Irina Moreira

My goal is to consolidate myself as a leading expert in my core research area (the interface between Computer Sciences and Structural Biology) merging chemistry, bioinformatics, biophysics and data-mining to develop and implement novel approaches and address emerging biological questions that cannot be tackled with traditional approaches alone.

Machine-learning; deep-learning; statistics; data-science; computer science; genomics; cancer; mutagenesis; drug design and discovery; computational chemistry; structural biology; bioinformatics; biophysics; molecular modeling; GPCR/G-protein interactions; GPCR/Arrestin interactions; protein-protein interactions; protein-ligand interactions; protein-DNA interactions; molecular docking; computational mutagenesis; structure prediction; virtual-screening; homology modeling; molecular dynamic simulations; binding free energy calculations; MM-PBSA; TI; protein-protein interfacial evolution.

CURRICULUM VITAE

PROFESSIONAL WEB-SITES

MoreiraLab: http://www.moreiralab.com

CienciaVitae: https://www.cienciavitae.pt/portal/E516-94C9-7B1B

Scopus: https://www.scopus.com/authid/detail.uri?authorId=57191249780

Google Scholar: https://scholar.google.com/citations?user=8D0bgIIAAAAJ&hl=en

ACADEMIC QUALIFICATIONS

2020: Master’s in Mathematical Engineering, Department of Mathematics, Faculty of Sciences, University of Porto, Portugal.

Thesis: “Supervised Classification applied to hot-spot detection in protein-protein interfaces”.

2008: PhD in Chemistry – Computational Biochemistry, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Portugal.

Thesis: “Design of Anti-cancer drugs that target the Vascular Endothelial Growth Factor”.

2003: Grad. Diploma in Biochemistry – Applied Biochemistry, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Portugal.

Thesis: “Genetic Study of Spinocerebellar Ataxias and Familial Hemiplegic Migraine caused by Calcium Channel”.

POSITIONS

2022-present: 3D-Bioinfo Community (ELIXIR – https://elixir-europe.org/) Portuguese Node Representative/Facilitator.

2021-present: Vice-president of BioData.pt – Portuguese distributed infrastructure for biological data and the Portuguese ELIXIR node.

2019-present: Assistant Professor at Life Sciences Department of Science and technology Faculty of University of Coimbra; tenure-track position attained in a competitive call.

2015-present: Group Leader of the “Data Driven Molecular Design” Lab at Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Portugal; position initially awarded under the highly competitive international programme FCT-Investigator for outstanding researchers (contract IF/00578/2014).

2016-2018: Sabbatical leave at Utrecht University, Netherlands, in A. Bonvin’s Lab, under a H2020 Marie Skłodowska-Curie Fellowship (MSCA-IF(EF)-659826).

2009-2014: Associate Researcher (Assistant Professor level), Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto; position awarded under FCT’s international programme “Investigator Ciência 2008” for attracting excellent researchers to Portugal.

2007-2009: Postdoctoral Researcher at Weill Cornell Medical College, NYC, USA; Supervisor: Harel Weinstein (USA).

DECLINED POSITIONS

2019: Assistant Professor at Data Science/Computer Science Department of Science and technology Faculty of University of Coimbra; tenure-track position attained in a competitive call; declined in favor of similar position at Life Sciences Department.

2019: Assistant Researcher (6-year contract CEECIND/03938/2018) awarded under FCT’s (the Portuguese Science Foundation) Employment Stimulus competitive international call.

FELLOWSHIPS

2016-2018: H2020 – Marie Sklodowska-Curie Individual Fellowship (MSCA-IF(EF)). [http://cordis.europa.eu/project/rcn/195851_en.html].

2015: FCT Individual Postdoctoral Fellowship – Declined in favor of the FCT-Investigator position.

2003-2007: FCT Individual PhD Fellowship – To support the PhD in Chemistry at Oporto University.

PEER-REVIEWED RESEARCH GRANTS

2021-2023: “Cutting-Edge Virus-Host Interactome Discovery: A Multi-Omics AI Driven Approach”; Agency: Fundação para a Ciência e a Tecnologia DSAIPA/DS/0118/2020; Role: Principal Investigator.

