Patrick O Brown

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. pmc Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types
    Julia Salzman
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS ONE 7:e30733. 2012
  2. pmc Widespread mRNA association with cytoskeletal motor proteins and identification and dynamics of myosin-associated mRNAs in S. cerevisiae
    Jason M Casolari
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS ONE 7:e31912. 2012
  3. pmc ESRRA-C11orf20 is a recurrent gene fusion in serous ovarian carcinoma
    Julia Salzman
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
    PLoS Biol 9:e1001156. 2011
  4. pmc Extensive gene-specific translational reprogramming in a model of B cell differentiation and Abl-dependent transformation
    Jamie G Bates
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS ONE 7:e37108. 2012
  5. pmc Stunned silence: gene expression programs in human cells infected with monkeypox or vaccinia virus
    Kathleen H Rubins
    Departments of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS ONE 6:e15615. 2011
  6. pmc The preclinical natural history of serous ovarian cancer: defining the target for early detection
    Patrick O Brown
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
    PLoS Med 6:e1000114. 2009
  7. pmc Transcriptional modulation of genes encoding structural characteristics of differentiating enterocytes during development of a polarized epithelium in vitro
    Jennifer M Halbleib
    Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
    Mol Biol Cell 18:4261-78. 2007
  8. pmc Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast
    Andre P Gerber
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
    PLoS Biol 2:E79. 2004
  9. pmc Determination of stromal signatures in breast carcinoma
    Robert B West
    Department of Pathology, Stanford University Medical Center, Stanford, California, USA
    PLoS Biol 3:e187. 2005
  10. pmc SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data
    Maximilian Diehn
    Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
    Nucleic Acids Res 31:219-23. 2003

Collaborators

Detail Information

Publications63

  1. pmc Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types
    Julia Salzman
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS ONE 7:e30733. 2012
    ..Our results suggest that a non-canonical mode of RNA splicing, resulting in a circular RNA isoform, is a general feature of the gene expression program in human cells...
  2. pmc Widespread mRNA association with cytoskeletal motor proteins and identification and dynamics of myosin-associated mRNAs in S. cerevisiae
    Jason M Casolari
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS ONE 7:e31912. 2012
    ....
  3. pmc ESRRA-C11orf20 is a recurrent gene fusion in serous ovarian carcinoma
    Julia Salzman
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
    PLoS Biol 9:e1001156. 2011
    ..Gene fusions involving adjacent or nearby genes can readily escape detection but may play important roles in the development and progression of cancer...
  4. pmc Extensive gene-specific translational reprogramming in a model of B cell differentiation and Abl-dependent transformation
    Jamie G Bates
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS ONE 7:e37108. 2012
    ..These results highlight a major role for gene-specific translational regulation in remodeling the gene expression program in differentiation and malignant transformation...
  5. pmc Stunned silence: gene expression programs in human cells infected with monkeypox or vaccinia virus
    Kathleen H Rubins
    Departments of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS ONE 6:e15615. 2011
    ..Thus, MPV selectively inhibits expression of genes with critical roles in cell-signaling pathways that activate innate immune responses, as part of its strategy for stealthy infection...
  6. pmc The preclinical natural history of serous ovarian cancer: defining the target for early detection
    Patrick O Brown
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
    PLoS Med 6:e1000114. 2009
    ..We can learn about this occult period by studying the unsuspected serous cancers that are discovered in a small fraction of apparently healthy women who undergo prophylactic bilateral salpingo-oophorectomy (PBSO)...
  7. pmc Transcriptional modulation of genes encoding structural characteristics of differentiating enterocytes during development of a polarized epithelium in vitro
    Jennifer M Halbleib
    Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
    Mol Biol Cell 18:4261-78. 2007
    ..Coordinated expression of genes encoding components of functional cell structures were often observed indicating temporal control of expression and assembly of multiprotein complexes...
  8. pmc Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast
    Andre P Gerber
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
    PLoS Biol 2:E79. 2004
    ....
