List of works by Patrick O. Brown

'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns

scientific article

2005 Curt Stern Award address. Exploring along a crooked path

scientific article published in September 2006

A DNA microarray survey of gene expression in normal human tissues

scientific article

A gene expression database for the molecular pharmacology of cancer

scientific article (publication date: March 2000)

A gene-expression program reflecting the innate immune response of cultured intestinal epithelial cells to infection by Listeria monocytogenes

scientific article

A landscape effect in tenosynovial giant-cell tumor from activation of CSF1 expression by a translocation in a minority of tumor cells

scholarly article

A method for detecting and correcting feature misidentification on expression microarrays

scientific article

A nucleoprotein complex mediates the integration of retroviral DNA.

scientific article published in April 1989

A specific gene expression program triggered by Gram-positive bacteria in the cytosol

scholarly article

A transcriptional response to Wnt protein in human embryonic carcinoma cells

scientific article

Adaptation to famine: a family of stationary-phase genes revealed by microarray analysis

scientific article

An interview with Patrick O Brown on the origins and future of open access

scientific article

Analysis of topoisomerase function in bacterial replication fork movement: use of DNA microarrays

scientific article

Anatomic demarcation by positional variation in fibroblast gene expression programs

scientific article

Apo D in soft tissue tumors: a novel marker for dermatofibrosarcoma protuberans

scientific article

Arrest, adaptation, and recovery following a chromosome double-strand break in Saccharomyces cerevisiae

scientific article

Autoantigen microarrays for multiplex characterization of autoantibody responses

scientific article

Automated Analysis and Classification of Histological Tissue Features by Multi-Dimensional Microscopic Molecular Profiling

scientific article published on 15 July 2015

Bethesda Statement on Open Access Publishing ⬇️

copyright manifesto

Bone morphogenetic protein antagonist gremlin 1 is widely expressed by cancer-associated stromal cells and can promote tumor cell proliferation

scholarly article

Cancer characterization and feature set extraction by discriminative margin clustering

scientific article

Catenation and knotting of duplex DNA by type 1 topoisomerases: a mechanistic parallel with type 2 topoisomerases

scientific article

Cell-type specific features of circular RNA expression

scientific article

Cell-type specific gene expression profiles of leukocytes in human peripheral blood

scientific article

Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae

scientific article

Characterization of heterotypic interaction effects in vitro to deconvolute global gene expression profiles in cancer

scientific article published on January 2007

Characterization of three related glucose repressors and genes they regulate in Saccharomyces cerevisiae.

scientific article

Circular RNA is expressed across the eukaryotic tree of life

scientific article

Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types

scientific article published in 2012

Climate change and the integrity of science

scientific article

Cluster analysis and display of genome-wide expression patterns

scientific article

Combining SSH and cDNA microarrays for rapid identification of differentially expressed genes

scientific article

Comparative analysis of viral gene expression programs during poxvirus infection: a transcriptional map of the vaccinia and monkeypox genomes

scientific article

Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization

scientific article

Computational Methods and Bioinformatic Tools

Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA

scientific article

Correct integration of retroviral DNA in vitro

scientific journal article

Correction: Cell-Type Specific Features of Circular RNA Expression.

scientific article published on 30 December 2013

Correction: Systematic Identification of mRNAs Recruited to Argonaute 2 by Specific microRNAs and Corresponding Changes in Transcript Abundance.

scientific article published on 14 November 2008

DNA arrays for analysis of gene expression

scientific article (publication date: 1999)

DNA methylation profiles of ovarian epithelial carcinoma tumors and cell lines

scientific article

DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli

scientific article

Defining the specificity of cotranslationally acting chaperones by systematic analysis of mRNAs associated with ribosome-nascent chain complexes

scientific article

Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays

scholarly article

Desferrioxamine-mediated iron uptake in Saccharomyces cerevisiae. Evidence for two pathways of iron uptake

scientific article published on 01 April 2000

Detection and characterization of cellular immune responses using peptide-MHC microarrays

scientific article

Determination of stromal signatures in breast carcinoma

scientific article

Development of the human infant intestinal microbiota

scientific article published in July 2007

Differential gene expression in anatomical compartments of the human eye.

