Center for Bioinformatics &
Genome Biology

Director - Dr. David S. Holmes

Articles, chapters and reports

Publications - 2000 present:

• 2011
• Stefanie Mangold, Jorge Valdés, David S. Holmes and Mark Dopson. Sulfur metabolism in the extreme acidophile Acidithiobacillus caldus (Front. Microbio. 2:17, 2011).

• Liljeqvist M, Valdes J, Holmes DS, Dopson M. Draft Genome of the Psychrotolerant Acidophile Acidithiobacillus ferrivorans SS3. J Bacteriol. 193:4304-5 (2011). .

• Bonnefoy, V. and D. S. Holmes. Genomic insights into microbial iron oxidation and iron homeostasis in extremely acidic environments (in press, Environ. Microbiol. Reports, 2011).

• Lefimil, C., Jedlicki, E. and D. S. Holmes. An artifact in studies of gene regulation using b-galactosidase reporter gene assays. (In press, Anal. Biochem, 2011).

• Raúl R Araya-Secchi, José A Garate, David S Holmes and Tomás Perez-Acle. Molecular Dynamics Study of the Archaeal Aquaporin AqpM (in press,  BMC Genomics, 2011).

• Jorge Valdes, Francisco Ossandon, Raquel Quatrini, Mark Dopson and David S. Holmes. Draft genome sequence of the extreme acidipohillic biomining proteobacterium Acidithiobacillus thiooxidans ATCC 19377 provides insights into the evolution of the Acidithiobacillus genus (in press, J. Bacteriol. 2011).

• 2010
  • Mario Esparza, Juan Pablo Cárdenas, Botho Bowien, Eugenia Jedlicki and David S. Holmes. Genes and pathways for CO2 fixation in the obligate, chemolithoautotrophic acidophile, Acidithiobacillus ferrooxidans. BMC Microbiology 10:229 (2010).

  • J. Valdés, J. P. Cárdenas, R. Quatrini, M. Esparza, H. Osorio, F. Duarte, C. Lefimil, R. Sepulveda, E. Jedlicki and D. S. Holmes. Comparative genomics begins to unravel the ecophysiology of bioleaching. Hydrometallurgy 104: 471-476 (2010).

  • Cárdenas, J. P., Valdés, J., Quatrini, R., Duarte, F. and D. S. Holmes. Lessons from the Genomes of Extremely Acidophilic Bacteria and Archaea with Special Emphasis on Bioleaching Microorganisms. Appl. Micobiol.Biotech. 88: 605-620,   (2010).

• 2009

• Holmes, D. S., Cárdenas, J. P., Valdés, J., Quatrini, R., Esparza, M., Osorio, H., Duarte, F., Lefimil, C. and E. Jedlicki. Comparative Genomics Begins to Unravel the  Ecophysiology of Bioleaching. Adv. Mat. Res. 71-73, 144-150, 2009.

• Valdes, J. H and D. S. Holmes. Genomic Lessons from Biomining Organisms: Case Study of the Acidithiobacillus Genus. Adv. Mat. Res. 71-73, 215-218, 2009.

• Duarte, F, Araya-Secchi, R., González, W., Perez-Acle, T.,  González-Nilo, D. and D. S. Holmes. Protein Function in Extremely Acidic Conditions: Molecular Simulation Studies of a Predicted Aquaporin and a Voltage Gated Potassium Channel in Acidithiobacillus ferrooxidans. Adv. Mat. Res. 71-73, 211-214, 2009.

• Shmaryahu, A. Lefimil, C., Jedlicki, E. and  D. S. Holmes. Small Regulatory RNA Genes in Acidithiobacillus ferrooxidans: case studies of  6S RNA and frr. Adv. Mat. Res. 71-73, 191-194, 2009.

• Castro, M., Ruiz, L., Díaz M., Mamani, S., Jerez, C. A., Holmes D., Guiliani N. C-Di-GMP Pathway in Biomining Bacteria. Adv. Mat. Res. 71-73, 223-226, 2009.

