David_holmes.jpeg_thumb90

David Holmes Salway

Head, Laboratory of Bioinformatics and Genome Biology

FUNDACION CIENCIA & VIDA

Santiago, Chile

Líneas de Investigación


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

Educación

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

Experiencia Académica

  •   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

Experiencia Profesional

  •   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

Formación de Capital Humano


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


Difusión y Transferencia


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


Premios y Distinciones

  •   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).


 

Article (134)

SinEx DB 2.0 update 2020: database for eukaryotic single-exon coding sequences
AciDB 1.0: a database of acidophilic organisms, their genomic information and associated metadata
Evolution of Predicted Acid Resistance Mechanisms in the Extremely Acidophilic Leptospirillum Genus
Genome-based classification of Acidihalobacter prosperus F5 (=DSM 105917=JCM 32255) as Acidihalobacter yilgarnensis sp. nov
Unlocking Survival Mechanisms for Metal and Oxidative Stress in the Extremely Acidophilic, Halotolerant Acidihalobacter Genus
Effect of CO2 Concentration on Uptake and Assimilation of Inorganic Carbon in the Extreme Acidophile Acidithiobacillus ferrooxidans
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
Identification and Unusual Properties of the Master Regulator FNR in the Extreme Acidophile Acidithiobacillus ferrooxidans
Uncovering the Mechanisms of Halotolerance in the Extremely Acidophilic Members of the Acidihalobacter Genus Through Comparative Genome Analysis
Improved ontology for eukaryotic single-exon coding sequences in biological databases
16S rRNA and Multilocus Phylogenetic Analysis of the Iron Oxidizing Acidophiles of the Acidiferrobacteraceae Family
Draft genome sequence of Acidithiobacillus thiooxidans CLST isolated from the acidic hypersaline Gorbea salt flat in northern Chile
Draft genome sequence of the type strain of the sulfur-oxidizing acidophile, Acidithiobacillus albertensis (DSM 14366)
Multiple Osmotic Stress Responses in Acidihalobacter prosperus Result in Tolerance to Chloride Ions
Multiple Osmotic Stress Responses in Acidihalobacter prosperus Result in Tolerance to Chloride Ions.
Mutantelec: An In Silico Mutation Simulation Platform for Comparative Electrostatic Potential Profiling of Proteins
Mutantelec=> An In Silico mutation simulation platform for comparative electrostatic potential profiling of proteins.
Aerobic Lineage of the Oxidative Stress Response Protein Rubrerythrin Emerged in an Ancient Microaerobic, (Hyper)Thermophilic Environment
Aerobic Lineage of the Oxidative Stress Response Protein Rubrerythrin Emerged in an Ancient Microaerobic, (Hyper)Thermophilic Environment.
Bioinformatic Analyses of Unique (Orphan) Core Genes of the Genus Acidithiobacillus: Functional Inferences and Use As Molecular Probes for Genomic and Metagenomic/Transcriptomic Interrogation
Bioinformatic Analyses of Unique (Orphan) Core Genes of the Genus Acidithiobacillus=> Functional Inferences and Use As Molecular Probes for Genomic and Metagenomic/Transcriptomic Interrogation
Draft genome sequence of chloride-tolerant Leptospirillum ferriphilum Sp-Cl from industrial bioleaching operations in northern Chile
Draft genome sequence of chloride-tolerant Leptospirillum ferriphilum Sp-Cl from industrial bioleaching operations in northern Chile
Gene Loss and Horizontal Gene Transfer Contributed to the Genome Evolution of the Extreme Acidophile "Ferrovum".
Gene Loss and Horizontal Gene Transfer Contributed to the Genome Evolution of the Extreme Acidophile “Ferrovum”
Genome Analysis of the Biotechnologically Relevant Acidophilic Iron Oxidising Strain JA12 Indicates Phylogenetic and Metabolic Diversity within the Novel Genus "Ferrovum"
Genomic and metagenomic challenges and opportunities for bioleaching: a mini-review
Graphlet Based Metrics for the Comparison of Gene Regulatory Networks
Graphlet Based Metrics for the Comparison of Gene Regulatory Networks.
SinEx DB: a database for single exon coding sequences in mammalian genomes
SinEx DB=> a database for single exon coding sequences in mammalian genomes.
Expression and activity of the Calvin-Benson-Bassham cycle transcriptional regulator CbbR from Acidithiobacillus ferrooxidans in Ralstonia eutropha
Metagenomic analysis reveals adaptations to a cold-adapted lifestyle in a low-temperature acid mine drainage stream
Reclassification of 'Thiobacillus prosperus' Huber and Stetter 1989 as Acidihalobacter prosperus gen. nov., sp nov., a member of the family Ectothiorhodospiraceae
