David A Nix

David A Nix

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David A Nix

David A Nix

Publications by authors named "David A Nix"

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Viral miRNA adaptor differentially recruits miRNAs to target mRNAs through alternative base-pairing.

Elife 2019 09 20;8. Epub 2019 Sep 20.

Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States.

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http://dx.doi.org/10.7554/eLife.50530DOI Listing
September 2019

Genome-wide profiling of the C. elegans dsRNAome.

RNA 2015 May 24;21(5):786-800. Epub 2015 Mar 24.

Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112-5650, USA.

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http://dx.doi.org/10.1261/rna.048801.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4408787PMC
May 2015

Potential role for snoRNAs in PKR activation during metabolic stress.

Proc Natl Acad Sci U S A 2015 Apr 6;112(16):5023-8. Epub 2015 Apr 6.

Department of Biochemistry, University of Utah, Salt Lake City, UT 84112;

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http://dx.doi.org/10.1073/pnas.1424044112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4413318PMC
April 2015

Reprogramming the maternal zebrafish genome after fertilization to match the paternal methylation pattern.

Cell 2013 May;153(4):759-72

Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.

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http://dx.doi.org/10.1016/j.cell.2013.04.030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4030421PMC
May 2013

DNA methylation profiling in zebrafish.

Methods Cell Biol 2011 ;104:327-39

Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.

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http://dx.doi.org/10.1016/B978-0-12-374814-0.00018-5DOI Listing
January 2012

Genome-wide RNA-seq analysis of human and mouse platelet transcriptomes.

Blood 2011 Oct 19;118(14):e101-11. Epub 2011 May 19.

Program in Molecular Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA.

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http://dx.doi.org/10.1182/blood-2011-03-339705DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3193274PMC
October 2011

Next generation tools for genomic data generation, distribution, and visualization.

BMC Bioinformatics 2010 Sep 9;11:455. Epub 2010 Sep 9.

Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, USA.

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http://dx.doi.org/10.1186/1471-2105-11-455DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2944281PMC
September 2010

Dicer's helicase domain is required for accumulation of some, but not all, C. elegans endogenous siRNAs.

RNA 2010 May 30;16(5):893-903. Epub 2010 Mar 30.

1Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112, USA.

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http://dx.doi.org/10.1261/rna.2122010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2856884PMC
May 2010

Distinctive chromatin in human sperm packages genes for embryo development.

Nature 2009 Jul 14;460(7254):473-8. Epub 2009 Jun 14.

Howard Hughes Medical Institute, Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA.

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http://dx.doi.org/10.1038/nature08162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2858064PMC
July 2009

Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks.

BMC Bioinformatics 2008 Dec 5;9:523. Epub 2008 Dec 5.

Huntsman Cancer Institute, Department of Research Informatics, University of Utah, Salt Lake City, Utah, 84105, USA.

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http://dx.doi.org/10.1186/1471-2105-9-523DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2628906PMC
December 2008

Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping.

Nat Genet 2008 Aug 20;40(8):977-86. Epub 2008 Jul 20.

Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah 84132, USA.

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http://dx.doi.org/10.1038/ng.196DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2538488PMC
August 2008

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill Gerard G Bouffard Xiaobin Guan Nancy F Hansen Jacquelyn R Idol Valerie V B Maduro Baishali Maskeri Jennifer C McDowell Morgan Park Pamela J Thomas Alice C Young Robert W Blakesley Donna M Muzny Erica Sodergren David A Wheeler Kim C Worley Huaiyang Jiang George M Weinstock Richard A Gibbs Tina Graves Robert Fulton Elaine R Mardis Richard K Wilson Michele Clamp James Cuff Sante Gnerre David B Jaffe Jean L Chang Kerstin Lindblad-Toh Eric S Lander Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007

Large-scale turnover of functional transcription factor binding sites in Drosophila.

PLoS Comput Biol 2006 Oct 21;2(10):e130. Epub 2006 Aug 21.

Graduate Group in Biophysics, University of California Berkeley, Berkeley, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.0020130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1599766PMC
October 2006

Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array.

Proc Natl Acad Sci U S A 2006 Aug 14;103(34):12763-8. Epub 2006 Aug 14.

Division of Genetics and Development, Department of Molecular Cell Biology, Center for Integrative Genomics, University of California, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1073/pnas.0604484103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1636694PMC
August 2006

Genome-wide analysis of Polycomb targets in Drosophila melanogaster.

Nat Genet 2006 Jun 28;38(6):700-5. Epub 2006 May 28.

Rutgers University, Department of Molecular Biology and Biochemistry, 604 Allison Road, Piscataway, New Jersey 08854, USA.

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http://escholarship.org/uc/item/4z0757zk.pdf
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http://www.nature.com/doifinder/10.1038/ng1817
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http://dx.doi.org/10.1038/ng1817DOI Listing
June 2006

Flexible promoter architecture requirements for coactivator recruitment.

BMC Mol Biol 2006 Apr 28;7:16. Epub 2006 Apr 28.

Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.

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http://bmcmolbiol.biomedcentral.com/articles/10.1186/1471-21
Publisher Site
http://dx.doi.org/10.1186/1471-2199-7-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1488866PMC
April 2006

Factors that predict prematurity and preeclampsia in pregnancies that are complicated by systemic lupus erythematosus.

Am J Obstet Gynecol 2005 Jun;192(6):1897-904

Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Palo Alto, CA 94304, USA.

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http://dx.doi.org/10.1016/j.ajog.2005.02.063DOI Listing
June 2005

GATA: a graphic alignment tool for comparative sequence analysis.

BMC Bioinformatics 2005 Jan 17;6. Epub 2005 Jan 17.

Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1186/1471-2105-6-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC546196PMC
January 2005

Comparison of calcaneus ultrasound and dual X-ray absorptiometry in children at risk of osteopenia.

J Clin Densitom 2003 ;6(1):7-15

Stanford University School of Medicine, Stanford, CA, USA.

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April 2003