Publications by authors named "Darren A Cusanovich"

19Publications

A human cell atlas of fetal chromatin accessibility.

Authors:
Silvia Domcke Andrew J Hill Riza M Daza Junyue Cao Diana R O'Day Hannah A Pliner Kimberly A Aldinger Dmitry Pokholok Fan Zhang Jennifer H Milbank Michael A Zager Ian A Glass Frank J Steemers Dan Doherty Cole Trapnell Darren A Cusanovich Jay Shendure

Science 2020 11;370(6518)

Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.

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November 2020

Rhinovirus Infections in Individuals with Asthma Increase ACE2 Expression and Cytokine Pathways Implicated in COVID-19.

Authors:
Eugene H Chang Amanda L Willis Casey E Romanoski Darren A Cusanovich Nima Pouladi Jianrong Li Yves A Lussier Fernando D Martinez

Am J Respir Crit Care Med 2020 09;202(5):753-755

University of Arizona Tucson, Arizona.

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September 2020

Single-cell ATAC-Seq in human pancreatic islets and deep learning upscaling of rare cells reveals cell-specific type 2 diabetes regulatory signatures.

Authors:
Vivek Rai Daniel X Quang Michael R Erdos Darren A Cusanovich Riza M Daza Narisu Narisu Luli S Zou John P Didion Yuanfang Guan Jay Shendure Stephen C J Parker Francis S Collins

Mol Metab 2020 02 20;32:109-121. Epub 2019 Dec 20.

National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA. Electronic address:

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February 2020

An upstream enhancer regulates expression in a tissue-specific manner.

Authors:
Christopher M Allan Patrick J Heizer Yiping Tu Norma P Sandoval Rachel S Jung Jazmin E Morales Eniko Sajti Ty D Troutman Thomas L Saunders Darren A Cusanovich Anne P Beigneux Casey E Romanoski Loren G Fong Stephen G Young

J Lipid Res 2019 04 31;60(4):869-879. Epub 2018 Dec 31.

Departments of Medicine University of California, Los Angeles, Los Angeles, CA 90095

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April 2019

Joint profiling of chromatin accessibility and gene expression in thousands of single cells.

Authors:
Junyue Cao Darren A Cusanovich Vijay Ramani Delasa Aghamirzaie Hannah A Pliner Andrew J Hill Riza M Daza Jose L McFaline-Figueroa Jonathan S Packer Lena Christiansen Frank J Steemers Andrew C Adey Cole Trapnell Jay Shendure

Science 2018 09 30;361(6409):1380-1385. Epub 2018 Aug 30.

Department of Genome Sciences, University of Washington, Seattle, WA, USA.

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September 2018

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data.

Authors:
Hannah A Pliner Jonathan S Packer José L McFaline-Figueroa Darren A Cusanovich Riza M Daza Delasa Aghamirzaie Sanjay Srivatsan Xiaojie Qiu Dana Jackson Anna Minkina Andrew C Adey Frank J Steemers Jay Shendure Cole Trapnell

Mol Cell 2018 09 2;71(5):858-871.e8. Epub 2018 Aug 2.

Department of Genome Sciences, University of Washington, Seattle, WA, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA. Electronic address:

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September 2018

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility.

Authors:
Darren A Cusanovich Andrew J Hill Delasa Aghamirzaie Riza M Daza Hannah A Pliner Joel B Berletch Galina N Filippova Xingfan Huang Lena Christiansen William S DeWitt Choli Lee Samuel G Regalado David F Read Frank J Steemers Christine M Disteche Cole Trapnell Jay Shendure

Cell 2018 08 2;174(5):1309-1324.e18. Epub 2018 Aug 2.

Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA. Electronic address:

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August 2018

The cis-regulatory dynamics of embryonic development at single-cell resolution.

Authors:
Darren A Cusanovich James P Reddington David A Garfield Riza M Daza Delasa Aghamirzaie Raquel Marco-Ferreres Hannah A Pliner Lena Christiansen Xiaojie Qiu Frank J Steemers Cole Trapnell Jay Shendure Eileen E M Furlong

Nature 2018 03 14;555(7697):538-542. Epub 2018 Mar 14.

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.

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March 2018

Comprehensive single-cell transcriptional profiling of a multicellular organism.

