Pedro T. Monteiro @ INESC-ID/IST

		Pedro T. Monteiro
		Affiliation:	INESC-ID / IST - Universidade de Lisboa
		Address:	INESC-ID Lisboa Rua Alves Redol 9 1000-029 Lisboa PORTUGAL
		Email:
		Telef:	Alameda campus - ext: 2320 / tel: +351 21 3100 320 TagusPark campus - ext: 5281 / tel: +351 21 0407 081

Research Interests - Formal methods: algorithms, formal verification, model checking, Boolean functions, model revision
- Computational systems biology: bioinformatics, gene regulatory networks, logical modeling

My research develops formal and static-analysis methods for biological regulatory networks, with the aim of characterizing the dynamical behaviors of qualitative (logical) models. I investigate how the structure of Boolean functions shapes model dynamics, and I design model revision procedures that repair or refine models so they agree with experimental observations.

A central goal of this work is to deliver these methods to the scientific community as Software tools. These include pyModRev (Boolean model revision), GINsim (modeling and analysis of gene regulatory networks), and EpiLog (simulatiion of epithelial pattern formation). I am a member of the CoLoMoTo consortium, which promotes standards and interoperability in logical modeling. I also maintain YEASTRACT+, a curated repository and analysis platform for cross-species regulatory network analysis in yeast.

Short CV Pedro T. Monteiro is an Associate Professor at the Department of Computer Science and Engineering of Instituto Superior Técnico (IST) - Universidade de Lisboa, and a researcher at INESC-ID Lisboa in the Automated Reasoning and Software Reliability (ARSR) scientific area.

He holds BSc and MSc degrees in Computer Science and Engineering from IST - Universidade Técnica de Lisboa, and worked for one year in the private sector before pursuing doctoral studies. In 2010 he received a joint PhD from IST - Universidade Técnica de Lisboa (Computer Science and Engineering) and Université Claude Bernard Lyon 1 (Bioinformatique), carried out largely in the IBIS Group at INRIA Grenoble - Rhône-Alpes, under the supervision of Hidde de Jong.
He subsequently held postdoctoral positions at Molecular Microbiology and Infection Unit (Mário Ramirez), Instituto de Medicina Molecular (IMM), and at the Network Modelling group (Claudine Chaouiya), Instituto Gulbenkian de Ciência (IGC). In 2013 he was awarded an Investigador FCT Starting Grant and joined INESC-ID Lisboa as a research fellow.
He joined the faculty of the Department of Computer Science and Engineering at IST in 2016 as an Assistant Professor and was promoted to Associate Professor in 2020.

He has held visiting researcher positions at the MABioS group - Institut de Mathématiques de Marseille (I2M) during spring 2019, and at the Computational Systems Biology of Cancer team - Institut Curie and the Institut de Biologie de l'École Normale Supérieure (IBENS) during spring 2026.

Alongside his research, he contributes to academic leadership at IST. Since 2021 he has been serving in the coordination of the MSc in Computer Science and Engineering (MEIC), IST's largest MSc programme, serving as Deputy Coordinator (2021-2022) and Coordinator (2023-2024 + 2025-2026). He also served on the IST Pedagogical Council (2025-2026) as Counselor representing the degree coordinators.

Projects - RevLog: Inference and revision of logical regulatory models: from cellular to multicellular models, PI, funded by FCT. Bilateral PHC-PESSOA with Elisabeth Remy at Institut de Mathématiques de Marseille (I2M), France.
- PiCaSSo: Pediatric Palliative Care Support System, Task leader, funded by FCT in collaboration with CHULN-HSM
- LAIfeBlood+: Artificial Intelligence for Blood Management, Task leader, funded by FCT in collaboration with IPST
- FAIRY: FAIRification of YEASTRACT+ to Support Yeast-based Bioeconomy and Health, PI, funded by O.S.C.A.R.S. (Open Science Clusters' Action for Research & Society) Horizon Europe
- LAIfeBlood: Artificial Intelligence for Blood Management, PI, funded by FCT in collaboration with IPST
- BioData.pt: Portuguese Biological Data Network, Task leader, funded by FCT
- MIXEDUP: Targeting pathogenesis and engineering cell factories: by developing mixed regulatory-metabolic genomic models in yeasts, Task leader, funded by FCT
- ERGODiC: Formal methods for the analysis of modular gEnetic ReGulatOry network DynamiCs, PI, funded by FCT
- CoMEDy: A COmputational Modelling platform for Epithelial DYnamics to explore the role of epithelial-mesenchymal transition and stemness acquisition in cancer recurrence, Task leader, funded by FCT
- CANTROL: Deciphering the mechanisms of transcriptional regulation that control antifungal drug resistance in the pathogenic yeast Candida glabrata: aiming the development of improved diagnosis and therapeutic approaches, Task leader, funded by FCT
- InvestigadorFCT: Towards a semi-automatic model revision of logical regulatory networks, PI, funded by FCT