a-fur, an antisense RNA gene to fur in the extreme acidophile Acidithiobacillus ferrooxidans
AFAL: a web service for profiling amino acids surrounding ligands in proteins
alpha-fur, an antisense RNA gene to fur in the extreme acidophile Acidithiobacillus ferrooxidans
Draft Genome Sequence of the Iron-Oxidizing Acidophile Leptospirillum ferriphilum Type Strain DSM 14647.
Draft Genome Sequence of the Iron-Oxidizing, Acidophilic, and Halotolerant "Thiobacillus prosperus" Type Strain DSM 5130
Draft Genome Sequence of the Iron-Oxidizing, Acidophilic, and Halotolerant "Thiobacillus prosperus" Type Strain DSM 5130.
Draft Genome Sequence of the Nominated Type Strain of
Draft genome sequence of the nominated type strain of “Ferrovum myxofaciens,” an acidophilic, iron-oxidizing betaproteobacterium
Genetic variability of psychrotolerant Acidithiobacillus ferrivorans revealed by (meta)genomic analysis
Metal resistance or tolerance? Acidophiles confront high metal loads via both abiotic and biotic mechanisms
Multi Locus Sequence Typing scheme for Acidithiobacillus caldus strain evaluation and differentiation
Anaerobic Sulfur Metabolism Coupled to Dissimilatory Iron Reduction in the Extremophile Acidithiobacillus ferrooxidans
Architecture and Gene Repertoire of the Flexible Genome of the Extreme Acidophile Acidithiobacillus caldus
Astrogenomics=> A convergence of disciplines spawning inspiration
An artifact in studies of gene regulation using beta-galactosidase reporter gene assays
Comparative genomics of the oxidative stress response in bioleaching microorganisms
Complete Genome Sequence of Temperate Bacteriophage AcaML1 from the Extreme Acidophile Acidithiobacillus caldus ATCC 51756
ICEAfe1, an Actively Excising Genetic Element from the Biomining Bacterium Acidithiobacillus ferrooxidans
TnpPred: AWeb Service for the Robust Prediction of Prokaryotic Transposases
Draft Genome of the Psychrotolerant Acidophile Acidithiobacillus ferrivorans SS3
Draft Genome Sequence of the Extremely Acidophilic Biomining Bacterium Acidithiobacillus thiooxidans ATCC 19377 Provides Insights into the Evolution of the Acidithiobacillus Genus
Molecular dynamics study of the archaeal aquaporin AqpM
Sulfur metabolism in the extreme acidophile Acidithiobacillus caldus
Comparative genomics begins to unravel the ecophysiology of bioleaching
Genes and pathways for CO2 fixation in the obligate, chemolithoautotrophic acidophile, Acidithiobacillus ferrooxidans, Carbon fixation in A. ferrooxidans
A 300 Kb Genome Segment, including a Complete Set of tRNA Genes, is Dispensable for Acidithiobacillus ferrooxidans
Comparative Genomics Begins to Unravel the Ecophysiology of Bioleaching
Draft Genome Sequence of the Extremely Acidophilic Bacterium Acidithiobacillus caldus ATCC 51756 Reveals Metabolic Versatility in the Genus Acidithiobacillus
Extending the models for iron and sulfur oxidation in the extreme Acidophile Acidithiobacillus ferrooxidans
Genomic Lessons from Biomining Organisms=> Case Study of the Acidithiobacillus Genus
Predicting the Function of Hypothetical Genes in Genomes of Bioleaching Microorganisms
Prediction of FNR Regulated Genes and Metabolic Pathways Potentially Involved in Anaerobic Growth of Acidithiobacillus Ferrooxidans
Protein Function in Extremely Acidic Conditions=> Molecular Simulations of a Predicted Aquaporin and a Potassium Channel in Acidithiobacillus Ferrooxidans
Regulation of expression of the PetI operon involved in iron oxidation in the biomining bacterium Acidithiobacillus ferrooxidans
Selection and evaluation of reference genes for improved interrogation of microbial transcriptomes: case study with the extremophile Acidithiobacillus ferrooxidans
Small Regulatory RNA Genes in Acidithiobacillus ferrooxidans=> case studies of 6S RNA and frr
AlterORF: a database of alternate open reading frames
Comparative genome analysis of Acidithiobacillus ferrooxidans, A. thiooxidans and A. caldus: Insights into their metabolism and ecophysiology
Iron homeostasis strategies in acidophilic iron oxidizers: Studies in Acidithiobacillus and Leptospirillum
Microbial iron management mechanisms in extremely acidic environments: comparative genomics evidence for diversity and versatility
Preparation and Analysis of an Expressed Sequence Tag Library from the Toxic Dinoflagellate Alexandrium catenella
Bioinformatic prediction and experimental verification of Fur-regulated genes in the extreme acidophile Acidithiobacillus ferrooxidans
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
Insights into the Metabolism and Ecophysiology of Three Acidithiobacilli by Comparative Genome Analysis
Regulation of a novel Acidithiobacillus caldus gene cluster involved in metabolism of reduced inorganic sulfur compounds
