Jacob J. W. Bakermans

Jacob J. W. Bakermans Postdoctoral researcher at the WIN University of Oxford https://github.com/jbakermans jacob.bakermans @ ndcn.ox.ac.uk

Research

• Relational representations for composition of knowledge and plans
  • Prof. dr. Tim Behrens and prof. dr. Mark Woolrich, Wellcome Centre For Integrative Neuroimaging, University of Oxford
• Modelling rat behaviour in a learning task with a latent causal structure
  • Prof. dr. Tim Behrens, Oxford Centre for Functional MRI of the Brain, University of Oxford
• MEG source reconstruction with dynamic network interactions
  • Prof. dr. Mark Woolrich, Oxford Centre for Human Brain Activity, University of Oxford
• Stable emission and excitation of the nitrogen-vacancy centre for quantum communication
  • Prof. dr. Ronald Hanson, QuTech, TU Delft
• RNA polymerase transcription initiation with single molecule FRET
• Prof. dr. Achillefs Kapanidis, Oxford Biological Physics, University of Oxford
• Electrophysiology of motor learning in mouse cerebellar nuclei
  • Prof. dr. Chris I. de Zeeuw, Department of Neuroscience, Erasmus MC Rotterdam
• A novel way to control STM-based manipulation: motion tracking and rapid molecular dynamics simulation
  • Prof. dr. Jan M. van Ruitenbeek, LION, Leiden University

Background

• 2016-2022 DPhil in Computational Neuroscience through Systems Biology DTC, University of Oxford, United Kingdom
• 2014-2016 MSc in Physics (Cum Laude), Leiden University, The Netherlands
• 2011-2014 BSc in Physics (Cum Laude), Leiden University, The Netherlands

Presentations and publications

• Bakermans, J.J.W, Warren, J., Whittington, J.C.R., Behrens, T.E. (2022).
  Constructing behaviour in structured environments. Poster at Computational and Systems Neuroscience, Lisbon, Portugal
• Warren, J., Bakermans, J.J.W, Whittington, J.C.R., Behrens, T.E. (2022).
  Learning generalised representations of behaviour within the hippocampal-entorhinal-prefrontal system. Poster at Computational and Systems Neuroscience, Lisbon, Portugal
• Shpektor, A., Bakermans, J.J.W., Baram, A.B., Fedele, T., Ledergerber, D., Imbach, L., Barron, H., Sarnthein, J., Behrens, T.E. (2022).
  A hierarchical representation of sequences in human entorhinal cortex. Talk at Computational and Systems Neuroscience, Lisbon, Portugal
• Whittington, J. C., McCaffary, D., Bakermans, J. J.W., & Behrens, T. E. (2022).
  How to build a cognitive map: insights from models of the hippocampal formation. arXiv preprint, arXiv:2202.01682.
• Malinen, A. M., Bakermans, J.J.W., Aalto-Setälä, E., Blessing, M., Bauer, D. L., Parilova, O., ... & Kapanidis, A. N. (2022).
  Real-Time Single-Molecule Studies of RNA Polymerase–Promoter Open Complex Formation Reveal Substantial Heterogeneity Along the Promoter-Opening Pathway. Journal of molecular biology, 434(2), 167383.
• Bakermans, J.J.W., & Behrens, T. E. (2021).
  Controlling precedence in sequential stimulus presentation with Euler tours. PsyArXiv preprint, https://doi.org/10.31234/osf.io/y8r6k
• Bakermans, J. J. W., Muller, T. H., Behrens, T. E. J. (2020).
  Reinforcement Learning: Full Glass or Empty — Depends Who You Ask. Current Biology, 30 (7), R321-R324.
• Tewari, S., Bakermans, J. J. W., Wagner, C., Galli, F., van Ruitenbeek, J. M. (2019).
  Intuitive human interface to a scanning tunnelling microscope: observation of parity oscillations for a single atomic chain. Beilstein Journal of Nanotechnoly, 10, 337–348.
• Van IJzendoorn, M. H., Bakermans, J. J. W., Steele, M., & Granqvist, P. (2018).
  Diagnostic use of Crittenden's attachment measures in Family Court is not beyond a reasonable doubt. Infant mental health journal, 39(6), 642-646.
• Dulin, D., Bauer, D. L., Malinen, A. M., Bakermans, J. J.W., Kaller, M., Morichaud, Z., ... & Kapanidis, A. N. (2018).
  Pausing controls branching between productive and non-productive pathways during initial transcription in bacteria. Nature Communications, 9(1), 1478.
• Ten Brinke, M. M., Heiney, S. A., Wang, X., Proietti-Onori, M., Boele, H. J., Bakermans, J. J. W., ... & De Zeeuw, C. I. (2017).
  Dynamic modulation of activity in cerebellar nuclei neurons during pavlovian eyeblink conditioning in mice. eLife, 6, e28132.
• Kalb, N., Reiserer, A. A., Humphreys, P. C., Bakermans, J. J. W., Kamerling, S. J., Nickerson, N. H., ... & Hanson, R. (2017).
  Entanglement distillation between solid-state quantum network nodes. Science, 356(6341), 928-932.

Awards

• DTC short project prize 2017, Systems Biology DTC Oxford
• Fully funded EPSRC scholarship for System Biology DTC
• Minerva Scholarship Fund scholarship for research project abroad
• SPIN Bachelor Project Competition 2015, best bachelor project in Physics
• Creative Game Challenge Student Edition 2011-2012, competition in game development (with Martijn Oei)
• Participants’ jury prize Make-a-Game 2007, competition in educational game development (with Niels Lodder)