{"id":3384,"date":"2020-02-02T10:54:40","date_gmt":"2020-02-02T08:54:40","guid":{"rendered":"http:\/\/cpsbb.eu\/?page_id=3384"},"modified":"2026-05-15T16:19:16","modified_gmt":"2026-05-15T14:19:16","slug":"departments-bioinformatics","status":"publish","type":"page","link":"https:\/\/cpsbb.eu\/bg\/departments\/departments-bioinformatics\/","title":{"rendered":"\u0411\u0438\u043e\u0438\u043d\u0444\u043e\u0440\u043c\u0430\u0442\u0438\u043a\u0430 \u0438 \u043c\u0430\u0442\u0435\u043c\u0430\u0442\u0438\u0447\u0435\u0441\u043a\u043e \u043c\u043e\u0434\u0435\u043b\u0438\u0440\u0430\u043d\u0435"},"content":{"rendered":"

\u0411\u0438\u043e\u0438\u043d\u0444\u043e\u0440\u043c\u0430\u0442\u0438\u043a\u0430 \u0438 \u043c\u0430\u0442\u0435\u043c\u0430\u0442\u0438\u0447\u0435\u0441\u043a\u043e \u043c\u043e\u0434\u0435\u043b\u0438\u0440\u0430\u043d\u0435<\/h1>\n

\u0411\u0438\u043e\u0438\u043d\u0444\u043e\u0440\u043c\u0430\u0442\u0438\u043a\u0430\u0442\u0430 \u0438 \u0432 \u043f\u043e \u043e\u0431\u0449 \u043f\u043b\u0430\u043d \u043c\u0430\u0442\u0435\u043c\u0430\u0442\u0438\u0447\u0435\u0441\u043a\u043e\u0442\u043e \u043c\u043e\u0434\u0435\u043b\u0438\u0440\u0430\u043d\u0435 \u043f\u0440\u0435\u0434\u0441\u0442\u0430\u0432\u043b\u044f\u0432\u0430\u0442 \u043a\u043b\u044e\u0447\u043e\u0432\u0438 \u0434\u0435\u0439\u043d\u043e\u0441\u0442\u0438 \u0432 \u0438\u0437\u0441\u043b\u0435\u0434\u0432\u0430\u043d\u0438\u044f\u0442\u0430, \u043e\u0440\u0438\u0435\u043d\u0442\u0438\u0440\u0430\u043d\u0438 \u043a\u044a\u043c \u0433\u0435\u043d\u043e\u043c\u0438\u043a\u0430\u0442\u0430 \u0438 \u0441\u0438\u0441\u0442\u0435\u043c\u043d\u0430\u0442\u0430 \u0431\u0438\u043e\u043b\u043e\u0433\u0438\u044f, \u0438 \u0441\u0430 \u043a\u043b\u044e\u0447\u043e\u0432\u0438 \u0437\u0430 \u0432\u0441\u0438\u0447\u043a\u0438 \u0435\u043a\u0441\u043f\u0435\u0440\u0438\u043c\u0435\u043d\u0442\u0430\u043b\u043d\u0438 \u043e\u0442\u0434\u0435\u043b\u0438 \u0432 \u0426\u0420\u0421\u0411\u0411. \u0422\u043e\u0437\u0438 \u043e\u0442\u0434\u0435\u043b \u0449\u0435 \u043e\u043a\u0430\u0437\u0432\u0430 \u043f\u043e\u0434\u043a\u0440\u0435\u043f\u0430 \u043d\u0430 \u0435\u043a\u0441\u043f\u0435\u0440\u0438\u043c\u0435\u043d\u0442\u0430\u043b\u043d\u0438\u0442\u0435 \u043e\u0442\u0434\u0435\u043b\u0438 \u0432 \u0426\u0420\u0421\u0411\u0411 \u0432\u044a\u0432 \u0432\u0441\u0438\u0447\u043a\u0438 \u043e\u0441\u043d\u043e\u0432\u043d\u0438 \u0430\u0441\u043f\u0435\u043a\u0442\u0438, \u0441\u0432\u044a\u0440\u0437\u0430\u043d\u0438 \u0441 \u0430\u043d\u0430\u043b\u0438\u0437\u0430 \u043d\u0430 \u043d\u0430\u0431\u043e\u0440\u0438 \u043e\u0442 “\u043e\u043c\u0438\u0447\u043d\u0438” \u0434\u0430\u043d\u043d\u0438 (\u0432\u043a\u043b\u044e\u0447\u0438\u0442\u0435\u043b\u043d\u043e \u043d\u0430\u043f\u0440\u0438\u043c\u0435\u0440 \u0434\u0430\u043d\u043d\u0438 \u043e\u0442 \u0441\u0435\u043a\u0432\u0435\u043d\u0438\u0440\u0430\u043d\u0435 \u043e\u0442 \u0441\u043b\u0435\u0434\u0432\u0430\u0449\u043e \u043f\u043e\u043a\u043e\u043b\u0435\u043d\u0438\u0435, \u043d\u0430\u043f\u0440\u0438\u043c\u0435\u0440 \u043e\u0442 RNA-seq, ChIP-seq \u0438\u043b\u0438 \u0441\u0435\u043a\u0432\u0435\u043d\u0438\u0440\u0430\u043d\u0435 \u043d\u0430 \u0446\u044f\u043b \u0433\u0435\u043d\u043e\u043c; \u0434\u0430\u043d\u043d\u0438 \u043e\u0442 \u043f\u0440\u043e\u0444\u0438\u043b\u0430 \u043d\u0430 \u043f\u044a\u0440\u0432\u0438\u0447\u043d\u0438 \u0438 \u0432\u0442\u043e\u0440\u0438\u0447\u043d\u0438 \u043c\u0435\u0442\u0430\u0431\u043e\u043b\u0438\u0442\u0438 \u0438 \u0434\u0440\u0443\u0433\u0438).<\/p>\n

 <\/p>\n

\n\n\n\n<\/p>\n\n\n\n\n\n\n
\u0420\u044a\u043a\u043e\u0432\u043e\u0434\u0438\u0442\u0435\u043b \u043e\u0442\u0434\u0435\u043b:<\/th>\n\u0418\u043c\u0435\u0439\u043b<\/th>\n<\/tr>\n<\/thead>\n
\u041f\u0440\u043e\u0444. \u0434-\u0440 \u0417\u043e\u0440\u0430\u043d \u041d\u0438\u043a\u043e\u043b\u043e\u0441\u043a\u0438<\/a><\/span><\/td>\nnikoloski@mpimp-golm.mpg.de<\/a><\/td>\n<\/tr>\n

<\/p>\n

\u041f\u043e\u0441\u0442\u0434\u043e\u043a\u0442\u043e\u0440\u0430\u043d\u0442\u0438:<\/th>\n\u0418\u043c\u0435\u0439\u043b<\/th>\n<\/tr>\n
\u0414-\u0440 \u0420\u0435\u0439\u0444 \u041b\u0430\u0439\u044a\u043b<\/a><\/span><\/td>\nlyall@cpsbb.eu<\/a><\/td>\n<\/tr>\n
\u0414-\u0440 \u042e\u0434\u0436\u0438\u0439\u043d \u041a\u0430\u0431\u0432\u0435<\/a><\/span><\/td>\nkabwe@cpsbb.eu<\/a><\/td>\n<\/tr>\n

<\/p>\n

\u0410\u043b\u0443\u043c\u043d\u0438:<\/th>\n\u0418\u043c\u0435\u0439\u043b<\/th>\n<\/tr>\n
\u0414-\u0440 \u0425\u0430\u043e \u0422\u043e\u043d\u0433<\/a><\/span><\/td>\n–<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n

<\/h1>\n
2025<\/strong><\/span><\/div>\n
\n
\n
Arend M., Paulitz E., Hsieh Y.E., Nikoloski Z. <\/strong> (2025)<\/span><\/div>\n
Scaling metabolic model reconstruction up to the pan-genome level: A systematic review and prospective applications to photosynthetic organisms.<\/a><\/div>\n
Metabolic Engineering. 90: 67-77. \u2022 IF 6.8<\/div>\n<\/div>\n
\n
Staykov N., Kanojia A., Lyall R., Ivanova V., Alseekh S., Petrov V., Gechev T.<\/strong> (2025)<\/span><\/div>\n
Sustainable agriculture through seaweed biostimulants: A two-year study demonstrates yield enhancement in pepper and eggplant.<\/a><\/div>\n
Frontiers in Plant Science. DOI: https:\/\/doi.org\/10.3389\/fpls.2025.1655340. \u2022 IF 4.8<\/div>\n<\/div>\n
\n
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., Brugi\u00e8re S., Cout\u00e9 Y., Kleman J.P., Sizova I., Schilling M., Jouhet J., Hegemann P., Li-Beisson Y., Nikoloski Z.,<\/strong> Bastien O., Hicks L.M., Petroutsos D. (2025)<\/span><\/div>\n
