Zoran Nikoloski

Scopus Author ID Loop profile ORCID

Publication Activity (10 Years)

Years Active: 2015-2024
Publications (10 Years): 64

Top Venues

Nature communications

Plant physiology

PLoS computational biology

Cellular and molecular life sciences : CMLS

University of Potsdam

University of Central Florida (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

University of Potsdam Apr 01 2017

Germany

Professor :: Bioinformatics

Max Planck Institute of Molecular Plant Physiology Apr 01 2017

Germany

Guest Group Leader

Education History

University of Central Florida Sep 01 2001 - Aug 06 2005

United States

PHD :: School of Computer Science

Publications

Yunli Eric Hsieh, Kshitij Tandon, Heroen Verbruggen, Zoran Nikoloski
Comparative analysis of metabolic models of microbial communities reconstructed from automated tools and consensus approaches. NPJ systems biology and applications 10 (1) (2024)
Saurabh Gupta, Veselin Petrov, Vanika Garg, Bernd Mueller-Roeber, Alisdair Robert Fernie, Zoran Nikoloski, Tsanko S Gechev
The genome of Haberlea rhodopensis provides insights into the mechanisms for tolerance to multiple extreme environments. Cellular and molecular life sciences : CMLS 81 (1) (2024)
Mahdis Habibpour, Zahra Razaghi-Moghadam, Zoran Nikoloski
Machine learning of metabolite-protein interactions from model-derived metabolic phenotypes. NAR genomics and bioinformatics 6 (3) (2024)
Saurabh Gupta, Veselin Petrov, Vanika Garg, Bernd Mueller-Roeber, Alisdair Robert Fernie, Zoran Nikoloski, Tsanko S Gechev
The genome of Haberlea rhodopensis provides insights into the mechanisms for tolerance to multiple extreme environments. Cellular and molecular life sciences : CMLS 81 (1) (2024)
Milad Rahimi-Majd, Alistair Leverett, Arne Neumann, Johannes Kromdijk, Zoran Nikoloski
Nonlinear models based on leaf architecture traits explain the variability of mesophyll conductance across plant species. Plant, cell & environment (2024)
Alice Pieri, Romina Beleggia, Tania Gioia, Hao Tong, Valerio Di Vittori, Giulia Frascarelli, Elena Bitocchi, Laura Nanni, Elisa Bellucci, Fabio Fiorani, Nicola Pecchioni, Stefania Marzario, Concetta De Quattro, Antonina Rita Limongi, Pasquale De Vita, Marzia Rossato, Ulrich Schurr, Jacques L David, Zoran Nikoloski, Roberto Papa
Transcriptomic response to nitrogen availability reveals signatures of adaptive plasticity during tetraploid wheat domestication. The Plant cell (2024)
Saurabh Gupta, Veselin Petrov, Vanika Garg, Bernd Mueller-Roeber, Alisdair Robert Fernie, Zoran Nikoloski, Tsanko S Gechev
The genome of Haberlea rhodopensis provides insights into the mechanisms for tolerance to multiple extreme environments. Cellular and molecular life sciences : CMLS 81 (1) (2024)
Saurabh Gupta, Veselin Petrov, Vanika Garg, Bernd Mueller-Roeber, Alisdair Robert Fernie, Zoran Nikoloski, Tsanko S Gechev
The genome of Haberlea rhodopensis provides insights into the mechanisms for tolerance to multiple extreme environments. Cellular and molecular life sciences : CMLS 81 (1) (2024)
Yunli Eric Hsieh, Kshitij Tandon, Heroen Verbruggen, Zoran Nikoloski
Comparative analysis of metabolic models of microbial communities reconstructed from automated tools and consensus approaches. NPJ systems biology and applications 10 (1) (2024)
