Ines Azevedo Isidro (2D10-210C-D29C)

Curriculum Vitae

Ines Azevedo Isidro

Inês Isidro is responsible for the Biosystems and Data Science Group at iBET, and a researcher within ITQB-NOVA, Portugal. Her current work combines machine learning, mechanistic modelling, systems biology, and other advanced data analytics concepts and approaches to design tailored, data-driven strategies to tackle complex biological systems, often integrating data from omics and process analytical technologies. Ongoing projects focus on three major goals: improving bioprocesses for cell and gene therapy, enabling precision medicine, and boosting drug discovery with advanced data analytics. She has over 20 published papers (4 as corresponding author) and 2 book chapters. She supervised 5 PhD students (4 concluded, 1 ongoing; 1 as main supervisor) and 5 MSc students (5 concluded). She graduated from Instituto Superior Técnico with an MSc in Biological Engineering and holds a PhD in Bioengineering Systems from the MIT-Portugal Program. During her PhD she developed and applied hybrid metabolic models to improve the production process for an antibody fragment. She was also a co-founder of the biotech startup MediaOmics, where she supported the development of a platform to customize culture media formulations.

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Identification

Personal identification

Full name: Ines Azevedo Isidro

Citation names

Inês A Isidro

Author identifiers

Ciência ID: 2D10-210C-D29C
ORCID iD: 0000-0002-0237-5805

Languages

Language	Speaking	Reading	Writing	Listening	Peer-review
Portuguese (Mother tongue)
English	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)

Education

	Degree	Classification
2010/09 - 2015/12 Concluded	Bioengineering Systems, MIT-Portugal Program (Doutoramento) Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal "Cell functional enviromics: applications to Pichia pastoris" (THESIS/DISSERTATION)
2004/09 - 2009/11 Concluded	Bioengineering (Mestrado integrado) Universidade de Lisboa Instituto Superior Técnico, Portugal "Update of the Yeast Transporter Information Database: Automatic assignment of genes to classes combining clustering and motif prediction tools" (THESIS/DISSERTATION)	17 (MSc); 15 (BSc)

Affiliation

Science

	Category Host institution	Employer
2018/01 - Current	Auxiliary Researcher (Research)	Instituto de Biologia Experimental e Tecnológica, Portugal

2016/04 - 2017/12	Postdoc (Research)	Instituto de Biologia Experimental e Tecnológica, Portugal

2011 - 2016/05	Researcher (Research)	Functional Enviromics Technologies SA, Portugal

2010/03 - 2010/09	Researcher (Research)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Projects

