Modeling Cancer Progression via Pathway Dependencies (2008)
Elena J. Edelman, Justin Guinney, Jen-Tsan Chi, Phillip G. Febbo, Sayan Mukherjee
Cancer is a heterogeneous disease often requiring a complexity of alterations to drive a normal cell to a malignancy and ultimately to a metastatic state. Certain genetic perturbations have been...
Jen-Tsan Chi, Edwin H. Rodriguez, Zhen Wang, Sayan Mukherjee, ...
Smooth muscle is present in a wide variety of anatomical locations, such as blood vessels, various visceral organs, and hair follicles. Contraction of smooth muscle is central to functions as diverse...
Predicting a local recurrence after breast-conserving therapy by gene expression profiling (2006)
Nuyten, Dimitry SA, Kreike, Bas, Hart, Augustinus AM, Chi, Jen-Tsan, Sneddon, Julie B, Wessels, Lodewyk FA, ...
Abstract Introduction To tailor local treatment in breast cancer patients there is a need for predicting ipsilateral recurrences after breast-conserving therapy. After adequate treatment (excision...
Jen-Tsan Chi, Zhen Wang, Edwin H. Rodriguez, Marci E. Schaner, Ali Salim, ...
The transcriptional response to hypoxia varies between cell types. A gene-expression signature of the cellular response to hypoxia is associated with a significantly poorer prognosis in breast and...
Jen-Tsan Chi, Zhen Wang, Edwin H. Rodriguez, Marci E. Schaner, Ali Salim, ...
Background Inadequate oxygen (hypoxia) triggers a multifaceted cellular response that has important roles in normal physiology and in many human diseases. A transcription factor, hypoxia-inducible...
Howard Y. Chang, Julie B. Sneddon, Ash A. Alizadeh, Ruchira Sood, Rob B. West, Kelli Montgomery, ...
The transcriptional signature of the response of fibroblasts to serum provides a possible link between cancer progression and wound healing, as well as a predictor of the clinical course in several...
Howard Y. Chang, Julie B. Sneddon, Ash A. Alizadeh, Ruchira Sood, Rob B. West, Kelli Montgomery, ...
Cancer invasion and metastasis have been likened to wound healing gone awry. Despite parallels in cellular behavior between cancer progression and wound healing, the molecular relationships between...
Diversity, topographic differentiation, and positional memory in human fibroblasts
Chang, Howard Y., Chi, Jen-Tsan, Dudoit, Sandrine, Bondre, Chanda, Van De Rijn, Matt, Botstein, David, ...
A fundamental feature of the architecture and functional design of vertebrate animals is a stroma, composed of extracellular matrix and mesenchymal cells, which provides a structural scaffold and...
Genomewide view of gene silencing by small interfering RNAs
Chi, Jen-Tsan, Chang, Howard Y., Wang, Nancy N., Chang, Dustin S., Dunphy, Nina, Brown, Patrick O.
RNA interference (RNAi) is an evolutionarily conserved mechanism in plant and animal cells that directs the degradation of messenger RNAs homologous to short double-stranded RNAs termed small...
Endothelial cell diversity revealed by global expression profiling
Chi, Jen-Tsan, Chang, Howard Y., Haraldsen, Guttorm, Jahnsen, Frode L., Troyanskaya, Olga G., Chang, Dustin S., ...
The vascular system is locally specialized to accommodate widely varying blood flow and pressure and the distinct needs of individual tissues. The endothelial cells (ECs) that line the lumens of...
Systemic and cell type-specific gene expression patterns in scleroderma skin
Whitfield, Michael L., Finlay, Deborah R., Murray, John Isaac, Troyanskaya, Olga G., Chi, Jen-Tsan, Pergamenschikov, Alexander, ...
We used DNA microarrays representing >12,000 human genes to characterize gene expression patterns in skin biopsies from individuals with a diagnosis of systemic sclerosis with diffuse scleroderma. We...