Yunli Eric Hsieh, Kshitij Tandon, Heroen Verbruggen, Zoran Nikoloski
Comparative analysis of metabolic models of microbial communities reconstructed from automated tools and consensus approaches. NPJ systems biology and applications 10 (1) (2024)
Mahdis Habibpour, Zahra Razaghi-Moghadam, Zoran Nikoloski
Machine learning of metabolite-protein interactions from model-derived metabolic phenotypes. NAR genomics and bioinformatics 6 (3) (2024)
Seirana Hashemi, Roosa Laitinen, Zoran Nikoloski
Models and molecular mechanisms for trade-offs in the context of metabolism. Molecular ecology (2023)
Philipp Wendering, Marius Arend, Zahra Razaghi-Moghadam, Zoran Nikoloski
Data integration across conditions improves turnover number estimates and metabolic predictions. Nature communications 14 (1) (2023)
Qiao Wen Tan, Peng Ken Lim, Zhong Chen, Asher Pasha, Nicholas J Provart, Marius Arend, Zoran Nikoloski, Marek Mutwil
Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses. Nature communications 14 (1) (2023)
Thekla von Bismarck, Philipp Wendering, Leonardo Perez de Souza, Jeremy Ruß, Linnéa Strandberg, Elmien Heyneke, And Berkley J Walker, Mark Aurel Schöttler, Alisdair Robert Fernie, Zoran Nikoloski, Ute Armbruster
Growth in fluctuating light buffers plants against photorespiratory perturbations. Nature communications 14 (1) (2023)
Marius Arend, Yizhong Yuan, M Águila Ruiz-Sola, Nooshin Omranian, Zoran Nikoloski, Dimitris Petroutsos
Widening the landscape of transcriptional regulation of green algal photoprotection. Nature communications 14 (1) (2023)
Marius Arend, David Zimmer, Rudan Xu, Frederik Sommer, Timo Mühlhaus, Zoran Nikoloski
Proteomics and constraint-based modelling reveal enzyme kinetic properties of Chlamydomonas reinhardtii on a genome scale. Nature communications 14 (1) (2023)
Philipp Wendering, Marius Arend, Zahra Razaghi-Moghadam, Zoran Nikoloski
Data integration across conditions improves turnover number estimates and metabolic predictions. Nature communications 14 (1) (2023)
Qiao Wen Tan, Peng Ken Lim, Zhong Chen, Asher Pasha, Nicholas J Provart, Marius Arend, Zoran Nikoloski, Marek Mutwil
Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses. Nature communications 14 (1) (2023)
Marius Arend, Yizhong Yuan, M Águila Ruiz-Sola, Nooshin Omranian, Zoran Nikoloski, Dimitris Petroutsos
Widening the landscape of transcriptional regulation of green algal photoprotection. Nature communications 14 (1) (2023)
Seirana Hashemi, Roosa Laitinen, Zoran Nikoloski
Models and molecular mechanisms for trade-offs in the context of metabolism. Molecular ecology (2023)
Qiao Wen Tan, Peng Ken Lim, Zhong Chen, Asher Pasha, Nicholas J Provart, Marius Arend, Zoran Nikoloski, Marek Mutwil
Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses. Nature communications 14 (1) (2023)
Mauricio Alexander de Moura Ferreira, Wendel Batista da Silveira, Zoran Nikoloski
PARROT: Prediction of enzyme abundances using protein-constrained metabolic models. PLoS computational biology 19 (10) (2023)
Philipp Wendering, Zoran Nikoloski
Toward mechanistic modelling and rational engineering of plant respiration. Plant physiology (2023)
Qiao Wen Tan, Peng Ken Lim, Zhong Chen, Asher Pasha, Nicholas J Provart, Marius Arend, Zoran Nikoloski, Marek Mutwil
Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses. Nature communications 14 (1) (2023)
Philipp Wendering, Marius Arend, Zahra Razaghi-Moghadam, Zoran Nikoloski
Data integration across conditions improves turnover number estimates and metabolic predictions. Nature communications 14 (1) (2023)
Hao Tong, Roosa A E Laitinen, Zoran Nikoloski
Predicting plasticity of rosette growth and metabolic fluxes in Arabidopsis thaliana. The New phytologist (2023)
Pedro Alonso Campana, Zoran Nikoloski
Self- and cross-attention accurately predicts metabolite-protein interactions. NAR genomics and bioinformatics 5 (1) (2023)
Pedro Alonso Campana, Zoran Nikoloski
Self- and cross-attention accurately predicts metabolite-protein interactions. NAR genomics and bioinformatics 5 (1) (2023)
Marius Arend, Yizhong Yuan, M Águila Ruiz-Sola, Nooshin Omranian, Zoran Nikoloski, Dimitris Petroutsos
Widening the landscape of transcriptional regulation of green algal photoprotection. Nature communications 14 (1) (2023)
Sandra Marcela Correa Cordoba, Hao Tong, Asdrúbal Burgos, Feng Zhu, Saleh Alseekh, Alisdair Robert Fernie, Zoran Nikoloski
Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism. Nature communications 14 (1) (2023)
Seirana Hashemi, Zahra Razaghi-Moghadam, Zoran Nikoloski
Maximizing multi-reaction dependencies provides more accurate and precise predictions of intracellular fluxes than the principle of parsimony. PLoS computational biology 19 (9) (2023)
Alain J Mbebi, Zoran Nikoloski
Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection. PLoS computational biology 19 (7) (2023)
Andrew D Hanson, A Harvey Millar, Zoran Nikoloski, Danielle A Way
Focus on Respiration. Plant physiology (2023)
Fayaz Soleymani Babadi, Zahra Razaghi-Moghadam, Fatemeh Zare-Mirakabad, Zoran Nikoloski
Prediction of metabolite-protein interactions based on integration of machine learning and constraint-based modeling. Bioinformatics advances 3 (1) (2023)
Fayezeh Aarabi, Apidet Rakpenthai, Rouhollah Barahimipour, Michał Gorka, Saleh Alseekh, Youjun Zhang, Mohamed A Salem, Franziska Brückner, Nooshin Omranian, Mutsumi Watanabe, Zoran Nikoloski, Patrick Giavalisco, Takayuki Tohge, Alexander Graf, Alisdair Robert Fernie, Rainer Hoefgen
Sulfur deficiency-induced genes affect seed protein accumulation and composition under sulfate deprivation. Plant physiology 187 (4) (2022)
Roosa A E Laitinen, Zoran Nikoloski
Strategies to identify and dissect trade-offs in plants. Molecular ecology (2022)
Zengyu Liu, Isabella Østerlund, Felix Ruhnow, Yiran Cao, Guoqiang Huang, Wenguo Cai, Jiao Zhang, Wanqi Liang, Zoran Nikoloski, Staffan Persson, Dabing Zhang
Fluorescent cytoskeletal markers reveal associations between the actin and microtubule cytoskeleton in rice cells. Development (Cambridge, England) 149 (12) (2022)
Sebastian Huß, Rika Siedah Judd, Kaan Koper, Hiroshi A Maeda, Zoran Nikoloski
An automated workflow that generates atom mappings for large-scale metabolic models and its application to Arabidopsis thaliana. The Plant journal : for cell and molecular biology 111 (5) (2022)
Anika Küken, Damoun Langary, Zoran Nikoloski
The hidden simplicity of metabolic networks is revealed by multireaction dependencies. Science advances 8 (13) (2022)