Contract

	Designation	Funders
2020/01 - 2024/12	BRAV3: Computational biomechanics and bioengineering 3D printing to develop a personalized regenerative biological ventricular assist device to provide lasting functional support to damaged hearts H2020 SC1-BHC-07-2019/874827 Researcher Instituto de Biologia Experimental e Tecnológica, Portugal Clínica Universidad de Navarra, Spain	European Commission Ongoing
2022/08 - 2024/10	Glyco-TAM Cracking glycan-lectin interactions to target immunosuppressive macrophages in triple-negative breast cancer PTDC/BTM-ORG/0971/2020 Researcher Instituto de Biologia Experimental e Tecnológica, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2017/10 - 2023/12	Build-up of precision medicine platform using patient derived cell models for prediction of drug efficacy in ovarian cancer patients 201707-05-34 Principal investigator Instituto de Biologia Experimental e Tecnológica, Portugal Instituto Português de Oncologia de Lisboa Francisco Gentil EPE, Portugal	iNOVA4Health – Advancing Precision Medicine Concluded
2019/01 - 2022/12	STACCATO: European Industrial Doctorate for enhancing upstream biopharmaceutical manufacturing process development through single cell analysis H2020 MSCA-ITN-2018/813453 Researcher Instituto de Biologia Experimental e Tecnológica, Portugal National Institute for Bioprocessing Research and Training, Ireland	European Commission Ongoing
2018/10 - 2022/09	ReaViVe: Surface enhanced Raman at- line detection of adeno-associated virus vectors for production optimization PTDC/BTM-SAL/29507/2017 Researcher Instituto de Biologia Experimental e Tecnológica, Portugal Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2020/03 - 2021/11	MintIC: Model-based intensification of AAV production in insect cells MintIC Principal investigator Instituto de Biologia Experimental e Tecnológica, Portugal	Instituto de Biologia Experimental e Tecnológica Ongoing
2018/04 - 2021/03	MetaCardio: Metabolic signatures of human pluripotent stem cells derived cardiomyocytes for improved cell therapy PTDC/BTM-SAL/32566/2017 Researcher Instituto de Biologia Experimental e Tecnológica, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2017/12 - 2020/10	DYNAMO: Elucidating the engineering principles in small-scale bioreactor systems for rational process intensification DYNAMO Researcher Instituto de Biologia Experimental e Tecnológica, Portugal	Instituto de Biologia Experimental e Tecnológica Ongoing
2018/01 - 2020/02	SysBIC: Leveraging systems biology to fine-tune production of AAV vectors in insect cells SysBIC Principal investigator Instituto de Biologia Experimental e Tecnológica, Portugal	Instituto de Biologia Experimental e Tecnológica Concluded
2017/12 - 2019/12	VOOmics: Omics approaches to investigate the anticancer properties of colonic metabolites derived from Virgin Olive OiL VOOmics Researcher Instituto de Biologia Experimental e Tecnológica, Portugal	Instituto de Biologia Experimental e Tecnológica Concluded
2017/12 - 2019/12	mAbs&CF: Cell-free systems: a powerful tool for biopharmaceuticals production and functional characterization mAbs&CF Researcher Instituto de Biologia Experimental e Tecnológica, Portugal	Instituto de Biologia Experimental e Tecnológica Concluded
2013/05 - 2015/08	Cell functional enviromics: unravelling the function of environmental factors PTDC/BBB-BSS/2800/2012 PhD Student Fellow Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal Instituto de Biologia Experimental e Tecnológica, Portugal Associação para a Inovação e Desenvolvimento da FCT, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2011/09 - 2012/03	Bridging Systems and Synthetic Biology for the development of Improved Microbial Cell Factories MIT-Pt/BSBB/0082/2008 PhD Student Fellow Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2010/03 - 2010/09	Multilevel modelling of physical and biochemical processes in phototrophic biofilms PTDC/BIA-MIC/72512/2006 Research Fellow Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal	Fundação para a Ciência e a Tecnologia Concluded

