Sandrine Dudoit

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Bioconductor: open software development for computational biology and bioinformatics
    Robert C Gentleman
    Department of Biostatistical Science, Dana Farber Cancer Institute, 44 Binney St, Boston, MA 02115, USA
    Genome Biol 5:R80. 2004
  2. pmc Resampling-based empirical Bayes multiple testing procedures for controlling generalized tail probability and expected value error rates: focus on the false discovery rate and simulation study
    Sandrine Dudoit
    Division of Biostatistics, University of California, Berkeley, 101 Haviland Hall, 7358, Berkeley, CA 94720 7358, USA
    Biom J 50:716-44. 2008
  3. pmc A prediction-based resampling method for estimating the number of clusters in a dataset
    Sandrine Dudoit
    Division of Biostatistics, School of Public Health, University of California Berkeley, 140 Earl Warren Hall, Berkeley, CA 94720 7360, USA
    Genome Biol 3:RESEARCH0036. 2002
  4. ncbi request reprint Bagging to improve the accuracy of a clustering procedure
    Sandrine Dudoit
    Division of Biostatistics, School of Public Health, University of California, Berkeley, 140 Earl Warren Hall, 7360, Berkeley, CA 94720 7360, USA
    Bioinformatics 19:1090-9. 2003
  5. pmc GenomeGraphs: integrated genomic data visualization with R
    Steffen Durinck
    Life Sciences Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
    BMC Bioinformatics 10:2. 2009
  6. ncbi request reprint A method to increase the power of multiple testing procedures through sample splitting
    Daniel Rubin
    Division of Biostatistics, School of Public Health, University of California, Berkeley, CA, USA
    Stat Appl Genet Mol Biol 5:Article19. 2006
  7. pmc Conservation of an RNA regulatory map between Drosophila and mammals
    Angela N Brooks
    Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
    Genome Res 21:193-202. 2011
  8. doi request reprint Silencing of odorant receptor genes by G protein βγ signaling ensures the expression of one odorant receptor per olfactory sensory neuron
    Todd Ferreira
    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA
    Neuron 81:847-59. 2014
  9. pmc A fine-scale linkage-disequilibrium measure based on length of haplotype sharing
    Yan Wang
    Division of Biostatistics, University of California, Berkeley, USA
    Am J Hum Genet 78:615-28. 2006
  10. ncbi request reprint Gene expression profiling of nonneoplastic mucosa may predict clinical outcome of colon cancer patients
    Alain Barrier
    Service de Chirurgie Digestive, Hopital Tenon, Universite Pierre et Marie Curie, Assistance Publique, Paris, France
    Dis Colon Rectum 48:2238-48. 2005

