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David Salway Holmes

Head, Laboratory of Bioinformatics and Genome Biology

FUNDACION CIENCIA & VIDA

Santiago, Chile

Bioinformatics; Genome Biology; Molecular Microbiology and Evolution; Molecular Biology; Microbiology, Astrobiology, Extremophile Microbiology

Biochemistry, CALIFORNIA INSTITUTE OF TECHNOLOGY. Estados Unidos, 1973
Genetics, UNIVERSITY OF DUBLIN, TRINITY COLLEGE. Irlanda, 1969

Full Professor Full Time

UNIVERSIDAD ANDRES BELLO

Santiago, Chile

2004 - 2018
Laboratory Head Full Time

Fundación Ciencia & Vida

Santiago, Chile

2004 - A la fecha
Full Professor Full Time

UNIVERSIDAD DE SANTIAGO DE CHILE

Santiago, Chile

1996 - 2004
Full Professor Full Time

UNIVERSIDAD DE CHILE

Santiago, Chile

1994 - 1996
Full Professor Full Time

CLARKSON UNIVERSITY

New York, Estados Unidos

1990 - 1994
Research Professor Full Time

Rensselaer Polytechnic Institute

New York, Estados Unidos

1988 - 1990
Assistant Professor Full Time

State University of New York

New York, Estados Unidos

1976 - 1980
Full Professor Full Time

Universidad Mayor

Facultad de Ciencias

Santiago, Chile

2019 - 2021

Head, Laboratory Bioinformatics and genome Biology Full Time

Fundación Ciencia & Vida

Santiago, Chile

2004 - A la fecha
Staff Scientist Full Time

General Electric Company

New York, Estados Unidos

1981 - 1988

Hiram Grimmond, Ph.D., "Chromatin Structural Studies", 1981
Steven Bodansky, M.S., "Chromatin Analysis of Gyrodinium sp.", 1982
Diane Rusigay, M.S., "Organization of Histone Genes", 1982
Christopher Bush, M.S., "Studies on Gel Electrophoresis", 1982
James Yates, Ph.D., "Repetitive Sequences in Thiobacillus ferrooxidans", 1989
Lisa Gieselhart, M.S., "Construction of a Mercury Biosensor", 1989
Todd Armstrong, M.S., "A Model Genetically Engineered Biosensor", 1989
Lu Zhao, M.S., "A Biosensor Based on Lux-LacZ Fusions", 1993
Farough Mahdahvi, M.S., "A Biosensor for Biphenol and PCBs", 1993
Huiling Zhao, Ph.D., "IST1: A New Insertion Sequence in Thiobacillus ferrooxidans", 1993
Seema Gangolli, M.S., "Construction and Evaluation of a Copper Biosensor", 1994
Minning Wu, M.S., "Studies on the Rusticyanin Gene of Thiobacillus ferrooxidans", 1994
Laurie Romanow, M.S., "Studies of Antibiotic Activity Using Biosensors", 1994
Gloria Levican, Ph.D, “Iron and Sulfur Oxidation in the Extremophile Acidithiobacillus ferrooxidans”, 2003
Raquel Quatrini, Ph.D, "Iron uptake and Homeostasis in the Extremophile Acidithiobacillus ferrooxidans: Gene regulation by Fur", 2004
Marlen Barreto, Ph.D, "Bioinformatic and Experimental Studies of Biofilm Formation in Acidithiobacillus ferrooxidans", 2005
Rodrigo Sagredo, M.S., (co-tutor with Dr. Max Chacón), "HMMProm: Búsqueda de promotores dependientes del factor Sigma70 mediante Modelos Ocultos de Markov", 2005
Rodrigo Guerrero, M.S., (co-tutor with Dr. Max Chacón), "Búsqueda de promotores en organismos procariontes mediante redes neuronales", 2005
Claudio Días, M.S., "Bioinformatic Analysis of Palindromic Sequences in Proteins", 2005
Maxamiliano Santa Ana, M.S., (co-tutor with Dr. Max Chacón), "La predicción de operones en Acidithiobacillus ferrooxidans", 2006
Mariella Rivas, Ph.D, "Estudio de la regulación "quorum sensing" en Acidithiobacillus ferrooxidans", 2006
Gustavo Rivera, M.S., (co-tutor with Dr. Max Chacón), "Implementación y Optimización de Software de Predicción de Promotores en Organismos Procariontes", 2007
Tomás Peréz, Ph.D, (co-tutor with P. Valenzuela), "Aplicaciones de Tecnología Bioinformática al Estudio de Fenómenos Biológicos", 2007
Felipe Lazo, M.S., (co-tutor with Dr. Max Chacón), "Análisis de Proveniencia Génica mediante Métodos de Agrupamiento", 2008
Mario Esparza, Ph.D, (co-tutor with Dr. Eugenia Jedlicki), "Función del regulador transcripcional CbbR durante la fijación de CO2 en la bacteria biolixiviante Acidithiobacillus ferroooxidans", 2009
Amir Shmaryahu, Ph.D, "Predicción bioinformática y validación experimental de genes RNA reguladores pequeños en la bacteria extremófila Acidithiobacillus ferrooxidans", 2010
Jorge Valdés, Ph.D, "Análisis Genómico-Comparativo de Bacterias Biolixiviantes del Género Acidithiobacillus: de la Secuencia Genómica a Rol Fisiológico", 2011
Claudia Lefimil, Ph.D, (Co-tutor Eugenia Jedlicki), "Regulación de los niveles intracelulares del represor transcripcional Fur en Acidithiobacillus ferrooxidans", 2012.
Felipe Veloso, Ph.D, "Análisis comparativo de la evolución de los genes", 2012.
Gonzalo Riadi. Ph.D, "Bioinformatic studies of bacterial mobile elements", 2012
Hector Osorio, Ph.D, "Investigaciones Bioinformáticas y Experimentales para el Análisis del Regulador Maestro FNR de Acidithiobacillus ferrooxidans en la Anaerobiosis", 2013
Mauricio Arenas, Ph.D, (Co-tutor Raquel Quatrini), "Modeling Fur from Acidithiobacillus ferrooxidans", 2013
Francisco Duarte, Ph.D, "Global comparative analysis of extra-cytoplasmic proteins in extremely acidophilic bacteria", 2013
Francisco Ossandón, Ph.D, "Generación de una base de datos (AlterORF) para mejorar el conocimiento y anotación genómica de los organismos secuenciados a través de sus marcos de lectura alternativos", 2014
Juan Pablo Cárdenas, Ph.D, (Co-tutor Raquel Quatrini), "Estudio genómico-comparativo de la respuesta a estrés oxidativo en organismos acidófilos: modelos de función, regulación y evolución", 2015
Carolina González, Ph.D, (Co-tutor, Jorge Valdés), "Estudio de la Ecofisiología y Evolución del Género Acidithiobacillus mediante Enfoques Genómicos", 2017
Gonzalo Neira, M.S., "Evolucio?n del estilo de vida acido?filo en el filo ancestral Verrucomicrobia", 2019
Joaquin Jil Basoalto, Lic., "Plataforma Web para el análisis y clasificación de organismos acidófilos", 2020
Pedro Sepúlveda Rebolledo, Ph.D, (co-tutor, Tutor Jorge Valdés), "A comparative assessment of Metabolic and Regulatory Modules in the Extremely Acidophilic Acidithiobacillus genus: Insights into Anaerobic Metabolism", 2022
Diego Ignacio Rivera Derpich, Lic. (Co-tutor with Carolina González), "Estudio del rol de proteínas expuestas de Acidithiobacillia en ambientes ácidos mediante análisis bioinformáticos", 2022

More than 470 invited and contributed oral presentations and posters at conferences in 25 countries.

Member of the American Society for Microbiology International Committee

American Society for Microbiology

Estados Unidos, 2003

Member of the American Society for Microbiology International Committee, 2003-2006
Member of the American Society for Microbiology International Committee

American Society for Microbiology

Chile, 2006

Member of the American Society for Microbiology International Committee, 2006-2009
Latin American Consul for Chile

American Society for Microbiology

Chile, 2003

Latin American Consul for Chile, American Society for Microbiology, 2003-2005
International Advisory Board

Sociedad Iberoamericana de Bioinformática

México, 2016

International Advisory Board, SoiBio Latin American Bioinformatics Congress, Mexico, April, 2016
International Advisory Board

Institut Teknologi Bandung

Indonesia, 2015

International Advisory Board, Biohydrymetallurgy Congress, Bali, Indonesia, Oct. 2015
International Advisory Board

UNIVERSIDAD DE SANTIAGO DE CHILE

Chile, 2015

International Advisory Board, International Thermophiles Congress, Chile, Aug. 2015
Elected Fellow

American Academy of Microbiology

Estados Unidos, 2015

Elected Fellow American Academy of Microbiology, Feb. 2015
International Advisory Board

Department of Chemistry and Bioengineering

Chile, 2013

International Advisory Board, Biohydrometallurgy Congress, Chile, Oct. 2013
Member Scientific Committee

Asociación Argentina de Bioinformática y Biología Computacional (A2B2C)

Chile, 2013

Member Scientific Committee, 4th Congresso Asociación Argentina de Bioinformática y Biología Computacional (A2B2C), Argentina, Oct., 2013.
International Advisory Board

MONTANA STATE UNIVERSITY

Estados Unidos, 2011

International Advisory Board, International Thermophiles Congress, Montana, Sept. 2011
International Advisory Board

CENTRAL SOUTH UNIVERSITY

China, 2011

International Advisory Board, 19th International Biohydrometallurgy Symposium (IBS2011), China, Sept. 2011
International Advisory Board

UNIVERSIDAD DE TALCA

Chile, 2010

International Advisory Board, 1st International Conference on Bioinformatics SoIBio, Chillán, Chile. Sept. 2010
International Advisory Board

EMBnet/CNB, Centro Nacional de Biotecnología, CSIC.