• Ossandón F. J., Lazo F., Rivera G., and D. S. Holmes. Predicting the Function of Hypothetical Genes in Genomes of Bioleaching Microorganisms.Adv. Mat. Res. 71-73, 203-206, 2009.

• Esparza, M., Bowien, B., Holmes, D. S. and E. Jedlicki . Gene Organization and CO2-Responsive Expression of Four Cbb Operons in Acidithiobacillus ferrooxidans. Adv. Mat. Res. 71-73, 207-210, 2009.

• Lefimil C., Osorio H., Quatrini R., Holmes D. and Jedlicki E. Making Crucial Regulatory Decisions in Acidithiobacillus ferrooxidans: Iron Oxidation versus Iron Uptake. Adv. Mat. Res. 71-73, 199-202, 2009.

• Osorio, H., Cárdenas, J.P.  Valdés, J. and  Holmes, D. S Prediction and Experimental Validation of Genes and Metabolic Pathways involved in Anaerobic Growth of Acidithiobacillus ferrooxidans.Adv. Mat. Res. 71-73, 195-198, 2009.

• Cárdenas, J-P., V, Martínez, P. Covarrubias, D. S. Holmes, and R. Quatrini, Predicting CO/CO2 Fixation in Ferroplasma spp. Through a Novel Chimaeric Pathway. Adv. Mat. Res. 71-73, 219-222, 2009.

• Levicán, G., Katz, A., Valdés, J., Quatrini, R., Holmes, D. S.  and O. Orellana. A 300 Kb Genome Segment, including a Complete Set of tRNA Genes, is Dispensable for Acidithiobacillus ferrooxidans. Adv. Mat. Res. 71-73, 187-190, 2009.

• 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 Mol Biol. 2009 Jun 25;10(1):63

• Raquel Quatrini, Corinne Appia-Ayme, Jorge Valdés, Yann Denis, Eugenia Jedlicki David S. Holmes and Violaine Bonnefoy. Extending the Models for Iron and Sulfur Oxidation in the extreme acidophile Acidithiobacillus ferrooxidans. In press.

• Jorge Valdes, Raquel Quatrini, Kevin Hallberg, Stefanie Mangold, Mark Dopson, Pablo D.T. Valenzuela and David S. Holmes. Draft genome sequence of the extremely acidophilic bacterium Acidithiobacillus caldus ATCC 51756 reveals metabolic versatility in the Acidithiobacillus genus. J. Bacteriol. Jul 17. [Epub ahead of print], 2009.

• 2008

• 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).

• Holmes, D. S. Review of International Biohydrometallurgy Symposium, Frankfurt, 2007. Hydrometallurgy, 92: 69-72  (2008).

• 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).

• Uribe, P., Fuentes, D., Valdes,  J., Shmaryahu, A.,  Zuñiga, A., Holmes D. S. and P. D.T. Valenzuela. Preparation and analysis of an expressed sequence tag library from the toxic dinoflagellate Alexandriun catenella. Marine Biotechnology 10:692-700 (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

• 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, 8:203 (2008).

• Valdés, 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).

• 2007

• Quatrini, R., Valdes, J., Jedlicki, 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]
  
  
• uatrini, 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). [Abstract] [Full text]

• 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 Genome Analysis. Advanced Mat. Res. 20-21, 531-534 (2007).

• 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).

• zhepishevska, 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).

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

• 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]
  
  
  

• 2005
  
  
• Felipe Veloso, Gonzalo Riadi, Daniela Aliaga, Ryan Lieph and David S. Holmes. Large Scale, Multi-Genome Analysis of Alternate Open Reading Frames in Bacteria and Archaea. OMICS 9, 91-105 (2005). [Abstract]
  
  
  
• Quatrini, R., Lefimil, C., Holmes, D. S. and E. Jedlicki. The Ferric Iron Uptake Regulator (Fur) from the Extreme Acidophile, Acidithiobacillus ferrooxidans. Microbiology, 151: 2005-2015 (2005). [Abstract] [Full text].
  
