Center for Bioinformatics &
Genome Biology

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Publications

Publications

Publications - 2000 present:

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)
Jorge Valdés, Inti Pedroso, Raquel Quatrini, Herve Tettelin, Jonathan A. Eisen and David S. Holmes. Acidithiobacillus ferrooxidans Metabolism: From Genome Sequence to Industrial Applications. BMC Genomics (In Press, 2008)

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. 3^rd 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]

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].

Publications prior to 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]

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].

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

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.

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].

Cabrejos, M-E., H-L Zhao, M. Guacucano, S. Bueno, G. Levican, E. Garcia, E. Jedlicki and D. S. Holmes. IST1 Insertional Inactivation of the resB Gene: Implications for Phenotypic Switching in Thiobacillus ferrooxidans. FEMS Microbiol. Lett., 175: 223-229 (1999).

Holmes, D. S. Biotechnology: Miners in miniature. Chemistry and Industry, 1: 20-24 (1999).

Holmes, D. S. , Jedlicki E., Cabrejos M. E., Vasquez O., Guacacano M., Levican, G., Varela P. and Garcia E. The use of insertion sequences to analyze gene function in Thiobacillus ferrrooxidans: a case study involving cytochrome c-type biogenesis proteins in iron oxidation, pp 139-147, in Biohydrometallurgy and the Environment: Toward the Mining of the 21st. Century. Eds. R . Amils and A. Ballester. Elsevier, Amsterdam (1999).

D.S. Holmes. "Biorecovery of Metals from Mining Wastes", pp 517-545 in Bioconversion of Waste Materials to Industrial Products, ed. A.M. Martin. Chapman Hall, London (1998).

Bengrine, N. Guiliani, C. Appia-Ayme, E. Jedlicki and D. S. Holmes, M. Chippaux and V. Bonneyfoy. Sequence and Expression of the Rusticyanin Structural Gene from Thiobacillus ferrooxidans ATCC33023 strain. Biochem. Biophys. Acta. 1443: 99-112 (1998).

S. K. Dubey and D. S. Holmes. Biological cyanide destruction mediated by microorganisms. World Journal of Microbiology and Biotechnology 11: 257-265 (1996).

Holmes, D. S. (1995). "Genetic and Phenotypic Switching Instability in Thiobacillus ferrooxidans and Why These Phenomena Are Important to Understand." pp 85-93 in Minerals Processing II eds. D.S. Holmes and R. W. Smith; TMS Publ.Warrendale, PA, USA.

Holmes, D. S. and R. W. Smith. (1995). "Advances in Mineral Processing." pp ix-xiii in Minerals Processing II, eds D.S. Holmes and R. W. Smith; TMS Publ.Warrendale, PA, USA.

Holmes, D.S. and S. Gangolli. (1995). "A Biosensor that Reports the Bioavailability of Copper Ions and its Use in the Design of New Reagents for Metal Binding." pp159-166 in Biohydrometallurgical Processing, eds C. A. Jerez, T. Vargas, H. Toledo and J. V. Wiertz; University of Chile, Santiago.

Cadiz, R., L. Gaete, E. Jedlicki, J. Yates, D. S. Holmes and O. Orellana. "Transposition of IST2 in Thiobacillus ferrooxidans." Mol. Microbiol. 12: 165-170 (1994).

Holmes, D. S., S. K. Dubey and S. S. Gangolli. "Development of Biosensors for the Detection of Mercury and Copper Ions". Environ. Geochem. & Health. 16: 229- 233 (1994).

Lau, P. C. K., M. Drolet, P. Zanga and D. S. Holmes (1993). "Plasmid Technology for Biomining Applications." pp 635-644 in Biohydrometallurgical Technologies Vol II eds A.E. Torma, M. L. Apel and C. L. Brierley, TMS, Warrendale, PA, USA (1993).

Zhao, H. and D. S. Holmes. "Insertion Sequence ISTI and Associated Phenotypic Switching in Thiobacillus ferrooxidans." pp 667-671 in Biohydrometallurgical Technologies Vol II eds A.E. Torma, M. L. Apel and C. L. Brierley, TMS, Warrendale, PA, USA (1993).

Holmes, D. S. Bioluminescent Biosensors, report for the Office of Naval Research, USA (1993).

Holmes, D. S. "The Story Behind the Development of the Rapid Boil Preparation of Bacterial Plasmids". Scientific Citation Classics 36: 7-8 (1993).

Holmes, D. S., S. K. Dubey and S. Gangolli. "Development of Biosensors to Measure Metal Ion Bioavailability in Mining and Metal Wastes", pp 659-666 in Biohydrometallurgical Technologies Vol II eds A.E. Torma, M. L. Apel and C. L. Brierley, TMS, Warrendale, PA, USA (1993).

