Bioinformatics and Genome Biology

PROFILE

The Bioinformatics and Genome Biology Lab carries out basic research in several areas of genome biology and bioinformatics. Current research focusses on the genomics of extremophile organisms including those that live in environments with ultra-low pH, high temperature, and high concentration of salt. Research questions include i) what are the thermodynamic limits of life? ii) how can an understanding of the extraordinary metabolisms of extremophiles suggest models for the emergence of life on Earth? and iii) how can extreme environments on Earth be used as surrogates to search for potential life-supporting habitats on exoplanets and moons (astrobiology)? Other research areas advance our understanding of the evolution of extremophiles and the metabolic potential and the ecophysiological interactions between acidophilic microorganisms involved in the industrial recovery of copper (bioleaching).

LAB MEMBERS

Research Head: David Holmes

Research Assistants: Eva Vergara • Diego Cortez • Gonzalo Neira

FORMER LAB MEMBERS

• Gloria Levicán (former Ph.D. student 2003). Associate Professor, Universidad de Santiago, Chile
• Raquel Quatrini (former Ph.D. student 2004). Lab Head, Fundación Ciencia & Vida, Chile
• Marlen Barreto (former Ph.D. student 2005). Assistant Professor, Universidad Autónoma de Chile
• Mariella Rivas (former Ph.D. student 2006). Associate Investigator, Universidad de Antofagasta, Chile
• Mario Esparza (former Ph.D. student 2009). Research Director, Universidad de Antofagasta, Chile
• Tomás Peréz-Acle (former Ph.D. student 2007). Lab Head, Fundación Ciencia & Vida, Chile
• Jorge Valdés (former Ph.D. student 2011). Associate Professor, Universidad Mayor, Chile
• Claudia Lefimil (former Ph.D. student 2012). Assistant Professor, Universidad de Chile
• Felipe Veloso (former Ph.D. student 2012). Scientific Advisor, Qualus Research, Chile
• Gonzalo Riadi (former Ph.D. student 2012). Assistant Professor, Universidad de Talca, Chile
• Hector Osorio (former Ph.D. student 2013). Postdoc, Pontifical Catholic University of Chile
• Mauricio Arenas (former Ph.D. student 2013). Assistant Professor, Universidad de Talca, Chile
• Francisco Duarte (former Ph.D. student 2013). Research investigator, Hospital Regional de Rancagua, Chile
• Francisco Ossandón (former Ph.D. student 2014). Data Science Manager, Biome Makers Inc., Chile
• Juan Pablo Cárdenas (former Ph.D. student 2015). Assistant Professor, Universidad Mayor, Chile
• Carolina González (former Ph.D. student 2017). Postdoc, Universidad Mayor, Chile
• Roddy Jorquera (former Ph.D. student 2017). Postdoc, Fundación Arturo López Pérez, Chile

COLLABORATIONS

National:
• Dr. Mario Esparza (Universidad de Antofagasta)
• Dr. Jorge Valdés (Universidad Mayor)
• Dr. Raquel Quatrini ( Fundación Ciencia & Vida)
• Dr. Roddy Jorquera (Fundación Arturo López Pérez)

International:

• Dr. Mark Dopson (Linnaeus University, Sweden)
• Dr. Elizabeth Watkin (Curtin University, Australia)
• Dr. Bent Petersen (Technical University of Denmark)

