João M.C. Teixeira

Computational structural biologist modeling protein dynamics.

  • Publications, talks, and posters are listed in the Publications page.
  • Produced software is listed in the Software page.
  • For summary of my research see the Research page.

Current Position

Senior developer. January 2024.
Zymvol Biomodeling

Education

Ph.D in Biochemistry with specialization in Biophysics. January 9th, 2014
CNC (University of Coimbra, Portugal) and CERM (University of Florence, Italy).
Title awarded by the University of Coimbra, Portugal.
Approved Unanimously with Distinction and Honours.
Grant: FCT Doctoral Research Grant for International Training (4 years)
Thesis title: “Paramagnetic NMR of Proteins to Study the Collagenolytic Mechanism of MMP-1.”
Supervisors: Carlos F.G.C. Geraldes and Claudio Luchinat.
Thesis PDF | Slides

Licentiate in Biochemistry. September 9th, 2008
University of Coimbra, Portugal.
Thesis title: “Study of the interaction of Ln3+ complexes of targeted contrast agents to HSA and RCA120 binding models using high resolution Saturation Transfer Difference (STD) NMR techniques.”
Supervisor: Carlos F.G.C. Geraldes
Thesis PDF

Previous positions

  1. AIRC-funded Research Software Engineer / Data Analyst. September 2022 - June 2023.
    Monika Fuxreiter Lab
    Department of Biomedical Sciences. University of Padua, Italy.
  2. BioExcel-funded Research Software Engineer. July 2021 - August 2022
    Alexandre Bonvin lab, Computational Structural Biology Group
    Bijvoet Center for Biomolecular Research, Utrecht University
    Utrecht, Holland.
  3. NIH-funded Research Software Engineer. April 2019 - May 2021
    Julie Forman-Kay lab
    Program in Molecular Medicine, Hospital for Sick Children
    Toronto, Canada.
  4. Postdoctoral Researcher / Research Software Engineer. February 2014 - June 2018
    Miquel Pons lab, BioNMR Group
    Department of Inorganic and Organic Chemistry, University of Barcelona
    Barcelona, Spain.
  5. FCT-funded Doctorate International Training. June 2009 - January 2013
    Claudio Luchinat lab
    Centro Risonanze Magnetiche (CERM), University of Florence
    Florence, Italy.
  6. FCT-funded Ph.D. candidate. May 2009 - January 2014
    Carlos F.G.C. Geraldes lab, Inorganic Biochemistry and Molecular Imaging Group
    CNC – Center for Neuroscience and Cell Biology, University of Coimbra
    Coimbra, Portugal.
  7. Research Assistant in Nuclear Magnetic Resonance (NMR). September 2007 - April 2009
    Carlos F.G.C. Geraldes lab, Inorganic Biochemistry and Molecular Imaging Group
    CNC – Center for Neuroscience and Cell Biology, University of Coimbra
    Coimbra, Portugal.

Research Missions

  1. Visiting Collaborator. September 2018
    Group of Structural Biology, School of Medicine Stanford University.
    Aim: Simulation of a multicomponent system using OpenMM.
    Collaborators: João P.G.L.M. Rodrigues, Susana Barrera-Vilarmau
    Group leader: Michael Levitt (2013 Nobel Prize in Chemistry)
    Palo Alto, The United States of America.
  2. Visiting Collaborator. September 2017
    Alexander L. Breeze Lab
    Astbury Centre for Structural Molecular Biology, University of Leeds
    Aim: Development of the Farseer-NMR Software user interface.
    Collaborators: Simon P. Skinner and Alexander L. Breeze
    Leeds, United Kingdom.
  3. Transnational Knowledge Transfer. November 2013
    Miquel Pons Lab, BioNMR Group, University of Barcelona
    Aim: Protocols to purify multidomain proteins for paramagnetic NMR strategies.
    Barcelona, Spain.
  4. Visiting PhD. Student. April 2013
    Alexandre Bonvin Lab, Computational Structural Biology Group
    Bijvoet Center for Biomolecular Research, Utrecht University
    Utrecht, Holland.
    Aim: Protein-protein docking calculations and analysis using HADDOCK Web Server.
    Collaborators: João P.G.L.M. Rodrigues
  5. Short Term Scientific Mission. September to November 2009
    Petr Hermann
    Charles University, Prague, Czech Republic
    Aim: Chemical Synthesis of Metal-based systems for Molecular Imaging A pplications and Paramagnetic Solution NMR Probes.
    Prague, Czech Republic.
  6. Short Term Scientific Mission. January 2009
    Jesús Jiménez-Barbero Lab
    NMR Group, Centro de Investigaciones Biológicas (CIB), CSIC, Spain.
    Aim: Protein-ligand interaction studies using Autodock 4.
    Madrid, Spain.

