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Items: 1 to 50 of 58


Filtering procedures for untargeted LC-MS metabolomics data.

Schiffman C, Petrick L, Perttula K, Yano Y, Carlsson H, Whitehead T, Metayer C, Hayes J, Rappaport S, Dudoit S.

BMC Bioinformatics. 2019 Jun 14;20(1):334. doi: 10.1186/s12859-019-2871-9.


Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq.

Cole MB, Risso D, Wagner A, DeTomaso D, Ngai J, Purdom E, Dudoit S, Yosef N.

Cell Syst. 2019 Apr 24;8(4):315-328.e8. doi: 10.1016/j.cels.2019.03.010.


Metabolomics of neonatal blood spots reveal distinct phenotypes of pediatric acute lymphoblastic leukemia and potential effects of early-life nutrition.

Petrick LM, Schiffman C, Edmands WMB, Yano Y, Perttula K, Whitehead T, Metayer C, Wheelock CE, Arora M, Grigoryan H, Carlsson H, Dudoit S, Rappaport SM.

Cancer Lett. 2019 Jun 28;452:71-78. doi: 10.1016/j.canlet.2019.03.007. Epub 2019 Mar 20.


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

Yano Y, Grigoryan H, Schiffman C, Edmands W, Petrick L, Hall K, Whitehead T, Metayer C, Dudoit S, Rappaport S.

Anal Bioanal Chem. 2019 Apr;411(11):2351-2362. doi: 10.1007/s00216-019-01675-8. Epub 2019 Feb 19.


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

Risso D, Perraudeau F, Gribkova S, Dudoit S, Vert JP.

Nat Commun. 2019 Feb 4;10(1):646. doi: 10.1038/s41467-019-08614-2.


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

Perttula K, Schiffman C, Edmands WMB, Petrick L, Grigoryan H, Cai X, Gunter MJ, Naccarati A, Polidoro S, Dudoit S, Vineis P, Rappaport SM.

BMC Cancer. 2018 Oct 19;18(1):996. doi: 10.1186/s12885-018-4894-4.


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

Risso D, Purvis L, Fletcher RB, Das D, Ngai J, Dudoit S, Purdom E.

PLoS Comput Biol. 2018 Sep 4;14(9):e1006378. doi: 10.1371/journal.pcbi.1006378. eCollection 2018 Sep. Erratum in: PLoS Comput Biol. 2019 Jan 11;15(1):e1006727.


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

Street K, Risso D, Fletcher RB, Das D, Ngai J, Yosef N, Purdom E, Dudoit S.

BMC Genomics. 2018 Jun 19;19(1):477. doi: 10.1186/s12864-018-4772-0.


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

Petrick L, Edmands W, Schiffman C, Grigoryan H, Perttula K, Yano Y, Dudoit S, Whitehead T, Metayer C, Rappaport S.

Metabolomics. 2017 Mar;13(3). pii: 27. doi: 10.1007/s11306-016-1153-z. Epub 2017 Feb 3.


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

Van den Berge K, Perraudeau F, Soneson C, Love MI, Risso D, Vert JP, Robinson MD, Dudoit S, Clement L.

Genome Biol. 2018 Feb 26;19(1):24. doi: 10.1186/s13059-018-1406-4.


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

Risso D, Perraudeau F, Gribkova S, Dudoit S, Vert JP.

Nat Commun. 2018 Jan 18;9(1):284. doi: 10.1038/s41467-017-02554-5. Erratum in: Nat Commun. 2019 Feb 4;10(1):646.


Injury Activates Transient Olfactory Stem Cell States with Diverse Lineage Capacities.

Gadye L, Das D, Sanchez MA, Street K, Baudhuin A, Wagner A, Cole MB, Choi YG, Yosef N, Purdom E, Dudoit S, Risso D, Ngai J, Fletcher RB.

Cell Stem Cell. 2017 Dec 7;21(6):775-790.e9. doi: 10.1016/j.stem.2017.10.014. Epub 2017 Nov 22.


Bioconductor workflow for single-cell RNA sequencing: Normalization, dimensionality reduction, clustering, and lineage inference.

Perraudeau F, Risso D, Street K, Purdom E, Dudoit S.

F1000Res. 2017 Jul 21;6:1158. doi: 10.12688/f1000research.12122.1. eCollection 2017.


Deconstructing Olfactory Stem Cell Trajectories at Single-Cell Resolution.

