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Results: 1 to 20 of 43

1.

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

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

Nat Biotechnol. 2014 Aug 24. doi: 10.1038/nbt.2931. [Epub ahead of print]

PMID:
25150836
[PubMed - as supplied by publisher]
2.

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.

PMID:
24559675
[PubMed - indexed for MEDLINE]
3.

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.

PMID:
22499689
[PubMed - indexed for MEDLINE]
4.

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.

PMID:
22177264
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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.

PMID:
21179090
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
20921232
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
20395217
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
20194736
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
20167110
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
19543372
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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.

PMID:
19543267
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
19529822
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
19123956
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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.

PMID:
19096707
[PubMed - indexed for MEDLINE]
Free PMC Article
15.
16.

[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.

PMID:
18402166
[PubMed - indexed for MEDLINE]
17.

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.

PMID:
17049030
[PubMed - indexed for MEDLINE]
18.

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.

PMID:
17043639
[PubMed - indexed for MEDLINE]
19.

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.

PMID:
16966692
[PubMed - indexed for MEDLINE]
Free Article
20.

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.

PMID:
16706714
[PubMed - indexed for MEDLINE]

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