Funding

  1. “Aberrant condensates as drug targets for cancer.”
    Fondazione AIRC per la Ricerca sul Cancro ETS, AIRC IG id. 26229
    PI: Monika Fuxreiter, University of Padua, Italy.
  2. “Virtual Research Environment for Integrative Modelling of Biomolecular Complexes.”
    i-VRESSE, The Netherlands eScience Center, eTEC 2020
    PI: Alexandre MJJ Bonvin, Utrecht University, Holland.
  3. “EGI Advanced Computing for EOSC.”
    EGI-ACE, EU Horizon 2020, Contract 101017567
    PI: EGI Foundation
  4. “Calculating Dynamic Ensembles of Intrinsically Disordered Proteins.”
    National Institute of Health (NIH) - R01 GM127627-01
    PI: Julie Forman-Kay, SickKids Research Institute, Toronto, Canada
  5. “BioExcel Centre of Excellence for Computational Biomolecular Research: BioExcel-2.”
    BioExcel, EU Horizon 2020, Contract 823830
    PI: Alexandre MJJ Bonvin, Utrecht University, Holland
  6. “El elemento regulador N-terminal de Src: métodos y estrategia hacia una nueva generación de fármacos contra el cáncer”
    MINECO-FEDER, Contract BIO2016-78006-R
    PR: Miquel Pons, University of Barcelona, Spain
  7. “Src unique domain signalling in colorectal cancer”
    Maratò 2012 cancer-20132830
    PI: Miquel Pons, University of Barcelona, Spain
  8. “The Unique Domain of c-Src: disordered protein domains at the cellular membrane surface”
    MINECO-FEDER, Contract BIO2013-45793-R
    PI: Miquel Pons, University of Barcelona, Spain
  9. “New methods and new concepts for the study of biomolecules with dynamic interactions involved in cell signalling.”
    MICINN, Contract BIO2010-15683
    PI: Miquel Pons, University of Barcelona, Spain
  10. “Transnational Activity Fellowship. Scientific Knowledge Transfer to and within BioNMR.”
    BIO-NMR: NMR for structural Biology. Task 3.4, EU-FP7 Contract no. 261863
    PI: Miquel Pons and João M.C. Teixeira, University of Barcelona, Spain
  11. “Chemical Synthesis of Metal-based systems for Molecular Imaging Applications and Paramagnetic Solution NMR Probes.”
    Short Term Scientific Mission. COST Action D38, COST-STSM-D38-05161
    PI: João M.C. Teixeira and Carlos FGC Geraldes, Charles University, Czech Republic
  12. “Paramagnetic NMR of Proteins to study the collagenolytic mechanism of MMP-1.”
    Foundation of Science and Technology (FCT), Doctoral Fellowship. Contract: SRFH/BD/45928/2008
    PI: João M.C. Teixeira and Carlos FGC Geraldes, University of Coimbra, Portugal
  13. “Nanostructures addressed to Multimodal Medical Molecular Imaging”.
    COMPETE, Contract PTDC/QUI/70063/2006
    PI: Carlos FGC Geraldes, University of Coimbra, Portugal.
  14. “Development of new lanthanide–based compounds as MRI Molecular Imaging agents.”
    Network of Excellence (NoE) “European Molecular Imaging Laboratory” (EMIL), LSCH-2004-503569
    PI: Carlos FGC Geraldes, University of Coimbra, Portugal
  15. Award of “Best Student” ROTARY Club. Secondary School “Escola E.B. 2-3 D. José de Vila Real de Santo António. Portugal. 1998.

Peer-review

Reviewer for the following editorials

Mentoring Experience

Students I have mentored and dedicated throughout the years. Thanks to all of them for the fantastic moments and the two-way learning.

  • 2023, Zi Hao Liu. Ph.D. student, SikKids, Toronto, Canada.
  • 2022, Zi Hao Liu. MSc graduate student, SikKids, Toronto, Canada.
  • 2021, Ashley Nanimi, Summer Student, SickKids, Toronto, Canada.
  • 2020, Serene Rodrigues, COOP Student SickKids-University of Waterloo, Toronto, Canada.
  • 2020, Alaa Shamandy, research student SickKids-University of Toronto, Toronto, Canada.
  • 2018, Héctor Fuentes de la Osa. BioNMR Group, University of Barcelona, Spain.
  • 2017, Stasė Bielskutė. BioNMR Group, University of Barcelona, Spain.
  • 2017, Xavier Sanz Daroca. BioNMR Group, University of Barcelona, Spain.
  • 2017, Josemari Urtasun Elizari. BioNMR Group, University of Barcelona, Spain.
  • 2017, Héctor Fuentes de la Osa. BioNMR Group, University of Barcelona, Spain.
  • 2015, Guillermo Iruela Martin, BSc. BioNMR Group, University of Barcelona, Spain.
  • 2015, Simone Höfler, BSc. BioNMR Group, University of Barcelona, Spain.
  • 2014, Pedro Garcia Lorente, Bsc & Msc. BioNMR Group, University of Barcelona, Spain.
  • 2012, Tommaso Martelli, CERM, University of Florence, Italy.
  • 2009, David M. Dias. CNC, University of Coimbra, Portugal.

