Center for Bioinformatics &
Genome Biology

Papers

2008

Pedroso, I., Rivera, G., Lazo, F., Chacon, M., Ossandon, F., Veloso, F. A. and Holmes, D.S. AlterOrf: A Database of Alternate Open Reading Frames. Nucleic Acid Res. D517-8, 2008.[PubMed]

Holmes, D. S. Superando los Principales Impedimentos para la Adopción Extendida de la e-Ciencia en Chile: ¿Qué Queda por Hacer? (Surmounting Impediments to the Widespread Adoption of e-Science in Chile: What remains to be Done?) Editorial, REDenACCIÓN # 17, Oct., 2008. [Spanish][English] Holmes, D.S. Review of International Biohydrometallurgy Symposium, Frankfurt, 2007. Hydrometallurgy. 92: 69-72, 2008.[Abstract]

Valdés, J., Pedroso, I., Quatrini, R. And D.S. Holmes. Comparative Genome Analysis of Acidithiobacillus ferrooxidans, A. thiooxidans and A. caldus: Insights into their Metabolism and Ecophysiology. Hydrometallurgy. 94: 180-184, 2008.

Osorio, H., Martínez, V., Veloso, F. A., Pedroso, I., Valdés, J., Jedlicki, E., Holmes, D. S. and R. Quatrini. Iron Homeostasis Strategies in Acidophilic Iron Oxidizers: Studies in Acidithiobacillus and Leptospirillum. (Hydrometallurgy, 94:175-179 2008) [FullText]

Paulina Uribe, Daniela Fuentes, Jorge Valdes, Amir Shmaryahu, Alicia Zuñiga, David S. Holmes and Pablo D.T. Valenzuela. Preparation and analysis of an expressed sequence tag library from the toxic dinoflagellate Alexandriun catenella. (e-version available), Marine Biotechnology, 2008.[PubMed]

Osorio, H., Martínez, V., Nieto, P. A., Holmes, D. S. and R. Quatrini. Microbial iron management mechanisms in extremely acidic environments: comparative genomics evidence for diversity and versatility. BMC Microbiology (Accepted, 2008)

JValdés, J., Pedroso, I., Quatrini, R., Tettelin, H., Eisen, J. A.  and D. S. Holmes. Acidithiobacillus ferrooxidans Metabolism: From Genome Sequence to Industrial Applications. BMC Genomics, 9:597 (2008)

Holmes, D. S. Superando los Principales Impedimentos para la Adopción Extendida de la e-Ciencia en Chile: ¿Qué Queda por Hacer? (Surmounting Impediments to the Widespread Adoption of e-Science in Chile: What remains to be Done?) Editorial, REDenACCIÓN # 17, Oct., 2008. www.reuna.cl/documentos/redenaccion/REDenACCION_17_octubre2008.pdf

Nieto, P. A., Covarrubias, P. C., Jedlicki, E., Holmes, D. S. and R. Quatrini. Selection and evaluation of reference genes for improved interrogation of microbial transcriptomes: case study with the extremophile Acidithiobacillus ferrooxidans. BMC Microbiology (under review, 2009).

2007

Quatrini, R., Valdes, J., Jedlicki, E. and D. Holmes. cki, E. and D. Holmes. The Use of Bioinformatics and Genome Biology to Advance Our Understanding of Bioleaching Microorganisms, pp 221-239 in “Microbial Processing of Metal Sulfides” eds. E. Donati and W. Sand. Springer (2007). [Abstract]

Bruscella, P., Appia-Ayme, C., Levicán, G., Ratouchniak, J., Jedlicki, E., Holmes, D. S., and V.Bonnefoy. Differential expression of two bc1 complexes in the acidophilic chemolithoautotrophic bacterium Acidthiobacillus ferrooxidans suggests a model for their respective roles in iron or sulfur oxidation. Microbiology, 153: 102-110, 2007. [Abstract]

Mariella Rivas, Michael Seeger, Eugenia Jedlicki, David S. Holmes. A second acyl homoserine lactone (AHL) producing system in the extreme acidophile, Acidithiobacillus ferrooxidans. Appl. Environ. Microbiol. (PMID:17351095 [PubMed, 2007). [Abstract]