Dubey, S. K., S. S. Gangolli and D. S. Holmes. "Development of Biosensors to Measure Metal Ion Bioavailability in Environmental Samples". Northeastern Geol. And Environmental Sci. 15: 188-194 (1993).

H. Bungay, L. Clesceri, Y-H Lin and D. S. Holmes."Metabolism of Toxic Wastes in Auxostat Mode of Continous Culture", Report for The Hazadous Waste Center, Buffalo, New York, USA. (1992).

L. Geiselhart, M. Osgood and D.S. Holmes. "Construction and Evaluation of a Self-Luminescent Biosensor". N.Y. Academy Sci. 646: 53-60 (1992).

D.S. Holmes and K.H Debus "Opportunities for Biological Metal Recovery". pp 57-78 in Minerals Bioprocessing. eds. Ross W. Smith and Manoranjan Misra, Reno, NV ( 1991).

D.S. Holmes. "The Use of DNA Probes for the Identification and Enumeration of Biomining Microorganisms: An Overview for the Non-Specialist", pp. 1-12, in Bioleaching: From Molecular Biology to Industrial Applications, eds R. Badilla-Ohlbaum, T. Vargas, L. Herrera.Editorial Universitaria, Santiago, Chile, (1991).

D.S. Holmes and K.H. Debus. "Biological Opportunities for Metal Recovery", pp. 341-358, in Biotechnology for Energy, Eds. K.A. Malik, S.H.M. Naqui and M.I.H. Aleem. NIAB Press, Faisalabad, Pakistan, (1991).

D.S. Holmes "Biohydrometallurgy" pp 44-46 in McGraw Hill Yearbook of Science and Technology (1991).

D.S. Holmes. "Biorecovery of Waste Materials from Mining Operations", Elsevier pp. 441-474 in Bioconversion of Waste Materials to Industrial Products, ed. A.M. Martin. Elsevier, London (1991).

D.S. Holmes and J.R. Yates. "Basic Principles of Genetic Manipulation of Thiobacillus ferrooxidans for Biohydrometallurgical Applications", pp. 29-54 in Microbial Mineral Recovery, eds H.L. Ehrlich and C.L. Brierley. McGraw Hill Publ. Co., N.Y. (1990).

J. Retamel and D.S. Holmes et al.. "Lixiviacion Bacteriana". Programma de las Naciones Unidas. Report for UNDP, Santiago, Chile. (1991).

D.S. Holmes and R. Haq. "Adaptation of Thiobacillus ferrooxidans for Industrial Applications", pp. 115-127 in Biohydrometallurgy ed., J. Salley, R.G.L. McCready and P.L. Wichlacz. Canmet, Ottawa, Canada (1990).

D.S. Holmes. "Genetic Engineering of Microorganisms for Pollution Control", pp. 29-39 in "Hazardous Waste Treatment: Biosystems for Pollution Control". Air & Waste Management Assoc., Pittsburgh, PA (1989).

D.S. Holmes. "Biotechnology in the Mining and Metal-Processing Industries. Challenges and Opportunities", Minerals Metallurgical Processing. 5: 49-56 (1988).

J.R. Yates, R.R. Cunningham and D.S. Holmes. "IST2: A New Insertion Sequence in Thiobacillus ferrooxidans", Proc. Natl. Acad. Sci. USA. 85: 7284-7287 (1988).

J. Schrader and D.S. Holmes. "Phenotypic Switching of Thiobacillus ferrooxidans", J. Bacteriol. 170: 3915-3923 (1988).

D.S. Holmes, J.R. Yates, J. Schrader and R. Ul Haq. "The Use of Thiobacillus ferrooxidans for Metal-Recovery: Problems and Prospects", Applications of Genetic Engineering, Lahore Press, Pakistan, pp. 19-26 (1988).

D.S. Holmes, J.R. Yates and J. Schrader. "Mobile Repeated DNA Sequences in Thiobacillus ferrooxidans and their Significance for Biomining", In: Biohydrometallurgy, P.R. Norris and D.P. Kelley eds., pp. 153-160 (1988). Science and Tech. Letters.

D.S. Holmes. "Molecular Enzyme Engineering", In: Advanced Biochemical Engineering. H.R. Bungay and G. Belford, eds., Wiley, New York, Sciences, Inc., pp. 129-165 (1987).

C.L. Spiro, D.S. Holmes, J.H., Lobos and D.H. Maylotte. "X-Ray Computed Tomographic Assay in in situ Microbial Desulfurization of Lump Coal", p 27-28, In: Industrial and Engineering Chemistry, 1st Int. Symp. on Separation Sciences, 191st Am. Chem. Soc. Meet., April 1986 (1987).

