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A prediction-based resampling method for estimating the number of clusters in a dataset
Sandrine Dudoit, Jane Fridlyand
Genome Biol. 2002; 3(7): research0036.1–research0036.21. Published online 2002 June 25.
PMCID:
PMC126241
Abstract Full Text PDF–484K

Is Cited by the Following 34 Articles in this Archive:

Integrative Subtype Discovery in Glioblastoma Using iCluster
Ronglai Shen, Qianxing Mo, Nikolaus Schultz, Venkatraman E. Seshan, Adam B. Olshen, Jason Huse, Marc Ladanyi, Chris Sander
PLoS One. 2012; 7(4): e35236. Published online 2012 April 23. doi: 10.1371/journal.pone.0035236
PMCID:
PMC3335101
Abstract Full Text PDF–910K Supplementary Material
Genome-wide analysis distinguishes hyperglycemia regulated epigenetic signatures of primary vascular cells
Luciano Pirola, Aneta Balcerczyk, Richard W. Tothill, Izhak Haviv, Antony Kaspi, Sebastian Lunke, Mark Ziemann, Tom Karagiannis, Stephen Tonna, Adam Kowalczyk, Bryan Beresford-Smith, Geoff Macintyre, Ma Kelong, Zhang Hongyu, Jingde Zhu, Assam El-Osta
Genome Res. 2011 October; 21(10): 1601–1615. doi: 10.1101/gr.116095.110
PMCID:
PMC3202278
Abstract Full Text PDF–1.7M
Transcriptional profiling of fetal hypothalamic TRH neurons
Magdalena Guerra-Crespo, Carlos Pérez-Monter, Sarath Chandra Janga, Santiago Castillo-Ramírez, Rosa María Gutiérrez-Rios, Patricia Joseph-Bravo, Leonor Pérez-Martínez, Jean-Louis Charli
BMC Genomics. 2011; 12: 222. Published online 2011 May 10. doi: 10.1186/1471-2164-12-222
PMCID:
PMC3126781
Abstract Full Text PDF–645K
Speeding up the Consensus Clustering methodology for microarray data analysis
Raffaele Giancarlo, Filippo Utro
Algorithms Mol Biol. 2011; 6: 1. Published online 2011 January 14. doi: 10.1186/1748-7188-6-1
PMCID:
PMC3035181
Abstract Full Text PDF–628K
Merged consensus clustering to assess and improve class discovery with microarray data
T Ian Simpson, J Douglas Armstrong, Andrew P Jarman
BMC Bioinformatics. 2010; 11: 590. Published online 2010 December 3. doi: 10.1186/1471-2105-11-590
PMCID:
PMC3002369
Abstract Full Text PDF–496K Supplementary Material
Identification of common microRNA-mRNA regulatory biomodules in human epithelial cancers
Xinan Yang, Younghee Lee, Hong Fan, Xiao Sun, Yves A Lussier
Chin Sci Bull. Author manuscript; available in PMC 2011 February 16.
Published in final edited form as: Chin Sci Bull. 2010 November; 55(31): 3576–3589. doi: 10.1007/s11434-010-4051-1
PMCID:
PMC3039912
Abstract Full Text PDF–1.2M Supplementary Material
Hepatic microRNA expression is associated with the response to interferon treatment of chronic hepatitis C
Yoshiki Murakami, Masami Tanaka, Hidenori Toyoda, Katsuyuki Hayashi, Masahiko Kuroda, Atsushi Tajima, Kunitada Shimotohno
BMC Med Genomics. 2010; 3: 48. Published online 2010 October 22. doi: 10.1186/1755-8794-3-48
PMCID:
PMC2984584
Abstract Full Text PDF–1.3M Supplementary Material
Dynamics of dendritic cell maturation are identified through a novel filtering strategy applied to biological time-course microarray replicates
Amy L Olex, Elizabeth M Hiltbold, Xiaoyan Leng, Jacquelyn S Fetrow
BMC Immunol. 2010; 11: 41. Published online 2010 August 3. doi: 10.1186/1471-2172-11-41
PMCID:
PMC2928180
Abstract Full Text PDF–1.6M Supplementary Material
Analysis of protein complexes through model-based biclustering of label-free quantitative AP-MS data
Hyungwon Choi, Sinae Kim, Anne-Claude Gingras, Alexey I Nesvizhskii
Mol Syst Biol. 2010; 6: 385. Published online 2010 June 22. doi: 10.1038/msb.2010.41
PMCID:
PMC2913403
Abstract Full Text PDF–1.6M Supplementary Material
Identifying Prototypical Components in Behaviour Using Clustering Algorithms
Elke Braun, Bart Geurten, Martin Egelhaaf
PLoS One. 2010; 5(2): e9361. Published online 2010 February 22. doi: 10.1371/journal.pone.0009361
