Emma Farley

Title(s)Associate Professor, Medicine
SchoolVc-health Sciences-schools
Address9500 Gilman Drive #
La Jolla CA 92093
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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

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    Collapse Research 
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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.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    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 benchmarked, high-efficiency prime editing platform for multiplexed dropout screening. Nat Methods. 2025 Jan; 22(1):92-101. Cirincione A, Simpson D, Yan W, McNulty R, Ravisankar P, Solley SC, Yan J, Lim F, Farley EK, Singh M, Adamson B. PMID: 39562753; PMCID: PMC11725502.
      View in: PubMed   Mentions:    Fields:    
    2. Protocol to electroporate DNA plasmids into Ciona robusta embryos at the 1-cell stage. STAR Protoc. 2024 Sep 20; 5(3):103107. Jindal GA, Lim F, Tellez K, Song BP, Bantle AT, Farley EK. PMID: 38963758; PMCID: PMC11269276.
      View in: PubMed   Mentions:    Fields:    
    3. Affinity-optimizing enhancer variants disrupt development. Nature. 2024 Feb; 626(7997):151-159. Lim F, Solvason JJ, Ryan GE, Le SH, Jindal GA, Steffen P, Jandu SK, Farley EK. PMID: 38233525; PMCID: PMC10830414.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCells
    4. Ciona, an ideal research organism to study the role of enhancers. Genesis. 2023 11; 61(6):e23577. Farley EK. PMID: 38009359.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    5. Predictive analyses of regulatory sequences with EUGENe. Nat Comput Sci. 2023 Nov; 3(11):946-956. Klie A, Laub D, Talwar JV, Stites H, Jores T, Solvason JJ, Farley EK, Carter H. PMID: 38177592; PMCID: PMC10768637.
      View in: PubMed   Mentions: 3     Fields:    
    6. Conserved enhancers control notochord expression of vertebrate Brachyury. Nat Commun. 2023 10 18; 14(1):6594. Kemmler CL, Smolikova J, Moran HR, Mannion BJ, Knapp D, Lim F, Czarkwiani A, Hermosilla Aguayo V, Rapp V, Fitch OE, Bötschi S, Selleri L, Farley E, Braasch I, Yun M, Visel A, Osterwalder M, Mosimann C, Kozmik Z, Burger A. PMID: 37852970; PMCID: PMC10584899.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimals
    7. Single-nucleotide variants within heart enhancers increase binding affinity and disrupt heart development. Dev Cell. 2023 11 06; 58(21):2206-2216.e5. Jindal GA, Bantle AT, Solvason JJ, Grudzien JL, D'Antonio-Chronowska A, Lim F, Le SH, Song BP, Ragsac MF, Klie A, Larsen RO, Frazer KA, Farley EK. PMID: 37848026; PMCID: PMC10720985.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    8. Conserved enhancer logic controls the notochord expression of vertebrate Brachyury. bioRxiv. 2023 Apr 20. Kemmler CL, Smolikova J, Moran HR, Mannion BJ, Knapp D, Lim F, Czarkwiani A, Hermosilla Aguayo V, Rapp V, Fitch OE, Bötschi S, Selleri L, Farley E, Braasch I, Yun M, Visel A, Osterwalder M, Mosimann C, Kozmik Z, Burger A. PMID: 37131681; PMCID: PMC10153258.
      View in: PubMed   Mentions:
    9. Diverse logics and grammar encode notochord enhancers. Cell Rep. 2023 02 28; 42(2):112052. Song BP, Ragsac MF, Tellez K, Jindal GA, Grudzien JL, Le SH, Farley EK. PMID: 36729834; PMCID: PMC10387507.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimalsCells
    10. 3D genomics across the tree of life reveals condensin II as a determinant of architecture type. Science. 2021 05 28; 372(6545):984-989. Hoencamp C, Dudchenko O, Elbatsh AMO, Brahmachari S, Raaijmakers JA, van Schaik T, Sedeño Cacciatore Á, Contessoto VG, van Heesbeen RGHP, van den Broek B, Mhaskar AN, Teunissen H, St Hilaire BG, Weisz D, Omer AD, Pham M, Colaric Z, Yang Z, Rao SSP, Mitra N, Lui C, Yao W, Khan R, Moroz LL, Kohn A, St Leger J, Mena A, Holcroft K, Gambetta MC, Lim F, Farley E, Stein N, Haddad A, Chauss D, Mutlu AS, Wang MC, Young ND, Hildebrandt E, Cheng HH, Knight CJ, Burnham TLU, Hovel KA, Beel AJ, Mattei PJ, Kornberg RD, Warren WC, Cary G, Gómez-Skarmeta JL, Hinman V, Lindblad-Toh K, Di Palma F, Maeshima K, Multani AS, Pathak S, Nel-Themaat L, Behringer RR, Kaur P, Medema RH, van Steensel B, de Wit E, Onuchic JN, Di Pierro M, Lieberman Aiden E, Rowland BD. PMID: 34045355; PMCID: PMC8172041.
      View in: PubMed   Mentions: 92     Fields:    Translation:HumansAnimalsCells
    11. 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: 46     Fields:    Translation:HumansCells
    12. 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: 10     Fields:    Translation:HumansAnimalsCells
    13. 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: 65     Fields:    Translation:HumansCells
    14. 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: 10     Fields:    Translation:HumansCells
    15. 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: 81     Fields:    Translation:HumansCells
    16. 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: 83     Fields:    Translation:AnimalsCells
    17. 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: 166     Fields:    Translation:AnimalsCells
    18. 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: 17     Fields:    Translation:HumansAnimalsCells
    19. 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
    20. 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
    21. 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
    22. 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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