Works by Dudoit, Sandrine

Results: 44

Power and robustness of a score test for linkage analysis of quantitative traits using identity by descent data on sib pairs.

Published in:

Genetic Epidemiology, 2001, v. 20, n. 4, p. 415, doi. 10.1002/gepi.1011

By:

Goldstein, Darlene R.;
Dudoit, Sandrine;
Speed, Terence P.

Publication type:

Article

Power of a score test for quantitative trait linkage analysis of relative pairs.

Published in:

Genetic Epidemiology, 2000, v. 19, n. S1, p. S85, doi. 10.1002/1098-2272(2000)19:1+<::AID-GEPI13>3.0.CO;2-7

By:

Goldstein, Darlene R.;
Dudoit, Sandrine;
Speed, Terence P.

Publication type:

Article

HSA Adductomics in the Shanghai Women's Health Study Links Lung Cancer in Never-Smokers with Air Pollution, Redox Biology, and One-Carbon Metabolism.

Published in:

Antioxidants, 2025, v. 14, n. 3, p. 335, doi. 10.3390/antiox14030335

By:

Imani, Partow;
Grigoryan, Hasmik;
Dudoit, Sandrine;
Shu, Xiao-Ou;
Wong, Jason;
Zhang, Luoping;
Zhang, Junfeng;
Hu, Wei;
Cai, Qiuyin;
Gao, Yutang;
Blechter, Batel;
Rahman, Mohammad;
Zheng, Wei;
Rothman, Nathaniel;
Lan, Qing;
Rappaport, Stephen M.

Publication type:

Article

CALDERA: finding all significant de Bruijn subgraphs for bacterial GWAS.

Published in:

Bioinformatics, 2022, v. 38, p. i36, doi. 10.1093/bioinformatics/btac238

By:

Bézieux, Hector Roux de;
Lima, Leandro;
Perraudeau, Fanny;
Mary, Arnaud;
Dudoit, Sandrine;
Jacob, Laurent

Publication type:

Article

Biases in Illumina transcriptome sequencing caused by random hexamer priming.

Published in:

Nucleic Acids Research, 2010, v. 38, n. 12, p. e131, doi. 10.1093/nar/gkq224

By:

Hansen, Kasper D.;
Brenner, Steven E.;
Dudoit, Sandrine

Publication type:

Article

Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation.

Published in:

Nucleic Acids Research, 2002, v. 30, n. 4, p. e15, doi. 10.1093/nar/30.4.e15

By:

Yang, Yee Hwa;
Dudoit, Sandrine;
Luu, Percy;
Lin, David M.;
Peng, Vivian;
Ngai, John;
Speed, Terence P.

Publication type:

Article

Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications.

Published in:

Genome Biology, 2018, v. 19, p. 1, doi. 10.1186/s13059-018-1406-4

By:

Van den Berge, Koen;
Perraudeau, Fanny;
Soneson, Charlotte;
Love, Michael I.;
Risso, Davide;
Vert, Jean-Philippe;
Robinson, Mark D.;
Dudoit, Sandrine;
Clement, Lieven

Publication type:

Article

The establishment of gene silencing at single-cell resolution.

Published in:

Nature Genetics, 2009, v. 41, n. 7, p. 800, doi. 10.1038/ng.402

By:

Osborne, Erin A.;
Dudoit, Sandrine;
Rine, Jasper

Publication type:

Article

Statistical methods for the characterisation of tumour types using cDNA microarray data.

Published in:

1999

By:

Dudoit, Sandrine

Publication type:

Abstract

Genome-Wide Identification of Alternative Splice Forms Down-Regulated by Nonsense-Mediated mRNA Decay in Drosophila.

Published in:

PLoS Genetics, 2009, v. 5, n. 6, p. 1, doi. 10.1371/journal.pgen.1000525

By:

Hansen, Kasper Daniel;
Lareau, Liana F.;
Blanchette, Marco;
Green, Richard E.;
Qi Meng;
Rehwinkel, Jan;
Gallusser, Fabian L.;
Izaurralde, Elisa;
Rio, Donald C.;
Dudoit, Sandrine;
Brenner, Steven E.

Publication type:

Article

Novel Low Abundance and Transient RNAs in Yeast Revealed by Tiling Microarrays and Ultra High- Throughput Sequencing Are Not Conserved Across Closely Related Yeast Species.

Published in:

PLoS Genetics, 2008, v. 4, n. 12, p. 1, doi. 10.1371/journal.pgen.1000299

By:

Lee, Albert;
Hansen, Kasper Daniel;
Bullard, James;
Dudoit, Sandrine;
Sherlock, Gavin

Publication type:

Article

Mycobacteria that cause tuberculosis have retained ancestrally acquired genes for the biosynthesis of chemically diverse terpene nucleosides.