México, 2009

International Advisory Board, RIB-EMBNet Bioinformatics Congress, Cancun, Mexico, 2009
International Advisory Board

Centro de Investigación y Desarrollo en Fermentaciones Industriales

Argentina, 2009

International Advisory Board, Biohydrometallurgy Congress, Argentina, 2009
Outstanding Service Award

American Society for Microbiology

Estados Unidos, 2009

Outstanding Service Award, International Board, Am. Soc. for Microbiol. 2009
Chairman

PONTIFICIA UNIVERSIDAD CATOLICA DE CHILE

Chile, 2008

Chairman, 5th RIB Conference (Red Iberoamerica de Bioinformática), Santiago, Chile, Oct. 2008
Scientific Advisory Board

RED UNIVERSITARIA NACIONAL REUNA

Chile, 2008

Scientific Advisory Board, 3er Congreso Nacional de e-Cienca, Santiago, Mayo, 2008
International Advisory Board

UNIVERSIDADE DO PORTO

Portugal, 2008

International Advisory Board, IberiGRID Conference, Universidade do Porto, Portugal, May12 -14, 2008
Scientific Advisory Board

RED UNIVERSITARIA NACIONAL REUNA

Chile, 2007

Scientific Advisory Board, 2do Congreso Nacional de e-Ciencia, Santiago, Sept., 2007
Scientific Advisory Board

DECHEMA

Alemania, 2007

Scientific Advisory Board, Biohydrometallurgy Congress, Germany, Sept, 2007
Local Scientific Committee

Asociación Latinoamericana de Microbiología

Chile, 2006

Local Scientific Committee, Congreso Latinoamericano de Microbiologia, Pucon, Oct., 2006
Scientific Advisory Board

RED UNIVERSITARIA NACIONAL REUNA

Chile, 2006

Scientific Advisory Board, 1er Congreso Nacional de e-Ciencia, Santiago, Sept., 2006
Planning Committee

UNIVERSIDAD DE TALCA

Chile, 2005

Planning Committee, Workshop: From Structure to Function, Talca, Chile, Oct., 2005
International liason officer

Red Iberoamericana de Bioinformática

Chile, 2003

International liason officer, Red Iberoamericana de Bioinformática 2003-present
International Advisory Board

National Technical University of Athens

Grecia, 2003

Internat. Advisory Board, Biohydrometallurgy Conference, Greece, 2003.
International Advisory Board

UNIVERSIDADE FEDERAL DE MINAS GERAIS

Brasil, 2001

Internat. Advisory Board, Biohydrometallurgy Conference, Brazil, 2001
International Advisory Board

Engineering Foundation

Suecia, 1999

Internat. Advisory Board, Engineering Foundation Conference, Sweden, 1999
Chairman

Biohydrometallurgy Conference

España, 1999

Chairman, Microbial Physiology Session, Biohydrometal. Conference, Spain, 1999.
International Advisory Board

Biohydrometallurgy Conference

Chile, 1999

Internat. Advisory Board, Biohydrometallurgy Conference, Spain, 1999
Chairman and Organizer

SOCIEDAD DE MICROBIOLOGÍA DE CHILE

Chile, 1996

Chairman and Organizer, Round Table, Microbiol Soc. Conference, Chile, 1996
Chairman

UNIVERSIDAD DE CHILE

Chile, 1995

Chairman, Mining Effluent Treatment Session, Biohydrometallurgy Conference, Chile, 1995.
International Advisory Board

UNIVERSIDAD DE CHILE

Chile, 1995

International Advisory Board, Biohydrometallurgy Conference, Chile, 1995
Chairman

CBET Div Of Chem, Bioeng, Env, & Transp Sys

Estados Unidos, 1994

Chairman, Minerals Bioprocessing II Conference, Engineering Foundation Conference, 1994
Scientific Citation Classic

Citation Classics

Chile, 1994

Scientific Citation Classic, 1994 (highly refrenced paper)
Invited Speaker

SOCIEDAD DE BIOLOGIA DE CHILE

Chile, 1993

Invited Speaker, Biological Soc. of Chile, Puyehue, Chile, 1993
Life Time Achievement Award

Bandung Institute of Technology

Indonesia, 2018

Life Time Achievement Award for his many contributions in the field of biohydrometallurgy.
Award for Scientific and Academic Trajectory

Sociadad Iberoamericana de Bioinformática

España, 2018

Award for Scientific and Academic Trajectory for Pioneering Development of Bioinformatics in Latin America, Sociadad Iberoamericana de Bioinformática (Soi Bio).