Second acyl homoserine lactone production system in the extreme acidophile Acidithiobacillus ferrooxidans
Generation and analysis of expressed sequence tags from Botrytis cinerea
Insights into the iron and sulfur energetic metabolism of Acidithiobacillus ferrooxidans by microarray transcriptome profiling
Microarray and bioinformatic analyses suggest models for carbon metabolism in the autotroph Acidithiobacillus ferrooxidans
Taking the pulse of Latin American microbiology
A Lux-like Quorum Sensing System in the Extreme Acidophile Acidithiobacillus ferrooxidans
Genomic insights into the iron uptake mechanisms of the biomining microorganism Acidithiobacillus ferrooxidans
Identification of a gene cluster for the formation of extracellular polysaccharide precursors in the chemolithoautotroph Acidithiobacillus ferrooxidans
Large-scale, multi-genome analysis of alternate open reading frames in bacteria and archaea
Role of complementary proteins in autoimmunity: an old idea re-emerges with new twists
The ferric iron uptake regulator (Fur) from the extreme acidophile Acidithiobacillus ferrooxidans
Apparent redundancy of electron transfer pathways via bc(1) complexes and terminal oxidases in the extremophilic chemolithoautotrophic Acidithiobacillus ferrooxidans
Aspects of the predicted physiology of Acidithiobacillus ferrooxidans deduced from an analysis of its partial genome sequence
Metabolic reconstruction of sulfur assimilation in the extremophile Acidithiobacillus ferrooxidans based on genome analysis
Characterization of the petI and res operons of Acidithiobacillus ferrooxidans
Latin American Genome Initiative, the Creation of a Network and Web Based Resource to Aid and Nurture Genome Biology in Developing Countries
ISAfe1, an ISL3 family insertion sequence from Acidithiobacillus ferrooxidans ATCC 19859
An RT-PCR Artifact in the Characterization of Bacterial Operons.
Functional Analysis of Gapped Microbial Genomes=> Principles with Examples from Thiobacillus ferrooxidans.
Biotechnology=> Miners in miniature.
IST1 Insertional Inactivation of the resB Gene=> Implications for Phenotypic Switching in Thiobacillus ferrooxidans.
Sequence and Expression of the Rusticyanin Structural Gene from Thiobacillus ferrooxidans ATCC33023 strain.
Biological cyanide destruction mediated by microorganisms.
Development of Biosensors for the Detection of Mercury and Copper Ions.
Transposition of IST2 in Thiobacillus ferrooxidans.
Development of Biosensors to Measure Metal Ion Bioavailability in Environmental Samples.
This Week's Citation Classic
Construction and evaluation of a self-luminescent biosensor.
Biotechnology in the Mining and Metal-Processing Industries. Challenges and Opportunities.
IST2=> A New Insertion Sequence in Thiobacillus ferrooxidans
Phenotypic Switching of Thiobacillus ferrooxidans.
Two Families of Repeated DNA Sequences in Thiobacillus ferrooxidans
Designed Metal-Binding Proteins
Use of X-ray Computed Tomographic to Examine Microbial Desulfurization of Lump Coal
Acidiphilium organovorum sp. nov., An Acidophilic Heterotroph Isolated from a Thiobacillus ferrooxidans Culture.
Strategy for the Establishment of a Genetic System for the Acidophilic Heterotroph, Acidiphilium organovorum.
The Use of Genetic Probes to Detect Microorganisms in Biomining Operations.
Cloning of a Thiobacillus ferrooxidans Plasmid in E. coli.
Improved Rapid Heating Technique for Screening Recombinant DNA Plasmids in E. coli.
The Cot Curve.
A Note on the Use of CsCl Centrifugation to Purify Bacterial Plasmids Prepared by the Rapid Boiling Method.
Rapid Purification of Bacterial Plasmids and Coliphage M13 RF Without CsCl Centrifugation.
The Use of Agar for Electrophoresis of DNA Fragments.
A Rapid Method for the Preparation of Plasmids.
Specific Increase of Perchloric Acid Extractable Chromosomal Proteins During Mammalian Erythropoieses.
Structure of the Chromosomal Material in Inactive Nuclei of Chicken Red Blood Cells.
The Mesokaryote Gyrodinium cohnii Lacks Nucleosomes
Applications of the Avidin biotin Methods of Gene Enrichment to the Isolation of Long Double-Stranded DNA Containing Specific Gene Sequences
Positions of Sea Urchin Histone Genes Relative to Restriction Endonuclease Sites on the Chimeric Plasmids pSp2 and pSp17.
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.
Interspersion of Repetitive and Single Copy Sequences in High Molecular Weight Nuclear RNA.
Sequence Composition of Rat Ascites Chromosomal RNA.
Sequence Composition of Rat Nuclear DNA and High Molecular RNA
Preparation, Molecular Weight, Base Composition and Secondary Structure of Giant Nuclear RNA.
Chromosomal RNA: Its Properties

