Ammonium Toxicity and Potassium Limitation in Yeast (2006)
David C. Hess, Wenyun Lu, Joshua D. Rabinowitz, David Botstein
DNA microarray analysis of gene expression in steady-state chemostat cultures limited for potassium revealed a surprising connection between potassium and ammonium: potassium limits growth only when...
Reguly, Teresa, Breitkreutz, Ashton, Boucher, Lorrie, Breitkreutz, Bobby-Joe, Hon, Gary C, Myers, Chad L, ...
Abstract Background The study of complex biological networks and prediction of gene function has been enabled by high-throughput (HTP) methods for detection of genetic and protein interactions....
Genome-Scale Identification of Membrane-Associated Human mRNAs (2006)
Maximilian Diehn, Ramona Bhattacharya, David Botstein, Patrick O. Brown
The subcellular localization of proteins is critical to their biological roles. Moreover, whether a protein is membrane-bound, secreted, or intracellular affects the usefulness of, and the strategies...
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.
Homeostatic Adjustment and Metabolic Remodeling in Glucose-limited Yeast Cultures (2005)
Brauer, Matthew J., Saldanha, Alok J., Dolinski, Kara, Botstein, David
We studied the physiological response to glucose limitation in batch and steady-state (chemostat) cultures of Saccharomyces cerevisiae by following global patterns of gene expression. Glucose-limited...
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...
GeneXplorer: an interactive web application for microarray data visualization and analysis (2004)
Rees, Christian A, Demeter, Janos, Matese, John C, Botstein, David, Sherlock, Gavin
Abstract Background When publishing large-scale microarray datasets, it is of great value to create supplemental websites where either the full data, or selected subsets corresponding to figures...
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...
Nutritional homeostasis in batch and steady-state culture of yeast (2004)
Saldanha, Alok J., Brauer, Matthew J., Botstein, David
We studied the physiological response to limitation by diverse nutrients in batch and steady-state (chemostat) cultures of S. cerevisiae. We found that the global pattern of transcription in...
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...
Universal Reference RNA as a standard for microarray experiments (2004)
Novoradovskaya, Natalia, Whitfield, Michael L, Basehore, Lee S, Novoradovsky, Alexey, Pesich, Robert, Usary, Jerry, ...
Abstract Background Obtaining reliable and reproducible two-color microarray gene expression data is critically important for understanding the biological significance of perturbations made on a...
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...
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...
Module Networks: Discovering Regulatory (2003)
Eran Segal, David Botstein, Daphne Koller, Nir Friedman
Introduction The complex functions of a living cell are carried out through the concerted activity of many genes and gene products. This activity is often coordinated by the organization of Computer...
Ranade, Koustubh, Hinds, David, Hsiung, Chao Agnes, Chuang, Lee-Ming, Chang, Mau-Song, Chen, Ying-Tsung, ...
Background: Our understanding of genes that predispose to essential hypertension is poor. Methods: A genome-wide scan for linkage at ~10 cM resolution was done on 1425 sibpairs of Chinese and...
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...
Olga Troyanskaya, Gavin Sherlock, Trevor Hastie, Robert Tibshirani, David Botstein, Russ B. Altman
Motivation: Gene expression microarray experiments can generate data sets with multiple missing expression values. Unfortunately, many algorithms for gene expression analysis require a complete...
Imputing Missing Data for Gene Expression Arrays (2001)
Trevor Hastie, Robert Tibshirani, Gavin Sherlock, Michael Eisen, Patrick Brown, David Botstein
this report. 1.2 SVD imputation using all the data
Cluster Validation By Prediction Strength (2001)
Robert Tibshirani, Guenther Walther, David Botstein
We propose a new quantity for assessing the number of groups or clusters in a dataset. The key idea is to view clustering as a supervised classication problem, in which we must also estimate the rue"...
Missing value estimation methods for DNA microarrays (2001)
Olga Troyanskaya, Gavin Sherlock, Pat Brown, Trevor Hastie, Robert Tibshirani, David Botstein, ...
