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Pedro Andrés Saa Higuera

Profesor Asistente

Pontificia Universidad Catolica de Chile

Santiago, Chile

My research interests include metabolic network and biosystems modelling. My main goal is to develop useful computational tools rooted in advanced optimization and statistical learning methods to gain novel insights about biological systems.

Systems biology, UNIVERSITY OF QUEENSLAND. Australia, 2017
Ingeneria Quimica y Bioprocesos, PONTIFICIA UNIVERSIDAD CATOLICA DE CHILE. Chile, 2012
Ingeniero civil de Biotecnologia, PONTIFICIA UNIVERSIDAD CATOLICA DE CHILE. Chile, 2012
Educación, PONTIFICIA UNIVERSIDAD CATOLICA DE CHILE. Chile, 2023

Ayudante de catedra - Algebra lineal Other

PONTIFICIA UNIVERSIDAD CATOLICA DE CHILE

Facultad de Matematicas

Santiago, Chile

2008 - 2008
Ayudante de catedra - Termodinamica Other

PONTIFICIA UNIVERSIDAD CATOLICA DE CHILE

Facultad de Ingenieria

Santiago, Chile

2009 - 2009
Ayudante de catedra - Fenomenos de transporte Other

PONTIFICIA UNIVERSIDAD CATOLICA DE CHILE

Facultad de Ingenieria

Santiago, Chile

2012 - 2012
Ayudante instructor - Dinamica y Control de Procesos Other

PONTIFICIA UNIVERSIDAD CATOLICA DE CHILE

Facultad de Ingenieria

Santiago, Chile

2012 - 2012
Ayudante instructor - Biotecnologia microbiana Other

PONTIFICIA UNIVERSIDAD CATOLICA DE CHILE

Facultad de Ingenieria

Santiago, Chile

2012 - 2012
Teaching Assistant - Metabolic Engineering Other

UNIVERSITY OF QUEENSLAND

Brisbane, Australia

2016 - 2016
Profesor Asistente Adjunto Part Time

PONTIFICIA UNIVERSIDAD CATOLICA DE CHILE

Facultad de Ingenieria

Santiago, Chile

2017 - 2018
Profesor Asistente Full Time

PONTIFICIA UNIVERSIDAD CATOLICA DE CHILE

Facultad de Ingenieria

Santiago, Chile

2018 - A la fecha

Project Engineer Full Time

Pontificia Universidad Catolica de Chile

Santiago, Chile

2013 - 2013
Project Engineer Full Time

Fraunhofer Chile Research Foundation

Santiago de Chile, Chile

2012 - 2013
Investigador Part Time

Universidad de Chile

Santiago, Chile

2017 - 2018
Investigador Part Time

Pontificia Universidad Católica de Chile

Santiago, Chile

2017 - 2018

1. Ibaceta M (2018 – 2019) Magíster en Ciencias de la Ingeniería, Pontificia Universidad Católica de Chile, Santiago Chile. Co-supervisor.
Título tesis: “Bioprocess engineering for the production of ionones in Saccharomyces cerevisiae”

2. Deantas C (2021 - 2023) Magíster en Ciencias de la Ingeniería, Pontificia Universidad Católica de Chile, Santiago Chile. Supervisor.
Título tesis: “Metabolic Optimization of Halomonas campaniensis for its use as a non-conventional platform for the biotechnological production of polyhydroxybutyrate”

3. Zapararte S (2022 - 2024) Magíster en Ciencias de la Ingeniería, Pontificia Universidad Católica de Chile, Santiago Chile. Supervisor.
Título tesis: “Optimization and random sampling methods for exploring thermodynamically feasible mass-balanced states of metabolic reaction networks”

4. Elizondo B (2021 - 2024). Magíster en Ciencias de la Ingeniería, Pontificia Universidad Católica de Chile, Santiago Chile. Supervisor.
Título tesis: “Development of detailed kinetic models of beta-carotene production in recombinant Saccharomyces cerevisiae strains”

1) Orellana C, Saa PA, Deantas C. Método para la producción de bioplástico polihidroxibutirato (phb) a partir de Halomonas spp. INAPI Chile. Patente solicitada PCT/CL/3429-2023, Nov. 17, 2023.
2) Agosin E, Saa PA, Barceló P, Arenas A. Test olfativo rápido para la identificación temprana de enfermedades que alteran la capacidad olfativa. INAPI Chile. Patente solicitada PCT/CL2020/0500992015904470, Oct. 02, 2020.

