Emma Farley

Title(s)Assistant Professor, Medicine
SchoolVc-health Sciences-schools
Address9500 Gilman Drive #
La Jolla CA 92093
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    Princeton UniversityPostdoc2015Lewis Sigler Institute for Integrative Genomics
    UC BerkeleyPostdoc2012Molecular and Cellular Biology
    Imperial College LondonPhD2011MRC Clinical Sciences Center
    Oxford UniversityMBiochem2007Department of Biochemistry

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    Statistical and high-throughput models of enhancer function and evolution
    NIH R01HG011485Feb 22, 2021 - Jan 31, 2025
    Role: Co-Principal Investigator
    Deciphering the regulatory principles governing enhancer specificity
    NIH DP2HG010013Sep 30, 2017 - May 31, 2022
    Role: Principal Investigator

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    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. 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. Diverse logics and grammar encode notochord enhancers. Cell Rep. 2023 Jan 31; 42(2):112052. Song BP, Ragsac MF, Tellez K, Jindal GA, Grudzien JL, Le SH, Farley EK. PMID: 36729834.
      View in: PubMed   Mentions: 1     Fields:    
    2. Enhancer grammar in development, evolution, and disease: dependencies and interplay. Dev Cell. 2021 03 08; 56(5):575-587. Jindal GA, Farley EK. PMID: 33689769; PMCID: PMC8462829.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCells
    3. Functional genomic approaches to elucidate the role of enhancers during development. Wiley Interdiscip Rev Syst Biol Med. 2020 03; 12(2):e1467. Ryan GE, Farley EK. PMID: 31808313; PMCID: PMC7027484.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    4. A global transcriptional network connecting noncoding mutations to changes in tumor gene expression. Nat Genet. 2018 04; 50(4):613-620. 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 EK, Snyder M, Fraley SI, Kreisberg JF, Ideker T. PMID: 29610481; PMCID: PMC5893414.
      View in: PubMed   Mentions: 52     Fields:    Translation:HumansCells
    5. Identifying DNase I hypersensitive sites as driver distal regulatory elements in breast cancer. Nat Commun. 2017 09 05; 8(1):436. 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 EK, Sunyaev SR, Frazer KA. PMID: 28874753; PMCID: PMC5585396.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    6. 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. 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 EK, Frazer KA. PMID: 28388430; PMCID: PMC5444918.
      View in: PubMed   Mentions: 70     Fields:    Translation:HumansCells
    7. 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. Farley EK, Olson KM, Zhang W, Rokhsar DS, Levine MS. PMID: 27155014; PMCID: PMC4988596.
      View in: PubMed   Mentions: 64     Fields:    Translation:AnimalsCells
    8. Suboptimization of developmental enhancers. Science. 2015 Oct 16; 350(6258):325-8. Farley EK, Olson KM, Zhang W, Brandt AJ, Rokhsar DS, Levine MS. PMID: 26472909; PMCID: PMC4970741.
      View in: PubMed   Mentions: 129     Fields:    Translation:AnimalsCells
    9. Regulatory Principles Governing Tissue Specificity of Developmental Enhancers. Cold Spring Harb Symp Quant Biol. 2015; 80:27-32. Farley EK, Olson KM, Levine MS. PMID: 27325706; PMCID: PMC4970742.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansAnimalsCells
    10. Gene transfer in developing chick embryos: in ovo electroporation. Methods Mol Biol. 2013; 1018:141-50. Farley EK. PMID: 23681625.
      View in: PubMed   Mentions: 1     Fields:    Translation:Animals
    11. HOT DNAs: a novel class of developmental enhancers. Genes Dev. 2012 May 01; 26(9):873-6. Farley E, Levine M. PMID: 22549952; PMCID: PMC3347785.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    12. 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. Gennet N, Gale E, Nan X, Farley E, Takacs K, Oberwallner B, Chambers D, Li M. PMID: 21576465; PMCID: PMC3107330.
      View in: PubMed   Mentions: 21     Fields:    Translation:AnimalsCells
    13. Effects of in ovo electroporation on endogenous gene expression: genome-wide analysis. Neural Dev. 2011 Apr 28; 6:17. Farley EK, Gale E, Chambers D, Li M. PMID: 21527010; PMCID: PMC3105949.
      View in: PubMed   Mentions: 3     Fields:    Translation:Animals
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