Current Position

Postdoctoral Researcher. Since July 2021
Lead Python software engineer/structural biologist developing HADDOCK v3
Dr. Alexandre Bonvin’s Lab, Computational Structural Biology Group
Bijvoet Center for Biomolecular Research, Science for Life, Faculty of Science - Chemistry
Utrecht University, Link to UU profile

HADDOCK3 is the new version of the HADDOCK2.x series which is the world’s most used docking platform for scientific research with +26,000 users and +400,000 jobs served worldwide since 2008. While version 2 was based on a predefined protocol, version 3 is a fully modular pipeline allowing the user to construct his/her docking workflows. The HADDOCK3 code and project is open-source and is hosted at GitHub. The HADDOCK project is part of the European funded BioExcel platform, the WeNMR grid, and the INSTRUCT-ERIC consortiums.

Education

Ph.D in Biochemistry with specialization in Biophysics. January 9th, 2014
CERM, University of Florence (Italy) and CNC, University of Coimbra (Portugal).
Title officially awarded by the University of Coimbra, Portugal. Approved Unanimously with Distinction and Honours.
Grant: Portuguese Doctoral Research Grant for International Training (4 years) - Foundation for Science and Technology.
Thesis title: Paramagnetic NMR of Proteins to Study the Collagenolitic Mechanism of MMP-1.
Supervisors: Prof. Dr. Carlos F.G.C. Geraldes and Prof. Dr. 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: Prof. Dr. Carlos F.G.C. Geraldes
Thesis PDF

Research Experience

  1. Postdoctoral Researcher. April/2019 to May/2021; 2 years and 2 months
    Dr. Julie Forman-Kay’s Lab, Program in Molecular Medicine
    Hospital for Sick Children, Toronto, Canada

  2. Independent and ad honorem scientific researcher. July/2018 to March/2019; 9 months
    Also software developer for Open Source scientific software projects: Farseer-NMR, taurenmd, pdb-tools. Salamanca, Spain. After leaving the University of Barcelona, I worked ad honorem to prepare myself for my next postdoctoral experience. I dedicated most of this period to the development of Open Source scientific software for the analysis of NMR data, molecular simmulations, and structural biology in general.

  3. Visiting Collaborator. September/2018; 2 weeks
    Group of Structural Biology, School of Medicine Stanford University.
    Theme: Simulation of a multicomponent system using OpenMM.
    Collaborators: Dr. João P.G.L.M. Rodrigues, Susana Barrera-Vilarmau
    Group leader: Dr. Michael Levitt

  4. Visiting Collaborator. September/2017; 1 week
    Astbury Centre for Structural Molecular Biology, University of Leeds.
    Theme: Development of the Farseer-NMR Software.
    Collaborators: Dr. Simon P. Skinner and Dr. Alexander L. Breeze

  5. Postdoctoral Researcher. February/2014 to June/2018; 4 years and 6 months
    Dr. Miquel Pons’s Lab, BioNMR Group
    Faculty of Chemistry Department of Inorganic and Organic Chemistry, University of Barcelona

  6. Transnational Knowledge Transfer. October/2013; 1 month
    Dr. Miquel Pons’s Lab, BioNMR Group
    Faculty of Chemistry Department of Inorganic and Organic Chemistry, University of Barcelona

  7. Visiting PhD. Student. April/2013; 2 weeks
    Dr. Alexandre Bonvin’s Lab, Computational Structural Biology Group
    Bijvoet Center for Biomolecular Research, Science for Life, Faculty of Science - Chemistry
    Utrecht University
    Theme: Protein-protein docking calculations and analysis using HADDOCK Web Server. Collaborators: Dr. João P.G.L.M. Rodrigues

  8. Short Term Scientific Mission. September/2009 to November/2009; 3 months
    Charles University, Prague, Czech Republic
    Theme: Chemical Synthesis of Metal-based systems for Molecular Imaging Applications and Paramagnetic Solution NMR Probes.
    Supervisor: Dr. Petr Hermann

  9. PhD. candidate in International Training. June/2009 to January 2013; 36 months
    Dr. Claudio Luchinat’s lab
    Centro Risonanze Magnetiche (CERM), University of Florence, Italy.

