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'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns
Trevor Hastie, Robert Tibshirani, Michael B Eisen, Ash Alizadeh, Ronald Levy, Louis Staudt, Wing C Chan, David Botstein, Patrick Brown
Genome Biol. 2000; 1(2): research0003.1–research0003.21. Published online 2000 August 4.
PMCID:
PMC15015
Abstract Full Text PDF–6.2M
 Is Cited by the Following 29 Articles in this Archive:
Partition decoupling for multi-gene analysis of gene expression profiling data
Rosemary Braun, Gregory Leibon, Scott Pauls, Daniel Rockmore
BMC Bioinformatics. 2011; 12: 497. Published online 2011 December 30. doi: 10.1186/1471-2105-12-497
PMCID:
PMC3276603
Abstract Full Text PDF–3.0M Supplementary Material
Strategy to Find Molecular Signatures in a Small Series of Rare Cancers: Validation for Radiation-Induced Breast and Thyroid Tumors
Nicolas Ugolin, Catherine Ory, Emilie Lefevre, Nora Benhabiles, Paul Hofman, Martin Schlumberger, Sylvie Chevillard
PLoS One. 2011; 6(8): e23581. Published online 2011 August 11. doi: 10.1371/journal.pone.0023581
PMCID:
PMC3154936
Abstract Full Text PDF–442K Supplementary Material
Robust consensus clustering for identification of expressed genes linked to malignancy of human colorectal carcinoma
Gatot Wahyudi, Ito Wasito, Tisha Melia, Indra Budi
Bioinformation. 2011; 6(7): 279–282. Published online 2011 June 23.
PMCID:
PMC3124694
Abstract Full Text PDF–150K Supplementary Material
Challenges in microarray class discovery: a comprehensive examination of normalization, gene selection and clustering
Eva Freyhult, Mattias Landfors, Jenny Önskog, Torgeir R Hvidsten, Patrik Rydén
BMC Bioinformatics. 2010; 11: 503. Published online 2010 October 11. doi: 10.1186/1471-2105-11-503
PMCID:
PMC3098084
Abstract Full Text PDF–849K Supplementary Material
An exploratory data analysis method to reveal modular latent structures in high-throughput data
Tianwei Yu
BMC Bioinformatics. 2010; 11: 440. Published online 2010 August 27. doi: 10.1186/1471-2105-11-440
PMCID:
PMC2940911
Abstract Full Text PDF–1.6M Supplementary Material
svdPPCS: an effective singular value decomposition-based method for conserved and divergent co-expression gene module identification
Wensheng Zhang, Andrea Edwards, Wei Fan, Dongxiao Zhu, Kun Zhang
BMC Bioinformatics. 2010; 11: 338. Published online 2010 June 22. doi: 10.1186/1471-2105-11-338
PMCID:
PMC2905369
Abstract Full Text PDF–1.6M Supplementary Material
Making Informed Choices about Microarray Data Analysis
Mark Reimers
PLoS Comput Biol. 2010 May; 6(5): e1000786. Published online 2010 May 27. doi: 10.1371/journal.pcbi.1000786
PMCID:
PMC2877726
Full Text PDF–428K Supplementary Material
STARNET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data
Daniel Jupiter, Hailin Chen, Vincent VanBuren
BMC Bioinformatics. 2009; 10: 332. Published online 2009 October 14. doi: 10.1186/1471-2105-10-332
PMCID:
PMC2765977
Abstract Full Text PDF–1.2M
Gene expression meta-analysis supports existence of molecular apocrine breast cancer with a role for androgen receptor and implies interactions with ErbB family
Sandeep Sanga, Bradley M Broom, Vittorio Cristini, Mary E Edgerton
BMC Med Genomics. 2009; 2: 59. Published online 2009 September 11. doi: 10.1186/1755-8794-2-59
PMCID:
PMC2753593
Abstract Full Text PDF–1.5M Supplementary Material
Semi-supervised gene shaving method for predicting low variation biological pathways from genome-wide data
Dongxiao Zhu
BMC Bioinformatics. 2009; 10(Suppl 1): S54. Published online 2009 January 30. doi: 10.1186/1471-2105-10-S1-S54
PMCID:
PMC2648790
Abstract Full Text PDF–2.0M Supplementary Material
The liver pharmacological and xenobiotic gene response repertoire
Georges Natsoulis, Cecelia I Pearson, Jeremy Gollub, Barrett P Eynon, Joe Ferng, Ramesh Nair, Radha Idury, May D Lee, Mark R Fielden, Richard J Brennan, Alan H Roter, Kurt Jarnagin
Mol Syst Biol. 2008; 4: 175. Published online 2008 March 25. doi: 10.1038/msb.2008.9
PMCID:
PMC2290941
Abstract Full Text PDF–318K Supplementary Material
A Visual Data Mining Tool that Facilitates Reconstruction of Transcription Regulatory Networks
Daniel C. Jupiter, Vincent VanBuren
PLoS ONE. 2008; 3(3): e1717. Published online 2008 March 5. doi: 10.1371/journal.pone.0001717
PMCID:
PMC2248622
Abstract Full Text PDF–318K
Data Mining in Genomics
Jae K. Lee, Paul D. Williams, Sooyoung Cheon
Clin Lab Med. Author manuscript; available in PMC 2009 March 1.
