Joao Fonseca Email & Phone Number

Almada, Pt

Porto, Portugal

- Led a project to enhance internal metabolic modeling capabilities, introducing new algorithms, methodologies, and software solutions.- Partnered in the development of Design of Experiments (DOE) strategies to improve data quality across the organization.- Developed customized dashboards to deliver actionable insights to scientists and stakeholders.- Deployed machine learning models to predict key performance indicators (KPIs) and estimate values that are challenging to measure directly.- Collaborated continuously with cross-functional teams to perform in-depth data analysis on a wide range of experiments.

Porto, Portugal

- Collaborated cross-functionally with software engineering, biology, fermentation, and process development teams to deliver integrated solutions.- Designed and developed backend microservices and frontend components for an internal web application used in metabolic modeling.- Contributed to the full-stack development of internal applications supporting fermentation and process development workflows.- Developed algorithms to automate the conversion of genetic modification representations between yeast strains and constraint-based models.- Implemented advanced zero-shot and low-n inference pipelines utilizing natural language models for protein optimization.

San Francisco

Prof. El-Samad Lab• Designed and conducted experiments in a team setting to create a mammalian cloning toolkit for the rapid and modular design and construction of synthetic gene circuits.• Designed and conducted experiments in a team setting to create a CAS9-based synthetic circuit capable of controlling the mean and noise of expression of endogenous genes in mammalian cells.

San Francisco

Prof. El-Samad Lab• Used a combination of molecular, biochemical, optogenetic, tissue culture, genome editing, next-generation sequencing, microscopy, flow cytometry, and computational techniques to address a wide range of research questions.• Independently designed and conducted experiments to identify fundamental rules of cAMP signaling in kidney epithelial cells.• Designed and conducted experiments in a team setting to create synthetic epithelial tissues that are responsive to light and able to generate highly localized intracellular signals.• Designed and conducted experiments in a collaboration setting to generate yeast mutants and measure the effect of calcium absence in their growth.• Co-wrote an NSF-funded grant to drive a new effort in multicellular models research in the lab.• Mentored six graduate students, one undergraduate student, and one high-school student.• Presented results in lab meetings and international conferences.• Interpreted results, summarized data, prepared figures, and wrote manuscripts for publication.

Vienna

Dr. Ringrose Lab• Designed and conducted experiments in a team setting to identify modifiers of the kinetic properties of Polycomb Group Proteins in Drosophila stem cells.

Vienna

Dr. Ringrose Lab• Used molecular, biochemical, flow cytometry, live-cell microscopy, computational modeling, and fly genetics to address the kinetic properties of PcG proteins in Drosophila.• Independently designed and conducted experiments to identify the kinetic properties of Polycomb proteins in Drosophila stem cells.• Mentored master students.• Interpreted results, summarized data, prepared figures, and wrote a dissertation and successful manuscripts for publication.• Presented results in lab meetings, national, and international conferences.

Vienna

Dr. Ringrose Lab• Used bisulfite sequencing and immunoprecipitation techniques to measure DNA methylation in mouse stem cells• Performed research in a team to detect changes in DNA methylation of mouse stem cells upon differentiation.

Oeiras

SOS response in S. aureus, performed in Dr. Mariana Pinho's lab• Used molecular cloning and live-cell microscopy to measure transcriptional responses of S. aureus to antibiotics.

Lisbon

Roles of actin in gene regulation, performed in Joao Ferreira's lab• Used small molecule inhibitors, immunoblotting, and immunofluorescence techniques to measure gene activity in mammalian cell culture in response to disruption of actin polymerization.

London, United Kingdom

Dr. Michael Antoniou Lab• Performed research in team generating integration-defective lentiviral vectors for muscle gene therapy.• Used molecular cloning and southern blotting to generate and quantify the effectiveness of new integration-defective HIV-1 based vectors for muscle gene therapy.

Dr. Rer. Nat. (Doctor Of Natural Sciences), Molecular Biology

Bachelor'S Degree, Cell/Cellular And Molecular Biology