  10. PhD. candidate. May/2009 to January/2014; 5 years
    Dr. Carlos F.G.C. Geraldes’s group, Inorganic Biochemistry and Molecular Imaging Group
    CNC – Center for Neuroscience and Cell Biology, University of Coimbra, Portugal

  11. Short Term Scientific Mission. 11/January/2009 to 31/Janruary/2009; 3 weeks
    NMR and molecular recognition Group, Centro de Investigaciones Biológicas (CIB), CSIC, Spain.
    Theme: Protein-ligand interaction studies using Autodock 4.
    Supervisor: Dr. Jesús Jiménez-Barbero

  12. NMR Research Technician. November/2008 to April/2009; 6 months Dr. Carlos F.G.C. Geraldes’s group, Inorganic Biochemistry and Molecular Imaging Group
    CNC – Center for Neuroscience and Cell Biology, University of Coimbra, Portugal
    Role: Biochemistry Licentiate with experience in NMR methodology. Supervisor: Carlos F.G.C. Geraldes.

Scientific Software

Most relevant public scientific software I developed or for which I was part of the lead developing team

  1. HADDOCK3:High-Ambiguity Driven Docking version 3
  2. Python Project Skeleton: a full-featured continuous integration template for scientific software
  3. pdb-tools: a swiss army knife for manipulating and editing PDB files
  4. taurenmd: a command client for analysis of molecular simulations
  5. FarSeer-NMR: multidimensional NMR peaklists data analysis
  6. mdacli: A command-line tool for MDAnalysis

Experienced Python software engineer. Highly proficient in both Object Oriented programming and Functional Programming in Python and git. Almost 20 years of experience with Linux systems and bash scripting. Experienced with Python Numpy, Pandas, Numba, and matplotlib. Good experience with R data frames and plotting with ggplot2. Able to quickly learn other programming languages, workflows, or platforms. Experienced and able to comply with Continuous Integration practices and best practices for team software development. Able to work in team, supervise, manage, and collaborate, as well as perform independently. Also, I enjoy writing about advanced programming concepts and possible solutions for particular problems. You can find my posts at DEV.to and PythonicThoughtsSnippets. Highlighted articles:

Scientific Publications

by inverse chronological order #: equal contribution; @: corresponding author

  1. “Learning to Evolve Structural Ensembles of Unfolded and Disordered Proteins Using Experimental Solution Data”
    Zhang, O.; Haghighatlari, M.; Li, J.; Teixeira, J. M. C.; Namini, A.; Liu, Z. H.; Forman-Kay, J. D.
    arXiv 2022 (preprint)
    https://doi.org/10.48550/arXiv.2206.12667

  2. “IDPConformerGenerator: A Flexible Software Suite for Sampling Conformational Space of Disordered Protein States”
    Teixeira, J. M. C.@; Liu, Z. H.; Namini, A.; Li, J.; Vernon, R. M.; Krzeminski, M.; Shamandy, A. A.; Zhang, O.; Haghighatlari, M.; Yu, L.; Head-Gordon, T.; Forman-Kay, J. D.@
    bioRxiv 2022 (preprint)
    https://doi.org/10.1101/2022.05.28.493726 (:unlock: open-access)

  3. “Effective open-science practices for organizing a scientific software repository”
    Teixeira, J. M. C.; Rodrigues, J. P. G. L. M.; Bonvin, A. M. J. J.
    Proceedings of Science 2022 (submitted)

  4. “Learning Correlations between Internal Coordinates to improve 3D Cartesian Coordinates for Proteins”
    Li, J.; Zhang, O.; Lee, S.; Namini, A.; Liu, Z. H.; Teixeira, J. M. C.; Forman-Kay, J. D.; Head-Gordon, T.
    arXiv 2022 (preprint)
    https://doi.org/10.48550/arXiv.2205.04676 (:unlock: open-access)

  5. “Protein Dynamics to Define and Refine Protein Ensembles”
    Pavithra, N.; Haghighatlari, M.; Ashley, N.; Teixeira, J. M. C.; Li, J.; Zhang, O.; Gradinaru, C.; Forman-Kay, J.; Head-Gordon, T.
    Journal of Physical Chemistry B 2022, 126, 9, 1885-1894.
    https://doi.org/10.1021/acs.jpcb.1c10925

  6. “A Methionine Chemical Shift Based Order Parameter Characterizing Global Protein Dynamics”
    Chashmniam, S.#; Teixeira, J. M. C.#; Paniagua, J. C.; Pons, M.
    ChemBioChem 2021, 22, 1001–1004.
    https://doi.org/10.1002/cbic.202000701

  7. “PDB-Tools Web: A User-Friendly Interface for the Manipulation of PDB Files”
    Jiménez‐García, B.; Teixeira, J. M. C.; Trellet, M.; Rodrigues, J. P. G. L. M.; Bonvin, A. M. J. J.
    Proteins: Structure, Function, and Bioinformatics 2021, 89 (3), 330–335.
    https://doi.org/10.1002/prot.26018 (:unlock: open-access)