scientific article

Differential gene-expression patterns in genital fibroblasts of normal males and 46,XY females with androgen insensitivity syndrome: evidence for early programming involving the androgen receptor

scientific article

Digital Compared with Screen-Film Mammography: Measures of Diagnostic Accuracy among Women Screened in the Ontario Breast Screening Program

scientific article published on 2 September 2015

Digital compared to screen-film mammography: breast cancer prognostic features in an organized screening program

scientific article published on 10 August 2014

Digital compared with screen-film mammography: performance measures in concurrent cohorts within an organized breast screening program

scientific article

Digital versus screen-film mammography: impact of mammographic density and hormone therapy on breast cancer detection

scientific article published on 30 October 2015

Directed Chemical Evolution with an Outsized Genetic Code

scientific article

Discovery and validation of breast cancer subtypes

scientific article

Discovery and validation of breast cancer subtypes.

scientific article

Dissecting eukaryotic translation and its control by ribosome density mapping

scientific article

Dissecting interferon-induced transcriptional programs in human peripheral blood cells

scientific article

Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments

scientific article

Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling

scientific article (publication date: 3 February 2000)

Distinctive gene expression patterns in human mammary epithelial cells and breast cancers

scientific article

Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system

scientific article published on 28 October 2008

Diverse and specific gene expression responses to stresses in cultured human cells

scientific article

Diversity of gene expression in adenocarcinoma of the lung

scientific article (publication date: 20 November 2001)

Diversity, topographic differentiation, and positional memory in human fibroblasts

scientific article

ESRRA-C11orf20 is a recurrent gene fusion in serous ovarian carcinoma

scientific article

Effects of mutations in residues near the active site of human immunodeficiency virus type 1 integrase on specific enzyme-substrate interactions

scientific article published on June 1998

Endothelial cell diversity revealed by global expression profiling

scientific article

Estimating the risk of bladder and kidney cancer from exposure to low-levels of arsenic in drinking water, Nova Scotia, Canada

scientific article published on 28 October 2017

Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets

scientific article

Examining the living genome in health and disease with DNA microarrays

scientific article published on 01 May 2000

Exploration of global gene expression patterns in pancreatic adenocarcinoma using cDNA microarrays

scientific article (publication date: April 2003)

Exploring drug-induced alterations in gene expression in Mycobacterium tuberculosis by microarray hybridization

scientific article published on October 1999

Exploring the metabolic and genetic control of gene expression on a genomic scale

scientific article (publication date: 24 October 1997)

Exploring the new world of the genome with DNA microarrays

scientific article (publication date: 1999)

Exploring the regulation of human neural precursor cell differentiation using arrays of signaling microenvironments

scientific article

Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast

scientific article

Functional analysis of the genes of yeast chromosome V by genetic footprinting

scientific article

Gene expression in the normal adult human kidney assessed by complementary DNA microarray

scholarly article

Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans

scientific article published in December 2003

Gene expression patterns in human embryonic stem cells and human pluripotent germ cell tumors ⬇️

scientific article published on October 31, 2003

Gene expression patterns in human liver cancers

scientific article

Gene expression patterns in human placenta

scholarly article

Gene expression patterns in ovarian carcinomas

scientific article

Gene expression patterns in pancreatic tumors, cells and tissues

scientific article

Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications

scientific article (publication date: 11 September 2001)

Gene expression profiling identifies clinically relevant subtypes of prostate cancer

scholarly article

Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme

scientific article

Gene expression programs in response to hypoxia: cell type specificity and prognostic significance in human cancers

scientific article

Gene expression programs of human smooth muscle cells: tissue-specific differentiation and prognostic significance in breast cancers

scientific article

Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds

scientific article

Gene-expression patterns reveal underlying biological processes in Kawasaki disease

scientific article

Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms

scientific article

Genetic footprinting: a genomic strategy for determining a gene's function given its sequence ⬇️

scientific article published on July 3, 1995

Genome-scale identification of membrane-associated human mRNAs

scientific article

Genome-wide analysis of DNA copy-number changes using cDNA microarrays

scientific article (publication date: September 1999)

Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae

scientific article

Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae

scientific article

Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae ⬇️

scholarly article

Genome-wide characterization of the Zap1p zinc-responsive regulon in yeast

scientific article

Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster

scholarly article

Genomewide demarcation of RNA polymerase II transcription units revealed by physical fractionation of chromatin

scientific article

Genomewide view of gene silencing by small interfering RNAs

scientific article

Genomic analysis of renal allograft dysfunction using cDNA microarrays.

scientific article published in February 2001

Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF

scientific article (publication date: 25 January 2001)

Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation

scientific article

Genomic expression programs in the response of yeast cells to environmental changes

scientific article (publication date: December 2000)

Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p

scientific article

Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli

scientific article

Global and specific translational regulation in the genomic response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source

scientific article published on February 2001

Global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae

scientific article

INFORMATION ACCESS: Building A "GenBank" of the Published Literature

scientific article (publication date: 23 March 2001)

Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome ⬇️

scientific article published on October 18, 2010

Identification of eukaryotic mRNAs that are translated at reduced cap binding complex eIF4F concentrations using a cDNA microarray

scientific article published on November 1999

Identification of genes periodically expressed in the human cell cycle and their expression in tumors

scientific article (publication date: June 2002)

Identification of the copper regulon in Saccharomyces cerevisiae by DNA microarrays

scientific article published on October 2000

Improved discovery of molecular interactions in genome-scale data with adaptive model-based normalization

scientific article

In vivo regulation of human skeletal muscle gene expression by thyroid hormone

scientific article

Individuality and variation in gene expression patterns in human blood

scientific article

Large-scale identification of secreted and membrane-associated gene products using DNA microarrays

scientific article

Marked differences in human melanoma antigen-specific T cell responsiveness after vaccination using a functional microarray

scientific article

Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors

scientific article

Microarrays in primary breast cancer--lessons from chemotherapy studies

scientific article published in September 2001

Minimizing off-target effects by using diced siRNAs for RNA interference

scientific article published on 17 July 2006

Missing value estimation methods for DNA microarrays

scientific article (publication date: June 2001)

Molecular portraits of human breast tumours

scientific article (publication date: 17 August 2000)

New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis

scientific article

Nonparametric methods for identifying differentially expressed genes in microarray data

scientific article

Novel Genome-Scale Correlation between DNA Replication and RNA Transcription During the Cell Cycle in Yeast is Predicted by Data-Driven Models

scientific report

Ongoing immunoglobulin somatic mutation in germinal center B cell-like but not in activated B cell-like diffuse large cell lymphomas

scientific article

PLoS Medicine— A Medical Journal for the Internet Age

scientific article

Parallel human genome analysis: microarray-based expression monitoring of 1000 genes

scientific article published on October 1996

Parallels between global transcriptional programs of polarizing Caco-2 intestinal epithelial cells in vitro and gene expression programs in normal colon and colon cancer

scientific article

Phospholipase A2 group IIA expression in gastric adenocarcinoma is associated with prolonged survival and less frequent metastasis

scientific article

Physical mapping of genes in somatic cell radiation hybrids by comparative genomic hybridization to cDNA microarrays

scientific article

Precision and functional specificity in mRNA decay

scientific article

Predicting a local recurrence after breast-conserving therapy by gene expression profiling

scientific article published on January 2006

Presynaptic homeostasis at CNS nerve terminals compensates for lack of a key Ca2+ entry pathway

scholarly article

Processing and Modeling Genome-Wide Expression Data Using Singular Value Decomposition

scientific book chapter

Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association

scientific article

Proteome-Wide Search Reveals Unexpected RNA-Binding Proteins in Saccharomyces cerevisiae ⬇️

scientific article published on September 10, 2010

Public-access group supports PubMed Central

scientific article (publication date: 12 September 2002)

Quantitative monitoring of gene expression patterns with a complementary DNA microarray

scholarly article

Quantitative proteomic analysis reveals concurrent RNA-protein interactions and identifies new RNA-binding proteins in Saccharomyces cerevisiae

scientific article published on May 2013

RERG is a novel ras-related, estrogen-regulated and growth-inhibitory gene in breast cancer

scientific article

Rapid global phaseout of animal agriculture has the potential to stabilize greenhouse gas levels for 30 years and offset 68 percent of CO2 emissions this century

scientific article

Rapid quantitative profiling of complex microbial populations

scientific article

Relation of gene expression phenotype to immunoglobulin mutation genotype in B cell chronic lymphocytic leukemia

scientific article

Repeated observation of breast tumor subtypes in independent gene expression data sets

scientific article (publication date: 8 July 2003)