Best Master Thesis

PONTIFICIA UNIVERSIDAD CATOLICA DE CHILE

Chile, 2013

Mejor Tesis de Magíster mención Ingeniería Química y Bioprocesos, Promoción 2012-2013
Top graduate student

PONTIFICIA UNIVERSIDAD CATOLICA CAMPINAS

Chile, 2013

Mejor alumno de Magíster mención Ingeniería Química y Bioprocesos, Promoción 2012-2013
Teaching Excellence Award

PONTIFICIA UNIVERSIDAD CATOLICA DE CHILE

Chile, 2018

Premio a la excelencia académica del Departamento de Ingeniería Química y Bioprocesos, Categoría Adjunta
Premio a la Innovación

PONTIFICIA UNIVERSIDAD CATOLICA DE CHILE

Chile, 2021

Premio anual a la Innovación otorgado por la Escuela de Ingeniería UC por el desarrollo de modelo y kit olfativo para la detección rápida de individuos sospechosos de tener COVID19
Conference Junior Researcher Grant

Organizing Committee Metabolic Engineering Conference

Alemania, 2018

Apoyo para asistir y presentar investigación en la conferencia internacional ME-12, München, Alemania. Junio 2018
Premio Excelencia a la Docencia Profesores Jornada Parcial

PONTIFICIA UNIVERSIDAD CATOLICA DE CHILE

Chile, 2018

Premio Excelencia a la Docencia Profesores Jornada Parcial. Escuela de Ingeniería UC
Premio Excelencia a la Docencia

PONTIFICIA UNIVERSIDAD CATOLICA DE CHILE

Chile, 2023

Premio a la Excelencia Docente entregado por la Escuela de Ingeniería anualmente a un académico/a destacado


Fractional adaptive observer for variable structure high cell density fed-batch cultures Article ISI IFAC PAPERSONLINE (2024)
Genome-scale metabolic modeling of the human milk oligosaccharide utilization by <i>Bifidobacterium longum</i> subsp. <i>infantis</i> Article ISI MSYSTEMS (2024)
Genome-scale metabolic modeling of the human milk oligosaccharide utilization by Bifidobacterium longum subsp. infantis Román, Loreto; Pröschle, Tomás Article MSYSTEMS (2024)
LooplessFluxSampler: an efficient toolbox for sampling the loopless flux solution space of metabolic models Drovandi, Christopher C. Article ISI BMC BIOINFORMATICS (2024)
Metabolic modeling of <i>Halomonas campaniensis</i> improves polyhydroxybutyrate production under nitrogen limitation Mendoza, Sebastian N. Article ISI APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2024)
Metabolic modeling of Halomonas campaniensis improves polyhydroxybutyrate production under nitrogen limitation Deantas-Jahn, Carolina; Mendoza, Sebastian Nelson Article Paper WoS Applied Microbiology and Biotechnology (2024)
Reliable calibration and validation of phenomenological and hybrid models of high-cell-density fed-batch cultures subject to metabolic overflow Agosin, Eduardo Article Paper WoS COMPUTERS AND CHEMICAL ENGINEERING (2024)
Sensitivities in protein allocation models reveal distribution of metabolic capacity and flux control van den Bogaard, Samira; Alter, Tobias B. Article ISI BIOINFORMATICS (2024)
Importance of microbial interactions in colonization resistance and gut dysbiosis: role of Bifidobacterium Article ISI Microbiome Research Reports (2023)
GRASP: A computational platform for building kinetic models of cell metabolism Matos, Marta; Volkova, Svetlana; de Leeuw, Marina Article ISI Bioinformatics advances (2022)
GRASP: a computational platform for building kinetic models of cellular metabolism Matos, Marta R. A. Article ISI BIOINFORMATICS ADVANCES (2022)
Metabolic Modeling and Bidirectional Culturing of Two Gut Microbes Reveal Cross-Feeding Interactions and Protective Effects on Intestinal Cells Hirmas, Belen; Saa, Pedro Article ISI MSYSTEMS (2022)
Modeling approaches for probing cross-feeding interactions in the human gut microbiome Saa, Pedro; Silva-Andrade, Claudia Article ISI COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2022)
The topology of genome-scale metabolic reconstructions unravels independent modules and high network flexibility Article ISI, WoS PLOS COMPUTATIONAL BIOLOGY (2022)
A robust hybrid observer for monitoring high-cell density cultures exhibiting overflow metabolism Ibanez-Espinel, Francisco; Gamboa-Labbe, Bastian Article ISI JOURNAL OF PROCESS CONTROL (2021)
Robust control of fed-batch high-cell density cultures: a simulation-based assessment Agosin, Eduardo Article ISI COMPUTERS & CHEMICAL ENGINEERING (2021)
Screening of COVID-19 cases through a Bayesian network symptoms model and psychophysical olfactory test Eyheramendy, Susana; Valencia, Carlos; Finkelstein-Kulka, Andres; Solari, Sandra; Bahamondes, Pedro; BarcelO, Pablo; Arenas, Marcelo; Agosin, Eduardo Article ISI ISCIENCE (2021)
Engineering Saccharomyces cerevisiae for the Overproduction of beta-Ionone and Its Precursor beta-Carotene Bustos, Diego; Camilo, Conrado; Agosin, Eduardo Article ISI FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY (2020)
Genomic integration of unclonable gene expression cassettes in Saccharomyces cerevisiae using rapid cloning-free workflows Salgado V.; Saa P.A. Article ISI SCOPUS MICROBIOLOGYOPEN (2020)
Inferring composition and function of the human gut microbiome in time and space: A review of genome-scale metabolic modelling tools Article ISI COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2020)
Build Your Bioprocess on a Solid Strain-beta-Carotene Production in Recombinant Saccharomyces cerevisiae Saa P.A. Article ISI SCOPUS FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY (2019)
Contextualized genome-scale model unveils high-order metabolic effects of the specific growth rate and oxygenation level in recombinant Pichia pastoris Saa P.A.; Albiol J. Article SCOPUS Metabolic Engineering Communications (2019)
From reconstruction to C-4 metabolic engineering: A case study for overproduction of polyhydroxybutyrate in bioenergy grasses Saa, Pedro A.; Palfreyman, Robin; Nielsen, Lars Keld Article ISI SCOPUS PLANT SCIENCE (2018)
Formulation, construction and analysis of kinetic models of metabolism: A review of modelling frameworks Nielsen, Lars K. Article ISI BIOTECHNOLOGY ADVANCES (2017)
A probabilistic framework for the exploration of enzymatic capabilities based on feasible kinetics and control analysis Article ISI BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS (2016)
Construction of feasible and accurate kinetic models of metabolism: A Bayesian approach Article ISI Scientific Reports (2016)
Fast-SNP: a fast matrix pre-processing algorithm for efficient loopless flux optimization of metabolic models Article ISI BIOINFORMATICS (2016)
ll-ACHRB: a scalable algorithm for sampling the feasible solution space of metabolic networks Article ISI BIOINFORMATICS (2016)
A General Framework for Thermodynamically Consistent Parameterization and Efficient Sampling of Enzymatic Reactions Saa, Pedro Article ISI PLOS COMPUTATIONAL BIOLOGY (2015)
A multi-tissue genome-scale metabolic modelling for the analysis of whole plant systems Gomes de Oliveira Dal'Molin, Cristiana; Quek, Lake-Ee; Nielsen, Lars K. Article FRONTIERS IN PLANT SCIENCE (2015)
Effective dissolved oxygen control strategy for high-cell-density cultures Cárcamo M.; Saa P.A.; Torres, J; Torres, S.; Mandujano, P,; Correa J.R.P.; Agosin, E Article SCOPUS IEEE Latin America Transactions (2014)
Oxygen Incorporation and Dissolution During Industrial-Scale Red Wine Fermentations Moenne, M.I.; Saa, P; Laurie, V. F.; Perez Correa J.R.; Agosin, E Article ISI SCOPUS FOOD AND BIOPROCESS TECHNOLOGY (2014)
Impact of carbon dioxide injection on oxygen dissolution rate during oxygen additions in a bubble column Perez-Correa, JR; Celentano, D; Agosin, E Article ISI SCOPUS Chemical Engineering Journal (2013)
Modeling oxygen dissolution and biological uptake during pulse oxygen additions in oenological fermentations Saa P.A.; Moenne, M.I.; Perez Correa J.R.; Agosin, E Article ISI SCOPUS BIOPROCESS AND BIOSYSTEMS ENGINEERING (2012)
Improved calibration of a solid substrate fermentation model Sacher,J; Saa, P; Cárcamo M.; Lopez J.; Perez-Correa, R Article ISI SCIELO SCOPUS ELECTRONIC JOURNAL OF BIOTECHNOLOGY (2011)


