@String{curopin = {Current Opinion in}}
@String{j = {Journal}}
@String{jof = {Journal of}}
@String{jofthe = {Journal of the}}
@String{jmb = {Journal of Molecular Biology}}
@String{jtb = {Journal of Theoretical Biology}}
@String{mbc = {Molecular Biology of the Cell}}
@String{mcb = {Molecular and Cellular Biology}}
@String{mkp = {Morgan Kaufmann Publishers}}
@String{mach = {Machine Learning}}
@String{nips = {Neural Information Processing Systems}}
@String{pnas = {Proceedings of the National Academy of Sciences, USA}}
@String{proc = {Proceedings}}
@String{procof = {Proceedings of}}
@String{procofthe = {Proceedings of the}}
@String{psb = {Pacific Symposium on Biocomputing}}
@String{uai = {Annual Conference on Uncertainty in Artificial Intelligence}}

@Book{kuhn70,
  author       = {Kuhn, Thomas S.},
  title	       = {The Structure of Scientific Revolutions},
  publisher    = {University of Chicago Press},
  address      = {Chicago, IL},
  isbn	       = {0-226-45804-0},
  year	       = 1970,
}

@Article{arkin97,
  author       = {Arkin, Adam and Shen, Peidong and Ross, John},
  title	       = {A Test Case of Correlation Metric Construction of a
                  Reaction Pathway from Measurements},
  journal      = {Science},
  year	       = 1997,
  month	       = Aug,
  volume       = 277,
  pages	       = {1275-1279},
}

@Article{lander01,
  author       = {Lander, Eric S. and others},
  title	       = {Initial sequencing and analysis of the human genome},
  journal      = {Nature},
  year	       = 2001,
  volume       = 409,
  pages	       = {860-921},
  month	       = Feb,
}

@Article{arkin98,
  author       = {Arkin, Adam and Ross, John and McAdams, Harley H.},
  title	       = {Stochastic Kinetic Analysis of Developmental Pathway
                  Bifurcation in Phage $\lambda$-infected
                  {E}scherichia coli Cells},
  journal      = {Genetics},
  year	       = 1998,
  volume       = 149,
  pages	       = {1633-1648},
}

@InProceedings{akutsu99,
  author       = {Akutsu, Tatsuya and Miyano, Satoru and Kuhara,
                  Satoru},
  title	       = {Identification of Genetic Networks from a Small
                  Number of Gene Expression Patterns under the
                  {B}oolean Network Model},
  booktitle    = psb,
  pages	       = {17-28},
  year	       = 1999,
  volume       = 4,
}

@Article{brown00,
  author       = {Brown, Michael P. S. and Grundy, William Noble and
                  Lin, David and Cristianini, Nello and Sugnet,
                  Charles Walsh and Furey, Terrence S. and Ares Jr.,
                  Manuel and Haussler, David},
  title	       = {Knowledge-based analysis of microarray gene
                  expression data by using support vector machines},
  journal      = pnas,
  year	       = 2000,
  month	       = Jan,
  volume       = 97,
  number       = 1,
  pages	       = {262-267},
}

@Article{arkin94,
  author       = {Arkin, Adam and Ross, John},
  title	       = {Computational Functions in Biochemical Reaction
                  Networks},
  journal      = {Biophysical } # j,
  year	       = 1994,
  month	       = Aug,
  volume       = 67,
  pages	       = {560-578},
}

@Article{burge98,
  author       = {Burge, Christopher B. and Karlin, Samuel},
  title	       = {Finding the genes in genomic {DNA}},
  journal      = curopin # { Structural Biology},
  year	       = 1998,
  volume       = 8,
  pages	       = {346-354},
}

@InProceedings{chavez94,
  author       = {Ch\'{a}vez, T. and Henrion, M.},
  title	       = {Efficient Estimation of the Value of Information in
                  {M}onte {C}arlo Models},
  booktitle    = procofthe # { Tenth } # uai,
  year	       = 1994,
  pages	       = {119-127},
}

@Article{eisen98,
  author       = {Eisen, Michael B. and Spellman, Paul T. and Brown,
                  Patrick O. and Botstein, David},
  title	       = {Cluster analysis and display of genome-wide
                  expression patterns},
  journal      = pnas,
  year	       = 1998,
  month	       = Dec,
  volume       = 95,
  pages	       = {14863-14868},
  url	       = {http://www.pnas.org/cgi/reprint/95/25/14863.pdf},
  abstract     = {A system of cluster analysis for genome-wide expression
                  data from DNA microarray hybridization is described
                  that uses standard statistical algorithms to arrange
                  genes according to similarity in pattern of gene
                  expression.  The output is displayed graphically,
                  conveying the clustering and the underlying
                  expression data simultaneously in a form intuitive
                  for biologists. We have found in the budding yeast
                  Saccharomyces cerevisiae that clustering gene
                  expression data groups together efficiently genes of
                  known similar function, and we find a similar
                  tendency in human data. Thus patterns seen in
                  genome-wide expression experiments can be
                  interpreted as indications of the status of cellular
                  processes. Also, coexpression of genes of known
                  function with poorly characterized or novel genes
                  may provide a simple means of gaining leads to the
                  functions of many genes for which information is not
                  available currently.},
  annote       = {In this seminal paper, Eisen and coauthors apply the
                  preexisting method of hierarchical clustering to
                  genome-wide expression data for the first time.
                  Though the clustering method is not novel, the
                  application in this domain was a significant step
                  forward and the methodology (and software) used here
                  are in widespread use today.},
  notetoself   = {should always remember that the method was developed
                  elsewhere first; still need to read the original
                  paper for future citation.},
  keywords     = {hierarchical clustering; red; green; visualization;
                  genomic expression data; yeast; sporulation; cell
                  division; cell cycle; diauxic shift},
}