  9. pmc Determination of stromal signatures in breast carcinoma
    Robert B West
    Department of Pathology, Stanford University Medical Center, Stanford, California, USA
    PLoS Biol 3:e187. 2005
    ..Our findings suggest that the host stromal response varies significantly among carcinomas and that gene expression patterns characteristic of soft tissue tumors can be used to discover new markers for normal connective tissue cells...
  10. pmc SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data
    Maximilian Diehn
    Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
    Nucleic Acids Res 31:219-23. 2003
    ..SOURCE is available at http://source.stanford.edu...
  11. pmc Characterization of heterotypic interaction effects in vitro to deconvolute global gene expression profiles in cancer
    Martin Buess
    Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
    Genome Biol 8:R191. 2007
    ..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 cancer...
  12. pmc Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA
    David G Hendrickson
    Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, USA
    PLoS Biol 7:e1000238. 2009
    ....
  13. pmc The Stanford Tissue Microarray Database
    Robert J Marinelli
    Department of Biochemistry, Stanford University School of Medicine, Howard Hughes Medical Institute, Stanford, CA, USA
    Nucleic Acids Res 36:D871-7. 2008
    ..The production server uses the Apache HTTP Server, Oracle Database and Perl application code. Source code is available to interested researchers under a no-cost license...
  14. pmc Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds
    Howard Y Chang
    Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
    PLoS Biol 2:E7. 2004
    ..Thus, the transcriptional signature of the response of fibroblasts to serum provides a possible link between cancer progression and wound healing, as well as a powerful predictor of the clinical course in several common carcinomas...
  15. pmc Gene expression patterns in pancreatic tumors, cells and tissues
    Anson W Lowe
    Department of Medicine, Stanford University Medical Center, Stanford, California, United States of America
    PLoS ONE 2:e323. 2007
    ..This study provides a comprehensive assessment of gene expression for pancreatic tumors, the normal pancreas, and nonneoplastic pancreatic disease...
  16. pmc Gene expression patterns in ovarian carcinomas
    Marci E Schaner
    Stanford University School of Medicine, Stanford, California 94305 5151, USA
    Mol Biol Cell 14:4376-86. 2003
    ....
  17. pmc Parallels between global transcriptional programs of polarizing Caco-2 intestinal epithelial cells in vitro and gene expression programs in normal colon and colon cancer
    Annika M Sääf
    Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
    Mol Biol Cell 18:4245-60. 2007
    ..The full data set is available at http://microarray-pubs.stanford.edu/CACO2...
  18. pmc Anatomic demarcation by positional variation in fibroblast gene expression programs
    John L Rinn
    Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
    PLoS Genet 2:e119. 2006
    ..Together, these findings suggest that site-specific variations in fibroblast gene expression programs are not idiosyncratic but rather are systematically related to their positional identities relative to major anatomic axes...
  19. pmc The temporal program of peripheral blood gene expression in the response of nonhuman primates to Ebola hemorrhagic fever
    Kathleen H Rubins
    Department of Microbiology and Immunology, 299 Campus Dr, Stanford University School of Medicine, Stanford, California 94305, USA
    Genome Biol 8:R174. 2007
    ..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 examined the molecular features of EBOV infection in vivo...
  20. pmc Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae
    Evan H Hurowitz
    Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305 5307, USA
    Genome Biol 5:R2. 2003
    ..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 of the untranslated regions of yeast mRNAs...
  21. pmc DNA methylation profiles of ovarian epithelial carcinoma tumors and cell lines
    Sahar Houshdaran
    Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, California, United States of America
    PLoS ONE 5:e9359. 2010
    ..This study applied recently developed methods for high-throughput DNA methylation profiling to characterize ovarian cancer cell lines and tumors, including representatives of three major histologies...
  22. pmc The host response to smallpox: analysis of the gene expression program in peripheral blood cells in a nonhuman primate model
    Kathleen H Rubins
    Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 101:15190-5. 2004
    ..These results provide a detailed picture of the host transcriptional response during smallpox infection, and may help guide the development of diagnostic, therapeutic, and prophylactic strategies...
