Publications by authors named "Aaron J Mackey"

33Publications

Risk-based Monitoring of Clinical Trials: An Integrative Approach.

Clin Ther 2018 07 4;40(7):1204-1212. Epub 2018 Jul 4.

Covance, the Drug Development Division of LabCorp, Princeton, New Jersey.

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http://dx.doi.org/10.1016/j.clinthera.2018.04.020DOI Listing
July 2018

Using SQL Databases for Sequence Similarity Searching and Analysis.

Curr Protoc Bioinformatics 2017 09 13;59:9.4.1-9.4.22. Epub 2017 Sep 13.

Department of Public Health Sciences, University of Virginia, School of Medicine, Charlottesville, Virginia.

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http://doi.wiley.com/10.1002/cpbi.32
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http://dx.doi.org/10.1002/cpbi.32DOI Listing
September 2017

Targeted Deep Sequencing in Multiple-Affected Sibships of European Ancestry Identifies Rare Deleterious Variants in PTPN22 That Confer Risk for Type 1 Diabetes.

Diabetes 2016 Mar 2;65(3):794-802. Epub 2015 Dec 2.

Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL Genetics Institute, University of Florida, Gainesville, FL

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http://dx.doi.org/10.2337/db15-0322DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4764149PMC
March 2016

An Islet-Targeted Genome-Wide Association Scan Identifies Novel Genes Implicated in Cytokine-Mediated Islet Stress in Type 2 Diabetes.

Endocrinology 2015 Sep 27;156(9):3147-56. Epub 2015 May 27.

Department of Medicine (P.R.S., E.A.D., J.W.R., C.S.N.), Center for Public Health Genomics (A.J.M., S.S.R.), and Department of Chemistry (E.A.D.), University of Virginia, Charlottesville, Virginia 22904; Department of Biochemistry (N.D.P.), Center for Genomics and Personalized Medicine Research (N.D.P.), Center for Diabetes Research (N.D.P.), Center for Public Health Genomics (C.D.L., N.D.P., L.E.W.), Department of Biostatistical Sciences (C.D.L.), and Division of Public Health Sciences (L.E.W.), Wake Forest School of Medicine, Winston-Salem, North Carolina 27157; Department of Physiology and Biophysics (R.M.W.), Department of Preventive Medicine, and USC Diabetes and Obesity Research Institute (R.M.W.), Keck School of Medicine of University of Southern California, Los Angeles, California 90033; and Institute for Translational Genomics and Population Sciences (K.D.T.) and Department of Pediatrics (K.D.T.), Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California 90502.

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http://dx.doi.org/10.1210/en.2015-1203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4541617PMC
September 2015

Leptin protects host cells from Entamoeba histolytica cytotoxicity by a STAT3-dependent mechanism.

Infect Immun 2012 May 13;80(5):1934-43. Epub 2012 Feb 13.

Biology Department, Drew University, Madison, New Jersey, USA.

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http://dx.doi.org/10.1128/IAI.06140-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3347425PMC
May 2012

Using relational databases for improved sequence similarity searching and large-scale genomic analyses.

Curr Protoc Bioinformatics 2004 Oct;Chapter 9:Unit 9.4

University of Virginia, Charlottesville, Virginia, USA.

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http://doi.wiley.com/10.1002/0471250953.bi0904s7
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http://dx.doi.org/10.1002/0471250953.bi0904s7DOI Listing
October 2004

The genome of the model beetle and pest Tribolium castaneum.

