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Clustering analysis of SAGE data using a Poisson approach
Li Cai, Haiyan Huang, Seth Blackshaw, Jun S Liu, Connie Cepko, Wing H Wong
Genome Biol. 2004; 5(7): R51. Published online 2004 June 29. doi: 10.1186/gb-2004-5-7-r51
PMCID:
PMC463327
Abstract Full Text PDF–328K Supplementary Material

Is Cited by the Following 20 Articles in this Archive:

Comparison of Gene Expression and Genome-Wide DNA Methylation Profiling between Phenotypically Normal Cloned Pigs and Conventionally Bred Controls
Fei Gao, Yonglun Luo, Shengting Li, Jian Li, Lin Lin, Anders Lade Nielsen, Charlotte Brandt Sørensen, Gábor Vajta, Jun Wang, Xiuqing Zhang, Yutao Du, Huanming Yang, Lars Bolund
PLoS One. 2011; 6(10): e25901. Published online 2011 October 11. doi: 10.1371/journal.pone.0025901
PMCID:
PMC3191147
Abstract Full Text PDF–1.1M Supplementary Material
Gene expression profiling of human breast tissue samples using SAGE-Seq
Zhenhua Jeremy Wu, Clifford A. Meyer, Sibgat Choudhury, Michail Shipitsin, Reo Maruyama, Marina Bessarabova, Tatiana Nikolskaya, Saraswati Sukumar, Armin Schwartzman, Jun S. Liu, Kornelia Polyak, X. Shirley Liu
Genome Res. 2010 December; 20(12): 1730–1739. doi: 10.1101/gr.108217.110
PMCID:
PMC2989999
Abstract Full Text PDF–888K
LNCaP Atlas: Gene expression associated with in vivo progression to castration-recurrent prostate cancer
Tammy L Romanuik, Gang Wang, Olena Morozova, Allen Delaney, Marco A Marra, Marianne D Sadar
BMC Med Genomics. 2010; 3: 43. Published online 2010 September 24. doi: 10.1186/1755-8794-3-43
PMCID:
PMC2956710
Abstract Full Text PDF–781K Supplementary Material
Genomic analysis distinguishes phases of early development of the mouse atrio-ventricular canal
Pavle Vrljicak, Alex C. Y. Chang, Olena Morozova, Elizabeth D. Wederell, Kyle Niessen, Marco A. Marra, Aly Karsan, Pamela A. Hoodless
Physiol Genomics. 2010 February; 40(3): 150–157. Published online 2009 December 1. doi: 10.1152/physiolgenomics.00142.2009
PMCID:
PMC2825764
Abstract Full Text
The maize root stem cell niche: a partnership between two sister cell populations
Keni Jiang, Tong Zhu, Zhaoyan Diao, Haiyan Huang, Lewis J. Feldman
Planta. 2010 January; 231(2): 411–424. Published online 2009 November 22. doi: 10.1007/s00425-009-1059-3
PMCID:
PMC2799627
Abstract Full Text PDF–1.2M Supplementary Material
Significance Analysis of Spectral Count Data in Label-free Shotgun Proteomics
Hyungwon Choi, Damian Fermin, Alexey I. Nesvizhskii
Mol Cell Proteomics. 2008 December; 7(12): 2373–2385. doi: 10.1074/mcp.M800203-MCP200
PMCID:
PMC2596341
Abstract Full Text Supplementary Material
A Seriation Approach for Visualization-Driven Discovery of Co-Expression Patterns in Serial Analysis of Gene Expression (SAGE) Data
Olena Morozova, Vyacheslav Morozov, Brad G. Hoffman, Cheryl D. Helgason, Marco A. Marra
PLoS ONE. 2008; 3(9): e3205. Published online 2008 September 12. doi: 10.1371/journal.pone.0003205
PMCID:
PMC2527533
Abstract Full Text PDF–734K Supplementary Material
Clustering-based approaches to SAGE data mining
Haiying Wang, Huiru Zheng, Francisco Azuaje
BioData Min. 2008; 1: 5. Published online 2008 July 17. doi: 10.1186/1756-0381-1-5
PMCID:
PMC2553774
Abstract Full Text PDF–446K
An en masse phenotype and function prediction system for Mus musculus
Murat Taşan, Weidong Tian, David P Hill, Francis D Gibbons, Judith A Blake, Frederick P Roth
Genome Biol. 2008; 9(Suppl 1): S8. Published online 2008 June 27. doi: 10.1186/gb-2008-9-s1-s8
PMCID:
PMC2447542
Abstract Full Text PDF–2.8M Supplementary Material
Identification of transcripts with enriched expression in the developing and adult pancreas
Brad G Hoffman, Bogard Zavaglia, Joy Witzsche, Teresa Ruiz de Algara, Mike Beach, Pamela A Hoodless, Steven JM Jones, Marco A Marra, Cheryl D Helgason
Genome Biol. 2008; 9(6): R99. Published online 2008 June 14. doi: 10.1186/gb-2008-9-6-r99
PMCID:
PMC2481431
Abstract Full Text PDF–2.2M Supplementary Material
Using a Seed-Network to Query Multiple Large-Scale Gene Expression Datasets from the Developing Retina in Order to Identify and Prioritize Experimental Targets
Laura A. Hecker, Timothy C. Alcon, Vasant G. Honavar, M. Heather West Greenlee
Bioinform Biol Insights. 2008; 2: 401–412. Published online 2008 February 1.