  23. pmc The novel marker, DOG1, is expressed ubiquitously in gastrointestinal stromal tumors irrespective of KIT or PDGFRA mutation status
    Robert B West
    Department of Pathology, Stanford University Medical Center, 300 Pasteur Drive, Stanford, CA 94305, USA
    Am J Pathol 165:107-13. 2004
    ..Reactivity for DOG1 may aid in the diagnosis of GISTs, including PDGFRA mutants that fail to express KIT antigen, and lead to appropriate treatment with imatinib mesylate, an inhibitor of the KIT tyrosine kinase...
  24. pmc The Stanford Microarray Database: implementation of new analysis tools and open source release of software
    Janos Demeter
    Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
    Nucleic Acids Res 35:D766-70. 2007
    ..In this article, we describe several data analysis tools implemented in SMD and we discuss features of our software release...
  25. pmc Bone morphogenetic protein antagonist gremlin 1 is widely expressed by cancer-associated stromal cells and can promote tumor cell proliferation
    Julie B Sneddon
    Department of Biochemistry, Stanford University Medical Center, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 103:14842-7. 2006
    ..Our data suggest that BMP antagonists may be important constituents of tumor stroma, providing a favorable microenvironment for cancer cell survival and expansion in many cancers...
  26. pmc The Stanford Microarray Database accommodates additional microarray platforms and data formats
    Catherine A Ball
    Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
    Nucleic Acids Res 33:D580-2. 2005
    ..The latest version of the source code for the complete database package was released in November 2004 (http://smd.stanford.edu/download/), allowing researchers around the world to deploy their own installations of SMD...
  27. pmc Cell-type specific gene expression profiles of leukocytes in human peripheral blood
    Chana Palmer
    Department of Genetics, Stanford University School of Medicine, Stanford, USA
    BMC Genomics 7:115. 2006
    ..We did this by comparing the global gene expression profiles of purified B-cells, CD4+ T-cells, CD8+ T-cells, granulocytes, and lymphocytes using cDNA microarrays...
  28. pmc Gene expression programs in response to hypoxia: cell type specificity and prognostic significance in human cancers
    Jen Tsan Chi
    Department of Biochemistry, Stanford University School of Medicine, Palo Alto, California, United States of America
    PLoS Med 3:e47. 2006
    ....
  29. pmc Dissecting eukaryotic translation and its control by ribosome density mapping
    Yoav Arava
    Howard Hughes Medical Institute, Stanford, CA 94305 5428, USA
    Nucleic Acids Res 33:2421-32. 2005
    ..These results provide new insights into eukaryotic translation in vivo...
  30. pmc Diverse and specific gene expression responses to stresses in cultured human cells
    John Isaac Murray
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
    Mol Biol Cell 15:2361-74. 2004
    ..The dataset is freely available for search and download at http://microarray-pubs.stanford.edu/human_stress/Home.shtml...
  31. pmc The yeast Rab GTPase Ypt1 modulates unfolded protein response dynamics by regulating the stability of HAC1 RNA
    Nikoleta G Tsvetanova
    Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
    PLoS Genet 8:e1002862. 2012
    ..Our findings establish that Ypt1 contributes to regulation of UPR signaling dynamics by promoting the decay of HAC1 RNA, suggesting a potential regulatory mechanism for linking vesicle trafficking to the UPR and ER homeostasis...
  32. pmc Comparative analysis of viral gene expression programs during poxvirus infection: a transcriptional map of the vaccinia and monkeypox genomes
    Kathleen H Rubins
    Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS ONE 3:e2628. 2008
    ..Poxviruses engage in a complex and intricate dialogue with host cells as part of their strategy for replication. However, relatively little molecular detail is available with which to understand the mechanisms behind this dialogue...
  33. pmc A DNA microarray survey of gene expression in normal human tissues
    Radha Shyamsundar
    Department of Pathology, Stanford University School of Medicine, 269 Campus Drive, CCSR 3245A, Stanford, CA 94305 5176, USA
    Genome Biol 6:R22. 2005
    ....
  34. ncbi request reprint Apo D in soft tissue tumors: a novel marker for dermatofibrosarcoma protuberans
    Robert B West
    Department of Pathology, Stanford University Medical Center, 300 Pasteur Drive, Stanford, CA 94305, USA
    Am J Surg Pathol 28:1063-9. 2004
    ..stanford.edu/tma_portal/apod/). We conclude that Apo D is strongly expressed in DFSPs and neural lesions and may be useful in differentiating DFSP from fibrous histiocytoma...