2020-2024: “Dynamic brain function: towards the understanding and treatment of brain disorders”; Agency: European Commission H2020-WIDESPE-2018-2020-6; Role: Team member.

2020-2023: “Potassium channel dysfunction in models of neurodevelopmental disorders”; Agency: Caixabank SA; Fundação para a Ciência e a Tecnologia (Iniciativa Ibérica de Investigaçao e Inovaçao Biomédica, i4b; HR20-00904; Role: Team member/Task Leader.

2021: “EuroCC Portugal – National Competence Centres in the framework of EuroHPC”; Agency: 951732 – EUROCC – H2020-JTI-EuroHPC-2019-2; Role: Member of Coimbra team led by Pedro Alberto.

2018-2021: “Deep learning in cancer drug discovery: a pipeline for the generation of new therapies”; Agency: FCT – POCI-01-0145-FEDER-031356; Role: Principal Investigator.

2018-2021: “Membrane proteins – development of new computational approaches and its application to G-Protein Coupled Receptors”; Agency: FCT – PTDC/QUI-OUT/32243/2017; Role: co-Principal Investigator.

2018-2021: “Targeting the transporters of cationic amino acids for cancer theranostics: experimental and computational chemistry approach”; Agency: FCT – PTDC/QUI-NUC/30147/2017; Role: Team-member/Task Leader.

2016-2020: “Early Detection, neuromodelation and advanced therapies to brain disorders”; Agency: Centro2020, Institutional driven Project CENTRO-01-0145-FEDER-000008: BrainHealth 2020; Role: Task Leader.

2015-2020: “Molecular mechanisms in signaling selectivity of GPCRs”; Agency: FCT – IF/00578/2014; Role: Principal Investigator.

2013-2015: “In-silico design of semi i-synthetic functional mimics of glutathione peroxidase: from the rational choice of the organochalcogen to its bioincorporation in protein scaffols”; Agency: Progetti de Ricerca di Ateneo (CPDA127392/12); University of Padova; Role: Team member.

2012-2015: “Re(I)/99mTc(I) complexes containing L-arginine derivatives as substrates or inhibitors of Nitric Oxide Synthase: A structure-activity study”; Agency: FCT – PTDC/QUI-QUI/121752/2010; Role: Team member.

PEER-REVIEWED RESEARCH ALLOCATIONS

2020-2021: “Dissecting dopamine receptor 2 functional mechanism” – (CPCA/A2/7219/2020); Agency: FCT-RNCA; Role: Principal-Investigator.

2021-2024: “Cutting-Edge Virus-Host Interactome Discovery: A Multi-Omics AI Driven Approach” – (DSAIPA/DS/0118/2020); Agency: FCT-RNCA; Role: Principal-Investigator.

2020-2021: “Structural and functional role of CACNG2 gene mutations in psychiatric diseases” – (CPCA/A0/7302/2020); Agency: FCT-RNCA; Role: Principal-Investigator.

2018-2019: “Conformational dynamics, assembly and inhibition of GPCR oligomers” – (2017174234); Agency: PRACE; Role: Team-member.

2017-2018: “Structural and dynamic understanding of the ghrelin receptor function on memory and learning: a computational perspective” – (NWO16425); Agency: Surfsara, Netherlands; Role: Co-Principal Investigator.

2015-2017: “Target-specific delivery of radioactivity to cancer cells by virus-like particles”; Agency: Icahn School of Medicine at Mount Sinai; Role: Task leader.

2015-2016: “Biased agonism in the dopamine receptor” – (ISCRA A BiaDop HP10CIQNJW); Agency: CINECA, Italy; Role: Team member.

2014-2015: “In-silico design of enzymatic anti-oxidant systems 2”; Agency: CINECA- IDEAS 2, Italy; Role: Team member.

2013-2014: “In-silico design of semi i-synthetic functional mimics of glutathione peroxidase: from the rational choice of the organochalcogen to its bioincorporation in protein scaffols”; Agency: CINECA – IDEAS, Italy; Role: Team member.