Motivation: Gene expression microarray experiments can generate data sets with multiple missing expression values. Unfortunately, many algorithms for gene expression analysis require a complete...
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...
Supervised harvesting of expression trees (2001)
Hastie, Trevor, Tibshirani, Robert, Botstein, David, Brown, Patrick
Abstract Background We propose a new method for supervised learning from gene expression data. We call it 'tree harvesting'. This technique starts with a hierarchical clustering of genes, then models...
Supervised Harvesting of Expression Trees (2000)
Trevor Hastie, Robert Tibshirani, David Botstein, Patrick Brown
Background We propose a new method for supervising learning from gene expression data. We call it Tree Harvesting". This technique starts with a hierarchical clustering of genes, and models the...
Hastie, Trevor, Tibshirani, Robert, Eisen, Michael B, Alizadeh, Ash, Levy, Ronald, Staudt, Louis, ...
Abstract Background Large gene expression studies, such as those conducted using DNA arrays, often provide millions of different pieces of data. To address the problem of analyzing such data, we...
Clustering methods for the analysis of DNA microarray data (1999)
Robert Tibshirani, Trevor Hastie, Mike Eisen, Doug Ross, David Botstein, Pat Brown
It is now possible to simultaneously measure the expression of thousands of genes during cellular differentiation and response, through the use of DNA microarrays. A major statistical task is to...
Clustering methods for the analysis of DNA microarray data (1999)
Robert Tibshirani, Trevor Hastie, Mike Eisen, Doug Ross, David Botstein, Pat Brown
It is now possible to simultaneously measure the expression of thousands of genes during cellular differentiation and response, through the use of DNA microarrays. A major statistical task is to...
Robert Tibshirani, Trevor Hastie, Mike Eisen, Doug Ross, David Botstein, Pat Brown
It is now possible to simultaneously measure the expression of thousands of genes during cellular differentiation and response, through the use of DNA microarrays. A major statistical task is to...
J. Michael Cherry, Caroline Adler, Catherine Ball, Stephen A. Chervitz, Selina S. Dwight, Erich T. Hester, ...
The Saccharomyces GenomeDatabase (SGD) provides Internet access to the complete Saccharomyces cerevisiae genomic sequence, its genes and their products, the phenotypes of its mutants, and the...
Synthesis and maturation of phage P22 DNA : I. Identification of intermediates (1968)
Two intermediates in the synthesis and maturation of phage P22 DNA have been identified by sedimentation of lysozyme-detergent lysates of induced lysogens or infected cells through sucrose...
Botstein, David, Levine, Myron
Three temperature-sensitive mutants of phage P22 have been isolated which are defective in phage DNA metabolism. After infection at restrictive temperature, one mutant (ts 12.1) fails to synthesize...
THE SYNTHESIS AND MATURATION OF PHAGE-P22 DNA. (1967)
DISSERTATION (PH.D.)--THE UNIVERSITY OF MICHIGAN
Structure–Function Relationships in Yeast TubulinsD⃞
Richards, Kristy L., Anders, Kirk R., Nogales, Eva, Schwartz, Katja, Downing, Kenneth H., Botstein, David
A comprehensive set of clustered charged-to-alanine mutations was generated that systematically alter TUB1, the major α-tubulin gene of Saccharomyces cerevisiae. A variety of phenotypes were...
'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns
Hastie, Trevor, Tibshirani, Robert, Eisen, Michael B, Alizadeh, Ash, Levy, Ronald, Staudt, Louis, ...
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...
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)...
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...
Supervised harvesting of expression trees
Hastie, Trevor, Tibshirani, Robert, Botstein, David, Brown, Patrick
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...
Pennica, Diane, Swanson, Todd A., Welsh, James W., Roy, Margaret A., Lawrence, David A., Lee, James, ...
Wnt family members are critical to many developmental processes, and components of the Wnt signaling pathway have been linked to tumorigenesis in familial and sporadic colon carcinomas. Here we...
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...