A Large-Scale Genome-Based Survey of Acidophilic Bacteria Suggests That Genome Streamlining Is an Adaption for Life at Low pH Cortez, Diego; Neira, Gonzalo; Gonzalez, Carolina; Vergara, Eva; Holmes, David S. Article ISI FRONTIERS IN MICROBIOLOGY (2022)
A Large-Scale Multiple Genome Comparison of Acidophilic Archaea (pH = 5.0) Extends Our Understanding of Oxidative Stress Responses in Polyextreme Environments Neira, Gonzalo; Vergara, Eva; Cortez, Diego; Holmes, David S. Article ISI ANTIOXIDANTS (2022)
Draft Genome Sequence of the Novel, Moderately Thermophilic, Iron-and Sulfur-Oxidizing Firmicute Strain Y002, Isolated from an Extremely Acidic Geothermal Environment Bitencourt, José; Scholte, Larissa; Oliveira, Renato; Morais, Daniel; Nunes, Gisele; Nancucheo, Ivan; Valadares, Rafael; Holmes, David S; Johnson, D Barrie; Alves, Ronnie; Oliveira, Guilherme Article Microbiology Resource Announcements (2022)
Integrative Genomics Sheds Light on Evolutionary Forces Shaping the Acidithiobacillia Class Acidophilic Lifestyle Gonzalez-Rosales, Carolina; Vergara, Eva; Dopson, Mark; Valdes, Jorge H.; Holmes, David S. Article ISI FRONTIERS IN MICROBIOLOGY (2022)
Prediction and Inferred Evolution of Acid Tolerance Genes in the Biotechnologically Important Acidihalobacter Genus Boase, Katelyn; González, Carolina; Vergara, Eva; Neira, Gonzalo; Holmes, David; Watkin, Elizabeth Article FRONTIERS IN MICROBIOLOGY (2022)
SinEx DB 2.0 update 2020: database for eukaryotic single-exon coding sequences Jorquera, R; González, C; Clausen, P T L C; Petersen, B; Holmes, D S Article DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2021)
AciDB 1.0: a database of acidophilic organisms, their genomic information and associated metadata Neira, Gonzalo; Cortez, Diego; Jil, Joaquin; Holmes, David S. Article ISI BIOINFORMATICS (2020)
Evolution of Predicted Acid Resistance Mechanisms in the Extremely Acidophilic Leptospirillum Genus Vergara E.; Neira G.; GonzÃ¡lez C.; Cortez D.; Dopson M.; Holmes D.S. Article ISI SCOPUS GENES (2020)
Genome-based classification of Acidihalobacter prosperus F5 (=DSM 105917=JCM 32255) as Acidihalobacter yilgarnensis sp. nov Khaleque, Himel Nahreen; Gonzalez, Carolina; Johnson, D. Barrie; Kaksonen, Anna H.; Holmes, David S.; Watkin, Elizabeth L. J. Article ISI INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2020)
Unlocking Survival Mechanisms for Metal and Oxidative Stress in the Extremely Acidophilic, Halotolerant Acidihalobacter Genus Khaleque, Himel Nahreen; Fathollazadeh, Homayoun; Gonzalez, Carolina; Shafique, Raihan; Kaksonen, Anna H.; Holmes, David S.; Watkin, Elizabeth L. J. Article ISI GENES (2020)
Effect of CO2 Concentration on Uptake and Assimilation of Inorganic Carbon in the Extreme Acidophile Acidithiobacillus ferrooxidans Esparza, Mario; Jedlicki, Eugenia; Gonzalez, Carolina; Dopson, Mark; Holmes, David S Article ISI SCOPUS FRONTIERS IN MICROBIOLOGY (2019)
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 Khaleque, Himel N.; González, Carolina; Kaksonen, Anna H.; Boxall, Naomi J.; Holmes, David S; Watkin, Elizabeth L. J. Article ISI SCOPUS INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2019)
Identification and Unusual Properties of the Master Regulator FNR in the Extreme Acidophile Acidithiobacillus ferrooxidans Osorio, Hector; Mettert, Erin; Kiley, Patricia; Dopson, Mark; Jedlicki, Eugenia; Holmes, David S Article ISI SCOPUS FRONTIERS IN MICROBIOLOGY (2019)
Uncovering the Mechanisms of Halotolerance in the Extremely Acidophilic Members of the Acidihalobacter Genus Through Comparative Genome Analysis Khaleque, Himel N.; Gonzalez, Carolina; Shafique, Raihan; Kaksonen, Anna H.; Holmes, David S; Watkin, Elizabeth L. J. Article ISI SCOPUS FRONTIERS IN MICROBIOLOGY (2019)
Improved ontology for eukaryotic single-exon coding sequences in biological databases Jorquera, R; Gonzalez, C; Clausen, P.; Petersen, B.; Holmes, DS Article ISI SCOPUS DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2018)
16S rRNA and Multilocus Phylogenetic Analysis of the Iron Oxidizing Acidophiles of the Acidiferrobacteraceae Family Issotta, Francisco; Covarrubias, Paulo C.; Moya-Beltrán, Ana; Bellenberg, Sören; Thyssen, Christian; Sand, Wolfgang; Nuñez, Harold; Mena, Cristóbal; Holmes, David S.; Quatrini, Raquel; Vera Véliz, Mario Article SCOPUS Solid State Phenomena (2017)
Draft genome sequence of Acidithiobacillus thiooxidans CLST isolated from the acidic hypersaline Gorbea salt flat in northern Chile Quatrini, R; Escudero, LV; Moya-Beltran, A; Galleguillos, PA; Issotta, F; Acosta, M; Cardenas, JP; Nunez, H; Salinas, K; Holmes, DS; Demergasso, C Article ISI SCOPUS Standards in Genomic Sciences (2017)
Draft genome sequence of the type strain of the sulfur-oxidizing acidophile, Acidithiobacillus albertensis (DSM 14366) Castro, M; Moya-Beltran, A; Covarrubias, PC; González, M; Cardenas, JP; Issotta, F; Nunez, H; Acuna, LG; Encina, G; Holmes, DS; Johnson, DB; Quatrini, R Article ISI SCOPUS Standards in Genomic Sciences (2017)
Multiple Osmotic Stress Responses in Acidihalobacter prosperus Result in Tolerance to Chloride Ions Dopson, Mark; Holmes, David S.; Lazcano, Marcelo; McCredden, Timothy J.; Bryan, Christopher G.; Mulroney, Kieran T.; Steuart, Robert; Jackaman, Connie; Watkin, Elizabeth L. J. Article ISI SCOPUS FRONTIERS IN MICROBIOLOGY (2017)
Multiple Osmotic Stress Responses in Acidihalobacter prosperus Result in Tolerance to Chloride Ions. Dopson, Mark; Holmes, David S; Lazcano, Marcelo; McCredden, Timothy J; Bryan, Christopher G; Mulroney, Kieran T; Steuart, Robert; Jackaman, Connie; Watkin, Elizabeth L.J. Article Frontiers in Microbiology (2017)
Mutantelec=> An In Silico mutation simulation platform for comparative electrostatic potential profiling of proteins. Valdebenito-Maturana, B; Reyes-Suarez, JA; Henriquez, J; Holmes, DS; Quatrini, R; Pohl, E; Arenas-Salinas, M. Article JOURNAL OF COMPUTATIONAL CHEMISTRY (2017)
Aerobic Lineage of the Oxidative Stress Response Protein Rubrerythrin Emerged in an Ancient Microaerobic, (Hyper)Thermophilic Environment Cardenas, JP; Quatrini, R; Holmes, DS Article ISI FRONTIERS IN MICROBIOLOGY (2016)
Aerobic Lineage of the Oxidative Stress Response Protein Rubrerythrin Emerged in an Ancient Microaerobic, (Hyper)Thermophilic Environment. Cardenas, JP.; Quatrini, R.; Holmes, DS. Article Frontiers in Microbiology (2016)
Bioinformatic Analyses of Unique (Orphan) Core Genes of the Genus Acidithiobacillus: Functional Inferences and Use As Molecular Probes for Genomic and Metagenomic/Transcriptomic Interrogation González, Carolina; Lazcano, Marcelo; Valdés, Jorge; Holmes, David S. Article ISI SCOPUS FRONTIERS IN MICROBIOLOGY (2016)
Bioinformatic Analyses of Unique (Orphan) Core Genes of the Genus Acidithiobacillus=> Functional Inferences and Use As Molecular Probes for Genomic and Metagenomic/Transcriptomic Interrogation González, Carolina; Lazcano, Marcelo; Valdés, Jorge; Holmes, David S. Article Frontiers in Microbiology (2016)
Draft genome sequence of chloride-tolerant Leptospirillum ferriphilum Sp-Cl from industrial bioleaching operations in northern Chile Issotta, Francisco; Galleguillos, Pedro A; Moya-Beltrán, Ana; Davis-Belmar, Carol S; Rautenbach, George; Covarrubias, Paulo C; Acosta, Mauricio; Ossandon, Francisco J; Contador, Yasna; Holmes, David S; Marín- Eliantonio, Sabrina; Quatrini, Raquel; Demergasso, Cecilia Article Standards in Genomic Sciences (2016)
Draft genome sequence of chloride-tolerant Leptospirillum ferriphilum Sp-Cl from industrial bioleaching operations in northern Chile Issotta, Francisco; Galleguillos, Pedro; Moya-Beltran, Ana; Davis-Belmar, Carol; Rautenbach, George; Covarrubias, Paulo; Acosta, Mauricio; Ossandon, Francisco; Contador, Yasna; Holmes, David; Marin, Sabrina A.; Quatrini, Raquel; Demergasso, Cecilia Article ISI SCOPUS STANDARDS IN GENOMIC SCIENCES (2016)
Gene Loss and Horizontal Gene Transfer Contributed to the Genome Evolution of the Extreme Acidophile "Ferrovum" Ullrich, Sophie R.; González, Carolina; Poehlein, Anja; Tischler, Judith S.; Daniel, Rolf; Schlömann, Michael; Holmes, David S.; Mühling, Martin Article ISI SCOPUS FRONTIERS IN MICROBIOLOGY (2016)
Gene Loss and Horizontal Gene Transfer Contributed to the Genome Evolution of the Extreme Acidophile "Ferrovum". Ullrich, Sophie R; González, Carolina; Poehlein, Anja; Tischler, Judith S; Daniel, Rolf; Schlömann, Michael; Holmes, David S; Mühling, Martin Article Frontiers in Microbiology (2016)
Genome Analysis of the Biotechnologically Relevant Acidophilic Iron Oxidising Strain JA12 Indicates Phylogenetic and Metabolic Diversity within the Novel Genus "Ferrovum" Ullrich, SR; Poehlein A.; Tischler, JS; González C; Ossandon FJ; Daniel R.; Holmes, DS; Schlomann, M; Muhling, M Article ISI PLOS ONE (2016)
Genomic and metagenomic challenges and opportunities for bioleaching: a mini-review Cárdenas, Juan Pablo; Quatrini, Raquel; Holmes, David S. Article ISI SCOPUS RESEARCH IN MICROBIOLOGY (2016)
Graphlet Based Metrics for the Comparison of Gene Regulatory Networks Martin, Alberto J. M.; Dominguez, Calixto; Contreras-Riquelme, Sebastián; Holmes, David S.; Pérez-Acle, Tomás; Virolle, Marie-Joelle Article ISI SCOPUS PLOS ONE (2016)
Graphlet Based Metrics for the Comparison of Gene Regulatory Networks. Martin, Alberto J M; Dominguez, Calixto; Contreras-Riquelme, Sebastián; Holmes, David S; Perez-Acle,Tomas Article PLoS One (2016)
SinEx DB: a database for single exon coding sequences in mammalian genomes Jorquera, Roddy; Ortiz, Rodrigo; Ossandon, F.; Cárdenas, Juan Pablo; Sepúlveda, Rene; González, Carolina; Holmes, David S. Article ISI DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2016)
SinEx DB=> a database for single exon coding sequences in mammalian genomes. Jorquera, Roddy; Ortiz, Rodrigo; Ossandon, F; Cárdenas, Juan Pablo; Sepúlveda, Rene; González, Carolina; Holmes, David S. Article Database-The Journal of Biological Databases and Curation (2016)
Expression and activity of the Calvin-Benson-Bassham cycle transcriptional regulator CbbR from Acidithiobacillus ferrooxidans in Ralstonia eutropha Esparza M.; Jedlicki, E; Dopson, M; Holmes, DS Article ISI SCOPUS FEMS Microbiology Letters (2015)
Metagenomic analysis reveals adaptations to a cold-adapted lifestyle in a low-temperature acid mine drainage stream Liljeqvist M; Ossandon FJ; González C; Rajan, S; Stell, A; Valdés J.; Holmes, DS; Dopson, M Article ISI SCOPUS FEMS Microbiology Ecology (2015)
Reclassification of 'Thiobacillus prosperus' Huber and Stetter 1989 as Acidihalobacter prosperus gen. nov., sp nov., a member of the family Ectothiorhodospiraceae Pablo Crdenas, Juan; Norris, Paul R.; Ortiz, Rodrigo; Holmes, David S; Watkin, Elizabeth Article ISI INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2015)
a-fur, an antisense RNA gene to fur in the extreme acidophile Acidithiobacillus ferrooxidans Lefimil, C; Jedlicki, E; Holmes, D S Article MICROBIOLOGY-SGM (2014)
AFAL: a web service for profiling amino acids surrounding ligands in proteins Arenas-Salinas, M; Ortega-Salazar, S; Gonzales-Nilo, F; Pohl E; Holmes, DS; Quatrini, R Article ISI SCOPUS JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2014)
alpha-fur, an antisense RNA gene to fur in the extreme acidophile Acidithiobacillus ferrooxidans Lefimil, C; Jedlicki, E; Holmes, DS Article ISI MICROBIOLOGY-SGM (2014)
Draft Genome Sequence of the Iron-Oxidizing Acidophile Leptospirillum ferriphilum Type Strain DSM 14647. Cárdenas, Juan Pablo; Lazcano, Marcelo; Ossandon, Francisco J; Corbett, Melissa; Holmes, David S; Watkin, Elizabeth Article Genome announcements (2014)
Draft Genome Sequence of the Iron-Oxidizing, Acidophilic, and Halotolerant "Thiobacillus prosperus" Type Strain DSM 5130 Ossandon, F. J.; Cardenas, J. P.; Corbett, M.; Quatrini, R.; Holmes, D. S.; Watkin, E. Article SCOPUS Genome Announcements (2014)
Draft Genome Sequence of the Iron-Oxidizing, Acidophilic, and Halotolerant "Thiobacillus prosperus" Type Strain DSM 5130. Ossandon, Francisco J; Cárdenas, Juan Pablo; Corbett, Melissa; Quatrini, Raquel; Holmes, David S; Watkin, Elizabeth Article Genome announcements (2014)
Draft Genome Sequence of the Nominated Type Strain of Moya-Beltrán, Ana; Cárdenas, Juan Pablo; Covarrubias, Paulo C; Issotta, Francisco; Ossandon, Francisco J; Grail, Barry M; Holmes, David S; Quatrini, Raquel; Johnson, D Barrie Article Genome announcements (2014)
Draft genome sequence of the nominated type strain of “Ferrovum myxofaciens,” an acidophilic, iron-oxidizing betaproteobacterium Moya-Beltrán, A.; Cárdenas, J. P; Covarrubias, P. C.; Issotta, F; Ossandon, F. J.; Grail, B. M.; Holmes, D.S.; Quatrini, R.; Johnson, D. B. Article (2014)
Genetic variability of psychrotolerant Acidithiobacillus ferrivorans revealed by (meta)genomic analysis González C; Yanquepe M; Cardenas, JP; Valdés J.; Quatrini, R; Holmes, DS; Dopson, M Article ISI SCOPUS RESEARCH IN MICROBIOLOGY (2014)
Metal resistance or tolerance? Acidophiles confront high metal loads via both abiotic and biotic mechanisms Dopson, M; Ossandon FJ; Lovgren, L; Holmes, DS Article ISI SCOPUS FRONTIERS IN MICROBIOLOGY (2014)
Multi Locus Sequence Typing scheme for Acidithiobacillus caldus strain evaluation and differentiation Núñez H; Loyola D.; Cardenas, JP; Holmes, DS; Johnson, DB; Quatrini, R Article ISI SCOPUS RESEARCH IN MICROBIOLOGY (2014)
Anaerobic Sulfur Metabolism Coupled to Dissimilatory Iron Reduction in the Extremophile Acidithiobacillus ferrooxidans Osorio H.; Mangold S.; Denis Y.; Nancucheo I.; Esparza M.; Johnson, DB; Bonnefoy, V; Dopson, M; Holmes, DS Article ISI SCOPUS Applied and Environmental Microbiology (2013)
Architecture and Gene Repertoire of the Flexible Genome of the Extreme Acidophile Acidithiobacillus caldus Acuña LG; Cardenas, JP; Covarrubias PC; Haristoy JJ; Flores R.; Núñez H; Riadi G.; Shmaryahu, A; Valdés J.; Dopson, M; Rawlings DE; Banfield, JF; Holmes, DS; Quatrini, R Article ISI SCOPUS PLOS ONE (2013)
Astrogenomics=> A convergence of disciplines spawning inspiration Holmes, David S Article Journal of Computer Science & Systems Biology (2013)
An artifact in studies of gene regulation using beta-galactosidase reporter gene assays Lefimil, C; Jedlicki, E; Holmes, D.S. Article ISI SCOPUS Analytical Biochemistry (2012)
Comparative genomics of the oxidative stress response in bioleaching microorganisms Cardenas J.P.; Moya, F; Covarrubias P; Shmaryahu, A; Levicán G; Holmes, D.S.; Quatrini, R Article ISI SCOPUS Hydrometallurgy (2012)
Complete Genome Sequence of Temperate Bacteriophage AcaML1 from the Extreme Acidophile Acidithiobacillus caldus ATCC 51756 Tapia, P; Flores F M.; Covarrubias, P. C.; Acuna L.G.; Holmes, D.S.; Quatrini, R Article ISI SCOPUS Journal of Virology (2012)
ICEAfe1, an Actively Excising Genetic Element from the Biomining Bacterium Acidithiobacillus ferrooxidans Bustamante, P; Covarrubias PC; Levicán G; Katz, A; Tapia, P; Holmes D; Quatrini, R; Orellana O. Article ISI SCOPUS Journal of Molecular Microbiology and Biotechnology (2012)
TnpPred: AWeb Service for the Robust Prediction of Prokaryotic Transposases Riadi G.; Medina-Moenne C.; Holmes, D.S. Article ISI SCOPUS Comparative and Functional Genomics (2012)
Draft Genome of the Psychrotolerant Acidophile Acidithiobacillus ferrivorans SS3 Liljeqvist M; Valdés J.; Holmes, DS; Dopson, M Article ISI SCOPUS Journal of Bacteriology (2011)
Draft Genome Sequence of the Extremely Acidophilic Biomining Bacterium Acidithiobacillus thiooxidans ATCC 19377 Provides Insights into the Evolution of the Acidithiobacillus Genus Valdés J.; Ossandon F; Quatrini, R; Dopson, M; Holmes, DS Article ISI SCOPUS Journal of Bacteriology (2011)