Phototropin connects blue light perception to starch metabolism in green algae.<\/a><\/div>\n
Nature Communications. 16(1): 2545. \u2022 IF 14.7<\/div>\n<\/div>\n
2024<\/strong><\/span><\/div>\n
\n
Gupta S., Petrov V<\/strong>., Garg V., Mueller-Roeber B., Fernie A.R., Nikoloski Z., Gechev T<\/strong>. (2024)<\/span><\/div>\n
The genome of Haberlea rhodopensis<\/em> provides insights into the mechanisms for tolerance to multiple extreme environments.<\/a><\/div>\n
Cellular and Molecular Life Sciences. 81: 117. \u2022 IF 8<\/div>\n<\/div>\n
2023<\/strong><\/span><\/div>\n
\n
Arend M., Yuan Y., Ruiz-Sola M.\u00c1., Omranian N., Nikoloski Z.,<\/strong> Petroutsos D. (2023)<\/span><\/div>\n
Widening the landscape of transcriptional regulation of green algal photoprotection.<\/a><\/div>\n
Nature Communications. 14(1): 2687. \u2022 IF 17.694<\/div>\n<\/div>\n
\n
C\u00f3rdoba S.C., Tong H., Burgos A., Zhu F., Alseekh S., Fernie A.R., Nikoloski Z.<\/strong> (2023)<\/span><\/div>\n
Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism.<\/a><\/div>\n
Nature Communications. 4(1): 4897. \u2022 IF 17.694<\/div>\n<\/div>\n
\n
Tong H., Laitinen R.A.E., Nikoloski Z.<\/strong> (2023)<\/span><\/div>\n
Predicting plasticity of rosette growth and metabolic fluxes in Arabidopsis thaliana.<\/em><\/a><\/div>\n
New Phytologyst. 40(1): 426-438. \u2022 IF 10.323<\/div>\n<\/div>\n
2022<\/strong><\/span><\/div>\n
\n
Mbebi A.J., Breitler J.C., Bordeaux M., Sulpice R., McHale M., Tong H.<\/strong>, Toniutti L., Castillo J.A., Bertrand B., Nikoloski Z<\/strong>. (2022)<\/span><\/div>\n
A comparative analysis of genomic and phenomic predictions of growth-related traits in 3-way coffee hybrids.<\/a><\/div>\n
Genes Genomes Genetics. 12(9): jkac170. \u2022 IF 3.542<\/div>\n<\/div>\n
\n
Tong H., Nankar A.N.<\/strong>, Liu J., Todorova V., Ganeva D., Grozeva S., Tringovska I., Pasev Gancho., Radeva-Ivanova V., Gechev T., Kostova D., Nikoloski Z.<\/strong> (2022)<\/span><\/div>\n
Genomic prediction of morphometric and colorimetric traits in Solanaceous fruits.<\/a><\/div>\n
Horticulture Research. Horticulture Research 9: uhac072. \u2022 IF 7.3 (Q1)<\/div>\n<\/div>\n
\n
Zhu F., Alseekh S.,<\/strong> Koper K., Tong H., Nikoloski Z.,<\/strong> Naake T., Liu H., Yan J., Brotman Y., Wen W., Maeda H., Cheng Y., Fernie A.R.<\/strong> (2022)<\/span><\/div>\n
Genome-wide association of the metabolic shifts underpinning dark-induced senescence in Arabidopsis.<\/a><\/div>\n
The Plant Cell. 34(1): 557-578. \u2022 IF 11.277<\/div>\n<\/div>\n
2021<\/strong><\/span><\/div>\n
\n
