclassification of “Thiobacillus prosperus” (Huber and Stetter 1989) as Acidihalobacter prosperus sp. nov., gen. nov., a member of the Ectothiorhodospiraceae. Int J Syst Evol Microbiol. Oct;65(10):3641-3644 (2015). | | ABSTRACT
  • Maria Liljeqvist, Francisco J. Ossandon, Carolina Gonzalez, Sukithar Rajan, Adam Stell, Jorge Valdes, David S. Holmes and Mark Dopson. Metagenomic Analysis Reveals Adaptations to a Cold Adapted Lifestyle in a Low Temperature Acid Mine Drainage Stream. FEMS Microbiol Ecol. 2015 Jan 27. pii: fiv011. [Epub ahead of print]. | | ABSTRACT
  • Juan Pablo Cárdenas, Marcelo Lazcano, Francisco J. Ossandon, Melissa Corbett, David S Holmes and Elizabeth Watkin. Draft genome sequence of the type strain of the iron oxidizing acidophile Leptospirillum ferriphilum DSM 14647T. Genome Announcements. 2014 Nov 6; 2(6). | | ABSTRACT
  • Francisco J. Ossandon, Juan Pablo Cárdenas, Melissa Corbett, Raquel Quatrini, David S. Holmes and Elizabeth Watkin. Draft genome sequence of the iron-oxidizing, acidophilic and halotolerant ‘Thiobacillus prosperus’ type strain DSM 5130. Genome Announcements, 2014 Nov 6;2(6). pii: e01153-14. | | ABSTRACT
  • Harold Nuñez, David Loyola, Juan Pablo Cárdenas, David S Holmes, D. Barrie Johnson, and Raquel Quatrini. Multi Locus Sequence Typing scheme for Acidithiobacillus caldus strain evaluation and differentiation. Research in Microbiology, Aug 28. pii: S0923-2508(14)00116-8, 2014. | | ABSTRACT
  • Ana Moya-Beltrán, Juan Pablo Cárdenas, Paulo Covarrubias, Francisco Issotta, Francisco Ossandon, David Holmes, Raquel Quatrini, and Barrie Johnson. Draft Genome Sequence of the Nominated Type Strain of "Ferrovum myxofaciens": an Acidophilic, Iron-Oxidizing Betaproteobacterium, Genome Announcements, Aug 21;2(4). pii: e00834-14. | | ABSTRACT
  • Mark Dopson and David S. Holmes. Metal resistance in acidophilic microorganisms and its significance for biotechnologies. Appl Microbiol Biotechnol 98(19):8133-8144, 2014. | | ABSTRACT
  • Carolina Gonzalez, María Yanquepe, Juan Pablo Cardenas, Jorge Valdes, Raquel Quatrini, David S. Holmes and Mark Dopson. Genetic variability of psychrotolerant Acidithiobacillus ferrivorans strains revealed by (meta)genomic analysis. (Research in Microbiology, Aug 27. pii: S0923-2508(14)00135-1. doi: 10.1016/j.resmic.2014.08.005, 2014. | | ABSTRACT
  • For the full list of publications, visit Dr. Holmes’ Google Scholar profile: | | ABSTRACT