  35. pmc Cell-type specific features of circular RNA expression
    Julia Salzman
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS Genet 9:e1003777. 2013
    ..These results suggest that biogenesis of circular RNA is an integral, conserved, and regulated feature of the gene expression program. ..
  36. pmc Dissecting interferon-induced transcriptional programs in human peripheral blood cells
    Simon J Waddell
    Department of Medicine, Stanford University, Stanford, California, United States of America
    PLoS ONE 5:e9753. 2010
    ..This information provides a detailed view of cellular activation by immune mediators, and contributes an interpretive framework for the definition of host immune responses in a variety of disease settings...
  37. pmc Genome-scale identification of membrane-associated human mRNAs
    Maximilian Diehn
    Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California, USA
    PLoS Genet 2:e11. 2006
    ..The large-scale annotation of subcellular localization reported here will serve as a reference database and will aid in the rational design of diagnostic tests and molecular therapies for diverse diseases...
  38. pmc Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae
    Yoav Arava
    Department of Biochemistry, Stanford University, Stanford, CA 94305 5307, USA
    Proc Natl Acad Sci U S A 100:3889-94. 2003
    ..Global analysis revealed an unexpected correlation: Ribosome density decreases with increasing ORF length. Models to account for this surprising observation are discussed...
  39. pmc Defining the specificity of cotranslationally acting chaperones by systematic analysis of mRNAs associated with ribosome-nascent chain complexes
    Marta del Alamo
    Department of Biology and BioX Program, Stanford University, Stanford, California, United States of America
    PLoS Biol 9:e1001100. 2011
    ..The strategy we used should be generally applicable to mapping the specificity, interplay, and dynamics of the cotranslational protein homeostasis network...
  40. pmc Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors
    Jonathan R Pollack
    Departments of Pathology, Genetics, Surgery, Health Research and Policy, and Biochemistry, and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 99:12963-8. 2002
    ..These findings provide evidence that widespread DNA copy number alteration can lead directly to global deregulation of gene expression, which may contribute to the development or progression of cancer...
  41. pmc Improved discovery of molecular interactions in genome-scale data with adaptive model-based normalization
    Julia Salzman
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
    PLoS ONE 8:e53930. 2013
    ....
  42. pmc 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
    Paul Martin Holterhus
    Department of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Genome Biol 4:R37. 2003
    ....
  43. pmc Discovery and validation of breast cancer subtypes
    Amy V Kapp
    Department of Statistics, Stanford University, Stanford, CA, USA
    BMC Genomics 7:231. 2006
    ..The most recent study presented evidence for the existence of five different subtypes: normal breast-like, basal, luminal A, luminal B, and ERBB2+...
  44. pmc Endothelial cell diversity revealed by global expression profiling
    Jen Tsan Chi
    Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 100:10623-8. 2003
    ..Tissue-specific expression patterns in different tissue microvascular ECs suggest they are distinct differentiated cell types that play roles in the local physiology of their respective organs and tissues...
  45. pmc Marked differences in human melanoma antigen-specific T cell responsiveness after vaccination using a functional microarray
    Daniel S Chen
    Department of Internal Medicine Division of Oncology, Stanford University, Stanford, California, United States of America
    PLoS Med 2:e265. 2005
    ..In contrast to many animal model studies, immunotherapeutic trials in humans suffering from cancer invariably result in a broad range of outcomes, from long-lasting remissions to no discernable effect...
  46. pmc Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival
    Howard Y Chang
    Program in Epithelial Biology, Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 102:3738-43. 2005
    ....
  47. pmc Exploring the regulation of human neural precursor cell differentiation using arrays of signaling microenvironments
    Yoav Soen
    Department of Biochemistry, Stanford University, Stanford, CA 94305 5307, USA
    Mol Syst Biol 2:37. 2006
    ....
  48. pmc Individuality and variation in gene expression patterns in human blood
    Adeline R Whitney
    Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 100:1896-901. 2003
    ..These data help to define human individuality and provide a database with which disease-associated gene expression patterns can be compared...
