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Sandrine Dudoit, PhD - Publications

Affiliations: 
Statistics University of California, Berkeley, Berkeley, CA, United States 
Area:
Statistical methods, Genomics, R,
Website:
http://www.stat.berkeley.edu/~sandrine/
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58 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Boileau P, Hejazi NS, van der Laan MJ, Dudoit S. Cross-Validated Loss-Based Covariance Matrix Estimator Selection in High Dimensions. Journal of Computational and Graphical Statistics : a Joint Publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America. 32: 601-612. PMID 37273839 DOI: 10.1080/10618600.2022.2110883  0.502
2022 Boileau P, Qi NT, van der Laan MJ, Dudoit S, Leng N. A flexible approach for predictive biomarker discovery. Biostatistics (Oxford, England). PMID 35861622 DOI: 10.1093/biostatistics/kxac029  0.5
2020 Boileau P, Hejazi NS, Dudoit S. Exploring High-Dimensional Biological Data with Sparse Contrastive Principal Component Analysis. Bioinformatics (Oxford, England). PMID 32176249 DOI: 10.1093/Bioinformatics/Btaa176  0.319
2020 Van den Berge K, Roux de Bézieux H, Street K, Saelens W, Cannoodt R, Saeys Y, Dudoit S, Clement L. Trajectory-based differential expression analysis for single-cell sequencing data. Nature Communications. 11: 1201. PMID 32139671 DOI: 10.1038/S41467-020-14766-3  0.401
2019 Cole MB, Risso D, Wagner A, DeTomaso D, Ngai J, Purdom E, Dudoit S, Yosef N. Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq. Cell Systems. 8: 315-328.e8. PMID 31022373 DOI: 10.1016/J.Cels.2019.03.010  0.379
2019 Risso D, Perraudeau F, Gribkova S, Dudoit S, Vert JP. Publisher Correction: A general and flexible method for signal extraction from single-cell RNA-seq data. Nature Communications. 10: 646. PMID 30718493 DOI: 10.1038/S41467-019-08614-2  0.311
2018 Van den Berge K, Perraudeau F, Soneson C, Love MI, Risso D, Vert JP, Robinson MD, Dudoit S, Clement L. Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications. Genome Biology. 19: 24. PMID 29478411 DOI: 10.1186/S13059-018-1406-4  0.352
2018 Risso D, Perraudeau F, Gribkova S, Dudoit S, Vert JP. A general and flexible method for signal extraction from single-cell RNA-seq data. Nature Communications. 9: 284. PMID 29348443 DOI: 10.1038/S41467-017-02554-5  0.398
2017 Perraudeau F, Risso D, Street K, Purdom E, Dudoit S. Bioconductor workflow for single-cell RNA sequencing: Normalization, dimensionality reduction, clustering, and lineage inference. F1000research. 6: 1158. PMID 28868140 DOI: 10.12688/F1000Research.12122.1  0.332
2017 Vallejos CA, Risso D, Scialdone A, Dudoit S, Marioni JC. Normalizing single-cell RNA sequencing data: challenges and opportunities. Nature Methods. PMID 28504683 DOI: 10.1038/Nmeth.4292  0.365
2014 Risso D, Ngai J, Speed TP, Dudoit S. Normalization of RNA-seq data using factor analysis of control genes or samples. Nature Biotechnology. 32: 896-902. PMID 25150836 DOI: 10.1038/Nbt.2931  0.42
2014 Cleynen A, Dudoit S, Robin S. Comparing Segmentation Methods for Genome Annotation Based on RNA-Seq Data Journal of Agricultural, Biological, and Environmental Statistics. 19: 101-118. DOI: 10.1007/S13253-013-0159-5  0.377
2012 Labbe A, Dudoit S. Special issue on computational statistical methods for genomics and systems biology. Statistical Applications in Genetics and Molecular Biology. 11. PMID 22499689 DOI: 10.2202/1544-6115.1759  0.316
