Normalization Benefits Microarray-Based Classification (2006)
Jianping Hua, Yoganand Balagurunathan, Yidong Chen, James Lowey, Michael L. Bittner, Zixiang Xiong, ...
When using cDNA microarrays, normalization to correct labeling bias is a common preliminary step before further data analysis is applied, its objective being to reduce the variation between arrays....
Huang, Shixia, Li, Yi, Chen, Yidong, Podsypanina, Katrina, Chamorro, Mario, Olshen, Adam B, ...
Abstract Background In human breast cancer normal mammary cells typically develop into hyperplasia, ductal carcinoma in situ , invasive cancer, and metastasis. The changes in gene expression...
Yoganand Balagurunathan (2004)
Yoganand Balagurunathan, Naisyin Wang, Edward R. Dougherty, Danh Nguyen, Yidong Chen, Michael L. Bittner, ...
A microarray-image model is used that takes into account many factors, including spot morphology, signal strength, background fluorescent noise, and shape and surface degradation. The model yields...
Xiongwu Wu, Yidong Chen, Bernard R. Brooks, Yan A. Su
An unsupervised data clustering method, called the local maximum clustering (LMC) method, is proposed for identifying clusters in experiment data sets based on research interest. A magnitude property...
Analysis of expression patterns: The scope of (2003)
Yidong Chen, Zohar Yakhini, Amir Ben-dor, Edward Dougherty, Jeffrey M. Trent, Michael Bittner, ...
Introduction The profiling of transcription patterns is a central and long-standing tool in molecular biology. Recently, it has become possible to gather this kind of data for many genes...
Analysis of expression patterns: The scope of (2003)
Yidong Chen, Zohar Yakhini, Amir Ben-dor, Edward Dougherty, Jeffrey M. Trent, Michael Bittner, ...
Introduction The profiling of transcription patterns is a central and long-standing tool in molecular biology. Recently, it has become possible to gather this kind of data for many genes...
Journal of Biological Systems, Vol. 10, No. 4 (2002) 337--357 c (2003)
Seungchan Kim, Edward R. Dougherty, Yidong Chen, Michael Bittner, Edward B. Suh
this paper is relatively small, it suggests that models incorporating rule-based transitions among states have a capacity to mimic biology. The ability of such models to enhance our understanding of...
Ratio-Based Decisions And The (2003)
Yidong Chen, Edward R. Dougherty, Michael L. Bittner
Gene expression can be quantitatively analyzed by hybridizing fluor-tagged mRNA to targets on a cDNA microarray. Comparison of gene expression levels arising from cohybridized samples is achieved by...
Yidong Chen, Edward R. Dougherty, L. Bittner, Paul S. Meltzer, Jeffery M. Trent
Motivation: Expression-based analysis for large families of genes has recently become possible owing to the development of cDNA microarrays, which allow simultaneous measurement of transcript levels...
Simulation of cDNA microarrays via a parameterized (2003)
Yoganand Balagurunathan, Edward R. Dougherty, Yidong Chen, Michael L. Bittner, J. M. Trent
cDNA microarrays provide simultaneous expression measurements for thousands of genes that are the result of processing images to recover the average signal intensity from a spot composed of pixels...
Ratio-Based Decisions And The (2003)
Yidong Chen, Edward R. Dougherty, Michael L. Bittner
Gene expression can be quantitatively analyzed by hybridizing fluor-tagged mRNA to targets on a cDNA microarray. Comparison of gene expression levels arising from cohybridized samples is achieved by...
Yidong Chen, Edward R. Dougherty, L. Bittner, Paul S. Meltzer, Jeffery M. Trent
Motivation: Expression-based analysis for large families of genes has recently become possible owing to the development of cDNA microarrays, which allow simultaneous measurement of transcript levels...
General Nonlinear Framework for the Analysis of Gene (2003)
Seungchan Kim, Edward R. Dougherty, Michael L. Bittner, Yidong Chen, Krishnamoorthy Sivakumar, Paul Meltzer, ...
A cDNA microarray is a complex biochemical-optical system whose purpose is the simultaneous measurement of gene expression for thousands of genes. In this paper we propose a general statistical...
Corresponding author. Tel.: 1-409-862-8154; fax: 1-409-862-3336. (2003)
Edward R. Dougherty, Seungchan Kim, Yidong Chen
For statistical design of an optimal "lter, it is probabilistically advantageous to employ a large number of observation random variables; however, estimation error increases with the number of...
Can Markov Chain Models Mimic Biological Regulation? (2003)
Seungchan Kim, Edward R. Dougherty, Yidong Chen, Michael Bittner, Edward B. Suh
this paper is relatively small, it suggests that models incorporating rule-based transitions among states have a capacity to mimic biology. The ability of such models to enhance our understanding of...