Timon W Matz, Yang Wang, Ritika Kulshreshtha, Arun Sampathkumar, Zoran Nikoloski
Topological properties accurately predict cell division events and organization of shoot apical meristem in Arabidopsis thaliana. Development (Cambridge, England) 149 (16) (2022)
Philipp Wendering, Zoran Nikoloski
Genome-Scale Modeling Specifies the Metabolic Capabilities of Rhizophagus irregularis . mSystems 7 (1) (2022)
Alain J Mbebi, Jean-Christophe Breitler, Mélanie Bordeaux, Ronan Sulpice, Marcus McHale, Hao Tong, Lucile Toniutti, Jonny Alonso Castillo, Benoît Bertrand, Zoran Nikoloski
A comparative analysis of genomic and phenomic predictions of growth-related traits in 3-way coffee hybrids. G3 (Bethesda, Md.) 12 (9) (2022)
Philipp Wendering, Zoran Nikoloski
COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions. PLoS computational biology 18 (3) (2022)
Jacqueline Nowak, Ryan Christopher Eng, Timon W Matz, Matti Waack, Staffan Persson, Arun Sampathkumar, Zoran Nikoloski
A network-based framework for shape analysis enables accurate characterization of leaf epidermal cells. Nature communications 12 (1) (2021)
David Zimmer, Corné Swart, Alexander Graf, Stéphanie Arrivault, Michael Tillich, Sebastian Proost, Zoran Nikoloski, Mark Stitt, Ralph Bock, Timo Mühlhaus, Alix Boulouis
Topology of the redox network during induction of photosynthesis as revealed by time-resolved proteomics in tobacco. Science advances 7 (51) (2021)
Haim Treves, Anika Küken, Stéphanie Arrivault, Hirofumi Ishihara, Ines Hoppe, Alexander Erban, Melanie Höhne, Thiago Alexandre Moraes, Joachim Kopka, Jedrzej Jakub Szymanski, Zoran Nikoloski, Mark Stitt
Carbon flux through photosynthesis and central carbon metabolism show distinct patterns between algae, C 3 and C 4 plants. Nature plants 8 (1) (2021)
Hao Tong, Anika Küken, Zahra Razaghi-Moghadam, Zoran Nikoloski
Characterization of effects of genetic variants via genome-scale metabolic modelling. Cellular and molecular life sciences : CMLS 78 (12) (2021)
Hao Tong, Anika Küken, Zoran Nikoloski
Integrating molecular markers into metabolic models improves genomic selection for Arabidopsis growth. Nature communications 11 (1) (2020)
Sandra Marcela Correa Cordoba, Saleh Alseekh, Lucia Atehortùa, Yariv Brotman, Rigoberto Ríos-Estepa, Alisdair Robert Fernie, Zoran Nikoloski
Model-assisted identification of metabolic engineering strategies for Jatropha curcas lipid pathways. The Plant journal : for cell and molecular biology 104 (1) (2020)
Zahra Razaghi-Moghadam, Zoran Nikoloski
Supervised learning of gene-regulatory networks based on graph distance profiles of transcriptomics data. NPJ systems biology and applications 6 (1) (2020)
Semidán Robaina-Estévez, Zoran Nikoloski
Flux-based hierarchical organization of Escherichia coli's metabolic network. PLoS computational biology 16 (4) (2020)
Anika Küken, Jeanne M O Eloundou-Mbebi, Georg Basler, Zoran Nikoloski
Cellular determinants of metabolite concentration ranges. PLoS computational biology 15 (1) (2019)
Anika Küken, Zoran Nikoloski
Computational Approaches to Design and Test Plant Synthetic Metabolic Pathways. Plant physiology 179 (3) (2019)
Yu Song, Gang Li, Jacqueline Nowak, Xiaoqing Zhang, Dongbei Xu, Xiujuan Yang, Guoqiang Huang, Wanqi Liang, Litao Yang, Canhua Wang, Vincent Bulone, Zoran Nikoloski, Jianping Hu, Staffan Persson, Dabing Zhang