2012 Jacob L, Neuvial P, Dudoit S. More power via graph-structured tests for differential expression of gene networks Annals of Applied Statistics. 6: 561-600. DOI: 10.1214/11-Aoas528  0.32
2011 Risso D, Schwartz K, Sherlock G, Dudoit S. GC-content normalization for RNA-Seq data. Bmc Bioinformatics. 12: 480. PMID 22177264 DOI: 10.1186/1471-2105-12-480  0.424
2011 Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, Artieri CG, van Baren MJ, Boley N, Booth BW, Brown JB, Cherbas L, Davis CA, Dobin A, Li R, ... ... Dudoit S, et al. The developmental transcriptome of Drosophila melanogaster. Nature. 471: 473-9. PMID 21179090 DOI: 10.1038/Nature09715  0.363
2011 Brooks AN, Yang L, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, Graveley BR. Conservation of an RNA regulatory map between Drosophila and mammals. Genome Research. 21: 193-202. PMID 20921232 DOI: 10.1101/Gr.108662.110  0.592
2010 Hansen KD, Brenner SE, Dudoit S. Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Research. 38: e131. PMID 20395217 DOI: 10.1093/Nar/Gkq224  0.587
2010 Bullard JH, Mostovoy Y, Dudoit S, Brem RB. Polygenic and directional regulatory evolution across pathways in Saccharomyces. Proceedings of the National Academy of Sciences of the United States of America. 107: 5058-63. PMID 20194736 DOI: 10.1073/Pnas.0912959107  0.748
2010 Bullard JH, Purdom E, Hansen KD, Dudoit S. Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. Bmc Bioinformatics. 11: 94. PMID 20167110 DOI: 10.1186/1471-2105-11-94  0.76
2009 Hansen KD, Lareau LF, Blanchette M, Green RE, Meng Q, Rehwinkel J, Gallusser FL, Izaurralde E, Rio DC, Dudoit S, Brenner SE. Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila. Plos Genetics. 5: e1000525. PMID 19543372 DOI: 10.1371/Journal.Pgen.1000525  0.607
2009 Durinck S, Bullard J, Spellman PT, Dudoit S. GenomeGraphs: integrated genomic data visualization with R. Bmc Bioinformatics. 10: 2. PMID 19123956 DOI: 10.1186/1471-2105-10-2  0.736
2008 Lee A, Hansen KD, Bullard J, Dudoit S, Sherlock G. 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. Plos Genetics. 4: e1000299. PMID 19096707 DOI: 10.1371/Journal.Pgen.1000299  0.738
2008 Dudoit S, Gilbert HN, van der Laan MJ. 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. Biometrical Journal. Biometrische Zeitschrift. 50: 716-44. PMID 18932138 DOI: 10.1002/Bimj.200710473  0.732
2008 Shilane D, Martikainen J, Dudoit S, Ovaska SJ. A general framework for statistical performance comparison of evolutionary computation algorithms Information Sciences. 178: 2870-2879. DOI: 10.1016/J.Ins.2008.03.007  0.717
2007 Barrier A, Roser F, Boëlle PY, Franc B, Tse C, Brault D, Lacaine F, Houry S, Callard P, Penna C, Debuire B, Flahault A, Dudoit S, Lemoine A. Prognosis of stage II colon cancer by non-neoplastic mucosa gene expression profiling. Oncogene. 26: 2642-8. PMID 17043639 DOI: 10.1038/Sj.Onc.1210060  0.323
2006 Rubin D, Dudoit S, van der Laan M. A method to increase the power of multiple testing procedures through sample splitting. Statistical Applications in Genetics and Molecular Biology. 5: Article19. PMID 17049030 DOI: 10.2202/1544-6115.1148  0.588
2006 Barrier A, Boelle PY, Roser F, Gregg J, Tse C, Brault D, Lacaine F, Houry S, Huguier M, Franc B, Flahault A, Lemoine A, Dudoit S. Stage II colon cancer prognosis prediction by tumor gene expression profiling. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. 24: 4685-91. PMID 16966692 DOI: 10.1200/Jco.2005.05.0229  0.316
