Publications
-
Local false discovery rate facilitates comparison of different microarray experiments.
Hong WJ,
Tibshirani R, Chu G.
Nucleic Acids Res.
2009
-
Lymphoma cell VEGFR2 expression detected by immunohistochemistry predicts poor overall survival in diffuse large B cell lymphoma treated with immunochemotherapy (R-CHOP).
Gratzinger D,
Advani R, Zhao S, Talreja N, Tibshirani RJ, Shyam R, Horning S, Sehn LH, Farinha P, Briones J, Lossos IS, Gascoyne RD, Natkunam Y.
Br J Haematol.
2009
-
Relationship of differential gene expression profiles in CD34+ myelodysplastic syndrome marrow cells to disease subtype and progression.
Sridhar K,
Ross DT, Tibshirani R, Butte AJ, Greenberg PL.
Blood.
2009
-
Disease signatures are robust across tissues and experiments.
Dudley JT,
Tibshirani R, Deshpande T, Butte AJ.
Mol Syst Biol.
2009:
5
307
-
Survival analysis with high-dimensional covariates.
Witten DM,
Tibshirani R.
Stat Methods Med Res.
2009
-
Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling.
Beck AH,
Lee CH, Witten DM, Gleason BC, Edris B, Espinosa I, Zhu S, Li R, Montgomery KD, Marinelli RJ, Tibshirani R, Hastie T, Jablons DM, Rubin BP, Fletcher CD, West RB, van de Rijn M.
Oncogene.
2009
-
Alteration of gene expression signatures of cortical differentiation and wound response in lethal clear cell renal cell carcinomas.
Zhao H,
Zongming Ma, Tibshirani R, Higgins JP, Ljungberg B, Brooks JD.
PLoS One.
2009;
4
(6):
e6039
-
Univariate shrinkage in the cox model for high dimensional data.
Tibshirani RJ,
Stat Appl Genet Mol Biol.
2009;
8
(1):
Article21
-
A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis.
Witten DM,
Tibshirani R, Hastie T.
Biostatistics.
2009;
10
(3):
515-34
-
Temporal changes in gene expression induced by sulforaphane in human prostate cancer cells.
Bhamre S,
Sahoo D, Tibshirani R, Dill DL, Brooks JD.
Prostate.
2009;
69
(2):
181-90
-
Extensions of sparse canonical correlation analysis with applications to genomic data.
Witten DM,
Tibshirani RJ.
Stat Appl Genet Mol Biol.
2009;
8
(1):
Article28
-
Complementary hierarchical clustering.
Nowak G,
Tibshirani R.
Biostatistics.
2008;
9
(3):
467-83
-
TESTING SIGNIFICANCE OF FEATURES BY LASSOED PRINCIPAL COMPONENTS.
Witten DM,
Tibshirani R.
Ann Appl Stat.
2008;
2
(3):
986-1012
-
IRF9 and STAT1 are required for IgG autoantibody production and B cell expression of TLR7 in mice.
Thibault DL,
Chu AD, Graham KL, Balboni I, Lee LY, Kohlmoos C, Landrigan A, Higgins JP, Tibshirani R, Utz PJ.
J Clin Invest.
2008;
118
(4):
1417-26
-
hCAP-D3 expression marks a prostate cancer subtype with favorable clinical behavior and androgen signaling signature.
Lapointe J,
Malhotra S, Higgins JP, Bair E, Thompson M, Salari K, Giacomini CP, Ferrari M, Montgomery K, Tibshirani R, van de Rijn M, Brooks JD, Pollack JR.
Am J Surg Pathol.
2008;
32
(2):
205-9
-
Multiplexed proximity ligation assays to profile putative plasma biomarkers relevant to pancreatic and ovarian cancer.
Fredriksson S,
Horecka J, Brustugun OT, Schlingemann J, Koong AC, Tibshirani R, Davis RW.
Clin Chem.
2008;
54
(3):
582-9
-
Sparse inverse covariance estimation with the graphical lasso.
Friedman J,
Hastie T, Tibshirani R.
Biostatistics.
2008;
9
(3):
432-41
-
LMO2 protein expression predicts survival in patients with diffuse large B-cell lymphoma treated with anthracycline-based chemotherapy with and without rituximab.
Natkunam Y,
Farinha P, Hsi ED, Hans CP, Tibshirani R, Sehn LH, Connors JM, Gratzinger D, Rosado M, Zhao S, Pohlman B, Wongchaowart N, Bast M, Avigdor A, Schiby G, Nagler A, Byrne GE, Levy R, Gascoyne RD, Lossos IS.