Research Grants

Detail Information

Publications28

  1. pmc Bioconductor: open software development for computational biology and bioinformatics
    Robert C Gentleman
    Department of Biostatistical Science, Dana Farber Cancer Institute, 44 Binney St, Boston, MA 02115, USA
    Genome Biol 5:R80. 2004
    ..We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples...
  2. pmc Resampling-based empirical Bayes multiple testing procedures for controlling generalized tail probability and expected value error rates: focus on the false discovery rate and simulation study
    Sandrine Dudoit
    Division of Biostatistics, University of California, Berkeley, 101 Haviland Hall, 7358, Berkeley, CA 94720 7358, USA
    Biom J 50:716-44. 2008
    ....
  3. pmc A prediction-based resampling method for estimating the number of clusters in a dataset
    Sandrine Dudoit
    Division of Biostatistics, School of Public Health, University of California Berkeley, 140 Earl Warren Hall, Berkeley, CA 94720 7360, USA
    Genome Biol 3:RESEARCH0036. 2002
    ..Here we address the first of these problems...
  4. ncbi request reprint Bagging to improve the accuracy of a clustering procedure
    Sandrine Dudoit
    Division of Biostatistics, School of Public Health, University of California, Berkeley, 140 Earl Warren Hall, 7360, Berkeley, CA 94720 7360, USA
    Bioinformatics 19:1090-9. 2003
    ..Essential aspects of this clustering problem include identifying accurate partitions of the tumor samples into clusters and assessing the confidence of cluster assignments for individual samples...
  5. pmc GenomeGraphs: integrated genomic data visualization with R
    Steffen Durinck
    Life Sciences Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
    BMC Bioinformatics 10:2. 2009
    ..In addition, genomic data analysis requires integrated visualization of experimental data along with constantly changing genomic annotation and statistical analyses...
  6. ncbi request reprint A method to increase the power of multiple testing procedures through sample splitting
    Daniel Rubin
    Division of Biostatistics, School of Public Health, University of California, Berkeley, CA, USA
    Stat Appl Genet Mol Biol 5:Article19. 2006
    ..This paper is an updated version of the work presented in Rubin et al. (2005), later expanded upon by Wasserman and Roeder (2006)...
  7. pmc Conservation of an RNA regulatory map between Drosophila and mammals
    Angela N Brooks
    Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
    Genome Res 21:193-202. 2011
    ..This observation suggests that the regulatory codes of individual RNA binding proteins may be nearly immutable, yet the regulatory modules controlled by these proteins are highly evolvable...
  8. doi request reprint Silencing of odorant receptor genes by G protein βγ signaling ensures the expression of one odorant receptor per olfactory sensory neuron
    Todd Ferreira
    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA
    Neuron 81:847-59. 2014
    ..These results link receptor activity with the epigenetic mechanisms responsible for ensuring the expression of one odorant receptor per olfactory sensory neuron...
  9. pmc A fine-scale linkage-disequilibrium measure based on length of haplotype sharing
    Yan Wang
    Division of Biostatistics, University of California, Berkeley, USA
    Am J Hum Genet 78:615-28. 2006
    ..These merits may offer new opportunities for mapping complex disease genes and for investigating recombination mechanisms on the basis of better-quantified LD...
  10. ncbi request reprint Gene expression profiling of nonneoplastic mucosa may predict clinical outcome of colon cancer patients
    Alain Barrier
    Service de Chirurgie Digestive, Hopital Tenon, Universite Pierre et Marie Curie, Assistance Publique, Paris, France
    Dis Colon Rectum 48:2238-48. 2005
    ..This study assessed the possibility to build a prognosis predictor, based on microarray gene expression measures, in Stage II and III colon cancer patients...
  11. ncbi request reprint Colon cancer prognosis prediction by gene expression profiling
    Alain Barrier
    Service de Chirurgie Digestive, Hopital Tenon, Universite Pierre et Marie Curie, Assistance Publique, 75020 Paris, France
    Oncogene 24:6155-64. 2005
    ..This study suggests that one can build an accurate prognosis predictor for stage II and III colon cancer patients, based on gene expression measures, and one can use either tumour or non-neoplastic mucosa for this purpose...
  12. pmc Biases in Illumina transcriptome sequencing caused by random hexamer priming
    Kasper D Hansen
    Division of Biostatistics, School of Public Health, UC Berkeley, 101 Haviland Hall, Berkeley, CA 94720 7358, USA
    Nucleic Acids Res 38:e131. 2010
    ..We provide a read count reweighting scheme, based on the nucleotide frequencies of the reads, that mitigates the impact of the bias...
  13. ncbi request reprint Open source software for the analysis of microarray data
    Sandrine Dudoit
    University of California, Berkeley, CA, USA
    Biotechniques . 2003
    ..bioconductor.org), the Java-based TM4 software system available from The Institute for Genomic Research (http://www.tigr.org/software), and BASE, the Web-based system developed at Lund University (http://base.thep.lu.se)...
  14. pmc Polygenic and directional regulatory evolution across pathways in Saccharomyces
    James H Bullard
    Division of Biostatistics, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 107:5058-63. 2010
    ..We suggest that pathway analyses, including our test for directional regulatory evolution, will prove to be a relevant and powerful strategy in many evolutionary genomic applications...
  15. pmc GC-content normalization for RNA-Seq data
    Davide Risso
    Division of Biostatistics and Department of Statistics, University of California, Berkeley, USA
    BMC Bioinformatics 12:480. 2011
    ..Normalization is therefore essential to ensure accurate inference of expression levels and subsequent analyses thereof...
