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  • Biophysical assay for tethered signaling reactions reveals tether-controlled activity for the phosphatase SHP-1 

    Goyette, Jesse; Salas, Citlali Solis; Coker-Gordon, Nicola; Bridge, Marcus; Isaacson, Samuel A.; Allard, Jun; Dushek, Omer (2017-03)
    Tethered enzymatic reactions are ubiquitous in signaling networks but are poorly understood. A previously unreported mathematical analysis is established for tethered signaling reactions in surface plasmon resonance (SPR). ...
  • Why we (usually) don't have to worry about multiple comparisons 

    Gelman, Andrew; Hill, Jennifer; Yajima, Masanao (2012)
    Applied researchers often find themselves making statistical inferences in settings that would seem to require multiple comparisons adjustments. We challenge the Type I error paradigm that underlies these corrections. ...
  • MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data 

    Finak, Greg; McDavid, Andrew; Yajima, Masanao; Deng, Jingyuan; Gersuk, Vivian; Shalek, Alex K.; Slichter, Chloe K.; Miller, Hannah W.; McElrath, M. Juliana; Prlic, Martin; Linsley, Peter S.; Gottardo, Raphael (2015-12-10)
    Single-cell transcriptomics reveals gene expression heterogeneity but suffers from stochastic dropout and characteristic bimodal expression distributions in which expression is either strongly non-zero or non-detectable. ...
  • Reactive boundary conditions as limits of interaction potentials for Brownian and Langevin dynamics 

    Chapman, S. Jonathan; Erban, Radek; Isaacson, Samuel A. (SIAM PUBLICATIONS, 2016-01-01)
  • Transient rapamycin treatment can increase lifespan and healthspan in middle-aged mice 

    Bitto, Alessandro; Ito, Takashi K.; Pineda, Victor V.; LeTexier, Nicolas J.; Huang, Heather Z.; Sutlief, Elissa; Tung, Herman; Vizzini, Nicholas; Chen, Belle; Smith, Kaleb; Meza, Daniel; Yajima, Masanao; Beyer, Richard P.; Kerr, Kathleen F.; Davis, Daniel J.; Gillespie, Catherine H.; Snyder, Jessica M.; Treuting, Piper M.; Kaeberlein, Matt (2016-08-03)
    The FDA approved drug rapamycin increases lifespan in rodents and delays age-related dysfunction in rodents and humans. Nevertheless, important questions remain regarding the optimal dose, duration, and mechanisms of action ...
  • Uniform asymptotic approximation of diffusion to a small target: Generalized reaction models 

    Isaacson, Samuel A.; Mauro, Ava J.; Newby, Jay (2016-10)
    The diffusion of a reactant to a binding target plays a key role in many biological processes. The reaction radius at which the reactant and target may interact is often a small parameter relative to the diameter of the ...
  • Hopf algebras for matroids over hyperfields 

    Szczesny, Matt M.; Jun, Jaiung; Eppolito, Chris
    Recently, M.~Baker and N.~Bowler introduced the notion of matroids over hyperfields as a unifying theory of various generalizations of matroids. In this paper we generalize the notion of minors and direct sums from ordinary ...
  • Quasicoherent sheaves on projective schemes over F_1 

    Lorscheid, Oliver; Szczesny, Matt (2017-07)
    Given a graded monoid A with 1, one can construct a projective monoid scheme MProj(A) analogous to Proj(R) of a graded ring R. This paper is concerned with the study of quasicoherent sheaves on MProj(A), and we prove several ...
  • Čech cohomology over 𝔽12 

    Flores, Jaret; Lorscheid, Oliver; Szczesny, Matt (2017-09)
    In this text, we generalize Cech cohomology to sheaves  with values in blue B-modules where B is a blueprint with −1. If X is an object of the underlying site, then the cohomology sets Hl(X,) turn out to be blue B-modules. ...
  • Wakimoto modules for twisted affine lie algebras 

    Szczesny, Matthew (2002)
    We construct Wakimoto modules for twisted affine Lie algebras, and interpret the construction in terms of vertex algebras and their twisted modules. Using the Wakimoto realization, we prove the Kac-Kazhdan conjecture on ...

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