  8. “Taurenmd: A Command-Line Interface for Analysis of Molecular Dynamics Simulations”
    Teixeira, J. M. C.@
    Journal of Open Source Software 2020, 5 (50), 2175.
    https://doi.org/10.21105/joss.02175 (:unlock: open-access)

  9. “Insights on Cross-Species Transmission of SARS-CoV-2 from Structural Modeling”
    Rodrigues, J. P. G. L. M.; Barrera-Vilarmau, S.#; Teixeira, J. M. C.#; Seckel, E.; Kastritis, P.; Levitt, M.
    PLOS Computational Biology 2020, 16, e1008449.
    https://doi.org/10.1371/journal.pcbi.1008449 (:unlock: open-access)
    Pre-print @bioRxiv (:unlock: open-access)

  10. “Structural Models of Human ACE2 Variants with SARS-CoV-2 Spike Protein for Structure-Based Drug Design”
    Sorokina, M.#; Teixeira, J. M. C.#; Barrera-Vilarmau, S.#; Paschke, R.#; Papasotiriou, I.#; Rodrigues, J. P. G. L. M.#; Kastritis, P. L.#
    Scientific Data 2020, 7 (1), 309.
    https://doi.org/10.1038/s41597-020-00652-6 (:unlock: open-access)

  11. “Extended Experimental Inferential Structure Determination Method in Determining the Structural Ensembles of Disordered Protein States”
    Lincoff, J.; Haghighatlari, M.; Krzeminski, M.; Teixeira, J. M. C.; Gomes, G.-N. W.; Gradinaru, C. C.; Forman-Kay, J. D.; Head-Gordon, T.
    Communications Chemistry 2020, 3 (1), 1–12. https://doi.org/10.1038/s42004-020-0323-0
    Pre-print @arxiv (:unlock: open-access)

  12. “Cis-Trans Proline Isomers in the Catalytic Domain of Calcineurin”
    Teixeira, J. M. C.; Guasch, A.; Biçer, A.; Aranguren‐Ibáñez, Á.; Chashmniam, S.; Paniagua, J. C.; Pérez‐Riba, M.; Fita, I.; Pons, M.
    The FEBS Journal 2019, 286 (6), 1230–1239.
    https://doi.org/10.1111/febs.14721 (:unlock: open-access)

  13. “A Myristoyl-Binding Site in the SH3 Domain Modulates c-Src Membrane Anchoring”
    Le Roux, A.-L.; Mohammad, I.-L.; Mateos, B.; Arbesú, M.; Gairí, M.; Khan, F. A.; Teixeira, J. M. C.; Pons, M.
    iScience 2019, 12, 194–203.
    https://doi.org/10.1016/j.isci.2019.01.010 (:unlock: open-access)

  14. “Pdb-Tools: A Swiss Army Knife for Molecular Structures”
    Rodrigues, J. P. G. L. M.; Teixeira, J. M. C.; Trellet, M.; Bonvin, A. M. J. J.
    F1000Res 2018, 7, 1961.
    https://doi.org/10.12688/f1000research.17456.1 (:unlock: open-access)

  15. “The Two Isoforms of Lyn Display Different Intramolecular Fuzzy Complexes with the SH3 Domain”
    Teixeira, J. M. C.; Fuentes, H.; Bielskutė, S.; Gairi, M.; Żerko, S.; Koźmiński, W.; Pons, M.
    Molecules 2018, 23 (11), 2731.
    https://doi.org/10.3390/molecules23112731 (:unlock: open-access)

  16. “Farseer-NMR: Automatic Treatment, Analysis and Plotting of Large, Multi-Variable NMR Data”
    Teixeira, J. M. C.@; Skinner, S. P.; Arbesú, M.; Breeze, A. L.; Pons, M.
    Journal Biomolecular NMR 2018, 71 (1), 1–9.
    https://doi.org/10.1007/s10858-018-0182-5 (:unlock: open-access)

  17. “Intramolecular Fuzzy Interactions Involving Intrinsically Disordered Domains”
    Arbesú, M.; Iruela, G.; Fuentes, H.; Teixeira, J. M. C.; Pons, M.
    Frontiers Molecular Biosciences 2018, 5.
    https://doi.org/10.3389/fmolb.2018.00039 (:unlock: open-access)

