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Juan Pablo Cardenas Astudillo

Assistant Professor

Universidad Mayor

Santiago, Chile

Líneas de Investigación


* Genómica comparativa y Filogenómica de organismos de la microbiota intestinal * Análisis de la composición, diversidad y función del microbioma intestinal humano con potenciales aplicaciones en enfermedades metabólicas

Educación

  •  Biochemistry, UNIVERSIDAD DE SANTIAGO DE CHILE. Chile, 2008
  •  Biochemistry, UNIVERSIDAD DE SANTIAGO DE CHILE. Chile, 2008
  •  Biotechnology, Universidad Andres Bello. Chile, 2015

Experiencia Académica

  •   Phd candidate Full Time

    Fundacion Ciencia y Vida (FCV)

    Santiago, Chile

    2011 - 2015

  •   Research Assistant Full Time

    Fundacion Ciencia y Vida (FCV)

    Santiago, Chile

    2008 - 2010

  •   Assistant Professor Full Time

    Universidad Mayor

    Biology

    Santiago, Chile

    2019 - A la fecha

Experiencia Profesional

  •   Senior Bioinformatician Full Time

    uBiome

    Santiago, Chile

    2016 - 2019

  •   Research assistant (INNOVA project 08CM01-03) Full Time

    Fundacion Ciencia y Vida

    Santiago, Chile

    2008 - 2010

  •   Profesor Asistente Full Time

    Universidad Mayor

    Chile

    2019 - A la fecha

Premios y Distinciones

  •   Beca de Estudios de Doctorado en Chile

    COMISION NACIONAL DE INVESTIGACION CIENTIFICA Y TECNOLOGICA

    Chile, 2010

    Beca para estudios de doctorado en Chile.

  •   "Evolutionary genomics of ?Akkermansia species: insights into its adaptation to the gut environment

    FONDECYT

    Chile, 2020

    Responsible researcher for ANID/Fondecyt Initiation Grant: "Evolutionary genomics of ?Akkermansia species: insights into its adaptation to the gut environment" (2020 - 2023)


 

Article (32)

Modification of the Trizol Method for the Extraction of RNA from <i>Prorocentrum triestinum</i> ACIZ_LEM2

Huarachi-Olivera, Ronald; Mata, Maria Teresa; Ardiles-Candia, Alonso; Escobar-Mendez, Valentina; Gatica-Cortes, Carlos; Ahumada, Matias; Orrego, Jose; Vidal-Veuthey, Boris; Cardenas, Juan P.; Gonzalez, Leonel; et al.

Article ISI
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES  (2024)

Contribution of -Omics Technologies in the Study of Porphyromonas gingivalis during Periodontitis Pathogenesis: A Minireview

Nuñez-Belmar, Josefa; Morales-Olavarria, Mauricio; Vernal, Rolando

Article ISI
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES  (2023)

Insights into early evolutionary adaptations of the <i>Akkermansia</i> genus to the vertebrate gut

Gonzalez, Damariz; Morales-Olavarria, Mauricio; Vidal-Veuthey, Boris; Cardenas, Juan P.

Article ISI
FRONTIERS IN MICROBIOLOGY  (2023)

Microbiota Profile of the Nasal Cavity According to Lifestyles in Healthy Adults in Santiago, Chile

Toro-Ascuy, Daniela; Cardenas, Juan P. P.; Fuenzalida, Loreto F. F.

Article ISI
Microorganisms  (2023)

Phylogenomic analysis of the <i>Porphyromonas gingivalis-Porphyromonas gulae</i> duo: approaches to the origin of periodontitis



Article ISI
FRONTIERS IN MICROBIOLOGY  (2023)

Transcriptional Signatures and Network-Based Approaches Identified Master Regulators Transcription Factors Involved in Experimental Periodontitis Pathogenesis

Vernal, Rolando

Article ISI
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES  (2023)

Role of microbial secreted proteins in gut microbiota-host interactions

Gonzalez, Damariz

Article ISI
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY  (2022)

Genomic Sequences and Analysis of Five SARS-CoV-2 Variants Obtained from Patients in Lambayeque, Peru

Romulo Aguilar-Gamboa, Franklin; Alberto Salcedo-Mejia, Luis; Miguel Serquen-Lopez, Luis; Mechan-Llontop, Marco Enrique; Omar Tullume-Vergara, Percy; Bonifacio-Briceno, Juan Jose; Salas-Asencios, Ramses; Silva Diaz, Heber

Article ISI
MICROBIOLOGY RESOURCE ANNOUNCEMENTS  (2021)

Insights on the Evolutionary Genomics of the Blautia Genus: Potential New Species and Genetic Content Among Lineages

Maturana, Jose Luis

Article ISI
Frontiers in Microbiology  (2021)

Draft Genome Sequence of Blautia luti DSM 14534(T), Isolated from Human Stool

Ortiz, Rodrigo L.