Abstract (1)

Apparent redundancy of electron transfer pathways to oxygen in the extremophilic chemolithautotrophic bacterium acidithiobacillus ferrooxidans

BookSection (16)

The Genomics of Acidophiles
Application of CellDesigner to the Selection of Anticancer Drug Targets: Test Case using P53
The Use of Bioinformatics and Genome Biology to Advance Our Understanding of Bioleaching Microorganisms
Genetic and Bioinformatic Insights into Iron and Sulfur Oxidation Mechanisms of Bioleaching Organisms
Detection and measurement of ultra-trace levels of mercury and copper by genetically engineered microbial sensors
Biorecovery of Metals from Mining Wastes
Biohydrometallurgy
Biorecovery of Waste Materials from Mining Operations
Opportunities for Biological Metal Recovery
Adaptation of Thiobacillus ferrooxidans for Industrial Applications
Basic Principles of Genetic Manipulation of Thiobacillus ferrooxidans for Biohydrometallurgical Applications
Genetic Engineering of Microorganisms for Pollution Control
Molecular Enzyme Engineering
Construction and Use of Molecular Probes to Identify and Quantitate Bioleaching Microorganisms
Genetic Engineering of Biomining Organisms
Sequence Composition and Organization of the Genome and Nuclear RNA of Higher Organisms: An Approach to Understanding Gene Regulation

ConferencePaper (9)

