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Emma Farley

TitleAssistant Professor
InstitutionUniversity of California San Diego
DepartmentMedicine
Address9500 Gilman Drive #0655
La Jolla CA 92093
Phone858-246-2552
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    Collapse Biography 
    Collapse Education and Training
    Princeton UniversityPostdoc2015Lewis Sigler Institute for Integrative Genomics
    UC BerkeleyPostdoc2012Molecular and Cellular Biology
    Imperial College LondonPhD2011MRC Clinical Sciences Center
    Oxford UniversityMBiochem2007Department of Biochemistry

    Collapse Research 
    Collapse Research Activities and Funding
    Deciphering the regulatory principles governing enhancer specificity
    NIH/NHGRI DP2HG010013Sep 30, 2017 - Jun 30, 2022
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Featured Publications
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    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. Zhang W, Bojorquez-Gomez A, Velez DO, Xu G, Sanchez KS, Shen JP, Chen K, Licon K, Melton C, Olson KM, Yu MK, Huang JK, Carter H, Farley E, Snyder M, Fraley SI, Kreisberg JF, Ideker T. A global transcriptional network connecting noncoding mutations to changes in tumor gene expression. Nat Genet. 2018 Apr; 50(4):613-620. PMID: 29610481.
      View in: PubMed
    2. D Antonio M, Weghorn D, D Antonio-Chronowska A, Coulet F, Olson KM, DeBoever C, Drees F, Arias A, Alakus H, Richardson AL, Schwab RB, Farley E, Sunyaev SR, Frazer KA. Identifying DNase I hypersensitive sites as driver distal regulatory elements in breast cancer. Nat Commun. 2017 09 05; 8(1):436. PMID: 28874753.
      View in: PubMed
    3. DeBoever C, Li H, Jakubosky D, Benaglio P, Reyna J, Olson KM, Huang H, Biggs W, Sandoval E, D'Antonio M, Jepsen K, Matsui H, Arias A, Ren B, Nariai N, Smith EN, D'Antonio-Chronowska A, Farley E, Frazer KA. Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells. Cell Stem Cell. 2017 04 06; 20(4):533-546.e7. PMID: 28388430.
      View in: PubMed
    4. Farley E, Olson KM, Zhang W, Rokhsar DS, Levine MS. Syntax compensates for poor binding sites to encode tissue specificity of developmental enhancers. Proc Natl Acad Sci U S A. 2016 06 07; 113(23):6508-13. PMID: 27155014; PMCID: PMC4988596 [Available on 12/07/16].
    5. Farley E, Olson KM, Zhang W, Brandt AJ, Rokhsar DS, Levine MS. Suboptimization of developmental enhancers. Science. 2015 Oct 16; 350(6258):325-8. PMID: 26472909; PMCID: PMC4970741 [Available on 10/16/16].
    6. Farley E, Olson KM, Levine MS. Regulatory Principles Governing Tissue Specificity of Developmental Enhancers. Cold Spring Harb Symp Quant Biol. 2015; 80:27-32. PMID: 27325706; PMCID: PMC4970742.
    7. Farley E. Gene transfer in developing chick embryos: in ovo electroporation. Methods Mol Biol. 2013; 1018:141-50. PMID: 23681625.
      View in: PubMed
    8. Farley E, Levine M. HOT DNAs: a novel class of developmental enhancers. Genes Dev. 2012 May 01; 26(9):873-6. PMID: 22549952; PMCID: PMC3347785.
    9. Gennet N, Gale E, Nan X, Farley E, Takacs K, Oberwallner B, Chambers D, Li M. Doublesex and mab-3-related transcription factor 5 promotes midbrain dopaminergic identity in pluripotent stem cells by enforcing a ventral-medial progenitor fate. Proc Natl Acad Sci U S A. 2011 May 31; 108(22):9131-6. PMID: 21576465; PMCID: PMC3107330.
    10. Farley E, Gale E, Chambers D, Li M. Effects of in ovo electroporation on endogenous gene expression: genome-wide analysis. Neural Dev. 2011 Apr 28; 6:17. PMID: 21527010; PMCID: PMC3105949.