Gene-expression patterns reveal underlying biological processes in Kawasaki disease (2007)
Popper, Stephen J, Shimizu, Chisato, Shike, Hiroko, Kanegaye, John T, Newburger, Jane W, Sundel, Robert P, ...
Abstract Background Kawasaki disease (KD) is an acute self-limited vasculitis and the leading cause of acquired heart disease in children in developed countries. No etiologic agent(s) has been...
Buess, Martin, Nuyten, Dimitry SA, Hastie, Trevor, Nielsen, Torsten, Pesich, Robert, Brown, Patrick O
Abstract Background Perturbations in cell-cell interactions are a key feature of cancer. However, little is known about the systematic effects of cell-cell interaction on global gene expression in...
Rubins, Kathleen H, Hensley, Lisa E, Wahl-Jensen, Victoria, Daddario DiCaprio, Kathleen M, Young, Howard A, Reed, Douglas S, ...
Abstract Background Infection with Ebola virus (EBOV) causes a fulminant and often fatal hemorrhagic fever. In order to improve our understanding of EBOV pathogenesis and EBOV-host interactions, we...
Correction: Discovery and validation of breast cancer subtypes (2007)
Kapp, Amy V, Jeffrey, Stefanie S, Langerød, Anita, Børresen-Dale, Anne-Lise, Han, Wonshik, Noh, Dong-Young, ...
Abstract Following the publication of our recent article (Kapp et al. , BMC Genomics 2006 , 7:231), we (the authors) regrettably found several errors in the published Table 5. This correction article...
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...
Discovery and validation of breast cancer subtypes (2006)
Kapp, Amy V, Jeffrey, Stefanie S, Langerød, Anita, Børresen-Dale, Anne-Lise, Han, Wonshik, Noh, Dong-Young, ...
Abstract Background Previous studies demonstrated breast cancer tumor tissue samples could be classified into different subtypes based upon DNA microarray profiles. The most recent study presented...
Cell-type specific gene expression profiles of leukocytes in human peripheral blood (2006)
Palmer, Chana, Diehn, Maximilian, Alizadeh, Ash A, Brown, Patrick O
Abstract Background Blood is a complex tissue comprising numerous cell types with distinct functions and corresponding gene expression profiles. We attempted to define the cell type specific gene...
Jen-Tsan Chi, Zhen Wang, Dimitry S. A. Nuyten, 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...
Daniel S. Chen, Yoav Soen, Tor B. Stuge, Peter P. Lee, Jeffrey S. Weber, Patrick O. Brown, ...
Patients vaccinated with melanoma-associated peptides show a wide diversity of responses, analysis of which may help us understand the differing clinical responses to such vaccines.
Correction: A DNA microarray survey of gene expression in normal human tissues (2005)
Shyamsundar, Radha, Kim, Young H, Higgins, John P, Montgomery, Kelli, Jorden, Michelle, Sethuraman, Anand, ...
No abstract available.
Differential gene expression in anatomical compartments of the human eye (2005)
Diehn, Jennifer J, Diehn, Maximilian, Marmor, Michael F, Brown, Patrick O
Abstract Background The human eye is composed of multiple compartments, diverse in form, function, and embryologic origin, that work in concert to provide us with our sense of sight. We set out to...
Determination of Stromal Signatures in Breast Carcinoma (2005)
Robert B. West, Dimitry S. A. Nuyten, Subbaya Subramanian, Torsten O. Nielsen, Christopher L. Corless, Brian P. Rubin, ...
The authors used two different fibroblastic tumors to identify markers expressed by normal stroma cells (the supporting framework of body tissues and/or tumors), and show that different stromal...
A DNA microarray survey of gene expression in normal human tissues (2005)
Shyamsundar, Radha, Kim, Young H, Higgins, John P, Montgomery, Kelli, Jorden, Michelle, Sethuraman, Anand, ...
Abstract Background Numerous studies have used DNA microarrays to survey gene expression in cancer and other disease states. Comparatively little is known about the genes expressed across the gamut...
Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli (2004)
Peter, Brian J, Arsuaga, Javier, Breier, Adam M, Khodursky, Arkady B, Brown, Patrick O, Cozzarelli, Nicholas R
Abstract Background The chromosome of Escherichia coli is maintained in a negatively supercoiled state, and supercoiling levels are affected by growth phase and a variety of environmental stimuli. In...
PLoS Medicine—A Medical Journal for the Internet Age (2004)
Michael B. Eisen, Patrick O. Brown, Harold E. Varmus
A message from the founders of the Public Library of Science.
