Genomes and Genes
Robert J Tibshirani
Affiliation: Stanford University
- Boolean implication networks derived from large scale, whole genome microarray datasetsDebashis Sahoo
Department of Computer Science, Stanford University, Stanford, CA 94305, USA
Genome Biol 9:R157. 2008..These relationships capture gender differences, tissue differences, development, and differentiation. New relationships are discovered that are preserved across all three species...
- Discovery and validation of breast cancer subtypesAmy 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+...
- Cancer characterization and feature set extraction by discriminative margin clusteringKamesh 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...
- 'Gene shaving' as a method for identifying distinct sets of genes with similar expression patternsT Hastie
Department of Statistics, Sequoia Hall, Stanford University, Stanford, CA 94305, USA
Genome Biol 1:RESEARCH0003. 2000..The technique can be 'unsupervised', that is, the genes and samples are treated as unlabeled, or partially or fully supervised by using known properties of the genes or samples to assist in finding meaningful groupings...
- Univariate shrinkage in the cox model for high dimensional dataRobert J Tibshirani
Stanford University, USA
Stat Appl Genet Mol Biol 8:Article21. 2009..We illustrate the new method on real and simulated data, and compare it to other proposed methods for survival prediction with a large number of predictors...
- Spatial smoothing and hot spot detection for CGH data using the fused lassoRobert Tibshirani
Department of Health, Stanford University Stanford, CA 94305, USA
Biostatistics 9:18-29. 2008..Estimates of false-discovery rate are also provided. Our studies show that the new method generally outperforms competing methods for calling gains and losses in CGH data...
- Outlier sums for differential gene expression analysisRobert Tibshirani
Department of Health Research and Policy, Stanford University, Stanford, CA 94305, USA
Biostatistics 8:2-8. 2007..We also compare our approach to the recent cancer profile outlier analysis proposal of Tomlins and others (2005)...
- Diagnosis of multiple cancer types by shrunken centroids of gene expressionRobert Tibshirani
Department of Health, Research and Policy, and Statistics, Stanford University, Stanford, CA 94305, USA
Proc Natl Acad Sci U S A 99:6567-72. 2002..The technique is general and can be used in many other classification problems. To demonstrate its effectiveness, we show that the method was highly efficient in finding genes for classifying small round blue cell tumors and leukemias...
- Prediction of survival in diffuse large B-cell lymphoma based on the expression of 2 genes reflecting tumor and microenvironmentAsh A Alizadeh
Department of Medicine, Division of Oncology, Stanford University, Stanford, CA, USA
Blood 118:1350-8. 2011..We conclude that the measurement of a single gene expressed by tumor cells (LMO2) and a single gene expressed by the immune microenvironment (TNFRSF9) powerfully predicts overall survival in patients with DLBCL...
- Predicting patient survival from longitudinal gene expressionYuping Zhang
Stanford University, USA
Stat Appl Genet Mol Biol 9:Article41. 2010..Moreover, our method is consistently better than prediction methods using individual time point gene expression or simply pooling gene expression from each time point...
- Prognostic significance of VEGF, VEGF receptors, and microvessel density in diffuse large B cell lymphoma treated with anthracycline-based chemotherapyDita Gratzinger
Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305 5324, USA
Lab Invest 88:38-47. 2008..Dependence on autocrine vascular endothelial growth factor receptor-1-mediated signaling may render a subset of diffuse large B-cell lymphomas susceptible to anthracycline-based therapy...
- In situ vaccination with a TLR9 agonist induces systemic lymphoma regression: a phase I/II studyJoshua D Brody
269 Campus Dr CCSR rm 1105, Stanford, CA 94305, USA
J Clin Oncol 28:4324-32. 2010..In a preclinical lymphoma model, intratumoral injection of a Toll-like receptor 9 (TLR9) agonist induced systemic antitumor immunity and cured large, disseminated tumors...
- Molecular assessment of surgical-resection margins of gastric cancer by mass-spectrometric imagingLivia S Eberlin
Department of Chemistry, Stanford University, Stanford, CA 94305 5080
Proc Natl Acad Sci U S A 111:2436-41. 2014..The results obtained suggest that DESI-MSI/Lasso may be valuable for routine intraoperative assessment of the specimen margins during gastric-cancer surgery. ..
- Blood autoantibody and cytokine profiles predict response to anti-tumor necrosis factor therapy in rheumatoid arthritisWolfgang Hueber
Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305, USA
Arthritis Res Ther 11:R76. 2009..Since no clinical or laboratory tests are available to predict response to anti-TNF therapies, great need exists for predictive biomarkers...
- Extensions of sparse canonical correlation analysis with applications to genomic dataDaniela M Witten
Stanford University, USA
Stat Appl Genet Mol Biol 8:Article28. 2009..We demonstrate these new methods on simulated data and on a recently published and publicly available diffuse large B-cell lymphoma data set...
- Microvessel density and expression of vascular endothelial growth factor and its receptors in diffuse large B-cell lymphoma subtypesDita Gratzinger
Department of Pathology, Stanford University, Stanford, California, Stanford, CA 94305 5324, USA
Am J Pathol 170:1362-9. 2007..These differences may have important implications for the responsiveness of the two diffuse large B-cell lymphoma subtypes to anti-vascular endothelial growth factor and anti-angiogenic therapies...
- Polymorphisms in hypoxia inducible factor 1 and the initial clinical presentation of coronary diseaseMark A Hlatky
Department of Health Research and Policy, Stanford University School of Medicine, Stanford, CA 94305 5405, USA
Am Heart J 154:1035-42. 2007..The goal of this study was to assess whether polymorphisms in genes encoding elements of pathways mediating the response to ischemia affect vulnerability to MI among patients with underlying CAD...