Authors:
Stephen Richards Richard A Gibbs George M Weinstock Susan J Brown Robin Denell Richard W Beeman Richard Gibbs Richard W Beeman Susan J Brown Gregor Bucher Markus Friedrich Cornelis J P Grimmelikhuijzen Martin Klingler Marce Lorenzen Stephen Richards Siegfried Roth Reinhard Schröder Diethard Tautz Evgeny M Zdobnov Donna Muzny Richard A Gibbs George M Weinstock Tony Attaway Stephanie Bell Christian J Buhay Mimi N Chandrabose Dean Chavez Kerstin P Clerk-Blankenburg Andrew Cree Marvin Dao Clay Davis Joseph Chacko Huyen Dinh Shannon Dugan-Rocha Gerald Fowler Toni T Garner Jeffrey Garnes Andreas Gnirke Alica Hawes Judith Hernandez Sandra Hines Michael Holder Jennifer Hume Shalini N Jhangiani Vandita Joshi Ziad Mohid Khan LaRonda Jackson Christie Kovar Andrea Kowis Sandra Lee Lora R Lewis Jon Margolis Margaret Morgan Lynne V Nazareth Ngoc Nguyen Geoffrey Okwuonu David Parker Stephen Richards San-Juana Ruiz Jireh Santibanez Joël Savard Steven E Scherer Brian Schneider Erica Sodergren Diethard Tautz Selina Vattahil Donna Villasana Courtney S White Rita Wright Yoonseong Park Richard W Beeman Jeff Lord Brenda Oppert Marce Lorenzen Susan Brown Liangjiang Wang Joël Savard Diethard Tautz Stephen Richards George Weinstock Richard A Gibbs Yue Liu Kim Worley George Weinstock Christine G Elsik Justin T Reese Eran Elhaik Giddy Landan Dan Graur Peter Arensburger Peter Atkinson Richard W Beeman Jim Beidler Susan J Brown Jeffery P Demuth Douglas W Drury Yu-Zhou Du Haruhiko Fujiwara Marce Lorenzen Vincenza Maselli Mizuko Osanai Yoonseong Park Hugh M Robertson Zhijian Tu Jian-jun Wang Suzhi Wang Stephen Richards Henry Song Lan Zhang Erica Sodergren Doreen Werner Mario Stanke Burkhard Morgenstern Victor Solovyev Peter Kosarev Garth Brown Hsiu-Chuan Chen Olga Ermolaeva Wratko Hlavina Yuri Kapustin Boris Kiryutin Paul Kitts Donna Maglott Kim Pruitt Victor Sapojnikov Alexandre Souvorov Aaron J Mackey Robert M Waterhouse Stefan Wyder Evgeny M Zdobnov Evgeny M Zdobnov Stefan Wyder Evgenia V Kriventseva Tatsuhiko Kadowaki Peer Bork Manuel Aranda Riyue Bao Anke Beermann Nicola Berns Renata Bolognesi François Bonneton Daniel Bopp Susan J Brown Gregor Bucher Thomas Butts Arnaud Chaumot Robin E Denell David E K Ferrier Markus Friedrich Cassondra M Gordon Marek Jindra Martin Klingler Que Lan H Michael G Lattorff Vincent Laudet Cornelia von Levetsow Zhenyi Liu Rebekka Lutz Jeremy A Lynch Rodrigo Nunes da Fonseca Nico Posnien Rolf Reuter Siegfried Roth Joël Savard Johannes B Schinko Christian Schmitt Michael Schoppmeier Reinhard Schröder Teresa D Shippy Franck Simonnet Henrique Marques-Souza Diethard Tautz Yoshinori Tomoyasu Jochen Trauner Maurijn Van der Zee Michel Vervoort Nadine Wittkopp Ernst A Wimmer Xiaoyun Yang Andrew K Jones David B Sattelle Paul R Ebert David Nelson Jeffrey G Scott Richard W Beeman Subbaratnam Muthukrishnan Karl J Kramer Yasuyuki Arakane Richard W Beeman Qingsong Zhu David Hogenkamp Radhika Dixit Brenda Oppert Haobo Jiang Zhen Zou Jeremy Marshall Elena Elpidina Konstantin Vinokurov Cris Oppert Zhen Zou Jay Evans Zhiqiang Lu Picheng Zhao Niranji Sumathipala Boran Altincicek Andreas Vilcinskas Michael Williams Dan Hultmark Charles Hetru Haobo Jiang Cornelis J P Grimmelikhuijzen Frank Hauser Giuseppe Cazzamali Michael Williamson Yoonseong Park Bin Li Yoshiaki Tanaka Reinhard Predel Susanne Neupert Joachim Schachtner Peter Verleyen Florian Raible Peer Bork Markus Friedrich Kimberly K O Walden Hugh M Robertson Sergio Angeli Sylvain Forêt Gregor Bucher Stefan Schuetz Ryszard Maleszka Ernst A Wimmer Richard W Beeman Marce Lorenzen Yoshinori Tomoyasu Sherry C Miller Daniela Grossmann Gregor Bucher

Nature 2008 Apr 23;452(7190):949-55. Epub 2008 Mar 23.

Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1038/nature06784DOI Listing
April 2008

Evigan: a hidden variable model for integrating gene evidence for eukaryotic gene prediction.

Bioinformatics 2008 Mar 10;24(5):597-605. Epub 2008 Jan 10.