Molecular dynamics study of the archaeal aquaporin AqpM Araya-Secchi R.; Garate J.A.; Perez-Acle, T; Holmes, D.S. Article ISI SCOPUS BMC GENOMICS (2011)
Sulfur metabolism in the extreme acidophile Acidithiobacillus caldus Mangold S.; Valdés J.; Holmes, DS; Dopson, M Article ISI SCOPUS FRONTIERS IN MICROBIOLOGY (2011)
Comparative genomics begins to unravel the ecophysiology of bioleaching Valdés J.; Cardenas, JP; Quatrini, R; Esparza M.; Osorio H.; Duarte F.; Lefimil, C; sepulveda, r; Jedlicki, E; Holmes, DS Article ISI SCOPUS Hydrometallurgy (2010)
Genes and pathways for CO2 fixation in the obligate, chemolithoautotrophic acidophile, Acidithiobacillus ferrooxidans, Carbon fixation in A. ferrooxidans Esparza M.; Cardenas, JP; Bowien B.; Jedlicki, E; Holmes, DS Article ISI SCOPUS BMC Microbiology (2010)
A 300 Kb Genome Segment, including a Complete Set of tRNA Genes, is Dispensable for Acidithiobacillus ferrooxidans G. Levicán, Katz; A., Valdés; J, Quatrini; R, Holmes; D. S, O. Orellana Article Advanced Materials Research (2009)
Comparative Genomics Begins to Unravel the Ecophysiology of Bioleaching D. S. Holmes, Cardenas JP; Valdez J, Quatrini; R, Esparza; M, Osorio; H., Duarte; F., Lefimil; C, E. Jedlicki Article Advanced Materials Research (2009)
Draft Genome Sequence of the Extremely Acidophilic Bacterium Acidithiobacillus caldus ATCC 51756 Reveals Metabolic Versatility in the Genus Acidithiobacillus Valdés J.; Quatrini, R; Hallberg K; Dopson, M; Valenzuela PDT; Holmes, DS Article ISI SCOPUS JOURNAL OF BACTERIOLOGY (2009)
Extending the models for iron and sulfur oxidation in the extreme Acidophile Acidithiobacillus ferrooxidans Quatrini, R; Appia-Ayme, C; Denis Y.; Jedlicki, E; Holmes, DS; Bonnefoy, V Article ISI SCOPUS BMC GENOMICS (2009)
Genomic Lessons from Biomining Organisms=> Case Study of the Acidithiobacillus Genus J. Valdes, D. S. Holmes Article Advanced Materials Research (2009)
Predicting the Function of Hypothetical Genes in Genomes of Bioleaching Microorganisms L. F. Ossandón, Rivera G; F. Lazo, D. S. Holmes Article Advanced Materials Research (2009)
Prediction of FNR Regulated Genes and Metabolic Pathways Potentially Involved in Anaerobic Growth of Acidithiobacillus Ferrooxidans H. Osorio, Cárdenas; J.P, Valdés; J, D. S. Holmes Article Advanced Materials Research (2009)
Protein Function in Extremely Acidic Conditions=> Molecular Simulations of a Predicted Aquaporin and a Potassium Channel in Acidithiobacillus Ferrooxidans F. A.-S. Duarte, González; W., Perez-Acle; T., González-Nilo; D., Holmes Article Advanced Materials Research (2009)
Regulation of expression of the PetI operon involved in iron oxidation in the biomining bacterium Acidithiobacillus ferrooxidans O. H. Lefimil, Quatrini R; Holmes DS, E. Jedlicki Article Advanced Materials Research (2009)
Selection and evaluation of reference genes for improved interrogation of microbial transcriptomes: case study with the extremophile Acidithiobacillus ferrooxidans Nieto, PA; Covarrubias PC; Jedlicki, E; Holmes, DS; Quatrini, R Article ISI SCOPUS BMC MOLECULAR BIOLOGY (2009)
Small Regulatory RNA Genes in Acidithiobacillus ferrooxidans=> case studies of 6S RNA and frr A. L. Shmaryahu, Jedlicki; E, D. S. Holmes Article Advanced Materials Research (2009)
AlterORF: a database of alternate open reading frames Pedroso, I.; Rivera G.; Lazo F.; Chacon M.; Ossandon F; Veloso FA; Holmes, DS Article ISI SCOPUS NUCLEIC ACIDS RESEARCH (2008)
Comparative genome analysis of Acidithiobacillus ferrooxidans, A. thiooxidans and A. caldus: Insights into their metabolism and ecophysiology Valdés J.; Pedroso, I.; Quatrini, R; Holmes, DS Article ISI SCOPUS HYDROMETALLURGY (2008)
Iron homeostasis strategies in acidophilic iron oxidizers: Studies in Acidithiobacillus and Leptospirillum Osorio H.; Martínez V; Veloso FA; Pedroso, I.; Valdés J.; Jedlicki, E; Holmes, DS; Quatrini, R Article ISI SCOPUS HYDROMETALLURGY (2008)
Microbial iron management mechanisms in extremely acidic environments: comparative genomics evidence for diversity and versatility Osorio H.; Martínez V; Nieto, PA; Holmes, DS; Quatrini, R Article ISI SCOPUS BMC MICROBIOLOGY (2008)
Preparation and Analysis of an Expressed Sequence Tag Library from the Toxic Dinoflagellate Alexandrium catenella Uribe, P; Fuentes, D; Valdés J.; Shmaryahu, A; Zuniga, A; Holmes D; Valenzuela PDT Article ISI SCOPUS MARINE BIOTECHNOLOGY (2008)
Bioinformatic prediction and experimental verification of Fur-regulated genes in the extreme acidophile Acidithiobacillus ferrooxidans Quatrini, R; Lefimil, C; Veloso FA; Pedroso, I.; Holmes, DS; Jedlicki, E Article ISI SCOPUS NUCLEIC ACIDS RESEARCH (2007)
Differential expression of two bc(1) complexes in the strict acidophilic chemolithoautotrophic bacterium Acidithiobacillus ferrooxidans suggests a model for their respective roles in iron or sulfur oxidation Bruscella, P; Appia-Ayme, C; Levicán G; Ratouchniak, J; Jedlicki, E; Holmes, DS; Bonnefoy, V Article ISI SCOPUS MICROBIOLOGY-SGM (2007)
Insights into the Metabolism and Ecophysiology of Three Acidithiobacilli by Comparative Genome Analysis Valdés,Jorge H.; Pedroso, Inti; Quatrini, Raquel; Hallberg, Kevin B.; Valenzuela, Pablo D.T.; Holmes, David S. Article Advanced Materials Research (2007)
Regulation of a novel Acidithiobacillus caldus gene cluster involved in metabolism of reduced inorganic sulfur compounds Rzhepishevska, OI; Valdés J.; Marcinkeviciene, L; Gallardo, CA; Meskys, R; Bonnefoy, V; Holmes, DS; Dopson, M Article ISI SCOPUS APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2007)
Second acyl homoserine lactone production system in the extreme acidophile Acidithiobacillus ferrooxidans Rivas, M; Seeger M.; Jedlicki, E; Holmes, DS Article ISI SCOPUS APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2007)
Generation and analysis of expressed sequence tags from Botrytis cinerea Silva, E.; Valdés J.; Holmes D; Shmaryahu, A; Valenzuela PDT Article ISI SCIELO SCOPUS BIOLOGICAL RESEARCH (2006)
Insights into the iron and sulfur energetic metabolism of Acidithiobacillus ferrooxidans by microarray transcriptome profiling 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 D; Bonnefoy, V Article ISI SCOPUS HYDROMETALLURGY (2006)
Microarray and bioinformatic analyses suggest models for carbon metabolism in the autotroph Acidithiobacillus ferrooxidans Appia-Ayme, C; Quatrini, R; Denis Y.; Denizot, F.; Silver, S; Roberto, F; Veloso F.; Valdés J.; Cardenas, JP; Esparza M.; Orellana O.; Jedlicki, E; Bonnefoy, V; Holmes, DS Article ISI SCOPUS HYDROMETALLURGY (2006)
Taking the pulse of Latin American microbiology HOLMES,DAVID S.; MORA, GUIDO Article INTERNATIONAL MICROBIOLOGY (2006)
A Lux-like Quorum Sensing System in the Extreme Acidophile Acidithiobacillus ferrooxidans Rivas, M; Seeger M.; Holmes, DS; Jedlicki, E Article ISI SCIELO SCOPUS BIOLOGICAL RESEARCH (2005)
Genomic insights into the iron uptake mechanisms of the biomining microorganism Acidithiobacillus ferrooxidans Quatrini, R; Jedlicki, E; Holmes, DS Article ISI SCOPUS JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY (2005)
Identification of a gene cluster for the formation of extracellular polysaccharide precursors in the chemolithoautotroph Acidithiobacillus ferrooxidans Barreto, M; Jedlicki, E; Holmes, DS Article ISI SCOPUS APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2005)
Large-scale, multi-genome analysis of alternate open reading frames in bacteria and archaea Veloso F.; Riadi G.; Aliaga, D.; Lieph, R; Holmes, DS Article ISI SCOPUS OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY (2005)
Role of complementary proteins in autoimmunity: an old idea re-emerges with new twists McGuire, KL; Holmes, DS Article ISI SCOPUS TRENDS IN IMMUNOLOGY (2005)
The ferric iron uptake regulator (Fur) from the extreme acidophile Acidithiobacillus ferrooxidans Quatrini, R; Lefimil, C; Holmes, DS; Jedlicki, E Article ISI SCOPUS MICROBIOLOGY-SGM (2005)
Apparent redundancy of electron transfer pathways via bc(1) complexes and terminal oxidases in the extremophilic chemolithoautotrophic Acidithiobacillus ferrooxidans Brasseur, G; Levicán G; Bonnefoy, V; Holmes D; Jedlicki, E; Lemesle-Meunier, D Article ISI SCOPUS BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS (2004)
Aspects of the predicted physiology of Acidithiobacillus ferrooxidans deduced from an analysis of its partial genome sequence Barreto, M; Quatrini, R; Bueno, S; Arriagada C.; Valdés J.; Silver, S; Jedlicki, E; Holmes, DS Article ISI HYDROMETALLURGY (2003)
Metabolic reconstruction of sulfur assimilation in the extremophile Acidithiobacillus ferrooxidans based on genome analysis Valdés J.; Veloso F.; Jedlicki, E; Holmes D Article ISI BMC GENOMICS (2003)
Characterization of the petI and res operons of Acidithiobacillus ferrooxidans Levicán G; Bruscella, P; Guacunano, M; Inostroza C.; Bonnefoy, V; Holmes, DS; Jedlicki, E Article ISI SCOPUS JOURNAL OF BACTERIOLOGY (2002)
Latin American Genome Initiative, the Creation of a Network and Web Based Resource to Aid and Nurture Genome Biology in Developing Countries Ramírez, Jose Luis; González, Alicia; Cantú, José María; Chavez-Crooker, Pamela; Leiva, Juan Carlos; Blamey, Jenny M.; Cortes, Hernan; Holmes, David Article Electronic Journal of Biotechnology (2002)
ISAfe1, an ISL3 family insertion sequence from Acidithiobacillus ferrooxidans ATCC 19859 Holmes, DS; Zhao, HL; Levicán G; Ratouchniak, J; Bonnefoy, V; Varela, P; Jedlicki, E Article ISI SCOPUS JOURNAL OF BACTERIOLOGY (2001)
An RT-PCR Artifact in the Characterization of Bacterial Operons. Holmes, D.S.; Guacucano, M.; Levican, G.; Jedlicki, E. Article ELECTRONIC JOURNAL OF BIOTECHNOLOGY (2000)
Functional Analysis of Gapped Microbial Genomes=> Principles with Examples from Thiobacillus ferrooxidans. Holmes, D.S.; Selkov, E.; Overbeek, R.; Kogan, Y.; Chu, L.; Vonstein, V.; Silver, S.; Fonstein, M. Article PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA-BIOLOGICAL SCIENCES (2000)
Biotechnology=> Miners in miniature. Holmes, D.S. Article Chemistry and Industry (1999)
IST1 Insertional Inactivation of the resB Gene=> Implications for Phenotypic Switching in Thiobacillus ferrooxidans. Holmes, D.S.; Cabrejos, M-E.; Zhao, H.L.; Guacucano, M.; Bueno, S.; Levican, G.; Garcia, E. Jedlicki and . Article FEMS MICROBIOLOGY LETTERS (1999)
Sequence and Expression of the Rusticyanin Structural Gene from Thiobacillus ferrooxidans ATCC33023 strain. Holmes, D.S.; Bengrine, A.; Guiliani, N.; Appia-Ayme, C.; Jedlicki, E.; Chippaux, M. and V. Bonneyfoy. Article BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS (1998)
Biological cyanide destruction mediated by microorganisms. Holmes, D.S. Article WORLD JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY (1996)
Development of Biosensors for the Detection of Mercury and Copper Ions. Holmes, D.S.; Dubey, S.K.; Gangolli, S.S. Article ENVIRONMENTAL GEOCHEMISTRY AND HEALTH (1994)
Transposition of IST2 in Thiobacillus ferrooxidans. Holmes, D.S.; Cadiz, R.; Gaete, L.; Jedlicki, E.; Yates, J.; Orellana, O. Article MOLECULAR MICROBIOLOGY (1994)
Development of Biosensors to Measure Metal Ion Bioavailability in Environmental Samples. Holmes, D.S.; Dubey, S.K.; Gangolli, S.S. Article Northeastern Geology and Environmental Science (1993)
This Week's Citation Classic Holmes, David S; Quigley, M. Article CURRENT CONTENTS (1993)
Construction and evaluation of a self-luminescent biosensor. Geiselhart, L; Osgood, M Article Annals of the New York Academy of Sciences (1991)
Biotechnology in the Mining and Metal-Processing Industries. Challenges and Opportunities. Holmes, D.S. Article MINERALS and METALLURGICAL PROCESSING (1988)
IST2=> A New Insertion Sequence in Thiobacillus ferrooxidans Holmes, D.S.; Yates, J.R. Cunningham Article PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (1988)
Phenotypic Switching of Thiobacillus ferrooxidans. Holmes, D.S.; Schrader, J. Article JOURNAL OF BACTERIOLOGY (1988)
Two Families of Repeated DNA Sequences in Thiobacillus ferrooxidans Holmes, D.S; Yates, J.R. Article JOURNAL OF BACTERIOLOGY (1988)
Designed Metal-Binding Proteins Holmes, D.S; Leib, T.K. Article Biotechnology (1987)
Use of X-ray Computed Tomographic to Examine Microbial Desulfurization of Lump Coal Holmes, D.S.; Spiro, C.L.; Lobos, J.H.; Maylotte, D.H. Article ENERGY & FUELS (1987)
Acidiphilium organovorum sp. nov., An Acidophilic Heterotroph Isolated from a Thiobacillus ferrooxidans Culture. Holmes, D.S.; Lobos, J.H.; Chisholm, T.E. Article INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (1986)
Strategy for the Establishment of a Genetic System for the Acidophilic Heterotroph, Acidiphilium organovorum. Holmes, D.S.; Yates, J.R.; Lobos, J.H.; Doyle, M.V. Article BIOTECHNOLOGY AND APPLIED BIOCHEMISTRY (1986)
The Use of Genetic Probes to Detect Microorganisms in Biomining Operations. Holmes, D.S. ; Yates, J.R.; Lobos, J.H. Article Journal of Industrial Microbiology and Biotechnology (1986)
Cloning of a Thiobacillus ferrooxidans Plasmid in E. coli. Holmes, D.S.; Lobos, J.H.; Bopp, L.H.; Welch, G.C. Article JOURNAL OF BACTERIOLOGY (1984)
Improved Rapid Heating Technique for Screening Recombinant DNA Plasmids in E. coli. Holmes, D.S. Article BIOTECHNIQUES (1984)
The Cot Curve. Holmes, D.S. Article TRENDS IN BIOCHEMICAL SCIENCES (1984)
A Note on the Use of CsCl Centrifugation to Purify Bacterial Plasmids Prepared by the Rapid Boiling Method. Holmes, D.S.; Eisenberg, A.J. Article ANALYTICAL BIOCHEMISTRY (1982)
Rapid Purification of Bacterial Plasmids and Coliphage M13 RF Without CsCl Centrifugation. Holmes, D.S. Article ANALYTICAL BIOCHEMISTRY (1982)
The Use of Agar for Electrophoresis of DNA Fragments. Holmes, D.S.; Bush, C. Article ANALYTICAL BIOCHEMISTRY (1982)
A Rapid Method for the Preparation of Plasmids. Holmes, D.S.; Quigley, M. Article ANALYTICAL BIOCHEMISTRY (1981)
Specific Increase of Perchloric Acid Extractable Chromosomal Proteins During Mammalian Erythropoieses. Holmes, D.S.; Grimmond, H. Article COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY (1981)
Structure of the Chromosomal Material in Inactive Nuclei of Chicken Red Blood Cells. Holmes, D.S.; Colquhoun, W. Article CHROMOSOMA (1980)
The Mesokaryote Gyrodinium cohnii Lacks Nucleosomes Holmes, D.S.; Bodansky, S.; Mintz, L.B. Article BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (1979)
Applications of the Avidin biotin Methods of Gene Enrichment to the Isolation of Long Double-Stranded DNA Containing Specific Gene Sequences Holmes, D.S.; Pellegriniand, M.; Manning, J. Article NUCLEIC ACIDS RESEARCH (1977)
Positions of Sea Urchin Histone Genes Relative to Restriction Endonuclease Sites on the Chimeric Plasmids pSp2 and pSp17. Holmes, D.S.; Davidson, N.; Cohn, R.H. ; Kedes, L.H. Article Biochemistry (1977)
The Relative Positions of the Coding and Spacer Regions on Sea Urchin Histone Genes on the Chimeric Plasmids pSp2 and pSp17 as Studied by Electron Microscopy. Holmes, D.S.; Wu, M.; Davidson, N.; Cohn, R.H.; Kedes, L.H. Article CELL (1976)
Interspersion of Repetitive and Single Copy Sequences in High Molecular Weight Nuclear RNA. Holmes, D.S.; Bonner, J. Article PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (1974)
Sequence Composition of Rat Ascites Chromosomal RNA. Holmes, D.S.; Mayfield, J.E.; Bonner, J. Article Biochemistry (1974)
Sequence Composition of Rat Nuclear DNA and High Molecular RNA Holmes, D.S.; Bonner, J. Article Biochemistry (1974)
Preparation, Molecular Weight, Base Composition and Secondary Structure of Giant Nuclear RNA. Holmes, D.S.; Bonner, J. Article Biochemistry (1973)
Chromosomal RNA: Its Properties Holmes, D. S.; Mayfield, J. E.; Sander, G.; Bonner, J. Article ISI SCIENCE (1972)