The Rice Actin-Binding Protein RMD Regulates Light-Dependent Shoot Gravitropism. Plant physiology 181 (2) (2019)
Georg Basler, Alisdair R Fernie, Zoran Nikoloski
Advances in metabolic flux analysis toward genome-scale profiling of higher organisms. Bioscience reports 38 (6) (2018)
Anika Küken, Frederik Sommer, Liliya Yaneva-Roder, Luke C M Mackinder, Melanie Höhne, Stefan Geimer, Martin C Jonikas, Michael Schroda, Mark Stitt, Zoran Nikoloski, Tabea Mettler-Altmann
Effects of microcompartmentation on flux distribution and metabolic pools in Chlamydomonas reinhardtii chloroplasts. eLife 7 (2018)
Federico Apelt, David Breuer, Justyna Jadwiga Olas, Justyna Jadwiga Olas, Anna Flis, Zoran Nikoloski, Friedrich Kragler, Mark Stitt
Circadian, Carbon, and Light Control of Expansion Growth and Leaf Movement. Plant physiology 174 (3) (2017)
Matthias Westhues, Tobias A Schrag, Claas Heuer, Georg Thaller, H Friedrich Utz, Wolfgang Schipprack, Alexander Thiemann, Felix Seifert, Anita Ehret, Armin Schlereth, Mark Stitt, Zoran Nikoloski, Lothar Willmitzer, Chris C Schön, Stefan Scholten, Albrecht E Melchinger
Omics-based hybrid prediction in maize. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik 130 (9) (2017)
Saleh Alseekh, Hao Tong, Federico Scossa, Yariv Brotman, Florian Vigroux, Takayuki Tohge, Itai Ofner, Dani Zamir, Zoran Nikoloski, Alisdair R Fernie
Canalization of Tomato Fruit Metabolism. The Plant cell 29 (11) (2017)
Zheng Li, Nooshin Omranian, Lutz Neumetzler, Ting Wang, Thomas Herter, Bjoern Usadel, Taku Demura, Patrick Giavalisco, Zoran Nikoloski, Staffan Persson
A Transcriptional and Metabolic Framework for Secondary Wall Formation in Arabidopsis. Plant physiology 172 (2) (2016)
Kevin Schwahn, Anika Küken, Daniel J Kliebenstein, Alisdair R Fernie, Zoran Nikoloski
Observability of Plant Metabolic Networks Is Reflected in the Correlation of Metabolic Profiles. Plant physiology 172 (2) (2016)
Jorge Gago, Danilo de Menezes Daloso, Carlos María Figueroa, Jaume Flexas, Alisdair Robert Fernie, Zoran Nikoloski
Relationships of Leaf Net Photosynthesis, Stomatal Conductance, and Mesophyll Conductance to Primary Metabolism: A Multispecies Meta-Analysis Approach. Plant physiology 171 (1) (2016)
Colin Ruprecht, Amelie Mendrinna, Takayuki Tohge, Arun Sampathkumar, Sebastian Klie, Alisdair R Fernie, Zoran Nikoloski, Staffan Persson, Marek Mutwil
FamNet: A Framework to Identify Multiplied Modules Driving Pathway Expansion in Plants. Plant physiology 170 (3) (2016)
Weiwei Wen, Kun Li, Saleh Alseekh, Nooshin Omranian, Lijun Zhao, Yang Zhou, Yingjie Xiao, Min Jin, Ning Yang, Haijun Liu, Alexandra Florian, Wenqiang Li, Qingchun Pan, Zoran Nikoloski, Jianbing Yan, Alisdair R Fernie
Genetic Determinants of the Network of Primary Metabolism and Their Relationships to Plant Performance in a Maize Recombinant Inbred Line Population. The Plant cell 27 (7) (2015)
Zoran Nikoloski, Richard Perez-Storey, Lee J Sweetlove
Inference and Prediction of Metabolic Network Fluxes. Plant physiology 169 (3) (2015)

Zoran Nikoloski.css-eqlu8i{font-size:small;padding-left:4px;}

Publication Activity (10 Years)

Top Topics

Top Venues

Zoran Nikoloski