Analysis of gene expression in response to copper stress in Acidithiobacillus ferrooxidans strain D2, isolated from a copper bioleaching operation
Temporal dynamics of genes involved in metabolic pathways of C and N of L. ferriphilum, in the industrial bioleaching process of Escondida mine, Chile
C-di-GMP pathway in biomining bacteria
Gene organization and CO(2)-responsive expression of four cbb operons in the biomining bacterium Acidithiobacillus ferrooxidans
Predicted CO/CO(2) fixation in Ferroplasma spp. via a novel chimaeric pathway
Preliminary genomic and functional analysis of a cDNA library from Botrytis cinerea
Discovery of small regulatory RNAs extends our understanding of gene regulation in the Acidithiobacillus genus
Insights into the metabolism and ecophysiology of three acidithiobacilli by comparative genome analysis
Iron homeostasis strategies in acidophilic iron oxidizers: Comparative genomic analyses

ConferencePoster (35)

Putting metabolism on the road: the case for the emergence of life in hot acid
Comparative Analyses of Metagenomes from Acid Mine Drainages
Metagenomic analyses reveal specific adaptations to metal efflux of Acidithiobacillus ferrivorans SS3
Microbial Iron Oxidation in High Salt: Implications for Martian Habitat Investigation
Potential Sources of Oxygen on Early Earth Before the Great Oxygenation Event (GOE)
Benchmarking Available Methods for Prediction of Mobile Genetic Elements in Complete Genomes
Benchmarking of Binning Methods Using a Conceptual Metagenome
Comparative Analysis of Metagenomes from Extremely Acidic Environments Using a Phylogenetic Approach
Inference of gene regulatory networks during embryonic development of Drosophila melanogaster
Investigating the Biochemical Potential of the Iron Oxidizing Betaproteobacterium Ferrovum sp. JA12 at the Genomic and Transcriptomic level
Acidithiobacillus phylogenomics: understanding ecophysiology in extreme acidic environments by whole genome evolutionary reconstruction (2013)
Analysis of gene expression in response to stress induced by copper in Acidithiobacillus ferrooxidans strain D2, an isolated from a copper bioleaching operation
Análisis filogenómico del complejo heterodisúlfuro reductasa (HdrABC) en genomas microbianos
Biomining on Mars: Challenges and Opportunities
Biomining on planetary bodies: challenges and opportunities
Eukaryotic Single Exon Genes
Evolution of terminal electron transfer proteins during the anaerobic/aerobic transition in the Archean era
Extremely acidic environments on earth as surrogates for habitable planetary bodies
Heterodisulfide reductase complex: a key to energetics in early evolution
Phenotypic analysis of an Acidithiobacillus caldus mutant defective in c-di-GMP production
Psychrotolerant acidophiles in a subsurface metal sulphide mine: from (meta)genomes to biomining
AFAL: a web service for determine the profiling amino acids surrounding ligands in Protein Data Bank
AFAL: a web service for profiling amino acids surrounding ligands in Protein Data Bank crystallographic data
Análisis fisiológico de bacterias (biolixiviantes) mesotermófilas del género Sulfobacillus empleando herramientas de biología genómica
Análisis metagenómico de comunidades microbianas de ambiente ácido y psicrófilo procedentes de desechos residuales mineros
Bioinformatic and Biophysical Characterization of FUR (Ferric Uptake Regulator) from an extreme Acidophile Thriving in an Iron Rich Environment
Comparative genomics of the oxidative stress response in acidophile microorganisms
Computational Pattern Recognition for the Identification of Transposases in Prokaryotic Genomes: Challenges and Advances
High Dimensional multi-genomic investigation into the function and evolution of eukaryotic single exon genes
High Dimensional, Multi-Genomic Investigation into the function and evolution of eukaryotic single exon genes
Human single exon genes
Niche specific oxidative stress response in extreme acidophiles
Regulando a un regulador: el caso de Fur en Acidithiobacillus ferrooxidans
Study and molecular characterization of the hypothetical representative of a third subfamily of aquaporins, AqpF from Acidothiobacillus ferrooxidans
Toxin-Antitoxin Systems Encoded in an Integrative Conjugative Element from the Biomining Bacterium Acidithiobacillus ferrooxidans

ConferenceProceedingWhole (56)