  18. “The Unique Domain Forms a Fuzzy Intramolecular Complex in Src Family Kinases”
    Arbesú, M.; Maffei, M.; Cordeiro, T. N.; Teixeira, J. M. C.; Pérez, Y.; Bernadó, P.; Roche, S.; Pons, M.
    Structure 2017, 25 (4), 630-640.e4.
    https://doi.org/10.1016/j.str.2017.02.011 (:unlock: open-access)

  19. “An Oxygen-Sensitive Toxin-Antitoxin System”
    Marimon, O.; Teixeira, J. M. C.; Cordeiro, T. N.; Soo, V. W. C.; Wood, T. L.; Mayzel, M.; Amata, I.; García, J.; Morera, A.; Gay, M.; Vilaseca, M.; Orekhov, V. Y.; Wood, T. K.; Pons, M.
    Nature Communications 2016, 7, 13634.
    https://doi.org/10.1038/ncomms13634 (:unlock: open-access)

  20. “A C2HC Zinc Finger Is Essential for the RING-E2 Interaction of the Ubiquitin Ligase RNF12”
    Bijlmakers, M.-J.; Teixeira, J. M. C.; Boer, R.; Mayzel, M.; Puig-Sàrries, P.; Karlsson, G.; Coll, M.; Pons, M.; Crosas, B.
    Scientific Reports 2016, 6 (1), 29232.
    https://doi.org/10.1038/srep29232 (:unlock: open-access)

  21. “A Bis(Pyridine N-Oxide) Analogue of DOTA: Relaxometric Properties of the Gd(III) Complex and Efficient Sensitization of Visible and NIR-Emitting Lanthanide(III) Cations Including Pr(III) and Ho(III)”
    Martins, A. F.; Eliseeva, S. V.; Carvalho, H. F.; Teixeira, J. M. C.; Paula, C. T. B.; Hermann, P.; Platas-Iglesias, C.; Petoud, S.; Tóth, E.; Geraldes, C. F. G. C.
    Chemistry 2014, 20 (45), 14834–14845.
    https://doi.org/10.1002/chem.201403856

  22. “Examination of Matrix Metalloproteinase-1 in Solution A PREFERENCE FOR THE PRE-COLLAGENOLYSIS STATE”
    Cerofolini, L.; Fields, G. B.; Fragai, M.; Geraldes, C. F. G. C.; Luchinat, C.; Parigi, G.; Ravera, E.; Svergun, D. I.; Teixeira, J. M. C.
    Journal of Biological Chemistry 2013, 288 (42), 30659–30671.
    https://doi.org/10.1074/jbc.M113.477240 (:unlock: open-access)

  23. “The Catalytic Domain of MMP-1 Studied through Tagged Lanthanides”
    Bertini, I.; Calderone, V.; Cerofolini, L.; Fragai, M.; Geraldes, C. F. G. C.; Hermann, P.; Luchinat, C.; Parigi, G.; Teixeira, J. M. C.
    FEBS Letters 2012, 586 (5), 557–567.
    https://doi.org/10.1016/j.febslet.2011.09.020 (:unlock: open-access)

  24. “The Interaction of La3+ Complexes of DOTA/DTPA Glycoconjugates with the RCA120 Lectin: A Saturation Transfer Difference NMR Spectroscopic Study”
    Teixeira, J. M. C.; Dias, D. M.; Cañada, F. J.; Martins, J. A.; André, J. P.; Jiménez-Barbero, J.; Geraldes, C. F. G. C.
    Journal of Biological Inorganic Chemistry 2011, 16 (5), 725.
    https://doi.org/10.1007/s00775-011-0773-z

  25. “Enantioselective Binding of a Lanthanide(III) Complex to Human Serum Albumin Studied by 1H STD NMR Techniques”
    Dias, D. M.; Teixeira, J. M. C.; Kuprov, I.; New, E. J.; Parker, D.; Geraldes, C. F. G. C.
    Organic & Biomolecular Chemistry 2011, 9 (14), 5047–5050.
    https://doi.org/10.1039/C1OB05524K

Newspapers highlights

  1. “Entre cães e gatos, galinhas e chimpanzés há animais imunes e susceptíveis ao SARS-CoV-2”. Publico.pt, 2020
  2. “Así es el coronavirus que ha mutado en Dinamarca”. El País, 2020
  3. Matrix Metalloproteinases: proteins in action. pNMR news, Paramagnetic NMR Newsletters of the FP7-PEOPLE-2012-ITN “PNMR”. www.pnmr.eu, 2012

Book chapters

  1. “Matrix Metallopeptidase-1/Interstitial Collagenase.”
    Handbook of Proteolytic Enzymes, 4th Edition, 2022, Elsevier.
    Invited by Dr Neil D. Rawlings. EMBL-European Bioinformatics Institute alumnus. 34 Brybank Road, Haverhill, Suffolk, CB9 7WD, UK. Tel: 01440 713859
    (Currently under review)

