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Academic Editor

Gerard R. Lazo

ORCID: 0000-0002-9160-2052

Summary

Geneticist with the Crop Improvement and Genetics Research Unit, Agricultural Research Service, Western Regional Research Center, Albany, CA, USA.

Bioinformatics Computational Biology Genetics Genomics Plant Science

Work details

Geneticist

United States Department of Agriculture

Crop Improvement and Genetics

Websites

PeerJ Contributions

Edited 37

Academic Editor on

October 11, 2019

Adapterama III: Quadruple-indexed, double/triple-enzyme RADseq libraries (2RAD/3RAD)

161 downloads

710 views

Natalia J. Bayona-Vásquez, Travis C. Glenn, Troy J. Kieran, Todd W. Pierson, Sandra L. Hoffberg, Peter A. Scott, Kerin E. Bentley, John W. Finger, Swarnali Louha, Nicholas Troendle, Pindaro Diaz-Jaimes, Rodney Mauricio, Brant C. Faircloth

https://doi.org/10.7717/peerj.7724 PubMed 31616583

October 11, 2019

Adapterama I: universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru & iNext)

1 citation

217 downloads

842 views

Travis C. Glenn, Roger A. Nilsen, Troy J. Kieran, Jon G. Sanders, Natalia J. Bayona-Vásquez, John W. Finger, Todd W. Pierson, Kerin E. Bentley, Sandra L. Hoffberg, Swarnali Louha, Francisco J. Garcia-De Leon, Miguel Angel del Rio Portilla, Kurt D. Reed, Jennifer L. Anderson, Jennifer K. Meece, Samuel E. Aggrey, Romdhane Rekaya, Magdy Alabady, Myriam Belanger, Kevin Winker, Brant C. Faircloth

https://doi.org/10.7717/peerj.7755 PubMed 31616586

October 11, 2019

Adapterama II: universal amplicon sequencing on Illumina platforms (TaggiMatrix)

1 citation

137 downloads

560 views

Travis C. Glenn, Todd W. Pierson, Natalia J. Bayona-Vásquez, Troy J. Kieran, Sandra L. Hoffberg, Jesse C. Thomas IV, Daniel E. Lefever, John W. Finger, Bei Gao, Xiaoming Bian, Swarnali Louha, Ramya T. Kolli, Kerin E. Bentley, Julie Rushmore, Kelvin Wong, Timothy I. Shaw, Michael J. Rothrock Jr, Anna M. McKee, Tai L. Guo, Rodney Mauricio, Marirosa Molina, Brian S. Cummings, Lawrence H. Lash, Kun Lu, Gregory S. Gilbert, Stephen P. Hubbell, Brant C. Faircloth

https://doi.org/10.7717/peerj.7786 PubMed 31616589

August 29, 2019

Analysis of the laccase gene family and miR397-/miR408-mediated posttranscriptional regulation in Salvia miltiorrhiza

234 downloads

275 views

Caili Li, Dongqiao Li, Hong Zhou, Jiang Li, Shanfa Lu

https://doi.org/10.7717/peerj.7605 PubMed 31528508

August 28, 2019

Cyclodipeptides from Pseudomonas aeruginosa modulate the maize (Zea mays L.) root system and promote S6 ribosomal protein kinase activation

214 downloads

357 views

Iván Corona-Sánchez, Cesar Arturo Peña-Uribe, Omar González-López, Javier Villegas, Jesus Campos-Garcia, Homero Reyes de la Cruz

https://doi.org/10.7717/peerj.7494 PubMed 31523498

July 10, 2019

Towards sex identification of Asian Palmyra palm (Borassus flabellifer L.) by DNA fingerprinting, suppression subtractive hybridization and de novo transcriptome sequencing

407 downloads

574 views

Kwanjai Pipatchartlearnwong, Piyada Juntawong, Passorn Wonnapinij, Somsak Apisitwanich, Supachai Vuttipongchaikij

https://doi.org/10.7717/peerj.7268 PubMed 31333909

May 14, 2019

PEST sequences from a cactus dehydrin regulate its proteolytic degradation

191 downloads

623 views

Adriana L. Salazar-Retana, Israel Maruri-López, Itzell E. Hernández-Sánchez, Alicia Becerra-Flora, María de la Luz Guerrero-González, Juan Francisco Jiménez-Bremont

https://doi.org/10.7717/peerj.6810 PubMed 31143531

April 11, 2019

Genome-wide analysis of maize OSCA family members and their involvement in drought stress

