Papers

  • Preprints
  • Widespread dysregulation of the circadian clock in human cancer.
    Shilts J, Chen G, Hughey JJ. bioRxiv (2017).
    Abstract   Journal   Results  
  • Postprints
  • Machine learning identifies a compact gene set for monitoring the circadian clock in human blood.
    Hughey JJ. Genome Med (2017).
    Abstract   PDF   Supp   Results   Reviews   Journal   Pubmed  
  • Differential phasing between circadian clocks in the brain and peripheral organs in humans.
    Hughey JJ and Butte AJ. J Biol Rhythms (2016).
    Abstract   PDF   Supp   Results   Reviews   Journal   Pubmed  
  • Is the Crowd Better as an Assistant or a Replacement in Ontology Engineering? An Exploration Through the Lens of the Gene Ontology.
    Mortensen JM, Telis N, Hughey JJ, Fan-Minogue H, Auken KV, Dumontier M, Musen MA. J Biomed Inform (2016).
    Abstract   PDF   Journal   Pubmed  
  • ZeitZeiger: supervised learning for high-dimensional data from an oscillatory system.
    Hughey JJ, Hastie T, Butte AJ. Nucleic Acids Res (2016).
    Abstract   PDF   Supp   Results   Journal   Pubmed  
  • Robust meta-analysis of gene expression using the elastic net.
    Hughey JJ and Butte AJ. Nucleic Acids Res (2015).
    Abstract   PDF   Supp   Results   Journal   Pubmed  
  • Single-cell variation leads to population invariance in NF-κB signaling dynamics.
    Hughey JJ*, Gutschow MV*, Bajar BT, Covert MW, *equal contribution. Mol Biol Cell (2015).
    Abstract   PDF   Supp   Results   Journal   Pubmed  
  • High-sensitivity measurements of multiple kinase activities in live single cells.
    Regot S, Hughey JJ, Bajar BT, Carrasco S, Covert MW. Cell (2014).
    Abstract   PDF   Supp   Journal   Pubmed  
  • The microfluidic multi-trap nanophysiometer for hematologic cancer cell characterization reveals temporal sensitivity of the calcein-AM efflux assay.
    Byrd TF IV, Hoang LT, Kim EG, Pfister ME, Werner EM, Arndt SE, Chamberlain JW, Hughey JJ, Nguyen BA, Schneibel EJ, Wertz LL, Whitfield JS, Wikswo JP, Seale KT. Sci Rep (2014).
    Abstract   PDF   Supp   Journal   Pubmed  
  • Single-cell and Population NF-κB Dynamic Responses Depend on Lipopolysaccharide Preparation.
    Gutschow MV*, Hughey JJ*, Ruggero NA, Bajar BT, Valle SD, Covert MW, *equal contribution. PLOS One (2013).
    Abstract   PDF   Journal   Pubmed  
  • Single-cell NF-κB dynamics reveal digital activation and analog information processing.
    Tay S*, Hughey JJ*, Lee TK, Lipniacki T, Quake SR, Covert MW, *equal contribution. Nature (2010).
    Abstract   PDF   Supp   Journal   Pubmed  
  • Computational modeling of mammalian signaling networks.
    Hughey JJ, Lee TK, Covert MW. Wiley Interdiscip Rev Syst Biol Med (2010).
    Abstract   PDF   Journal   Pubmed  
  • A Noisy Paracrine Signal Determines the Cellular NF-κB Response to Lipopolysaccharide.
    Lee TK, Denny EM, Sanghvi JC, Gaston JE, Maynard ND, Hughey JJ, Covert MW. Sci Signal (2009).
    Abstract   PDF   Supp   Journal   Pubmed  
  • Microfluidic platform for real-time signaling analysis of multiple single T cells in parallel.
    Faley S, Seale K, Hughey J, Schaffer DK, VanCompernolle S, McKinney B, Baudenbacher F, Unutmaz D, Wikswo JP. Lab Chip (2008).
    Abstract   PDF   Journal   Pubmed