Are We Alone in the Universe?
Astrobiology: When Disciplines Collide Innovation Happens (2017)
Probing the Deep Evolutionary Roots of Thermo-Acidophiles (2017)
Acidihalobacter prosperus, a halophilic acidophile, has unique mechanisms to survive high chloride concentrations at low pH
Acidihalobacter prosperus, a halophilic acidophile, has unique mechanisms to survive high chloride concentrations at low pH. (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
Comparative Genomics Sheds Light on the Evolutionary Dynamics and Sympatric Speciation of Life in Extremely Acidic Environments
Comparative Genomics Sheds Light on the Evolutionary Dynamics and Sympatric Speciation of Life in Extremely Acidic Environments (<pH 2)
Comparative Genomics Sheds Light on the Evolutionary Mechanisms and Dynamics of Extreme Acidophiles
Genomes in Turmoil: Frugality Drives Microbial Community Structure in Extremely Acidic Environments
Insights into the Evolutionary Mechanisms and Dynamics of Extreme Acidophiles
Probing the Deep Evolutionary Roots of Thermo-Acidophiles (2016)
Astrobiology: When Disciplines Collide Innovation Happens
Astrobiology: When Disciplines Collide Innovation Happens (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
Forces shaping microbial speciation in extremely acidic environments: insights from the Acidithiobacillus genus
Genomics and Metagenomics of Extreme Acidophiles in Biomining Environments
Navigating the Genomes-to-Ecosystems Cascade in Biomining Environments
Probing the Deep Evolutionary Roots of Thermo-acidophiles
Probing the Deep Evolutionary Roots of Thermo-acidophiles (2015)
Acidithiobacillus Phylogenomics: Understanding Ecophysiology In Extreme Acidic Environments By Whole Genome Evolutionary Reconstruction
Advances in Our Understanding of Bioleaching using Omic Approaches
Astrobiology: Emerging Opportunities for Environmental Microbiologists
Astrobiology: The Next Frontier
Biological Challenges and Opportunities in Biomining: Biooxidation Tank Reactors, Heap, Dump and In Situ Bioleaching and Acid Mine Drainage Bioremediation
Genomic and evolutionary insights into adaptation of "Thiobacillus prosperus" (Acidihalobacillus prosperus sp. nov) to saline and acidic environments
Genomic Project of Acidiferrobacter “MURCIENSIS” Sp. Spiii/3: insights into Biofilm Formation and Cell-to-Cell Communication Mechanisms
Genomics and Metagenomics of Acidophiles
Modeling Sulfur Oxido-Reduction Pathways in Early Evolution
Non-similarity Techniques for Predicting Gene Function
Potential for the Early Evolution of Life in Acidic Conditions
The role of iron and sulfur exergonic oxido-reduction pathways in the early evolution of life
Thiobacillus prosperus, a halophilic acidophile, has unique mechanisms to survive high chloride concentrations at low pH
Unraveling evolutionary pathways for genomic and phenotypic diversification and its predicted impact on the ecophysiology of biomining Acidithiobacilli
Astrogenomics: A Convergence of Disciplines Spawning Inspiration
At the Interface of Genomics and Astrobiology: When Disciplines Collide Innovations Happen
Bioinformatics and Genome Biology of Prokaryotes
Bioinformatics Workshop: Hands-on
Bioleaching: opportunities, challenges and future directions
Oxidative stress response in acidophilic bacteria: the role of Fur and PerR regulators
Protein Evolution during the Archean Anaerobic/Aerobic Transition
Psychrotolerant Acidophiles in a Subsurface Metal Sulphide Mine: From (Meta)Genomes to Biomining (2013)
Recent advances in iron biogeochemistry in extremely acidic conditions
Stabilization of proteins in extreme thermo-acidic environments
Summary of investigations at the Center for Bioinformatics and Genome Biology
The ecophysiology of bioleaching: A genomics perspective
Understanding functional relationships across an evolutionary gradient within the Acidithiobacillus genus
Bioleaching heaps provide special opportunities for studying the adaption, ecophysiology and evolution of extreme acidophiles
Challenges for life at pH 1: a genomics and metagenomics perspective
Characterization of Fur protein from Acidithiobacillus ferrooxidans an extreme acidophile thriving in an iron rich environment using bioinformatic and biophysical techniques.
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.
Genomics and metagenomics of extremely acidic environments
Microbial Diversity: the “Copernican” Revolution of Biology
Omics and Meta-Omics of Extremely Acidic Environments
Psychrotolerant acidophiles in a subsurface metal sulfide mine: from (meta)genomes to biotechnological applications
The evolution of electron transport chains during the anaerobic to aerobic transition before or during the “Great Oxygenation Event” 2.4 billion years ago