Collaborators

Past and present main collaborators in successful research projects

Peer review

Peer-reviewer for the following editorials

Fellowships and Awards

  1. Transnational Activity Fellowship. Scientific Knowledge Transfer to and within BioNMR, NMR for structural Biology. Task 3.4, contract no. 261863. 2013. (1 month)
  2. Short Term Scientific Mission. COST Action D38, COST-STSM-D38-05161. 2009. (3 months)
  3. Doctoral Fellowship. Foundation of Science and Technology (FCT), Portugal. SRFH/BD/45928/2008. 2008. (4 years)
  4. Research Technician Fellowship contracted (BIT from FCT). Center of Neurosciences and Cellular Biology of the University of Coimbra. Project No. LSCH-2004-503569 (EMIL), funded by EU “Development of new lanthanide-based compounds as MRI Molecular Imaging agents”. 2008. (6 months)
  5. Research team member associated to FCT Project “Nanostructures addressed to Multimodal Medical Molecular Imaging”. Portugal. PTDC/QUI/70063/2006. 2008. (1 year)
  6. Award of “Best Student” ROTARY Club. Secondary School “Escola E.B. 2-3 D. José de Vila Real de Santo António. Portugal. 1998.

Scientific Workshops

Organized workshops and participations as lecturer or tutor

  1. “Protein docking”
    Hands-on Session tutor
    EMBL-EBI Structural Bioinformatics virtual course, 11-15th October, 2021

  2. “Farseer-NMR: automatic treatment, analysis and plotting of large scale, multi-variable BioNMR data – knowledge exchange within the community.”
    Organizer and speaker
    NMR Groups at Utrecht University and Leiden, The Netherlands. 2018.
    Hosted by: Dr. Hugo van Ingen.
    Slides | DOI

  3. “Farseer-NMR: automatic treatment, analysis and plotting of large scale, multi-variable BioNMR data.”
    Organizer and speaker
    Parc Cientific de Barcelona, CCiTUB, University of Barcelona, Spain. 2018.
    Hosteg by: NMR Facility of the University of Barcelona.
    Slides | DOI

  4. “Farseer-NMR: automatic treatment, analysis and plotting of large scale, multi-variable BioNMR data”
    Organizer and speaker
    Nuclear Magnetic Resonance Spectroscopy Facility, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Portugal. 9th May 2018
    Hosted by: Dr. Eurico J. Cabrita
    Slides

  5. “Farseer-NMR: automatic treatment, analysis and plotting of large scale, multi-variable BioNMR data”
    Organizer and Speaker
    Seminar and Hands-on Session at the Workshop NMR FOCUS entitled: “NMR in health and disease: From Protein-Ligand Interactions to Small Molecules in Tissues”, 7th-11th of May 2018.
    PTNMR, University of Coimbra, Portugal.
    Hosted by: Dr. Rui Brito
    Slides

  6. “2D- and 3D-NMR Processing and Analysis with introduction to CCPNMR Analysis Suite v2.4.” Speaker
    Hands-on Session at the Workshop NMR FOCUS entitled: “NMR in health and disease: From Protein-Ligand Interactions to Small Molecules in Tissues”, 7th-11th of May 2018.
    PTNMR, University of Coimbra, Portugal.
    Hosted by: Dr. Rui Brito

  7. “Chemical Shift Perturbation – Protein Based Studies”
    Speaker
    Workshop NMR FOCUS entitled: “NMR in health and disease: From Protein-Ligand Interactions to Small Molecules in Tissues”, 7th-11th of May 2018
    PTNMR, University of Coimbra, Portugal.

  8. “Introductory workshops on Farseer-NMR Software.”
    Organizer and Speaker
    CIC bioGUNE Institute of the Bizkaia Technology Park and the University of Basque Country, Spain, 2017. Hosted by: Dr. Jesús Jiménez-Barbero
    Slides

Oral Communications

  1. “Modular code for a modular software: developing HADDOCK3”.
    Instruct Software Developers Exchange Webinar 5, June 10th, 2022, invited.
    Website | Twitter | LinkedIn | Youtube | Slides

  2. “Introducing HADDOCK3: Enabling modular integrative modelling pipelines”
    BioExcel Webminar, June 7th, 2022, invited
    Website | Twitter | LinkedIn | Youtube | Slides

  3. “Effective open-science practices for organizing a scientific software repository - extended”
    International Symposium on Grids & Clouds (ISGC), 20-25th March, 2022, Virtual Conference.
    Abstract | Slides