Aarabi F., Rakpenthai A., Barahimipour R., Gorka M., Alseekh S.,<\/strong> Zhang Y.,<\/strong> Salem M. A., Br\u00fcckner F., Omranian N., Watanabe M., Nikoloski Z.,<\/strong> Giavalisco P., Tohge T., Graf A., Fernie A.R.,<\/strong> Hoefgen R. (2021)<\/span><\/div>\n
Sulfur deficiency-induced genes affect seed protein accumulation and composition under sulfate deprivation.<\/a><\/div>\n
Plant Physiology. 187(4): 2419\u20132434. \u2022 IF 8.340<\/div>\n<\/div>\n
\n
Gechev T., Lyall R., Petrov V.<\/strong>, Bartels D. (2021)<\/span><\/div>\n
Systems biology of resurrection plants.<\/a><\/div>\n
Cellular and Molecular Life Sciences. 78: 6365\u20136394. \u2022 IF 9.261<\/div>\n<\/div>\n
\n
Duarte G. T., Pandey P. K., Vaid N., Alseekh S.,<\/strong> Fernie A.R.,<\/strong> Nikoloski Z.,<\/strong> Laitinen. R. (2021)<\/span><\/div>\n
Plasticity of rosette size in response to nitrogen availability is controlled by an RCC1-family protein.<\/a><\/div>\n
Plant cell and environment. 44(10) :3398-3411. \u2022 IF 7.228<\/div>\n<\/div>\n
\n
Mbebi AJ, Tong H, Nikoloski Z.<\/strong> (2021)<\/span><\/div>\n
L2,1-norm regularized multivariate regression model with applications to genomic prediction.<\/a><\/div>\n
Bioinformatics. 37(18): 2896-904. \u2022 IF 6.937<\/div>\n<\/div>\n
\n
Moreno J. C., Vicente R., Bruno E. R., Gorka M., Kosmacz M., Peralta-Ariza J. S., Zhang Y.<\/strong>, Saleh A.<\/strong>, Dorothee C., Luzarowski M., Nikoloski Z.,<\/strong> Hartman M. D., Figueroa C. M., Iglesias A. A., Fernie A.R.<\/strong>, A. Skirycz (2021)<\/span><\/div>\n
Tyr-Asp inhibition of glyceraldehyde 3-phosphate dehydrogenase affects plant redox metabolism.<\/a><\/div>\n
EMBO Journal. 40(15): e106800. \u2022 IF 11.598<\/div>\n<\/div>\n
\n
Omranian S., Angeleska A., Nikoloski Z.<\/strong> (2021)<\/span><\/div>\n
PC2P: Parameter-free network-based prediction of protein complexes.<\/a><\/div>\n
Bioinformatics. 37(1): 73\u201381. \u2022 IF 6.937<\/div>\n<\/div>\n
\n
Tong H<\/strong>., Nikoloski Z.<\/strong> (2021)<\/span><\/div>\n
Machine learning approaches for crop improvement: leveraging phenotypic and genotypic big data<\/a><\/div>\n
Journal of Plant Physiology. 257: 153354. \u2022 IF 3.549<\/div>\n<\/div>\n
\n
Tong H<\/strong>., K\u00fcken A., Razaghi-Moghadam Z., Nikoloski Z. <\/strong> (2021)<\/span><\/div>\n
Characterization of effects of genetic variants via genome-scale metabolic modelling.<\/a><\/div>\n
Cellular and Molecular Life Sciences. 78: 5123\u20135138. \u2022 IF 9.261<\/div>\n<\/div>\n
2020<\/strong><\/span><\/div>\n
\n
Correa S.M., Alseekh S.<\/strong>, Atehort\u00faa L., Brotman Y., R\u00edos-Estepa R., Fernie A.R.<\/strong>, Nikoloski Z.<\/strong> (2020)<\/span><\/div>\n
Model-assisted identification of metabolic engineering strategies for Jatropha curcas lipid pathways.<\/a><\/div>\n
The Plant Journal. 104(1): 76-95. \u2022 IF 6.417<\/div>\n<\/div>\n
