DR. JOHANNA M. M. BAYER, M.Sc., B.Sc.

EDUCATION/ACADEMIC QUALIFICATIONS

Year Qualification Institution
2023- now Post Doctoral Fellow Donders Institute for Brain, Cognition and Behaviour, Radboud UMC, Nijmegen Topics: Longitudinal and lifespan normative modelling, PCNtoolkit development and maintenance, normative modelling development
2018-2025 PhD candidate. Computational Psychiatry, supported by Melbourne Research Scholarship based on GPA of 94% PhD awarded Feb 2025 The University of Melbourne, Melbourne
Orygen, the National Institute of Excellence in Youth Mental Health
PhD Topic: Machine learning methods development and application in big data - towards the identification and evaluation of a neuroimaging biomarker for major depressive disorder. supervisor by A/Prof. Lianne Schmaal
  • Working with ENIGMA MDD big open neuroimaging dataset and machine learning methods
  • Collaboration with A/Prof. Andre Marquand
  • Collaboration with PI Philipp Saemann
  • Project 1: Development of a normative model that can deal with site effects in a big, open neuroimaging data set (ABIDE)
  • Project II: Application of this normative model to a large neuroimaging depression data set (ENIGMA) to study biomarkers in depression
  • Project III: Overview over the site effect correction literature, comparison of methods
2017-2018 Smart Start Fellow Smart Start Fellowship of the Bernstein Center for Computational Neuroscience Germany
2017-2018 Student Acceptance to Graduate School of Systemic Neuroscience, Munich
2014-2016 Master of Neuro- Cognitive Psychology, highly competitive Elite Master Program of State of Bavaria Ludwig Maximillian University Munich, Munich, Germany GPA 1.06, (pass range 1.0 - 4.7, lower values are better, 2nd best of cohort of 14 individuals, see conversion of German to US grades here)

Master thesis: Multimodal path integration in distance estimation based on Bayesian principles (Supervisors: Prof. Dr. Ing. Stefan Glasauer , LMU, Munich; Prof. Zhuanghua Shi, LMU, Munich) Grade: 1.0 (see conversion of German to US grades here)

Refinement of a Kalman filter model to estimate the perception of distance travelled from visual and vestibular sensory cues in an optokinetic drum

2010-2014 Bachelor of Psychology Otto-Friedrich University Bamberg, Bamberg, Germany, GPA 1.3 (pass range 1.0 - 4.7, lower values are better, < 5% best of cohort of 150 individuals, see conversion of German to US grades here)

Bachelor thesis: Electrophysiological Correlates of Intentional and Unintentional Errors in Relation to Conscientiousness Grade: 1.0 (see conversion of German to US grades here)

Acquisition and Analysis of EEG data of 47 subjects

2010 Abitur (University Entrance Certificate) Majors: Physics, Spanish, Latin; GPA = 1.4 (pass range = 1.0 - 4.7, lower values are better, <5% best of cohort of 120 individuals, see conversion of German to US grades here)

TEACHING

Date Role/Course Taught/Developed
09/2025 Advanced Registration, Lecture, Donders fmri Toolkit, September 2025
Normative modelling tutorial. Tutorial, Donders fmri Toolkit, September 2025
05/2025 Research Software Engineering for PhD Students, Forschungszentrum Juelich
09/2024 Advanced Registration, Lecture, Donders fmri Toolkit, September 2024
Normative modelling tutorial. Tutorial, Donders fmri Toolkit, September 2024
06/2024 Normative modelling educational course, half day educational course, OHBM 2024, Korea, material
05/2024 Site effects for normative modelling tutorial
03/24-04/24 NASA Tops Open Science Curriculum Instructor & Coach, first Nebula Cohort
10/25-04/26 Teaching Assistant at ReproRehab, University of Southern California, https://www.reprorehab.usc.edu/teaching-assistants
10/24-04/25 Teaching Assistant at ReproRehab, University of Southern California, https://www.reprorehab.usc.edu/teaching-assistants
10/23-04/24 Teaching Assistant at ReproRehab, University of Southern California, https://www.reprorehab.usc.edu/teaching-assistants
10/22-04/23 Teaching Assistant at ReproRehab, University of Southern California, https://www.reprorehab.usc.edu/teaching-assistants
18-19/07/23 Git for Librarians; Teaching Assistant at VALA Tech Camp 2023
07/22- 08/22 Paid Curriculum Developer role for Open Software with NASA Open Science.
03/2022 Teaching Assistant under Caroline Gao: Doing statistical and non-statistical things using R without tears
12/2021 Train track Git Intro course, global hackathon 2021, Australia Hub
2014 Design and development of an online tutorial supporting the lecture of biological psychology (not publicly available)