J Clin Oncol.
2008;
26
(3):
447-54
-
Prognostic significance of VEGF, VEGF receptors, and microvessel density in diffuse large B cell lymphoma treated with anthracycline-based chemotherapy.
Gratzinger D,
Zhao S, Tibshirani RJ, Hsi ED, Hans CP, Pohlman B, Bast M, Avigdor A, Schiby G, Nagler A, Byrne GE, Lossos IS, Natkunam Y.
Lab Invest.
2008;
88
(1):
38-47
-
Spatial smoothing and hot spot detection for CGH data using the fused lasso.
Tibshirani R,
Wang P.
Biostatistics.
2008;
9
(1):
18-29
-
Regularized linear discriminant analysis and its application in microarrays.
Guo Y,
Hastie T, Tibshirani R.
Biostatistics.
2007;
8
(1):
86-100
-
Averaged gene expressions for regression.
Park MY,
Hastie T, Tibshirani R.
Biostatistics.
2007;
8
(2):
212-27
-
Notch signals positively regulate activity of the mTOR pathway in T-cell acute lymphoblastic leukemia.
Chan SM,
Weng AP, Tibshirani R, Aster JC, Utz PJ.
Blood.
2007;
110
(1):
278-86
-
Extracting binary signals from microarray time-course data.
Sahoo D,
Dill DL, Tibshirani R, Plevritis SK.
Nucleic Acids Res.
2007;
35
(11):
3705-12
-
Outlier sums for differential gene expression analysis.
Tibshirani R,
Hastie T.
Biostatistics.
2007;
8
(1):
2-8
-
Oncogenic regulators and substrates of the anaphase promoting complex/cyclosome are frequently overexpressed in malignant tumors.
Lehman NL,
Tibshirani R, Hsu JY, Natkunam Y, Harris BT, West RB, Masek MA, Montgomery K, van de Rijn M, Jackson PK.
Am J Pathol.
2007;
170
(5):
1793-805
-
Expression and prognostic significance of a panel of tissue hypoxia markers in head-and-neck squamous cell carcinomas.
Le QT,
Kong C, Lavori PW, O'byrne K, Erler JT, Huang X, Chen Y, Cao H, Tibshirani R, Denko N, Giaccia AJ, Koong AC.
Int J Radiat Oncol Biol Phys.
2007;
69
(1):
167-75
-
Polymorphisms in hypoxia inducible factor 1 and the initial clinical presentation of coronary disease.
Hlatky MA,
Quertermous T, Boothroyd DB, Priest JR, Glassford AJ, Myers RM, Fortmann SP, Iribarren C, Tabor HK, Assimes TL, Tibshirani RJ, Go AS.
Am Heart J.
2007;
154
(6):
1035-42
-
Are clusters found in one dataset present in another dataset?
Kapp AV,
Tibshirani R.
Biostatistics.
2007;
8
(1):
9-31
-
Microvessel density and expression of vascular endothelial growth factor and its receptors in diffuse large B-cell lymphoma subtypes.
Gratzinger D,
Zhao S, Marinelli RJ, Kapp AV, Tibshirani RJ, Hammer AS, Hamilton-Dutoit S, Natkunam Y.
Am J Pathol.
2007;
170
(4):
1362-9
-
Disease-specific genomic analysis: identifying the signature of pathologic biology.
Nicolau M,
Tibshirani R, Børresen-Dale AL, Jeffrey SS.
Bioinformatics.
2007;
23
(8):
957-65
-
Global transcriptional response to interferon is a determinant of HCV treatment outcome and is modified by race.
He XS,
Ji X, Hale MB, Cheung R, Ahmed A, Guo Y, Nolan GP, Pfeffer LM, Wright TL, Risch N, Tibshirani R, Greenberg HB.
Hepatology.
2006;
44
(2):
352-9
-
Discovery and validation of breast cancer subtypes.
Kapp AV,
Jeffrey SS, Langerød A, Børresen-Dale AL, Han W, Noh DY, Bukholm IR, Nicolau M, Brown PO, Tibshirani R.
BMC Genomics.
2006:
7
231
-
Gene expression profiling predicts survival in conventional renal cell carcinoma.
Zhao H,
Ljungberg B, Grankvist K, Rasmuson T, Tibshirani R, Brooks JD.
PLoS Med.
2006;
3
(1):
e13
-
A tail strength measure for assessing the overall univariate significance in a dataset.
