Scott Rifkin

Title(s)	Associate Professor, Ecology, Behavior, and Evolution
School	Vc-academic Affairs
Address	9500 Gilman Drive # La Jolla CA 92093
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Research

Research Activities and Funding

Dynamics and regulatory logic of the endodermal cell-fate decision in C. elegans
NIH R01GM103782Sep 1, 2013 - Aug 31, 2019
Role: Principal Investigator

Effects of mutations on gene expression noise and cellular memory
NIH F32GM080966May 1, 2007 - Apr 30, 2010
Role: Principal Investigator

Bibliographic

Publications

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.

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Networks of Causal Linkage Between Eigenmodes Characterize Behavioral Dynamics of Caenorhabditis elegans. PLoS Comput Biol. 2021 09; 17(9):e1009329. Saberski E, Bock AK, Goodridge R, Agarwal V, Lorimer T, Rifkin SA, Sugihara G. PMID: 34506477; PMCID: PMC8494368.

View in: PubMed Mentions: 1 Fields:
Com Computational Biology
Translation:Animals
Tracking changes in behavioural dynamics using prediction error. PLoS One. 2021; 16(5):e0251053. Lorimer T, Goodridge R, Bock AK, Agarwal V, Saberski E, Sugihara G, Rifkin SA. PMID: 33979384; PMCID: PMC8115816.

View in: PubMed Mentions: 1 Fields:
Med Medicine (General)Sci Science
Translation:Animals
A larger target leads to faster evolution. Elife. 2020 10 14; 9. Yang B, Rifkin SA. PMID: 33052100; PMCID: PMC7556857.

View in: PubMed Mentions: Fields:
Bio Biology
Translation:Animals
The circadian clock and darkness control natural competence in cyanobacteria. Nat Commun. 2020 04 03; 11(1):1688. Taton A, Erikson C, Yang Y, Rubin BE, Rifkin SA, Golden JW, Golden SS. PMID: 32245943; PMCID: PMC7125226.

View in: PubMed Mentions: 36 Fields:
Bio Biology Sci Science
Translation:Cells
Genome-wide fitness assessment during diurnal growth reveals an expanded role of the cyanobacterial circadian clock protein KaiA. Proc Natl Acad Sci U S A. 2018 07 24; 115(30):E7174-E7183. Welkie DG, Rubin BE, Chang YG, Diamond S, Rifkin SA, LiWang A, Golden SS. PMID: 29991601; PMCID: PMC6064986.

View in: PubMed Mentions: 27 Fields:
Sci Science
Translation:Cells
High-throughput interaction screens illuminate the role of c-di-AMP in cyanobacterial nighttime survival. PLoS Genet. 2018 04; 14(4):e1007301. Rubin BE, Huynh TN, Welkie DG, Diamond S, Simkovsky R, Pierce EC, Taton A, Lowe LC, Lee JJ, Rifkin SA, Woodward JJ, Golden SS. PMID: 29608558; PMCID: PMC5897029.

View in: PubMed Mentions: 20 Fields:
Gen Genetics
Translation:Cells
A living vector field reveals constraints on galactose network induction in yeast. Mol Syst Biol. 2017 01 30; 13(1):908. Stockwell SR, Rifkin SA. PMID: 28137775; PMCID: PMC5293160.

View in: PubMed Mentions: 9 Fields:
Com Computational Biology Mol Molecular Biology
Translation:Animals
Erratum to: 'Aro: a machine learning approach to identifying single molecules and estimating classification error in fluorescence microscopy images'. BMC Bioinformatics. 2016 May 09; 17:207. Wu AC, Rifkin SA. PMID: 27161120; PMCID: PMC4862211.

View in: PubMed Mentions: 1 Fields:
Com Computational Biology
Mutagenesis of GATA motifs controlling the endoderm regulator elt-2 reveals distinct dominant and secondary cis-regulatory elements. Dev Biol. 2016 Apr 01; 412(1):160-170. Du L, Tracy S, Rifkin SA. PMID: 26896592; PMCID: PMC4814310.

View in: PubMed Mentions: 7 Fields:
Bio Biology Emb Embryology
Translation:Animals
MED GATA factors promote robust development of the C. elegans endoderm. Dev Biol. 2015 Aug 01; 404(1):66-79. Maduro MF, Broitman-Maduro G, Choi H, Carranza F, Wu AC, Rifkin SA. PMID: 25959238; PMCID: PMC4469534.

View in: PubMed Mentions: 21 Fields:
Bio Biology Emb Embryology
Translation:Animals
Aro: a machine learning approach to identifying single molecules and estimating classification error in fluorescence microscopy images. BMC Bioinformatics. 2015 Mar 27; 16:102. Wu AC, Rifkin SA. PMID: 25880543; PMCID: PMC4450985.

View in: PubMed Mentions: 11 Fields:
Com Computational Biology
Translation:Animals
The yeast galactose network as a quantitative model for cellular memory. Mol Biosyst. 2015 Jan; 11(1):28-37. Stockwell SR, Landry CR, Rifkin SA. PMID: 25328105; PMCID: PMC4252300.

View in: PubMed Mentions: 23 Fields:
Bio Biochemistry Mol Molecular Biology
Translation:Animals Cells
Ubiquitin-mediated response to microsporidia and virus infection in C. elegans. PLoS Pathog. 2014 Jun; 10(6):e1004200. Bakowski MA, Desjardins CA, Smelkinson MG, Dunbar TL, Dunbar TA, Lopez-Moyado IF, Rifkin SA, Cuomo CA, Troemel ER. PMID: 24945527; PMCID: PMC4063957.

