Research Interests

The major topics of my research include image analysis, graph theory and statistics. I work on automated, computational frameworks to analyze microscopy images by quantifying certain processes in plants. These frameworks include the automated extraction and analysis of cytoskeletal components, such as actin filaments, by representing them as networks. The extracted networks can then be used for quantitative analysis of actin in time series, between different conditions or for the testing against random networks.

Furthermore, I work on the development of a framework to describe the complex shape of pavement cells in the upper epidermis of plant leaves. Due to their shape complexity, pavement cell shapes are hard to describe in a quantitative manner. We developed a network-based framework to quantify, compare and classify cell shapes by analyzing global and local shape features.

Education

University of Melbourne, University of Potsdam, Joint PhD, 2021

MSc in Bioinformatics, University of Potsdam, 2015

BSc in Biosciences, University of Potsdam, 2012

Selected Publications

Breuer D, Nowak J, Ivakov A, Somssich M, Persson S, Nikoloski (2017).
System-wide organization of actin cytoskeleton determines organelle transport in hypocotyl plant cells
PNAS 114(28): E5741-5749

Yu Y, Wu S, Nowak J, Wang G, Han L, Feng Z, Mendrinna A, Ma Y, Wang H, Zhang X, Tian J, Dong L, Nikoloski Z, Persson S, Kong Z (2019).
Live-cell imaging of the cytoskeleton in elongating cotton fibers
Nature Plants 5: 498-504

Song Y, Li G, Nowak J, Zhang X, Xu D, Yang X, Huang G, Liang W, Yang L, Wang C, Bulone V, Nikoloski Z, Hu J, Persson S, Zhang D (2019).
The rice actin-binding protein RMD regulates light-dependent shoot gravitropism
Plant Physiology 181: 630-644

Nowak J, Gennermann, K, Persson S, Nikoloski Z (2020).
CytoSeg 2.0: automated extraction of actin filaments.
Bioinformatics. 2020 May 1;36(9):2950-2951

Nowak J, Eng RC, Matz T, Waack M, Persson S, Sampathkumar A, Nikoloski Z (2021).
A network-based framework for shape analysis enables accurate characterization and classification of leaf epidermis cells.
Nat Commun, 2021 Jan; 12(1):458