I use a variety of computational and systems biology approaches to study the physiology of human red blood cells. Our goal is to provide the framework for identifying, computing, and understanding systems-level properties by integrating disparate multi-omic data types into multi-scale models.
In my dissertation, I examined the metabolic physiology of red cells under storage conditions for use in transfusion medicine. We combined statistical and mechanistic modeling approaches to characterize the state of the metabolic network. Link to my dissertation.
2018, Postdoctoral Scholar, Bioengineering Department, University of California, San Diego, La Jolla, CA
2018, Ph.D. Bioinformatics and Systems Biology, University of California, San Diego, La Jolla, CA
2013, B.S. Electrical Engineering, University of Notre Dame, Notre Dame, IN
- E Brunk, RL Chang, J Xia, H Hefzi, JT Yurkovich, D Kim, E Buckmiller, HH Wang, BK Cho, C Yang, BO Palsson, G Church, and NE Lewis. "Characterizing post-translational modifications in prokaryotic metabolism using a multi-scale workflow." PNAS (in press).
- E Kavvas, E Catoiu, N Mih, JT Yurkovich, Y Seif, N Dillon, D Heckmann, A Anand, L Yang, V Nizet, J Monk, and BO Palsson. "Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance." Nature Communications, (in press).
- Y Gao, JT Yurkovich, SW Seo, I Kabimoldayev, A Draeger, K Chen, A Sastry, X Fang, N Mih, L Yang, J Eichner, BK Cho, D Kim, and BO Palsson. Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655. Nucleic Acids Research, gky752 (2018).
- Y Seif, E Kavvas, JC Lachance, JT Yurkovich, SP Nuccio, E Catoiu, X Fang, M Raffatellu, and BO Palsson. "Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits." Nature Communications (in press).
- JT Yurkovich*, MA Alcantar*, Z Haiman, and BO Palsson. Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials. PLOS Computational Biology, 14(8): e1006356.
- L Heirendt et al. Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0. Nature Protocols (in press).
- B Du, Z Zhang, S Grubner, JT Yurkovich, BO Palsson, and DC Zielinski. Temperature-dependent estimation of Gibbs energies using an updated group contribution method. Biophysical Journal, 114(11):2691-2702 (2018).
- KS Choudhary, N Mih, J Monk, E Kavvas, JT Yurkovich, G Sakoulas, and BO Palsson. The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures. Frontiers in Microbiology, 9:1082 (2018).
- 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