Published in:

PLoS Biology, 2024, v. 22, n. 9, p. 1, doi. 10.1371/journal.pbio.3002813

By:

Mayfield, Jacob A.;
Raman, Sahadevan;
Ramnarine, Alexandrea K.;
Mishra, Vivek K.;
Huang, Annie D.;
Dudoit, Sandrine;
Buter, Jeffrey;
Cheng, Tan-Yun;
Young, David C.;
Nair, Yashodhan M.;
Ouellet, Isobel G.;
Griebel, Braden T.;
Ma, Shuyi;
Sherman, David R.;
Mallet, Ludovic;
Rhee, Kyu Y.;
Minnaard, Adriaan J.;
Branch Moody, D.

Publication type:

Article

Filtering procedures for untargeted LC-MS metabolomics data.

Published in:

BMC Bioinformatics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12859-019-2871-9

By:

Schiffman, Courtney;
Petrick, Lauren;
Perttula, Kelsi;
Yano, Yukiko;
Carlsson, Henrik;
Whitehead, Todd;
Metayer, Catherine;
Hayes, Josie;
Rappaport, Stephen;
Dudoit, Sandrine

Publication type:

Article

An untargeted metabolomics method for archived newborn dried blood spots in epidemiologic studies.

Published in:

Metabolomics, 2017, v. 13, n. 3, p. 1, doi. 10.1007/s11306-016-1153-z

By:

Petrick, Lauren;
Edmands, William;
Schiffman, Courtney;
Grigoryan, Hasmik;
Perttula, Kelsi;
Yano, Yukiko;
Dudoit, Sandrine;
Whitehead, Todd;
Metayer, Catherine;
Rappaport, Stephen

Publication type:

Article

Trajectory inference across multiple conditions with condiments.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-44823-0

By:

Roux de Bézieux, Hector;
Van den Berge, Koen;
Street, Kelly;
Dudoit, Sandrine

Publication type:

Article

Untargeted lipidomic features associated with colorectal cancer in a prospective cohort.

Published in:

2018

By:

Perttula, Kelsi;
Schiffman, Courtney;
Edmands, William M. B.;
Petrick, Lauren;
Grigoryan, Hasmik;
Xiaoming Cai;
Gunter, Marc J.;
Naccarati, Alessio;
Polidoro, Silvia;
Dudoit, Sandrine;
Vineis, Paolo;
Rappaport, Stephen M.;
Cai, Xiaoming

Publication type:

journal article

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics.

Published in:

BMC Genomics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12864-018-4772-0

By:

Street, Kelly;
Risso, Davide;
Fletcher, Russell B.;
Das, Diya;
Ngai, John;
Yosef, Nir;
Purdom, Elizabeth;
Dudoit, Sandrine

Publication type:

Article

Evaluation of statistical methods fornormalization and differential expression inmRNA-Seq experiments.

Published in:

BMC Bioinformatics, 2010, v. 11, p. 94, doi. 10.1186/1471-2105-11-94

By:

Bullard, James H.;
Purdom, Elizabeth;
Hansen, Kasper D.;
Dudoit, Sandrine

Publication type:

Article

GenomeGraphs: integrated genomic data visualization with R.

Published in:

BMC Bioinformatics, 2009, v. 10, p. 1, doi. 10.1186/1471-2105-10-2

By:

Durinck, Steffen;
Bullard, James;
Spellman, Paul T;
Dudoit, Sandrine

Publication type:

Article

A flexible approach for predictive biomarker discovery.

Published in:

Biostatistics, 2023, v. 24, n. 4, p. 1085, doi. 10.1093/biostatistics/kxac029

By:

Boileau, Philippe;
Qi, Nina Ting;
Laan, Mark J van der;
Dudoit, Sandrine;
Leng, Ning

Publication type:

Article

A score test for the linkage analysis of qualitative and quantitative traits based on identity by descent data from sib-pairs.

Published in:

Biostatistics, 2000, v. 1, n. 1, p. 1, doi. 10.1093/biostatistics/1.1.1

By:

Dudoit, Sandrine;
P.Speed, Terence

Publication type:

Article

A general and flexible method for signal extraction from single-cell RNA-seq data.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-017-02554-5

By:

Risso, Davide;
Perraudeau, Fanny;
Gribkova, Svetlana;
Dudoit, Sandrine;
Vert, Jean-Philippe

Publication type:

Article

One-Carbon (Folate) Metabolism Pathway at Birth and Risk of Childhood Acute Lymphoblastic Leukemia: A Biomarker Study in Newborns.