Outputs

Publications

Book chapter	Inês A Isidro; Daniel AM Pais; Paula M Alves; Manuel JT Carrondo. "Online Control Strategies". In Comprehensive Biotechnology, 943-951. 2019. Published Inês A Isidro; Ana R Ferreira; João J Clemente; António E Cunha; João ML Dias; Rui Oliveira. "Design of pathway-level bioprocess monitoring and control strategies supported by metabolic networks". In Measurement, Monitoring, Modelling and Control of Bioprocesses, 193-215. Springer Berlin Heidelberg, 2012. 10.1007/10_2012_168
Journal article	Marta H.G. Costa; Inês Carrondo; Inês A. Isidro; Margarida Serra. "Harnessing Raman spectroscopy for cell therapy bioprocessing". Biotechnology Advances (2024): http://dx.doi.org/10.1016/j.biotechadv.2024.108472. 10.1016/j.biotechadv.2024.108472 Pedro Vicente; Joana I. Almeida; Inês E. Crespo; Nikolaus Virgolini; Inês A. Isidro; Maria Eréndira Calleja-Cervantes; Juan R. Rodriguez-Madoz; et al. "Oxygen control in bioreactor drives high yield production of functional hiPSC-like hepatocytes for advanced liver disease modelling". Scientific Reports (2024): http://dx.doi.org/10.1038/s41598-024-75582-z. 10.1038/s41598-024-75582-z Nikolaus Virgolini; Marco Silvano; Ryan Hagan; Ricardo Correia; Paula M. Alves; Colin Clarke; António Roldão; Inês A. Isidro. Corresponding author: Inês A. Isidro. "Impact of dual-baculovirus infection on the Sf9 insect cell transcriptome during rAAV production using single-cell RNA-seq". Biotechnology and Bioengineering (2023): https://doi.org/10.1002/bit.28377. 10.1002/bit.28377 Marta H G Costa; Margarida S Costa; Beatriz Painho; Carolina D Sousa; Inês Carrondo; Enrique Oltra; Beatriz Pelacho; et al. "Enhanced bioprocess control to advance the manufacture of mesenchymal stromal cell-derived extracellular vesicles in stirred-tank bioreactors". Biotechnology and Bioengineering (2023): https://doi.org/10.1002/bit.28378. 10.1002/bit.28378 Marco Silvano; Nikolaus Virgolini; Ricardo Correia; Colin Clarke; Inês A. Isidro; Paula M. Alves; António Roldão. "Dissecting insect cell heterogeneity during influenza VLP production using single-cell transcriptomics". Frontiers in Bioengineering and Biotechnology 11 (2023): http://dx.doi.org/10.3389/fbioe.2023.1143255. 10.3389/fbioe.2023.1143255 Nikolaus Virgolini; Ryan Hagan; Ricardo Correia; Marco Silvano; Sofia Fernandes; Paula M. Alves; Colin Clarke; António Roldão; Inês A Isidro. "Transcriptome analysis of Sf9 insect cells during production of recombinant Adeno-associated virus". Biotechnology Journal (2022): http://dx.doi.org/10.1002/biot.202200466. 10.1002/biot.202200466 Alexandre B. Murad; Marcos Q. Sousa; Ricardo Correia; Inês A. Isidro; Manuel J. T. Carrondo; António Roldão. "Targeted metabolic analysis and MFA of insect cells expressing influenza HA-VLP". Processes 10 11 (2022): 2283. https://doi.org/10.3390/pr10112283. Open access • 10.3390/pr10112283 Marco Silvano; Ricardo Correia; Nikolaus Virgolini; Colin Clarke; Paula M. Alves; Inês A. Isidro; António Roldão. "Gene expression analysis of adapted insect cells during influenza VLP production using RNA-sequencing". Viruses 14 10 (2022): 2238. https://doi.org/10.3390/v14102238. Open access • 10.3390/v14102238 Rita Mendes; Gonçalo Graça; fernanda silva; Ana Catarina Leite Guerreiro; Patrícia Gomes-Alves; Jacinta Serpa; Erwin R. Boghaert; et al. Corresponding author: Inês A Isidro. "Exploring metabolic signatures of ex vivo tumor tissue cultures for prediction of chemosensitivity in ovarian cancer". Cancers 14 18 (2022): 4460. https://www.mdpi.com/2072-6694/14/18/4460. Open access • 10.3390/cancers14184460 Sofia B Carvalho; Ricardo A Gomes; Anja Pfenninger; Martina Fischer; Michaela Strotbek; Inês A Isidro; Nihal Tugçu; Patrícia Gomes-Alves. "Multi attribute method implementation using a High Resolution Mass Spectrometry platform: From sample preparation to batch analysis". PLOS ONE 17 1 (2022): e0262711-e0262711. http://dx.doi.org/10.1371/journal.pone.0262711. 