Apparent redundancy of electron transfer pathways to oxygen in the extremophilic chemolithautotrophic bacterium acidithiobacillus ferrooxidans Brasseur, G; Levicán G; Bonnefoy, V; Holmes D; Jedlicki, E; Lemesle-Meunier, D Abstract ISI BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS (2004)


The Genomics of Acidophiles Cardenas, J.P.; Quatrini, Raquel; Holmes, David S.; Quatrini, Raquel; Johnson, D.B. BookSection (2016)
Application of CellDesigner to the Selection of Anticancer Drug Targets: Test Case using P53 Isea, Raúl; Hoebeke, Johan; Mayo, Rafael; Alvarez, Fernando; Holmes, David S.; Aguiló, J.; Freire, A.; de la Iglesia, D.; López, V.; Pazos, A. BookSection (2013)
The Use of Bioinformatics and Genome Biology to Advance Our Understanding of Bioleaching Microorganisms Quatrini, Raquel; Valdés, Jorge; Jedlicki, Eugenia; Holmes, David S.; Donati, E.; Sand, W. BookSection (2007)
Genetic and Bioinformatic Insights into Iron and Sulfur Oxidation Mechanisms of Bioleaching Organisms Holmes, D. S.; Bonnefoy, V; Rawlings, D.; Johnson, B. BookSection (2006)
Detection and measurement of ultra-trace levels of mercury and copper by genetically engineered microbial sensors Dubey, S. K.; Holmes, D. S.; Rao, G. R.; Gangolli, S.; Hiremath, K. G. BookSection (2002)
Biorecovery of Metals from Mining Wastes Holmes, D. S.; Martin, A. M. BookSection (1998)
Biohydrometallurgy Holmes, D. S. BookSection (1991)
Biorecovery of Waste Materials from Mining Operations Holmes, D. S.; Martin, A. M. BookSection (1991)
Opportunities for Biological Metal Recovery Holmes, D. S.; Debus, K. H.; Smith, R. W.; Misra, M. BookSection (1991)
Adaptation of Thiobacillus ferrooxidans for Industrial Applications Holmes, D. S.; Haq, R.; Salley, J.; McCready, R. G. L.; Wichlacz, P. L. BookSection (1990)
Basic Principles of Genetic Manipulation of Thiobacillus ferrooxidans for Biohydrometallurgical Applications Holmes, D. S.; Yates, J. R.; Ehrlich, H. L.; Brierley, C. L. BookSection (1990)
Genetic Engineering of Microorganisms for Pollution Control Holmes, D. S. BookSection (1989)
Molecular Enzyme Engineering Holmes, D. S.; Bungay, H. R.; Belford, G. BookSection (1987)
Construction and Use of Molecular Probes to Identify and Quantitate Bioleaching Microorganisms Yates, J. R.; Holmes, D. S.; Branion, R. M. R.; Ebner, H. G. BookSection (1986)
Genetic Engineering of Biomining Organisms Holmes, D. S.; Yates, J. R.; Lobos, J. H.; Doyle, M. V. BookSection (1984)
Sequence Composition and Organization of the Genome and Nuclear RNA of Higher Organisms: An Approach to Understanding Gene Regulation Holmes, D. S.; Bonner, J.; Niu, M.; Segal, S. BookSection (1973)


