Research Interests

My main research goal is to assemble genome-scale models of cellular processes such as gene regulation and metabolism. In this regard I focus on the integration of omics data sets and biological knowledge bases in order to come up with novel hyptheses and testable predictions.

Education

Freie Universität Berlin, M.Sc. Biochemistry, 2020

Freie Universität Berlin, B. Sc. Biochemistry, 2017

Teaching

Exercise "Constraint-based modelling of cellular systems" WS2021/22

Exercise "Analysis of cellular networks" SS2022

Publications

Ferreira M A d M, Wendering P, Arend M, Silveira W B d, Nikoloski Z.
Accurate prediction of in vivo protein abundances by coupling constraint-based modelling and machine learning
bioRxiv 2023.04.11.536445

Wendering P, Arend M, Razaghi-Moghadam Z, Nikoloski Z.
Data integration across conditions improves turnover number estimates and metabolic predictions.
Nat Commun 14, 1485 (2023).

Tan Q W, Lim P K, Chen Z, Arend M, Nikoloski Z. et al.
Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses.
Nat Commun 14, 986 (2023).

Arend M, Yuan Y, Águila Ruiz-Sola M, Omranian N, Nikoloski Z, Petroutsos D. (2022)
Widening the landscape of transcriptional regulation of algal photoprotection
bioRxiv 2022.02.25.482034

Wendering P, Arend M, Razaghi-Moghadamkashani Z, Nikoloski Z. (2022)
Data integration across conditions improves turnover number estimates and metabolic predictions
bioRxiv 2022.04.01.486742

Arend M,  Zimmer D,  Xu R, Sommer F, Muhlhaus T, Nikoloski Z. (2022)
Proteomics and constraint-based modelling reveal enzyme kinetic properties of Chlamydomonas reinhardtii on a genome scale

https://doi.org/10.1101/2022.11.06.515318

Tan QW, Lim PK, Chen Z, Pasha A, Provart N, Arend M, Nikoloski Z, Mutwil M. (2022)
Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses
https://doi.org/10.1101/2021.11.12.468350

Ruiz-Sola MA, Flori S, Yuan S, Villain G, Sanz-Luque E, Redekop P, Tokutsu R, Kueken A, Tsichla A, Kepesidis G, Allorent G, Arend M, Iacono F, Finazzi G, Hippler M, Nikoloski Z, Minagawa J, Grossman AR, Petroutsos D. (2021)

Photoprotection is regulated by light-independent CO2 availability

https://doi.org/10.1101/2021.10.23.465040

Malik V., Glaser L.V., Zimmer D., Velychko S., Weng M., Holzner M., Arend M., Chen Y., Srivastava Y., Veerapandian V., Shah Z., Esteban M.A., Wang H., Chen J., Schöler H.R., Hutchins A.P., Meijsing S.H., Pott S., Jauch R. (2019)
Pluripotency reprogramming by competent and incompetent POU factors uncovers temporal dependency for Oct4 and Sox2.

Nature Communications volume 10, Article number: 3477 (2019)