2006 Keleş S, van der Laan MJ, Dudoit S, Cawley SE. Multiple testing methods for ChIP-Chip high density oligonucleotide array data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 13: 579-613. PMID 16706714 DOI: 10.1089/Cmb.2006.13.579  0.571
2006 Wang Y, Zhao LP, Dudoit S. A fine-scale linkage-disequilibrium measure based on length of haplotype sharing. American Journal of Human Genetics. 78: 615-28. PMID 16532392 DOI: 10.1086/502632  0.372
2006 Hothorn T, Bühlmann P, Dudoit S, Molinaro A, van der Laan MJ. Survival ensembles. Biostatistics (Oxford, England). 7: 355-73. PMID 16344280 DOI: 10.1093/biostatistics/kxj011  0.452
2006 Laan MJvd, Dudoit S, Vaart AWvd. The cross-validated adaptive epsilon-net estimator Statistics & Decisions. 24. DOI: 10.1524/Stnd.2006.24.3.373  0.32
2006 Vaart AWvd, Dudoit S, Laan MJvd. Oracle inequalities for multi-fold cross validation Statistics & Decisions. 24. DOI: 10.1524/Stnd.2006.24.3.351  0.325
2006 Barrier A, Brault D, Houry S, Dudoit S, Lemoine A, Flahault A, Boelle P. Prognosis prediction of stage II colon cancer by gene expression profiling Journal of Clinical Oncology. 24: 3565-3565. DOI: 10.1200/Jco.2006.24.18_Suppl.3565  0.325
2005 Barrier A, Boelle PY, Lemoine A, Tse C, Brault D, Chiappini F, Lacaine F, Houry S, Huguier M, Flahault A, Dudoit S. Gene expression profiling of nonneoplastic mucosa may predict clinical outcome of colon cancer patients. Diseases of the Colon and Rectum. 48: 2238-48. PMID 16228831 DOI: 10.1007/S10350-005-0175-9  0.333
2005 Barrier A, Lemoine A, Boelle PY, Tse C, Brault D, Chiappini F, Breittschneider J, Lacaine F, Houry S, Huguier M, Van der Laan MJ, Speed T, Debuire B, Flahault A, Dudoit S. Colon cancer prognosis prediction by gene expression profiling. Oncogene. 24: 6155-64. PMID 16091735 DOI: 10.1038/Sj.Onc.1208984  0.531
2005 Dudoit S, Van Der Laan MJ. Asymptotics of cross-validated risk estimation in estimator selection and performance assessment Statistical Methodology. 2: 131-154. DOI: 10.1016/J.Stamet.2005.02.003  0.329
2004 van der Laan MJ, Dudoit S, Keles S. Asymptotic optimality of likelihood-based cross-validation. Statistical Applications in Genetics and Molecular Biology. 3: Article4. PMID 16646820 DOI: 10.2202/1544-6115.1036  0.543
2004 van der Laan MJ, Dudoit S, Pollard KS. Augmentation procedures for control of the generalized family-wise error rate and tail probabilities for the proportion of false positives. Statistical Applications in Genetics and Molecular Biology. 3: Article15. PMID 16646793 DOI: 10.2202/1544-6115.1042  0.709
2004 van der Laan MJ, Dudoit S, Pollard KS. Multiple testing. Part II. Step-down procedures for control of the family-wise error rate. Statistical Applications in Genetics and Molecular Biology. 3: Article14. PMID 16646792 DOI: 10.2202/1544-6115.1041  0.725
2004 Dudoit S, van der Laan MJ, Pollard KS. Multiple testing. Part I. Single-step procedures for control of general type I error rates. Statistical Applications in Genetics and Molecular Biology. 3: Article13. PMID 16646791 DOI: 10.2202/1544-6115.1040  0.728
2004 Kele? S, Van Der Laan M, Dudoit S. Asymptotically optimal model selection method with right censored outcomes Bernoulli. 10: 1011-1037. DOI: 10.3150/Bj/1106314848  0.351
