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Scott Rifkin

TitleAssociate Researcher
InstitutionUniversity of California San Diego
DepartmentEcology, Behavior, and Evolution
Address9500 Gilman Drive #0349
La Jolla CA 92093
Phone858-822-5748
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    Collapse Research 
    Collapse Research Activities and Funding
    Dynamics and regulatory logic of the endodermal cell-fate decision in C. elegans
    NIH/NIGMS R01GM103782Sep 1, 2013 - Aug 31, 2018
    Role: Principal Investigator
    Effects of mutations on gene expression noise and cellular memory
    NIH/NIGMS F32GM080966May 1, 2007 - Apr 30, 2010
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse 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.
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    1. Welkie DG, Rubin BE, Chang YG, Diamond S, Rifkin SA, LiWang A, Golden SS. 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 Jul 10. PMID: 29991601.
      View in: PubMed
    2. Rubin BE, Huynh TN, Welkie DG, Diamond S, Simkovsky R, Pierce EC, Taton A, Lowe LC, Lee JJ, Rifkin SA, Woodward JJ, Golden SS. High-throughput interaction screens illuminate the role of c-di-AMP in cyanobacterial nighttime survival. PLoS Genet. 2018 Apr; 14(4):e1007301. PMID: 29608558.
      View in: PubMed
    3. Stockwell SR, Rifkin SA. A living vector field reveals constraints on galactose network induction in yeast. Mol Syst Biol. 2017 01 30; 13(1):908. PMID: 28137775.
      View in: PubMed
    4. Wu AC, Rifkin SA. 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. PMID: 27161120; PMCID: PMC4862211.
    5. Du L, Tracy S, Rifkin SA. 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. PMID: 26896592; PMCID: PMC4814310 [Available on 04/01/17].
    6. Maduro MF, Broitman-Maduro G, Choi H, Carranza F, Wu AC, Rifkin SA. MED GATA factors promote robust development of the C. elegans endoderm. Dev Biol. 2015 Aug 01; 404(1):66-79. PMID: 25959238; PMCID: PMC4469534.
    7. Wu AC, Rifkin SA. Aro: a machine learning approach to identifying single molecules and estimating classification error in fluorescence microscopy images. BMC Bioinformatics. 2015 Mar 27; 16:102. PMID: 25880543; PMCID: PMC4450985.
    8. Stockwell SR, Landry CR, Rifkin SA. The yeast galactose network as a quantitative model for cellular memory. Mol Biosyst. 2015 Jan; 11(1):28-37. PMID: 25328105; PMCID: PMC4252300.
    9. Bakowski MA, Desjardins CA, Smelkinson MG, Dunbar TL, Dunbar TA, Lopez-Moyado IF, Rifkin SA, Cuomo CA, Troemel ER. Ubiquitin-mediated response to microsporidia and virus infection in C. elegans. PLoS Pathog. 2014 Jun; 10(6):e1004200. PMID: 24945527; PMCID: PMC4063957.
    10. Landry CR, Rifkin SA. The genotype-phenotype maps of systems biology and quantitative genetics: distinct and complementary. Adv Exp Med Biol. 2012; 751:371-98. PMID: 22821467.
      View in: PubMed
    11. Rifkin SA. Identifying fluorescently labeled single molecules in image stacks using machine learning. Methods Mol Biol. 2011; 772:329-48. PMID: 22065448.
      View in: PubMed
    12. Landry CR, Rifkin SA. Chromatin regulators shape the genotype-phenotype map. Mol Syst Biol. 2010 Nov 30; 6:434. PMID: 21119628; PMCID: PMC3010109.
    13. Raj A, Rifkin SA, Andersen E, van Oudenaarden A. Variability in gene expression underlies incomplete penetrance. Nature. 2010 Feb 18; 463(7283):913-8. PMID: 20164922; PMCID: PMC2836165.
    14. Raj A, van den Bogaard P, Rifkin SA, van Oudenaarden A, Tyagi S. Imaging individual mRNA molecules using multiple singly labeled probes. Nat Methods. 2008 Oct; 5(10):877-9. PMID: 18806792; PMCID: PMC3126653.
    15. Gilad Y, Rifkin SA, Pritchard JK. Revealing the architecture of gene regulation: the promise of eQTL studies. Trends Genet. 2008 Aug; 24(8):408-15. PMID: 18597885; PMCID: PMC2583071.
    16. Landry CR, Lemos B, Rifkin SA, Dickinson WJ, Hartl DL. Genetic properties influencing the evolvability of gene expression. Science. 2007 Jul 06; 317(5834):118-21. PMID: 17525304.
      View in: PubMed
    17. Gilad Y, Oshlack A, Rifkin SA. Natural selection on gene expression. Trends Genet. 2006 Aug; 22(8):456-61. PMID: 16806568.
      View in: PubMed
    18. Rifkin SA, Houle D, Kim J, White KP. A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression. Nature. 2005 Nov 10; 438(7065):220-3. PMID: 16281035.
      View in: PubMed
    19. Gilad Y, Rifkin SA, Bertone P, Gerstein M, White KP. Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Res. 2005 May; 15(5):674-80. PMID: 15867429; PMCID: PMC1088295.
    20. 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. A gene expression map for the euchromatic genome of Drosophila melanogaster. Science. 2004 Oct 22; 306(5696):655-60. PMID: 15499012.
      View in: PubMed
    21. 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. 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. PMID: 15492032; PMCID: PMC543832.
    22. Gu Z, Rifkin SA, White KP, Li WH. Duplicate genes increase gene expression diversity within and between species. Nat Genet. 2004 Jun; 36(6):577-9. PMID: 15122255.
      View in: PubMed
    23. Rifkin SA, Kim J, White KP. Evolution of gene expression in the Drosophila melanogaster subgroup. Nat Genet. 2003 Feb; 33(2):138-44. PMID: 12548287.
      View in: PubMed