Metabolic modelling of wine fermentation at genome scale Mendoza, Sebastian; Agosin, Eduardo; Cortassa, Sonia; Aon, Miguel BookSection (2022)
Rational metabolic pathway prediction and design: Computational tools and their applications for yeast systems and synthetic biology BookSection (2022)


Model-guided analysis of microbial interactions leading to colonization resistance and dysbiosis in the gut microbiota Daniel Garrido Proyecto (2023)
Sustainable production of mealybug pheromones using engineered biological systems Agosin, Eduardo; Zaviezo, Tania Proyecto (2020)
A general Bayesian framework for leveraging existing kinetic data and thermodynamic constraints for constructing accurate models of cellular metabolism Proyecto (2019)
Identification and modeling of cross-feeding interactions in the gut microbiome for designing microbial communities Proyecto (2019)
Gestión del potencial redox en la cadena de elaboración del vino y su impacto en la calidad FONDEF (D11I1139) Proyecto 2011-2014 Investigador(a)
Oxygen Management during Winemaking FONDECYT (1090520) Proyecto 2009-2012 Tesista


Microbial interactions and the homeostasis of the gut microbiome: the role of<i> Bifidobacterium</i> Riquelme, Erick Review ISI MICROBIOME RESEARCH REPORTS (2023)
Expanding Metabolic Capabilities Using Novel Pathway Designs: Computational Tools and Case Studies Saa P.A. Review ISI SCOPUS BIOTECHNOLOGY JOURNAL (2019)