  16. pmc The establishment of gene silencing at single-cell resolution
    Erin A Osborne
    Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
    Nat Genet 41:800-6. 2009
    ..Our findings showed that removal of methyl modifications at H3K4 and H3K79 were important steps in silent chromatin formation and that Jhd2 and Set1 had competing roles in the process...
  17. pmc Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
    James H Bullard
    Division of Biostatistics, University of California, Berkeley, Berkeley, CA, USA
    BMC Bioinformatics 11:94. 2010
    ..We provide a detailed evaluation of statistical methods for normalization and differential expression (DE) analysis of Illumina transcriptome sequencing (mRNA-Seq) data...
  18. pmc Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation
    Yee Hwa Yang
    Department of Statistics, Helen Wills Neuroscience Institute, University of California, Berkeley, CA 94720 3860, USA
    Nucleic Acids Res 30:e15. 2002
    ..Lastly, to allow for comparisons of expression levels across slides, a robust method based on maximum likelihood estimation is proposed to adjust for scale differences among slides...
  19. pmc Diverse transcriptional programs associated with environmental stress and hormones in the Arabidopsis receptor-like kinase gene family
    Lee Chae
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Mol Plant 2:84-107. 2009
    ..Taken as a whole, our study represents a preliminary, working model of processes and interactions in which the members of the RLK gene family may be involved, where such information has remained elusive for so many of its members...
  20. ncbi request reprint [Gene expression profiling in colon cancer]
    Alain Barrier
    Service de Chirurgie Digestive, Hopital Tenon, Paris
    Bull Acad Natl Med 191:1091-101; discussion 1102-3. 2007
    ..This study supports the possibility of predicting the prognosis of non-metastatic colon cancer by tumor gene expression profiling. It also shows the highly variable gene composition of predictive combinations...
  21. ncbi request reprint Stage II colon cancer prognosis prediction by tumor gene expression profiling
    Alain Barrier
    Service de Chirurgie Digestive, Hopital Tenon, 4 rue de la Chine, 75020 Paris, France
    J Clin Oncol 24:4685-91. 2006
    ..This study mainly aimed to identify and assess the performance of a microarray-based prognosis predictor (PP) for stage II colon cancer. A previously suggested 23-gene prognosis signature (PS) was also evaluated...
  22. ncbi request reprint Multiple testing methods for ChIP-Chip high density oligonucleotide array data
    Sunduz Keles
    Department of Statistics, University of Wisconsin, Madison, Madison, WI 53706, USA
    J Comput Biol 13:579-613. 2006
    ..Moreover, these target segments include the 13 experimentally verified p53 binding regions of Cawley et al. (2004), as well as 49 additional regions that show higher hybridization signal than these 13 experimentally verified regions...
  23. ncbi request reprint Exploration of global gene expression in human liver steatosis by high-density oligonucleotide microarray
    Franck Chiappini
    INSERM 602, Service de Biochimie et Biologie Moléculaire, Hôpital Universitaire Paul Brousse, Universite Paris XI, Villejuif Cedex, France
    Lab Invest 86:154-65. 2006
    ..Activation of inflammatory pathways is present at a very early stage of steatosis, even if no morphological sign of inflammation is observed...
  24. ncbi request reprint Survival ensembles
    Torsten Hothorn
    Institut für Medizininformatik, Biometrie und Epidemiologie, Friedrich Alexander Universitat Erlangen Nurnberg, Waldstrasse 6, D 91054 Erlangen, Germany
    Biostatistics 7:355-73. 2006
    ....
  25. ncbi request reprint Ischemic preconditioning modulates the expression of several genes, leading to the overproduction of IL-1Ra, iNOS, and Bcl-2 in a human model of liver ischemia-reperfusion
    Alain Barrier
    Inserm 602 Service de Biochimie et Biologie Moléculaire Hôpital Universitaire Paul Brousse Université Paris Sud XI, Villejuif Cedex Assistance Publique Hôpitaux de Paris, France
    FASEB J 19:1617-26. 2005
    ..Therefore, the benefits of IP may be associated with the overproduction of IL-1Ra, Bcl-2, and NO countering the proinflammatory and proapoptotic effects generated during ischemia-reperfusion...
  26. pmc Diversity, topographic differentiation, and positional memory in human fibroblasts
    Howard Y Chang
    Departments of Dermatology, Biochemistry, Pathology, and Genetics, and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 99:12877-82. 2002
    ....
  27. pmc Gene expression patterns in human liver cancers
    Xin Chen
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
    Mol Biol Cell 13:1929-39. 2002
    ..Some features of the gene expression patterns were associated with specific phenotypic and genotypic characteristics of the tumors, including growth rate, vascular invasion, and p53 overexpression...
  28. pmc Stereotyped and specific gene expression programs in human innate immune responses to bacteria
    Jennifer C Boldrick
    Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 99:972-7. 2002
    ..Modulation of this host-response program by bacterial virulence mechanisms was an important source of variation in the response to different bacteria...

Research Grants3

  1. Statistical Design & Analysis of Microarray Experiments
    Sandrine Dudoit; Fiscal Year: 2002
    ..To facilitate use and integration with biological information resources a web-browser interface will be provided. ..
  2. Statistical Design & Analysis of Microarray Experiments
    Sandrine Dudoit; Fiscal Year: 2003
    ..To facilitate use and integration with biological information resources a web-browser interface will be provided. ..
  3. Statistical Design & Analysis of Microarray Experiments
    Sandrine Dudoit; Fiscal Year: 2004
    ..To facilitate use and integration with biological information resources a web-browser interface will be provided. ..