MENTORING/SUPERVISING

Date Role/Topic
2022-2025 ReproRehab Teaching Assistant, supervision of cohorts between 5-10 students https://www.reprorehab.usc.edu/teaching-assistants
2024 OLS Nebula cohort. Project supervision of 2 students
2024 OLS Open Seeds DRIA EDI track: Mentoring of 3 students from the field of machine learning (Open Science)
2023 Google Summer of Code Mentor, shared project between INCF and the Turing Way
2020 Machine Learning to peers (on voluntary basis)
2019/20 Mentor in mentoring network at Orygen

SOFTWARE CONTRIBUTIONS/MAINTENANCE

Date Tool Role
06/2025 ReproInventory Data collation, curation, front end developer
10/23-now Physio Toolbox (Matlab) Core contributor. Added a BIDS writer tool that formats output to BIDS and a switch that toggles the verbosity of image output when being run in a cluster environment.
10/23-now PCNtoolkit (Python) Core contributor. Adding Velocity centiles logic.
Small refactoring tasks and bug fixes
10/23-now PCNtoolkit Demo repository (Python) Developer of Site effect correction in normative modelling tutorial. Small refactoring tasks and bug fixes
07/23-now Matlab Open Neuro Toolbox Open Neuro Matlab Interface. I authored this toolbox
2022-now The Carpentries Maintainer of the Social Sciences and Geospatial repositories
2020-now The Turing Way Book Core maintainer, community governance group, individual contributor
02/2024 Scikit learn Contribution to scikit learn (examples).

WORK AND INTERNSHIPS

Date Role
10/23-now Handling editor, Journal of Open Source Software (JOSS)
10/23- now Freelance contract with MathWorks, Boston Massachusetts – working on OpenNeuro/BIDS toolbox
07/23-now Consultant, Lab Amanda Meija, Indiana University, USA. Working on pre-processing the ADNI data set.
15/08/22- 15/08/23 0.4FTE Research fellow in mood and anxiety disorders, Centre for Youth Mental Health, The University of Melbourne: working on using machine learning methods in the search of biomarkers for depression
01/09/22- 01/10/24 Research fellow in psychosis risk research, Faculty for Medicine Dentistry and Health Sciences, The University of Melbourne: working on translating machine learning models of psychosis risk research (1.0 FTE from 15/08/23 on)
12/22-05/23 Freelance contract with MathWorks, Boston Massachusetts -working on the PhysIO Toolbx
06/22-09/22 Machine learning engineer, SAMA Therapeutics
07/22 10/22 Paid Mathworks Summer Project Internship, a joined initiative by Mathworks and INCF, working on the PhysIO toolbox (part time).
07/21-09/22 Research Fellow Role with Prof. Barnaby Nelson, Orygen (Analysis, writing of manuscripts)
04/20-11/21 Research Assistant with Prof. Alison Yung, group-based trajectory modelling of large-scale data set of individuals with ultra-high-risk for and first-episode psychosis (Stata, R, SAS)
05/18-01/19 Research Assistant in the Horyzons study with Orygen digital, , Prof. Mario Alvarez, computer based (scripts in R) scoring, pre-processing analysis, visualisation of 40 questionnaires of 168 individuals in 3year lasting longitudinal study
04/17-09/17 Lab rotation and working experience at the Translational Neuromodelling Unit, under the direction of Prof. Klaas Enno Stephan, Eidgenössische Technische Hochschule Zürich, Switzerland direct supervisors: Dr. Lars Kasper, Dr. Jakob Heinzle
Project: Mismatch Negativity in different layers of the auditory cortex at 7-tesla MRI: developing a probabilistic brain mask to delineate an inner and outer layer of the cortex; data analysis
2017 Research assistant with the LAYMM study at the TNU; in charge of concurrent magnetic field monitoring during data acquisition
09/16-04/17 Lab rotation at the Neural Information Processing Group under the direction of Prof. Klaus Obermayer, direct supervisor: Dr. Rong Guo
Project: A Bayesian approach to sequence learning data, developing a Bayesian model of surprise in the BOLD response fMRI after stimulus/reward sequence changes in a learning task
11/17 Lab Internship at Cognition and DecisionMaking Lab at the Psychology Department of Boston University, MA, Boston, USA under the supervision of Prof. Joseph McGuire, 2 weeks
2015/16: Research assistant/scientific secretary at the sleeping lab of Prof. Dr. Axel Steiger at Max Planck Institute for Psychiatry, Munich
08/15-02-16 Research Project under the supervision of Prof. Dr. Ing. Glasauer, at the Department of Neurology & German Center for Dizziness at Klinikum Großhadern and at the Bernstein Center for Computational Neurosciences (former D2 project), Munich, in Collaboration with the Vestibulo-Oculomotor lab Zürich (Prof. Dr. Straumann, University Hospital, Zurich, Switzerland) Research Topic: Path reproduction in body- vs. environmentally caused angular displacement
2015 Research Project under the supervision of Dr. Dragan Rangelov, Department of General and Experimental Psychology, LMU Munich, data analysis project with Python Topic: Investigating the characteristics of face detectors using normal and scrambled faces
2015 Work as research assistant for Dr. Agnieszka Wykowska, Experimental Psychology Unit, Department Psychology, LMU Munich, pre-processing of behavioural data
2014 Work as a research assistant at the Chair for General Psychology, Otto-Friedrich-Universität Bamberg, under the direction of Prof. Dr. Rüsseler, data collection of EEG data

