Written by Ivan Dulgerov

Bioinformatics and Mathematical Modeling

Bioinformatics and more generally mathematical modelling represent key activities in genomics and systems biology-oriented research and are key to all experimental departments in the CPSBB. This department will provide support to the experimental departments at CPSBB in all major aspects related to the analysis of “omics” data sets (including e.g. next generation sequencing data from e.g. RNA-seq, ChIP-seq or whole-genome sequencing; primary and secondary metabolite profile data, and others).

 

Head of Department: Email
Prof. Dr. Zoran Nikoloski nikoloski@cpsbb.eu
Postdoctoral Researchers: Email
Dr. Rafe Lyall lyall@cpsbb.eu
Dr. Eugene Kabwe kabwe@cpsbb.eu
Alumni: Email
Dr. Hao Tong –

 

2025
Arend M., Paulitz E., Hsieh Y.E., Nikoloski Z. (2025)
Scaling metabolic model reconstruction up to the pan-genome level: A systematic review and prospective applications to photosynthetic organisms.
Metabolic Engineering. 90: 67-77. • IF 6.8
Staykov N., Kanojia A., Lyall R., Ivanova V., Alseekh S., Petrov V., Gechev T. (2025)
Sustainable agriculture through seaweed biostimulants: A two-year study demonstrates yield enhancement in pepper and eggplant.
Frontiers in Plant Science. DOI: https://doi.org/10.3389/fpls.2025.1655340. • IF 4.8
Yuan Y., Iannetta A.A., Kim M., Sadecki P.W., Arend M., Tsichla A., Ruiz-Sola M.A., Kepesidis G., Falconet D., Thevenon E., Tardif M., Brugière S., Couté Y., Kleman J.P., Sizova I., Schilling M., Jouhet J., Hegemann P., Li-Beisson Y., Nikoloski Z., Bastien O., Hicks L.M., Petroutsos D. (2025)
Phototropin connects blue light perception to starch metabolism in green algae.
Nature Communications. 16(1): 2545. • IF 14.7
2024
Gupta S., Petrov V., Garg V., Mueller-Roeber B., Fernie A.R., Nikoloski Z., Gechev T. (2024)
The genome of Haberlea rhodopensis provides insights into the mechanisms for tolerance to multiple extreme environments.
Cellular and Molecular Life Sciences. 81: 117. • IF 8
2023
Arend M., Yuan Y., Ruiz-Sola M.Á., Omranian N., Nikoloski Z., Petroutsos D. (2023)
Widening the landscape of transcriptional regulation of green algal photoprotection.
Nature Communications. 14(1): 2687. • IF 17.694
Córdoba S.C., Tong H., Burgos A., Zhu F., Alseekh S., Fernie A.R., Nikoloski Z. (2023)
Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism.
Nature Communications. 4(1): 4897. • IF 17.694
Tong H., Laitinen R.A.E., Nikoloski Z. (2023)
Predicting plasticity of rosette growth and metabolic fluxes in Arabidopsis thaliana.
New Phytologyst. 40(1): 426-438. • IF 10.323
2022
Mbebi A.J., Breitler J.C., Bordeaux M., Sulpice R., McHale M., Tong H., Toniutti L., Castillo J.A., Bertrand B., Nikoloski Z. (2022)
A comparative analysis of genomic and phenomic predictions of growth-related traits in 3-way coffee hybrids.
Genes Genomes Genetics. 12(9): jkac170. • IF 3.542
Tong H., Nankar A.N., Liu J., Todorova V., Ganeva D., Grozeva S., Tringovska I., Pasev Gancho., Radeva-Ivanova V., Gechev T., Kostova D., Nikoloski Z. (2022)
Genomic prediction of morphometric and colorimetric traits in Solanaceous fruits.
Horticulture Research. Horticulture Research 9: uhac072. • IF 7.3 (Q1)
Zhu F., Alseekh S., Koper K., Tong H., Nikoloski Z., Naake T., Liu H., Yan J., Brotman Y., Wen W., Maeda H., Cheng Y., Fernie A.R. (2022)
Genome-wide association of the metabolic shifts underpinning dark-induced senescence in Arabidopsis.
The Plant Cell. 34(1): 557-578. • IF 11.277
2021
Aarabi F., Rakpenthai A., Barahimipour R., Gorka M., Alseekh S., Zhang Y., Salem M. A., Brückner F., Omranian N., Watanabe M., Nikoloski Z., Giavalisco P., Tohge T., Graf A., Fernie A.R., Hoefgen R. (2021)