1 citation

270 downloads

820 views

Shuangcheng Ding, Xin Feng, Hewei Du, Hongwei Wang

https://doi.org/10.7717/peerj.6765 PubMed 30997296

April 10, 2019

virMine: automated detection of viral sequences from complex metagenomic samples

1 citation

630 downloads

2,548 views

Andrea Garretto, Thomas Hatzopoulos, Catherine Putonti

https://doi.org/10.7717/peerj.6695 PubMed 30993039

April 10, 2019

MetaMSD: meta analysis for mass spectrometry data

330 downloads

817 views

So Young Ryu, George A. Wendt

https://doi.org/10.7717/peerj.6699 PubMed 30993040

April 1, 2019

Identification of the GRAS gene family in the Brassica juncea genome provides insight into its role in stem swelling in stem mustard

1 citation

341 downloads

723 views

Mengyao Li, Bo Sun, Fangjie Xie, Ronggao Gong, Ya Luo, Fen Zhang, Zesheng Yan, Haoru Tang

https://doi.org/10.7717/peerj.6682 PubMed 30972257

March 27, 2019

Pixel: a content management platform for quantitative omics data

310 downloads

1,002 views

Thomas Denecker, William Durand, Julien Maupetit, Charles Hébert, Jean-Michel Camadro, Pierre Poulain, Gaëlle Lelandais

https://doi.org/10.7717/peerj.6623 PubMed 30944779

October 17, 2018

Genome-wide identification and analysis of the CNGC gene family in maize

1 citation

314 downloads

1,076 views

Lidong Hao, Xiuli Qiao

https://doi.org/10.7717/peerj.5816 PubMed 30356996

September 28, 2018

Leaf photosynthetic function duration during yield formation of large-spike wheat in rainfed cropping systems

169 downloads

680 views

Lifang Wang, Jutao Sun, Chenyang Wang, Zhouping Shangguan

https://doi.org/10.7717/peerj.5532 PubMed 30280014

September 19, 2018

Identification of MOS9 as an interaction partner for chalcone synthase in the nucleus

2 citations

171 downloads

925 views

Jonathan I. Watkinson, Peter A. Bowerman, Kevin C. Crosby, Sherry B. Hildreth, Richard F. Helm, Brenda S.J. Winkel

https://doi.org/10.7717/peerj.5598 PubMed 30258711

July 3, 2018

Recombination between T-DNA insertions to cause chromosomal deletions in Arabidopsis is a rare phenomenon

153 downloads

840 views

John F. Seagrist, Shih-Heng Su, Patrick J. Krysan

https://doi.org/10.7717/peerj.5076 PubMed 30002957

June 20, 2018

GEsture: an online hand-drawing tool for gene expression pattern search

283 downloads

2,017 views

Chunyan Wang, Yiqing Xu, Xuelin Wang, Li Zhang, Suyun Wei, Qiaolin Ye, Youxiang Zhu, Hengfu Yin, Manoj Nainwal, Luis Tanon-Reyes, Feng Cheng, Tongming Yin, Ning Ye

https://doi.org/10.7717/peerj.4927 PubMed 29942676

May 24, 2018

Identification of stem rust resistance genes in wheat cultivars in China using molecular markers

1 citation

486 downloads

1,097 views

Xiaofeng Xu, Depeng Yuan, Dandan Li, Yue Gao, Ziyuan Wang, Yang Liu, Siting Wang, Yuanhu Xuan, Hui Zhao, Tianya Li, Yuanhua Wu

https://doi.org/10.7717/peerj.4882 PubMed 29844997

March 6, 2018

Genome-wide identification and characterization of Dof transcription factors in eggplant (Solanum melongena L.)