Chang, Howard Y, Sneddon, Julie B, Alizadeh, Ash A, Sood, Ruchira, West, Rob B, Montgomery, Kelli, ...
Cancer invasion and metastasis have been likened to wound healing gone awry. Despite parallels in cellular behavior between cancer progression and wound healing, the molecular relationships between...
Chi, Jen-Tsan, Wang, Zhen, Nuyten, Dimitry S. A, Rodriguez, Edwin H, Schaner, Marci E, Salim, Ali, ...
The transcriptional response to hypoxia varies between cell types. A gene-expression signature of the cellular response to hypoxia is associated with a significantly poorer prognosis in breast and...
Diversity, topographic differentiation, and positional memory in human fibroblasts
Chang, Howard Y., Chi, Jen-Tsan, Dudoit, Sandrine, Bondre, Chanda, Van De Rijn, Matt, Botstein, David, ...
A fundamental feature of the architecture and functional design of vertebrate animals is a stroma, composed of extracellular matrix and mesenchymal cells, which provides a structural scaffold and...
Genomewide view of gene silencing by small interfering RNAs
Chi, Jen-Tsan, Chang, Howard Y., Wang, Nancy N., Chang, Dustin S., Dunphy, Nina, Brown, Patrick O.
RNA interference (RNAi) is an evolutionarily conserved mechanism in plant and animal cells that directs the degradation of messenger RNAs homologous to short double-stranded RNAs termed small...
Endothelial cell diversity revealed by global expression profiling
Chi, Jen-Tsan, Chang, Howard Y., Haraldsen, Guttorm, Jahnsen, Frode L., Troyanskaya, Olga G., Chang, Dustin S., ...
The vascular system is locally specialized to accommodate widely varying blood flow and pressure and the distinct needs of individual tissues. The endothelial cells (ECs) that line the lumens of...
Systemic and cell type-specific gene expression patterns in scleroderma skin
Whitfield, Michael L., Finlay, Deborah R., Murray, John Isaac, Troyanskaya, Olga G., Chi, Jen-Tsan, Pergamenschikov, Alexander, ...
We used DNA microarrays representing >12,000 human genes to characterize gene expression patterns in skin biopsies from individuals with a diagnosis of systemic sclerosis with diffuse scleroderma. We...
Chang, Howard Y, Sneddon, Julie B, Alizadeh, Ash A, Sood, Ruchira, West, Rob B, Montgomery, Kelli, ...
Cancer invasion and metastasis have been likened to wound healing gone awry. Despite parallels in cellular behavior between cancer progression and wound healing, the molecular relationships between...
Chi, Jen-Tsan, Wang, Zhen, Nuyten, Dimitry S. A, Rodriguez, Edwin H, Schaner, Marci E, Salim, Ali, ...
The transcriptional response to hypoxia varies between cell types. A gene-expression signature of the cellular response to hypoxia is associated with a significantly poorer prognosis in breast and...
Chi, Jen-Tsan, Rodriguez, Edwin H, Wang, Zhen, Nuyten, Dimitry S. A, Mukherjee, Sayan, Van De Rijn, Matt, ...
Smooth muscle is present in a wide variety of anatomical locations, such as blood vessels, various visceral organs, and hair follicles. Contraction of smooth muscle is central to functions as diverse...
Messika, Eric J., Lu, Peter S., Sung, Yen-Jen, Yao, Tony, Chi, Jen-Tsan, Chien, Yueh-hsiu, ...
The B lymphocyte–induced maturation protein (Blimp-1) upregulates the expression of syndecan-1 and J chain and represses that of c-myc. We have transfected Blimp-1 into two sublines of the BCL1 B...
Modeling Cancer Progression via Pathway Dependencies
Edelman, Elena J, Guinney, Justin, Chi, Jen-Tsan, Febbo, Phillip G, Mukherjee, Sayan
Cancer is a heterogeneous disease often requiring a complexity of alterations to drive a normal cell to a malignancy and ultimately to a metastatic state. Certain genetic perturbations have been...