Article WOS-ESCI
MICROBIOLOGY RESOURCE ANNOUNCEMENTS  (2020)

A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis

Bustamante, Juan P.; Addae, Kwasi; Alegria-Mera, Victor; Bravo, Cristian; Bravo, Denisse; Carson, Glenn A.; Caughey, Adam; Gass, Graham; Gupta, Sarah L.; Harman, Kira; et al.

Article ISI
PLOS ONE  (2019)

Self-Sampling for Human Papillomavirus Testing: Increased Cervical Cancer Screening Participation and Incorporation in International Screening Programs

Gupta, Sarah; Palmer, Christina; Bowers, Jennie

Article ISI
FRONTIERS IN PUBLIC HEALTH  (2018)

16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome

Budovskaya, Yelena V.

Article ISI
PLOS ONE  (2017)

Draft genome sequence of Acidithiobacillus thiooxidans CLST isolated from the acidic hypersaline Gorbea salt flat in northern Chile



Article ISI SCOPUS
Standards in Genomic Sciences  (2017)

Draft genome sequence of the type strain of the sulfur-oxidizing acidophile, Acidithiobacillus albertensis (DSM 14366)



Article ISI SCOPUS
Standards in Genomic Sciences  (2017)

Molecular Systematics of the Genus Acidithiobacillus: Insights into the Phylogenetic Structure and Diversification of the Taxon

Issotta, Francisco; Atavales, Joaquín; Johnson, D. Barrie

Article SCOPUS
Frontiers in Microbiology  (2017)

Aerobic Lineage of the Oxidative Stress Response Protein Rubrerythrin Emerged in an Ancient Microaerobic, (Hyper)Thermophilic Environment



Article SCOPUS
FRONTIERS IN MICROBIOLOGY  (2016)

Genomic and metagenomic challenges and opportunities for bioleaching: a mini-review



Article ISI SCOPUS
RESEARCH IN MICROBIOLOGY  (2016)

SinEx DB: a database for single exon coding sequences in mammalian genomes

Jorquera, Roddy; Sepúlveda, Rene

Article ISI
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION  (2016)

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)

Draft genome sequence of the iron-oxidizing acidophile Leptospirillum ferriphilum type strain DSM 14647

Corbett M.; Watkin E.

Article SCOPUS
Genome Announcements  (2014)

Draft Genome Sequence of the Iron-Oxidizing, Acidophilic, and Halotolerant "Thiobacillus prosperus" Type Strain DSM 5130

Ossandon, F. J.; Holmes, D. S.

Article SCOPUS
Genome Announcements  (2014)

Draft genome sequence of the nominated type strain of "Ferrovum myxofaciens,"" an acidophilic, iron-oxidizing betaproteobacterium"



Article SCOPUS
Genome Announcements  (2014)

Genetic variability of psychrotolerant Acidithiobacillus ferrivorans revealed by (meta)genomic analysis

González, C.; Yanquepe M; Valdés J.; Quatrini, R; Holmes, DS; Dopson, M

Article ISI SCOPUS
RESEARCH IN MICROBIOLOGY  (2014)

Multi Locus Sequence Typing scheme for Acidithiobacillus caldus strain evaluation and differentiation

Núñez H; Loyola D.; Holmes, DS; Johnson, DB; Quatrini, R

Article ISI SCOPUS
RESEARCH IN MICROBIOLOGY  (2014)

Architecture and Gene Repertoire of the Flexible Genome of the Extreme Acidophile Acidithiobacillus caldus

Acuña LG; Covarrubias PC; Haristoy JJ; Flores R.; Núñez H; Riadi G.; Shmaryahu, A; Valdés J.; Dopson, M; Rawlings DE; et al.

