P41 HG004059/HG/NHGRI NIH HHS/United States[Grant Number] - Search Results

Year	Number of Results
2007	1
2008	5
2009	5
2010	5
2011	1
2012	2
2013	1
2015	1
2017	1
2019	2
2020	1
2021	0

1

Orchestrating high-throughput genomic analysis with Bioconductor.

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M. Huber W, et al. Nat Methods. 2015 Feb;12(2):115-21. doi: 10.1038/nmeth.3252. Nat Methods. 2015. PMID: 25633503 Free PMC article. Review.

2

Tackling the widespread and critical impact of batch effects in high-throughput data.

Leek JT, Scharpf RB, Bravo HC, Simcha D, Langmead B, Johnson WE, Geman D, Baggerly K, Irizarry RA. Leek JT, et al. Nat Rev Genet. 2010 Oct;11(10):733-9. doi: 10.1038/nrg2825. Epub 2010 Sep 14. Nat Rev Genet. 2010. PMID: 20838408 Free PMC article. Review.

3

An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors.

Ben-Porath I, Thomson MW, Carey VJ, Ge R, Bell GW, Regev A, Weinberg RA. Ben-Porath I, et al. Nat Genet. 2008 May;40(5):499-507. doi: 10.1038/ng.127. Nat Genet. 2008. PMID: 18443585 Free PMC article.

4

Reproducible and replicable comparisons using SummarizedBenchmark.

Kimes PK, Reyes A. Kimes PK, et al. Bioinformatics. 2019 Jan 1;35(1):137-139. doi: 10.1093/bioinformatics/bty627. Bioinformatics. 2019. PMID: 30016409 Free PMC article.

5

Machine learning and its applications to biology.

Tarca AL, Carey VJ, Chen XW, Romero R, Drăghici S. Tarca AL, et al. PLoS Comput Biol. 2007 Jun;3(6):e116. doi: 10.1371/journal.pcbi.0030116. PLoS Comput Biol. 2007. PMID: 17604446 Free PMC article. Review. No abstract available.

6

Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model.

Townes FW, Hicks SC, Aryee MJ, Irizarry RA. Townes FW, et al. Genome Biol. 2019 Dec 23;20(1):295. doi: 10.1186/s13059-019-1861-6. Genome Biol. 2019. PMID: 31870412 Free PMC article.

7

Accessible, curated metagenomic data through ExperimentHub.

Pasolli E, Schiffer L, Manghi P, Renson A, Obenchain V, Truong DT, Beghini F, Malik F, Ramos M, Dowd JB, Huttenhower C, Morgan M, Segata N, Waldron L. Pasolli E, et al. Nat Methods. 2017 Oct 31;14(11):1023-1024. doi: 10.1038/nmeth.4468. Nat Methods. 2017. PMID: 29088129 Free PMC article. No abstract available.

8

Quantile normalization of single-cell RNA-seq read counts without unique molecular identifiers.

Townes FW, Irizarry RA. Townes FW, et al. Genome Biol. 2020 Jul 3;21(1):160. doi: 10.1186/s13059-020-02078-0. Genome Biol. 2020. PMID: 32620142 Free PMC article.

9

Model-based quality assessment and base-calling for second-generation sequencing data.

Bravo HC, Irizarry RA. Bravo HC, et al. Biometrics. 2010 Sep;66(3):665-74. doi: 10.1111/j.1541-0420.2009.01353.x. Biometrics. 2010. PMID: 19912177 Free PMC article. Review.

10

Genotyping in the cloud with Crossbow.

Gurtowski J, Schatz MC, Langmead B. Gurtowski J, et al. Curr Protoc Bioinformatics. 2012 Sep;Chapter 15:Unit15.3. doi: 10.1002/0471250953.bi1503s39. Curr Protoc Bioinformatics. 2012. PMID: 22948728 Free PMC article.

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