\n
Correa S. M., Fernie A.R.,<\/strong> Nikoloski Z.,<\/strong> Brotman Y. (2020)<\/span><\/div>\n
Towards model-driven characterization and manipulation of plant lipid metabolism<\/a><\/div>\n
Progress in Lipid Research. 80: 101051. \u2022 IF 16.195<\/div>\n<\/div>\n
\n
Lyall R.<\/strong>, Gechev T.<\/strong> (2020)<\/span><\/div>\n
Multi-omics insights into the evolution of angiosperm resurrection plants<\/a><\/div>\n
Annual Plant Reviews Online. 3(1): 77-110.<\/div>\n<\/div>\n
\n
Lyall R.<\/strong>, Nikoloski Z.<\/strong>, Gechev T.<\/strong> (2020)<\/span><\/div>\n
Comparative analysis of ROS network genes in extremophile eukaryotes<\/a><\/div>\n
International Journal of Molecular Sciences. 21: 9131. \u2022 IF 5.923<\/div>\n<\/div>\n
\n
Omidbakhshfard M.A., Sujeeth N., Gupta S., Omranian N.,<\/strong> Guinan K.J., Brotman Y., Nikoloski Z.<\/strong>, Fernie A.R.<\/strong>, Mueller-Roeber B.<\/strong>, Gechev T.<\/strong> (2020)<\/span><\/div>\n
A biostimulant obtained from the seaweed Ascophyllum nodosum<\/em> protects Arabidopsis thaliana<\/em> from severe oxidative stress<\/a><\/div>\n
International Journal of Molecular Sciences. 21(2): 1\u201326. \u2022 IF 5.923<\/div>\n<\/div>\n
\n
Tong H.<\/strong>, K\u00fcken A., Nikoloski Z.<\/strong> (2020)<\/span><\/div>\n
Integrating molecular markers into metabolic models improves genomic selection for Arabidopsis<\/em> growth<\/a><\/div>\n
Nature Communications 11: 2410. \u2022 IF 14.919<\/div>\n<\/div>\n
2019<\/strong><\/span><\/div>\n
\n
Pandey P.K., Yu J., Omranian N., Alseekh S.<\/strong>, Vaid N, Fernie A.R.<\/strong>, Nikoloski Z.<\/strong>, Laitinen R.A.E. (2019)<\/span><\/div>\n
Plasticity in metabolism underpins local responses to nitrogen in Arabidopsis thaliana populations<\/a><\/div>\n
Plant Direct. 3(11): e00186. \u2022 IF 1.725<\/div>\n<\/div>\n
\n
Nunes-Nesi A., Alseekh S.<\/strong>, de Oliveira Silva F., Omranian N., Lichtenstein G., Mirnezhad M., Gonzalez R., Sabio Y Garcia J., Conte M., Leiss K., Klinkhamer P., Nikoloski Z.<\/strong>, Carrari F., Fernie A.R.<\/strong> (2019)<\/span><\/div>\n
Identification and characterization of metabolite quantitative trait loci in tomato leaves and comparison with those reported for fruits and seeds<\/a><\/div>\n
Metabolomics. 15(4): 46. \u2022 IF 3.167<\/div>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"