Fletcher RB, Das D, Gadye L, Street KN, Baudhuin A, Wagner A, Cole MB, Flores Q, Choi YG, Yosef N, Purdom E, Dudoit S, Risso D, Ngai J.

Cell Stem Cell. 2017 Jun 1;20(6):817-830.e8. doi: 10.1016/j.stem.2017.04.003. Epub 2017 May 11.


Normalizing single-cell RNA sequencing data: challenges and opportunities.

Vallejos CA, Risso D, Scialdone A, Dudoit S, Marioni JC.

Nat Methods. 2017 Jun;14(6):565-571. doi: 10.1038/nmeth.4292. Epub 2017 May 15.


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

Risso D, Ngai J, Speed TP, Dudoit S.

Nat Biotechnol. 2014 Sep;32(9):896-902. doi: 10.1038/nbt.2931. Epub 2014 Aug 24.


Silencing of odorant receptor genes by G protein βγ signaling ensures the expression of one odorant receptor per olfactory sensory neuron.

Ferreira T, Wilson SR, Choi YG, Risso D, Dudoit S, Speed TP, Ngai J.

Neuron. 2014 Feb 19;81(4):847-59. doi: 10.1016/j.neuron.2014.01.001.


Special issue on computational statistical methods for genomics and systems biology.

Labbe A, Dudoit S.

Stat Appl Genet Mol Biol. 2012 Jan 6;11(2). pii: /j/sagmb.2012.11.issue-2/1544-6115.1759/1544-6115.1759.xml. doi: 10.2202/1544-6115.1759.


GC-content normalization for RNA-Seq data.

Risso D, Schwartz K, Sherlock G, Dudoit S.

BMC Bioinformatics. 2011 Dec 17;12:480. doi: 10.1186/1471-2105-12-480.


The developmental transcriptome of Drosophila melanogaster.

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, Lin W, Malone JH, Mattiuzzo NR, Miller D, Sturgill D, Tuch BB, Zaleski C, Zhang D, Blanchette M, Dudoit S, Eads B, Green RE, Hammonds A, Jiang L, Kapranov P, Langton L, Perrimon N, Sandler JE, Wan KH, Willingham A, Zhang Y, Zou Y, Andrews J, Bickel PJ, Brenner SE, Brent MR, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Oliver B, Celniker SE.

Nature. 2011 Mar 24;471(7339):473-9. doi: 10.1038/nature09715. Epub 2010 Dec 22.


Conservation of an RNA regulatory map between Drosophila and mammals.

Brooks AN, Yang L, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, Graveley BR.

Genome Res. 2011 Feb;21(2):193-202. doi: 10.1101/gr.108662.110. Epub 2010 Oct 4.


Biases in Illumina transcriptome sequencing caused by random hexamer priming.

Hansen KD, Brenner SE, Dudoit S.

Nucleic Acids Res. 2010 Jul;38(12):e131. doi: 10.1093/nar/gkq224. Epub 2010 Apr 14.


Polygenic and directional regulatory evolution across pathways in Saccharomyces.

Bullard JH, Mostovoy Y, Dudoit S, Brem RB.

Proc Natl Acad Sci U S A. 2010 Mar 16;107(11):5058-63. doi: 10.1073/pnas.0912959107. Epub 2010 Mar 1.


Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments.

Bullard JH, Purdom E, Hansen KD, Dudoit S.

BMC Bioinformatics. 2010 Feb 18;11:94. doi: 10.1186/1471-2105-11-94.


Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila.

Hansen KD, Lareau LF, Blanchette M, Green RE, Meng Q, Rehwinkel J, Gallusser FL, Izaurralde E, Rio DC, Dudoit S, Brenner SE.

PLoS Genet. 2009 Jun;5(6):e1000525. doi: 10.1371/journal.pgen.1000525. Epub 2009 Jun 19.


The establishment of gene silencing at single-cell resolution.

Osborne EA, Dudoit S, Rine J.

Nat Genet. 2009 Jul;41(7):800-6. doi: 10.1038/ng.402. Epub 2009 Jun 21.


Diverse transcriptional programs associated with environmental stress and hormones in the Arabidopsis receptor-like kinase gene family.

Chae L, Sudat S, Dudoit S, Zhu T, Luan S.

Mol Plant. 2009 Jan;2(1):84-107. doi: 10.1093/mp/ssn083.


GenomeGraphs: integrated genomic data visualization with R.

Durinck S, Bullard J, Spellman PT, Dudoit S.

BMC Bioinformatics. 2009 Jan 6;10:2. doi: 10.1186/1471-2105-10-2.


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.