EditorialMaterial (2)

Taking the pulse of Latin American microbiology: the 18th ALAM Congress (Pucon, 23-26 October 2006)
Latin American genome initiative, the creation of a network and web based resource to aid and nurture genome biology in developing countries

Proyecto (19)

Comparative genomic, metagenomic and bioinformatic approaches to generating fundamental and applied knowledge for bioleaching and other acidic econiches
Application of Bioinformatics and Comparative Genomics to Investigate the Ecophysiology of Bioleaching Microorganisms
Desarrollo de Arreglos de ADN Especializados para el Monitoreo de Transcriptomas Industriales de Biolixiviación
Sistema de Aprendizaje Colaborativo Basado en Infraestructura Grid (SACGRID)=> Aplicaciones en Ciencias Biológicas y Biotecnología.
Genomic Analysis of Biomining Bacteria present at La Escondida Mine
Microsoft Sponsored Research
Modeling Acidithiobacillus ferrooxidans metabolism by Microarray Transcript Profiling
Bioinformatic and Functional Genomic Analysis for Understanding the Unusual Physiology of Acidithiobacillus ferrooxidans
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
Microarray analysis to measure transcript expression in Acidithiobacillus ferrooxidans
Functional and Genomic Analysis of Acidithiobacillus ferrooxidans (formerly Thiobacillus ferrooxidans).
A new model for the oxidation of iron in Thiobacillus ferrooxidans=> implications for the evolution of electron transport
Development of Genetically Engineered Biosensors
Papel de la Secuencía de la Inserción IST1 en la generación de Thiobacillus ferrooxidans que difieren en sus capacidades para oxidar fierro
Minerals Bioprocessing II
Construction and Evaluation of a Novel Metal Ion Biosensor
Genetic Engineering of a Biosensor to Detect PCB's
High Rate Biodegradation of Hazardous Wastes in Situ
Construction and Evaluation of Self-Luminescent Biosensors

Review (6)

Metal resistance in acidophilic microorganisms and its significance for biotechnologies
Genomic insights into microbial iron oxidation and iron uptake strategies in extremely acidic environments
Lessons from the genomes of extremely acidophilic bacteria and archaea with special emphasis on bioleaching microorganisms
Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications
Review of International Biohydrometallurgy Symposium, Frankfurt, 2007
Thermophiles like hot T
199
David Holmes