2004 Molinaro AM, Dudoit S, Van Der Laan MJ. Tree-based multivariate regression and density estimation with right-censored data Journal of Multivariate Analysis. 90: 154-177. DOI: 10.1016/J.Jmva.2004.02.003  0.346
2003 Keles S, van der Laan MJ, Dudoit S, Xing B, Eisen MB. Supervised detection of regulatory motifs in DNA sequences. Statistical Applications in Genetics and Molecular Biology. 2: Article5. PMID 16646783 DOI: 10.2202/1544-6115.1015  0.556
2003 Dudoit S, Gentleman RC, Quackenbush J. Open source software for the analysis of microarray data. Biotechniques. 45-51. PMID 12664684 DOI: 10.2144/Mar03Dudoit  0.309
2003 Dudoit S, van der Laan MJ, Keleş S, Molinaro AM, Sinisi SE, Teng SL. Loss-based estimation with cross-validation Acm Sigkdd Explorations Newsletter. 5: 56-68. DOI: 10.1145/980972.980981  0.355
2003 Ge Y, Dudoit S, Speed TP, Glonek G, Solomon P, Grant GR, Kendziorski CM, Maindonald JH, Storey JD, Westfall PH. Resampling-based multiple testing for microarray data analysis Test. 12: 1-77. DOI: 10.1007/Bf02595811  0.417
2002 Chang HY, Chi JT, Dudoit S, Bondre C, van de Rijn M, Botstein D, Brown PO. Diversity, topographic differentiation, and positional memory in human fibroblasts. Proceedings of the National Academy of Sciences of the United States of America. 99: 12877-82. PMID 12297622 DOI: 10.1073/Pnas.162488599  0.305
2002 Dudoit S, Fridlyand J. A prediction-based resampling method for estimating the number of clusters in a dataset. Genome Biology. 3: RESEARCH0036. PMID 12184810 DOI: 10.1186/Gb-2002-3-7-Research0036  0.307
2002 Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Research. 30: e15. PMID 11842121 DOI: 10.1093/Nar/30.4.E15  0.366
2002 Yang YH, Buckley MJ, Dudoit S, Speed TP. Comparison of methods for image analysis on cDNA microarray data Journal of Computational and Graphical Statistics. 11: 108-136. DOI: 10.1198/106186002317375640  0.334
2002 Dudoit S, Fridlyand J, Speed TP. Comparison of discrimination methods for the classification of tumors using gene expression data Journal of the American Statistical Association. 97: 77-86. DOI: 10.1198/016214502753479248  0.331
2001 Goldstein DR, Dudoit S, Speed TP. Power and robustness of a score test for linkage analysis of quantitative traits using identity by descent data on sib pairs. Genetic Epidemiology. 20: 415-31. PMID 11319783 DOI: 10.1002/Gepi.1011  0.359
2000 Dudoit S, Speed TP. A score test for the linkage analysis of qualitative and quantitative traits based on identity by descent data from sib-pairs. Biostatistics (Oxford, England). 1: 1-26. PMID 12933522 DOI: 10.1093/Biostatistics/1.1.1  0.375
2000 Callow MJ, Dudoit S, Gong EL, Speed TP, Rubin EM. Microarray expression profiling identifies genes with altered expression in HDL-deficient mice. Genome Research. 10: 2022-9. PMID 11116096 DOI: 10.1101/Gr.10.12.2022  0.307
2000 Goldstein DR, Dudoit S, Speed TP. Power of a score test for quantitative trait linkage analysis of relative pairs. Genetic Epidemiology. 19: S85-91. PMID 11055375 DOI: 10.1002/1098-2272(2000)19:1+<::Aid-Gepi13>3.0.Co;2-7  0.339
1999 Dudoit S, Speed TP. A score test for linkage using identity by descent data from sibships Annals of Statistics. 27: 943-986. DOI: 10.1214/Aos/1018031264  0.308
1999 Dudoit S. Statistical methods for the characterisation of tumour types using cDNA microarray data Nature Genetics. 23: 42-42. DOI: 10.1038/14296  0.364
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