Analysis of gene expression in response to copper stress in Acidithiobacillus ferrooxidans strain D2, isolated from a copper bioleaching operation Salazar C.; Acosta M.; Galleguillos, P.; Shmaryahu, A; Quatrini, R; Holmes, DS; Demergasso, C ConferencePaper ISI SCOPUS ADVANCED MATERIALS RESEARCH (2013)
Temporal dynamics of genes involved in metabolic pathways of C and N of L. ferriphilum, in the industrial bioleaching process of Escondida mine, Chile Galleguillos, PA; Music V; Acosta M.; Salazar CN; Quatrini, R; Shmaryahu, A; Holmes D; Velásquez A; Espoz C.; Pinilla C.; Demergasso, CS ConferencePaper ISI BIOHYDROMETALLURY: FROM THE SINGLE CELL TO THE ENVIRONMENT (2013)
C-di-GMP pathway in biomining bacteria Castro M.; Ruiz, LM; Barriga, A.; JEREZ, CA; Holmes D; Guiliani N. ConferencePaper ISI BIOHYDROMETALLURY: FROM THE SINGLE CELL TO THE ENVIRONMENT (2009)
Gene organization and CO(2)-responsive expression of four cbb operons in the biomining bacterium Acidithiobacillus ferrooxidans Esparza M.; Bowien B.; Jedlicki, E; Holmes, DS ConferencePaper ISI BIOHYDROMETALLURY: FROM THE SINGLE CELL TO THE ENVIRONMENT (2009)
Predicted CO/CO(2) fixation in Ferroplasma spp. via a novel chimaeric pathway Cardenas, JP; Martínez V; Covarrubias P; Holmes, DS; Quatrini, R ConferencePaper ISI BIOHYDROMETALLURY: FROM THE SINGLE CELL TO THE ENVIRONMENT (2009)
Preliminary genomic and functional analysis of a cDNA library from Botrytis cinerea Silva, EM; Valdés J.; Shmaryahu, A; Holmes D; Valenzuela P. ConferencePaper ISI XXXI INTERNATIONAL HORTICULTURAL CONGRESS, IHC2022: INTERNATIONAL SYMPOSIUM ON INNOVATIVE PERENNIAL CROPS MANAGEMENT (2008)
Discovery of small regulatory RNAs extends our understanding of gene regulation in the Acidithiobacillus genus Shmaryahu, A; Holmes, DS ConferencePaper ISI BIOHYDROMETALLURY: FROM THE SINGLE CELL TO THE ENVIRONMENT (2007)
Insights into the metabolism and ecophysiology of three acidithiobacilli by comparative genome analysis Valdés J.; Pedroso, I.; Quatrini, R; Holmes, D.S.; Valenzuela P.D.T.; Hallberg, K. B. ConferencePaper SCOPUS BIOHYDROMETALLURY: FROM THE SINGLE CELL TO THE ENVIRONMENT (2007)
Iron homeostasis strategies in acidophilic iron oxidizers: Comparative genomic analyses Quatrini, R; Martínez V; Osorio H.; Veloso FA; Pedroso, I.; Valdés J.; Jedlicki, E; Holmes, DS ConferencePaper ISI BIOHYDROMETALLURY: FROM THE SINGLE CELL TO THE ENVIRONMENT (2007)


Putting metabolism on the road: the case for the emergence of life in hot acid Holmes, D. S.; González, C. ConferencePoster Poster participation (2017)
Comparative Analyses of Metagenomes from Acid Mine Drainages Moya-Beltrán, A.; Issotta, F.; Nuñez, H.; Ossandón, F.; Holmes, D. S.; Quatrini, R. ConferencePoster Poster participation (2015)
Metagenomic analyses reveal specific adaptations to metal efflux of Acidithiobacillus ferrivorans SS3 González, C.; Yanquepe, M.; Cárdenas, J. P.; Valdés, J.; Quatrini, R.; Dopson, M.; Holmes, D. S. ConferencePoster Poster participation (2015)
Microbial Iron Oxidation in High Salt: Implications for Martian Habitat Investigation Lazcano M.; Cárdenas J.P.; Holmes, D. S. ConferencePoster Poster participation (2015)
Potential Sources of Oxygen on Early Earth Before the Great Oxygenation Event (GOE) Ortiz, R.; Sepúlveda R.; Holmes, D. S. ConferencePoster Poster participation (2015)
Benchmarking Available Methods for Prediction of Mobile Genetic Elements in Complete Genomes Ossandon, F.; Yanquepe, M.; Holmes, D. S.; Quatrini, R. ConferencePoster Poster participation (2014)
Benchmarking of Binning Methods Using a Conceptual Metagenome Issota, F.; Riadi, G.; Holmes, D. S.; Quatrini, R. ConferencePoster Poster participation (2014)
Comparative Analysis of Metagenomes from Extremely Acidic Environments Using a Phylogenetic Approach Moya, A.; Riadi, G.; Quatrini, R.; Holmes, D. S. ConferencePoster Poster participation (2014)
Inference of gene regulatory networks during embryonic development of Drosophila melanogaster Domínguez, C.; Santos, A.; Jensen, L. J.; Perez-Acle, T.; Holmes, D. S. ConferencePoster Poster participation (2014)
Investigating the Biochemical Potential of the Iron Oxidizing Betaproteobacterium Ferrovum sp. JA12 at the Genomic and Transcriptomic level Ullrich, S. R.; Poehlein, A.; Daniel, R.; Tischler, J. S.; Ossandon, F.; Holmes, D. S.; Schlömann, M.; Mühling, M. ConferencePoster Poster participation (2014)
Acidithiobacillus phylogenomics: understanding ecophysiology in extreme acidic environments by whole genome evolutionary reconstruction (2013) González, C.; Guzmán, D.; Tapia, P.; Valdés, J.; Holmes, D. S. ConferencePoster Poster participation (2013)
Analysis of gene expression in response to stress induced by copper in Acidithiobacillus ferrooxidans strain D2, an isolated from a copper bioleaching operation Salazar, C.; Acosta, M.; Galleguillos, P.; Demergasso, C.; Shmaryahu, A.; Quatrini, R.; Holmes, D. S. ConferencePoster Poster participation (2013)
Análisis filogenómico del complejo heterodisúlfuro reductasa (HdrABC) en genomas microbianos García-González, R.; Cárdenas, J. P.; Quatrini, R.; Holmes, D. S. ConferencePoster Poster participation (2013)
Biomining on Mars: Challenges and Opportunities Sepúlveda, R.; Ortiz,R.; Holmes, D. S. ConferencePoster Poster participation (2013)
Biomining on planetary bodies: challenges and opportunities Ortiz, R.; Sepúlveda, R.; Holmes, D. S. ConferencePoster Poster participation (2013)
Eukaryotic Single Exon Genes Ortiz, R.; Jorquera, R.; Holmes, D. S. ConferencePoster Poster participation (2013)
Evolution of terminal electron transfer proteins during the anaerobic/aerobic transition in the Archean era Sepúlveda, R.; Ortiz, R.; Holmes, D. S. ConferencePoster Poster presentation (2013)
Extremely acidic environments on earth as surrogates for habitable planetary bodies Holmes, D. S. ConferencePoster Poster participation (2013)
Heterodisulfide reductase complex: a key to energetics in early evolution Cárdenas, J. P.; Holmes, D. S. ConferencePoster Poster participation (2013)
Phenotypic analysis of an Acidithiobacillus caldus mutant defective in c-di-GMP production Castro, M.; Guiliani, N.; Deane, S.; Rawlings, D. E.; Holmes, D. S. ConferencePoster Poster participation (2013)
Psychrotolerant acidophiles in a subsurface metal sulphide mine: from (meta)genomes to biomining Liljeqvist, M.; Dopson, M.; Stell, A.; Ossandon, F.; González, C.; Holmes, D. S.; Valdés, J. ConferencePoster Poster participation (2013)
AFAL: a web service for determine the profiling amino acids surrounding ligands in Protein Data Bank Arenas-Salinas, M.; Ortega-Salasar, S.; Holmes, D. S.; Pohl, E.; Quatrini, R. ConferencePoster Poster participation (2012)
AFAL: a web service for profiling amino acids surrounding ligands in Protein Data Bank crystallographic data Arenas, M.; Ortega, S.; González-Nilo, D.; Holmes, D. S.; Pohl, E.; Quatrini, R. ConferencePoster Poster participation (2012)
Análisis fisiológico de bacterias (biolixiviantes) mesotermófilas del género Sulfobacillus empleando herramientas de biología genómica Monsalve, A.; Cárdenas, J.P.; Acosta, M.; Levicán, G.; Demergasso, C.; Holmes, D. S.; Quatrini, R. ConferencePoster Poster participation (2012)
Análisis metagenómico de comunidades microbianas de ambiente ácido y psicrófilo procedentes de desechos residuales mineros González, C.; Ossandon, F.; Stell, A.; Liljeqvist, M.; Dopson.M; Valdés, J.; Holmes, D. S. ConferencePoster Poster participation (2012)
Bioinformatic and Biophysical Characterization of FUR (Ferric Uptake Regulator) from an extreme Acidophile Thriving in an Iron Rich Environment Arenas, M.; Pohl, E.; Marquez, N.; Holmes, D. S.; Quatrini, R. ConferencePoster Poster participation (2012)
Comparative genomics of the oxidative stress response in acidophile microorganisms Cárdenas, J. P.; Holmes, D. S.; Quatrini, R.; Levican, G. ConferencePoster Poster participation (2012)
Computational Pattern Recognition for the Identification of Transposases in Prokaryotic Genomes: Challenges and Advances Riadi, G.; Holmes, D. S. ConferencePoster Poster participation (2012)
High Dimensional multi-genomic investigation into the function and evolution of eukaryotic single exon genes Jorquera, R.; Ortiz, R.; Pedroso, A.; Holmes, D. S. ConferencePoster Poster participation (2012)
High Dimensional, Multi-Genomic Investigation into the function and evolution of eukaryotic single exon genes Jorquera, R.; Ortiz, R.; Pedroso, A.; Holmes, D. S. ConferencePoster Poster participation (2012)
Human single exon genes Jorquera, R.; Ortiz, R.; Holmes, D. S. ConferencePoster Poster participation (2012)
Niche specific oxidative stress response in extreme acidophiles Cárdenas, J. P.; Arenas, M.; Quatrini, R.; Holmes, D. S. ConferencePoster Poster participation (2012)
Regulando a un regulador: el caso de Fur en Acidithiobacillus ferrooxidans Lefimil, C.; Leiva, M.; Acuña, L.; Holmes, D. S.; Jedlicki, E. ConferencePoster Poster participation (2012)
Study and molecular characterization of the hypothetical representative of a third subfamily of aquaporins, AqpF from Acidothiobacillus ferrooxidans Flores, S.; Araya-Secchi, R.; Pérez-Acle, T.; Holmes, D. S. ConferencePoster Poster participation (2012)
Toxin-Antitoxin Systems Encoded in an Integrative Conjugative Element from the Biomining Bacterium Acidithiobacillus ferrooxidans Bustamante, P.; Levicán, G.; Quatrini, R.; Holmes, D. S.; orellana, o. ConferencePoster Poster participation (2012)


