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Publications 2023

University of Potsdam - Institute of Biochemistry and Biology- Bioinformatics group - Publications - 2023

Arend M, Zimmer D, Xu R, Sommer F, Mühlhaus T, Nikoloski Z.
Proteomics and constraint-based modelling reveal enzyme kinetic properties of Chlamydomonas reinhardtii on a genome scale.
Nat Commun 14, 4781 (2023).

Mbebi AJ, Nikoloski Z.
Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection.
PLOS Computational Biology, 2023

Tong H, Laitinen R A E, Nikoloski Z.
Predicting plasticity of rosette growth and metabolic fluxes in Arabidopsis thaliana.
New Phytol. (2023)

Soleymani Babadi F, Razaghi-Moghadam Z, Zare-Mirakabad F, Nikoloski Z.
Prediction of metabolite-protein intreactions based on integration of machine learning and constraint-based modeling.
Bioinformatics Advances, vbad098,2023.

Bezold F, Scheffer J, Wendering P, Razaghi-Moghadam Z, Trauth J, Pook B, Nußhär H, Hasenjäger S, Nikoloski Z, Essen LO, Taxis C.
Optogenetic control of Cdc48 for dynamic metabolic engineering in yeast.
Metabolic Engineering. 2023 Jul;79:97-107.

Wendering P, Nikoloski Z.
Model-driven insights into the effects of temperature on metabolism.
Biotechnology Advances, 108203

Huß S, Nikoloski Z.
Systematic comparison of local approaches for isotopically nonstationary metabolic flux analysis.
Frontiers in Plant Science 14, 1178239

Matz T W, Eng R C, Sampathkumar A, Nikoloski Z.
Microtubule-mediated cell shape regulation contributes to efficient cell packing in Arabidopsis thaliana cotyledons.
bioRxiv 2023.05.16.540958.

Arend M, Yuan Y, Ruiz-Sola M Á, Omranian N, Nikoloski Z, Petroutsos D.
Widening the landscape of transcriptional regulation of green algal photoprotection.
Nat Commun 14, 2687 (2023)

Ruiz-Sola, M A, Flori S, Yuan Y, Villain G, Sanz-Luque E, Redekop P, Tokutsu R, Küken A, Tsichla A, Kepesidis G, Allorent G, Arend M, Iacono F, Finazzi G, Hippler M, Nikoloski Z, Minagawa J, Grossman A R, Petroutsos D.
Light-independent regulation of algal photoprotection by CO2 availability.
Nat Commun 14, 1977 (2023)

Hanson AD, Millar AH, Nikoloski Z, Way DA.
Focus on Respiration.
Plant physiology.:kiad041

Langary D, Küken A, Nikoloski Z.
The unraveling of balanced complexes in metabolic networks.
Sci Rep 13, 5712 (2023)

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, Nikoloski Z.
Toward mechanistic modeling and rational engineering of plant respiration.
Plant Physiology, Volume 191, Issue 4, April 2023, p 2150–2166

Andreou G, Messer M, Tong  H, Nikoloski, Z, Laitinen R.
Heritability of temperature-mediated flower size plasticity in Arabidopsis thaliana.
Quantitative Plant Biology, 4, E4.

Campana P A, Nikoloski Z.
Self- and cross-attention accurately predicts metabolite–protein interactions.
NAR Genomics and Bioinformatics, Volume 5, Issue 1, March 2023, lqad008

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, Nikoloski Z.
Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses.
Nat Commun 14, 986 (2023).

Hashemi S, Laitinen R, Nikoloski Z.
Models and molecular mechanisms for trade-offs in the context of metabolism.
Molecular Ecology, 00, 1– 11.

Østerlund I, Persson S, Nikoloski Z.
Tracing and tracking filamentous structures across scales: A systematic review.
Computational and Structural Biotechnology Journal,Volume 21, 2023, p 452-462