Smith AD - Search Results

1

Identifying dispersed epigenomic domains from ChIP-Seq data.

Song Q, Smith AD. Song Q, et al. Among authors: smith ad. Bioinformatics. 2011 Mar 15;27(6):870-1. doi: 10.1093/bioinformatics/btr030. Epub 2011 Feb 16. Bioinformatics. 2011. PMID: 21325299 Free PMC article.

2

Mining ChIP-chip data for transcription factor and cofactor binding sites.

Smith AD, Sumazin P, Das D, Zhang MQ. Smith AD, et al. Bioinformatics. 2005 Jun;21 Suppl 1:i403-12. doi: 10.1093/bioinformatics/bti1043. Bioinformatics. 2005. PMID: 15961485

3

Updates to the RMAP short-read mapping software.

Smith AD, Chung WY, Hodges E, Kendall J, Hannon G, Hicks J, Xuan Z, Zhang MQ. Smith AD, et al. Bioinformatics. 2009 Nov 1;25(21):2841-2. doi: 10.1093/bioinformatics/btp533. Epub 2009 Sep 7. Bioinformatics. 2009. PMID: 19736251 Free PMC article.

4

Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment.

Hodges E, Molaro A, Dos Santos CO, Thekkat P, Song Q, Uren PJ, Park J, Butler J, Rafii S, McCombie WR, Smith AD, Hannon GJ. Hodges E, et al. Among authors: smith ad. Mol Cell. 2011 Oct 7;44(1):17-28. doi: 10.1016/j.molcel.2011.08.026. Epub 2011 Sep 15. Mol Cell. 2011. PMID: 21924933 Free PMC article.

5

Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates.

Molaro A, Hodges E, Fang F, Song Q, McCombie WR, Hannon GJ, Smith AD. Molaro A, et al. Among authors: smith ad. Cell. 2011 Sep 16;146(6):1029-41. doi: 10.1016/j.cell.2011.08.016. Cell. 2011. PMID: 21925323 Free PMC article.

6

Site identification in high-throughput RNA-protein interaction data.

Uren PJ, Bahrami-Samani E, Burns SC, Qiao M, Karginov FV, Hodges E, Hannon GJ, Sanford JR, Penalva LO, Smith AD. Uren PJ, et al. Among authors: smith ad. Bioinformatics. 2012 Dec 1;28(23):3013-20. doi: 10.1093/bioinformatics/bts569. Epub 2012 Sep 28. Bioinformatics. 2012. PMID: 23024010 Free PMC article.

7

MLML: consistent simultaneous estimates of DNA methylation and hydroxymethylation.

Qu J, Zhou M, Song Q, Hong EE, Smith AD. Qu J, et al. Among authors: smith ad. Bioinformatics. 2013 Oct 15;29(20):2645-6. doi: 10.1093/bioinformatics/btt459. Epub 2013 Aug 21. Bioinformatics. 2013. PMID: 23969133 Free PMC article.

8

A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics.

Song Q, Decato B, Hong EE, Zhou M, Fang F, Qu J, Garvin T, Kessler M, Zhou J, Smith AD. Song Q, et al. Among authors: smith ad. PLoS One. 2013 Dec 6;8(12):e81148. doi: 10.1371/journal.pone.0081148. eCollection 2013. PLoS One. 2013. PMID: 24324667 Free PMC article.

9

The Amordad database engine for metagenomics.

Behnam E, Smith AD. Behnam E, et al. Among authors: smith ad. Bioinformatics. 2014 Oct 15;30(20):2949-55. doi: 10.1093/bioinformatics/btu405. Epub 2014 Jun 27. Bioinformatics. 2014. PMID: 24974201 Free PMC article.

10

Modeling genome coverage in single-cell sequencing.

Daley T, Smith AD. Daley T, et al. Among authors: smith ad. Bioinformatics. 2014 Nov 15;30(22):3159-65. doi: 10.1093/bioinformatics/btu540. Epub 2014 Aug 8. Bioinformatics. 2014. PMID: 25107873 Free PMC article.

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