PMCID:
PMC2825265
Abstract Full Text PDF–1.9M Supplementary Material
MULTI-K: accurate classification of microarray subtypes using ensemble k-means clustering
Eun-Youn Kim, Seon-Young Kim, Daniel Ashlock, Dougu Nam
BMC Bioinformatics. 2009; 10: 260. Published online 2009 August 22. doi: 10.1186/1471-2105-10-260
PMCID:
PMC2743671
Abstract Full Text PDF–876K Supplementary Material
Transcriptional profiling of human cavernosal endothelial cells reveals distinctive cell adhesion phenotype and role for claudin 11 in vascular barrier function
Hunter Wessells, Chris J. Sullivan, Yoshiaki Tsubota, Karen L. Engel, Bryan Kim, N. Eric Olson, Daniel Thorner, Kanchan Chitaley
Physiol Genomics. 2009 October; 39(2): 100–108. Published online 2009 July 21. doi: 10.1152/physiolgenomics.90354.2008
PMCID:
PMC2765067
Abstract Full Text
Natural genetic variation in transcriptome reflects network structure inferred with major effect mutations: insulin/TOR and associated phenotypes in Drosophila melanogaster
Sergey V Nuzhdin, Jennifer A Brisson, Andrew Pickering, Marta L Wayne, Lawrence G Harshman, Lauren M McIntyre
BMC Genomics. 2009; 10: 124. Published online 2009 March 24. doi: 10.1186/1471-2164-10-124
PMCID:
PMC2674066
Abstract Full Text PDF–671K Supplementary Material
Cbf genes of the Fr-A2 allele are differentially regulated between long-term cold acclimated crown tissue of freeze-resistant and – susceptible, winter wheat mutant lines
Fedora Sutton, Ding-Geng Chen, Xijin Ge, Don Kenefick
BMC Plant Biol. 2009; 9: 34. Published online 2009 March 23. doi: 10.1186/1471-2229-9-34
PMCID:
PMC2663559
Abstract Full Text PDF–650K
NIFTI: An evolutionary approach for finding number of clusters in microarray data
Sudhakar Jonnalagadda, Rajagopalan Srinivasan
BMC Bioinformatics. 2009; 10: 40. Published online 2009 January 30. doi: 10.1186/1471-2105-10-40
PMCID:
PMC2669482
Abstract Full Text PDF–781K Supplementary Material
WGCNA: an R package for weighted correlation network analysis
Peter Langfelder, Steve Horvath
BMC Bioinformatics. 2008; 9: 559. Published online 2008 December 29. doi: 10.1186/1471-2105-9-559
PMCID:
PMC2631488
Abstract Full Text PDF–1.7M
Computational cluster validation for microarray data analysis: experimental assessment of Clest, Consensus Clustering, Figure of Merit, Gap Statistics and Model Explorer
Raffaele Giancarlo, Davide Scaturro, Filippo Utro
BMC Bioinformatics. 2008; 9: 462. Published online 2008 October 29. doi: 10.1186/1471-2105-9-462
PMCID:
PMC2657801
Abstract Full Text PDF–1.1M
An Integrative Analysis of microRNA and mRNA Expression—A Case Study
Li-Xuan Qin
Cancer Inform. 2008; 6: 369–379. Published online 2008 June 17.
PMCID:
PMC2623315
Abstract Full Text PDF–702K Supplementary Material
Using iterative cluster merging with improved gap statistics to perform online phenotype discovery in the context of high-throughput RNAi screens
Zheng Yin, Xiaobo Zhou, Chris Bakal, Fuhai Li, Youxian Sun, Norbert Perrimon, Stephen TC Wong
BMC Bioinformatics. 2008; 9: 264. Published online 2008 June 5. doi: 10.1186/1471-2105-9-264
PMCID:
PMC2443381
Abstract Full Text PDF–3.2M Supplementary Material
Genetic weighted k-means algorithm for clustering large-scale gene expression data
Fang-Xiang Wu
BMC Bioinformatics. 2008; 9(Suppl 6): S12. Published online 2008 May 28. doi: 10.1186/1471-2105-9-S6-S12
PMCID:
PMC2423435
Abstract Full Text PDF–278K
Discovering multi–level structures in bio-molecular data through the Bernstein inequality
Alberto Bertoni, Giorgio Valentini
BMC Bioinformatics. 2008; 9(Suppl 2): S4. Published online 2008 March 26. doi: 10.1186/1471-2105-9-S2-S4
PMCID:
PMC2323667
Abstract Full Text PDF–396K
Bayesian Weibull tree models for survival analysis of clinico-genomic data
Jennifer Clarke, Mike West
Stat Methodol. Author manuscript; available in PMC 2008 July 10.
