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@article{kanehisa04,
	Author = {Minoru Kanehisa and Susumu Goto and Shuichi Kawashima and Yasushi Okuno and Masahiro Hattori},
	Date-Added = {2009-10-08 19:24:18 +0200},
	Date-Modified = {2009-10-08 19:25:55 +0200},
	Journal = {Nucleic Acids Research},
	Pages = {D277-D280},
	Title = {The {KEGG} resource for deciphering the genome},
	Volume = {32},
	Year = {2004}}

@article{ashburner00,
	Author = {Michael Ashburner and Catherine A. Ball and Judith A. Blake and David Botstein and Heather Butler and J. Michael Cherry and Allan P. Davis and Kara Dolinski and Selina S. Dwight and Janan T. Eppig and Midori A. Harris and David P. Hill and Laurie Issel-Tarver and Andrew Kasarskis and Suzanna Lewis and John C. Matese and Joel E. Richardson and Martin Ringwald and Gerald M. Rubin and Gavin Sherlock},
	Date-Added = {2009-10-08 19:15:01 +0200},
	Date-Modified = {2009-10-08 19:23:45 +0200},
	Journal = {Nature Genetics},
	Pages = {25 - 29},
	Title = {Gene Ontology: tool for the unification of biology},
	Volume = {25},
	Year = {2000}}

@article{turner04,
	Author = {Heather Turner and Trevor Baileya and Wojtek Krzanowski},
	Date-Added = {2009-10-08 11:27:12 +0200},
	Date-Modified = {2009-10-08 14:59:14 +0200},
	Journal = {Computational Statistics \& Data Analysis},
	Lastchecked = {Thursday, October 8, 2009},
	Pages = {235-254},
	Title = {Improved biclustering of microarray data demonstrated through systematic performance tests},
	Volume = {48},
	Year = {2004},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.csda.2004.02.003}}

@article{madeira04,
	Author = {Madeira, S.C. and Oliveira, A.L.},
	Date-Added = {2009-09-16 10:08:38 +0200},
	Date-Modified = {2009-10-08 15:00:52 +0200},
	Issue = {1},
	Journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics},
	Pages = {24-45},
	Title = {Biclustering algorithms for biological data analysis: a survey},
	Volume = {1},
	Year = {2004}}

@techreport{kaiser08,
	Author = {Sebastian Kaiser and Friedrich Leisch},
	Date-Added = {2009-09-12 14:51:55 +0200},
	Date-Modified = {2009-09-12 14:54:27 +0200},
	Institution = {Department of Statistics, University of Munich},
	Number = {028},
	Title = {A Toolbox for Bicluster Analysis in {R}},
	Url = {http://epub.ub.uni-muenchen.de/3293/},
	Year = {2008},
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@article{csardi09,
	Author = {G{\'a}bor Cs{\'a}rdi and Zolt{\'a}n Kutalik and Sven Bergmann},
	Date-Added = {2009-09-09 09:42:27 +0200},
	Date-Modified = {2009-09-09 09:50:07 +0200},
	Journal = {Bioinformatics},
	Title = {EISA},
	Year = {2009}}

@article{gentleman04,
	Abstract = {The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples.},
	Author = {Gentleman, Robert C and Carey, Vincent J and Bates, Douglas M and Bolstad, Ben and Dettling, Marcel and Dudoit, Sandrine and Ellis, Byron and Gautier, Laurent and Ge, Yongchao and Gentry, Jeff and Hornik, Kurt and Hothorn, Torsten and Huber, Wolfgang and Iacus, Stefano and Irizarry, Rafael and Leisch, Friedrich and Li, Cheng and Maechler, Martin and Rossini, Anthony J and Sawitzki, Gunther and Smith, Colin and Smyth, Gordon and Tierney, Luke and Yang, Jean Y H and Zhang, Jianhua},
	Date-Added = {2009-09-06 20:57:14 +0200},
	Date-Modified = {2009-10-08 15:00:58 +0200},
	Doi = {10.1186/gb-2004-5-10-r80},
	Journal = {Genome Biol},
	Journal-Full = {Genome biology},
	Mesh = {Computational Biology; Internet; Reproducibility of Results; Software},
	Pages = {R80},
	Pmid = {15461798},
	Title = {Bioconductor: open software development for computational biology and bioinformatics},
	Volume = {5},
	Year = {2004},
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	Bdsk-Url-1 = {http://dx.doi.org/10.1186/gb-2004-5-10-r80}}

@article{grothaus06,
	Abstract = {BACKGROUND:Biclustering has emerged as a powerful algorithmic tool for analyzing measurements of gene expression. A number of different methods have emerged for computing biclusters in gene expression data. Many of these algorithms may output a very large number of biclusters with varying degrees of overlap. There are no systematic methods that create a two-dimensional layout of the computed biclusters and display overlaps between them.RESULTS:We develop a novel algorithm for laying out biclusters in a two-dimensional matrix whose rows (respectively, columns) are rows (respectively, columns) of the original dataset. We display each bicluster as a contiguous submatrix in the layout. We allow the layout to have repeated rows and/or columns from the original matrix as required, but we seek a layout of the smallest size. We also develop a web-based search interface for the user to query the genes and samples of interest and visualise the layout of biclusters matching the queries.CONCLUSION:We demonstrate the usefulness of our approach on gene expression data for two types of leukaemia and on protein-DNA binding data for two growth conditions in Saccharomyces cerevisiae. The software implementing the layout algorithm is available at http://bioinformatics.cs.vt.edu/~murali/papers/bivoc.},
	Author = {Grothaus, Gregory and Mufti, Adeel and Murali, TM},
	Date-Added = {2009-09-04 14:53:00 +0200},
	Date-Modified = {2009-10-08 15:00:42 +0200},
	Doi = {10.1186/1748-7188-1-15},
	Issn = {1748-7188},
	Journal = {Algorithms for Molecular Biology},
	Pages = {15},
	Pubmedid = {16952321},
	Title = {Automatic layout and visualization of biclusters},
	Url = {http://www.almob.org/content/1/1/15},
	Volume = {1},
	Year = {2006},
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	Bdsk-Url-1 = {http://dx.doi.org/10.1186/1748-7188-1-15}}

@article{bergmann03,
	Author = {Sven Bergmann and Jan Ihmels and Naama Barkai},
	Date-Added = {2009-09-04 14:35:15 +0200},
	Date-Modified = {2009-10-08 15:01:12 +0200},
	Doi = {10.1103/PhysRevE.67.031902},
	Eid = {031902},
	Journal = {Physical Review E},
	Keywords = {iterative methods; genetics; molecular biophysics},
	Numpages = {18},
	Pages = {031902},
	Publisher = {APS},
	Title = {Iterative signature algorithm for the analysis of large-scale gene expression data},
	Url = {http://link.aps.org/abstract/PRE/v67/e031902},
	Volume = {67},
	Year = {2003},
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	Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevE.67.031902}}