Published in:

Cancers, 2023, v. 15, n. 4, p. 1011, doi. 10.3390/cancers15041011

By:

Metayer, Catherine;
Imani, Partow;
Dudoit, Sandrine;
Morimoto, Libby;
Ma, Xiaomei;
Wiemels, Joseph L.;
Petrick, Lauren M.

Publication type:

Article

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.

Published in:

FASEB Journal, 2005, v. 19, n. 12, p. 1617, doi. 10.1096/fj.04-3445com

By:

Barrier, Alain;
Olaya, Natalia;
Chiappini, Franck;
Roser, François;
Scatton, Olivier;
Artus, Cédric;
Franc, Brigitte;
Dudoit, Sandrine;
Flahault, Antoine;
Debuire, Brigitte;
Azoulay, Daniel;
Lemoine, Antoinette

Publication type:

Article

Assessment of transcript reconstruction methods for RNA-seq.

Published in:

Nature Methods, 2013, v. 10, n. 12, p. 1177, doi. 10.1038/nmeth.2714

By:

Steijger, Tamara;
Abril, Josep F;
Engström, Pär G;
Kokocinski, Felix;
Akerman, Martin;
Alioto, Tyler;
Ambrosini, Giovanna;
Antonarakis, Stylianos E;
Behr, Jonas;
Bertone, Paul;
Bohnert, Regina;
Bucher, Philipp;
Cloonan, Nicole;
Derrien, Thomas;
Djebali, Sarah;
Du, Jiang;
Dudoit, Sandrine;
Gerstein, Mark;
Gingeras, Thomas R;
Gonzalez, David

Publication type:

Article

clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets.

Published in:

PLoS Computational Biology, 2018, v. 14, n. 9, p. 1, doi. 10.1371/journal.pcbi.1006378

By:

Risso, Davide;
Purvis, Liam;
Fletcher, Russell B.;
Das, Diya;
Ngai, John;
Dudoit, Sandrine;
Purdom, Elizabeth

Publication type:

Article

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.

Published in:

Biometrical Journal, 2008, v. 50, n. 5, p. 716, doi. 10.1002/bimj.200710473

By:

Dudoit, Sandrine;
Gilbert1, Houston N.;
van der Laan, Mark J.

Publication type:

Article

A nonparametric framework for treatment effect modifier discovery in high dimensions.

Published in:

Journal of the Royal Statistical Society: Series B (Statistical Methodology), 2025, v. 87, n. 1, p. 157, doi. 10.1093/jrsssb/qkae084

By:

Boileau, Philippe;
Leng, Ning;
Hejazi, Nima S;
van der Laan, Mark;
Dudoit, Sandrine

Publication type:

Article

Trajectory-based differential expression analysis for single-cell sequencing data.

Published in:

Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-14766-3

By:

Van den Berge, Koen;
Roux de Bézieux, Hector;
Street, Kelly;
Saelens, Wouter;
Cannoodt, Robrecht;
Saeys, Yvan;
Dudoit, Sandrine;
Clement, Lieven

Publication type:

Article

Special Issue on Computational Statistical Methods for Genomics and Systems Biology.

Published in:

Statistical Applications in Genetics & Molecular Biology, 2012, v. 11, n. 2, p. 1, doi. 10.2202/1544-6115.1759

By:

Labbe, Aurélie;
Dudoit, Sandrine

Publication type:

Article

A Method to Increase the Power of Multiple Testing Procedures Through Sample Splitting.

Published in:

Statistical Applications in Genetics & Molecular Biology, 2006, v. 5, n. 1, p. 1, doi. 10.2202/1544-6115.1148

By:

Rubin, Daniel;
Dudoit, Sandrine;
Van der Laan, Mark

Publication type:

Article

Asymptotic Optimality of Likelihood-Based Cross-Validation.

Published in:

Statistical Applications in Genetics & Molecular Biology, 2004, v. 3, n. 1, p. 1, doi. 10.2202/1544-6115.1036

By:

van der Laan, Mark J.;
Dudoit, Sandrine;
Keles, Sunduz

Publication type:

Article

Augmentation Procedures for Control of the Generalized Family-Wise Error Rate and Tail Probabilities for the Proportion of False Positives.

Published in:

Statistical Applications in Genetics & Molecular Biology, 2004, v. 3, n. 1, p. 1, doi. 10.2202/1544-6115.1042

By:

Van der Laan, Mark J.;
Dudoit, Sandrine;
Pollard, Katherine S.

