Tristan Cragnolini

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Post-doctoral researcher

2018-2021 Topf and Thalassinos groups , Birbeck, University of London, London.

Cryo-EM data modelling, mass spectrometry data analysis.

Rigid and flexible fitting of molecular model in cryo-EM maps. Development of statistical models for interpreting Ion Moblity-Mass Spectrometry data of protein assemblies.

2014-2016 Wales group,University of Cambridge, Cambridge

Path sampling of coarse-grained biomolecules.

+Path sampling of G-quadruplex conformational transitions.
+Monte-carlo simulations of RNA and protein folding.
+Benchmarking of RNA and protein forcefields

• September 2021, Invited Speaker, S2C2 CryoEM Map Modeling and Validation Workshop, Stanford, Online. Cragnolini T., Topf M., “Improving and validating map/model fits with TEMPy”.
• August 2021, Speaker, New directions of AI in structural biology, CIRM. §Cragnolini T., Kryshtafovych A., Topf M., “ML for cryo-EM”.
• December 2020, Speaker, CASP 14, Online. Cragnolini T., Topf M., Kryshtafovych A., “Evaluating and refining EM structures with TEMPy”.
• June 2020 Speaker, Annual Conference of the American Society for Mass Spectrometry, Online. Cragnolini T., Eldrid C., Brit H., Menneteau T., Ben-Younis A., Thalassinos K., “Automated, web-based analysis and visualisation of tandem ion mobility mass spectrometry data
• June 2019 Poster, Annual Conference of the American Society for Mass Spectrometry, Manchester, UK. Cragnolini T., Eldrid C., Brit H., Thalassinos K., “Automated, web-based analysis and visualisation of data from a Cyclic Ion Mobility Spectrometry Travelling Wave Device”.
• February 2014, Biophysical Society Meeting, San Francisco Poster: Cragnolini T., Sutherland-Cash K.H., Wales D., Pasquali S., Derreumaux P., “Wide exploration of OPEP protein energy landscapes using advanced Monte Carlo methods”.
• Poster: Cragnolini T., Laurin Y., Derreumaux P., Pasquali S., “Predicting RNA complex architectures”. May 2013, “Computational Biology: Then and Now” symposium, Weizmann Institute
• Poster: Cragnolini T., Derreumaux P., Pasquali S., “Multiscale modelling of RNAs combining coarse-grain folding with detailed all-atom dynamics”. April 2013, CFCAM Meeting, Paris, France
• Presentation: “Fully flexible coarse-grained model for RNA and DNA” January 2012, Amsterdam, Netherlands
• MOLSIM 2012 school: Understanding Molecular Simulation
• May 2011, groupe de graphisme et modélisation moléculaire (GGMM), La Rochelle Poster: Cragnolini T., Derreumaux P., Pasquali, S., “All-atom reconstruction of predicted coarse-grained RNA structures”

• Post-doc Department of Chemistry, University of Cambridge
  Supervisor: Lucy Colwell
  RNA folding, detection of structural motifs
• Post-doc Department of Chemistry, University of Cambridge10/2014 - 09/2016
  Supervisor: David Wales
  Path sampling of coarse-grained biomolecules
• PhD thesis, Laboratoire de Biochimie Théorique, Paris, France10/2011 - 09/2014
  Supervisors: Dr. Samuela Pasquali and Pr. Philippe Derreumaux
  Predicting RNA structures and the large scale motions of RNA
  using computer simulations and coarse-grained models.
  • Development of HiRE-RNA, a coarse-grain forcefield for RNA
  • Optimization of the forcefield using a genetic algorithm
  • Implementation of the forcefield in the OPEP package (Fortran)
  • Development of analysis tools, in C++, Python and R
  • All-atom RNA simulations with AMBER and Gromacs
• Masters intership, Computational Biology Unit, Bergen, Norway03/2010 - 06/2010
  Supervisors: Dr. Nathalie Reuter and Svenn Grindhaug
• Contribution to webnm@, a normal mode webserver for analysis and visualisation
  Web address: http://apps.cbu.uib.no/webnma
  • Experience with MMTK, for the normal mode calculation (Python)
  • Addition of a Jmol viewing applet, with visualisation of the modes (Javascript)
  • Modification of the webserver to handle new analysis (Python, HTML, CSS, XML)
• Bachelor course, San Jose State University, San Jose, California, USA 03/2009 - 09/2009
  Supervisor: Pr. Steve White
• Work in a molecular biology laboratory (HeLa cell culture, Western Blot, PCR)
  

• 2011-2014 PhD thesis in molecular modelling, Université Paris Diderot-Paris 7, Paris, France
• 2009-2011 Master in bioinformatics, Université Paris Diderot-Paris 7, Paris, France
• 2008-2009 Exchange student at San José State University, San José, California, USA
• 2005-2009 Bachelor in chemistry and biology, Université Paris 12, Créteil, France

• 2015-2017 Supervision of classes in: computational techniques, quantum mechanics, perturbation theory, symmetry and bonding, University of Cambridge, UK
• 2011-2014 Teaching assistant for classes in Python(masters), bioinformatics(bachelor),
  molecular modelling(masters), Université Paris Diderot-Paris 7, Paris, France
• 2007-2008 Teaching assistant, Lycée Léon Blum (high school), Créteil, France

  

Molecular modelling Molecular modelling using Amber, GMIN, Gromacs, MMTK Models used: Amber99 (and variants), HiRE-RNA, Martini, OPEP Visualisation softwares: Chimera, Jmol, PyMol and VMD   

Software development Programming languages : C, C++, Fortran(77/90), Python Data formatting using CSS, JSON, L ^AT _EX, HTML, XML Parallel programming (MPI and pthreads), objected oriented programming Limited knowledge of Haskell, Java, Javascript, Perl, PHP, Development tools: Eclipse, Emacs, GDB, Git, SVN, Valgrind, Vi

Fluent English (2008, TOEFL: 105/120; 2011, Oxford placement test: level C2)

French (native language)

Beginner in Portuguese

Beginner in Spanish

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This document was translated from L ^AT _EX by H ^E V ^E A .