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Eva Colla’kova'

Eva Collakova
308 Latham Hall
Blacksburg, Va. 24060


My appointment in the School of Plant and Environmental Sciences involves 70% research and 30% teaching.  My research program is focused on understanding how plants and algae regulate their metabolism, particularly production of oil and protein in seeds and lipids in algal cells. Lipids and proteins are products important for food and biofuel uses. I currently teach three courses within the School pertaining to plant physiology and metabolism and bioinformatics.


  • Plant Metabolism
  • Multi-OMICs


  • Ph.D. Plant Biology, Michigan State University, 2003 
  • B.A. Biochemistry, University of P.J. Safarik, Kosice, Slovakia, 1995

Photosynthetic organisms regulate their metabolism at different levels and in a very complex way, which can be explored by a combination of experimental and modeling multi-OMICs approaches. In my lab, we employ genomics, transcriptomics, metabolomics, fluxomics, and phenomics to probe several levels of regulation and unravel interactions of different molecules (DNA, RNA, proteins, and metabolites). One of the proposed projects include investigating metabolic fluxes to understand how peanut seeds, which develop underground, can make so much oil without light, which normally provides substantial amounts of energy for oil synthesis in green seeds. A different collaborative project involves generating and testing predictive transcript regulatory networks to understand how transcription and RNA splicing regulate seed metabolism in the model plant Arabidopsis. I also collaborate with several faculty at the School who require my metabolomics and fluxomics expertise.

  • PPWS 5534: Advanced Plant Physiology and Metabolism II
  • GBCB 5314: Biological Paradigms for Bioinformatics
  • GBCB 5874: Problem Solving

Associate Professor | 2015 – present
School of Plant and Environmental Sciences and
Department of Plant Pathology Physiology, & Weed Science
Virginia Polytechnic Institute and State University

Assistant Professor | 2009 – 2015
Department of Plant Pathology, Physiology, & Weed Science
Virginia Polytechnic Institute and State University

Postdoctoral Fellow | 2003 – 2008
Department of Plant Biology
Michigan State University

  1. Clermont K, Wang Y, Liu S, Yang Z, dePamphilis CW, Yoder JI, Collakova E, Westwood JH (2019) Comparative metabolomics of early development of parasitic plants Pelipanche aegyptiaca and Tryphysaria vesicolor. Metabolites 9: E114
  2. Gupta C, Krishnan A, Collakova E, Wolinski P, Pereira A (2017) SANe: The Seed Active Network For Mining Transcriptional Regulatory Programs of Seed Development. bioRxiv
  3. Aziz M, Sturtevant D, Winston J, Collakova E, Jelesko JG, Chapman KD (2017) MALDI-MS imaging of urushiol in poison ivy stems. Molecules 22: Article E711 (1-11)
  4. Ni Y, Aghamirzaie D, Collakova E, Li S, Grene R, Heath LS (2016) A machine learning approach to predict gene regulatory networks in seed development in Arabidopsis. Front Plant Sci 7: Article 1936 (1-13)
  5. Besnard J, Pratelli R, Zhao C, Sonawala U, Collakova E, Pilot G, Okumoto S (2016) UMAMIT14 is an amino acid exporter involved in phloem unloading in Arabidopsis roots. J Exp Bot 67: 6385-6397
  6. Aghamirzaie D, Collakova E, Li S, Grene R (2016) CoSpliceNet: A framework for co-splicing network inference from transcriptomics data. BMC Genomics 17: Article 845 (1-16)
  7. Schneider A, Aghamirzaie D, Elamarakeby H, Poudel AN, Koo AJ, Heath LS, Grene R, Collakova E (2016) Potential targets of VIVIPAROUS1/ABI3-LIKE1 (VAL1) repression in developing Arabidopsis thaliana embryos. Plant J 85: 305-319
  8. Aghamirzaie D, Batra D, Heath LS, Schneider A, Grene R, Collakova E (2015) Transcriptome-wide functional characterization reveals novel relationships among differentially expressed transcripts in developing soybean embryos. BMC Genomics 16: Article 928 (1-23)
  9. Nourbakhsh A, Collakova E, Gillaspy GE (2015) Characterization of the inositol monophosphatase gene family in Arabidopsis. Front Plant Sci 5: Article 725 (1-14)
  10. Zu TNK, Athamneh AIM, Collakova E, Robertson J, Aardema C, Senger RS (2015) Assessment of ex vivo perfused liver health by Raman spectroscopy. J Raman Spectrosc 46: 551-558
  11. Zu TNK, Athamneh AIM, Wallace RS, Collakova E, Senger RS (2014) Near real-time analysis of the phenotypic responses of Escherichia coli to 1-butanol exposure using Raman spectroscopy. J Bacteriol 196: 3983-3991
  12. Singh D, Balota M, Isleib TG, Collakova E, Welbaum GE (2014) Suitability of canopy temperature depression, specific leaf area, and SPAD chlorophyll reading for genotypic comparison of peanut grown in a sub-humid environment. Peanut Sci 41: 100-110
  13. Singh D, Collakova E, Isleib TG, Welbaum GE, Tallury SP, Balota M (2014) Differential physiological and metabolic responses to drought stress of peanut cultivars and breeding lines. Crop Sci 54: 2262-2274
  14. Aghamirzaie D, Nabiyouni M, Fang Y, Klumas C, Heath LS, Grene R, Collakova E (2013) Changes in RNA splicing in developing soybean (Glycine max) embryos. Biology 2: 1311-1337
  15. Collakova E, Aghamirzaie D, Fang Y, Klumas C, Tabataba F, Kakumanu A, Myers E, Heath L, Grene R (2013) Metabolic and transcriptional reprogramming in developing soybean (Glycine max) embryos. Metabolites 3: 347-372
  16. Collakova E, Klumas C, Suren H, Myers E, Heath LS, Holliday JA, Grene R (2013) Evidence for extensive heterotrophic metabolism, antioxidant action, and associated regulatory events during winter hardening in Sitka spruce. BMC Plant Biol 13: 72-87
  17. Grene R, Klumas C, Suren H, Yang K, Collakova E, Myers E, Heath LS, Holliday JA (2012) Mining and visualization of microarray and metabolomic data reveal extensive cell wall remodeling during winter hardening in Sitka spruce (Picea sitchensis). Front Plant Sci 3: Article 241 (1-14)
  18. Collakova E, Yen JY, Senger R (2012) Are we ready for genome-scale modeling in plants? Plant Sci 191-192: 53-70

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