T.K. Leib amd D.S. Holmes. "Designed Metal-Binding Proteins", Biotech. 87: 208-215 (1987).

J.R. Yates and D.S. Holmes. "Two Families of Repeated DNA Sequences in Thiobacillus ferrooxidans", J. Bacteriol., 169: 1861-1870 (1988).

C.L.Spiro, D.S. Holmes, J.H. Lobos and D.H. Maylotte. "Use of X-ray Computed Tomographic to Examine Microbial Desulfurization of Lump Coal", J. Energy and Fuels 1: 76-79 (1987).

T.K. Leib, T-M Su and D.S. Holmes. "Metal-binding Proteins for Strategic Metal Recovery and Metal Detoxification", Energy Res. Abstr. 11: 32796-32807 (1986).

D.S. Holmes. "Biotechnological Considerations for Designed Metal-Recovery Operations", R.M.L. McCready, ed., Biominet Proc. Energy, Mines and Resources Conf., Canada, Report SP85/6, pp. 25-36 (1986).

T-M Su and D.S. Holmes. "A Novel Technique for On-Line Detection of Cupro-protein by HPLC", Proc. Int. Sump. on HPLC of Proteins and Peptides, Toronto, Canada. 1985 (1986).

D. Maylotte, C.L. Spiro, J.H. Lobos and D.S. Holmes. "A Study of Thiobacillus ferrooxidans Penetration Depth into Lump Coal Using X-Ray Computed Tomography", In: Fundamental and Applied Biohydrometallurgy, R.W. Lawrence, R.M.R. Branion and H.G. Ebner, eds., Elsevier Science Publ., Amsterdam, The Netherlands, pp. 483 (1986).

H. Ehrlich and D.S. Holmes. "Biotechnology for Mining, Metal-Refining Fossil Fuel Processing Industries", Biotechnol. Bioeng. Symp. 16: 2-3 (1986), ISBN: 0471851027)

J. R. Yates and D.S. Holmes. "Construction and Use of Molecular Probes to Identify and Quantitate Bioleaching Microorganisms", R.M.R. Branion and H.G. Ebner, eds., Fundamental and Applied Biohydrometallurgy , Elsevier Science Publ., Amsterdam, The Netherlands, pp. 409-418 (1986).

J.R. Yates and D.S. Holmes. "Molecular Probes for the Identification and Quantification of Microorganisms found in Mines and Mine Tailing", Biotechnol. Bioeng. Symp. 16: 310-319 (1986).

D.S. Holmes, J.R. Yates, J.H. Lobos and M.V. Doyle. "Strategy for the Establishment of a Genetic System for the Acidophilic Heterotroph, Acidiphilium organovorum", Biotech. Appl. Biochem, 8: 1-11 (1986).

J.R. Yates, J. H. Lobos and D.S. Holmes. "The Use of Genetic Probes to Detect Microorganisms in Biomining Operations", J. Ind. Microbiol. and Biotechnology 1: 129-135 (1986).

J.H. Lobos, T.E. Chisholm, L.H. Bopp and D.S. Holmes, "Acidiphilium organovorum sp. nov., An Acidophilic Heterotroph Isolated from a Thiobacillus ferrooxidans Culture", Int. J. Syst. Bacteriol. 36: 139-144 (1986).

T-M Su and D.S. Holmes. "A Novel Technique for the Detection of Copper-Containing Proteins", R.H. Sarma, ed., 4th Conversation in Biomolecular Stereodynamics, Adenine Press, Albany, NY, pp 317-318 (1985).

D. S. Holmes, J.R. Yates, J.H. Lobos and M.V. Doyle. "Genetic Engineering of Biomining Organisms", Biotech. 84, 67-84 . Online Publications, New York, NY (1984).

• D.S. Holmes. "Improved Rapid Heating Technique for Screening Recombinant DNA Plasmids in E. coli", Biotechniques 2: 68-69 (1984).

D.S. Holmes, J.H. Lobos, L.H. Bopp and G.C. Welch. "Cloning of a Thiobacillus ferrooxidans Plasmid in E. coli.", J. Bacteriol., 157: 324-326 (1984).

D.S. Holmes. "The Cot Curve", Trends in Biochemistry. 8: 437 (1984).

D.S. Holmes. "Biotechnology: Applications for Microbiology", Am. Soc. Microbiol. Eastern New York Branch Newsletter, Nov.-Dec., pp. 2-3 (1983).