Sulfur deficiency-induced genes affect seed protein accumulation and composition under sulfate deprivation.
Plant Physiology. 187(4): 2419–2434. • IF 8.340
Gechev T., Lyall R., Petrov V., Bartels D. (2021)
Systems biology of resurrection plants.
Cellular and Molecular Life Sciences. 78: 6365–6394. • IF 9.261
Duarte G. T., Pandey P. K., Vaid N., Alseekh S., Fernie A.R., Nikoloski Z., Laitinen. R. (2021)
Plasticity of rosette size in response to nitrogen availability is controlled by an RCC1-family protein.
Plant cell and environment. 44(10) :3398-3411. • IF 7.228
Mbebi AJ, Tong H, Nikoloski Z. (2021)
L2,1-norm regularized multivariate regression model with applications to genomic prediction.
Bioinformatics. 37(18): 2896-904. • IF 6.937
Moreno J. C., Vicente R., Bruno E. R., Gorka M., Kosmacz M., Peralta-Ariza J. S., Zhang Y., Saleh A., Dorothee C., Luzarowski M., Nikoloski Z., Hartman M. D., Figueroa C. M., Iglesias A. A., Fernie A.R., A. Skirycz (2021)
Tyr-Asp inhibition of glyceraldehyde 3-phosphate dehydrogenase affects plant redox metabolism.
EMBO Journal. 40(15): e106800. • IF 11.598
Omranian S., Angeleska A., Nikoloski Z. (2021)
PC2P: Parameter-free network-based prediction of protein complexes.
Bioinformatics. 37(1): 73–81. • IF 6.937
Tong H., Nikoloski Z. (2021)
Machine learning approaches for crop improvement: leveraging phenotypic and genotypic big data
Journal of Plant Physiology. 257: 153354. • IF 3.549
Tong H., Küken A., Razaghi-Moghadam Z., Nikoloski Z. (2021)
Characterization of effects of genetic variants via genome-scale metabolic modelling.
Cellular and Molecular Life Sciences. 78: 5123–5138. • IF 9.261
2020
Correa S.M., Alseekh S., Atehortúa L., Brotman Y., Ríos-Estepa R., Fernie A.R., Nikoloski Z. (2020)
Model-assisted identification of metabolic engineering strategies for Jatropha curcas lipid pathways.
The Plant Journal. 104(1): 76-95. • IF 6.417
Correa S. M., Fernie A.R., Nikoloski Z., Brotman Y. (2020)
Towards model-driven characterization and manipulation of plant lipid metabolism
Progress in Lipid Research. 80: 101051. • IF 16.195
Lyall R., Gechev T. (2020)
Multi-omics insights into the evolution of angiosperm resurrection plants
Annual Plant Reviews Online. 3(1): 77-110.
Lyall R., Nikoloski Z., Gechev T. (2020)
Comparative analysis of ROS network genes in extremophile eukaryotes
International Journal of Molecular Sciences. 21: 9131. • IF 5.923
Omidbakhshfard M.A., Sujeeth N., Gupta S., Omranian N., Guinan K.J., Brotman Y., Nikoloski Z., Fernie A.R., Mueller-Roeber B., Gechev T. (2020)
A biostimulant obtained from the seaweed Ascophyllum nodosum protects Arabidopsis thaliana from severe oxidative stress
International Journal of Molecular Sciences. 21(2): 1–26. • IF 5.923
Tong H., Küken A., Nikoloski Z. (2020)
Integrating molecular markers into metabolic models improves genomic selection for Arabidopsis growth
Nature Communications 11: 2410. • IF 14.919
2019
Pandey P.K., Yu J., Omranian N., Alseekh S., Vaid N, Fernie A.R., Nikoloski Z., Laitinen R.A.E. (2019)
Plasticity in metabolism underpins local responses to nitrogen in Arabidopsis thaliana populations
Plant Direct. 3(11): e00186. • IF 1.725
Nunes-Nesi A., Alseekh S., de Oliveira Silva F., Omranian N., Lichtenstein G., Mirnezhad M., Gonzalez R., Sabio Y Garcia J., Conte M., Leiss K., Klinkhamer P., Nikoloski Z., Carrari F., Fernie A.R. (2019)
Identification and characterization of metabolite quantitative trait loci in tomato leaves and comparison with those reported for fruits and seeds
Metabolomics. 15(4): 46. • IF 3.167