\u0411\u0438\u043e\u0438\u043d\u0444\u043e\u0440\u043c\u0430\u0442\u0438\u043a\u0430 \u0438 \u043c\u0430\u0442\u0435\u043c\u0430\u0442\u0438\u0447\u0435\u0441\u043a\u043e \u043c\u043e\u0434\u0435\u043b\u0438\u0440\u0430\u043d\u0435 \u0411\u0438\u043e\u0438\u043d\u0444\u043e\u0440\u043c\u0430\u0442\u0438\u043a\u0430\u0442\u0430 \u0438 \u0432 \u043f\u043e \u043e\u0431\u0449 \u043f\u043b\u0430\u043d \u043c\u0430\u0442\u0435\u043c\u0430\u0442\u0438\u0447\u0435\u0441\u043a\u043e\u0442\u043e \u043c\u043e\u0434\u0435\u043b\u0438\u0440\u0430\u043d\u0435 \u043f\u0440\u0435\u0434\u0441\u0442\u0430\u0432\u043b\u044f\u0432\u0430\u0442 \u043a\u043b\u044e\u0447\u043e\u0432\u0438 \u0434\u0435\u0439\u043d\u043e\u0441\u0442\u0438 \u0432 \u0438\u0437\u0441\u043b\u0435\u0434\u0432\u0430\u043d\u0438\u044f\u0442\u0430, \u043e\u0440\u0438\u0435\u043d\u0442\u0438\u0440\u0430\u043d\u0438 \u043a\u044a\u043c \u0433\u0435\u043d\u043e\u043c\u0438\u043a\u0430\u0442\u0430 \u0438 \u0441\u0438\u0441\u0442\u0435\u043c\u043d\u0430\u0442\u0430 \u0431\u0438\u043e\u043b\u043e\u0433\u0438\u044f, \u0438 \u0441\u0430 \u043a\u043b\u044e\u0447\u043e\u0432\u0438 \u0437\u0430 \u0432\u0441\u0438\u0447\u043a\u0438 \u0435\u043a\u0441\u043f\u0435\u0440\u0438\u043c\u0435\u043d\u0442\u0430\u043b\u043d\u0438 \u043e\u0442\u0434\u0435\u043b\u0438 \u0432 \u0426\u0420\u0421\u0411\u0411. \u0422\u043e\u0437\u0438 \u043e\u0442\u0434\u0435\u043b \u0449\u0435 \u043e\u043a\u0430\u0437\u0432\u0430 \u043f\u043e\u0434\u043a\u0440\u0435\u043f\u0430 \u043d\u0430 \u0435\u043a\u0441\u043f\u0435\u0440\u0438\u043c\u0435\u043d\u0442\u0430\u043b\u043d\u0438\u0442\u0435 \u043e\u0442\u0434\u0435\u043b\u0438 \u0432 \u0426\u0420\u0421\u0411\u0411 \u0432\u044a\u0432 \u0432\u0441\u0438\u0447\u043a\u0438 \u043e\u0441\u043d\u043e\u0432\u043d\u0438 \u0430\u0441\u043f\u0435\u043a\u0442\u0438, \u0441\u0432\u044a\u0440\u0437\u0430\u043d\u0438 \u0441 \u0430\u043d\u0430\u043b\u0438\u0437\u0430 \u043d\u0430 \u043d\u0430\u0431\u043e\u0440\u0438 \u043e\u0442 “\u043e\u043c\u0438\u0447\u043d\u0438” \u0434\u0430\u043d\u043d\u0438 (\u0432\u043a\u043b\u044e\u0447\u0438\u0442\u0435\u043b\u043d\u043e<\/p>\n","protected":false},"author":17,"featured_media":0,"parent":102,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":"","_links_to":"","_links_to_target":""},"_links":{"self":[{"href":"https:\/\/cpsbb.eu\/bg\/wp-json\/wp\/v2\/pages\/3384"}],"collection":[{"href":"https:\/\/cpsbb.eu\/bg\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/cpsbb.eu\/bg\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/cpsbb.eu\/bg\/wp-json\/wp\/v2\/users\/17"}],"replies":[{"embeddable":true,"href":"https:\/\/cpsbb.eu\/bg\/wp-json\/wp\/v2\/comments?post=3384"}],"version-history":[{"count":5,"href":"https:\/\/cpsbb.eu\/bg\/wp-json\/wp\/v2\/pages\/3384\/revisions"}],"predecessor-version":[{"id":12330,"href":"https:\/\/cpsbb.eu\/bg\/wp-json\/wp\/v2\/pages\/3384\/revisions\/12330"}],"up":[{"embeddable":true,"href":"https:\/\/cpsbb.eu\/bg\/wp-json\/wp\/v2\/pages\/102"}],"wp:attachment":[{"href":"https:\/\/cpsbb.eu\/bg\/wp-json\/wp\/v2\/media?parent=3384"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}