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Daniel P. Farrell
Researcher at University of Washington
Publications - 28
Citations - 496
Daniel P. Farrell is an academic researcher from University of Washington. The author has contributed to research in topics: Protein filament & Bacterial outer membrane. The author has an hindex of 8, co-authored 24 publications receiving 206 citations. Previous affiliations of Daniel P. Farrell include Roy J. and Lucille A. Carver College of Medicine.
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Journal ArticleDOI
A Structural Model of the Endogenous Human BAF Complex Informs Disease Mechanisms
Nazar Mashtalir,Nazar Mashtalir,Hiroshi Suzuki,Daniel P. Farrell,Akshay Sankar,Akshay Sankar,Jie Luo,Martin Filipovski,Martin Filipovski,Andrew R. D’Avino,Andrew R. D’Avino,Roodolph St. Pierre,Roodolph St. Pierre,Alfredo M. Valencia,Alfredo M. Valencia,Takashi Onikubo,Robert G. Roeder,Yan Han,Yuan He,Jeffrey A. Ranish,Frank DiMaio,Thomas Walz,Cigall Kadoch,Cigall Kadoch +23 more
TL;DR: A structural model of the endogenously purified human canonical BAF complex bound to the nucleosome, generated using cryoelectron microscopy, cross-linking mass spectrometry, and homology modeling provides important biophysical foundations for understanding the mechanisms of BAFcomplex function in normal and disease states.
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Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge
Catherine L. Lawson,Andriy Kryshtafovych,Paul D. Adams,Pavel V. Afonine,Matthew L. Baker,Benjamin A Barad,Paul S. Bond,Tom Burnley,Renzhi Cao,Jianlin Cheng,Grzegorz Chojnowski,Kevin Cowtan,Ken A. Dill,Frank DiMaio,Daniel P. Farrell,James S. Fraser,Mark A. Herzik,Soon Wen Hoh,Jie Hou,Li-Wei Hung,Maxim Igaev,Agnel Praveen Joseph,Daisuke Kihara,Dilip Kumar,Sumit Mittal,Bohdan Monastyrskyy,Mateusz Olek,Colin M. Palmer,Ardan Patwardhan,Alberto Perez,Jonas Pfab,Grigore D. Pintilie,Jane S. Richardson,Peter B. Rosenthal,Daipayan Sarkar,Daipayan Sarkar,Luisa U. Schäfer,Michael F. Schmid,Gunnar F. Schröder,Gunnar F. Schröder,Mrinal Shekhar,Mrinal Shekhar,Dong Si,Singharoy A,Genki Terashi,Thomas C. Terwilliger,Andrea C. Vaiana,Liguo Wang,Zhe Wang,Stephanie A. Wankowicz,Christopher J. Williams,Martyn Winn,Tianqi Wu,Xiaodi Yu,Kaiming Zhang,Helen M. Berman,Wah Chiu,Wah Chiu +57 more
TL;DR: The 2019 Cryo-EM Model Challenge as discussed by the authors evaluated the quality of models that can be produced from Cryogenic EM maps using current modeling software, evaluating reproducibility of modeling results from different software developers and users and comparing performance of current metrics used for model evaluation, particularly Fit-to-Map metrics.
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DNA binding drives the association of BRG1/hBRM bromodomains with nucleosomes
Emma A. Morrison,Julio C. Sanchez,Jehnna L. Ronan,Daniel P. Farrell,Katayoun Varzavand,Jenna K. Johnson,Brian X. Gu,Gerald R. Crabtree,Catherine A. Musselman +8 more
TL;DR: This work shows that the human BRM (hBRM) bromodomain (BRD) has moderate specificity for H3K14ac, and finds that both BRG1 and hBRM BRDs have DNA-binding activity, suggesting that association of theBRG1/h BRM BRD with nucleosomes plays a regulatory rather than targeting role in BAF activity.
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The Molecular Architecture of Native BBSome Obtained by an Integrated Structural Approach.
Hui-Ting Chou,Luise Apelt,Daniel P. Farrell,Susan Roehl White,Jonathan Woodsmith,Vladimir Svetlov,Jaclyn S. Goldstein,Andrew R. Nager,Zixuan Li,Jean Muller,Hélène Dollfus,Evgeny Nudler,Ulrich Stelzl,Frank DiMaio,Maxence V. Nachury,Maxence V. Nachury,Thomas Walz,Thomas Walz +17 more
TL;DR: This model provides the first detailed view of the machinery enabling ciliary exit and finds that BBSome subunits have a very high degree of interconnectivity, explaining the obligate nature of the complex.
Journal ArticleDOI
BRCA1/BARD1 site-specific ubiquitylation of nucleosomal H2A is directed by BARD1
Samuel R. Witus,Anika L. Burrell,Daniel P. Farrell,Jianming Kang,Meiling Wang,Jesse M Hansen,Alex Pravat,Lisa M. Tuttle,Mikaela D. Stewart,Mikaela D. Stewart,Peter S. Brzovic,Champak Chatterjee,Weixing Zhao,Frank DiMaio,Justin M. Kollman,Rachel E. Klevit +15 more
TL;DR: In this article, the BRCA1/BARD1 RING heterodimer with the E2 enzyme UbcH5c bound to its cellular target, the nucleosome, along with biochemical data that explain how the complex selectively ubiquitylates lysines 125, 127 and 129 in the flexible C-terminal tail of H2A in a fully human system.