Coefficient of Determination in Nonlinear Signal Processing (2003)
Edward R. Dougherty, Seungchan Kim, Yidong Chen
For statistical design of an optimal filter, it is probabilistically advantageous to employ a large number of observation random variables; however, estimation error increases with the number of...
Seungchan Kim, Edward R. Dougherty, Michael L. Bittner, Yidong Chen, Krishnamoorthy Sivakumar, Paul Meltzer, ...
A cDNA microarray is a complex biochemical-optical system whose purpose is the simultaneous measurement of gene expression for thousands of genes. In this paper we propose a general statistical...
Abdelghani Bellaachia, David Portnoy, Yidong Chen, Abdel G. Elkahloun
Data clustering methods have been proven to be a successful data mining technique in the analysis of gene expression data. The Cluster affinity search technique (CAST) developed by Ben-Dor, et. al.,...
Typescript.
Chen, Yidong, Dougherty, Edward, Totterman, Saara, Hornak, Joseph
Article may be found at: http://www3.interscience.wiley.com/cgi-bin/abstract/112150097/ABSTRACT
Chen, Yidong, Dougherty, Edward, Totterman, Saara, Hornak, Joseph
Article may be found at: http://www3.interscience.wiley.com/cgi-bin/abstract/112150097/ABSTRACT
Comprehensive copy number and gene expression profiling of the 17q23 amplicon in human breast cancer
Monni, Outi, Bärlund, Maarit, Mousses, Spyro, Kononen, Juha, Sauter, Guido, Heiskanen, Mervi, ...
The biological significance of DNA amplification in cancer is thought to be due to the selection of increased expression of a single or few important genes. However, systematic surveys of the copy...
Molecular characteristics of non-small cell lung cancer
Nacht, Mariana, Dracheva, Tatiana, Gao, Yuhong, Fujii, Takeshi, Chen, Yidong, Player, Audrey, ...
We used hierarchical clustering to examine gene expression profiles generated by serial analysis of gene expression (SAGE) in a total of nine normal lung epithelial cells and non-small cell lung...
Transcription Program of Human Herpesvirus 8 (Kaposi's Sarcoma-Associated Herpesvirus)
Paulose-Murphy, Mini, Ha, Nguyen-Khoi, Xiang, Chunsheng, Chen, Yidong, Gillim, Laura, Yarchoan, Robert, ...
Human herpesvirus 8 (HHV-8), a gammaherpesvirus implicated in Kaposi's sarcoma, primary effusion lymphoma, and Castleman's disease, encodes several pathogenically important cellular homologs. To...
Mutation of melanosome protein RAB38 in chocolate mice
Loftus, Stacie K., Larson, Denise M., Baxter, Laura L., Antonellis, Anthony, Chen, Yidong, Wu, Xufeng, ...
Mutations of genes needed for melanocyte function can result in oculocutaneous albinism. Examination of similarities in human gene expression patterns by using microarray analysis reveals that RAB38,...
Molecular classification of familial non-BRCA1/BRCA2 breast cancer
Hedenfalk, Ingrid, Ringnér, Markus, Ben-Dor, Amir, Yakhini, Zohar, Chen, Yidong, Chebil, Gunilla, ...
In the decade since their discovery, the two major breast cancer susceptibility genes BRCA1 and BRCA2, have been shown conclusively to be involved in a significant fraction of families segregating...
Changes in gene expression during the development of mammary tumors in MMTV-Wnt-1 transgenic mice
Huang, Shixia, Li, Yi, Chen, Yidong, Podsypanina, Katrina, Chamorro, Mario, Olshen, Adam B, ...
cDNA microarray-derived expression profiles of MMTV-Wnt-1 and MMTV-Neu transgenic mice reveal several hundred genes to be differentially expressed at each stage of breast tumor development.
Yen, Paul M., Feng, Xu, Flamant, Frederic, Chen, Yidong, Walker, Robert L., Weiss, Roy E., ...
Little is known about the overall patterns of thyroid hormone (Th)-mediated gene regulation by the main Th receptor (Tr) isoforms, Tr-α and Tr-β, in vivo. We used 48 complementary DNA microarrays...
Crawford, Gregory E., Holt, Ingeborg E., Whittle, James, Webb, Bryn D., Tai, Denise, Davis, Sean, ...
A major goal in genomics is to understand how genes are regulated in different tissues, stages of development, diseases, and species. Mapping DNase I hypersensitive (HS) sites within nuclear...
Wolf, Maija, Mousses, Spyro, Hautaniemi, Sampsa, Karhu, Ritva, Huusko, Pia, Allinen, Minna, ...
Identification of target genes for genetic rearrangements in prostate cancer and the impact of copy number changes on gene expression are currently not well understood. Here, we applied...