  49. pmc Development of the human infant intestinal microbiota
    Chana Palmer
    Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS Biol 5:e177. 2007
    ..By the end of the first year of life, the idiosyncratic microbial ecosystems in each baby, although still distinct, had converged toward a profile characteristic of the adult gastrointestinal tract...
  50. pmc Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system
    Daniel J Hogan
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS Biol 6:e255. 2008
    ..These results strongly suggest that combinatorial binding of RBPs to specific recognition elements in mRNAs is a pervasive mechanism for multi-dimensional regulation of their post-transcriptional fate...
  51. pmc A landscape effect in tenosynovial giant-cell tumor from activation of CSF1 expression by a translocation in a minority of tumor cells
    Robert B West
    Department of Pathology, Stanford University Medical Center, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 103:690-5. 2006
    ....
  52. pmc Virtual Northern analysis of the human genome
    Evan H Hurowitz
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS ONE 2:e460. 2007
    ..We applied the Virtual Northern technique to human brain mRNA to systematically measure human mRNA transcript lengths on a genome-wide scale...
  53. pmc Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome
    Daniel P Riordan
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
    Nucleic Acids Res 39:1501-9. 2011
    ....
  54. pmc Three-dimensional tracking of single mRNA particles in Saccharomyces cerevisiae using a double-helix point spread function
    Michael A Thompson
    Department of Chemistry, Stanford University, Stanford, CA 94305 5080, USA
    Proc Natl Acad Sci U S A 107:17864-71. 2010
    ..The quantitative methods detailed in this paper can be broadly applied to the study of mRNA localization and the dynamics of diverse other biomolecules in a wide variety of cell types...
  55. pmc Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance
    David G Hendrickson
    Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS ONE 3:e2126. 2008
    ..Microarray analysis of Ago2 immunopurified samples provides a simple, direct method for experimentally identifying the targets of miRNAs and for elucidating roles of miRNAs in cellular regulation...
  56. pmc Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation
    Maximilian Diehn
    Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 99:11796-801. 2002
    ....
  57. pmc Variation in gene expression patterns in follicular lymphoma and the response to rituximab
    Sean P Bohen
    Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 100:1926-30. 2003
    ..These findings suggest the possibility that the response of follicular lymphoma to rituximab treatment may be predicted from the gene expression pattern of tumors...
  58. pmc Quantitative proteomic analysis reveals concurrent RNA-protein interactions and identifies new RNA-binding proteins in Saccharomyces cerevisiae
    Daniel M Klass
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
    Genome Res 23:1028-38. 2013
    ..While existing methods can identify sets of RBPs that interact with common RNA targets, our approach can determine which of those interactions are concurrent-a crucial distinction for understanding post-transcriptional regulation...
  59. pmc A method for detecting and correcting feature misidentification on expression microarrays
    I Ping Tu
    Functional Genomics Facility, Stanford University School of Medicine, Stanford, CA, USA
    BMC Genomics 5:64. 2004
    ..In this paper, we describe our statistical methods to detect the inconsistencies in microarray data that arise from process errors, and discuss our technique to locate and fix these errors...
  60. pmc Cancer characterization and feature set extraction by discriminative margin clustering
    Kamesh Munagala
    Department of Biochemistry, Stanford University School of Medicine, 466 Gates Computer Science, Stanford, CA 94305, USA
    BMC Bioinformatics 5:21. 2004
    ..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 cancer, from all normal cells and tissues...
  61. pmc Identification of genes periodically expressed in the human cell cycle and their expression in tumors
    Michael L Whitfield
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
    Mol Biol Cell 13:1977-2000. 2002
    ..The data in this report provide a comprehensive catalog of cell cycle regulated genes that can serve as a starting point for functional discovery. The full dataset is available at http://genome-www.stanford.edu/Human-CellCycle/HeLa/...
  62. pmc Repeated observation of breast tumor subtypes in independent gene expression data sets
    Therese Sorlie
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 100:8418-23. 2003
    ..Our results strongly support the idea that many of these breast tumor subtypes represent biologically distinct disease entities...