Are We Alone in the Universe? Holmes, D. S. ConferenceProceedingWhole Invited talk (2017)
Astrobiology: When Disciplines Collide Innovation Happens (2017) Holmes, D. S. ConferenceProceedingWhole Keynote opening talk (2017)
Probing the Deep Evolutionary Roots of Thermo-Acidophiles (2017) Holmes, D. S. ConferenceProceedingWhole Talk (2017)
Acidihalobacter prosperus, a halophilic acidophile, has unique mechanisms to survive high chloride concentrations at low pH Watkin, E.L.J.; Holmes, D. S.; Dopson, M. ConferenceProceedingWhole Talk (2016)
Acidihalobacter prosperus, a halophilic acidophile, has unique mechanisms to survive high chloride concentrations at low pH. (2016) Watkin, E.L.J.; Holmes, D. S.; Dopson, M. ConferenceProceedingWhole Talk (2016)
Comparative genomic analysis of acidophilic iron oxidizing bacteria from a pilot plant for the microbial remediation of AMD water: Insights into strategies for speciation and metabolic adaptation to life at low pH and under low nutrient concentration Mühling, M.; Ullrich, S. R.; Poehlein, A.; Daniel, R.; Voitel, M.; Drechsel, A.; Tischler, J. S.; González, C.; Ossandon, F.; Holmes, D. S.; Schlömann, M. ConferenceProceedingWhole Talk (2016)
Comparative Genomics Sheds Light on the Evolutionary Dynamics and Sympatric Speciation of Life in Extremely Acidic Environments González, C.; Cárdenas, J.P.; Lazcano, M.; Guzmán, D.; Tapia, P.; Valdés, J.; Holmes, D. S. ConferenceProceedingWhole Talk (2016)
Comparative Genomics Sheds Light on the Evolutionary Dynamics and Sympatric Speciation of Life in Extremely Acidic Environments (<pH 2) González, C.; Cárdenas, J. P.; Lazcano, M.; Guzmán, D.; Tapia, P.; Valdés, J.; Holmes, D. S. ConferenceProceedingWhole Talk (2016)
Comparative Genomics Sheds Light on the Evolutionary Mechanisms and Dynamics of Extreme Acidophiles González, C.; Lazcano, M.; Valdés, J.; Holmes, D. S. ConferenceProceedingWhole Talk (2016)
Genomes in Turmoil: Frugality Drives Microbial Community Structure in Extremely Acidic Environments Holmes, D. S. ConferenceProceedingWhole Talk (2016)
Insights into the Evolutionary Mechanisms and Dynamics of Extreme Acidophiles González, C.; Lazcano, M.; Valdés, J.; Holmes, D. S. ConferenceProceedingWhole Talk (2016)
Probing the Deep Evolutionary Roots of Thermo-Acidophiles (2016) Holmes, D. S. ConferenceProceedingWhole Invited talk (2016)
Astrobiology: When Disciplines Collide Innovation Happens Holmes, D. S. ConferenceProceedingWhole Invited talk (2015)
Astrobiology: When Disciplines Collide Innovation Happens (2015) Holmes, D. S. ConferenceProceedingWhole Invited talk (2015)
Exploring patterns of chromatin modification and binding proteins to identify Cis-regulatory modules (CRMs) driving the restricted expression of genes in dorsal cells of D. melanogaster embryos Dominguez, C.; Medina, D.; Cambiazo, V.; Perez-Acle, T.; Holmes, D. S. ConferenceProceedingWhole Talk (2015)
Forces shaping microbial speciation in extremely acidic environments: insights from the Acidithiobacillus genus González, C.; Valdés, J.; Holmes, D. S. ConferenceProceedingWhole Talk (2015)
Genomics and Metagenomics of Extreme Acidophiles in Biomining Environments Holmes, D. S. ConferenceProceedingWhole Talk (2015)
Navigating the Genomes-to-Ecosystems Cascade in Biomining Environments Holmes, D. S. ConferenceProceedingWhole Invited opening keynote talk (2015)
Probing the Deep Evolutionary Roots of Thermo-acidophiles Holmes, D. S.; Ortiz, R.; Cárdenas, J. P.; Sepulveda, R. ConferenceProceedingWhole Talk (2015)
Probing the Deep Evolutionary Roots of Thermo-acidophiles (2015) Holmes, D. S.; Ortiz, R.; Cárdenas, J. P.; Sepúlveda, R. ConferenceProceedingWhole Invited keynote talk (2015)
Acidithiobacillus Phylogenomics: Understanding Ecophysiology In Extreme Acidic Environments By Whole Genome Evolutionary Reconstruction González, C.; Guzmán, D.; Tapia, P.; Valdés, J.; Holmes, D. S. ConferenceProceedingWhole Talk (2014)
Advances in Our Understanding of Bioleaching using Omic Approaches Holmes, D. S. ConferenceProceedingWhole Invited talk (2014)
Astrobiology: Emerging Opportunities for Environmental Microbiologists Holmes, D. S. ConferenceProceedingWhole Invited Opening keynote Talk (2014)
Astrobiology: The Next Frontier Holmes, D. S. ConferenceProceedingWhole Invited public lecture (2014)
Biological Challenges and Opportunities in Biomining: Biooxidation Tank Reactors, Heap, Dump and In Situ Bioleaching and Acid Mine Drainage Bioremediation Holmes, D. S. ConferenceProceedingWhole Invited talk (2014)
Genomic and evolutionary insights into adaptation of "Thiobacillus prosperus" (Acidihalobacillus prosperus sp. nov) to saline and acidic environments Cárdenas, J. P.; Ossandon, F.; Ortiz, R.; Watkin, E.; Holmes, D.S. ConferenceProceedingWhole Talk (2014)
Genomic Project of Acidiferrobacter “MURCIENSIS” Sp. Spiii/3: insights into Biofilm Formation and Cell-to-Cell Communication Mechanisms Bellenberg; Zhang, R.; Moya-Beltran, A.; Isotta, F.; Covarrubias, P.; Ossandon, F.; Sand, W.; Holmes, D. S.; Quatrini, R.; Vera, M. ConferenceProceedingWhole Talk (2014)
Genomics and Metagenomics of Acidophiles Holmes, D. S. ConferenceProceedingWhole Invited Talk (2014)
Modeling Sulfur Oxido-Reduction Pathways in Early Evolution Holmes, D. S. ConferenceProceedingWhole Invited talk (2014)
Non-similarity Techniques for Predicting Gene Function Holmes, D. S. ConferenceProceedingWhole Invited talk (2014)
Potential for the Early Evolution of Life in Acidic Conditions Holmes, D. S. ConferenceProceedingWhole Invited talk (2014)
The role of iron and sulfur exergonic oxido-reduction pathways in the early evolution of life Holmes, D. S.; Ortiz, R.; Sepúlveda, R. ConferenceProceedingWhole Invited talk (2014)
Thiobacillus prosperus, a halophilic acidophile, has unique mechanisms to survive high chloride concentrations at low pH Watkin, E. L. J.; Ossandon, F.; Holmes, D. S. ConferenceProceedingWhole Talk (2014)
Unraveling evolutionary pathways for genomic and phenotypic diversification and its predicted impact on the ecophysiology of biomining Acidithiobacilli González, C.; Guzmán, D.; Tapia, P.; Holmes, D. S.; Valdés, J. ConferenceProceedingWhole Invited Talk (2014)
Astrogenomics: A Convergence of Disciplines Spawning Inspiration Holmes, D. S. ConferenceProceedingWhole Invited keynote talk (2013)
At the Interface of Genomics and Astrobiology: When Disciplines Collide Innovations Happen Holmes, D. S. ConferenceProceedingWhole Talk (2013)
Bioinformatics and Genome Biology of Prokaryotes Holmes, D. S. ConferenceProceedingWhole Invited workshop (2013)
Bioinformatics Workshop: Hands-on Holmes, D. S. ConferenceProceedingWhole Invited workshop (2013)
Bioleaching: opportunities, challenges and future directions Holmes, D. S. ConferenceProceedingWhole Invited keynote talk (2013)
Oxidative stress response in acidophilic bacteria: the role of Fur and PerR regulators Cárdenas, J. P.; Holmes, D. S.; Quatrini, R. ConferenceProceedingWhole Talk (2013)
Protein Evolution during the Archean Anaerobic/Aerobic Transition Sepúlveda, R.; Ortiz, R.; Holmes, D. S. ConferenceProceedingWhole Invited talk (2013)
Psychrotolerant Acidophiles in a Subsurface Metal Sulphide Mine: From (Meta)Genomes to Biomining (2013) González, C.; Ossandon, F.; Liljeqvist, M.; Adam, A.; Holmes, D. S.; Dopson, M.; Valdés, J. ConferenceProceedingWhole Talk (2013)
Recent advances in iron biogeochemistry in extremely acidic conditions Holmes, D. S. ConferenceProceedingWhole Invited keynote talk (2013)
Stabilization of proteins in extreme thermo-acidic environments Duarte, F.; Holmes, D. S. ConferenceProceedingWhole Talk (2013)
Summary of investigations at the Center for Bioinformatics and Genome Biology Holmes, D. S. ConferenceProceedingWhole Invited talk (2013)
The ecophysiology of bioleaching: A genomics perspective Cárdenas, J. P.; Holmes, D. S.; Núñez, H.; Ossandon, F.; Shmaryahu, A.; Quatrini, R.; Galleguillos, P.; Acosta, M.; Demergasso, C. ConferenceProceedingWhole Talk (2013)
Understanding functional relationships across an evolutionary gradient within the Acidithiobacillus genus González, C.; Guzmán, D.; Tapia, P.; Valdés, J.; Holmes, D. S. ConferenceProceedingWhole Talk (2013)
Bioleaching heaps provide special opportunities for studying the adaption, ecophysiology and evolution of extreme acidophiles Quatrini, R.; Holmes, D. S. ConferenceProceedingWhole Talk (2012)
Challenges for life at pH 1: a genomics and metagenomics perspective Holmes, D. S. ConferenceProceedingWhole Invited talk (2012)
Characterization of Fur protein from Acidithiobacillus ferrooxidans an extreme acidophile thriving in an iron rich environment using bioinformatic and biophysical techniques. Arenas, M.; Marquez, S.; Pohl, E.; Quatrini, R.; Holmes, D. S. ConferenceProceedingWhole Talk (2012)
Dinámica temporal de la expresión de genes involucrados en metabolismos de C y N de L. ferriphilum en el proceso de biolixiviación de cobre en pila de Minera Escondida Ltda. Galleguillos, P.; Music, V.; Acosta, M.; Salazar, C.; Quatrini, R.; Shmaryahu, A.; Holmes, D. S.; Velásquez, A.; Espoz, C.; Pinilla, C.; Demergasso, C. ConferenceProceedingWhole Talk (2012)
Genomics and metagenomics of extremely acidic environments Holmes, D. S. ConferenceProceedingWhole Invited talk (2012)
Microbial Diversity: the “Copernican” Revolution of Biology Holmes, D. S. ConferenceProceedingWhole Invited talk (2012)
Omics and Meta-Omics of Extremely Acidic Environments Holmes, D. S. ConferenceProceedingWhole Invited talk (2012)
Psychrotolerant acidophiles in a subsurface metal sulfide mine: from (meta)genomes to biotechnological applications Stell, A.; Liljeqvist, M.; Valdés, J.; Holmes, D. S.; Dopson, M. ConferenceProceedingWhole Talk (2012)
The evolution of electron transport chains during the anaerobic to aerobic transition before or during the “Great Oxygenation Event” 2.4 billion years ago Sepúlveda, R.; Holmes, D. S. ConferenceProceedingWhole Invited talk (2012)


Taking the pulse of Latin American microbiology: the 18th ALAM Congress (Pucon, 23-26 October 2006) Holmes, DS; Mora, G EditorialMaterial ISI INTERNATIONAL MICROBIOLOGY (2006)
Latin American genome initiative, the creation of a network and web based resource to aid and nurture genome biology in developing countries Ramirez J.L.; González A; Cantu J.M.; Chavez-Crooker, P; Leiva J.C.; Blarney J.M.; Cortes, H; Holmes D EditorialMaterial ISI ELECTRONIC JOURNAL OF BIOTECHNOLOGY (2002)