AWARDS

2021: Born for Knowledge (BFK) award 2021 “Health and Wellbeing” – Agência Nacional de Inovação.

2019: Concurso Estímulo ao Emprego Científico Individual – CEECIND/03938/2018 – Highly competitive, declined.

2015: Investigador FCT – IF/00578/2014 – Highly competitive.

2009: Investigator Ciência 2008.

2008: Luso-American Foundation Network Grant (FLAD) – To support the postdoctoral research at the Weill Cornell Medical College.

2003: FCT PhD Fellowship.

2003: Eng. António de Almeida’s Prize – For the top-ranking student in the Biochemistry Degree.

1998: Excellence Prize – For the top-ranking student in the Secondary School.

HONORS

2022: BfK Acceleration Program: INNOV@RISE – winning prize from BFK 2021.

2022: HiEngine program from HiSeed Tech.

2022: Selected for HiTech program from HiSeedTech.

2018: Interview Stage of ERC Starting Grant – LS7 panel.

2014: Committee for Professional Opportunities for Women Travel Award – Biophysical Society Meeting, San Francisco, USA.

2006: MGMS Registration Fellowship – Quantum Pharmacology – 30 years on, Oxford, UK.

2006: NBCR Summer Institute Travel and Registration Fellowship – NBCR Summer Institute: Cyberinfrastructure & Multiscale Modeling Approaches”, La Jolla, California.

2006: Marie Curie Travel and Registration Fellowship – CCP5 and Marie Curie Actions: Methods in Molecular Simulation Summer School 2006”, University of Cardiff, Wales

2006: Italian Physical Society Scholarship – International School of Physics “E. Fermi”, “Protein Folding and Drug Design”, Varenna, Italy.

2006: EMBO Fellowship – “Biomolecular simulation – an EMBO course”, Paris, France.

ering, Oporto University, Portugal.

2008: PhD in Chemistry, Science Faculty, Oporto University, Portugal.

2003: Grad. Diploma in Biochemistry, Science Faculty, Oporto University, Portugal.

PENDING ACADEMIC QUALIFICATIONS

2023 [expected]: Bachelor´s in Mathematical Engineering (87 out of 180 ECTs concluded), Oporto University, Portugal.

POSITIONS

2019-present: Assistant Professor at Life Sciences Department of Science and technology Faculty of University of Coimbra; tenure-track position attained in an international highly competitive call.

2015-present: Group Leader (Assistant Professor level) of the Data Driven Molecular Design Lab at Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Portugal; position awarded under the highly competitive international programme FCT¹– Investigator for outstanding researchers.

2016-2018: Sabbatical leave at Utrecht University, Netherlands, in A. Bonvin’s Lab, under a H2020 Marie Skłodowska-Curie Fellowship (vide infra).

2009-2014: Associate Researcher (Assistant Professor level), Science Faculty, Oporto University, Portugal; position awarded under FCT¹’s international programme “Investigator Ciência 2008” for attracting excellent researchers to Portugal.

2007-2009: Postdoctoral Researcher at Weill Cornell Medical College, NYC, USA; Supervisor: Harel Weinstein (USA).

FELLOWSHIPS

2016-2018: H2020 – Marie Sklodowska-Curie Individual Fellowship(MSCA-IF(EF)). [http://cordis.europa.eu/project/rcn/195851_en.html].

2015: FCT¹ Individual Postdoctoral Fellowship; Declined in favour of the FCT¹– Investigator position.

2003-2007: FCT¹ Individual PhD Fellowship; To support the PhD in Chemistry at Oporto University.

PEER-REVIEWED RESEARCH GRANTS

2020-2024: “Dynamic brain function: towards the understanding and treatment of brain disorders”; Agency: European Commission H2020-WIDESPE–2018-2020-6; Role: Team member.

2018-2021: “Cancer Research Advancement through Deep Learning”; Agency: FCT¹; Role: Principal Investigator.