View in: PubMed Mentions: 100 Fields:
Mic Microbiology
Translation:Animals Cells
The genotype-phenotype maps of systems biology and quantitative genetics: distinct and complementary. Adv Exp Med Biol. 2012; 751:371-98. Landry CR, Rifkin SA. PMID: 22821467.

View in: PubMed Mentions: 9 Fields:
Bio Biology Med Medicine (General)
Translation:Animals Cells
Identifying fluorescently labeled single molecules in image stacks using machine learning. Methods Mol Biol. 2011; 772:329-48. Rifkin SA. PMID: 22065448.

View in: PubMed Mentions: 5 Fields:
Mol Molecular Biology
Translation:Animals
Chromatin regulators shape the genotype-phenotype map. Mol Syst Biol. 2010 Nov 30; 6:434. Landry CR, Rifkin SA. PMID: 21119628; PMCID: PMC3010109.

View in: PubMed Mentions: 2 Fields:
Com Computational Biology Mol Molecular Biology
Translation:Animals
Variability in gene expression underlies incomplete penetrance. Nature. 2010 Feb 18; 463(7283):913-8. Raj A, Rifkin SA, Andersen E, van Oudenaarden A. PMID: 20164922; PMCID: PMC2836165.

View in: PubMed Mentions: 344 Fields:
Sci Science
Translation:Animals Cells
Imaging individual mRNA molecules using multiple singly labeled probes. Nat Methods. 2008 Oct; 5(10):877-9. Raj A, van den Bogaard P, Rifkin SA, van Oudenaarden A, Tyagi S. PMID: 18806792; PMCID: PMC3126653.

View in: PubMed Mentions: 992 Fields:
Cli Clinical Laboratory Techniques
Translation:Animals
Revealing the architecture of gene regulation: the promise of eQTL studies. Trends Genet. 2008 Aug; 24(8):408-15. Gilad Y, Rifkin SA, Pritchard JK. PMID: 18597885; PMCID: PMC2583071.

View in: PubMed Mentions: 264 Fields:
Gen Genetics
Translation:Humans Animals
Genetic properties influencing the evolvability of gene expression. Science. 2007 Jul 06; 317(5834):118-21. Landry CR, Lemos B, Rifkin SA, Dickinson WJ, Hartl DL. PMID: 17525304.

View in: PubMed Mentions: 178 Fields:
Sci Science
Translation:Animals Cells
Natural selection on gene expression. Trends Genet. 2006 Aug; 22(8):456-61. Gilad Y, Oshlack A, Rifkin SA. PMID: 16806568.

View in: PubMed Mentions: 105 Fields:
Gen Genetics
Translation:Humans Animals
A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression. Nature. 2005 Nov 10; 438(7065):220-3. Rifkin SA, Houle D, Kim J, White KP. PMID: 16281035.

View in: PubMed Mentions: 93 Fields:
Sci Science
Translation:Humans Animals
Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Res. 2005 May; 15(5):674-80. Gilad Y, Rifkin SA, Bertone P, Gerstein M, White KP. PMID: 15867429; PMCID: PMC1088295.

View in: PubMed Mentions: 87 Fields:
Gen Genetics
Translation:Humans Animals Cells
A gene expression map for the euchromatic genome of Drosophila melanogaster. Science. 2004 Oct 22; 306(5696):655-60. 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. PMID: 15499012.

View in: PubMed Mentions: 157 Fields:
Sci Science
Translation:Animals Cells
A high productivity/low maintenance approach to high-performance computation for biomedicine: four case studies. J Am Med Inform Assoc. 2005 Jan-Feb; 12(1):90-8. Carriero N, Osier MV, Cheung KH, Miller PL, Gerstein M, Zhao H, Wu B, Rifkin S, Chang J, Zhang H, White K, Williams K, Schultz M. PMID: 15492032; PMCID: PMC543832.

View in: PubMed Mentions: 2 Fields:
Med Medical Informatics
Translation:Cells
Duplicate genes increase gene expression diversity within and between species. Nat Genet. 2004 Jun; 36(6):577-9. Gu Z, Rifkin SA, White KP, Li WH. PMID: 15122255.

View in: PubMed Mentions: 86 Fields:
Gen Genetics
Translation:Animals
Evolution of gene expression in the Drosophila melanogaster subgroup. Nat Genet. 2003 Feb; 33(2):138-44. Rifkin SA, Kim J, White KP. PMID: 12548287.

View in: PubMed Mentions: 164 Fields:
Gen Genetics
Translation:Animals Cells
Geometry of gene expression dynamics. Bioinformatics. 2002 Sep; 18(9):1176-83. Rifkin SA, Kim J. PMID: 12217909.

View in: PubMed Mentions: 5 Fields:
Com Computational Biology
Translation:Animals
Constraint structure analysis of gene expression. Funct Integr Genomics. 2000 Nov; 1(3):174-85. Rifkin SA, Atteson K, Kim J. PMID: 11793235.

View in: PubMed Mentions: 4 Fields:
Gen Genetics Mol Molecular Biology
Translation:Animals Cells
Microarray analysis of Drosophila development during metamorphosis. Science. 1999 Dec 10; 286(5447):2179-84. White KP, Rifkin SA, Hurban P, Hogness DS. PMID: 10591654.

View in: PubMed Mentions: 124 Fields:
Sci Science
Translation:Animals