Languages

  • Portuguese - Native
  • Spanish - Bilingual
  • English - Professional proficiency
  • Italian - Independent user
  • Catalan - Proficient in reading and listening

Outreach

Analysis and philosophy articles:

  • “Choque de gerações”
    RNA Mensageiro, Nº13 “O estado da nossa arte”, 2018.
    Núcleo Estudantes de Bioquímica da Associação Académica de Coimbra.
    English title: “A clash of generations [in academia]”, issue “The state of our art”. 2018
  • “Egoísmo na hora da morte”
    RNA Mensageiro, Nº7 “Envelhecimento”, 2011.
    Núcleo Estudantes de Bioquímica da Associação Académica de Coimbra.
    English title: “Selfishness with those at death”, issue title: “Ageing”. 2011

Activities with children:

  • Communication with children: “Descobreix la Recerca”. Programme Research in Society, Parc Cientific de Barcelona, Spain. 2014 to 2018 I guided children at Primary School through a tour that explains the process of pharmacological drug development from the researcher perspective. The tour visits the laboratory of organic synthesis and the laboratory for Drosophila observation. Children are also introduced through a video to the basic concepts in research with mice, always prioritizing animal safety and respect. Laboratory safety rules and sterile conditions are also discussed.

Courses attended:

  • 08/2021. “Techniques to tell science” for science communication in public by BigVan Ciencia - 20 hours

General Activities:

  • Organized “Treasures of the RI”, Display of the Molecular Medicine Program. SickKids, Toronto, Canada. February 2020.

Continuous Learning

  • 2021. “Inferential Statistical Analysis with Python”, Coursera Course Certificate, certificate.
  • 2019, “Academic Writing in English”, Series of workshops and classes, School of Graduate Studies, University of Toronto, Canada.
  • 2017, “Environmental Omics Integration & Modelling, International Workshop”, Cosmo Caixa, Barcelona, Spain.
  • 2017, CECAM Workshop: “Disordered protein segments: revisiting the structure-function paradigm”, Paris, France.
  • 2015, “Python for Scientists”, University of Barcelona, Spain.
  • 2015, “Advanced Isotopic Labelling Methods for Integrated Structural Biology”, AILM2015, International Workshop, IBS-Grenoble, France.
  • 2014, “Communication and Scientific Culture”, Campus Gutenberg, Universitat Pompeu Fabra, Spain.
  • 2014, “Iniciació a la utilizació dels equips de RMN, Varian en mode automàtic”, University of Barcelona, Spain.
  • 2013, “Advanced methods for the investigation of other structural data with NMR data”, CERM, University of Florence, Italy.
  • 2012, “Principles and rules for security and accident prevention in CERM’s laboratories”, CERM, University of Florence, Italy.
  • 2012, “Learn to Program: The Fundamentals”, Cousera.org, University of Toronto, Canada.
  • 2012, “Introduction to the Python Programming language”, V Edition. CEV – University of Granada, Spain.
  • 2012, “Writing in Sciences”, Cousera.org – Standford University, USA.
  • 2009, “Biomedical Magnetic Resonance: Molecular Imaging and Metabolism”, Center for Neuroscience and Cell Biology PDBEB Program, Portugal.
  • 2007, 7th Short Course of the Portuguese Biophysical Society – Biospectroscopy and Imaging. Portuguese Biophysical Society, Portugal.

Other Academic Activities

  • Facilitator in a discussion-active workshop about “Work/Life Balance”. Postdoctoral Advisor Committee at SickKids Research Institute. 2020
  • Organizing volunteer at the Pycon Toronto, Canada. 2019
  • International Postdocs Sub-committee of the Postdoctoral Advisor Committee at SickKids, Toronto, Canada. 2019-2020
  • Postdoctoral Adviser Committee at SickKids, Toronto, Canada. 2019-2020
  • Mendeley Adviser. Mendeley Desktop – Free reference manager and PDF organizer, mendeley.com. 2010-2019
  • Participation as staff assistant in the 12th Chianti/INSTRUCT Workshop on BioNMR. Electron and Nuclear Relaxation for Structural Biology, Montecatini Terme, Italy. 2012
  • Participation as staff assistant in the Joint EUROMAR 2010 and 17th ISMAR conference/Wordwide Magnetic Resonance conference, Florence, Italy.

Other Passions

I am decade long mountaineer with a heartful compromise towards nature and a purist approach to climbing. I am also an international Advanced ACUC scuba diver and caver.