Authors:
Junyue Cao Jonathan S Packer Vijay Ramani Darren A Cusanovich Chau Huynh Riza Daza Xiaojie Qiu Choli Lee Scott N Furlan Frank J Steemers Andrew Adey Robert H Waterston Cole Trapnell Jay Shendure

Science 2017 08;357(6352):661-667

Department of Genome Sciences, University of Washington, Seattle, WA, USA.

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August 2017

CRISPR/Cas9-Mediated Scanning for Regulatory Elements Required for HPRT1 Expression via Thousands of Large, Programmed Genomic Deletions.

Authors:
Molly Gasperini Gregory M Findlay Aaron McKenna Jennifer H Milbank Choli Lee Melissa D Zhang Darren A Cusanovich Jay Shendure

Am J Hum Genet 2017 Aug 14;101(2):192-205. Epub 2017 Jul 14.

Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA. Electronic address:

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August 2017

Mapping 3D genome architecture through in situ DNase Hi-C.

Authors:
Vijay Ramani Darren A Cusanovich Ronald J Hause Wenxiu Ma Ruolan Qiu Xinxian Deng C Anthony Blau Christine M Disteche William S Noble Jay Shendure Zhijun Duan

Nat Protoc 2016 11 29;11(11):2104-21. Epub 2016 Sep 29.

Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA.

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November 2016

Integrated analyses of gene expression and genetic association studies in a founder population.

Authors:
Darren A Cusanovich Minal Caliskan Christine Billstrand Katelyn Michelini Claudia Chavarria Sherryl De Leon Amy Mitrano Noah Lewellyn Jack A Elias Geoffrey L Chupp Roberto M Lang Sanjiv J Shah Jeanne M Decara Yoav Gilad Carole Ober

Hum Mol Genet 2016 05 29;25(10):2104-2112. Epub 2016 Feb 29.

Department of Human Genetics and,

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May 2016

Genome-Wide Association Studies of the Human Gut Microbiota.

Authors:
Emily R Davenport Darren A Cusanovich Katelyn Michelini Luis B Barreiro Carole Ober Yoav Gilad

PLoS One 2015 3;10(11):e0140301. Epub 2015 Nov 3.

Department of Human Genetics, University of Chicago, Chicago, IL, United States of America.

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June 2016

Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing.

Authors:
Darren A Cusanovich Riza Daza Andrew Adey Hannah A Pliner Lena Christiansen Kevin L Gunderson Frank J Steemers Cole Trapnell Jay Shendure

Science 2015 May 7;348(6237):910-4. Epub 2015 May 7.

University of Washington, Department of Genome Sciences, Seattle, WA, USA.

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May 2015

The functional consequences of variation in transcription factor binding.

Authors:
Darren A Cusanovich Bryan Pavlovic Jonathan K Pritchard Yoav Gilad

PLoS Genet 2014 Mar 6;10(3):e1004226. Epub 2014 Mar 6.

Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America.

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March 2014

Primate transcript and protein expression levels evolve under compensatory selection pressures.

Authors:
Zia Khan Michael J Ford Darren A Cusanovich Amy Mitrano Jonathan K Pritchard Yoav Gilad

Science 2013 Nov 17;342(6162):1100-4. Epub 2013 Oct 17.

Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.

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November 2013

Regulatory element copy number differences shape primate expression profiles.

Authors:
Rebecca C Iskow Omer Gokcumen Alexej Abyzov Joanna Malukiewicz Qihui Zhu Ann T Sukumar Athma A Pai Ryan E Mills Lukas Habegger Darren A Cusanovich Meagan A Rubel George H Perry Mark Gerstein Anne C Stone Yoav Gilad Charles Lee

Proc Natl Acad Sci U S A 2012 Jul 13;109(31):12656-61. Epub 2012 Jul 13.

Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA.

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July 2012

The combination of a genome-wide association study of lymphocyte count and analysis of gene expression data reveals novel asthma candidate genes.

Authors:
Darren A Cusanovich Christine Billstrand Xiang Zhou Claudia Chavarria Sherryl De Leon Katelyn Michelini Athma A Pai Carole Ober Yoav Gilad

Hum Mol Genet 2012 May 27;21(9):2111-23. Epub 2012 Jan 27.

Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.

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May 2012

The effects of EBV transformation on gene expression levels and methylation profiles.

Authors:
Minal Caliskan Darren A Cusanovich Carole Ober Yoav Gilad

Hum Mol Genet 2011 Apr 2;20(8):1643-52. Epub 2011 Feb 2.

Department of Human Genetics, University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA.

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April 2011