Department of Computer and Information Science, University of Pennsylvania, Philadelphia PA 19104, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn004DOI Listing
March 2008

Periplasmic proteins of the extremophile Acidithiobacillus ferrooxidans: a high throughput proteomics analysis.

Mol Cell Proteomics 2007 Dec 2;6(12):2239-51. Epub 2007 Oct 2.

Department of Biology and Cell Dynamics and Biotechnology Institute, Faculty of Sciences, University of Chile, Santiago 7800024, Chile.

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http://www.mcponline.org/lookup/doi/10.1074/mcp.M700042-MCP2
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http://dx.doi.org/10.1074/mcp.M700042-MCP200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631397PMC
December 2007

Assessing performance of orthology detection strategies applied to eukaryotic genomes.

PLoS One 2007 Apr 18;2(4):e383. Epub 2007 Apr 18.

Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0000383PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1849888PMC
April 2007

Creating a honey bee consensus gene set.

Genome Biol 2007 ;8(1):R13

Department of Animal Science, Texas A&M University, TAMU, College Station, Texas 77843, USA.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2007-8-1-r13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1839126PMC
April 2007

The genome of the sea urchin Strongylocentrotus purpuratus.

Authors:
Erica Sodergren George M Weinstock Eric H Davidson R Andrew Cameron Richard A Gibbs Robert C Angerer Lynne M Angerer Maria Ina Arnone David R Burgess Robert D Burke James A Coffman Michael Dean Maurice R Elphick Charles A Ettensohn Kathy R Foltz Amro Hamdoun Richard O Hynes William H Klein William Marzluff David R McClay Robert L Morris Arcady Mushegian Jonathan P Rast L Courtney Smith Michael C Thorndyke Victor D Vacquier Gary M Wessel Greg Wray Lan Zhang Christine G Elsik Olga Ermolaeva Wratko Hlavina Gretchen Hofmann Paul Kitts Melissa J Landrum Aaron J Mackey Donna Maglott Georgia Panopoulou Albert J Poustka Kim Pruitt Victor Sapojnikov Xingzhi Song Alexandre Souvorov Victor Solovyev Zheng Wei Charles A Whittaker Kim Worley K James Durbin Yufeng Shen Olivier Fedrigo David Garfield Ralph Haygood Alexander Primus Rahul Satija Tonya Severson Manuel L Gonzalez-Garay Andrew R Jackson Aleksandar Milosavljevic Mark Tong Christopher E Killian Brian T Livingston Fred H Wilt Nikki Adams Robert Bellé Seth Carbonneau Rocky Cheung Patrick Cormier Bertrand Cosson Jenifer Croce Antonio Fernandez-Guerra Anne-Marie Genevière Manisha Goel Hemant Kelkar Julia Morales Odile Mulner-Lorillon Anthony J Robertson Jared V Goldstone Bryan Cole David Epel Bert Gold Mark E Hahn Meredith Howard-Ashby Mark Scally John J Stegeman Erin L Allgood Jonah Cool Kyle M Judkins Shawn S McCafferty Ashlan M Musante Robert A Obar Amanda P Rawson Blair J Rossetti Ian R Gibbons Matthew P Hoffman Andrew Leone Sorin Istrail Stefan C Materna Manoj P Samanta Viktor Stolc Waraporn Tongprasit Qiang Tu Karl-Frederik Bergeron Bruce P Brandhorst James Whittle Kevin Berney David J Bottjer Cristina Calestani Kevin Peterson Elly Chow Qiu Autumn Yuan Eran Elhaik Dan Graur Justin T Reese Ian Bosdet Shin Heesun Marco A Marra Jacqueline Schein Michele K Anderson Virginia Brockton Katherine M Buckley Avis H Cohen Sebastian D Fugmann Taku Hibino Mariano Loza-Coll Audrey J Majeske Cynthia Messier Sham V Nair Zeev Pancer David P Terwilliger Cavit Agca Enrique Arboleda Nansheng Chen Allison M Churcher F Hallböök Glen W Humphrey Mohammed M Idris Takae Kiyama Shuguang Liang Dan Mellott Xiuqian Mu Greg Murray Robert P Olinski Florian Raible Matthew Rowe John S Taylor Kristin Tessmar-Raible D Wang Karen H Wilson Shunsuke Yaguchi Terry Gaasterland Blanca E Galindo Herath J Gunaratne Celina Juliano Masashi Kinukawa Gary W Moy Anna T Neill Mamoru Nomura Michael Raisch Anna Reade Michelle M Roux Jia L Song Yi-Hsien Su Ian K Townley Ekaterina Voronina Julian L Wong Gabriele Amore Margherita Branno Euan R Brown Vincenzo Cavalieri Véronique Duboc Louise Duloquin Constantin Flytzanis Christian Gache François Lapraz Thierry Lepage Annamaria Locascio Pedro Martinez Giorgio Matassi Valeria Matranga Ryan Range Francesca Rizzo Eric Röttinger Wendy Beane Cynthia Bradham Christine Byrum Tom Glenn Sofia Hussain Gerard Manning Esther Miranda Rebecca Thomason Katherine Walton Athula Wikramanayke Shu-Yu Wu Ronghui Xu C Titus Brown Lili Chen Rachel F Gray Pei Yun Lee Jongmin Nam Paola Oliveri Joel Smith Donna Muzny Stephanie Bell Joseph Chacko Andrew Cree Stacey Curry Clay Davis Huyen Dinh Shannon Dugan-Rocha Jerry Fowler Rachel Gill Cerrissa Hamilton Judith Hernandez Sandra Hines Jennifer Hume Laronda Jackson Angela Jolivet Christie Kovar Sandra Lee Lora Lewis George Miner Margaret Morgan Lynne V Nazareth Geoffrey Okwuonu David Parker Ling-Ling Pu Rachel Thorn Rita Wright

