Publications

Jindal GA; Lim F; Tellez K; Song BP; Bantle AT; Farley EK, 2024. Protocol to electroporate DNA plasmids into Ciona robusta embryos at the 1-cell stage.  STAR Protoc 5(3):103107

Lim F; Solvason JJ; Ryan GE; Le SH; Jindal GA; Steffen P; Jandu SK; Farley EK, 2024. Affinity-optimizing enhancer variants disrupt development.  Nature 626(7997):151-159

Klie A; Laub D; Talwar JV; Stites H; Jores T; Solvason JJ; Farley EK; Carter H, 2023. Predictive analyses of regulatory sequences with EUGENe.  Nat Comput Sci 3(11):946-956

Farley EK, 2023. Ciona, an ideal research organism to study the role of enhancers.  Genesis 61(6):e23577

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, 2023. Conserved enhancers control notochord expression of vertebrate Brachyury.  Nat Commun 14(1):6594

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, 2023. Single-nucleotide variants within heart enhancers increase binding affinity and disrupt heart development.  Dev Cell 58(21):2206-2216.e5

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, 2023. Conserved enhancer logic controls the notochord expression of vertebrate Brachyury.  bioRxiv.

Song BP; Ragsac MF; Tellez K; Jindal GA; Grudzien JL; Le SH; Farley EK, 2023. Diverse logics and grammar encode notochord enhancers.  Cell Rep 42(2):112052

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, 2021. 3D genomics across the tree of life reveals condensin II as a determinant of architecture type.  Science 372(6545):984-989

Jindal GA; Farley EK, 2021. Enhancer grammar in development, evolution, and disease: dependencies and interplay.  Dev Cell 56(5):575-587

Ryan GE; Farley EK, 2020. Functional genomic approaches to elucidate the role of enhancers during development.  Wiley Interdiscip Rev Syst Biol Med 12(2):e1467

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, 2018. A global transcriptional network connecting noncoding mutations to changes in tumor gene expression.  Nat Genet 50(4):613-620

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, 2017. Identifying DNase I hypersensitive sites as driver distal regulatory elements in breast cancer.  Nat Commun 8(1):436

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, 2017. Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells.  Cell Stem Cell 20(4):533-546.e7

Farley EK; Olson KM; Zhang W; Rokhsar DS; Levine MS, 2016. Syntax compensates for poor binding sites to encode tissue specificity of developmental enhancers.  Proc Natl Acad Sci U S A 113(23):6508-13

Farley EK; Olson KM; Zhang W; Brandt AJ; Rokhsar DS; Levine MS, 2015. Suboptimization of developmental enhancers.  Science 350(6258):325-8

Farley EK; Olson KM; Levine MS, 2015. Regulatory Principles Governing Tissue Specificity of Developmental Enhancers.  Cold Spring Harb Symp Quant Biol 80:27-32

Farley EK, 2013. Gene transfer in developing chick embryos: in ovo electroporation.  Methods Mol Biol 1018:141-50

Farley E; Levine M, 2012. HOT DNAs: a novel class of developmental enhancers.  Genes Dev 26(9):873-6

Gennet N; Gale E; Nan X; Farley E; Takacs K; Oberwallner B; Chambers D; Li M, 2011. 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 108(22):9131-6

Farley EK; Gale E; Chambers D; Li M, 2011. Effects of in ovo electroporation on endogenous gene expression: genome-wide analysis.  Neural Dev 6:17

Publication list retrieved from NCBI using ImpactPubs

.