Article ISI SCOPUS
PLOS ONE  (2013)

Comparative genomics of the oxidative stress response in bioleaching microorganisms

Cardenas J.P.; Moya, F; Covarrubias P; Shmaryahu, A; Levicán G; Quatrini, R

Article ISI SCOPUS
Hydrometallurgy  (2012)

Thiol/Disulfide System Plays a Crucial Role in Redox Protection in the Acidophilic Iron-Oxidizing Bacterium Leptospirillum ferriphilum

Norambuena, J.; Flores R.; Cardenas J.P.; Quatrini, R; Chavez, R; Levicán G

Article ISI SCOPUS
PLOS ONE  (2012)

Comparative genomics begins to unravel the ecophysiology of bioleaching

Valdés J.; 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.; Bowien B.; Jedlicki, E; Holmes, DS

Article ISI SCOPUS
BMC Microbiology  (2010)

Predicted CO/CO2 fixation in Ferroplasma spp. via a novel chimaeric pathway

Juan Pablo Cárdenas, Veronica Martínez; Paulo Covarrubias, David S. Holmes

Article
Advanced Materials Research  (2009)

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.; Esparza M.; Orellana O.; et al.

Article ISI SCOPUS
HYDROMETALLURGY  (2006)

BookSection (1)

Chapter 11: Progress in Acidophile Genomics



BookSection
 (2016)

ConferencePaper (3)

Comparative study of redox stress response in the acidophilic bacteria Leptospirillum ferriphilum and Acidithiobacillus ferrooxidans

Norambuena, J.

ConferencePaper
 (2011)

Predicted CO/CO(2) fixation in Ferroplasma spp. via a novel chimaeric pathway

Martínez V; Covarrubias P; Holmes, DS; Quatrini, R

ConferencePaper ISI
BIOHYDROMETALLURY: FROM THE SINGLE CELL TO THE ENVIRONMENT  (2009)

Prediction of FNR regulated genes and metabolic pathways potentially involved in anaerobic growth of Acidithiobacillus ferrooxidans

Osorio H.; Cardenas J.P.; Valdes J.; Holmes D.S.

ConferencePaper ISI SCOPUS
ADVANCED MATERIALS RESEARCH  (2009)

Correction (1)

Transcriptional Signatures and Network-Based Approaches Identified Master Regulators Transcription Factors Involved in Experimental Periodontitis Pathogenesis. <i>(vol</i> <i>24</i>, 14835, 2023)

Vicencio, Emiliano; Nuñez-Belmar, Josefa; Cardenas, Juan P.; Cortes, Bastian I.; Martin, Alberto J. M.; Maracaja-Coutinho, Vinicius; Rojas, Adolfo; Cafferata, Emilio A.; Gonzalez-Osuna, Luis; Vernal, Rolando; et al.

Correction ISI
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES  (2024)

Patent (1)

Method and system for panel characterizations

Apte Z; Richman, J.; Almonacid D; Kraal L; Ossandon F; Bik E; Goddard A

Patent Patent filled and published.
 (2018)

Proyecto (2)

“Desarrollo de Arreglos de ADN Especializados para el monitoreo de Transcriptomas Industriales de Biolixiviacio&#769;n”

Innova CORFO (08CM01-03)

Proyecto
2009-2011
Personal técnico y/o de apoyo

ESTRATEGIAS BIOINFORMATICAS Y DE GENOMICA FUNCIONAL EN LA COMPRENSION DE LA INUSUAL FISIOLOGIA DE LA BACTERIANA ACIDITHIOBACILLUS FERROOXIDANS.

FONDECYT (1050063)

Proyecto
2005-2008
Tesista

Review (1)

Lessons from the genomes of extremely acidophilic bacteria and archaea with special emphasis on bioleaching microorganisms

Valdés J.; Quatrini, R; Duarte F.; Holmes, DS

Review ISI SCOPUS
Applied Microbiology and Biotechnology  (2010)