Visualization of Receptor-mediated Endocytosis in Yeast
Mulholland, Jon, Konopka, James, Singer-Kruger, Birgit, Zerial, Marino, Botstein, David
We studied the ligand-induced endocytosis of the yeast α-factor receptor Ste2p by immuno-electron microscopy. We observed and quantitated time-dependent loss of Ste2p from the plasma membrane of...
Multiple Functions for Actin during Filamentous Growth of Saccharomyces cerevisiaeV⃞
Cali, Brian M., Doyle, Timothy C., Botstein, David, Fink, Gerald R.
Saccharomyces cerevisiae is dimorphic and switches from a yeast form to a pseudohyphal (PH) form when starved for nitrogen. PH cells are elongated, bud in a unipolar manner, and invade the agar...
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...
BIM1 Encodes a Microtubule-binding Protein in Yeast
Schwartz, Katja, Richards, Kristy, Botstein, David
A previously uncharacterized yeast gene (YER016w) that we have named BIM1 (binding to microtubules) was obtained from a two-hybrid screen of a yeast cDNA library using as bait the entire coding...
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...
Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data
Ball, Catherine A., Jin, Heng, Sherlock, Gavin, Weng, Shuai, Matese, John C., Andrada, Rey, ...
Upon the completion of the Saccharomyces cerevisiae genomic sequence in 1996 [Goffeau,A. et al. (1997) Nature, 387, 5], several creative and ambitious projects have been initiated to explore the...
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...
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 patterns derived from cDNA microarrays and to correlate tumor characteristics to clinical outcome. A...
Gasch, Audrey P., Huang, Mingxia, Metzner, Sandra, Botstein, David, Elledge, Stephen J., Brown, Patrick O.
Eukaryotic cells respond to DNA damage by arresting the cell cycle and modulating gene expression to ensure efficient DNA repair. The human ATR kinase and its homolog in yeast, MEC1, play central...
Dominant-Lethal α-Tubulin Mutants Defective in Microtubule Depolymerization in YeastV⃞
Anders, Kirk R., Botstein, David
The dynamic instability of microtubules has long been understood to depend on the hydrolysis of GTP bound to β-tubulin, an event stimulated by polymerization and necessary for depolymerization....
Genetic variation in aldosterone synthase predicts plasma glucose levels
Ranade, Koustubh, Wu, Kwan Dun, Risch, Neil, Olivier, Michael, Pei, Dee, Hsiao, Chin-Fu, ...
The mineralocorticoid hormone, aldosterone, is known to play a role in sodium homeostasis. We serendipitously found, however, highly significant association between single-nucleotide polymorphisms in...
Diversity of gene expression in adenocarcinoma of the lung
Garber, Mitchell E., Troyanskaya, Olga G., Schluens, Karsten, Petersen, Simone, Thaesler, Zsuzsanna, Pacyna-Gengelbach, Manuela, ...
The global gene expression profiles for 67 human lung tumors representing 56 patients were examined by using 24,000-element cDNA microarrays. Subdivision of the tumors based on gene expression...
Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO)
Dwight, Selina S., Harris, Midori A., Dolinski, Kara, Ball, Catherine A., Binkley, Gail, Christie, Karen R., ...
The Saccharomyces Genome Database (SGD) resources, ranging from genetic and physical maps to genome-wide analysis tools, reflect the scientific progress in identifying genes and their functions over...
Integrating functional genomic information into the Saccharomyces Genome Database
Ball, Catherine A., Dolinski, Kara, Dwight, Selina S., Harris, Midori A., Issel-Tarver, Laurie, Kasarskis, Andrew, ...
The Saccharomyces Genome Database (SGD) stores and organizes information about the nearly 6200 genes in the yeast genome. The information is organized around the ‘locus page’ and directs users to...
Systematic Structure-Function Analysis of the Small GTPase Arf1 in Yeast D⃞
Click, Eleanor S., Stearns, Tim, Botstein, David
Members of the ADP-ribosylation factor (Arf) family of small GTPases are implicated in vesicle traffic in the secretory pathway, although their precise function remains unclear. We generated a series...