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Maciej Dobrzyński
A computational biologist and a mathematical modeller with 10+ years of experience in academia and industry, focusing on data analysis and visualisation. Superb at building pipelines for diverse biological data that provide actionable insights through interactive visualisations. An interdisciplinary mind with organisational skills to conduct and lead computational biology projects under tight deadlines. Strong science communicator with a proven track record of designing and teaching courses, training the staff, publishing in scientific journals.
Education
PhD., Mathematics & Computer Science
Centre for Mathematics and Computer Science (CWI)
Amsterdam, The Netherlands
2009 - 2004
M.Sc., Physics, Theoretical Biophysics
Faculty of Physics, Warsaw University
Warsaw, Poland
2003 - 1997
- Thesis: Particle-based algorithm for modelling of biochemical networks
- Erasmus Scholarship at Vrije Universiteit Amsterdam
Experience
Postdoctoral Researcher
Cellular Dynamics Lab, Institute of Cell Biology, University of Bern
Bern, Switzerland
current - 2016
- Developed an R/Shiny app to explore and cluster time series
- Developed a web portal to visualise drug screen imaging data
- Set up a computational cluster and developed pipelines to process data from high-content screening and time-lapse microscopy experiments.
Data Scientist
TickerFit (start-up)
Dublin, Ireland
2018 - 2014
- Consulted and analysed in R patient activity during cardiac rehabilitation
Data Scientist
AstraZeneca Discovery Sciences
Cambridge, UK
2016 - 2015
- Used CellProfiler/R to analyse single-cell data from high-content screens
- Used Matlab/Mathematica to develop a mathematical model of cell-cell heterogeneity in a mitogenic signalling pathway
Postdoctoral Researcher
Systems Biology Ireland, University College Dublin
Dublin, Ireland
2015 - 2010
- Developed deterministic and stochastic models of oncogenic signalling
- Performed wet-lab experiments: flow cytometry and live cell imaging
- Programmed in Python, Matlab, Mathematica, R
Research Assistant
Institute of Theoretical Biology, Humboldt University
Berlin, Germany
2009
- Studied the robustness of a bacterial chemotactic network
Undergraduate Researcher
Interdisciplinary Centre for Mathematical and Computational Modelling (ICM)
Warsaw, Poland
2004 - 2003
- Vectorized a gene sequence alignment algorithm on Cray X1 architecture
- Programmed in C/C++, Perl, MPI
Undergraduate Researcher
FOM Institute for Atomic and Molecular Physics (AMOLF)
Amsterdam, The Netherlands
2002
- Developed a method for simulation of biochemical networks
- Programmed in C/C++, Fortran 77 & 95
I have bridged academia and industry, have worked in interdisciplinary, fast-paced, collaborative R&D environments.
Teaching Experience
I have held numerous invited lectures and workshops about biological image processing, statistical analysis, and visualisation of experimental data.
Course: Imaging statistics
Bern, Switzerland
2021
- Held a lecture & practicals on data analysis for microscopy
Course: Modern data analysis in R/RStudio
Bern, Switzerland
2020
- Held a workshop on advanced topics of data analysis in R
Course: Analysis on microscopy images with CellProfiler
Bern, Switzerland
2019
- Assisted a workshop on image analysis with CellProfiler
Processing data from single-cell time-lapse microscopy
Fiesch, Switzerland
2019
- Held a workshop on analysis of data from time-lapse microscopy
Semi-advanced R programming tricks
Bern, Switzerland
2019
- Held a lecture on advanced topics in R programming
Shiny from basics to awesome in 26 minutes
Bern, Switzerland
2019
- Held a lecture on R/Shiny programming
Image analysis with ImageJ and CellProfiler
Institute of Cell Biology, University of Bern
Bern, Switzerland
2018 - 2017
- Held a lecture for undergraduate students
Course: Introduction to modelling of signalling networks
2nd Porto Meeting in Mathematics and Biology
Porto, Portugal
2016
- Invited lecture series on cell-cell heterogeneity in signalling networks
Course: Introduction to Systems Biology
Systems Biology Ireland, University College Dublin
Dublin, Ireland
2015 - 2013
- Gave a lecture series to (under-)graduate students
Course: Principles of Object-Oriented Programming in Java
Faculty of Physics, Warsaw University
Warsaw, Poland
2004
- Teaching assistant
Selected Peer-reviewed Publications
I design and perform image/data analysis and ensure statistical rigour during results dissemination.
High-Content Screening Pipeline for Natural Products Targeting Oncogenic Signaling in Melanoma
N/A
2022
- Analysed and visualised HCS data
CODEX, a neural network approach to explore signaling dynamics landscapes
N/A
2021
- Supervised the project
- R/Python coding by MA Jacques, a PhD student in the lab
Collective ERK/Akt activity waves orchestrate epithelial homeostasis by driving apoptosis-induced survival
N/A
2021
- Analysed single-cell ERK/Akt activity waves that induce survival in neighbouring cells of the epithelium
- Developed an R package to quantify collective signalling
Mining single-cell time-series datasets with Time-Course Inspector
N/A
2020
- Developed an R/Shiny app to interactively process, visualise, and cluster time series
Temporal perturbation of Erk dynamics reveals network architecture of FGF2-MAPK signaling
N/A
2019
- Modelled the FGF2-MAPK network
- Analysed single-cell time series data in R and Matlab
Automated Comparative Metabolite Profiling of Large LC-ESIMS Data Sets in an ACD/MS Workbook Suite Add-in, and Data Clustering on a New Open-Source Web Platform FreeClust
N/A
2017
- Developed an R/Shiny web application to cluster LC-MS data
Stabilization of C-RAF:KSR1 complex by DiRas3 reduces availability of C-RAF for dimerization with B-RAF
N/A
2016
- Perfomed image and statistical analysis
Frequency modulation of ERK activation dynamics rewires cell fate
N/A
2015
- Studied cell fate determination by ERK signalling dynamics
- Analysed single-cell time series data in R and Matlab
Nonlinear signalling networks and cell-to-cell variability transform external signals into broadly distributed or bimodal responses
Journal of the Royal Society Interface
N/A
2014
- Studied the emergence of cell-cell heterogeneity in signalling pathways
- Developed a model in Wolfram Mathematica
Elongation dynamics shape bursty transcription and translation
Proceedings of the National Academy of Sciences of the USA
N/A
2009
- Studied stochasticity during mRNA transcription and protein translation
- Wrote code in C, Matlab, R
Computational methods for diffusion-influenced biochemical reactions
N/A
2007
- Evaluated methods for simulating cell signalling in space and time
- Wrote code in Python and C
Selected Press (By)
I write popular science articles about the role of computational biology in knowledge discovery.
The Era of Personalised Medicine
N/A
2015
- Leveraging personalised data to improve health
- Spider’s Web is a Polish technology portal with ~4M monthly users
Healing with a computer
N/A
2012
- How computational biology helps to predict new treatments
- Polityka is Poland’s biggest selling weekly magazine
Selected Press (About)
Math replaces lab animals
Experiment NL: Science in The Netherlands
N/A
2009
- A feature about my PhD research and how mathematical modelling can help to alleviate animal testing of drugs