D.S. Holmes, J.H. Lobos, L.P. Bopp and G.C. Welch. "Setting up a de novo Genetic System for Studying the Acidophilic Bacterium Thiobacillus ferrooxidans", GE Report 83CRD160 (1983).

D.S. Holmes, J.H. Lobos, L.H. Bopp and G.C. Welch. "Setting Up a Genetic System de novo for Studying the Acidophilic Thiobacillus T. ferrooxidans", In: Recent Progress in Biohydrometallurgy. G. Rossi and A.E. Torma, eds., Associazione Mineroria Sarda Inglesias, Italy, pp. 541-544 (1983).

A.J. Eisenberg and D.S. Holmes. "A Note on the Use of CsCl Centrifugation to Purify Bacterial Plasmids Prepared by the Rapid Boiling Method", Anal. Biochem. 127, 434 (1982).

D.S. Holmes. "Rapid Purification of Bacterial Plasmids and Colifage M13 RF Without CsCl Centrifugation", Anal. Biochem. 127: 428-439 (1982).

Bush and D.S. Holmes. "The Use of Agar for Electrophoresis of DNA Fragments", Anal. Biochem. 119: 164-166 (1982).

D.S. Holmes and M. Quigley. "A Rapid Method for Plasmid DNA Preparations", Focus 3, 2 (1981).

D.S. Holmes and M. Quigley. "Rapid Plasmid Preparation", Biotechnology News 1, 4 (1981).

D.S. Holmes and M. Quigley. "A Rapid Method for the Preparation of Plasmids", Anal. Biochem. 114: 193-197 (1981).

H. Grimmond and D.S. Holmes. "Specific Increase of Perchloric Acid Extractable Chromosomal Proteins During Mammalian Erythropoieses", Comp. Biochem. Physiol. 698: 303-306 (1981).

W. Colquhoun and D.S. Holmes. "Structure of the Chromosomal Material in Inactive Nuclei of Chicken Red Blood Cells", Chromosoma 79: 159-167 (1980).

S. Bodansky, L.B. Mintz and D.S. Holmes. "The Mesokaryote Gyrodinium cohnii Lacks Nucleosomes", Biochem. Biophys. Res. Commun. 88: 1329-1336 (1979).

M. Pellegrini, D.S. Holmes and J. Manning. "Applications of the Avidin biotin Methods of Gene Enrichment to the Isolation of Long Double-Stranded DNA Containing Specific Gene Sequences", Nucleic Acids Res. 9: 2961-2973 (1977).

D.S. Holmes, N. Davidson, R.H. Cohn and L.H. Kedes. "Positions of Sea Urchin Histone Genes Relative to Restriction Endonuclease Sites on the Chimeric Plasmids pSp2 and pSp17", Biochemistry 16: 1504-1512 (1977).

M. Wu, D.S. Holmes, N. Davidson, R.H. Cohn and L.H. Kedes. "The Relative Positions of the Coding and Spacer Regions on Sea Urchin Histone Genes on the Chimeric Plasmids pSp2 and pSp17 as Studies by Electron Microscopy", Cell 9: 163-169 (1976).

D.S. Holmes and J. Bonner. "Interspersion of Repetitive and Single Copy Sequences in High Molecular Weight Nuclear RNA", Proc. Natl. Acad. Sci. USA 71: 1108-1112 (1974).

D.S. Holmes, J.E. Mayfield and J. Bonner. "Sequence Composition of Chromosomal RNA", Biochemistry 13, 849-855 (1974).

D.S. Holmes and J. Bonner. "Sequence Composition of Rat Nuclear DNA and High Molecular RNA", Biochemistry 13: 841-848 (1974).

D. S. Holmes and J. Bonner. "Sequence Composition and Organization of the Genome and Nuclear RNA of Higher Organisms: An Approach to Understanding Gene Regulation". In: The Role of RNA in Development, M. Niu and S. Segal, eds., American Elsevier Publishing Co., Inc., New York, NY, pp. 204-323 (1973).

S. Holmes. Sequence Composition and Organization of the High Molecular Weight Nuclear RNA of Rat. Ph.D thesis, California Institute of Technology (1973)

• D.S. Holmes and J. Bonner. "Preparation, Molecular Weight, Base Composition and Secondary Structure of Giant Nuclear RNA", Biochemistry 12: 2322-2329 (1973).

D.S. Holmes, J.E. Mayfield, G. Sander and J. Bonner. "Composition and Secondary Structure of Giant Nuclear RNA", Biochemistry 12: 2330-2338 (1973).

S. Holmes, J.E. Mayfield and J. Bonner. Chromosomal RNA: its properties. Science, 177: 72-74 (1973)

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