Publication type:

Article

Multiple Testing. Part II. Step-Down Procedures for Control of the Family-Wise Error Rate.

Published in:

Statistical Applications in Genetics & Molecular Biology, 2004, v. 3, n. 1, p. 1, doi. 10.2202/1544-6115.1041

By:

Van der Laan, Mark J.;
Dudoit, Sandrine;
Pollard, Katherine S.

Publication type:

Article

Multiple Testing. Part I. Single-Step Procedures for Control of General Type I Error Rates.

Published in:

Statistical Applications in Genetics & Molecular Biology, 2004, v. 3, n. 1, p. 1, doi. 10.2202/1544-6115.1040

By:

Dudoit, Sandrine;
Van der Laan, Mark J.;
Pollard, Katherine S.

Publication type:

Article

Comparison of Discrimination Methods for the Classification of Tumors Using Gene Expression Data.

Published in:

Journal of the American Statistical Association, 2002, v. 97, n. 457, p. 77, doi. 10.1198/016214502753479248

By:

Dudoit, Sandrine;
Fridlyand, Jane;
Speed, Terence P.

Publication type:

Article

Improving replicability in single-cell RNA-Seq cell type discovery with Dune.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05814-6

By:

Roux de Bézieux, Hector;
Street, Kelly;
Fischer, Stephan;
Van den Berge, Koen;
Chance, Rebecca;
Risso, Davide;
Gillis, Jesse;
Ngai, John;
Purdom, Elizabeth;
Dudoit, Sandrine

Publication type:

Article

Untargeted adductomics of Cys34 modifications to human serum albumin in newborn dried blood spots.

Published in:

Analytical & Bioanalytical Chemistry, 2019, v. 411, n. 11, p. 2351, doi. 10.1007/s00216-019-01675-8

By:

Yano, Yukiko;
Grigoryan, Hasmik;
Schiffman, Courtney;
Edmands, William;
Petrick, Lauren;
Hall, Katie;
Whitehead, Todd;
Metayer, Catherine;
Dudoit, Sandrine;
Rappaport, Stephen

Publication type:

Article

Comparing Segmentation Methods for Genome Annotation Based on RNA-Seq Data.

Published in:

Journal of Agricultural, Biological & Environmental Statistics (JABES), 2014, v. 19, n. 1, p. 101, doi. 10.1007/s13253-013-0159-5

By:

Cleynen, Alice;
Dudoit, Sandrine;
Robin, Stéphane

Publication type:

Article

Colon cancer prognosis prediction by gene expression profiling.

Published in:

Oncogene, 2005, v. 24, n. 40, p. 6155, doi. 10.1038/sj.onc.1208984

By:

Barrier, Alain;
Lemoine, Antoinette;
Boelle, Pierre-Yves;
Tse, Chantal;
Brault, Didier;
Chiappini, Franck;
Breittschneider, Julia;
Lacaine, François;
Houry, Sidney;
Huguier, Michel;
Van der Laan, Mark J;
Speed, Terry;
Debuire, Brigitte;
Flahault, Antoine;
Dudoit, Sandrine

Publication type:

Article

Cross-Validated Loss-based Covariance Matrix Estimator Selection in High Dimensions.

Published in:

Journal of Computational & Graphical Statistics, 2023, v. 32, n. 2, p. 601, doi. 10.1080/10618600.2022.2110883

By:

Boileau, Philippe;
Hejazi, Nima S.;
van der Laan, Mark J.;
Dudoit, Sandrine

Publication type:

Article

Comparison of Methods for Image Analysis on cDNA Microarray Data.

Published in:

Journal of Computational & Graphical Statistics, 2002, v. 11, n. 1, p. 108, doi. 10.1198/106186002317375640

By:

Yee Hwa Yang;
Buckley, Michael J.;
Dudoit, Sandrine;
Speed, Terence C.

Publication type:

Article

Publisher Correction: A general and flexible method for signal extraction from single-cell RNA-seq data.

Published in:

Nature Communications, 2019, v. 10, n. 1, p. 1, doi. 10.1038/s41467-019-08614-2

By:

Risso, Davide;
Perraudeau, Fanny;
Gribkova, Svetlana;
Dudoit, Sandrine;
Vert, Jean-Philippe

Publication type:

Article

Normalization of RNA-seq data using factor analysis of control genes or samples.

Published in:

Nature Biotechnology, 2014, v. 32, n. 9, p. 896, doi. 10.1038/nbt.2931

By:

Risso, Davide;
Ngai, John;
Speed, Terence P;
Dudoit, Sandrine

Publication type:

Article