1 citation

488 downloads

2,120 views

Qingzhen Wei, Wuhong Wang, Tianhua Hu, Haijiao Hu, Weihai Mao, Qinmei Zhu, Chonglai Bao

https://doi.org/10.7717/peerj.4481 PubMed 29527420

July 27, 2017

Identification of ecogeographical gaps in the Spanish Aegilops collections with potential tolerance to drought and salinity

4 citations

470 downloads

1,956 views

Rosa María Garcia, Mauricio Parra-Quijano, Jose María Iriondo

https://doi.org/10.7717/peerj.3494 PubMed 28761779

July 3, 2017

Quantitative proteome-level analysis of paulownia witches’ broom disease with methyl methane sulfonate assistance reveals diverse metabolic changes during the infection and recovery processes

7 citations

374 downloads

1,791 views

Zhe Wang, Wenshan Liu, Guoqiang Fan, Xiaoqiao Zhai, Zhenli Zhao, Yanpeng Dong, Minjie Deng, Yabing Cao

https://doi.org/10.7717/peerj.3495 PubMed 28690927

May 18, 2017

StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees

14 citations

809 downloads

2,791 views

Märt Roosaare, Mihkel Vaher, Lauris Kaplinski, Märt Möls, Reidar Andreson, Maarja Lepamets, Triinu Kõressaar, Paul Naaber, Siiri Kõljalg, Maido Remm

https://doi.org/10.7717/peerj.3353 PubMed 28533988

February 15, 2017

ToxGen: an improved reference database for the identification of type B-trichothecene genotypes in Fusarium

6 citations

344 downloads

1,773 views

Tomasz Kulik, Kessy Abarenkov, Maciej Buśko, Katarzyna Bilska, Anne D. van Diepeningen, Anna Ostrowska-Kołodziejczak, Katarzyna Krawczyk, Balázs Brankovics, Sebastian Stenglein, Jakub Sawicki, Juliusz Perkowski

https://doi.org/10.7717/peerj.2992 PubMed 28229023

January 24, 2017

The DNA methylation level against the background of the genome size and t-heterochromatin content in some species of the genus Secale L

3 citations

407 downloads

1,902 views

Anna Kalinka, Magdalena Achrem, Paulina Poter

https://doi.org/10.7717/peerj.2889 PubMed 28149679

November 8, 2016

RGFA: powerful and convenient handling of assembly graphs

1 citation

303 downloads

2,273 views

Giorgio Gonnella, Stefan Kurtz

https://doi.org/10.7717/peerj.2681 PubMed 27843717

October 25, 2016

Proliferation of group II introns in the chloroplast genome of the green alga Oedocladium carolinianum (Chlorophyceae)

6 citations

413 downloads

1,618 views

Jean-Simon Brouard, Monique Turmel, Christian Otis, Claude Lemieux

https://doi.org/10.7717/peerj.2627 PubMed 27812423

August 31, 2016

Genome-wide identification and characterization of GRAS transcription factors in sacred lotus (Nelumbo nucifera)

11 citations

490 downloads

2,337 views

Yu Wang, Shenglu Shi, Ying Zhou, Yu Zhou, Jie Yang, Xiaoqing Tang

https://doi.org/10.7717/peerj.2388 PubMed 27635351

February 23, 2016

Unravelling potential virulence factor candidates in Xanthomonas citri. subsp. citri by secretome analysis

8 citations

653 downloads

2,874 views

Rafael M. Ferreira, Leandro M. Moreira, Jesus A. Ferro, Marcia R.R. Soares, Marcelo L. Laia, Alessandro M. Varani, Julio C.F. de Oliveira, Maria Ines T. Ferro

https://doi.org/10.7717/peerj.1734 PubMed 26925342

August 25, 2015

Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls

65 citations

2,773 downloads

17,694 views

Eduardo Castro-Nallar, Matthew L. Bendall, Marcos Pérez-Losada, Sarven Sabuncyan, Emily G. Severance, Faith B. Dickerson, Jennifer R. Schroeder, Robert H. Yolken, Keith A. Crandall

https://doi.org/10.7717/peerj.1140 PubMed 26336637

March 17, 2015

GROM-RD: resolving genomic biases to improve read depth detection of copy number variants

9 citations

652 downloads

2,334 views

Sean D. Smith, Joseph K. Kawash, Andrey Grigoriev

https://doi.org/10.7717/peerj.836 PubMed 25802807

March 3, 2015

VaRank: a simple and powerful tool for ranking genetic variants

45 citations

1,016 downloads