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Scott Rifkin

Title(s)Associate Professor, Ecology, Behavior, and Evolution
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
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    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 - Jun 30, 2009
    Role: Principal Investigator

    Collapse Bibliographic 
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    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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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. A larger target leads to faster evolution. Elife. 2020 Oct 14; 9. Yang B, Rifkin SA. PMID: 33052100.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    2. 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.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    3. 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.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    4. 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.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    5. 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.
      View in: PubMed   Mentions: 4     Fields:    Translation:Animals
    6. 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.
      View in: PubMed   Mentions: 1     Fields:    
    7. 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.
      View in: PubMed   Mentions: 2     Fields:    Translation:Animals
    8. 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.
      View in: PubMed   Mentions: 13     Fields:    Translation:Animals
    9. 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.
      View in: PubMed   Mentions: 5     Fields:    Translation:Animals
    10. 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.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    11. 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.
      View in: PubMed   Mentions: 51     Fields:    Translation:AnimalsCells
    12. 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:    Translation:AnimalsCells
    13. 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: 4     Fields:    Translation:Animals
    14. Chromatin regulators shape the genotype-phenotype map. Mol Syst Biol. 2010 Nov 30; 6:434. Landry CR, Rifkin SA. PMID: 21119628.
      View in: PubMed   Mentions: 1     Fields:    Translation:Animals
    15. 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.
      View in: PubMed   Mentions: 267     Fields:    Translation:AnimalsCells
    16. 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.
      View in: PubMed   Mentions: 595     Fields:    Translation:Animals
    17. 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.
      View in: PubMed   Mentions: 206     Fields:    Translation:HumansAnimals
    18. 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: 146     Fields:    Translation:AnimalsCells
    19. 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: 76     Fields:    Translation:HumansAnimals
    20. 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: 79     Fields:    Translation:HumansAnimals
    21. 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.
      View in: PubMed   Mentions: 84     Fields:    Translation:HumansAnimalsCells
    22. 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: 149     Fields:    Translation:AnimalsCells
    23. 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.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    24. 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: 79     Fields:    Translation:Animals
    25. 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: 148     Fields:    Translation:AnimalsCells
    26. Geometry of gene expression dynamics. Bioinformatics. 2002 Sep; 18(9):1176-83. Rifkin SA, Kim J. PMID: 12217909.
      View in: PubMed   Mentions: 4     Fields:    Translation:Animals
    27. 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:    Translation:AnimalsCells
    28. 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: 114     Fields:    Translation:Animals
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