  4. “Effective open-science practices for organizing a scientific software repository - short”
    OSCU Open Science Symposium - Faculty of Science, October 10th, 2021, Utrecht University, Netherlands.
    Slides on OSF | Slides on GDrive

  5. “Modelling Intrinsically Disorder Proteins by experimental data.”
    SickKids Postdoctoral Seminar Series, 2021, invited.
    Slides

  6. “A summary of the Farseer-NMR project and its current state.”
    Invited Researcher at SickKids, Toronto, Canada, 2019.
    Hosted by: Dr. Julie Forman-Kay
    Slides

  7. “Lyn’s natural isoforms display different fuzzy complexes in UD-SH3 interaction.”
    Invited Researcher at SickKids, Toronto, Canada, 2019.
    Hosted by: Dr. Julie Forman-Kay
    Slides

  8. Cis-trans proline isomers and ligand binding in the catalytic domain of Calcineurin.
    Open seminar, RMBLab, Protein Biophysical Chemistry Group, University of Coimbra, Portugal, May 4th, 2018, invited.
    Slides

  9. “Automated NMR data treatment of simple and complex experimental datasets.”
    1 minute flash-presentation at CECAM Workshop: “Disordered protein segments: revisiting the structure-function paradigm”, Paris, France, October, 2017.
    Slide

  10. “The concept of Farseer-NMR: automatic treatment and plotting of lage-scale NMR titration data.”
    Barcelona Biomed Seminars, Parc Scientific de la Universitat de Barcelona, Spain, 2017.

  11. “Analysis of Calcineurin’s structure and conformational changes via methionine labelling NMR spectroscopy.”
    Barcelona Biomed Seminars, Parc Scientific de la Universitat de Barcelona, Spain, February, 2016.
    Slides

  12. “On the ‘tectonics’ of MMP-1 catalyzed collagenolysis: joint use of paramagnetic NMR and computational tools.”
    Barcelona Biomed Seminars, Parc Scientific de la Universitat de Barcelona, Spain, Februrary, 2014.
    Slides

  13. “Joint use of NMR and bioinformatic tools to unveil the dynamics and the ‘tectonic’ enzymatic mechanism of MMP-1”.
    EJIBCE, December 20th, 2013, Oporto, Portugal.
    Slides

  14. “MMP-1: intradomain mobility and substract interaction.”
    Visiting researcher at the NMR Spectroscopy Research Group, Utrech University, The Netherlands, 2013.

  15. “Molecular Biology preparation of paramagnetic equipped MMP-1.”
    Ph.D. Day 3, University of Florence, Italy, 2012.

  16. “Characterizing MMP-1 Internal Dynamics.”
    IX Annual Meeting of CNC – Center for Neuroscience and Cell Biology, Coimbra, Portugal, 2011.

Poster presentations

Main presenting author:

  1. “Effectively developing, distributing, and managing a Python package with a large community”
    ISMB/BOSC, July 11-14th, 2022, virtual.
    Abstract | Poster | LinkedIn
  2. “Introducing HADDOCK v3”: A rebuilt, renewed, modern, extensible, and modular version”
    Bijvoet Symposium, April 2022. Utrecht, The Netherlands.
    Poster
  3. “Introducing HADDOCK v3”: A rebuilt, renewed, modern, extensible, and modular version”
    EMBO-Workshop: Advances and challenges in biomolecular workshop, October 21st, 2021. Virtual conference.
    Poster
  4. “Automated NMR Data treatment of simple and complex experimental datasets”
    CECAM Workshop 2017: “Disordered protein segments: revisiting the structure-function paradigm”, Paris, France.
    Poster
  5. “Farseer - Automatic treatment, calculation and plotting of NMR data. Reducing weeks to seconds”
    First All Hands Meeting of iNEXT (iNEXT AHM 2016), Alcalá de Henares, Spain.
    Poster
  6. “A python tool to automatically treat, calculate and plot NMR-derived peaklists data”
    16th CCPN / CCPBioSim joint conference 2016, Buxton, United Kingdom.
  7. “A python tool to instantly treat, calculate and plot NMR-derived peaklists data”
    8th GERMN/5th Iberian NMR Meeting 2016, Valencia, Spain. Awarded Travel Fellowship from GERMN (RSEQ).
  8. “The interdomain mobility of MMP-1 and its mechanism of interaction with a collagen analogue explored by paramagnetic NMR”
    5th CAPRI Evaluation Meeting, 17-19 April 2013, Utrecht, The Netherlands.
  9. “Analysis of conformational heterogeneity in multidomain enzymes: the prologue of the collagenolysis mechanism”
    IV Ibero-American NMR Meeting – VI GERMN Bienal Meeting – III Iberian NMR Meeting 2012, Aveiro, Portugal.
  10. “3D-view of MMP-1 conformational heterogeneity in solution: the prologue of the collagenolysis mechanism”
    12th Chianti/INSTRUCT Workshop on BioNMR 2012. Electron and Nuclear Relaxation for Structural Biology, Montecatini Terme, Italy.
  11. “3D-view of MMP-1 conformational heterogeneity in solution: the prologue of the collagenolysis mechanism”
    Breakthroughs in NMR of Structural Biology - 2nd BioNMR Annual User Meeting 2012, Portoroz, Slovenia.
  12. “Lanthanide binding CLaNP-5.2 for NMR of proteins: exploring PCS and RDCs in MMP-1 internal dynamics”
    BioNMR and EAST-NMR Annual User Meeting 2011, Brno, Czech Republic.
  13. “Interaction of Ln3+-based MRI contrast agents with HSA using Saturation Transfer Difference NMR Techniques”
    Joint EUROMAR 2010 and 17th ISMAR conference / Worldwide Magnetic Resonance conference, Florence, Italy.
  14. “Study of the interaction of Ln3+ complexes of BOPTA or DTPA-cholate with HSA and of DOTA/DTPA-glycoconjugates with RCA120 using the High Resolution Saturation Transfer Difference (STD) NMR technique”
    IV Reunión Bienal del GERM-I Reunión Iberica de RMN 2008, Sevilla, Spain.