Published in final edited form as: Stat Methodol. 2008; 5(3): 238–262.
PMCID:
PMC2447923
Abstract Full Text PDF–1.6M
Cell Cycle Genes Are the Evolutionarily Conserved Targets of the E2F4 Transcription Factor
Caitlin M. Conboy, Christiana Spyrou, Natalie P. Thorne, Elizabeth J. Wade, Nuno L. Barbosa-Morais, Michael D. Wilson, Arindam Bhattacharjee, Richard A. Young, Simon Tavaré, Jacqueline A. Lees, Duncan T. Odom
PLoS ONE. 2007; 2(10): e1061. Published online 2007 October 24. doi: 10.1371/journal.pone.0001061
PMCID:
PMC2020443
Abstract Full Text PDF–345K Supplementary Material
Model order selection for bio-molecular data clustering
Alberto Bertoni, Giorgio Valentini
BMC Bioinformatics. 2007; 8(Suppl 2): S7. Published online 2007 May 3. doi: 10.1186/1471-2105-8-S2-S7
PMCID:
PMC1892076
Abstract Full Text PDF–369K
Recursive Cluster Elimination (RCE) for classification and feature selection from gene expression data
Malik Yousef, Segun Jung, Louise C Showe, Michael K Showe
BMC Bioinformatics. 2007; 8: 144. Published online 2007 May 2. doi: 10.1186/1471-2105-8-144
PMCID:
PMC1877816
Abstract Full Text PDF–419K Supplementary Material
Functional genomics analysis of low concentration of ethanol in human hepatocellular carcinoma (HepG2) cells. Role of genes involved in transcriptional and translational processes
Francisco Castaneda, Sigrid Rosin-Steiner, Klaus Jung
Int J Med Sci. 2007; 4(1): 28–35. Published online 2006 December 21.
PMCID:
PMC1752234
Abstract Full Text PDF–410K
Cluster analysis of protein array results via similarity of Gene Ontology annotation
Cheryl Wolting, C Jane McGlade, David Tritchler
BMC Bioinformatics. 2006; 7: 338. Published online 2006 July 12. doi: 10.1186/1471-2105-7-338
PMCID:
PMC1539024
Abstract Full Text PDF–541K Supplementary Material
Intra- and Interindividual Epigenetic Variation in Human Germ Cells
James M. Flanagan, Violeta Popendikyte, Natalija Pozdniakovaite, Martha Sobolev, Abbas Assadzadeh, Axel Schumacher, Masood Zangeneh, Lynette Lau, Carl Virtanen, Sun-Chong Wang, Arturas Petronis
Am J Hum Genet. 2006 July; 79(1): 67–84. Published online 2006 May 25.
PMCID:
PMC1474120
Abstract Full Text PDF–3.2M
Classification and risk stratification of invasive breast carcinomas using a real-time quantitative RT-PCR assay
Laurent Perreard, Cheng Fan, John F Quackenbush, Michael Mullins, Nicholas P Gauthier, Edward Nelson, Mary Mone, Heidi Hansen, Saundra S Buys, Karen Rasmussen, Alejandra Ruiz Orrico, Donna Dreher, Rhonda Walters, Joel Parker, Zhiyuan Hu, Xiaping He, Juan P Palazzo, Olufunmilayo I Olopade, Aniko Szabo, Charles M Perou, Philip S Bernard
Breast Cancer Res. 2006; 8(2): R23. Published online 2006 April 20. doi: 10.1186/bcr1399
PMCID:
PMC1557722
Abstract Full Text PDF–1.4M Supplementary Material
Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts
Yudi Pawitan, Judith Bjöhle, Lukas Amler, Anna-Lena Borg, Suzanne Egyhazi, Per Hall, Xia Han, Lars Holmberg, Fei Huang, Sigrid Klaar, Edison T Liu, Lance Miller, Hans Nordgren, Alexander Ploner, Kerstin Sandelin, Peter M Shaw, Johanna Smeds, Lambert Skoog, Sara Wedrén, Jonas Bergh
Breast Cancer Res. 2005; 7(6): R953–R964. Published online 2005 October 3. doi: 10.1186/bcr1325
PMCID:
PMC1410752
Abstract Full Text PDF–1.4M Supplementary Material
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