Hogenesch JB - Search Results

1

Design and analysis of large-scale biological rhythm studies: a comparison of algorithms for detecting periodic signals in biological data.

Deckard A, Anafi RC, Hogenesch JB, Haase SB, Harer J. Deckard A, et al. Among authors: hogenesch jb. Bioinformatics. 2013 Dec 15;29(24):3174-80. doi: 10.1093/bioinformatics/btt541. Epub 2013 Sep 20. Bioinformatics. 2013. PMID: 24058056 Free PMC article.

2

Genomics and systems approaches in the mammalian circadian clock.

Baggs JE, Hogenesch JB. Baggs JE, et al. Among authors: hogenesch jb. Curr Opin Genet Dev. 2010 Dec;20(6):581-7. doi: 10.1016/j.gde.2010.08.009. Curr Opin Genet Dev. 2010. PMID: 20926286 Free PMC article. Review.

3

Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM).

Grant GR, Farkas MH, Pizarro AD, Lahens NF, Schug J, Brunk BP, Stoeckert CJ, Hogenesch JB, Pierce EA. Grant GR, et al. Among authors: hogenesch jb. Bioinformatics. 2011 Sep 15;27(18):2518-28. doi: 10.1093/bioinformatics/btr427. Epub 2011 Jul 19. Bioinformatics. 2011. PMID: 21775302 Free PMC article.

4

CircaDB: a database of mammalian circadian gene expression profiles.

Pizarro A, Hayer K, Lahens NF, Hogenesch JB. Pizarro A, et al. Among authors: hogenesch jb. Nucleic Acids Res. 2013 Jan;41(Database issue):D1009-13. doi: 10.1093/nar/gks1161. Epub 2012 Nov 24. Nucleic Acids Res. 2013. PMID: 23180795 Free PMC article.

5

Machine learning helps identify CHRONO as a circadian clock component.

Anafi RC, Lee Y, Sato TK, Venkataraman A, Ramanathan C, Kavakli IH, Hughes ME, Baggs JE, Growe J, Liu AC, Kim J, Hogenesch JB. Anafi RC, et al. Among authors: hogenesch jb. PLoS Biol. 2014 Apr 15;12(4):e1001840. doi: 10.1371/journal.pbio.1001840. eCollection 2014 Apr. PLoS Biol. 2014. PMID: 24737000 Free PMC article.

6

Considerations for RNA-seq analysis of circadian rhythms.

Li J, Grant GR, Hogenesch JB, Hughes ME. Li J, et al. Among authors: hogenesch jb. Methods Enzymol. 2015;551:349-67. doi: 10.1016/bs.mie.2014.10.020. Epub 2014 Dec 26. Methods Enzymol. 2015. PMID: 25662464

7

Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data.

Hayer KE, Pizarro A, Lahens NF, Hogenesch JB, Grant GR. Hayer KE, et al. Among authors: hogenesch jb. Bioinformatics. 2015 Dec 15;31(24):3938-45. doi: 10.1093/bioinformatics/btv488. Epub 2015 Sep 3. Bioinformatics. 2015. PMID: 26338770 Free PMC article.

8

Discovering Biology in Periodic Data through Phase Set Enrichment Analysis (PSEA).

Zhang R, Podtelezhnikov AA, Hogenesch JB, Anafi RC. Zhang R, et al. Among authors: hogenesch jb. J Biol Rhythms. 2016 Jun;31(3):244-57. doi: 10.1177/0748730416631895. Epub 2016 Mar 8. J Biol Rhythms. 2016. PMID: 26955841

9

MetaCycle: an integrated R package to evaluate periodicity in large scale data.

Wu G, Anafi RC, Hughes ME, Kornacker K, Hogenesch JB. Wu G, et al. Among authors: hogenesch jb. Bioinformatics. 2016 Nov 1;32(21):3351-3353. doi: 10.1093/bioinformatics/btw405. Epub 2016 Jul 4. Bioinformatics. 2016. PMID: 27378304 Free PMC article.

10

The Local Edge Machine: inference of dynamic models of gene regulation.

McGoff KA, Guo X, Deckard A, Kelliher CM, Leman AR, Francey LJ, Hogenesch JB, Haase SB, Harer JL. McGoff KA, et al. Among authors: hogenesch jb. Genome Biol. 2016 Oct 19;17(1):214. doi: 10.1186/s13059-016-1076-z. Genome Biol. 2016. PMID: 27760556 Free PMC article.

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