I am a fifth year PhD student in the Bioinformatics and Systems Biology program. I primarily study systems theory and develop modeling methods and computational approaches to study intracellular metabolite concentrations with applications in transfusion medicine. My research attempts to answer three fundamental questions:
- What physiological states are possible?
- How do these states behave?
- Why do these behaviors manifest themselves?
Using modeling approaches that span different timescales, we can provide the framework for identifying, computing, and understanding systems-level properties.
2013, B.S. Electrical Engineering, University of Notre Dame, Notre Dame, IN
- JT Yurkovich, A Bordbar, O Sigurjonsson, and BO Palsson. Systems biology as an emerging paradigm in transfusion medicine. BMC Systems Biology, 12:31 (2018).
- E Kavvas, Y Seif, JT Yurkovich, C Norsigian, S Poudel, WW Greenwald, S Ghatak, BO Palsson, and J Monk. Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions. BMC Systems Biology, 12:25 (2018).
- JT Yurkovich and BO Palsson. Quantitative -omic data empowers bottom-up systems biology. Current Opinion in Biotechnology, 51:130-136 (2018).
- L Yang, JT Yurkovich, ZA King, and BO Palsson. Modeling the multi-scale mechanisms of macromolecular resource allocation. Current Opinion in Microbiology, 45:8-15 (2018).
- JT Yurkovich, DC Zielinski, L Yang, G Paglia, O Rolfsson, OE Sigurjonsson, JT Broddrick, A Bordbar, K Wichuk, S Brynjolfsson, S Palsson, S Gudmundsson, and BO Palsson. Quantitative time-course metabolomics in human red blood cells reveal the temperature dependence of human metabolic networks. Journal of Biological Chemistry, 292(48):19556-19564 (2017). Cover of the December 1, 2017 (Vol. 292, Num. 48) issue.
- JT Yurkovich, L Yang, and BO Palsson. Utilizing biomarkers to forecast quantitative metabolite concentration profiles in human red blood cells. Proceedings of the IEEE Conference on Control Technology and Applications (CCTA), Kohala Coast, HI (August 27-30, 2017).
- JT Yurkovich, BJ Yurkovich, A Draeger, BO Palsson, and ZA King. A Padawan Programmer's Guide to Developing Software Libraries. Cell Systems, 5(5):431-437 (2017).
- X Fang*, A Sastry*, N Mih, D Kim, J Tan, JT Yurkovich, CJ Lloyd, Y Gao, L Yang, and BO Palsson. Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities. PNAS, 114(38):10286-10291 (2017).
- A Bordbar*, JT Yurkovich*, G Paglia, O Rolfsson, O Sigurjonsson, and BO Palsson. Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics. Scientific Reports, 7:46249 (2017).
- JT Yurkovich*, L Yang*, and BO Palsson. Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells. PLOS Computational Biology, 13(3):e1005424 (2017).
- L Yang*, JT Yurkovich*, CJ Lloyd, A Ebrahim, MA Saunders, and BO Palsson. Principles of proteome allocation are revealed using proteomic data and genome-scale models. Scientific Reports, 6:36734 (2016).
- D Waltemath et al. Toward community standards and software for whole-cell modeling. IEEE Transactions on Biomedical Engineering, 63(10):2007-2014 (2016).
- JT Yurkovich and BO Palsson. Solving Puzzles With Missing Pieces: The Power of Systems Biology. Proceedings of the IEEE, 104(1):2-7 (2016).
- L Yang*, J Tan*, E O'Brien, J Monk, D Kim, H Li, P Charusanti, A Ebrahim, C Lloyd, JT Yurkovich, B Du, A Draeger, A Thomas, Y Sun, M Saunders, and BO Palsson. Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data. PNAS, 112(34):10810-10815 (2015).
- I Tolbatov, P Bartl, JT Yurkovich, P Scheier, DM Chipman, S Denifl, and S Ptasinska. Monocarbon cationic cluster yields from N2/CH4 mixtures embedded in He nanodroplets and their calculated binding energies. J. Chem. Phys. 140 (2014) 034316.
- S Ptasinska, I Tolbatov, P Bartl, JT Yurkovich, B Coffey, DM Chipman, C Leidlmair, H Schobel, P Scheier, and NJ Mason. Electron impact on N2/CH4 mixtures in He droplets – Probing chemistry in Titan’s atmosphere. RSC Advances 2 (2012) 10492.
(* - Equal contribution)
Email Address: jyurkovich AT ucsd.edu