@article{Shiga07,
  author =       {Shiga, Motoki and Takigawa, Ichigaku and Mamitsuka,
                  Hiroshi},
  title =        {{Annotating gene function by combining expression
                  data with a modular gene network}},
  journal =      {Bioinformatics},
  volume =       23,
  number =       13,
  pages =        {i468-478},
  doi =          {10.1093/bioinformatics/btm173},
  year =         2007,
  URL =
                  {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/13/i468},
  eprint =
                  {http://bioinformatics.oxfordjournals.org/cgi/reprint/23/13/i468.pdf}
}

@InCollection{Shiga07kdd,
  author =       {M. Shiga and I. Takigawa and H. Mamitsuka},
  title =        {A Spectral Clustering Approach to Optimally
                  Combining Numerical Vectors with a Modular Network},
  booktitle =    {Proceedings of KDD'07, the 13th ACM SIGKDD
                  International Conference on Knowledge Discovery and
                  Data Mining},
  pages =        {647-656},
  publisher =    {ACM Press},
  year =         2007,
  address =      {San Jose, CA},
  annote =       {Keywords: gene expression, metabolic network,
                  modularity, spectral clustering. Same cost
                  function as in Shiga07ismb but solution with
                  spectral clustering => fast and less prone to local
                  minima}
}

@Article{Reiss06,
  AUTHOR =       {Reiss, David and Baliga, Nitin and Bonneau, Richard},
  TITLE =        {Integrated biclustering of heterogeneous genome-wide
                  datasets for the inference of global regulatory
                  networks},
  JOURNAL =      {BMC Bioinformatics},
  VOLUME =       7,
  YEAR =         2006,
  NUMBER =       1,
  PAGES =        280,
  URL =          {http://www.biomedcentral.com/1471-2105/7/280},
  DOI =          {10.1186/1471-2105-7-280},
  PubMedID =     16749936,
  ISSN =         {1471-2105},
  annote =       {cMonkey. MCMC biclustering, using network
                  information.}
}

@Article{Vert03,
  author =       {J.-P. Vert and M. Kanehisa},
  title =        {Extracting active pathways from gene expression data},
  journal =      {Bioinformatics},
  year =         {2003},
  volume =       {19},
  number =       {suppl.~2},
  pages =        {i238--i244}
}

@Article{Segal03b,
  author =       {Discovering molecular pathways from protein
                  interaction and gene expression data},
  title =        {E. Segal and H. Wang and D. Koller},
  journal =      {Bioinformatics},
  year =         2003,
  volume =       19,
  number =       {Suppl.~1},
  pages =        {i264--i272},
  annote =       {Assumes that genes in
                  the same process have same expression (from Gaussian), and
                  each gene belongs only to one
                  process. Gene-process-assignments are a hidden
                  variable and network guides this
                  search.}
}


@article{Hanisch02,
  author =       {Hanisch, Daniel and Zien, Alexander and Zimmer, Ralf
                  and Lengauer, Thomas},
  title =        {{Co-clustering of biological networks and gene
                  expression data}},
  journal =      {Bioinformatics},
  volume =       18,
  number =       90001,
  pages =        {145S-154},
  year =         2002,
  annote =       {Distance measure made for genes by combining
                  correlation-based expression profile distances and
                  corresponding metabolic network graph distances by
                  using a logistic function.}
}

@Article{Ulitsky07,
  AUTHOR =       {Ulitsky, Igor and Shamir, Ron},
  TITLE =        {Identification of functional modules using network
                  topology and high-throughput data},
  JOURNAL =      {BMC Systems Biology},
  VOLUME =       1,
  YEAR =         2007,
  NUMBER =       1,
  PAGES =        8,
  URL =          {http://www.biomedcentral.com/1752-0509/1/8},
  DOI =          {10.1186/1752-0509-1-8},
  PubMedID =     17408515,
  ISSN =         {1752-0509}
}

@Article{Maraziotis07,
  author =       {Ioannis A. Maraziotis and Konstantina
                  Dimitrakopoulou and Anastasios Bezerianos},
  title =        {Growing functional modules from a seed protein via
                  integration of protein interaction and gene
                  expression data},
  journal =      {BMC Bioinformatics},
  year =         2007,
  volume =       8,
  pages =        408
}

@article{Nacu07,
  author =       {Nacu, Serban and Critchley-Thorne, Rebecca and Lee,
                  Peter and Holmes, Susan},
  title =        {{Gene expression network analysis and applications
                  to immunology}},
  journal =      {Bioinformatics},
  volume =       23,
  number =       7,
  pages =        {850-858},
  doi =          {10.1093/bioinformatics/btm019},
  year =         2007,
  URL =
                  {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/7/850},
  eprint =
                  {http://bioinformatics.oxfordjournals.org/cgi/reprint/23/7/850.pdf},
  annote =       {Greedy search
                  from seed genes to find active subnetworks. Various
                  proposed scoring functions.}
}