Retroviral integration: structure of the initial covalent product and its precursor, and a role for the viral IN protein

scientific journal article

Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival

scientific article

Role of thioredoxin reductase in the Yap1p-dependent response to oxidative stress in Saccharomyces cerevisiae

scientific article published on February 2001

SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data

scientific article

Singular Value Decomposition for Gene Expression Data Processing and Modeling

scientific report

Singular value decomposition for genome-wide expression data processing and modeling

scientific article

Small-area spatio-temporal analyses of bladder and kidney cancer risk in Nova Scotia, Canada

scientific article published on 19 February 2016

Stereotyped and specific gene expression programs in human innate immune responses to bacteria

scientific article

Still Elegantly Muddling Through? NICE and Uncertainty in Decision Making About the Rationing of Expensive Medicines in England

scientific article published on January 2017

Stunned silence: gene expression programs in human cells infected with monkeypox or vaccinia virus

scientific article

Supervised harvesting of expression trees

scientific article

Systematic changes in gene expression patterns following adaptive evolution in yeast

scientific article

Systematic evaluation of candidate blood markers for detecting ovarian cancer

scientific article

Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance

scientific article published in 2008

Systematic variation in gene expression patterns in human cancer cell lines

scientific article (publication date: March 2000)

Systemic and cell type-specific gene expression patterns in scleroderma skin

scientific article

T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression

scientific article

The Stanford Microarray Database

scientific article

The Stanford Microarray Database accommodates additional microarray platforms and data formats

scientific article

The Stanford Microarray Database: data access and quality assessment tools

scientific article

The Stanford Microarray Database: implementation of new analysis tools and open source release of software

scientific article

The Stanford Tissue Microarray Database

scientific article

The host response to smallpox: analysis of the gene expression program in peripheral blood cells in a nonhuman primate model

scholarly article

The lymphochip: a specialized cDNA microarray for the genomic-scale analysis of gene expression in normal and malignant lymphocytes.

scientific article

The novel marker, DOG1, is expressed ubiquitously in gastrointestinal stromal tumors irrespective of KIT or PDGFRA mutation status

scientific article

The preclinical natural history of serous ovarian cancer: defining the target for early detection

scientific article

The temporal program of peripheral blood gene expression in the response of nonhuman primates to Ebola hemorrhagic fever

scientific article published on January 2007

The transcriptional program in the response of human fibroblasts to serum

scientific article

The transcriptional program of sporulation in budding yeast

scientific article

The yeast Rab GTPase Ypt1 modulates unfolded protein response dynamics by regulating the stability of HAC1 RNA.

scientific article

Three cell wall mannoproteins facilitate the uptake of iron in Saccharomyces cerevisiae

scientific article published on 22 October 2001

Three-dimensional tracking of single mRNA particles in Saccharomyces cerevisiae using a double-helix point spread function ⬇️

scientific article published on October 4, 2010

Tissue microarray validation of epidermal growth factor receptor and SALL2 in synovial sarcoma with comparison to tumors of similar histology

scientific article

Transcriptional modulation of genes encoding structural characteristics of differentiating enterocytes during development of a polarized epithelium in vitro

scientific article

Transcriptional program induced by Wnt protein in human fibroblasts suggests mechanisms for cell cooperativity in defining tissue microenvironments

scientific article

Transcriptional programs activated by exposure of human prostate cancer cells to androgen

scientific article

Transcriptional remodeling in response to iron deprivation in Saccharomyces cerevisiae

scientific article (publication date: March 2004)

Transcriptional response of human mast cells stimulated via the Fc(epsilon)RI and identification of mast cells as a source of IL-11

scientific article

Transcriptome-wide mapping of pseudouridines: pseudouridine synthases modify specific mRNAs in S. cerevisiae

scientific article

Transformation of follicular lymphoma to diffuse large-cell lymphoma: alternative patterns with increased or decreased expression of c-myc and its regulated genes

scientific article

Trust, regulatory processes and NICE decision-making: Appraising cost-effectiveness models through appraising people and systems

scientific article published in February 2016

Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth

scientific article

Variation in gene expression patterns in follicular lymphoma and the response to rituximab

scientific article

Variation in gene expression patterns in human gastric cancers

scientific article published on 17 April 2003

Virtual Northern analysis of the human genome

scientific article

Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles

scientific article

Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae

scientific article

Why PLoS became a publisher

scientific article

Widespread cytoplasmic mRNA transport in yeast: identification of 22 bud-localized transcripts using DNA microarray analysis

scientific article

Widespread mRNA association with cytoskeletal motor proteins and identification and dynamics of myosin-associated mRNAs in S. cerevisiae

scientific article

Yeast microarrays for genome wide parallel genetic and gene expression analysis

scientific article

miR-142 regulates the tumorigenicity of human breast cancer stem cells through the canonical WNT signaling pathway

scientific article

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