A method for detecting and correcting feature misidentification on expression microarrays (2004)
Tu, I-Ping, Schaner, Marci, Diehn, Maximilian, Sikic, Branimir I, Brown, Patrick O, Botstein, David, ...
Abstract Background Much of the microarray data published at Stanford is based on mouse and human arrays produced under controlled and monitored conditions at the Brown and Botstein laboratories and...
Olga G. Troyanskaya, Mitchell E. Garber, Patrick O. Brown, David Botstein, Russ B. Altman
Motivation: Gene expression experiments provide a fast and systematic way to identify disease markers relevant to clinical care. In this study, we address the problem of robust identification of...
Cancer characterization and feature set extraction by discriminative margin clustering (2004)
Munagala, Kamesh, Tibshirani, Robert, Brown, Patrick O
Abstract Background A central challenge in the molecular diagnosis and treatment of cancer is to define a set of molecular features that, taken together, distinguish a given cancer, or type of...
André P. Gerber, Daniel Herschlag, Patrick O. Brown
Messenger RNAs that are associated with each of the five Puf RNA-binding proteins can be grouped according to function and localization, suggesting that tagging of transcripts by specific RNA-binding...
André P. Gerber, Daniel Herschlag, Patrick O. Brown
Genes encoding RNA-binding proteins are diverse and abundant in eukaryotic genomes. Although some have been shown to have roles in post-transcriptional regulation of the expression of specific genes,...
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...
Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae (2003)
Hurowitz, Evan H, Brown, Patrick O
Abstract Background Although the protein-coding sequences in the Saccharomyces cerevisiae genome have been studied and annotated extensively, much less is known about the extent and characteristics...
Detection and Characterization of Cellular Immune Responses Using Peptide–MHC Microarrays (2003)
Yoav Soen, Daniel S. Chen, Daniel L. Kraft, Mark M. Davis, Patrick O. Brown
An array-based screening strategy using microarrays of immobilized peptide-MHC complexes has been developed for the rapid identification, isolation, activation, and characterization of multiple...
Detection and Characterization of Cellular Immune Responses Using Peptide–MHC Microarrays (2003)
Yoav Soen, Daniel S. Chen, Daniel L. Kraft, Mark M. Davis, Patrick O. Brown
The detection and characterization of antigen-specific T cell populations is critical for understanding the development and physiology of the immune system and its responses in health and disease. We...
Jeroen P. Roose, Maximilian Diehn, Michael G. Tomlinson, Joseph Lin, Ash A. Alizadeh, David Botstein, ...
In the absence of basal signaling, RAG activity is high at a time during T cell development when it is otherwise normally suppressed.
Jeroen P. Roose, Maximilian Diehn, Michael G. Tomlinson, Joseph Lin, Ash A. Alizadeh, David Botstein, ...
Signal transduction pathways guided by cellular receptors commonly exhibit low-level constitutive signaling in a continuous, ligand-independent manner. The dynamic equilibrium of positive and...
Why PLoS Became a Publisher (2003)
Patrick O. Brown, Michael B. Eisen, Harold E. Varmus
Public Library of Science has grown from a grassroots movement to a nonprofit publisher, in order to catalyze change towards open-access publishing of the scientific literature.
Holterhus, Paul-Martin, Hiort, Olaf, Demeter, Janos, Brown, Patrick O, Brooks, James D
Abstract Background Androgen insensitivity syndrome (AIS) comprises a range of phenotypes from male infertility to complete feminization. Most individuals with AIS carry germline mutations of the...
Baldwin, David N, Vanchinathan, Veena, Brown, Patrick O, Theriot, Julie A
Abstract Background Listeria monocytogenes is a Gram-positive, facultative, intracellular bacterial pathogen found in soil, which occasionally causes serious food-borne disease in humans. The outcome...
A transcriptional response to Wnt protein in human embryonic carcinoma cells (2002)
Willert, Jennifer, Epping, Mirjam, Pollack, Jonathan R, Brown, Patrick O, Nusse, Roel
Abstract Background Wnt signaling is implicated in many developmental decisions, including stem cell control, as well as in cancer. There are relatively few target genes known of the Wnt pathway....
Transcriptional programs activated by exposure of human prostate cancer cells to androgen (2002)
DePrimo, Samuel E, Diehn, Maximilian, Nelson, Joel B, Reiter, Robert E, Matese, John, Fero, Mike, ...
Abstract Background Androgens are required for both normal prostate development and prostate carcinogenesis. We used DNA microarrays, representing approximately 18,000 genes, to examine the temporal...
