Dr. Jędrzej Jakub Szymański

Machine Learning, Data Science, Bioinformatics, Gene Regulation, Plant Metabolism, Genomics, Citizen Science, Computer Games

Contact

+49 2461/61-84142

E-Mail

https://www.fz-juelich.de/profile/szymanski_j

Address

Wilhelm-Johnen-Straße

Institute of Bio- and Geosciences (IBG)

Bioinformatics (IBG-4)

Building 14.6y / Room 4044

You can find us here

About me:

I am a Data Scientist with a background in Molecular Biology and Biochemistry, specializing in gene regulation and plant metabolism. My interest lies in understanding how genetic variations impact molecular networks and manifest as visible macro-phenotypes. Additionally, I advocate for citizen science initiatives and the integration of computer games in education and scientific exploration. On a personal note, I am most and foremost a dad, a nature enthusiast, and a bit of a Dungeons & Dragons geek.

Vita

since 2022: Member of the Cluster of Excellence on Plant Sciences (CEPLAS)

since 2022: Head of Omics Data Research Group, Institute of Bio- and Geosciences, IBG-4: Bioinformatik, Forschungszentrum Jülich GmbH, Jülich, Germany

since 2019: Bioinformatics Coordinator at the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Germany

since 2018: Head of Network Analysis and Modelling Research Group, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) in Gatersleben, Germany

2015-2018: Postdoc, Department of Plant and Environmental Sciences at the Weizmann Institute of Science, Rehovot, Israel

2014-2015: Postdoc, Department of Computer Science at the Tel Aviv University, Tel Aviv, Israel

2009-2014: Postdoc, Max Planck Institute of Molecular Plant Physiology, Golm, Germany

2009: PhD at the Max Planck Institute of Molecular Plant Physiology, degree awarded by University of Potsdam, Germany

2005: MSc Degree in Biotechnology, University of Wrocław, Poland

Publications

Some of my representative papers:

Deep learning the cis-regulatory code for gene expression in selected model plants

Nature Communications (2024) https://doi.org/10.1038/s41467-024-47744-0

Carbon flux through photosynthesis and central carbon metabolism show distinct patterns between algae, C3 and C4 plants

Nature plants (2022) https://doi.org/10.1038/s41477-021-01042-5

From data to knowledge-big data needs stewardship, a plant phenomics perspective

The Plant Journal (2022) https://doi.org/10.1111/tpj.15804

Rhizosphere microbiome mediates systemic root metabolite exudation by root-to-root signaling

Proceedings of the National Academy of Sciences (2020) https://doi.org/10.1073/pnas.1912130117

Multi-omics reveals mechanisms of total resistance to extreme illumination of a desert alga

Nature Plants (2020) https://doi.org/10.1038/s41477-020-0729-9

Analysis of wild tomato introgression lines elucidates the genetic basis of transcriptome and metabolome variation underlying fruit traits and pathogen response

Nature Genetics (2020) https://doi.org/10.1038/s41588-020-0690-6

Pathways to defense metabolites and evading fruit bitterness in genus Solanum evolved through 2-oxoglutarate-dependent dioxygenases

Nature Communications (2019) https://doi.org/10.1038/s41467-019-13211-4

Data integration, metabolic networks and systems biology

Annual Plant Reviews (2018) https://doi.org/10.1002/9781444339956.ch9

Label?free deep shotgun proteomics reveals protein dynamics during tomato fruit tissues development

The Plant Journal (2017) https://doi.org/10.1111/tpj.13490

Involvement of a gut-retina axis in protection against dietary glycemia-induced age-related macular degeneration

Proceedings of the National Academy of Sciences (2017) https://doi.org/10.1073/pnas.1702302114

Linking gene expression and membrane lipid composition of Arabidopsis

The Plant Cell (2014) https://doi.org/10.1105/tpc.113.118919

Last Modified: 05.06.2024