Lab and alumni

Current Lab members

  • Dan Vasilescu, programmer working on VCell software
    • Schaff, J. C., Vasilescu, D., Moraru, I. I., Loew, L. M., & Blinov, M. L. (2016). Rule-based modeling with Virtual Cell. Bioinformatics (Oxford, England), 32(18), 2880–2882. https://doi.org/10.1093/bioinformatics/btw353
    • Blinov, M. L., Schaff, J. C., Vasilescu, D., Moraru, I. I., Bloom, J. E., & Loew, L. M. (2017). Compartmental and Spatial Rule-Based Modeling with Virtual Cell. Biophysical journal, 113(7), 1365–1372. https://doi.org/10.1016/j.bpj.2017.08.022
    • Blinov, M. L., Schaff, J. C., Ruebenacker, O., Wei, X., Vasilescu, D., Gao, F., Morgan, F., Ye, L., Lakshminarayana, A., Moraru, I. I., & Loew, L. M. (2014). Pathway Commons at virtual cell: use of pathway data for mathematical modeling. Bioinformatics (Oxford, England), 30(2), 292–294.
    • Shaikh, B., Smith, L. P., Vasilescu, D., …, Blinov, M. L., Sauro, H., Moraru, I. I., Karr, J. R. (2022). BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic acids research, 50(W1), W108–W114. https://doi.org/10.1093/nar/gkac331
  • Logan Drescher, programmer working on VCell software

Alumni

PostDocs

  • Cibele Falkenberg
    • Falkenberg, C. V., Carson, J. H., & Blinov, M. L. (2017). Multivalent Molecules as Modulators of RNA Granule Size and Composition. Biophysical journal, 113(2), 235–245. https://doi.org/10.1016/j.bpj.2017.01.031
    • Falkenberg, C. V., Blinov, M. L., & Loew, L. M. (2013). Pleomorphic ensembles: formation of large clusters composed of weakly interacting multivalent molecules. Biophysical journal, 105(11), 2451–2460. https://doi.org/10.1016/j.bpj.2013.10.016.
  • Oliver Ruebenacker
    • Blinov, M. L., Schaff, J. C., Ruebenacker, O., Wei, X., Vasilescu, D., Gao, F., Morgan, F., Ye, L., Lakshminarayana, A., Moraru, I. I., & Loew, L. M. (2014). Pathway Commons at Virtual Cell: use of pathway data for mathematical modeling. Bioinformatics (Oxford, England), 30(2), 292–294.
    • Ruebenacker, O., & Blinov, M. (2011). Using views of Systems Biology Cloud: application for model building. Theory in biosciences = Theorie in den Biowissenschaften, 130(1), 45–54. https://doi.org/10.1007/s12064-010-0108-6.
    • Blinov, M. L., Ruebenacker, O., Schaff, J. C., & Moraru, I. I. (2010). Modeling without borders: creating and annotating VCell Models using the web. In International Symposium on Bioinformatics Research and Applications (pp. 3-17). Springer, Berlin, Heidelberg.
    • Ruebenacker, O., Moraru, I. I., Schaff, J. C., & Blinov, M. L. (2009). Integrating BioPAX pathway knowledge with SBML models. IET systems biology, 3(5), 317–328. https://doi.org/10.1049/iet-syb.2009.0007
    • Blinov, M. L., Ruebenacker, O., & Moraru, I. I. (2008). Complexity and modularity of intracellular networks: a systematic approach for modelling and simulation. IET systems biology, 2(5), 363–368. https://doi.org/10.1049/iet-syb:20080092
    • Ruebenacker, O., Moraru, I. I., Schaff, J. C., & Blinov, M. L. (2007). Kinetic Modeling using BioPAX ontology. Proceedings. IEEE International Conference on Bioinformatics and Biomedicine, 2007, 339–348. https://doi.org/10.1109/BIBM.2007.55

Graduate Students

  • Aniruddha Chattaraj
    • Chattaraj, A., Blinov, M. L., & Loew, L. M. (2021). The solubility product extends the buffering concept to heterotypic biomolecular condensates. eLife, 10, e67176. PMID: 34236318
    • Chattaraj, A., Nalagandla, I., Loew, L. M., & Blinov, M. L. (2023). MolClustPy: a Python package to characterize multivalent biomolecular clusters. Bioinformatics, 39(6), btad385. PMID: 37326981/

Undergraduate Students

  • Noah Liguori-Bills
  • Nathan Schaumburger, Joel Pally
    • Schaumburger, N., Pally, J., Moraru, I. I., Kositsawat, J., Kuchel, G. A., & Blinov, M. L. (2023). Dynamic model assuming mutually inhibitory biomarkers of frailty suggests bistability with contrasting mobility phenotypes. Frontiers in Network Physiology, 3, 1079070. PMID: 37216041
  • John Albanese
    • Rougny, A., Touré, V., Albanese, J., Waltemath, D., Shirshov, D., Sorokin, A., Bader, G. D., Blinov, M. L., & Mazein, A. (2021). SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks. Briefings in bioinformatics, 22(5), bbab049. https://doi.org/10.1093/bib/bbab049
  • James Green
    • Vasilescu,D., Greene,J., Schaff, J.C., Moraru, I.I., Blinov, M.L. (2018) Molecular Process Diagram: a precise, scalable and compact visualization of rule-based models bioRxiv 503359; https://doi.org/10.1101/503359
  • Daniel Fryer
  • Maria Heredia Chavez
  • Keeyan Goreshi
  • Raman Allawirdi
  • Kevin Reid
  • Mitchell Clough
  • Thomas Vecca
  • Tyler McLoughlin
  • Dhruv Vig
  • Xiaozhou Liu
  • Max Win
  • Ritika Sahni

High School Students

  • Ricky Paul
  • Bushrah Khan
  • Zaiba Khan
  • Arundeep Singh
  • Nathan Schaumburger
  • Laurie Yousman
  • Tanya Miller
  • Summer Xu
  • Patrick Demkowitz
  • Thomas Vecca
  • Joel Pally