Sayama, Koichi, Diehn, Maximilian, Matsuda, Kentaro, Lunderius, Carolina, Tsai, Mindy, Tam, See-Ying, ...
Abstract Background In asthma and other allergic disorders, the activation of mast cells by IgE and antigen induces the cells to release histamine and other mediators of inflammation, as well as to...
Lin, Johann Y, Pollack, Jonathan R, Chou, Fan-Li, Rees, Christian A, Christian, Allen T, Bedford, Joel S, ...
Abstract Background Somatic cell mutants can be informative in the analysis of a wide variety of cellular processes. The use of map-based positional cloning strategies in somatic cell hybrids to...
Derek Y. Chiang, Patrick O. Brown, Michael B. Eisen
The combination of genome-wide expression patterns and full genome sequences offers a great opportunity to further our understanding of the mechanisms and logic of transcriptional regulation. Many...
Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes (2001)
Audrey P. Gasch, Paul T. Spellman, Camilla M. Kao, Orna Carmel-harel, Michael B. Eisen, Gisela Storz, ...
this article contains data set material, and is available at www.molbiolcell.org.
The Stanford Microarray Database (2001)
Gavin Sherlock, Tina Hern, Andrew Kasarskis, Gail Binkley, John C. Matese, Selina S. Dwight, ...
The Stanford Microarray Database (SMD) stores raw and normalized data from microarray experiments, and provides web interfaces for researchers to retrieve, analyze and visualize their data. The two...
Haab, Brian B, Dunham, Maitreya J, Brown, Patrick O
Abstract Background We have developed and tested a method for printing protein microarrays and using these microarrays in a comparative fluorescence assay to measure the abundance of many specific...
Haab, Brain B, Dunham, Maitreya J, Brown, Patrick O
Abstract Background We describe a method for printing protein microarrays, and using these microarrays in a comparative fluorescence assay to measure the abundance of many specific proteins in...
Microarray Hybridization, Paul T. Spellman, Gavin Sherlock, Michael Q. Zhang, Vishwanath R, Kirk Anders, ...
this article is available at www.molbiolcell.org.
Genomic Expression Programs in the Response of Yeast Cells to Environmental ChangesD⃞
Gasch, Audrey P., Spellman, Paul T., Kao, Camilla M., Carmel-Harel, Orna, Eisen, Michael B., Storz, Gisela, ...
We explored genomic expression patterns in the yeast Saccharomyces cerevisiae responding to diverse environmental transitions. DNA microarrays were used to measure changes in transcript levels over...
Ogawa, Nobuo, DeRisi, Joseph, Brown, Patrick O.
The PHO regulatory pathway is involved in the acquisition of phosphate (Pi) in the yeast Saccharomyces cerevisiae. When extracellular Pi concentrations are low, several genes are transcriptionally...
Mediator protein mutations that selectively abolish activated transcription
Myers, Lawrence C., Gustafsson, Claes M., Hayashibara, Kathleen C., Brown, Patrick O., Kornberg, Roger D.
Deletion of any one of three subunits of the yeast Mediator of transcriptional regulation, Med2, Pgd1 (Hrs1), and Sin4, abolished activation by Gal4–VP16 in vitro. By contrast, other Mediator...
Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae
Sudarsanam, Priya, Iyer, Vishwanath R., Brown, Patrick O., Winston, Fred
The Saccharomyces cerevisiae Snf/Swi complex has been previously demonstrated to control transcription and chromatin structure of particular genes in vivo and to remodel nucleosomes in vitro. We have...
Genome-wide characterization of the Zap1p zinc-responsive regulon in yeast
Lyons, Thomas J., Gasch, Audrey P., Gaither, L. Alex, Botstein, David, Brown, Patrick O., Eide, David J.
The Zap1p transcription factor senses cellular zinc status and increases expression of its target genes in response to zinc deficiency. Previously known Zap1p-regulated genes encode the Zrt1p, Zrt2p,...
Analysis of topoisomerase function in bacterial replication fork movement: Use of DNA microarrays
Khodursky, Arkady B., Peter, Brian J., Schmid, Molly B., DeRisi, Joseph, Botstein, David, Brown, Patrick O., ...
We used DNA microarrays of the Escherichia coli genome to trace the progression of chromosomal replication forks in synchronized cells. We found that both DNA gyrase and topoisomerase IV (topo IV)...
Global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae
Gerton, Jennifer L., DeRisi, Joseph, Shroff, Robert, Lichten, Michael, Brown, Patrick O., Petes, Thomas D.
In the yeast Saccharomyces cerevisiae, meiotic recombination is initiated by double-strand DNA breaks (DSBs). Meiotic DSBs occur at relatively high frequencies in some genomic regions (hotspots) and...
