Eric Lyons

Eric Lyons

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Eric Lyons

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Chickspress: a resource for chicken gene expression.

Database (Oxford) 2019 01;2019

School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson AZ, USA.

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http://dx.doi.org/10.1093/database/baz058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6556980PMC
January 2019

N-Methyladenosine Inhibits Local Ribonucleolytic Cleavage to Stabilize mRNAs in Arabidopsis.

Cell Rep 2018 10;25(5):1146-1157.e3

Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.10.020DOI Listing
October 2018

EPIC-CoGe: managing and analyzing genomic data.

Bioinformatics 2018 08;34(15):2651-2653

BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6061785PMC
August 2018

SynMap2 and SynMap3D: web-based whole-genome synteny browsers.

Bioinformatics 2017 Jul;33(14):2197-2198

Genetics GIDP, University of Arizona, Tucson AZ, USA.

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http://dx.doi.org/10.1093/bioinformatics/btx144DOI Listing
July 2017

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms.

J Vis Exp 2017 05 9(123). Epub 2017 May 9.

BIO5 Institute, University of Arizona; The School of Plant Sciences, University of Arizona; Genetics GIDP, University of Arizona.

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http://dx.doi.org/10.3791/55009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5607918PMC
May 2017

A Global View of RNA-Protein Interactions Identifies Post-transcriptional Regulators of Root Hair Cell Fate.

Dev Cell 2017 04;41(2):204-220.e5

Department of Biology, University of Pennsylvania, 433 South University Avenue, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2017.03.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5605909PMC
April 2017

FractBias: a graphical tool for assessing fractionation bias following polyploidy.

Bioinformatics 2017 02;33(4):552-554

BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btw666DOI Listing
February 2017

Optical mapping in plant comparative genomics.

Gigascience 2015 10;4. Epub 2015 Feb 10.

J. Craig Venter Institute, Rockville, MD 20850 USA.

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http://dx.doi.org/10.1186/s13742-015-0044-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332928PMC
December 2016

The genome of black raspberry (Rubus occidentalis).

Plant J 2016 09 20;87(6):535-47. Epub 2016 Jul 20.

Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA.

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http://dx.doi.org/10.1111/tpj.13215DOI Listing
September 2016

Bringing your tools to CyVerse Discovery Environment using Docker.

F1000Res 2016 21;5:1442. Epub 2016 Jun 21.

CyVerse, University of Arizona, Tucson, AR, 85721, USA.

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http://dx.doi.org/10.12688/f1000research.8935.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5070597PMC
June 2016

The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences.

PLoS Biol 2016 Jan 11;14(1):e1002342. Epub 2016 Jan 11.

The University of Arizona, Tucson, Arizona, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1002342DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4709069PMC
January 2016

Relevance of in vitro agar based screens to characterize the anti-fungal activities of bacterial endophyte communities.

BMC Microbiol 2016 Jan 16;16. Epub 2016 Jan 16.

Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada.

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http://dx.doi.org/10.1186/s12866-016-0623-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4715354PMC
January 2016

SynFind: Compiling Syntenic Regions across Any Set of Genomes on Demand.

Genome Biol Evol 2015 Nov 11;7(12):3286-98. Epub 2015 Nov 11.

School of Plant Sciences, iPlant Collaborative, University of Arizona

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http://dx.doi.org/10.1093/gbe/evv219DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4700967PMC
November 2015

Identification of dopamine receptors across the extant avian family tree and analysis with other clades uncovers a polyploid expansion among vertebrates.

Front Neurosci 2015 7;9:361. Epub 2015 Oct 7.

Genetics GIDP, University of Arizona Tucson, AZ, USA ; BIO5 Institute, University of Arizona Tucson, AZ, USA ; The School of Plant Sciences, University of Arizona Tucson, AZ, USA.

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http://journal.frontiersin.org/Article/10.3389/fnins.2015.00
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http://dx.doi.org/10.3389/fnins.2015.00361DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4595791PMC
October 2015

ALLMAPS: robust scaffold ordering based on multiple maps.

Genome Biol 2015 Jan 13;16. Epub 2015 Jan 13.

Heilongjiang River Fisheries Research Institute, Harbin, 150070, China.

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http://dx.doi.org/10.1186/s13059-014-0573-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4305236PMC
January 2015

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.

Science 2014 Dec 11;346(6215):1254449. Epub 2014 Dec 11.

Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA.

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http://jarvislab.net/wp-content/uploads/2012/02/Green-et-al-
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http://www.sciencemag.org/cgi/doi/10.1126/science.1254449
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http://dx.doi.org/10.1126/science.1254449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4386873PMC
December 2014

Whole genome and tandem duplicate retention facilitated glucosinolate pathway diversification in the mustard family.

Genome Biol Evol 2013 ;5(11):2155-73

Biosystematics Group, Wageningen University & Research Center, Wageningen, Gelderland, The Netherlands.

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http://dx.doi.org/10.1093/gbe/evt162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3845643PMC
October 2014

Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome.

Science 2014 Aug 21;345(6199):950-3. Epub 2014 Aug 21.

Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France. Université d'Evry Val d'Essone, UMR 8030, CP5706, Evry, France. Centre National de Recherche Scientifique (CNRS), UMR 8030, CP5706, Evry, France.

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http://dx.doi.org/10.1126/science.1253435DOI Listing
August 2014

Unleashing the genome of brassica rapa.

Front Plant Sci 2012 31;3:172. Epub 2012 Jul 31.

J. Craig Venter Institute Rockville, MD, USA.

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http://dx.doi.org/10.3389/fpls.2012.00172DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3408644PMC
August 2012

Genome-wide analysis of syntenic gene deletion in the grasses.

Genome Biol Evol 2012 23;4(3):265-77. Epub 2012 Jan 23.

Department of Plant and Microbial Biology, University of California-Berkeley, CA, USA.

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http://dx.doi.org/10.1093/gbe/evs009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3318446PMC
July 2012

Long identical multispecies elements in plant and animal genomes.

Proc Natl Acad Sci U S A 2012 May 10;109(19):E1183-91. Epub 2012 Apr 10.

Department of Computer Science, University of Missouri, Columbia, MO 65211, USA.

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http://dx.doi.org/10.1073/pnas.1121356109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3358895PMC
May 2012

Novel temporal, fine-scale and growth variation phenotypes in roots of adult-stage maize (Zea mays L.) in response to low nitrogen stress.

Plant Cell Environ 2011 Dec 12;34(12):2122-37. Epub 2011 Sep 12.

Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada.

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http://doi.wiley.com/10.1111/j.1365-3040.2011.02409.x
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http://dx.doi.org/10.1111/j.1365-3040.2011.02409.xDOI Listing
December 2011

The Selaginella genome identifies genetic changes associated with the evolution of vascular plants.

Authors:
Jo Ann Banks Tomoaki Nishiyama Mitsuyasu Hasebe John L Bowman Michael Gribskov Claude dePamphilis Victor A Albert Naoki Aono Tsuyoshi Aoyama Barbara A Ambrose Neil W Ashton Michael J Axtell Elizabeth Barker Michael S Barker Jeffrey L Bennetzen Nicholas D Bonawitz Clint Chapple Chaoyang Cheng Luiz Gustavo Guedes Correa Michael Dacre Jeremy DeBarry Ingo Dreyer Marek Elias Eric M Engstrom Mark Estelle Liang Feng Cédric Finet Sandra K Floyd Wolf B Frommer Tomomichi Fujita Lydia Gramzow Michael Gutensohn Jesper Harholt Mitsuru Hattori Alexander Heyl Tadayoshi Hirai Yuji Hiwatashi Masaki Ishikawa Mineko Iwata Kenneth G Karol Barbara Koehler Uener Kolukisaoglu Minoru Kubo Tetsuya Kurata Sylvie Lalonde Kejie Li Ying Li Amy Litt Eric Lyons Gerard Manning Takeshi Maruyama Todd P Michael Koji Mikami Saori Miyazaki Shin-ichi Morinaga Takashi Murata Bernd Mueller-Roeber David R Nelson Mari Obara Yasuko Oguri Richard G Olmstead Naoko Onodera Bent Larsen Petersen Birgit Pils Michael Prigge Stefan A Rensing Diego Mauricio Riaño-Pachón Alison W Roberts Yoshikatsu Sato Henrik Vibe Scheller Burkhard Schulz Christian Schulz Eugene V Shakirov Nakako Shibagaki Naoki Shinohara Dorothy E Shippen Iben Sørensen Ryo Sotooka Nagisa Sugimoto Mamoru Sugita Naomi Sumikawa Milos Tanurdzic Günter Theissen Peter Ulvskov Sachiko Wakazuki Jing-Ke Weng William W G T Willats Daniel Wipf Paul G Wolf Lixing Yang Andreas D Zimmer Qihui Zhu Therese Mitros Uffe Hellsten Dominique Loqué Robert Otillar Asaf Salamov Jeremy Schmutz Harris Shapiro Erika Lindquist Susan Lucas Daniel Rokhsar Igor V Grigoriev

Science 2011 May 5;332(6032):960-3. Epub 2011 May 5.

Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA.

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http://sites.psu.edu/axtell/wp-content/uploads/sites/21458/2
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http://www.sciencemag.org/cgi/doi/10.1126/science.1203810
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http://dx.doi.org/10.1126/science.1203810DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166216PMC
May 2011

Screening synteny blocks in pairwise genome comparisons through integer programming.

BMC Bioinformatics 2011 Apr 18;12:102. Epub 2011 Apr 18.

Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.

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https://bmcbioinformatics.biomedcentral.com/articles/10.1186
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http://dx.doi.org/10.1186/1471-2105-12-102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3088904PMC
April 2011

Using genomic sequencing for classical genetics in E. coli K12.

PLoS One 2011 Feb 25;6(2):e16717. Epub 2011 Feb 25.

Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0016717PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3045373PMC
February 2011

The evolution of a high copy gene array in Arabidopsis.

J Mol Evol 2010 Jun 22;70(6):531-44. Epub 2010 May 22.

Department of Plant and Microbial Biology, University of California at Berkeley, 311 Koshland Hall, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1007/s00239-010-9350-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2886086PMC
June 2010

Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs.

PLoS Biol 2010 Jun 29;8(6):e1000409. Epub 2010 Jun 29.

Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1000409DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2893956PMC
June 2010

cis-Inhibition of Notch by endogenous Delta biases the outcome of lateral inhibition.

Curr Biol 2009 Aug 23;19(16):1378-83. Epub 2009 Jul 23.

Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.

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http://dx.doi.org/10.1016/j.cub.2009.06.042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2761761PMC
August 2009

Many or most genes in Arabidopsis transposed after the origin of the order Brassicales.

Genome Res 2008 Dec 3;18(12):1924-37. Epub 2008 Oct 3.

Department of Plant and Microbial Biology, University of California at Berkeley, California 94720, USA.

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http://dx.doi.org/10.1101/gr.081026.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2593585PMC
December 2008

Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids.

Plant Physiol 2008 Dec 24;148(4):1772-81. Epub 2008 Oct 24.

Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1104/pp.108.124867DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2593677PMC
December 2008

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).

Nature 2008 Apr;452(7190):991-6

Hawaii Agriculture Research Center, Aiea, Hawaii 96701, USA.

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http://dx.doi.org/10.1038/nature06856DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2836516PMC
April 2008

How to usefully compare homologous plant genes and chromosomes as DNA sequences.

Plant J 2008 Feb;53(4):661-73

Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA.

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http://doi.wiley.com/10.1111/j.1365-313X.2007.03326.x
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http://dx.doi.org/10.1111/j.1365-313X.2007.03326.xDOI Listing
February 2008

G-boxes, bigfoot genes, and environmental response: characterization of intragenomic conserved noncoding sequences in Arabidopsis.

Plant Cell 2007 May 11;19(5):1441-57. Epub 2007 May 11.

Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.

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http://www.plantcell.org/cgi/doi/10.1105/tpc.107.050419
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http://dx.doi.org/10.1105/tpc.107.050419DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1913728PMC
May 2007

Arabidopsis intragenomic conserved noncoding sequence.

Proc Natl Acad Sci U S A 2007 Feb 14;104(9):3348-53. Epub 2007 Feb 14.

College of Natural Resources and Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1073/pnas.0611574104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1805546PMC
February 2007

Culture-independent molecular analysis of microbial constituents of the healthy human outer ear.

J Clin Microbiol 2003 Jan;41(1):295-303

Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309-0347, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC149572PMC
http://dx.doi.org/10.1128/jcm.41.1.295-303.2003DOI Listing
January 2003