1
Carlos Riquelme

Director Centro de Bioinnovacion

UNIVERSIDAD DE ANTOFAGASTA

Antofagasta, Chile

16
David Holmes

Head, Laboratory of Bioinformatics and Genome Biology

Center for Bioinformatics and Genome Biology

FUNDACION CIENCIA & VIDA

Santiago, Chile

1
Lorena Escudero

Investigador

Medio ambiente

CICITEM

Antofagasta, Chile

1
Renato Chavez

Full Professor

Biology

UNIVERSIDAD DE SANTIAGO DE CHILE

Santiago, Chile

1
Denisse Bravo

Profesora Titular

Odontología

Universidad Andrés Bello

Santiago, Chile

1
Rolando Vernal

Profesor Titular

Departamento de Odontología Conservadora

UNIVERSIDAD DE CHILE

Santiago, Chile

2
Gloria Levican

Académica Profesora Titular

Departamento de Biología

UNIVERSIDAD DE SANTIAGO DE CHILE

Santiago, Chile

3
Harold Nuñez

PostDoc

FUNDACIÓN CIENCIA PARA LA VIDA

Santiago, Chile

1
Francisco Zorondo

Profesor Asociado

Departamento de Gestión Agraria

Universidad de Santiago de Chile

Santiago, Chile

1
Katia Soto

Académica

Universidad de Chile

Santiago, Chile

5
Jorge Valdes

PROFESOR ASOCIADO

CENTRO DE BIOINFORMÁTICA Y BIOLOGÍA INTEGRATIVA

Universidad Andrés Bello

Santiago, Chile

1
Pedro Galleguillos

Investigador Titular

Minería

CICITEM

Antofagasta, Chile

1
Alberto Martin

Associate professor

Centro Ciencia & Vida

Universidad San Sebastián

Santiago, Chile

1
Vinicius Ramos Henriques

Associate Professor

Advanced Center for Chronic Diseases - ACCDiS

Univesidad de Chile

Santiago, Chile

1
Alexia Núñez

Profesora Asistente

Departamento de Biología

Universidad de Chile

Santiago, Chile

1
Luis Leon

Head of Bioinformatics and Computational Biology

Technology

PhageLab

Santiago, Chile

1
SEBASTIAN REYES

Profesor Asistente

Centro de Genómica y Bioinformática

Universidad Mayor de Chile

Santiago, Chile

1
Claudia Lefimil

Profesor Asistente

Instituto de Investigación en Ciencias odontológicas

UNIVERSIDAD DE CHILE

Santiago, Chile

1
Daniela Toro

Profesor Asistente

Facultad de ciencias

Universidad de Chile

Santiago, Chile

3
Cristian Cortez

Profesor Asociado

Facultad de Ciencias

Pontificia Universidad Católica de Valparaíso

Valparaíso, Chile

1
Juan Jiménez

Investigador I+D Senior

Multiplex SpA

Santiago, Chile

1
CRISTIAN BRAVO

Profesional

Laboratorio Biomédico

Instituto Salud Publica

Santiago, Chile

14
Raquel Quatrini

Research Associate

Fundación Ciencia & Vida

Santiago, Chile

1
LILLIAN ACUÑA

INVESTIGADOR POST-DOCTORAL FONDECYT

Laboratorio de Genética y Patógenesis Bacteriana

Universidad Andrés Bello

SANTIAGO, Chile

1
Héctor Osorio

Postdoctorado

Departamento de Biología

Universidad de Santiago de Chile

Santiago, Chile

1
David Loyola

1
Jaime Rivas

Profesor Asociado

Facultad de Ciencias

Universidad Mayor

Santiago, Chile

4
Ana Moya

Profesor Asistente

Departamento de Informática y Computación

Universidad Tecnológica Metropolitana

Ñuñoa, Chile

2
Juan Ugalde

Assistant Professor

Facultad de Ciencias de la Vida

Universidad Andrés Bello

Santiago, Chile

38
Juan Cardenas

Assistant Professor

Centro de Genómica y Bioinformatica

Universidad Mayor

Santiago, Chile

1
Mauricio Acosta

Profesor Adjunto

Vicerrectoría de Investigación y Desarrollo Tecnológico

Universidad Católica del Norte

Antofagasta, Chile

7
Paulo Covarrubias

Profesional

Biomédico

Instituto de Salud Pública

Santiago, Chile

1
Francisco Moya

Postdoctoral Associate

Medicina

MICROB-R

Santiago, Chile

2
RODRIGO FLORES

Investigador

Biología Celular y Molecular

Universidad de Chile

Macul, Chile

4
Josefa Núñez

Investigadora

Centro de Genómica y Bioinformática

Universidad Mayor de Chile

Santiago, Chile

1
Gonzalo Riadi

Assistant Professor

Bioinformatics

Universidad de Talca

Talca, Chile

4
Francisco Issotta

Investigador Postoctoral

Genética Molecular y Microbiología

Pontificia Universidad Católica de Chile

Santiago, Chile

1
Roddy Jorquera

Investigador

Investigación del cáncer

Fundación Arturo López Pérez

Santiago, Chile

1
Javiera Norambuena

Post-Doctoral Associate

Biochemistry and Microbiology

Rutgers University

New Brunswick, Estados Unidos

1
Alonso Ardiles

Técnico/investigador

Centro de Bioinnovación

Universidad de Antofagasta

Antofagasta , Chile