Khodursky, Arkady B., Peter, Brian J., Cozzarelli, Nicholas R., Botstein, David, Brown, Patrick O., Yanofsky, Charles
We investigated the global changes in mRNA abundance in Escherichia coli elicited by various perturbations of tryptophan metabolism. To do so we printed DNA microarrays containing 95% of all...
Distinctive gene expression patterns in human mammary epithelial cells and breast cancers
Perou, Charles M., Jeffrey, Stefanie S., Van De Rijn, Matt, Rees, Christian A., Eisen, Michael B., Ross, Douglas T., ...
cDNA microarrays and a clustering algorithm were used to identify patterns of gene expression in human mammary epithelial cells growing in culture and in primary human breast tumors. Clusters of...
Systematic changes in gene expression patterns following adaptive evolution in yeast
Ferea, Tracy L., Botstein, David, Brown, Patrick O., Rosenzweig, R. Frank
Culturing a population of Saccharomyces cerevisiae for many generations under conditions to which it is not optimally adapted selects for fitter genetic variants. This simple experimental design...
Yeager, Mark, Wilson-Kubalek, Elizabeth M., Weiner, Scott G., Brown, Patrick O., Rein, Alan
We have used electron cryo-microscopy and image analysis to examine the native structure of immature, protease-deficient (PR−) and mature, wild-type (WT) Moloney murine leukemia virus (MuLV)....
Wilson, Michael, DeRisi, Joseph, Kristensen, Hans-Henrik, Imboden, Paul, Rane, Sangeeta, Brown, Patrick O., ...
Tuberculosis is a chronic infectious disease that is transmitted by cough-propelled droplets that carry the etiologic bacterium, Mycobacterium tuberculosis. Although currently available drugs kill...
Johannes, Gregg, Carter, Mark S., Eisen, Michael B., Brown, Patrick O., Sarnow, Peter
Although most eukaryotic mRNAs need a functional cap binding complex eIF4F for efficient 5′ end- dependent scanning to initiate translation, picornaviral, hepatitis C viral, and a few cellular RNAs...
Yeast microarrays for genome wide parallel genetic and gene expression analysis
Lashkari, Deval A., DeRisi, Joseph L., McCusker, John H., Namath, Allen F., Gentile, Cristl, Hwang, Seung Y., ...
We have developed high-density DNA microarrays of yeast ORFs. These microarrays can monitor hybridization to ORFs for applications such as quantitative differential gene expression analysis and...
Cluster analysis and display of genome-wide expression patterns
Eisen, Michael B., Spellman, Paul T., Brown, Patrick O., Botstein, David
A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according to similarity in...
Spellman, Paul T., Sherlock, Gavin, Zhang, Michael Q., Iyer, Vishwanath R., Anders, Kirk, Eisen, Michael B., ...
We sought to create a comprehensive catalog of yeast genes whose transcript levels vary periodically within the cell cycle. To this end, we used DNA microarrays and samples from yeast cultures...
Singular value decomposition for genome-wide expression data processing and modeling
Alter, Orly, Brown, Patrick O., Botstein, David
We describe the use of singular value decomposition in transforming genome-wide expression data from genes × arrays space to reduced diagonalized “eigengenes” × “eigenarrays” space, where...
Lossos, Izidore S., Alizadeh, Ash A., Eisen, Michael B., Chan, Wing C., Brown, Patrick O., Botstein, David, ...
B cell diffuse large cell lymphoma (B-DLCL) is a heterogeneous group of tumors, based on significant variations in morphology, clinical presentation, and response to treatment. Gene expression...
The Stanford Microarray Database
Sherlock, Gavin, Hernandez-Boussard, Tina, Kasarskis, Andrew, Binkley, Gail, Matese, John C., Dwight, Selina S., ...
The Stanford Microarray Database (SMD) stores raw and normalized data from microarray experiments, and provides web interfaces for researchers to retrieve, analyze and visualize their data. The two...
Miki, Rika, Kadota, Koji, Bono, Hidemasa, Mizuno, Yosuke, Tomaru, Yasuhiro, Carninci, Piero, ...
We have systematically characterized gene expression patterns in 49 adult and embryonic mouse tissues by using cDNA microarrays with 18,816 mouse cDNAs. Cluster analysis defined sets of genes that...
Sørlie, Therese, Perou, Charles M., Tibshirani, Robert, Aas, Turid, Geisler, Stephanie, Johnsen, Hilde, ...
The purpose of this study was to classify breast carcinomas based on variations in gene expression patter