Zobrazeno 1 - 10
of 21
pro vyhledávání: '"Emma K. Farley"'
Autor:
Benjamin P. Song, Michelle F. Ragsac, Krissie Tellez, Granton A. Jindal, Jessica L. Grudzien, Sophia H. Le, Emma K. Farley
Publikováno v:
Cell Reports, Vol 42, Iss 2, Pp 112052- (2023)
Summary: 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 Ciona embryos to understand
Externí odkaz:
https://doaj.org/article/0a07ee4646954a249ff52c80c196b956
Autor:
Matteo D′Antonio, Donate Weghorn, Agnieszka D′Antonio-Chronowska, Florence Coulet, Katrina M. Olson, Christopher DeBoever, Frauke Drees, Angelo Arias, Hakan Alakus, Andrea L. Richardson, Richard B. Schwab, Emma K. Farley, Shamil R. Sunyaev, Kelly A Frazer
Publikováno v:
Nature Communications, Vol 8, Iss 1, Pp 1-16 (2017)
Cancer driver mutations can occur within noncoding genomic sequences. Here, the authors develop a statistical approach to identify candidate noncoding driver mutations in DNase I hypersensitive sites in breast cancer and experimentally demonstrate th
Externí odkaz:
https://doaj.org/article/fed8c71471284e789fe9fe3936d957c5
Deep learning (DL) has become a popular tool to study cis-regulatory element function. Yet efforts to design software for DL analyses in genomics that are Findable, Accessible, Interoperable and Reusable (FAIR) have fallen short of fully meeting thes
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::360a670347fd1086dd1761bb970f9166
https://doi.org/10.1101/2022.10.24.513593
https://doi.org/10.1101/2022.10.24.513593
Autor:
Granton A Jindal, Alexis T Bantle, Joe J Solvason, Jessica L Grudzien, Agnieszka D’Antonio-Chronowska, Fabian Lim, Sophia H Le, Reid O Larsen, Adam Klie, Kelly A Frazer, Emma K Farley
SummaryEnhancers direct precise gene expression patterns during development and harbor the majority of variants associated with disease. We find that suboptimal affinity ETS transcription factor binding sites are prevalent within Ciona and human deve
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::c28fdfda915bfaeb65ad5eb7faf659e1
https://doi.org/10.1101/2022.05.27.493636
https://doi.org/10.1101/2022.05.27.493636
SummaryAn emerging regulatory principle governing enhancers is the use of suboptimal affinity binding sites to encode tissue-specific gene expression. Here we investigate if optimizing single-nucleotide variants that violate this principle can disrup
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::16d3128782325b0fae7031059b7a26c6
https://doi.org/10.1101/2022.05.27.493789
https://doi.org/10.1101/2022.05.27.493789
Autor:
Granton A. Jindal, Emma K. Farley
Publikováno v:
Developmental cell, vol 56, iss 5
Dev Cell
Dev Cell
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 on enhancer grammar. We
Autor:
Judy St. Leger, Bram van den Broek, Ahmed M.O. Elbatsh, Leonid L. Moroz, Evin Hildebrandt, Namita Mitra, Parwinder Kaur, Roger D. Kornberg, Federica Di Palma, Nils Stein, Weijie Yao, Theresa L.U. Burnham, Christopher J. Knight, Suhas S.P. Rao, Kazuhiro Maeshima, Asha S. Multani, Veronica F. Hinman, Aditya N. Mhaskar, José N. Onuchic, David Weisz, Sen Pathak, René H. Medema, Kevin A. Hovel, Arina D. Omer, Alexandria Mena, Andrea B. Kohn, Andrew J. Beel, Liesl Nel-Themaat, Benjamin D. Rowland, José Luis Gómez-Skarmeta, Bas van Steensel, Maria Cristina Gambetta, Claire Hoencamp, Christopher Lui, Roy G.H.P. van Heesbeen, Emma K. Farley, Olga Dudchenko, Michele Di Pierro, Neil D. Young, Meng C. Wang, Kerstin Lindblad-Toh, Pierre Jean Mattei, Tom van Schaik, Melanie Pham, Ruqayya Khan, Fabian Lim, Wesley C. Warren, Vinícius G. Contessoto, Richard R. Behringer, Hans H. Cheng, Alexander Haddad, Gregory A. Cary, Daniel Chauss, Zane Colaric, Hans Teunissen, Ayse Sena Mutlu, Zhenzhen Yang, Ángela Sedeño Cacciatore, Elzo de Wit, Sumitabha Brahmachari, Erez Lieberman Aiden, Karen Holcroft, Jonne A. Raaijmakers, Brian Glenn St Hilaire
Publikováno v:
Science
Science (New York, N.Y.), vol 372, iss 6545
Digital.CSIC. Repositorio Institucional del CSIC
instname
Scopus
Repositório Institucional da UNESP
Universidade Estadual Paulista (UNESP)
instacron:UNESP
Science (New York, N.Y.), vol 372, iss 6545
Digital.CSIC. Repositorio Institucional del CSIC
instname
Scopus
Repositório Institucional da UNESP
Universidade Estadual Paulista (UNESP)
instacron:UNESP
We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional(3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedlyduring eukaryotic evolution. The type of genome arc
Autor:
Emma K. Farley, Genevieve E. Ryan
Publikováno v:
Wiley Interdisciplinary Reviews. Systems Biology and Medicine
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 for development, and the majority of
Autor:
Katherine Licon, Daniel Ortiz Velez, Trey Ideker, John Paul Shen, Hannah Carter, Wei Zhang, Michael Ku Yu, Kevin Chen, Justin K. Huang, Emma K. Farley, Jason F. Kreisberg, Ana Bojorquez-Gomez, Collin Melton, Guorong Xu, Michael Snyder, Katrina M. Olson, Stephanie I. Fraley, Kyle S. Sanchez
Publikováno v:
Nature genetics, vol 50, iss 4
Nature genetics
Nature genetics
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, identifying a network of 193 nonc
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2701e0d381a041d05eb73b98a65ab9aa
https://escholarship.org/uc/item/88f7k0gz
https://escholarship.org/uc/item/88f7k0gz
Publikováno v:
Cold Spring Harbor Symposia on Quantitative Biology. 80:27-32
Transcriptional enhancers are short segments of genomic DNA (50 bp to 1 kb in length) that can work over long distances (≥1 Mb) to regulate gene expression in specific cells and tissues. Genomic assays have identified on the order of 400,000 to one