Comparative genomic, metagenomic and bioinformatic approaches to generating fundamental and applied knowledge for bioleaching and other acidic econiches FONDECYT (1130683) Proyecto 2013-2017 Inv. Principal
Application of Bioinformatics and Comparative Genomics to Investigate the Ecophysiology of Bioleaching Microorganisms FONDEF (1090451) Proyecto 2009-2013 Inv. Principal
Desarrollo de Arreglos de ADN Especializados para el Monitoreo de Transcriptomas Industriales de Biolixiviación Innova-Corfo Proyecto 2009-2012 Coinvestigador(a)
Sistema de Aprendizaje Colaborativo Basado en Infraestructura Grid (SACGRID)=> Aplicaciones en Ciencias Biológicas y Biotecnología. FONDEF (TE08I1021) Proyecto 2009-2012 Coinvestigador(a)
Genomic Analysis of Biomining Bacteria present at La Escondida Mine BHP Billiton Proyecto 2008-2009 Coinvestigador(a)
Microsoft Sponsored Research Microsoft Research Proyecto 2006-2009 Inv. Principal
Modeling Acidithiobacillus ferrooxidans metabolism by Microarray Transcript Profiling Conicyt (C05B01) Proyecto 2006-2007 Inv. Principal
Bioinformatic and Functional Genomic Analysis for Understanding the Unusual Physiology of Acidithiobacillus ferrooxidans FONDEF (1050063) Proyecto 2005-2009 Inv. Principal
Global protein-DNA binding site analysis in Acidithiobacillus ferrooxidans=> a microarray-based genomic mapping of protein binding sites for the iron responsive transcriptional regulator Fur Universidad Andrés Bello Proyecto 2005-2006 Inv. Principal
Microarray analysis to measure transcript expression in Acidithiobacillus ferrooxidans CNRS/Conicyt Proyecto 2003-2005 Coinvestigador(a)
Functional and Genomic Analysis of Acidithiobacillus ferrooxidans (formerly Thiobacillus ferrooxidans). FONDEF (1010623) Proyecto 2001-2005 Inv. Principal
A new model for the oxidation of iron in Thiobacillus ferrooxidans=> implications for the evolution of electron transport FONDECYT (1980665) Proyecto 1998-2001 Inv. Principal
Development of Genetically Engineered Biosensors DICYT Proyecto 1997-2005 Inv. Principal
Papel de la Secuencía de la Inserción IST1 en la generación de Thiobacillus ferrooxidans que difieren en sus capacidades para oxidar fierro FONDEF (1950560) Proyecto 1995-1998 Inv. Principal
Minerals Bioprocessing II National Science Fundation Proyecto 1994-1995 Inv. Principal
Construction and Evaluation of a Novel Metal Ion Biosensor Office of Naval Research Proyecto 1990-1993 Inv. Principal
Genetic Engineering of a Biosensor to Detect PCB's NYS Science and Technology Foundation with Matching funds from General Electric Proyecto 1990-1993 Inv. Principal
High Rate Biodegradation of Hazardous Wastes in Situ NYS Center for Hazardous Waste Proyecto 1990-1992 Coinvestigador(a)
Construction and Evaluation of Self-Luminescent Biosensors National Science Fundation Proyecto 1989-1993 Inv. Principal


Metal resistance in acidophilic microorganisms and its significance for biotechnologies Dopson, M; Holmes, DS Review ISI SCOPUS APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2014)
Genomic insights into microbial iron oxidation and iron uptake strategies in extremely acidic environments Bonnefoy, V; Holmes, D.S. Review ISI SCOPUS Environmental Microbiology (2012)
Lessons from the genomes of extremely acidophilic bacteria and archaea with special emphasis on bioleaching microorganisms Cardenas, JP; Valdés J.; Quatrini, R; Duarte F.; Holmes, DS Review ISI SCOPUS Applied Microbiology and Biotechnology (2010)
Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications Valdés J.; Pedroso, I.; Quatrini, R; Dodson RJ; Tettelin H; Blake R; Eisen JA; Holmes, DS Review ISI SCOPUS BMC GENOMICS (2008)
Review of International Biohydrometallurgy Symposium, Frankfurt, 2007 Holmes, DS Review ISI SCOPUS HYDROMETALLURGY (2008)
Thermophiles like hot T Lieph, R; Veloso FA; Holmes, DS Review ISI TRENDS IN MICROBIOLOGY (2006)

203

David Holmes

Head, Laboratory of Bioinformatics and Genome Biology

Center for Bioinformatics and Genome Biology

FUNDACION CIENCIA & VIDA

Santiago, Chile

Raquel Quatrini

Research Associate

Fundación Ciencia & Vida

Santiago, Chile

Jorge Valdes

PROFESOR ASOCIADO

CENTRO DE BIOINFORMÁTICA Y BIOLOGÍA INTEGRATIVA

Universidad Andrés Bello

Santiago, Chile

Juan Cardenas

Assistant Professor

Universidad Mayor de Chile

Santiago, Chile

Paulo Covarrubias

Profesional

Genética Molecular

Instituto de Salud Pública

Santiago, Chile

Gloria Levican

Académica Profesora Titular

Departamento de Biología

UNIVERSIDAD DE SANTIAGO DE CHILE

Santiago, Chile

Carolina González

Post Doctoral Fellow

Department of Biology and Environmental Science

Linnaeus University

Kalmar, Suecia

Inti Pedroso

Profesor Asistente

Facultad de Ciencias

Universidad Mayor

Santiago, Chile

Claudia Lefimil

Profesor Asistente

Instituto de Investigación en Ciencias odontológicas

UNIVERSIDAD DE CHILE

Santiago, Chile

Héctor Osorio

Postdoctorado

Departamento de Biología

Universidad de Santiago de Chile

Santiago, Chile

Diego Cortez

Ana Moya

Profesor Asistente

Departamento de Informática y Computación

Universidad Tecnológica Metropolitana

Ñuñoa, Chile

Francisco Issotta

Investigador Postoctoral

Genética Molecular y Microbiología

Pontificia Universidad Católica de Chile

Santiago, Chile

Pedro Galleguillos

Investigador Titular

Minería

CICITEM

Antofagasta, Chile

Pablo Valenzuela

Founder and Scientific Director

Fundación Ciencia & Vida

Santiago, Chile

Mauricio Acosta

Profesor Adjunto

Vicerrectoría de Investigación y Desarrollo Tecnológico

Universidad Católica del Norte

Antofagasta, Chile

Cecilia Demergasso

Directora

Centro de Biotecnología "Profesor Alberto Ruiz"

UNIVERSIDAD CATÓLICA DEL NORTE

Antofagasta, Chile

Gonzalo Riadi

Assistant Professor

Bioinformatics

Universidad de Talca

Talca, Chile

Francisco Moya

Postdoctoral Associate

Medicina

MICROB-R

Santiago, Chile

Michael Seeger

Full Professor

Chemistry

UNIVERSIDAD TÉCNICA FEDERICO SANTA MARÍA

Valparaíso, Chile

Omar Orellana

Profesor Titular

Programa de Biología Celular y Molecular

FACULTAD DE MEDICINA, UNIVERSIDAD DE CHILE

Santiago, Chile

Mariella Rivas

Profesor Asistente

Biotecnología

Universidad de Antofagasta

Antofagasta, Chile

Harold Nuñez

PostDoc

FUNDACIÓN CIENCIA PARA LA VIDA

Santiago, Chile

Marlén Barreto

Profesor asociado

UNIVERSIDAD AUTONOMA DE CHILE

Santiago de Chile, Chile

Tomas Perez-Acle

Full Professor

Computational Biology Lab

Fundación Ciencia para la Vida

Santiago, Chile

Camila Salazar

Investigador

Biomédico

Universidad de Antofagasta

Antofagasta, Chile

Roddy Jorquera

Investigador

Investigación del cáncer

Fundación Arturo López Pérez

Santiago, Chile

Nicolas Guiliani

Profesor Titular

Biología

UNIVERSIDAD DE CHILE

Santiago, Chile

Lorena Escudero

Investigador

Medio ambiente

CICITEM

Antofagasta, Chile

RODRIGO FLORES

Investigador

Biología Celular y Molecular

Universidad de Chile

Macul, Chile

Lina Ruiz

Academico Docente Investigador

Instituto de Ciencias Biomédicas

Universidad Autónoma de Chile

Santiago, Chile

Raul Araya

Profesor Asistente

Facultad de Ingenieria y Tecnologia

Universidad San Sebastián

Santiago, Chile

Sabrina Marin

Profesor(a) Adjunto(a)

Centro de Biotecnología CBAR

Universidad Católica del Norte

Antofagasta, Chile

Ivan Nancucheo

Profesor Titular

Facultad de Ingeniería, Arquitectura y Diseño

Universidad San Sebastián

Concepción, Chile

Pedro Galleguillos

Investigador

Centro de Investigación Científico y Tecnológico para la Minería

Antofagasta, Chile

Max Chacón

Profesor Titular

Ingeniería Informática

UNIVERSIDAD DE SANTIAGO DE CHILE

Santiago, Chile

Mauricio Arenas

Profesor Asistente

Bioinformática

UNIVERSIDAD DE TALCA

talca, Chile

Alberto Martin

Associate professor

Centro Ciencia & Vida

Universidad San Sebastián

Santiago, Chile

Cristóbal Medina

CEO

Lircaytech

Santiago, Chile

Susan Bueno

Profesor Asociado

Genética Molecular y Microbiología

PONTIFICIA UNIVERSIDAD CATOLICA DE CHILE

Santiago, Chile

David Loyola

carolina inostroza

investigador

Universidad de Los Andes

Santiago, Chile

Matías Castro

Investigador

Ingeniería y Tecnología

Universidad San Sebastián

Concepción, Chile

David Salway Holmes

Líneas de Investigación

Educación

Biochemistry, CALIFORNIA INSTITUTE OF TECHNOLOGY. Estados Unidos, 1973

Genetics, UNIVERSITY OF DUBLIN, TRINITY COLLEGE. Irlanda, 1969

Experiencia Académica

Full Professor Full Time

Laboratory Head Full Time

Full Professor Full Time

Full Professor Full Time

Full Professor Full Time

Research Professor Full Time

Assistant Professor Full Time

Full Professor Full Time

Experiencia Profesional

Head, Laboratory Bioinformatics and genome Biology Full Time

Staff Scientist Full Time

Formación de Capital Humano

Difusión y Transferencia

Premios y Distinciones

Member of the American Society for Microbiology International Committee

Member of the American Society for Microbiology International Committee

Latin American Consul for Chile

International Advisory Board

International Advisory Board

International Advisory Board

Elected Fellow

International Advisory Board

Member Scientific Committee

International Advisory Board

International Advisory Board

International Advisory Board

International Advisory Board

International Advisory Board

Outstanding Service Award

Chairman

Scientific Advisory Board

International Advisory Board

Scientific Advisory Board

Scientific Advisory Board

Local Scientific Committee

Scientific Advisory Board

Planning Committee

International liason officer

International Advisory Board

International Advisory Board

International Advisory Board

Chairman

International Advisory Board

Chairman and Organizer

Chairman

International Advisory Board

Chairman

Scientific Citation Classic

Invited Speaker

Life Time Achievement Award

Award for Scientific and Academic Trajectory

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