10.1371/journal.pone.0262711 Inês A Isidro; Pedro Vicente; Daniel AM Pais; Joana I. Almeida; Mara Domingues; Bernardo Abecasis; Natalia Zapata-Linares; et al. "Online monitoring of hiPSC expansion and hepatic differentiation in 3D culture by dielectric spectroscopy". Biotechnology and Bioengineering 118 9 (2021): 3610-3617. https://doi.org/10.1002/bit.27751. 10.1002/bit.27751 Meghan C Cox; Rita Mendes; Fernanda Silva; Teresa F Mendes; Adelyn Zelaya-Lazo; Kathleen Halwachs; Julie J Purkal; et al. "Application of LDH assay for therapeutic efficacy evaluation of ex vivo tumor models". Scientific Reports 11 1 (2021): https://doi.org/10.1038/s41598-021-97894-0. 10.1038/s41598-021-97894-0 Ana Luísa Cartaxo; Almeida, Jaime; Emilio J. Gualda; Maria Marsal; Pablo Loza-Alvarez; Catarina Brito ; Inês A Isidro. Corresponding author: Inês A Isidro. "A computational diffusion model to study antibody transport within reconstructed tumor microenvironments". BMC Bioinformatics 21 1 (2020): 529. http://dx.doi.org/10.1186/s12859-020-03854-2. Open access • 10.1186/s12859-020-03854-2 Daniel AM Pais; Chris Brown; Anastasia Neuman; Krishanu Mathur; Inês A Isidro; Paula M Alves; Peter G Slade. "Dielectric spectroscopy to improve theproduction of rAAV used in gene therapy". Processes 8 11 (2020): 1456-1456. https://doi.org/10.3390/pr8111456. Open access • Published • 10.3390/pr8111456 Daniel AM Pais; Paulo RS Galrão; Anastasiya Kryzhanska; Jérémie Barbau; Inês A Isidro; Paula M Alves. "Holographic imaging of insect cell cultures: online non-invasive monitoring of adeno-associated virus production and cell concentration". Processes 8 4 (2020): 487. http://dx.doi.org/10.3390/pr8040487. Open access • Published • 10.3390/pr8040487 João V Sá; Daniel Simão; Ana P Terrasso; Marta M Silva; Catarina Brito; Inês A Isidro; Paula M Alves; Manuel JT Carrondo. "Unveiling dynamic metabolic signatures in human induced pluripotent and neural stem cells". PLOS Computational Biology (2020): http://dx.doi.org/10.1371/journal.pcbi.1007780. Open access • Published • 10.1371/journal.pcbi.1007780 Daniel AM Pais; Rui MC Portela; Manuel JT Carrondo; Inês A Isidro; Paula M Alves. "Enabling PAT in insect cell bioprocesses: In situ monitoring of recombinant adeno-associated virus production by fluorescence spectroscopy". Biotechnology and Bioengineering 116 11 (2019): 2803-2814. http://dx.doi.org/10.1002/bit.27117. 10.1002/bit.27117 Inês A Isidro; Rui MC Portela; Rui Oliveira. "Hybrid metabolic flux analysis and recombinant protein prediction in Pichia pastoris X-33 cultures expressing a single-chain antibody fragment". Bioprocess Biosyst Eng (2016): http://dx.doi.org/10.1007/s00449-016-1611-z. 10.1007/s00449-016-1611-z Inês A Isidro; Ana R Ferreira; João C Clemente; António E Cunha; Rui Oliveira. "Analysis of culture media screening data by projection to latent pathways: The case of Pichia pastoris X-33". Journal of Biotechnology 217 (2016): 82-89. http://dx.doi.org/10.1016/j.jbiotec.2015.10.014. 10.1016/j.jbiotec.2015.10.014 Abel Folch-Fortuny; Rodolfo Marques; Inês A Isidro; Rui Oliveira; Alberto Ferrer. "Principal elementary mode analysis (PEMA)". Mol. BioSyst. 12 3 (2016): 737-746. http://dx.doi.org/10.1039/c5mb00828j. 10.1039/c5mb00828j Ana R Ferreira; João ML Dias; Ana P Teixeira; Nuno Carinhas; Rui MC Portela; Inês A Isidro; Moritz von Stosch; Rui Oliveira. "Projection to latent pathways (PLP): a constrained projection to latent variables (PLS) method for elementary flux modes discrimination". BMC Systems Biology 5 1 (2011): 181. http://dx.doi.org/10.1186/1752-0509-5-181. 10.1186/1752-0509-5-181
Thesis / Dissertation	Inês A Isidro. "Cell functional enviromics: applications to Pichia pastoris". PhD, Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, 2015. Inês A Isidro. "Update of the Yeast Transporter Information Database: Automatic assignment of genes to classes combining clustering and motif prediction tools". Master, Universidade de Lisboa Instituto Superior Técnico, 2009.