Taylor J,
Tibshirani R.
Biostatistics.
2006;
7
(2):
167-81
-
A simple method for assessing sample sizes in microarray experiments.
Tibshirani R,
BMC Bioinformatics.
2006:
7
106
-
Changes of gene expression in gastric preneoplasia following Helicobacter pylori eradication therapy.
Tsai CJ,
Herrera-Goepfert R, Tibshirani RJ, Yang S, Mohar A, Guarner J, Parsonnet J.
Cancer Epidemiol Biomarkers Prev.
2006;
15
(2):
272-80
-
An evaluation of tumor oxygenation and gene expression in patients with early stage non-small cell lung cancers.
Le QT,
Chen E, Salim A, Cao H, Kong CS, Whyte R, Donington J, Cannon W, Wakelee H, Tibshirani R, Mitchell JD, Richardson D, O'Byrne KJ, Koong AC, Giaccia AJ.
Clin Cancer Res.
2006;
12
(5):
1507-14
-
Combined microarray analysis of small cell lung cancer reveals altered apoptotic balance and distinct expression signatures of MYC family gene amplification.
Kim YH,
Girard L, Giacomini CP, Wang P, Hernandez-Boussard T, Tibshirani R, Minna JD, Pollack JR.
Oncogene.
2006;
25
(1):
130-8
-
Signature patterns of gene expression in mouse atherosclerosis and their correlation to human coronary disease.
Tabibiazar R,
Wagner RA, Ashley EA, King JY, Ferrara R, Spin JM, Sanan DA, Narasimhan B, Tibshirani R, Tsao PS, Efron B, Quertermous T.
Physiol Genomics.
2005;
22
(2):
213-26
-
Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival.
Chang HY,
Nuyten DS, Sneddon JB, Hastie T, Tibshirani R, Sørlie T, Dai H, He YD, van't Veer LJ, Bartelink H, van de Rijn M, Brown PO, van de Vijver MJ.
Proc Natl Acad Sci U S A.
2005;
102
(10):
3738-43
-
The 'miss rate' for the analysis of gene expression data.
Taylor J,
Tibshirani R, Efron B.
Biostatistics.
2005;
6
(1):
111-7
-
A method for calling gains and losses in array CGH data.
Wang P,
Kim Y, Pollack J, Narasimhan B, Tibshirani R.
Biostatistics.
2005;
6
(1):
45-58
-
Mouse strain-specific differences in vascular wall gene expression and their relationship to vascular disease.
Tabibiazar R,
Wagner RA, Spin JM, Ashley EA, Narasimhan B, Rubin EM, Efron B, Tsao PS, Tibshirani R, Quertermous T.
Arterioscler Thromb Vasc Biol.
2005;
25
(2):
302-8
-
Genome-wide characterization of gene expression variations and DNA copy number changes in prostate cancer cell lines.
Zhao H,
Kim Y, Wang P, Lapointe J, Tibshirani R, Pollack JR, Brooks JD.
Prostate.
2005;
63
(2):
187-97
-
Array-based comparative genomic hybridization identifies localized DNA amplifications and homozygous deletions in pancreatic cancer.
Bashyam MD,
Bair R, Kim YH, Wang P, Hernandez-Boussard T, Karikari CA, Tibshirani R, Maitra A, Pollack JR.
Neoplasia.
2005;
7
(6):
556-62
-
Gene expression profiling differentiates germ cell tumors from other cancers and defines subtype-specific signatures.
Juric D,
Sale S, Hromas RA, Yu R, Wang Y, Duran GE, Tibshirani R, Einhorn LH, Sikic BI.
Proc Natl Acad Sci U S A.
2005;
102
(49):
17763-8
-
Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes.
Lossos IS,
Czerwinski DK, Alizadeh AA, Wechser MA, Tibshirani R, Botstein D, Levy R.
N Engl J Med.
2004;
350
(18):
1828-37
-
Efficient quadratic regularization for expression arrays.
Hastie T,
Tibshirani R.
Biostatistics.
2004;
5
(3):
329-40
-
Gene expression profiling identifies clinically relevant subtypes of prostate cancer.
Lapointe J,
Li C, Higgins JP, van de Rijn M, Bair E, Montgomery K, Ferrari M, Egevad L, Rayford W, Bergerheim U, Ekman P, DeMarzo AM, Tibshirani R, Botstein D, Brown PO, Brooks JD, Pollack JR.
Proc Natl Acad Sci U S A.
