Emma K Farley
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Explore the profile of Emma K Farley including associated specialties, affiliations and a list of published articles.
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16
Citations
558
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Recent Articles
1.
Cirincione A, Simpson D, Yan W, McNulty R, Ravisankar P, Solley S, et al.
Nat Methods
. 2024 Nov;
22(1):92-101.
PMID: 39562753
Prime editing installs precise edits into the genome with minimal unwanted byproducts, but low and variable editing efficiencies have complicated application of the approach to high-throughput functional genomics. Here we...
2.
Jindal G, Lim F, Tellez K, Song B, Bantle A, Farley E
STAR Protoc
. 2024 Jul;
5(3):103107.
PMID: 38963758
Electroporation is a technique to introduce DNA constructs into cells using electric current. Here, we present a protocol to electroporate DNA plasmids into Ciona robusta embryos at the 1-cell stage....
3.
Lim F, Solvason J, Ryan G, Le S, Jindal G, Steffen P, et al.
Nature
. 2024 Jan;
626(7997):151-159.
PMID: 38233525
Enhancers control the location and timing of gene expression and contain the majority of variants associated with disease. The ZRS is arguably the most well-studied vertebrate enhancer and mediates the...
4.
Klie A, Laub D, Talwar J, Stites H, Jores T, Solvason J, et al.
Nat Comput Sci
. 2024 Jan;
3(11):946-956.
PMID: 38177592
Deep learning has become a popular tool to study cis-regulatory function. Yet efforts to design software for deep-learning analyses in regulatory genomics that are findable, accessible, interoperable and reusable (FAIR)...
5.
Jindal G, Bantle A, Solvason J, Grudzien J, DAntonio-Chronowska A, Lim F, et al.
Dev Cell
. 2023 Oct;
58(21):2206-2216.e5.
PMID: 37848026
Transcriptional enhancers direct precise gene expression patterns during development and harbor the majority of variants associated with phenotypic diversity, evolutionary adaptations, and disease. Pinpointing which enhancer variants contribute to changes...
6.
Song B, Ragsac M, Tellez K, Jindal G, Grudzien J, Le S, et al.
Cell Rep
. 2023 Feb;
42(2):112052.
PMID: 36729834
The notochord is a defining feature of all chordates. The transcription factors Zic and ETS regulate enhancer activity within the notochord. We conduct high-throughput screens of genomic elements within developing...
7.
Jindal G, Farley E
Dev Cell
. 2021 Mar;
56(5):575-587.
PMID: 33689769
Each language has standard books describing that language's grammatical rules. Biologists have searched for similar, albeit more complex, principles relating enhancer sequence to gene expression. Here, we review the literature...
8.
Ryan G, Farley E
Wiley Interdiscip Rev Syst Biol Med
. 2019 Dec;
12(2):e1467.
PMID: 31808313
Successful development depends on the precise tissue-specific regulation of genes by enhancers, genetic elements that act as switches to control when and where genes are expressed. Because enhancers are critical...
9.
Zhang W, Bojorquez-Gomez A, Ortiz Velez D, Xu G, Sanchez K, Shen J, et al.
Nat Genet
. 2018 Apr;
50(4):613-620.
PMID: 29610481
Although cancer genomes are replete with noncoding mutations, the effects of these mutations remain poorly characterized. Here we perform an integrative analysis of 930 tumor whole genomes and matched transcriptomes,...
10.
D Antonio M, Weghorn D, D Antonio-Chronowska A, Coulet F, Olson K, DeBoever C, et al.
Nat Commun
. 2017 Sep;
8(1):436.
PMID: 28874753
Efforts to identify driver mutations in cancer have largely focused on genes, whereas non-coding sequences remain relatively unexplored. Here we develop a statistical method based on characteristics known to influence...