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    Scott Rifkin

    TitleAssociate Professor
    SchoolUniversity of California, San Diego
    DepartmentEcology, Behavior, and Evolution
    Address9500 Gilman Drive #0349
    CA La Jolla 92093
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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. Stockwell SR, Rifkin S. A living vector field reveals constraints on galactose network induction in yeast. Mol Syst Biol. 2017 Jan 30; 13(1):908. PMID: 28137775.
        View in: PubMed
      2. Wu AC, Rifkin S. 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.
      3. Du L, Tracy S, Rifkin S. 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].
      4. Maduro MF, Broitman-Maduro G, Choi H, Carranza F, Wu AC, Rifkin S. MED GATA factors promote robust development of the C. elegans endoderm. Dev Biol. 2015 Aug 01; 404(1):66-79. PMID: 25959238; PMCID: PMC4469534.
      5. Wu AC, Rifkin S. 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.
      6. Stockwell SR, Landry CR, Rifkin S. The yeast galactose network as a quantitative model for cellular memory. Mol Biosyst. 2015 Jan; 11(1):28-37. PMID: 25328105; PMCID: PMC4252300.
      7. Bakowski MA, Desjardins CA, Smelkinson MG, Dunbar TL, Dunbar TA, Lopez-Moyado IF, Rifkin S, 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.
      8. Landry CR, Rifkin S. 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
      9. Rifkin S. Identifying fluorescently labeled single molecules in image stacks using machine learning. Methods Mol Biol. 2011; 772:329-48. PMID: 22065448.
        View in: PubMed
      10. Landry CR, Rifkin S. Chromatin regulators shape the genotype-phenotype map. Mol Syst Biol. 2010 Nov 30; 6:434. PMID: 21119628; PMCID: PMC3010109.
      11. Raj A, Rifkin S, Andersen E, van Oudenaarden A. Variability in gene expression underlies incomplete penetrance. Nature. 2010 Feb 18; 463(7283):913-8. PMID: 20164922; PMCID: PMC2836165.
      12. Raj A, van den Bogaard P, Rifkin S, 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.
      13. Gilad Y, Rifkin S, 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.
      14. Landry CR, Lemos B, Rifkin S, 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
      15. Gilad Y, Oshlack A, Rifkin S. Natural selection on gene expression. Trends Genet. 2006 Aug; 22(8):456-61. PMID: 16806568.
        View in: PubMed
      16. Rifkin S, 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
      17. Gilad Y, Rifkin S, 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.
      18. Stolc V, Gauhar Z, Mason C, Halasz G, van Batenburg MF, Rifkin S, 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
      19. 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.
      20. Gu Z, Rifkin S, 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
      21. Rifkin S, 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
      22. Rifkin S, Kim J. Geometry of gene expression dynamics. Bioinformatics. 2002 Sep; 18(9):1176-83. PMID: 12217909.
        View in: PubMed
      23. Rifkin S, Atteson K, Kim J. Constraint structure analysis of gene expression. Funct Integr Genomics. 2000 Nov; 1(3):174-85. PMID: 11793235.
        View in: PubMed
      24. White KP, Rifkin S, Hurban P, Hogness DS. Microarray analysis of Drosophila development during metamorphosis. Science. 1999 Dec 10; 286(5447):2179-84. PMID: 10591654.
        View in: PubMed
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