2004;
101
(3):
811-6
-
Different gene expression patterns in invasive lobular and ductal carcinomas of the breast.
Zhao H,
Langerød A, Ji Y, Nowels KW, Nesland JM, Tibshirani R, Bukholm IK, Kåresen R, Botstein D, Børresen-Dale AL, Jeffrey SS.
Mol Biol Cell.
2004;
15
(6):
2523-36
-
Cancer characterization and feature set extraction by discriminative margin clustering.
Munagala K,
Tibshirani R, Brown PO.
BMC Bioinformatics.
2004:
5
21
-
Use of gene-expression profiling to identify prognostic subclasses in adult acute myeloid leukemia.
Bullinger L,
Döhner K, Bair E, Fröhling S, Schlenk RF, Tibshirani R, Döhner H, Pollack JR.
N Engl J Med.
2004;
350
(16):
1605-16
-
Semi-supervised methods to predict patient survival from gene expression data.
Bair E,
Tibshirani R.
PLoS Biol.
2004;
2
(4):
E108
-
Sample classification from protein mass spectrometry, by 'peak probability contrasts'.
Tibshirani R,
Hastie T, Narasimhan B, Soltys S, Shi G, Koong A, Le QT.
Bioinformatics.
2004;
20
(17):
3034-44
-
Gene expression profiles at diagnosis in de novo childhood AML patients identify FLT3 mutations with good clinical outcomes.
Lacayo NJ,
Meshinchi S, Kinnunen P, Yu R, Wang Y, Stuber CM, Douglas L, Wahab R, Becton DL, Weinstein H, Chang MN, Willman CL, Radich JP, Tibshirani R, Ravindranath Y, Sikic BI, Dahl GV.
Blood.
2004;
104
(9):
2646-54
-
The use of plasma surface-enhanced laser desorption/ionization time-of-flight mass spectrometry proteomic patterns for detection of head and neck squamous cell cancers.
Soltys SG,
Le QT, Shi G, Tibshirani R, Giaccia AJ, Koong AC.
Clin Cancer Res.
2004;
10
(14):
4806-12
-
Developmental response to hypoxia.
Huang ST,
Vo KC, Lyell DJ, Faessen GH, Tulac S, Tibshirani R, Giaccia AJ, Giudice LC.
FASEB J.
2004;
18
(12):
1348-65
-
Toxicity from radiation therapy associated with abnormal transcriptional responses to DNA damage.
Rieger KE,
Hong WJ, Tusher VG, Tang J, Tibshirani R, Chu G.
Proc Natl Acad Sci U S A.
2004;
101
(17):
6635-40
-
Statistical methods for identifying differentially expressed genes in DNA microarrays.
Storey JD,
Tibshirani R.
Methods Mol Biol.
2003:
224
149-57
-
Note on "Comparison of model selection for regression" by Vladimir Cherkassky and Yunqian Ma.
Hastie T,
Tibshirani R, Friedman J.
Neural Comput.
2003;
15
(7):
1477-80
-
Repeated observation of breast tumor subtypes in independent gene expression data sets.
Sorlie T,
Tibshirani R, Parker J, Hastie T, Marron JS, Nobel A, Deng S, Johnsen H, Pesich R, Geisler S, Demeter J, Perou CM, Lønning PE, Brown PO, Børresen-Dale AL, Botstein D.
Proc Natl Acad Sci U S A.
2003;
100
(14):
8418-23
-
Gene expression patterns in ovarian carcinomas.
Schaner ME,
Ross DT, Ciaravino G, Sorlie T, Troyanskaya O, Diehn M, Wang YC, Duran GE, Sikic TL, Caldeira S, Skomedal H, Tu IP, Hernandez-Boussard T, Johnson SW, O'Dwyer PJ, Fero MJ, Kristensen GB, Borresen-Dale AL, Hastie T, Tibshirani R, van de Rijn M, Teng NN, Longacre TA, Botstein D, Brown PO, Sikic BI.
Mol Biol Cell.
2003;
14
(11):
4376-86
-
Characterization of variant patterns of nodular lymphocyte predominant hodgkin lymphoma with immunohistologic and clinical correlation.
Fan Z,
Natkunam Y, Bair E, Tibshirani R, Warnke RA.
Am J Surg Pathol.
2003;
27
(10):
1346-56
-
HGAL is a novel interleukin-4-inducible gene that strongly predicts survival in diffuse large B-cell lymphoma.
Lossos IS,
Alizadeh AA, Rajapaksa R, Tibshirani R, Levy R.