Lee A, Hansen KD, Bullard J, Dudoit S, Sherlock G.

PLoS Genet. 2008 Dec;4(12):e1000299. doi: 10.1371/journal.pgen.1000299. Epub 2008 Dec 19.


[Gene expression profiling in colon cancer].

Barrier A, Boelle PY, Lemoine A, Flahault A, Dudoit S, Huguier M.

Bull Acad Natl Med. 2007 Jun;191(6):1091-101; discussion 1102-3. French.


A method to increase the power of multiple testing procedures through sample splitting.

Rubin D, Dudoit S, van der Laan M.

Stat Appl Genet Mol Biol. 2006;5:Article19. Epub 2006 Aug 1.


Prognosis of stage II colon cancer by non-neoplastic mucosa gene expression profiling.

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.

Oncogene. 2007 Apr 19;26(18):2642-8. Epub 2006 Oct 9.


Stage II colon cancer prognosis prediction by tumor gene expression profiling.

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.

J Clin Oncol. 2006 Oct 10;24(29):4685-91. Epub 2006 Sep 11.


Multiple testing methods for ChIP-Chip high density oligonucleotide array data.

Keleş S, van der Laan MJ, Dudoit S, Cawley SE.

J Comput Biol. 2006 Apr;13(3):579-613.


Asymptotic optimality of likelihood-based cross-validation.

van der Laan MJ, Dudoit S, Keles S.

Stat Appl Genet Mol Biol. 2004;3:Article4. Epub 2004 Mar 22.


Augmentation procedures for control of the generalized family-wise error rate and tail probabilities for the proportion of false positives.

van der Laan MJ, Dudoit S, Pollard KS.

Stat Appl Genet Mol Biol. 2004;3:Article15. Epub 2004 Jun 15.


Multiple testing. Part II. Step-down procedures for control of the family-wise error rate.

van der Laan MJ, Dudoit S, Pollard KS.

Stat Appl Genet Mol Biol. 2004;3:Article14. Epub 2004 Jun 14.


Multiple testing. Part I. Single-step procedures for control of general type I error rates.

Dudoit S, van der Laan MJ, Pollard KS.

Stat Appl Genet Mol Biol. 2004;3:Article13. Epub 2004 Jun 9.


Supervised detection of regulatory motifs in DNA sequences.

Keles S, van der Laan MJ, Dudoit S, Xing B, Eisen MB.

Stat Appl Genet Mol Biol. 2003;2:Article5. Epub 2003 Aug 25.


A fine-scale linkage-disequilibrium measure based on length of haplotype sharing.

Wang Y, Zhao LP, Dudoit S.

Am J Hum Genet. 2006 Apr;78(4):615-28. Epub 2006 Feb 13.


Exploration of global gene expression in human liver steatosis by high-density oligonucleotide microarray.

Chiappini F, Barrier A, Saffroy R, Domart MC, Dagues N, Azoulay D, Sebagh M, Franc B, Chevalier S, Debuire B, Dudoit S, Lemoine A.

Lab Invest. 2006 Feb;86(2):154-65.


Survival ensembles.

Hothorn T, Bühlmann P, Dudoit S, Molinaro A, van der Laan MJ.

Biostatistics. 2006 Jul;7(3):355-73. Epub 2005 Dec 12.


Gene expression profiling of nonneoplastic mucosa may predict clinical outcome of colon cancer patients.

Barrier A, Boelle PY, Lemoine A, Tse C, Brault D, Chiappini F, Lacaine F, Houry S, Huguier M, Flahault A, Dudoit S.

Dis Colon Rectum. 2005 Dec;48(12):2238-48.


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.

Barrier A, Olaya N, Chiappini F, Roser F, Scatton O, Artus C, Franc B, Dudoit S, Flahault A, Debuire B, Azoulay D, Lemoine A.

FASEB J. 2005 Oct;19(12):1617-26.


Colon cancer prognosis prediction by gene expression profiling.

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.

Oncogene. 2005 Sep 8;24(40):6155-64.


Bioconductor: open software development for computational biology and bioinformatics.

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J.

Genome Biol. 2004;5(10):R80. Epub 2004 Sep 15.


Bagging to improve the accuracy of a clustering procedure.

Dudoit S, Fridlyand J.

Bioinformatics. 2003 Jun 12;19(9):1090-9.


Open source software for the analysis of microarray data.

Dudoit S, Gentleman RC, Quackenbush J.

Biotechniques. 2003 Mar;Suppl:45-51. Review.


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