Comprehensive copy number and gene expression profiling of the 17q23 amplicon in human breast cancer
Monni, Outi, Bärlund, Maarit, Mousses, Spyro, Kononen, Juha, Sauter, Guido, Heiskanen, Mervi, ...
The biological significance of DNA amplification in cancer is thought to be due to the selection of increased expression of a single or few important genes. However, systematic surveys of the copy...
Molecular characteristics of non-small cell lung cancer
Nacht, Mariana, Dracheva, Tatiana, Gao, Yuhong, Fujii, Takeshi, Chen, Yidong, Player, Audrey, ...
We used hierarchical clustering to examine gene expression profiles generated by serial analysis of gene expression (SAGE) in a total of nine normal lung epithelial cells and non-small cell lung...
Transcription Program of Human Herpesvirus 8 (Kaposi's Sarcoma-Associated Herpesvirus)
Paulose-Murphy, Mini, Ha, Nguyen-Khoi, Xiang, Chunsheng, Chen, Yidong, Gillim, Laura, Yarchoan, Robert, ...
Human herpesvirus 8 (HHV-8), a gammaherpesvirus implicated in Kaposi's sarcoma, primary effusion lymphoma, and Castleman's disease, encodes several pathogenically important cellular homologs. To...
Mutation of melanosome protein RAB38 in chocolate mice
Loftus, Stacie K., Larson, Denise M., Baxter, Laura L., Antonellis, Anthony, Chen, Yidong, Wu, Xufeng, ...
Mutations of genes needed for melanocyte function can result in oculocutaneous albinism. Examination of similarities in human gene expression patterns by using microarray analysis reveals that RAB38,...
Molecular classification of familial non-BRCA1/BRCA2 breast cancer
Hedenfalk, Ingrid, Ringnér, Markus, Ben-Dor, Amir, Yakhini, Zohar, Chen, Yidong, Chebil, Gunilla, ...
In the decade since their discovery, the two major breast cancer susceptibility genes BRCA1 and BRCA2, have been shown conclusively to be involved in a significant fraction of families segregating...
Changes in gene expression during the development of mammary tumors in MMTV-Wnt-1 transgenic mice
Huang, Shixia, Li, Yi, Chen, Yidong, Podsypanina, Katrina, Chamorro, Mario, Olshen, Adam B, ...
cDNA microarray-derived expression profiles of MMTV-Wnt-1 and MMTV-Neu transgenic mice reveal several hundred genes to be differentially expressed at each stage of breast tumor development.
Yen, Paul M., Feng, Xu, Flamant, Frederic, Chen, Yidong, Walker, Robert L., Weiss, Roy E., ...
Little is known about the overall patterns of thyroid hormone (Th)-mediated gene regulation by the main Th receptor (Tr) isoforms, Tr-α and Tr-β, in vivo. We used 48 complementary DNA microarrays...
Crawford, Gregory E., Holt, Ingeborg E., Whittle, James, Webb, Bryn D., Tai, Denise, Davis, Sean, ...
A major goal in genomics is to understand how genes are regulated in different tissues, stages of development, diseases, and species. Mapping DNase I hypersensitive (HS) sites within nuclear...
Wolf, Maija, Mousses, Spyro, Hautaniemi, Sampsa, Karhu, Ritva, Huusko, Pia, Allinen, Minna, ...
Identification of target genes for genetic rearrangements in prostate cancer and the impact of copy number changes on gene expression are currently not well understood. Here, we applied...
A Novel Role of Myosin VI in Human Prostate Cancer
Dunn, Thomas A., Chen, Shenglin, Faith, Dennis A., Hicks, Jessica L., Platz, Elizabeth A., Chen, Yidong, ...
Myosin VI is an actin motor that moves to the minus end of the polarized actin filament, a direction opposite to all other characterized myosins. Using expression microarrays, we identified myosin VI...
Allander, Susanne V., Illei, Peter B., Chen, Yidong, Antonescu, Cristina R., Bittner, Mike, Ladanyi, Marc, ...
Synovial sarcoma is an aggressive spindle cell sarcoma with two major histological subtypes, biphasic and monophasic, defined respectively by the presence or absence of areas of glandular epithelial...
Huang, Shixia, Chen, Yidong, Podsypanina, Katrina, Li, Yi
Distant metastases of human breast cancers have been suggested to be more different from each other than from their respective primary tumors, based on expression profiling. The mechanism behind this...
Normalization Benefits Microarray-Based Classification
Hua, Jianping, Balagurunathan, Yoganand, Chen, Yidong, Lowey, James, Bittner, Michael L., Xiong, Zixiang, ...
When using cDNA microarrays, normalization to correct labeling bias is a common preliminary step before further data analysis is applied, its objective being to reduce the variation between arrays....