Activities

Oral presentation

	Presentation title	Event name Host (Event location)
2022/10	Enabling PAT in insect cell bioprocesses: a monitoring toolbox for AAV production	Integrated Continuous Biomanufacturing V (Sitges, Spain)
2020/11	Improving AAV production in insect cells through metabolic modulation by targeted supplements	PEGS Europe Cambridge Healthtech Institute (Virtual)
2020/07	Enabling PAT in insect cell processes for rAAV production	Bioprocessing Summit Europe Cambridge Healthtech Institute (Virtual)
2019/03	Metabolic modulation of insect cells by baculovirus infection: insights for bioprocess optimization	ISBioTech 9th Spring Meeting International Society for BioProcess Technology (Norfolk, Virginia, Portugal)
2018/03	Hybrid metabolic modelling in upstream process development	Bioprocessing Summit Europe Cambridge Healthtech Institute (Lisbon, Portugal)

Supervision

	Thesis Title Role	Degree Subject (Type) Institution / Organization
2022/11 - Current	Defining the landscape of immunosuppressive myeloid lectins in breast cancer and their potential as therapeutic targets Co-supervisor of Gonçalo Trindade	Molecular BioSciences (PhD) Instituto de Biologia Experimental e Tecnológica, Portugal
2019/06 - 2023/04	Combining single-cell analysis with systems biology to fine-tune production of rAAV vectors in insect cells Co-supervisor of Nikolaus Virgolini	Molecular Biosciences / Staccato European Industrial Doctorate (PhD) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal Instituto de Biologia Experimental e Tecnológica, Portugal
2021/10 - 2022/09	Targeted metabolomics of biofluids and extracellular vesicles of ovarian cancer patients Supervisor	Pharmacy, ERASMUS Program (Master) Universität Wien, Austria Instituto de Biologia Experimental e Tecnológica, Portugal
2018/12 - 2022/07	Harnessing complex metabolic signatures to predict drug efficacy in ovarian cancer Supervisor of Ana Rita Mendes	Bioengineering, MIT-Portugal Program (PhD) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal Instituto de Biologia Experimental e Tecnológica, Portugal
2020/09 - 2022/02	Characterization of extracellular vesicles from ascitic fluid in ovarian cancer patients Supervisor	Biotechnology (Master) Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2016/05 - 2020/04	Metabolic systems biology for stem cell bioprocesses Co-supervisor of João V Sá	Bioengineering - Cell Therapies and Regenerative Medicine Program (PhD) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal Instituto de Biologia Experimental e Tecnológica, Portugal
2016/05 - 2020/04	Development of advanced monitoring and control tools for rAAV production in insect cell system Co-supervisor of Daniel AM Pais	Bioengineering, MIT-Portugal Program (PhD) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal Instituto de Biologia Experimental e Tecnológica, Portugal
2019/02 - 2019/11	Optimization of an insect cell-based manufacturing platform for AAV vectors: a metabolomics-driven approach Supervisor	Pharmaceutical Engineering (Master) Universidade de Lisboa Instituto Superior Técnico, Portugal Instituto de Biologia Experimental e Tecnológica, Portugal
2018/10 - 2019/02	Development of MS-based analytical tools to support discovery of metabolic biomarkers in breast cancer cell Co-supervisor	Pharmacy, ERASMUS Program (Master) Universität Wien, Austria Instituto de Biologia Experimental e Tecnológica, Portugal
2018/02 - 2018/11	Optimization of an insect-based manufacturing platform for AAV vectors Supervisor	Biological Engineering (Master) Universidade de Lisboa Instituto Superior Técnico, Portugal Instituto de Biologia Experimental e Tecnológica, Portugal

Jury of academic degree

	Topic Role	Candidate name (Type of degree) Institution / Organization
2020/04/21	Metabolic systems biology for stem cell bioprocesses Supervisor	João Vasconcelos e Sá (PhD) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2017/11/20	Metabolomic analysis of the reconstructed epidermis cultivation protocol as a tool to improve the skin barrier properties (Thesis) Main arguer	Sandro Filipe Silva Evaristo (Master) Universidade de Lisboa Faculdade de Ciências, Portugal

Course / Discipline taught

	Academic session	Degree Subject (Type)	Institution / Organization
2017 - Current	Tutorial “Bioreaction Principles in Animal Cell Culture”, Animal Cell Technology module, Biochemical Engineering II course	Chemical and Biochemical Engineering (Mestrado integrado)	Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2019 - 2019	Invited lecture "Introduction to QbD and PAT in vaccine and drug manufacturing", Fundamentals of Bioengineering module	Molecular Biosciences (Doutoramento)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2018 - 2018	Invited lecture “Introduction to Process Analytical Technologies”, Animal Cell Technology module, Biochemical Engineering II course	Chemical and Biochemical Engineering (Mestrado integrado)	Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2017 - 2018	Invited lecture “Introduction to Systems Biology”, Animal Cell Technology module	Bioengineering - Cell Therapies and Regenerative Medicine (Doutoramento)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2011 - 2011	Workshop “MATLAB training with applications to bioprocesses”, Bioprocess Engineering module	Bioengineering, MIT-Portugal Program (Doutoramento)	Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal