A
Audra K. Johnson
Researcher at University of Washington
Publications - 27
Citations - 15788
Audra K. Johnson is an academic researcher from University of Washington. The author has contributed to research in topics: Human genome & Gene. The author has an hindex of 17, co-authored 25 publications receiving 13789 citations.
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Journal ArticleDOI
An expansive human regulatory lexicon encoded in transcription factor footprints
Shane Neph,Jeff Vierstra,Andrew B. Stergachis,Alex Reynolds,Eric Haugen,Benjamin Vernot,Robert E. Thurman,Sam John,Richard Sandstrom,Audra K. Johnson,Matthew T. Maurano,Richard Humbert,Eric Rynes,Hao Wang,Shinny Vong,Kristen Lee,Daniel Bates,Morgan Diegel,Vaughn Roach,Douglas Dunn,Jun Neri,Anthony Schafer,R. Scott Hansen,Tanya Kutyavin,Erika Giste,Molly Weaver,Theresa K. Canfield,Peter J. Sabo,Miaohua Zhang,Gayathri Balasundaram,Rachel Byron,Michael J. MacCoss,Joshua M. Akey,Michaël Bender,Michaël Bender,Mark Groudine,Mark Groudine,Rajinder Kaul,John A. Stamatoyannopoulos +38 more
TL;DR: A stereotyped 50-base-pair footprint is identified that precisely defines the site of transcript origination within thousands of human promoters, and a large collection of novel regulatory factor recognition motifs that are highly conserved in both sequence and function are described.
Journal ArticleDOI
BEDOPS: high-performance genomic feature operations.
Shane Neph,Scott Kuehn,Alex Reynolds,Eric Haugen,Robert E. Thurman,Audra K. Johnson,Eric Rynes,Matthew T. Maurano,Jeff Vierstra,Sean Thomas,Richard Sandstrom,Richard Humbert,John A. Stamatoyannopoulos +12 more
TL;DR: BEDOPS is introduced, a software suite for common genomic analysis tasks which offers improved flexibility, scalability and execution time characteristics over previously published packages, and includes a utility to compress large inputs into a lossless format that can provide greater space savings and faster data extractions than alternatives.
Journal ArticleDOI
Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics.
Alvaro N. Barbeira,Scott P. Dickinson,Rodrigo Bonazzola,Jiamao Zheng,Heather E. Wheeler,Jason M. Torres,Eric S. Torstenson,Kaanan P. Shah,Tzintzuni Garcia,Todd L. Edwards,Eli A. Stahl,Laura M. Huckins,François Aguet,Kristin G. Ardlie,Beryl B. Cummings,Ellen Gelfand,Gad Getz,Kane Hadley,Robert E. Handsaker,Katherine H. Huang,Seva Kashin,Konrad J. Karczewski,Monkol Lek,Xiao Li,Xiao Li,Daniel G. MacArthur,Jared L. Nedzel,Duyen T. Nguyen,Michael S. Noble,Ayellet V. Segrè,Casandra A. Trowbridge,Taru Tukiainen,Nathan S. Abell,Brunilda Balliu,Ruth Barshir,Omer Basha,Alexis Battle,Gireesh K. Bogu,Andrew A. Brown,Andrew A. Brown,Christopher D. Brown,Stephane E. Castel,Lin Chen,Colby Chiang,Donald F. Conrad,Farhan N. Damani,Joe R. Davis,Olivier Delaneau,Olivier Delaneau,Emmanouil T. Dermitzakis,Emmanouil T. Dermitzakis,Barbara E. Engelhardt,Eleazar Eskin,Pedro G. Ferreira,Laure Fresard,Eric R. Gamazon,Eric R. Gamazon,Diego Garrido-Martín,Ariel D. H. Gewirtz,Genna Gliner,Michael J. Gloudemans,Roderic Guigó,Ira M. Hall,Buhm Han,Yuan He,Farhad Hormozdiari,Cédric Howald,Cédric Howald,Brian Jo,Eun Yong Kang,Yungil Kim,Sarah Kim-Hellmuth,Tuuli Lappalainen,Gen Li,Xin Li,Boxiang Liu,Serghei Mangul,Mark I. McCarthy,Ian C. McDowell,Pejman Mohammadi,Jean Monlong,Jean Monlong,Stephen B. Montgomery,Manuel Muñoz-Aguirre,Manuel Muñoz-Aguirre,Anne Ndungu,Andrew B. Nobel,Meritxell Oliva,Halit Ongen,Halit Ongen,John Palowitch,Nikolaos I Panousis,Nikolaos I Panousis,Panagiotis Papasaikas,YoSon Park,Princy Parsana,Anthony Payne,Christine B. Peterson,Jie Quan,Ferran Reverter,Ferran Reverter,Chiara Sabatti,Ashis Saha,Michael Sammeth,Alexandra J. Scott,Andrey A. Shabalin,Reza Sodaei,Matthew Stephens,Barbara E. Stranger,Benjamin J. Strober,Jae Hoon Sul,Emily K. Tsang,Sarah Urbut,Martijn van de Bunt,Gao Wang,Xiaoquan Wen,Fred A. Wright,Hualin S. Xi,Esti Yeger-Lotem,Zachary Zappala,Judith B. Zaugg,Yi-Hui Zhou,Joshua M. Akey,Daniel Bates,Joanne Chan,Melina Claussnitzer,Melina Claussnitzer,Kathryn Demanelis,Morgan Diegel,Jennifer A. Doherty,Andrew P. Feinberg,Marian S. Fernando,Jessica Halow,Kasper D. Hansen,Eric Haugen,Peter Hickey,Lei Hou,Lei Hou,Farzana Jasmine,Ruiqi Jian,Lihua Jiang,Audra K. Johnson,Rajinder Kaul,Manolis Kellis,Manolis Kellis,Muhammad G. Kibriya,Kristen Lee,Jin Billy Li,Qin Li,Jessica Lin,Jessica Lin,Shin Lin,Shin Lin,Sandra Linder,Caroline Linke,Yaping Liu,Yaping Liu,Matthew T. Maurano,Benoit Molinie,Jemma Nelson,Fidencio J. Neri,Yongjin Park,Yongjin Park,Brandon L. Pierce,Nicola J. Rinaldi,Nicola J. Rinaldi,Lindsay F. Rizzardi,Richard Sandstrom,Andrew D. Skol,Kevin S. Smith,Michael Snyder,John A. Stamatoyannopoulos,Hua Tang,Li Wang,Meng Wang,Nicholas Van Wittenberghe,Fan Wu,Rui Zhang,Concepcion R. Nierras,Philip A. Branton,Latarsha J. Carithers,Ping Guan,Helen M. Moore,Abhi Rao,Jimmie B. Vaught,Sarah E. Gould,Nicole C. Lockart,Casey Martin,Jeffery P. Struewing,Simona Volpi,Anjené M. Addington,Susan E. Koester,A. Roger Little,Lori E. Brigham,Richard Hasz,Marcus Hunter,Christopher Johns,Mark H. Johnson,Gene Kopen,William F. Leinweber,John T. Lonsdale,Alisa McDonald,Bernadette Mestichelli,Kevin Myer,Brian Roe,Michael F. Salvatore,Saboor Shad,Jeffrey A. Thomas,Gary Walters,Michael Washington,Joseph Wheeler,Jason Bridge,Barbara A. Foster,Bryan Gillard,Ellen Karasik,Rachna Kumar,Mark Miklos,Michael T. Moser,Scott D. Jewell,Robert G. Montroy,Daniel C. Rohrer,Dana R. Valley,David A. Davis,Deborah C. Mash,Anita H. Undale,Anna M. Smith,David E. Tabor,Nancy Roche,Jeffrey McLean,Negin Vatanian,Karna Robinson,Leslie H. Sobin,Mary Barcus,Kimberly M. Valentino,Liqun Qi,Steven Hunter,Pushpa Hariharan,Shilpi Singh,Ki Sung Um,Takunda Matose,Maria M. Tomaszewski,Laura Barker,Maghboeba Mosavel,Laura A. Siminoff,Heather M. Traino,Paul Flicek,Thomas Juettemann,Magali Ruffier,Dan Sheppard,Kieron Taylor,Stephen J. Trevanion,Daniel R. Zerbino,Brian Craft,Mary Goldman,Maximilian Haeussler,W. James Kent,Christopher Lee,Benedict Paten,Kate R. Rosenbloom,John Vivian,Jingchun Zhu,Dan L. Nicolae,Nancy J. Cox,Hae Kyung Im +263 more
TL;DR: A mathematical expression is derived to compute PrediXcan results using summary data, and the effects of gene expression variation on human phenotypes in 44 GTEx tissues and >100 phenotypes are investigated.
Journal ArticleDOI
An encyclopedia of mouse DNA elements (Mouse ENCODE)
John A. Stamatoyannopoulos,Michael Snyder,Ross C. Hardison,Bing Ren,Thomas R. Gingeras,David M. Gilbert,Mark Groudine,M. A. Bender,Rajinder Kaul,Theresa K. Canfield,Erica Giste,Audra K. Johnson,Mia Zhang,Gayathri Balasundaram,Rachel Byron,Vaughan Roach,Peter J. Sabo,Richard Sandstrom,A Sandra Stehling,Robert E. Thurman,Sherman M. Weissman,Philip Cayting,Manoj Hariharan,Jin Lian,Yong Cheng,Stephen G. Landt,Zhihai Ma,Barbara J. Wold,Job Dekker,Gregory E. Crawford,Cheryl A. Keller,Weisheng Wu,Christopher T. Morrissey,Swathi Ashok Kumar,Tejaswini Mishra,Deepti Jain,Marta Byrska-Bishop,Daniel Blankenberg,Bryan R. Lajoie,Gaurav Jain,Amartya Sanyal,Kaun-Bei Chen,Olgert Denas,James Taylor,Gerd A. Blobel,Mitchell J. Weiss,Max Pimkin,Wulan Deng,Georgi K. Marinov,Brian A. Williams,Katherine I. Fisher-Aylor,Gilberto DeSalvo,Anthony Kiralusha,Diane Trout,Henry Amrhein,Ali Mortazavi,Lee Edsall,David McCleary,Samantha Kuan,Yin Shen,Feng Yue,Zhen Ye,Carrie A. Davis,Chris Zaleski,Sonali Jha,Chenghai Xue,Alexander Dobin,Wei Lin,Meagan Fastuca,Huaien Wang,Roderic Guigó,Sarah Djebali,Julien Lagarde,Tyrone Ryba,Takayo Sasaki,Venkat S. Malladi,Melissa S. Cline,Vanessa M. Kirkup,Katrina Learned,Kate R. Rosenbloom,W. James Kent,Elise A. Feingold,Peter J. Good,Michael J. Pazin,Rebecca F. Lowdon,Leslie B Adams +85 more
TL;DR: The Mouse E NCODE Consortium is applying the same experimental pipelines developed for human ENCODE to annotate the mouse genome to enable a broad range of mouse genomics efforts.
Journal ArticleDOI
Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution
Jeff Vierstra,Eric Rynes,Richard Sandstrom,Miaohua Zhang,Theresa K. Canfield,R. Scott Hansen,Sandra Stehling-Sun,Peter J. Sabo,Rachel Byron,Richard Humbert,Robert E. Thurman,Audra K. Johnson,Shinny Vong,Kristen Lee,Daniel Bates,Fidencio Neri,Morgan Diegel,Erika Giste,Eric Haugen,Douglas Dunn,Matthew S. Wilken,Steven Z. Josefowicz,Steven Z. Josefowicz,Robert M. Samstein,Robert M. Samstein,Kai Hsin Chang,Evan E. Eichler,Evan E. Eichler,Marella F. T. R. de Bruijn,Thomas A. Reh,Arthur I. Skoultchi,Alexander Y. Rudensky,Alexander Y. Rudensky,Stuart H. Orkin,Stuart H. Orkin,Thalia Papayannopoulou,Piper M. Treuting,Licia Selleri,Rajinder Kaul,Mark Groudine,Mark Groudine,Michaël Bender,Michaël Bender,John A. Stamatoyannopoulos +43 more
TL;DR: The mouse and human genomes have undergone extensive cis-regulatory rewiring that combines branch-specific evolutionary innovation and loss with widespread repurposing of conserved DHSs to alternative cell fates, and this process is mediated by turnover of transcription factor (TF) recognition elements.