SELECTED PUBLICATIONS

  • Jorquera R, González C, Clausen P.T.L.C., Petersen B and Holmes D.S. "SinEx DB 2.0 update 2020: Database for Eukaryotic Single-Exon Coding Sequences". Database, Volume 2021, 2021, baab002, https://doi.org/10.1093/database/baab002 | | ABSTRACT
  • Khaleque, Himel Nahreen, et al. “Unlocking Survival Mechanisms for Metal and Oxidative Stress in the Extremely Acidophilic, Halotolerant Acidihalobacter Genus”. Genes 11.12 (2020): 1392. | | ABSTRACT
  • Himel N. Khaleque, Carolina González, Barry Johnson, Anna H. Kaksonen, David S. Holmes and Elizabeth L.J. Watkin. "Genome-based classification of “Acidihalobacter prosperus F5” (=DSM 14174 =JCM 32253) as Acidihalobacter yilgarnensisT sp. nov. International Journal of Systematic and Evolutionary Microbiology 70.12 (2020): 6226-6234. | | ABSTRACT
  • Neira, G., Cortez, D., Jil, J., Holmes, D. S. AciDB 1.0: A database of acidophilic organisms, their genomic information and associated metadata. Bioinformatics (Oxford, England) DOI: 10.1093/bioinformatics/btaa638 (2020). | PDF | ABSTRACT
  • Vergara, E., Neira, G., González, C., Cortez, D., Dopson, M., Holmes, D. S. Evolution of Predicted Acid Resistance Mechanisms in the Extremely Acidophilic Leptospirillum Genus. Genes, 11(4), 389. DOI: 10.3390/genes11040389 (2020). | PDF | ABSTRACT
  • Osorio, H., Mettert, E. L., Kiley, P., Dopson, M., Jedlicki, E., Holmes, D. S. Identification and Unusual Properties of the Master Regulator FNR in the Extreme Acidophile Acidithiobacillus ferrooxidans. Frontiers in microbiology, 10, 1642. DOI: 10.3389/fmicb.2019.01642 (2019). | PDF | ABSTRACT
  • Esparza, M., Jedlicki, E., González, C., Dopson, M., Holmes, D. S. Effect of CO2 Concentration on Uptake and Assimilation of Inorganic Carbon in the Extreme Acidophile Acidithiobacillus ferrooxidans. Frontiers in microbiology, 10, 603. DOI: 10.3389/fmicb.2019.00603 (2019). | PDF | ABSTRACT
  • Khaleque, H. N., González, C., Shafique, R., Kaksonen, A. H., Holmes, D. S., Watkin, E. L. Uncovering the mechanisms of halotolerance in the extremely acidophilic members of the Acidihalobacter genus through comparative genome analysis. Frontiers in microbiology, 10, 155. DOI: 10.3389/fmicb.2019.00155 (2019). | PDF | ABSTRACT
  • Khaleque, H. N., González, C., Kaksonen, A. H., Boxall, N. J., Holmes, D. S., Watkin, E. L. Genome-based classification of two halotolerant extreme acidophiles, Acidihalobacter prosperus V6 (= DSM 14174= JCM 32253) and 'Acidihalobacter ferrooxidans' V8 (= DSM 14175= JCM 32254) as two new species, Acidihalobacter aeolianus sp. nov. and Acidihalobacter ferrooxydans sp. nov., respectively. International journal of systematic and evolutionary microbiology, 69(6), 1557-1565. DOI: 10.1099/ijsem.0.003313 (2019). | PDF | ABSTRACT
  • Jorquera, R., González, C., Clausen, P., Petersen, B., Holmes, D. S. Improved ontology for eukaryotic single-exon coding sequences in biological databases. Database, 2018. DOI: 10.1093/database/bay089 (2018). | PDF | ABSTRACT
  • Issotta, F., Covarrubias, P. C., Moya-Beltrán, A., Bellenberg, S., Thyssen, C., Sand, W., Nuñez, H., Mena, C., Holmes, D.S., Quatrini, R., Vera Véliz, M. 16S rRNA and multilocus phylogenetic analysis of the iron oxidizing acidophiles of the acidiferrobacteraceae family. In Solid State Phenomena (Vol. 262, pp. 339-343). Trans Tech Publications Ltd. DOI:10.4028/www.scientific.net/SSP.262.339 (2017). | PDF | ABSTRACT
  • Castro, M., Moya-Beltrán, A., Covarrubias, P. C., Gonzalez, M., Cardenas, J. P., Issotta, F., Salgado, O. A., Acuña, L. G., Encina, G., Holmes, D. S., Johnson, D. B. Draft genome sequence of the type strain of the sulfur-oxidizing acidophile, Acidithiobacillus albertensis (DSM 14366). Standards in genomic sciences, 12(1), 77. DOI: 10.1186/s40793-017-0282-y (2017). | PDF | ABSTRACT
  • Quatrini, R., Escudero, L. V., Moya-Beltrán, A., Galleguillos, P. A., Issotta, F., Acosta, M., Cárdenas, J. P., Nuñez, H., Holmes, D. S., Demergasso, C. Draft genome sequence of Acidithiobacillus thiooxidans CLST isolated from the acidic hypersaline Gorbea salt flat in northern Chile. Standards in Genomic Sciences, 12(1), 84. DOI: 10.1186/s40793-017-0305-8 (2017). | PDF | ABSTRACT
  • Valdebenito‐Maturana, B., Reyes‐Suarez, J. A., Henriquez, J., Holmes, D. S., Quatrini, R., Pohl, E., & Arenas‐Salinas, M. Mutantelec: An In Silico mutation simulation platform for comparative electrostatic potential profiling of proteins. Journal of Computational Chemistry, 38(7), 467-474. DOI: 10.1002/jcc.24712 (2017). | PDF | ABSTRACT
  • 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, doi.org/10.3389/fmicb.2016.02132 (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: https://scholar.google.cl/citations?user=pKM2MPYAAAAJ&hl=en | | ABSTRACT