2015-2020: “Molecular mechanisms in signaling selectivity of GPCRs”; Agency: FCT¹ – IF/00578/2014; Role: Principal Investigator.

2016-2020: “Early Detection, neuromodelation and advanced therapies to brain disorders”; Agency: Centro2020, Institutional driven project; Role: Task Leader.

2013-2015: “In silico design of semi i-synthetic functional mimics of glutathione peroxidase: from the rational choice of the organochalcogen to its bioincorporation in protein scaffols”; Agency: Progetti de Ricerca di Ateneo (CPDA127392/12); University of Padova; Role: Team member.

2012-2015: “Re(I)/99mTc(I) complexes containing L-arginine derivatives as substrates or inhibitors of Nitric Oxide Synthase: A structure-activity study”; Agency: FCT¹; Role: Team member.

PEER-REVIEWED RESEARCH ALLOCATIONS

2020-2021: “Dissecting dopamine receptor 2 functional mechanism” – (CPCA/A2/7219/2020); Agency: FCT-RNCA; Role: Principal-Investigator.

2021-2024: “Cutting-Edge Virus-Host Interactome Discovery: A Multi-Omics AI Driven Approach” – (DSAIPA/DS/0118/2020); Agency: FCT-RNCA; Role: Principal-Investigator.

2020-2021: “Structural and functional role of CACNG2 gene mutations in psychiatric diseases” – (CPCA/A0/7302/2020); Agency: FCT-RNCA; Role: Principal-Investigator.

2018-2019: “Conformational dynamics, assembly and inhibition of GPCR oligomers” – 2017174234; Budget: 20.000.000 CPU hours; Agency: PRACE; Role: Team-member.

2017-2018: “Structural and dynamic understanding of the ghrelin receptor function on memory and learning: a computational perspective” – NWO16425; Budget: 4.000.000 CPU hours; Agency: Surfsara, Netherlands; Role: Co-Principal investigator.

2015-2017: “Target-specific delivery of radioactivity to cancer cells by virus-like particles”; Budget: 700.000 CPU hours; Agency: Icahn School of Medicine at Mount Sinai; Role: Task leader.

2015-2016: “Biased agonism in the dopamine receptor” – ISCRA A BiaDop HP10CIQNJW; Budget: 200.000 CPU hours; Agency: CINECA, Italy; Role: Team member.

2014-2015: “In silico design of enzymatic anti-oxidant systems 2”; Budget: 90.000 CPU hours; Agency: CINECA- IDEAS 2, Italy; Role: Team member.

2013-2014: “In silico design of semi i-synthetic functional mimics of glutathione peroxidase: from the rational choice of the organochalcogen to its bioincorporation in protein scaffols”; Budget: 110.000 CPU hours; Agency: CINECA – IDEAS, Italy; Role: Team member.

AWARDS

2008: Luso-American Foundation Network Grant (FLAD) – To support research at an American University.

2003: Eng. António de Almeida’s Prize – For the top-ranking student in the Biochemistry Degree.

1998: Excellence Prize – For the top-ranking student in the Secondary School.

HONORS

2018: Interview Stage of ERC Starting Grant – LS7 panel.

2014: Committee for Professional Opportunities for Women Travel Award – Biophysical Society Meeting, San Francisco, USA.

2006: MGMS Registration Fellowship – Quantum Pharmacology – 30 years on, Oxford, UK.

2006: NBCR Summer Institute Travel and Registration Fellowship – NBCR Summer Institute: Cyberinfrastructure & Multiscale Modeling Approaches”, La Jolla, California.

2006: Marie Curie Travel and Registration Fellowship – CCP5 and Marie Curie Actions: Methods in Molecular Simulation Summer School 2006”, University of Cardiff, Wales.

2006: Italian Physical Society Scholarship – International School of Physics “E. Fermi”, “Protein Folding and Drug Design”, Varenna, Italy.

2006: EMBO Fellowship – “Biomolecular simulation: an EMBO course”, Paris, France.

FACULTY DUTIES

2020-present: Coordinator of Master ´s Degree in Computational Biology, Coimbra University.

