Research Statement:

  • Click here for my research statement. (This statement was last updated October, 2010.)


    • Preprints:

    1. q-bio.BM/0603012: A Chemical Kinetic Model of Transcriptional Elongation.
      Yamada, Y.R. and C.S.Peskin.


    Publications:

    1. Multiscale Complexity in the Mammalian Circadian Clock
      Y.R.Yamada and D.B.Forger
      Curr. Opin. Genet. Develop. 2010; 20:626-633

    2. Emergence of Noise-Induced Oscillations in the Central Circadian Pacemaker
      C.H.Ko*, Y.R.Yamada*, D.K.Welsh*, E.D.Buhr, A.C.Liu, E.E.Zhang, M.R.Ralph, S.A.Kay, D.B.Forger, and J.S.Takahashi
      PLoS Biology. 2010 Oct; 10(8):e1000513 (* equal contributions)

    3. The Influence of Look-Ahead on the Error Rate of Transcription
      Y.R.Yamada and C.S.Peskin
      Math. Mod. Nat. Phen. 2010 Apr; 5(3):206-227

    4. A Look-Ahead Model for the Elongation Dynamics of Transcription
      Y.R.Yamada and C.S.Peskin
      Biophys J. 2009 Apr; 96(8):3015-3031

      For an illustration of the look-ahead model, please see the accompanying 'movie' here.

    5. Quantitative Models of Transcriptional Elongation
      Y.R.Yamada
      Ph.D Thesis: Applied Mathematics, Cornell University, Ithaca, NY. 2007. 173 pages.

    6. IR Spectroscopy of Mammalian Cells
      Mourant, J.R., Y.R.Yamada, S.Carpenter, A.Guerra, J.Schoonover, and J.P.Freyer
      Biophys J. 2003 Sep; 85(3):1938-47

    7. Methods for Measuring the Infrared Spectra of Biological Cells
      Mourant, J.R., R.R.Gibson, T.M.Johnson, S.Carpenter, K.W.Short, Y.R.Yamada, and J.P.Freyer
      Phys Med Biol. 2003 Jan; 48(2):243-57

    8. Vibrational Spectroscopy of Viable, Paired Tumorigenic, and non-Tumorigenic Cells
      Mourant, J.R., Y.R.Yamada, S.Carpenter, A.Guerra, J.Schoonover, and J.P.Freyer
      Proceed.SPIE 2002 4614:109-116

      9.

    Publications in Preparation:

    1. Enright's Hypothesis Revisited: A Genetic Oscillator Approach (with K. Fulton and D. Forger)

    2. Transcription Regulation Mechanisms in Cellular Oscillators (with D. Forger)

    3. Mathematical Analysis of the Look-ahead Model of Transcription Elongation (with A. Matteson and C. Peskin)

    4. A Supra-Chiasmatic Nuclei Network Model with Inter-Cellular Coupling (with C. Ko, J. Takahashi, and D. Forger)


    Talk Slides:

    1. Talk for Students at the 2008 Michigan Math and Science Scholars. Link for the program can be found here.


    Research Colleagues:
    Below is a list of labs and individuals I have worked with.

  • Prof. Zachary Burton (Michigan State University, Department of Biochemistry.): 2009-present

  • Prof. Joseph Takahashi (HHMI and UT-Southwestern Medical Center at Dallas.): 2007-present

  • Prof. Daniel B. Forger (University of Michigan): 2007-present

  • Prof. Charles Peskin (Courant Institute): 2003-present


    • Research Students:
    I enjoy interacting, conversing, and working with students of all backgrounds! Please contact me if you would like to work with me!!!

    Undergraduate Students:

  • Tyler Bridge Johnson (University of Michigan, UROP and REU): 2008-2009

  • Alban Xhaferllari (University of Michigan, UROP): 2008-2009

  • David Yang (University of Michigan, UROP and REU): 2008-2009

  • Lars Johnson (University of Michigan, UROP): 2009-2010

  • Garrett Swaney (University of Michigan, UROP):2009-2010

  • Lisa Kalenkiewicz (University of Michigan, Math 499: Independent Study): Winter 2010 Term

  • Liz Kennedy (University of Michigan, Math 499: Independent Study): Winter 2010 Term

  • Kara Fulton (University of Michigan, Math 499: Independent Study):Winter 2010 Term

  • Kara Vogel (University of Michigan, Math 499: Independent Study): Spring/Summer 2010 Term

  • Toniesha Jones (University of Michigan, Junior/Senior UROP): 2010-2011

  • Christopher Luoma (University of Michigan, UROP): 2010-2011

  • Vikas Velagapudi (University of Michigan, UROP): 2010-2011

    Graduate Students:

    • Last modified 11/30/2010