Published in final edited form as: Clin Lab Med. 2008 March; 28(1): 145–viii. doi: 10.1016/j.cll.2007.10.010
PMCID:
PMC2253491
Abstract Full Text PDF–901K
Response projected clustering for direct association with physiological and clinical response data
Sung-Gon Yi, Taesung Park, Jae K Lee
BMC Bioinformatics. 2008; 9: 76. Published online 2008 January 31. doi: 10.1186/1471-2105-9-76
PMCID:
PMC2275250
Abstract Full Text PDF–874K
Transcription factor target prediction using multiple short expression time series from Arabidopsis thaliana
Henning Redestig, Daniel Weicht, Joachim Selbig, Matthew A Hannah
BMC Bioinformatics. 2007; 8: 454. Published online 2007 November 18. doi: 10.1186/1471-2105-8-454
PMCID:
PMC2198923
Abstract Full Text PDF–725K Supplementary Material
Measuring similarities between gene expression profiles through new data transformations
Kyungpil Kim, Shibo Zhang, Keni Jiang, Li Cai, In-Beum Lee, Lewis J Feldman, Haiyan Huang
BMC Bioinformatics. 2007; 8: 29. Published online 2007 January 27. doi: 10.1186/1471-2105-8-29
PMCID:
PMC1804284
Abstract Full Text PDF–1.2M Supplementary Material
Bayesian profiling of molecular signatures to predict event times
Dabao Zhang, Min Zhang
Theor Biol Med Model. 2007; 4: 3. Published online 2007 January 19. doi: 10.1186/1742-4682-4-3
PMCID:
PMC1796541
Abstract Full Text PDF–477K
A biological question and a balanced (orthogonal) design: the ingredients to efficiently analyze two-color microarrays with Confirmatory Factor Analysis
Anne PG Crijns, Frans Gerbens, A Edo D Plantinga, Gert Jan Meersma, Steven de Jong, Robert MW Hofstra, Elisabeth GE de Vries, Ate GJ van der Zee, Geertruida H de Bock, Gerard J te Meerman
BMC Genomics. 2006; 7: 232. Published online 2006 September 12. doi: 10.1186/1471-2164-7-232
PMCID:
PMC1590029
Abstract Full Text PDF–762K
Differential and trajectory methods for time course gene expression data
Yulan Liang, Bamidele Tayo, Xueya Cai, Arpad Kelemen
Bioinformatics. Author manuscript; available in PMC 2008 October 27.
Published in final edited form as: Bioinformatics. 2005 July 1; 21(13): 3009–3016. Published online 2005 May 10. doi: 10.1093/bioinformatics/bti465
PMCID:
PMC2574001
Abstract Full Text PDF–1.7M
Targeting c-Myc-activated genes with a correlation method: Detection of global changes in large gene expression network dynamics
D. Remondini, B. O'Connell, N. Intrator, J. M. Sedivy, N. Neretti, G. C. Castellani, L. N. Cooper
Proc Natl Acad Sci U S A. 2005 May 10; 102(19): 6902–6906. Published online 2005 May 2. doi: 10.1073/pnas.0502081102
PMCID:
PMC1100785
Abstract Full Text PDF–261K
Finding Groups in Gene Expression Data
David J. Hand, Nicholas A. Heard
J Biomed Biotechnol. 2005; 2005(2): 215–225. doi: 10.1155/JBB.2005.215
PMCID:
PMC1184051
Abstract Full Text PDF–160K
A method for detecting and correcting feature misidentification on expression microarrays
I-Ping Tu, Marci Schaner, Maximilian Diehn, Branimir I Sikic, Patrick O Brown, David Botstein, Michael J Fero
BMC Genomics. 2004; 5: 64. Published online 2004 September 9. doi: 10.1186/1471-2164-5-64
PMCID:
PMC521069
Abstract Full Text PDF–1.4M
SED, a normalization free method for DNA microarray data analysis
Huajun Wang, Hui Huang
BMC Bioinformatics. 2004; 5: 121. Published online 2004 September 2. doi: 10.1186/1471-2105-5-121
PMCID:
PMC517708
Abstract Full Text PDF–278K
Joint analysis of two microarray gene-expression data sets to select lung adenocarcinoma marker genes
Hongying Jiang, Youping Deng, Huann-Sheng Chen, Lin Tao, Qiuying Sha, Jun Chen, Chung-Jui Tsai, Shuanglin Zhang
BMC Bioinformatics. 2004; 5: 81. Published online 2004 June 24. doi: 10.1186/1471-2105-5-81
PMCID:
PMC476733
Abstract Full Text PDF–1.4M Supplementary Material
Neural network analysis of lymphoma microarray data: prognosis and diagnosis near-perfect
Michael C O'Neill, Li Song
BMC Bioinformatics. 2003; 4: 13. Published online 2003 April 10. doi: 10.1186/1471-2105-4-13
PMCID:
PMC155539
Abstract Full Text PDF–414K
Supervised clustering of genes
Marcel Dettling, Peter Bühlmann
Genome Biol. 2002; 3(12): research0069.1–research0069.15. Published online 2002 November 25.
PMCID:
PMC151171
Abstract Full Text PDF–176K
Permutation-validated principal components analysis of microarray data
Jobst Landgrebe, Wolfgang Wurst, Gerhard Welzl
Genome Biol. 2002; 3(4): research0019.1–research0019.11. Published online 2002 March 22.
PMCID:
PMC115254
Abstract Full Text PDF–353K
Expression Profiling of Human Tumors: The End of Surgical Pathology?
Marc Ladanyi, Wing C. Chan, Timothy J. Triche, William L. Gerald
J Mol Diagn. 2001 August; 3(3): 92–97.
PMCID:
PMC1906955
Full Text PDF–63K
Supervised harvesting of expression trees
Trevor Hastie, Robert Tibshirani, David Botstein, Patrick Brown
Genome Biol. 2001; 2(1): research0003.1–research0003.12. Published online 2001 January 10.
PMCID:
PMC17599
Abstract Full Text PDF–1.4M Supplementary Material
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