Head, Laboratory of Bioinformatics and Genome Biology

Center for Bioinformatics and Genome Biology

FUNDACION CIENCIA & VIDA

Santiago, Chile

34
Raquel Quatrini

Research Associate

Fundación Ciencia & Vida

Santiago, Chile

19
Jorge Valdes

I

CENTRO DE GENOMICA Y BIOINFORMATICA

UNIVERSIDAD MAYOR

Santiago, Chile

15
Juan Cardenas

Assistant Professor

Universidad Mayor de Chile

Santiago, Chile

8
Paulo Covarrubias

Profesional

Genética Molecular

Instituto de Salud Pública

Santiago, Chile

7
Gloria Levican

Académica Profesora Titular

Departamento de Biología

UNIVERSIDAD DE SANTIAGO DE CHILE

Santiago, Chile

6
Héctor Osorio

Postdoctorado

Departamento Genética Molecular y Microbiología

Pontificia Universidad Católica de Chile

Santiago, Chile

6
Inti Pedroso

Profesor Asistente

Facultad de Ciencias

Universidad Mayor

Santiago, Chile

6
Claudia Lefimil

Profesor Asistente

Instituto de Investigación en Ciencias odontológicas

UNIVERSIDAD DE CHILE

Santiago, Chile

5
Carolina González

Postdoctorado

Centro de Genómica y Bioinformática

Universidad mayor

Santiago, Chile

4
Pedro Galleguillos

Investigador Titular

Minería

CICITEM

Antofagasta, Chile

4
Pablo Valenzuela

Founder and Scientific Director

Fundación Ciencia & Vida

Santiago, Chile

3
Gonzalo Riadi

Assistant Professor

Bioinformatics

Universidad de Talca

Talca, Chile

3
Mauricio Acosta

Investigador

Universidad Católica del Norte

Antofagasta, Chile

3
Cecilia Demergasso

Directora

Vicerrectoría de Investigación y Desarrollo Tecnológico

UNIVERSIDAD CATÓLICA DEL NORTE

Antofagasta, Chile

2
Harold Nuñez

PostDoc

FUNDACIÓN CIENCIA PARA LA VIDA

Santiago, Chile

2
Omar Orellana

Profesor Titular

Programa de Biología Celular y Molecular

FACULTAD DE MEDICINA, UNIVERSIDAD DE CHILE

Santiago, Chile

2
Michael Seeger

Full Professor

Chemistry

UNIVERSIDAD TÉCNICA FEDERICO SANTA MARÍA

Valparaíso, Chile

2
Mauricio Arenas

Profesor Asistente

Bioinformática

UNIVERSIDAD DE TALCA

talca, Chile

2
Marlén Barreto

Profesor asociado

UNIVERSIDAD AUTONOMA DE CHILE

Santiago de Chile, Chile

2
Tomas Perez-Acle

Full Professor

Computational Biology Lab

Fundación Ciencia para la Vida

Santiago, Chile

2
Mariella Rivas

Profesor Asistente

Biotecnología

Universidad de Antofagasta

Antofagasta, Chile

2
Francisco Moya

Postdoctoral Associate

Medicina

MICROB-R

Santiago, Chile

1
Raul Araya

Docente Investigador

Facultad de Ingenieria y Tecnologia

Universidad San Sebastián

Santiago, Chile

1
Braulio Valdebenito

.

.

.

TALCA, Chile

1
Sabrina Marín

Investigadora

Centro de Biotecnología CBAR

Universidad Católica del Norte

Antofagasta, Chile

1
Lina Ruiz

Academico Docente Investigador

Instituto de Ciencias Biomédicas

Universidad Autónoma de Chile

Santiago, Chile

1
Nicolas Guiliani

Profesor Titular

Biología

UNIVERSIDAD DE CHILE

Santiago, Chile

1
Jose Reyes

Académico Jornada Completa

Bioinformática

UNIVERSIDAD DE TALCA

Talca, Chile

1
Lorena Escudero

Investigador

Medio ambiente

CICITEM

Antofagasta, Chile

1
Pedro Galleguillos

Investigador

Centro de Investigación Científico y Tecnológico para la Minería

Antofagasta, Chile

1
Ivan Nancucheo

Docente Investigador

Universidad San Sebastián

Concepción, Chile

1
Alberto Martin

Assistant professor

Centro de Genómica y Bioinformática

Universidad Mayor

Santiago, Chile

1
Cristóbal Medina

CEO

Lircaytech

Santiago, Chile

1
Camila Salazar

Investigador

Biomédico

Universidad de Antofagasta

Antofagasta, Chile

1
Susan Bueno

Profesor Asociado

Genética Molecular y Microbiología

PONTIFICIA UNIVERSIDAD CATOLICA DE CHILE

Santiago, Chile

1
RODRIGO FLORES

Investigador

Biología Celular y Molecular

Universidad de Chile

Macul, Chile

1
JOSE GARATE

Profesor Asistente

Instituto de Neurociencia

Universidad de Valparaíso

Valaparaiso, Chile

1
Matías Castro

Investigador

Ingeniería y Tecnología

Universidad San Sebastián

Concepción, Chile