Quatrini, R., Lefimil, C., Veloso, F., Pedroso, I., D. S. Holmes and Jedlicki, E. Bioinformatic prediction and experimental verification of Fur-regulated genes in the extreme acidophile Acidithiobacillus ferrooxidans. Nuc. Acid Research (MID: 17355989 [PubMed, 2007). [Full text]

Rivas, M., Seeger, M., Jedlicki, E. and Holmes, D. S. A second acyl homoserine lactone (AHL) producing system in the extreme acidophile, Acidithiobacillus ferrooxidans. Appl. Environ. Microbiol. 73: 3225-3231 (2007).[Abstract]

Quatrini, R., Martínez, V., Osorio, H., Veloso, F. A., Pedroso, I., Valdés, J., Jedlicki, E. and Holmes, D. S. F. A., Pedroso, I., Valdés, J., Jedlicki, E. and Holmes, D. S. Iron Homeostasis Strategies in Acidophilic Iron Oxidizers, 439-442 (2007).[Abstract]

Valdés, J., Pedroso, I., Quatrini, R., Hallberg, K., Valenzuela, P. T. D. and Holmes, D. S. Valdés, J., Pedroso, I., Quatrini, R., Hallberg, K., Valenzuela, P. T. D. and Holmes, D. S. Insights into the Metabolism and Ecophysiology of Three Acidithiobacilli Species by Comparative , 531-534 (2007).[Abstract]

Shmaryahu, A. and Holmes, D. S. Discovery of Small Regulatory RNAs in the Extremophile Acidithiobacillus Genus Suggests Novel Genetic Regulation. Advanced Mat. Res. 20-21, 535-538 (2007).[Abstract]

Holmes, D. S., González-Nilo, F., Perez, T. and R. Isea. Holmes, D. S., González-Nilo, F., Perez, T. and R. Isea. Virtual Institute for Integrative Biology (VIIB) (Proc. 3rd EELA Congress, 2007, www. www.eu-eela.org/3_conference , pp111-120) [Abstract]

Pedroso, I., Rivera, G., Lazo, F., Chacón, M., Ossandón, F., Veloso, F. A. and Holmes, D. S. AlterOrf: A Database of Alternate Open Reading Frames(Nucleic Acid Res. D517-8, 2008). [Abstract]

Rzhepishevska, O., Valdés, J., Marcinkeviciene, L., Gallardo, C. A., Meskys, R., Bonnefoy, V., Holmes, D. S. and Dopson, M. Regulation of a Novel Acidithiobacillus caldus Gene Cluster Involved in Reduced Sulfur Compound Metabolism. Appl. Environ. Microbiol. 73: 7367-7372 (2007). [Abstract]

2006

Quatrini., R., Appia-Ayme, C., Denis, Y., Ratouchniak, J., Veloso, F., Valdes, J., Lefimil, C., Silver, S., Roberto, F., Orellana, O., Denizot, F., Jedlicki, E., Holmes D. S., Bonnefoy, V. Insights into the Iron and Sulfur Energetic Metabolism of Acidthiobacillus ferrooxidans by Microarray Transcriptome Profiling, Hydrometallurgy ,83: 263-272, (2006). [Abstract]

Appia-Ayme C, Quatrini R, Denis Y, Denizot F, Silver S, Roberto F, Veloso F, Valdes J, Cárdenas JP, Esparza M, Orellana O, Jedlicki E, Bonnefoy V, Holmes DS. Microarray and Bioinformatic Analyses Suggest Models for Carbon Metabolism in the Autotroph Acidithiobacillus ferrooxidans, Hydrometallurgy,83: 273-280, (2006). [Abstract]

Silva, E., Valdés, J., Holmes, D., Shmaryahu, A. and Pablo D. T. Valenzuela. Generation and analysis of expressed sequence tags from Botrytis cinerea. Biol Res 39: 367-376, 2006. [Abstract] [Full text]

Holmes, D and V. Bonnefoy. Genetic and Bioinformatic Insights into Iron and Sulfur Oxidation Mechanisms of Bioleaching Organisms, pp 281-307 in: “Biomining” eds. D. Rawlings and B. Johnson. Springer-Verlag, Berlin (2006). [Abstract]

Lieph, R., Veloso, F. and D. S. Holmes. Thermophiles like Hot T. Trends Microbiol. 14: 423-426 (2006). [Abstract]

Holmes, D. S and G. Mora. Taking the Pulse of Latin American Microbiology. (Int. J. Micriobiol., 9: 306-308, 2006). [Full text]