Genomes and Genes
Affiliation: University of California
- Bioconductor: open software development for computational biology and bioinformaticsRobert 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...
- Bagging to improve the accuracy of a clustering procedureSandrine 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...
- 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 studySandrine Dudoit
Division of Biostatistics, University of California, Berkeley, 101 Haviland Hall, 7358, Berkeley, CA 94720 7358, USA
Biom J 50:716-44. 2008....
- A prediction-based resampling method for estimating the number of clusters in a datasetSandrine 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...
- GenomeGraphs: integrated genomic data visualization with RSteffen 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...
- A method to increase the power of multiple testing procedures through sample splittingDaniel 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)...
- Conservation of an RNA regulatory map between Drosophila and mammalsAngela 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...
- Colon cancer prognosis prediction by gene expression profilingAlain 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...
- Gene expression profiling of nonneoplastic mucosa may predict clinical outcome of colon cancer patientsAlain 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...
- A fine-scale linkage-disequilibrium measure based on length of haplotype sharingYan 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...
- Biases in Illumina transcriptome sequencing caused by random hexamer primingKasper 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...
- Open source software for the analysis of microarray dataSandrine 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)...
- Polygenic and directional regulatory evolution across pathways in SaccharomycesJames 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...
- GC-content normalization for RNA-Seq dataDavide 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...
- The establishment of gene silencing at single-cell resolutionErin 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...
- Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experimentsJames 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...
- Diverse transcriptional programs associated with environmental stress and hormones in the Arabidopsis receptor-like kinase gene familyLee 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...
- Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variationYee 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...
- Stage II colon cancer prognosis prediction by tumor gene expression profilingAlain 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...
- [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...
- Gene expression patterns in human liver cancersXin 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...
- Diversity, topographic differentiation, and positional memory in human fibroblastsHoward 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....
- Multiple testing methods for ChIP-Chip high density oligonucleotide array dataSunduz 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...
- 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-reperfusionAlain 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...
- Survival ensemblesTorsten Hothorn
Institut für Medizininformatik, Biometrie und Epidemiologie, Friedrich Alexander Universitat Erlangen Nurnberg, Waldstrasse 6, D 91054 Erlangen, Germany
Biostatistics 7:355-73. 2006....
- Exploration of global gene expression in human liver steatosis by high-density oligonucleotide microarrayFranck 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...
- Stereotyped and specific gene expression programs in human innate immune responses to bacteriaJennifer 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...
- Statistical Design & Analysis of Microarray ExperimentsSandrine Dudoit; Fiscal Year: 2004..To facilitate use and integration with biological information resources a web-browser interface will be provided. ..