Participating author

  1. “pdb-tools: a swiss army knife for molecular structures”
    ISMB/ECCB 2019, Basel, Switzerland. F1000 poster publication: https://f1000research.com/posters/8-1173. Best poster prize.
  2. “Fuzzy intramolecular interactions in Src family kinases”
    EUROMAR 2017, Warsaw, Poland.
  3. “A conserved aromatic-residue code shapes the intrinsically disordered Unique domain of c-Src”
    16th CCPN / CCPBioSim joint conference 2016, Buxton, United Kingdom.
  4. “A conserved aromatic-residue code shapes the intrinsically disordered Unique domain of c-Src”
    EUROMAR 2016, Aarhus, Denmark.
  5. “Transient contacts in the instrinsically Disordered Unique Domain of c-Src”
    Chemical Complexity & Biology, Strasbourg, France.
  6. “A C2HC zinc finger is essential for the activity of the RING ubiquitin ligase RNG125”
    EMBO Conference 2015 “Ubiquitin and ubiquitin-like modifiers: from molecular mechanisms to human diseases”, Cavtat, Croatia.
  7. “Transient contacts in the instrinsically Disordered Unique Domain of c-Src”
    VII GERMN Biennal Meeting / IV Iberian NMR Meeting / VI Iberoamerican NMR Meeting 2015, Alcalá de Henares, Spain.
  8. “Paramagnetic analysis of collagenolysis by matrix metalloproteinase-1 (MMP-1)”
    EMBO Workshop – Magnetic Resonance for cellular structural biology 2014, Grosseto, Italy.
  9. “Interactions of an essential Zn-finger in the ubiquitin ligase RNF125”
    4th Annual User group Meeting of BioNMR 2014, Warsaw, Poland.
  10. “3D-view of MMP-1 conformational heterogeneity in solution: the prologue to the collagenolysis mechanism”
    XXVth International Conference on Mangetic Resonance in Biological Systems 2012, Lyon, France.
  11. “Study of the interaction of La3+ complexes of DOTA/DTPA-glycoconjugates with RCA120 using the High Resolution Saturation Transfer Difference (STD) NMR technique”
    COST Chemistry D38 “Metal Based Systems for Molecular Imaging Applications” 2009, Warsaw, Poland.

