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Items: 25

1.

Genome-wide fitness assessment during diurnal growth reveals an expanded role of the cyanobacterial circadian clock protein KaiA.

Welkie DG, Rubin BE, Chang YG, Diamond S, Rifkin SA, LiWang A, Golden SS.

Proc Natl Acad Sci U S A. 2018 Jul 24;115(30):E7174-E7183. doi: 10.1073/pnas.1802940115. Epub 2018 Jul 10.

2.

High-throughput interaction screens illuminate the role of c-di-AMP in cyanobacterial nighttime survival.

Rubin BE, Huynh TN, Welkie DG, Diamond S, Simkovsky R, Pierce EC, Taton A, Lowe LC, Lee JJ, Rifkin SA, Woodward JJ, Golden SS.

PLoS Genet. 2018 Apr 2;14(4):e1007301. doi: 10.1371/journal.pgen.1007301. eCollection 2018 Apr.

3.

A living vector field reveals constraints on galactose network induction in yeast.

Stockwell SR, Rifkin SA.

Mol Syst Biol. 2017 Jan 30;13(1):908. doi: 10.15252/msb.20167323.

4.

Erratum to: 'Aro: a machine learning approach to identifying single molecules and estimating classification error in fluorescence microscopy images'.

Wu AC, Rifkin SA.

BMC Bioinformatics. 2016 May 9;17:207. doi: 10.1186/s12859-016-1049-y. No abstract available.

5.

Mutagenesis of GATA motifs controlling the endoderm regulator elt-2 reveals distinct dominant and secondary cis-regulatory elements.

Du L, Tracy S, Rifkin SA.

Dev Biol. 2016 Apr 1;412(1):160-170. doi: 10.1016/j.ydbio.2016.02.013. Epub 2016 Feb 16.

6.

MED GATA factors promote robust development of the C. elegans endoderm.

Maduro MF, Broitman-Maduro G, Choi H, Carranza F, Wu AC, Rifkin SA.

Dev Biol. 2015 Aug 1;404(1):66-79. doi: 10.1016/j.ydbio.2015.04.025. Epub 2015 May 8.

7.
8.

The yeast galactose network as a quantitative model for cellular memory.

Stockwell SR, Landry CR, Rifkin SA.

Mol Biosyst. 2015 Jan;11(1):28-37. doi: 10.1039/c4mb00448e. Epub 2014 Oct 20. Review.

9.

Ubiquitin-mediated response to microsporidia and virus infection in C. elegans.

Bakowski MA, Desjardins CA, Smelkinson MG, Dunbar TL, Lopez-Moyado IF, Rifkin SA, Cuomo CA, Troemel ER.

PLoS Pathog. 2014 Jun 19;10(6):e1004200. doi: 10.1371/journal.ppat.1004200. eCollection 2014 Jun. Erratum in: PLoS Pathog. 2014 Aug;10(8):e1004371. Dunbar, Tiffany A [corrected to Dunbar, Tiffany L].

10.

The genotype-phenotype maps of systems biology and quantitative genetics: distinct and complementary.

Landry CR, Rifkin SA.

Adv Exp Med Biol. 2012;751:371-98. doi: 10.1007/978-1-4614-3567-9_17.

PMID:
22821467
11.

Identifying fluorescently labeled single molecules in image stacks using machine learning.

Rifkin SA.

Methods Mol Biol. 2011;772:329-48. doi: 10.1007/978-1-61779-228-1_20.

PMID:
22065448
12.

Chromatin regulators shape the genotype-phenotype map.

Landry CR, Rifkin SA.

Mol Syst Biol. 2010 Nov 30;6:434. doi: 10.1038/msb.2010.97. No abstract available.

13.

Variability in gene expression underlies incomplete penetrance.

Raj A, Rifkin SA, Andersen E, van Oudenaarden A.

Nature. 2010 Feb 18;463(7283):913-8. doi: 10.1038/nature08781.

14.

Imaging individual mRNA molecules using multiple singly labeled probes.

Raj A, van den Bogaard P, Rifkin SA, van Oudenaarden A, Tyagi S.

Nat Methods. 2008 Oct;5(10):877-9. doi: 10.1038/nmeth.1253. Epub 2008 Sep 21.

15.

Revealing the architecture of gene regulation: the promise of eQTL studies.

Gilad Y, Rifkin SA, Pritchard JK.

Trends Genet. 2008 Aug;24(8):408-15. doi: 10.1016/j.tig.2008.06.001. Epub 2008 Jul 1. Review.

16.

Genetic properties influencing the evolvability of gene expression.

Landry CR, Lemos B, Rifkin SA, Dickinson WJ, Hartl DL.

Science. 2007 Jul 6;317(5834):118-21. Epub 2007 May 24.

17.

Natural selection on gene expression.

Gilad Y, Oshlack A, Rifkin SA.

Trends Genet. 2006 Aug;22(8):456-61. Epub 2006 Jun 27. Review.

PMID:
16806568
18.

A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression.

Rifkin SA, Houle D, Kim J, White KP.

Nature. 2005 Nov 10;438(7065):220-3.

PMID:
16281035
19.

Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles.

Gilad Y, Rifkin SA, Bertone P, Gerstein M, White KP.

Genome Res. 2005 May;15(5):674-80.

20.

A gene expression map for the euchromatic genome of Drosophila melanogaster.

Stolc V, Gauhar Z, Mason C, Halasz G, van Batenburg MF, Rifkin SA, Hua S, Herreman T, Tongprasit W, Barbano PE, Bussemaker HJ, White KP.

Science. 2004 Oct 22;306(5696):655-60.

21.

Duplicate genes increase gene expression diversity within and between species.

Gu Z, Rifkin SA, White KP, Li WH.

Nat Genet. 2004 Jun;36(6):577-9. Epub 2004 May 2.

PMID:
15122255
22.

Evolution of gene expression in the Drosophila melanogaster subgroup.

Rifkin SA, Kim J, White KP.

Nat Genet. 2003 Feb;33(2):138-44. Epub 2003 Jan 27.

PMID:
12548287
23.

Geometry of gene expression dynamics.

Rifkin SA, Kim J.

Bioinformatics. 2002 Sep;18(9):1176-83.

PMID:
12217909
24.

Constraint structure analysis of gene expression.

Rifkin SA, Atteson K, Kim J.

Funct Integr Genomics. 2000 Nov;1(3):174-85.

PMID:
11793235
25.

Microarray analysis of Drosophila development during metamorphosis.

White KP, Rifkin SA, Hurban P, Hogness DS.

Science. 1999 Dec 10;286(5447):2179-84.

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