Genome-Wide Analysis of KAP1 Binding Suggests Autoregulation of KRAB-ZNFs (2007)
Henriette O'Geen, Sharon L. Squazzo, Sushma Iyengar, Kim Blahnik, John L. Rinn, Howard Y. Chang, ...
We performed a genome-scale chromatin immunoprecipitation (ChIP)-chip comparison of two modifications (trimethylation of lysine 9 [H3me3K9] and trimethylation of lysine 27 [H3me3K27]) of histone H3...
A Transcriptional Program Mediating Entry into Cellular Quiescence (2007)
Helen Liu, Adam S. Adler, Eran Segal, Howard Y. Chang
The balance of quiescence and cell division is critical for tissue homeostasis and organismal health. Serum stimulation of fibroblasts is well studied as a classic model of entry into the cell...
Genome-Wide Analysis of KAP1 Binding Suggests Autoregulation of KRAB-ZNFs (2007)
Henriette O'Geen, Sharon L Squazzo, Sushma Iyengar, Kim Blahnik, John L. Rinn, Howard Y. Chang, ...
We performed a genome-scale chromatin immunoprecipitation (ChIP)-chip comparison of two modifications (trimethylation of lysine 9 [H3me3K9] and trimethylation of lysine 27 [H3me3K27]) of histone H3...
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...
Anatomic Demarcation by Positional Variation in Fibroblast Gene Expression Programs (2006)
John L. Rinn, Chanda Bondre, Hayes B. Gladstone, Patrick O. Brown, Howard Y. Chang
Fibroblasts are ubiquitous mesenchymal cells with many vital functions during development, tissue repair, and disease. Fibroblasts from different anatomic sites have distinct and characteristic gene...
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...
Chang, Howard Y., Yang, Xiaolu, Baltimore, David
Fas is a cell surface death receptor that regulates peripheral tolerance and lymphoid homeostasis. In many pathologic conditions, ectopic Fas activation mediates tissue destruction. Several proteins...
Chang, Howard Y., Yang, Xiaolu, Baltimore, David
Fas is a cell surface death receptor that regulates peripheral tolerance and lymphoid homeostasis. In many pathologic conditions, ectopic Fas activation mediates tissue destruction. Several proteins...
Proteases for Cell Suicide: Functions and Regulation of Caspases
Chang, Howard Y., Yang, Xiaolu
Caspases are a large family of evolutionarily conserved proteases found from Caenorhabditis elegans to humans. Although the first caspase was identified as a processing enzyme for interleukin-1β,...
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...
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...
Anatomic Demarcation by Positional Variation in Fibroblast Gene Expression Programs
Rinn, John L, Bondre, Chanda, Gladstone, Hayes B, Brown, Patrick O, Chang, Howard Y
Fibroblasts are ubiquitous mesenchymal cells with many vital functions during development, tissue repair, and disease. Fibroblasts from different anatomic sites have distinct and characteristic gene...
Chang, Howard Y., Yang, Xiaolu, Baltimore, David
Fas is a cell surface death receptor that regulates peripheral tolerance and lymphoid homeostasis. In many pathologic conditions, ectopic Fas activation mediates tissue destruction. Several proteins...
Proteases for Cell Suicide: Functions and Regulation of Caspases
Chang, Howard Y., Yang, Xiaolu
Caspases are a large family of evolutionarily conserved proteases found from Caenorhabditis elegans to humans. Although the first caspase was identified as a processing enzyme for interleukin-1β,...
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...
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...
Chang, Howard Y., Nuyten, Dimitry S. A., Sneddon, Julie B., Hastie, Trevor, Tibshirani, Robert, Sørlie, Therese, ...
Based on the hypothesis that features of the molecular program of normal wound healing might play an important role in cancer metastasis, we previously identified consistent features in the...
Anatomic Demarcation by Positional Variation in Fibroblast Gene Expression Programs
Rinn, John L, Bondre, Chanda, Gladstone, Hayes B, Brown, Patrick O, Chang, Howard Y
Fibroblasts are ubiquitous mesenchymal cells with many vital functions during development, tissue repair, and disease. Fibroblasts from different anatomic sites have distinct and characteristic gene...
Predicting a local recurrence after breast-conserving therapy by gene expression profiling
Nuyten, Dimitry SA, Kreike, Bas, Hart, Augustinus AM, Chi, Jen-Tsan Ashley, Sneddon, Julie B, Wessels, Lodewyk FA, ...
Sneddon, Julie B., Zhen, Hanson H., Montgomery, Kelli, Van De Rijn, Matt, Tward, Aaron D., West, Robert, ...
Although tissue microenvironments play critical roles in epithelial development and tumorigenesis, the factors mediating these effects are poorly understood. In this work, we used a genomic approach...
Genome-Wide Analysis of KAP1 Binding Suggests Autoregulation of KRAB-ZNFs
O'Geen, Henriette, Squazzo, Sharon L, Iyengar, Sushma, Blahnik, Kim, Rinn, John L, Chang, Howard Y, ...
We performed a genome-scale chromatin immunoprecipitation (ChIP)-chip comparison of two modifications (trimethylation of lysine 9 [H3me3K9] and trimethylation of lysine 27 [H3me3K27]) of histone H3...
A Transcriptional Program Mediating Entry into Cellular Quiescence
Liu, Helen, Adler, Adam S, Segal, Eran, Chang, Howard Y
The balance of quiescence and cell division is critical for tissue homeostasis and organismal health. Serum stimulation of fibroblasts is well studied as a classic model of entry into the cell...
Mechanisms of an autoimmunity syndrome in mice caused by a dominant mutation in Aire
Su, Maureen A., Giang, Karen, Žumer, Kristina, Jiang, Huimin, Oven, Irena, Rinn, John L., ...
Homozygous loss-of-function mutations in AIRE cause autoimmune polyglandular syndrome type 1 (APS 1), which manifests in a classic triad of hypoparathyroidism, adrenal insufficiency, and candidiasis....
Motif module map reveals enforcement of aging by continual NF-κB activity
Adler, Adam S., Sinha, Saurabh, Kawahara, Tiara L.A., Zhang, Jennifer Y., Segal, Eran, Chang, Howard Y.
Aging is characterized by specific alterations in gene expression, but their underlying mechanisms and functional consequences are not well understood. Here we develop a systematic approach to...
A dermal HOX transcriptional program regulates site-specific epidermal fate
Rinn, John L., Wang, Jordon K., Allen, Nancy, Brugmann, Samantha A., Mikels, Amanda J., Liu, Helen, ...
Reciprocal epithelial–mesenchymal interactions shape site-specific development of skin. Here we show that site-specific HOX expression in fibroblasts is cell-autonomous and epigenetically...
Systematic functional characterization of cis-regulatory motifs in human core promoters
Sinha, Saurabh, Adler, Adam S., Field, Yair, Chang, Howard Y., Segal, Eran
A large number of cis-regulatory motifs involved in transcriptional control have been identified, but the regulatory context and biological processes in which many of them function are unknown. Here,...