Mentoring Experience

  1. 2022, Zi Hao Liu. MSc graduate student, Department of Molecular Medicine, The Hospital of Sick Children, Toronto, Canada. Supervisor: Dr. Julie Forman-Kay.
  2. 2021, Ashley Nanimi, Summer Student, Department of Molecular Medicine, The Hospital of Sick Children, Toronto, Canada. Supervisor: Dr. Julie Forman-Kay.
  3. 2020, Serene Rodrigues, COOP Student SickKids-University of Waterloo, Bachelors of Science, Faculty of Science, Honours Co-operative Physics and Astronomy, University of Waterloo, Canada. Supervisor: Dr. Julie Forman-Kay.
  4. 2020, Alaa Shamandy, research student SickKids-University of Toronto, Honours Bachelor of Science, Faculty of Arts & Science. University of Toronto, Canada. Supervisor: Dr. Julie Forman-Kay.
  5. 2018, Héctor Fuentes de la Osa. BioNMR Group, University of Barcelona, Spain. MSc Thesis: “Understanding SFKs regulation, the case of Lyn.” Supervisor: Prof. Dr. Miquel Pons Vallès.
  6. 2017, Stasė Bielskutė. BioNMR Group, University of Barcelona, Spain. MSc Thesis: “Understanding SFKs regulation, the case of Lyn.” Supervisor: Prof. Dr. Miquel Pons Vallès.
  7. 2017, Xavier Sanz Daroca. BioNMR Group, University of Barcelona, Spain. BSc Thesis: “GlcNAcylation of the Unique Domain of proteins of the Src Family”. Supervisor: Prof. Dr. Miquel Pons Vallès
  8. 2017, Josemari Urtasun Elizari. BioNMR Group, University of Barcelona, Spain. Master Thesis: “New mechanisms of c-Src regulation”. Supervisor: Prof. Dr. Miquel Pons Vallès.
  9. 2017, Héctor Fuentes de la Osa. BioNMR Group, University of Barcelona, Spain. BSc Thesis: “Understanding SFKs regulation, the case of Lyn.” Supervisor: Prof. Dr. Miquel Pons Vallès.
  10. 2015, Guillermo Iruela Martin, BSc. BioNMR Group, University of Barcelona, Spain. Theme: Clonning of recombinant proteins. Supervisor: Prof. Dr. Miquel Pons Vallès.
  11. 2015, Simone Höfler, BSc. BioNMR Group, University of Barcelona, Spain. MSc Thesis: “Insights into modulation of the interaction between the Unique and SH3 domains in Src Family kinases.” Supervisor: Prof. Dr. Miquel Pons Valles.
  12. 2014, Pedro Garcia Lorente, Bsc & Msc. BioNMR Group, University of Barcelona, Spain. Bachelor’s Thesis: Evaluation of the oxidative potential of YmoB Protein. Supervisor: Prof. Dr. Miquel Pons Vallès.
  13. 2012, Tommaso Martelli, PhD. CERM, University of Florence, Italy. Theme: Molecular Biology techniques for the expression of Matrix Metalloproteinases constructurs. Supervisor: Prof. Dr. Claudio Luchinat.
  14. 2009, David M. Dias. Licentiate Thesis, CNC, University of Coimbra, Portugal. Licentiate Thesis: Strategies for protein-ligand binding evaluation by STD-NMR. Supervisor: Carlos F.G.C. Geraldes.

Scientific Outreach

Courses attended:

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

Social networks:

  • Twitter. I have two twitter accounts for dissemination and communication purposes. One for my profile and other shared with my wife who is also a researcher. @joaomcteixeira and @vvcientificos
  • Instagram. Shared with my life-partner (Susana Barrera Vilarmau) for communication purposes. @viviendocientificos
  • DEV.to. Blog where I discuss advanced programming concepts and implementations, for dissemination and communication purposes. https://dev.to/joaomcteixeira
  • 10/2021. Participant of Science Art communication with SURKxInktober (with a scientific twist). https://www.instagram.com/srukceru/ :point_right: #srukxinktober2021

Analysis and phylosophy 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.

Other:

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

Courses attended

  • 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. 02/2020
  • Organizing volunteer at the Pycon Toronto, Canada. 11/2019
  • International Postdocs Sub-committee of the Postdoctoral Advisrr Committee at SickKids, Toronto, Canada. 2019/2020
  • Postdoctoral Adviser Committee at SickKids, Toronto, Canada. 2019/20
  • 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.

Languages

Reading Writing Listening Speaking
Portuguese Native
Spanish C2+ C2 C2+ C2
English C1 C1 C1 C1
Italian B1 B1 C1 B2
Catalan B2 A1 B2 A1

Transferable skills

ACUC Advanced scuba-diver by CIB. Advanced techniques for speleology caving exploration (Speleo Discovery Barcelona). Advanced techniques for winter mountaineering. Advanced techniques for sport, classic, and multi-pitch climbing (see outdoors courses). Knowledgeable in safety and rescue techniques for mountaineering and caving. Tae-Know-Do black belt and Portuguese National Champion Juniors in combat (2003) for TKD-Club VRSA. Occasional bass-guitar player. Able to lead with high-risk and compromised situations. Able to work in team and independently. Able to lead and to support a leader.