2015-present: Member of Grading Committee for 7 Master thesis and 1 PhD thesis proposal at Coimbra University.

2015-2019: Member of the Institute for Interdisciplinary Research (3IIIs), Coimbra University.

SUPERVISION/CO-SUPERVISION

Ongoing: 3 post-doctoral fellows, 5 PhD students, 9 master students.

Previous: 7 bachelor students, 7 master students, 8 technicians, 3 ERAMUS master students; 1 PhD rotation student, 4 Master rotation students, 1 postdoctoral fellow at Oporto and Coimbra Universities.

TEACHING ACTIVITIES

Graduate programs

2017-present: Head Lecturer ‒ Computational Biochemistry course of the BEB PhD programme at CNC, Portugal.

2018: Invited lecturer at Infection course of the BEB PhD programme at CNC, Coimbra, Portugal.

2018: Invited lecturer at Therapeutics course of the BEB PhD programme at CNC, Coimbra, Portugal.

Master programs

2020-present: Professor, Applied Omics (theoretical and practical classes), Master’s in Computational Biology, Coimbra University.

2020-present: Professor, Data Analytics in Biology (theoretical and practical classes), Master’s in Computational Biology, Coimbra University.

2018: Invited professor, Computational Analysis of Proteomes and Genomes Class of Biostatistics and Bioinformatics applied to Health Master Program, Polytechnic Institute of Porto, Portugal.

2015-2017: Invited lecturer ‒ Cell Regulation Class of the Cellular Molecular Biology/Neurasmus Joint Master Program, University of Coimbra, Portugal.

2010-2013: Invited lecturer ‒ Biochemistry Class of the Biotechnology Master’s degree, Science Faculty and Polytechnic Institute of Porto, Portugal.

2010-2011: Professor, Bioinformatics Course, Oporto University, Portugal.

2010: Invited lecturer at the European Master in Theoretical Chemistry and Computational Modelling, Oporto University, Portugal.

Undergraduate programs

2020-present: Professor, Biochemistry (theoretical classes), Introduction to Structural Biochemistry (theoretical and practical classes), Coimbra University, Portugal.

2019-2020: Professor, Introduction to Biology Course (theoretical and practical classes), Introduction to Biochemistry Laboratory (practical classes), Biochemistry (theoretical and practical classes), Introduction to Structural Biochemistry (theoretical and practical classes), Differentiation and Development (practical classes), Coimbra University, Portugal.

2010-2011: Professor, Computational Biological Chemistry Course, Oporto University, Portugal.

Workshops

2020: Lecturer a Coimbra, Portugal.

2019: Lecturer at Advanced Experimental Courses for students and teachers of Secondary Education, Institute of education and citizenship, Cantanhede, Portugal.

2015-present: Lecturer at the annual Summer School in Computational Biology, Coimbra, Portugal.

2016: Lecturer at R: Hands-ON Workshop, CNC, Coimbra, Portugal.

2006-2014: Various teaching activities to promote computational chemistry for Secondary School.

SCIENTIFIC COMMITTEE/ORGANISATION OF SCIENTIFIC MEETINGS

2013-present: Organising committed of EJIBCE – “Encounter of Young investigators in Computational and Structural Biology”, Portugal (organisation of 4 out the 5 editions).

2016-present: Scientific Committee of MOL2NET, International Conference of Multidisciplinary Sciences.

EDITORIAL ACTIVITIES

2020-2021: Co-Editor of Book to Methods in Molecular Biology on the theme: “Computational Design of membrane proteins”.

2020-2021: Guest Editor, Biochem Issue: “Computational Analysis of Proteomes and Genomes”.

2020-2021: Guest Editor, International Journal of Molecular Sciences Issue: “Artificial Intelligence and Machine Learning in Drug Development”.

2017-2019: Guest Editor, Molecules Issue: “GPCR Mechanism and Drug Design”.

2017-2018: Guest Editor, Current Topics of Medicinal Chemistry Issue: “Modulation of Protein-protein Interactions for Development of Effective Therapeutics – from a Joint Perspective of Experiment and Computation”.