Science 2006 Nov;314(5801):941-52

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http://dx.doi.org/10.1126/science.1133609DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159423PMC
November 2006

SynView: a GBrowse-compatible approach to visualizing comparative genome data.

Bioinformatics 2006 Sep 14;22(18):2308-9. Epub 2006 Jul 14.

Center for Tropical and Emerging Global Diseases, University of Georgia Athens, GA 30602-2606, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl389DOI Listing
September 2006

OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups.

Nucleic Acids Res 2006 Jan;34(Database issue):D363-8

Department of Chemistry, Center for Bioinformatics, Penn Genomics Institute, University of Pennsylvania, Philadelphia, PA 19104-6018, USA.

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http://dx.doi.org/10.1093/nar/gkj123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347485PMC
January 2006

The transcriptome of Toxoplasma gondii.

BMC Biol 2005 Dec 2;3:26. Epub 2005 Dec 2.

Department of Veterinary Molecular Biology, Montana State University, Bozeman, MT 59717, USA.

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http://bmcbiol.biomedcentral.com/articles/10.1186/1741-7007-
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http://dx.doi.org/10.1186/1741-7007-3-26DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1325263PMC
December 2005

The genome of Cryptosporidium hominis.

Nature 2004 Oct;431(7012):1107-12

Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284-2030, USA.

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http://dx.doi.org/10.1038/nature02977DOI Listing
October 2004

CRP: Cleavage of Radiolabeled Phosphoproteins.

Nucleic Acids Res 2003 Jul;31(13):3859-61

Department of Microbiology, University of Virginia, Charlottesville, VA 22908, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC168920PMC
http://dx.doi.org/10.1093/nar/gkg513DOI Listing
July 2003

Identification of residues in glutathione transferase capable of driving functional diversification in evolution. A novel approach to protein redesign.

J Biol Chem 2003 Mar 16;278(10):8733-8. Epub 2002 Dec 16.

Department of Biochemistry, Uppsala University, Biomedical Center, Box 576, Sweden.

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http://dx.doi.org/10.1074/jbc.M211776200DOI Listing
March 2003

Entamoeba histolytica: sequence conservation of the Gal/GalNAc lectin from clinical isolates.

Exp Parasitol 2002 Jun-Jul;101(2-3):157-63

Department of Internal Medicine, University of Virginia, Charlottesville, VA 22908-1340, USA.

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http://dx.doi.org/10.1016/s0014-4894(02)00113-3DOI Listing
December 2002

Getting more from less: algorithms for rapid protein identification with multiple short peptide sequences.

Mol Cell Proteomics 2002 Feb;1(2):139-47

Department of Microbiology, University of Virginia, Charlottesville, Virginia 22908, USA.

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http://dx.doi.org/10.1074/mcp.m100004-mcp200DOI Listing
February 2002

A strategy for the rapid identification of phosphorylation sites in the phosphoproteome.

Mol Cell Proteomics 2002 Apr;1(4):314-22

Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina 27710, USA.

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http://dx.doi.org/10.1074/mcp.m200002-mcp200DOI Listing
April 2002