  
• Raquel Quatrini, Eugenia Jedlicki and David S. Holmes. Genomic Insights into the Iron Uptake Mechanisms of the Biomining Microorganism Acidithiobacillus ferrooxidans. J. Industrial Microbiology and Biotechnology, 32: 606-614 (2005). [Abstract] [Full text].
  
  
• Marlen Barreto, Eugenia Jedlicki and David S Holmes. A Gene Cluster for the Formation of Extracellular Polysaccharide (EPS) Precursors in the Chemolithoautotroph Acidithiobacilus ferrooxidans. Appl. Environ. Microbiol. 71: 2907-2909 (2005). [Abstract] [Full text].
  
  
• Kathleen L. McGuire and David S. Holmes. The role of complementary proteins in autoimmunity: an old idea reemerges with new twists. Trends in Immunology, 26, 367-372 (2005). [Abstract].
  
  
• Marlen Barreto, Tilman Gehrke, Kerstin Harneit, Wolfgang Sand, Eugenia Jedlicki and David Holmes. Unexpected Insights into Biofilm Formation by Acidithiobacillus ferrooxidans Revealed by Genome Analysis and Experimental Approaches, pp 817-825 in: Proc. 16th International Biohydrometallurgy Symposium, Cape Town, South Africa, 2005, eds S. Harrison, D Rawlings and J. Peterson, Compress www.compress.co.za.
  
  
• Quatrini R, Appia-Ayme C, Denis Y, Ratouchniak J, Veloso F, Valdés J, Lefimil C, Silver S, Roberto F, Orellana O, Denizot F, Jedlicki E, Holmes DS & Bonnefoy V. Global analysis of the ferrous iron and sulfur energetic metabolism of Acidithiobacillus ferrooxidans by microarray transcriptome profiling, pp 761-771 in: Proc. 16th International Biohydrometallurgy Symposium, Cape Town, South Africa, Eds S. Harrison, D Rawlings and J. Peterson, 2005.
  


• Appia-Ayme C, Quatrini R, Denis Y, Denizot F, Silver S, Roberto F, Veloso F, Valdés J, Cárdenas JP, Esparza M, Orellana O, Jedlicki E, Bonnefoy V & Holmes DS. Insights Into The Central Carbon Metabolism Of Acidithiobacillus ferrooxidans Revealed By Bioinformatic And Microarray Analysis, pp 753-760 in: Proc. 16th International Biohydrometallurgy Symposium, Cape Town, South Africa, Eds S. Harrison, D Rawlings and J. Peterson, 2005.
  
  
• Rivas, M., Seeger, M., Holmes, D. S. and E. Jedlicki. A Lux-like quorum sensing system in the extreme acidophile Acidithiobacillus ferrooxidans. Biological Res. 38: 283-297 (2005) [Abstract] [Full text].
  
  
• 2004

• Valdés, J., Jedlicki, E. and Holmes, D. Bioinformatic Analysis of Sulfur Assimilation in Acidithiobacillus ferrooxidans, pp 1187-1194 in: BioHydrometallurgy: A Sustainable Technology in Evolution. Eds: M. Tsezos, A. Hatzikioseyian and E. Remoudaki. National Technical University of Athens, ISBN numbers 960-88415-0-X, 2004.
  
  
• Quatrini, R., Veloso F., Jedlicki E. and D.S. Holmes. Bioinformatic Analysis of Iron Uptake in Acidithiobacillus ferrooxidans, pp 989-996 in: BioHydrometallurgy: A Sustainable Technology in Evolution. Eds: M. Tsezos, A. Hatzikioseyian and E. Remoudaki. National Technical University of Athens, ISBN numbers 960-88415-0-X, 2004.
  