AWARDS & FELLOWSHIPS

Date Award/Fellowship
2025 Open Science Prize, RadboudUMC, with my lab (~500 Euro)
2025 OHBM Merit Abstract Award (USD$850)
2022 INCF-Repronim-Fellowship by the INCF: Re-organisation/Improvement of teaching of training material, with final presentation in the community. Conference travel support (AUD$1200)
2022 Oracle Cloud Grant over AUD$230,000.00 of computing hours for development of “brainhack cloud”. I am collaborator on the grant and main admin of the cloud;
2019 ECR OHBM bursary (AUD$200)
2019 2nd prize student showcase held at Orygen Youth Health
2018 Melbourne Research Scholarship, waiving tuition fees, living allowance (~ AUD$500000)
2017 Smart start Fellowship – one year support of living allowance (~ 21000 Euro)
2017 Travel scholarship Smart Start (1000 Euro)
2016 Travel Grant for SFN in San Diego by the Graduate Center of Systemic Neurosciences (1100 Euro)

ADDITIONAL/EXTRACURRICULAR COURSES

Date Course
01/24-now Probabilistic Deep Learning. Part of the AI Masters programme, Radboud University, Nijmegen, Netherlands
03/21 -now Student of Bachelor Computer Science, FernUniversitaet Hagen, Hagen, Germany
05/22-now ML Ops Zoomcamp, course on the automiatisation of machine learning workflows on the cloud using python
01/22-04/22 ABCD Repronim course and ABCD Prepronim machine learning/artificial intelligence course, teaching how to analyse the large ABCD data set using machine learning and reproducible tools
08/18 Machine Learning Summer School, MLSS, Spain (10 days)
05/18 Australian Connectomics School (2 day course)
04/18 Advanced Scientific Programming in Python Course, Melbourne University (2-day course)
03/18 Introduction to Linux and Shell Scripting (2 day course)
08/17 Computational Psychiatry Course, 1 week, TNU/ETH Zurich, Switzerland part of staff
05/17 Connectomics workshop TNU/ETH Zurich, Switzerland (3 days), part of the organisation staff
2016/17 Machine Intelligence 1 + tutorials (Lecture as part of the SmartStart program by the Bernstein Center for Computational Neuroscience, Germany, passed)
2016/17 Neuronal Networks (seminar, passed)
02/2016 Winter school Ethics and Neuroscience, hosted by the Bernstein Center for Computational Neuroscience Berlin and the Berlin School of Mind and Brain
2015/16 Computational neuroscience: A lecture series from Models to Applications (Lecture at the Bernstein Center for Computational Neuroscience, Munich, passed)
2015/16 Programming and Modelling with Java (Part of the curriculum of Bachelor Informatics, Munich, passed) + practical programming lessons
2015/16 Applied statistics for Neuroscientists (Part of the curriculum of Graduate School of Systemic Neuroscience, Munich)
2015/16 Neurobiology of Cognition (Seminar at the Max Planck Institute of Biology, Munich, passed)
2015/16 Matlab-Course (passed)
2015 Mathematik für Nebenfach (Mathematics as minor, passed)
2015 Working with PsychoPy (Python) and R during the Research Project
2014 Introduction to computer- and operating systems (Part of the curriculum of Bachelor Informatics, Bamberg, passed)
2014 Introduction to Cognitive Neurosciences (ungraded)
2014 Introduction to Cognitive Informatics (ungraded)

SKILLS

Languages Python, R, Matlab, C++, Bash, Html, JAVA, Stan, JavaScript, CSS
Frameworks Scikit, TensorFlow, Django, Flask, Hugo, DiPy, Jekyll, Keras, Freesurfer, SPM, Pytorch
Tools Kubernetes, Docker, Singularity, Git
Platforms Mac OS, Windows, Linux
Soft Skills Leadership, Writing, Mentoring, Teaching, Social Media Management & Outreach, Community Building, Website Development
Spoken languages German, English, Spanish, Dutch

CONFERENCES/TALKS

OPEN SCIENCE & EXTRACURRICULAR ACTIVITIES

EXTRACURRICULAR NON-ACADEMIC ACTIVITIES

Johanna Bayer