Blood.
2003;
101
(2):
433-40
-
Precision and functional specificity in mRNA decay.
Wang Y,
Liu CL, Storey JD, Tibshirani RJ, Herschlag D, Brown PO.
Proc Natl Acad Sci U S A.
2002;
99
(9):
5860-5
-
Diagnosis of multiple cancer types by shrunken centroids of gene expression.
Tibshirani R,
Hastie T, Narasimhan B, Chu G.
Proc Natl Acad Sci U S A.
2002;
99
(10):
6567-72
-
Empirical bayes methods and false discovery rates for microarrays.
Efron B,
Tibshirani R.
Genet Epidemiol.
2002;
23
(1):
70-86
-
Transcriptional programs activated by exposure of human prostate cancer cells to androgen.
DePrimo SE,
Diehn M, Nelson JB, Reiter RE, Matese J, Fero M, Tibshirani R, Brown PO, Brooks JD.
Genome Biol.
2002;
3
(7):
RESEARCH0032
-
Pre-validation and inference in microarrays.
Tibshirani RJ,
Efron B.
Stat Appl Genet Mol Biol.
2002:
1
Article1
-
Expression of cytokeratins 17 and 5 identifies a group of breast carcinomas with poor clinical outcome.
van de Rijn M,
Perou CM, Tibshirani R, Haas P, Kallioniemi O, Kononen J, Torhorst J, Sauter G, Zuber M, Köchli OR, Mross F, Dieterich H, Seitz R, Ross D, Botstein D, Brown P.
Am J Pathol.
2002;
161
(6):
1991-6
-
Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors.
Pollack JR,
Sørlie T, Perou CM, Rees CA, Jeffrey SS, Lonning PE, Tibshirani R, Botstein D, Børresen-Dale AL, Brown PO.
Proc Natl Acad Sci U S A.
2002;
99
(20):
12963-8
-
Expression of a single gene, BCL-6, strongly predicts survival in patients with diffuse large B-cell lymphoma.
Lossos IS,
Jones CD, Warnke R, Natkunam Y, Kaizer H, Zehnder JL, Tibshirani R, Levy R.
Blood.
2001;
98
(4):
945-51
-
Supervised harvesting of expression trees.
Hastie T,
Tibshirani R, Botstein D, Brown P.
Genome Biol.
2001;
2
(1):
RESEARCH0003
-
Significance analysis of microarrays applied to the ionizing radiation response.
Tusher VG,
Tibshirani R, Chu G.
Proc Natl Acad Sci U S A.
2001;
98
(9):
5116-21
-
Missing value estimation methods for DNA microarrays.
Troyanskaya O,
Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R, Botstein D, Altman RB.
Bioinformatics.
2001;
17
(6):
520-5
-
Molecular analysis of immunoglobulin genes in diffuse large B-cell lymphomas.
Lossos IS,
Okada CY, Tibshirani R, Warnke R, Vose JM, Greiner TC, Levy R.
Blood.
2000;
95
(5):
1797-803
-
The inference of antigen selection on Ig genes.
Lossos IS,
Tibshirani R, Narasimhan B, Levy R.
J Immunol.
2000;
165
(9):
5122-6
-
'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns.
Hastie T,
Tibshirani R, Eisen MB, Alizadeh A, Levy R, Staudt L, Chan WC, Botstein D, Brown P.
Genome Biol.
2000;
1
(2):
RESEARCH0003
-
Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling.
Alizadeh AA,
Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J, Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Levy R, Wilson W, Grever MR, Byrd JC, Botstein D, Brown PO, Staudt LM.
Nature.
2000;
403
(6769):
503-11
-
Association between cellular phones and car collisions
Tibshirani, R.,
Redelmeier, D.,.
{\it New. Engl. J. Med}.
1997
-
The lasso method for variable selection in the Cox model.
Tibshirani R,
Stat Med.
1997;
16
(4):
385-95
-
Generalized additive models for medical research.
Hastie T,
Tibshirani R.
Stat Methods Med Res.
1995;
4
(3):
187-96
-
Flexible discriminant analysis
Tibshirani, R.,
Hastie, T., and Buja, A..
{\it J. Amer. Statist. Assoc. }.
1994
-
An Introduction to the Bootstrap
Tibshirani. R.,
Efron, B..
Chapman and Hall, New York and London..
1993
-
{\it Generalized additive models},
Tibshirani, R.,
Hastie, T..
Chapman and Hall, London.
1990
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