  
• Marlen Barreto, Mariella Rivas, Eugenia Jedlicki and David Holmes. Bioinformatic Analysis of Biofilm Formation in Acidithiobacillus ferrooxidans, pp 1271-1278 in BioHydrometallurgy: A Sustainable Technology in Evolution. Eds: M. Tsezos, A. Hatzikioseyian and E. Remoudaki. National Technical University of Athens, 2004. ISBN numbers 960-88415-0-X
  
  
• Brasseur G, Levican G, Bonnefoy V, Holmes D, Jedlicki E, Lemesle-Meunier D. Apparent redundancy of electron transfer pathways via bc(1) complexes and terminal oxidases in the extremophilic chemolithoautotrophic Acidithiobacillus ferrooxidans. Biochem. Biophys. Acta. 1656:114-126 (2004) [Abstract]
  
  
• 2003

• Barreto M, Quatrini R, Bueno S, Arraigada C, Valdés J, Silver S, Jedlicki E, Holmes DS. Aspects of the predicted physiology of Acidithiobacillus ferrooxidans deduced from an analysis of its partial genome sequence. Hydrometallurgy 71: 97–105. 2003. [Abstract]
  
  
• José Luis Ramírez and David Holmes. The need for Genomics Networking in Latin America. Science Development, 21 Aug. 2003, [Abstract].
  
  
• Valdes, J., Jedlicki E. and David Holmes. Metabolic Reconstruction of Sulfur Assimilation in the Extremophile Acidithiobacillus ferrooxidans Based on Genome Analysis BMC Genomics 4, 2003, online: [Abstract] [Full text].
  
  
• 2002

• Levican, G., P. Bruscella, M. Guacucano, C. Inostroza, V. Bonnefoy, D. S Holmes and E. Jedlicki. Characterization of the petC and resB Operons in Acidithiobacillus ferrooxidans. J. Bacteriol. 184: 1498-1501 (2002). [Abstract] [Full text].
  
  
• Ramírez, J. L., Alicia González, José María Cantú, Pamela Chavez-Crooker, Juan Carlos Leiva, Jenny Blamey, Hernan Cortes and David Holmes. Latin-American Genome Initiative, the Creation of a Network and Web-Based Resource to Aid and Nurture Genome Biology in Developing Countries. Electronic Journal of Biotechnology 5, Dec 15, 2002 accessible at
  
  
• 2001
  

• Holmes, D. S., Zhao, H-L, Levican, G., Ratouchniak, J., Bonneyfoy, V., Varela, P., and Jedlicki E. ISAfe1, an ISL3 Family Insertion Sequence in Acidihiobacillus ferrooxidans. J. Bacteriol. 183: 4323-4329 (2001) [Abstract] [Full text].
  
  
• Holmes, D. S., Barreto, M., Valdes, J., Dominguez, C., Arriagada, C., Silver, S. Bueno, S. and E. Jedlicki. Whole Genome Sequence of Acidithiobacillus ferrooxidans: Metabolic Reconstruction, Heavy Metal Resistance and Other Characteristics. pp 237-251, in Biohydrometallurgy: Fundamentals, Technology and Sustainable Development. eds Ciminelli, V. and O Garcia, Elsevier Press, 2001.
  
• 2000
  

• Selkov, E., R. Overbeek, Y. Kogan, L. Chu, V. Vonstein, D. Holmes, S. Silver and M. Fonstein. Functional Analysis of Gapped Microbial Genomes: Principles with Examples from Thiobacillus ferrooxidans. Proc. Natl. Acad. Sci. U S A. 97: 3509- 3514 (2000) [Abstract] [Full text].
  
  
• Guacucano, M., Levican, G., Holmes D. S. and E. Jedlicki. An RT-PCR Artifact in the Characterization of Bacterial Operons. Electronic Journal of Biotechnology [online]. 15 December vol. 3, No. 3. (2000) [Abstract] [Full text].
  

CC - [Rene S.. 2006] - [ Last update 19/10/2011 ]