PMCID:
PMC2735966
Abstract Full Text PDF–636K Supplementary Material
Modeling SAGE tag formation and its effects on data interpretation within a Bayesian framework
Michael A Gilchrist, Hong Qin, Russell Zaretzki
BMC Bioinformatics. 2007; 8: 403. Published online 2007 October 18. doi: 10.1186/1471-2105-8-403
PMCID:
PMC2217564
Abstract Full Text PDF–408K Supplementary Material
Simcluster: clustering enumeration gene expression data on the simplex space
Ricardo ZN Vêncio, Leonardo Varuzza, Carlos A de B Pereira, Helena Brentani, Ilya Shmulevich
BMC Bioinformatics. 2007; 8: 246. Published online 2007 July 11. doi: 10.1186/1471-2105-8-246
PMCID:
PMC2147035
Abstract Full Text PDF–418K Supplementary Material
LongSAGE analysis of skeletal muscle at three prenatal stages in Tongcheng and Landrace pigs
Zhonglin Tang, Yong Li, Ping Wan, Xiaoping Li, Shuhong Zhao, Bang Liu, Bin Fan, Mengjin Zhu, Mei Yu, Kui Li
Genome Biol. 2007; 8(6): R115. Published online 2007 June 16. doi: 10.1186/gb-2007-8-6-r115
PMCID:
PMC2394763
Abstract Full Text PDF–498K Supplementary Material
Large-scale clustering of CAGE tag expression data
Kazuro Shimokawa, Yuko Okamura-Oho, Takio Kurita, Martin C Frith, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki
BMC Bioinformatics. 2007; 8: 161. Published online 2007 May 21. doi: 10.1186/1471-2105-8-161
PMCID:
PMC1890301
Abstract Full Text PDF–602K
Heritable clustering and pathway discovery in breast cancer integrating epigenetic and phenotypic data
Zailong Wang, Pearlly Yan, Dustin Potter, Charis Eng, Tim H-M Huang, Shili Lin
BMC Bioinformatics. 2007; 8: 38. Published online 2007 February 1. doi: 10.1186/1471-2105-8-38
PMCID:
PMC1800873
Abstract Full Text PDF–374K
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
Machine learning approaches to supporting the identification of photoreceptor-enriched genes based on expression data
Haiying Wang, Huiru Zheng, David Simpson, Francisco Azuaje
BMC Bioinformatics. 2006; 7: 116. Published online 2006 March 8. doi: 10.1186/1471-2105-7-116
PMCID:
PMC1421439
Abstract Full Text PDF–389K Supplementary Material
GO-Diff: Mining functional differentiation between EST-based transcriptomes
Zuozhou Chen, Weilin Wang, Xuefeng Bruce Ling, Jane Jijun Liu, Liangbiao Chen
BMC Bioinformatics. 2006; 7: 72. Published online 2006 February 16. doi: 10.1186/1471-2105-7-72
PMCID:
PMC1388240
Abstract Full Text PDF–489K Supplementary Material
Theme discovery from gene lists for identification and viewing of multiple functional groups
Petri Pehkonen, Garry Wong, Petri Törönen
BMC Bioinformatics. 2005; 6: 162. Published online 2005 June 29. doi: 10.1186/1471-2105-6-162
PMCID:
PMC1190153
Abstract Full Text PDF–1.1M Supplementary Material
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