Emma Farley • UCSD Profiles (original) (raw)

  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: 15 Fields:
    Translation:Humans
  2. Protocol to electroporate DNA plasmids into Ciona robusta embryos at the 1-cell stage. STAR Protoc. 2024 09 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:
    Translation:Animals
  3. Affinity-optimizing enhancer variants disrupt development. Nature. 2024 02; 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: 52 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 11; 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: 10 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: 6 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: 20 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.
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  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: 9 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: 145 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: 67 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 Systematic Review of the Current Status of Safer Conception Strategies for HIV Affected Heterosexual Couples in Sub-Saharan Africa. AIDS Behav. 2018 Sep; 22(9):2916-2946. Joseph Davey D, West S, Umutoni V, Taleghani S, Klausner H, Farley E, Shah R, Madni S, Orewa S, Kottamasu V, Rice V, Robbin Z, Wall KM. PMID: 29869184; PMCID: PMC6466619.
    View in: PubMed Mentions: 27 Fields:
    Translation:HumansPHPublic Health
  14. 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: 73 Fields:
    Translation:HumansCells
  15. 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
  16. 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: 94 Fields:
    Translation:HumansCells
  17. 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: 98 Fields:
    Translation:AnimalsCells
  18. 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: 188 Fields:
    Translation:AnimalsCells
  19. 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: 18 Fields:
    Translation:HumansAnimalsCells
  20. 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
  21. 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
  22. 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: 22 Fields:
    Translation:AnimalsCells
  23. 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

This graph shows the number and percent of publications by field. Fields are based on how the National Library of Medicine (NLM) classifies the publications' journals and might not represent the specific topics of the publications. Note that an individual publication can be assigned to more than one field. As a result, the publication counts in this graph might add up to more than the number of publications the person has written. To see the data as text, click here.

This graph shows the number and percent of publications by field. Fields are based on how the National Library of Medicine (NLM) classifies the publications' journals and might not represent the specific topics of the publications. Note that an individual publication can be assigned to more than one field. As a result, the publication counts in this graph might add up to more than the number of publications the person has written. To see the data as text, click here.

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