Honors & Awards

  • NSF Graduate Research Fellowship, National Science Foundation (2013)
  • ADVANCE Fellowship, Stanford ADVANCE (2013)
  • EXROP Fellowship, Howard Hughes Medical Institute (2012)
  • Genentech Fellowship, Columbia University (2011)


Journal Articles

  • Markov State Models Provide Insights into Dynamic Modulation of Protein Function Accounts of Chemical Research Shukla, D., Hernandez, C. X., Weber, J. K., Pande, V. S. 2015

    View details for DOI 10.1021/ar5002999

  • MDTraj: a modern, open library for the analysis of molecular dynamics trajectories bioRxiv McGibbon, R. T., Beauchamp, K. A., Schwantes, C. R., Wang, L., Hernandez, C. X., Harrigan, M. P., Lane, T. J., Swails, J. M., Pande, V. S. 2014

    View details for DOI 10.1101/008896

  • Structure-based network analysis of an evolved G protein-coupled receptor homodimer interface PROTEIN SCIENCE Nichols, S. E., Hernandez, C. X., Wang, Y., McCammon, J. A. 2013; 22 (6): 745-754


    Crystallographic structures and experimental assays of human CXC chemokine receptor type 4 (CXCR4) provide strong evidence for the capacity to homodimerize, potentially as a means of allosteric regulation. Even so, how this homodimer forms and its biological significance has yet to be fully characterized. By applying principles from network analysis, sequence-based approaches such as statistical coupling analysis to determine coevolutionary residues, can be used in conjunction with molecular dynamics simulations to identify residues relevant to dimerization. Here, the predominant coevolution sector lies along the observed dimer interface, suggesting functional relevance. Furthermore, coevolution scoring provides a basis for determining significant nodes, termed hubs, in the network formed by residues found along the interface of the homodimer. These node residues coincide with hotspots indicating potential druggability. Drug design efforts targeting such key residues could potentially result in modulation of binding and therapeutic benefits for disease states, such as lung cancers, lymphomas and latent HIV-1 infection. Furthermore, this method may be applied to any protein-protein interaction.

    View details for DOI 10.1002/pro.2258

    View details for Web of Science ID 000319422500007

    View details for PubMedID 23553730

  • Understanding the Origins of a Pandemic Virus arXiv Hernández, C. X., Chan, J., Khiabanian, H., Rabadan, R. 2011

Conference Proceedings

  • The Origin and Evolution of a Pandemic Virus MAGNet/C2B2 Annual Retreat Carpenter, Z. W., Hernández, C. X., Chan, J., Rabadan, R. 2011

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