Gerard R. Lazo

Academic Editor on

May 19, 2021

K-mer-based machine learning method to classify LTR-retrotransposons in plant genomes

Simon Orozco-Arias, Mariana S. Candamil-Cortés, Paula A. Jaimes, Johan S. Piña, Reinel Tabares-Soto, Romain Guyot, Gustavo Isaza

https://doi.org/10.7717/peerj.11456 PubMed 34055489

April 7, 2021

Transcriptomic dynamics changes related to anthocyanin accumulation in the fleshy roots of carmine radish (Raphanus sativus L.) characterized using RNA-Seq

Xia Song, Jian Gao, Hua Peng

https://doi.org/10.7717/peerj.10978 PubMed 33868802

March 4, 2021

Comparative transcriptome and flavonoids components analysis reveal the structural genes responsible for the yellow seed coat color of Brassica rapa L.

Yanjing Ren, Ning Zhang, Ru Li, Xiaomin Ma, Lugang Zhang

https://doi.org/10.7717/peerj.10770 PubMed 33717670

March 3, 2021

Comparative transcriptomic analysis reveals the cold acclimation during chilling stress in sensitive and resistant passion fruit (Passiflora edulis) cultivars

Yanyan Wu, Weihua Huang, Qinglan Tian, Jieyun Liu, Xiuzhong Xia, Xinghai Yang, Haifei Mou

https://doi.org/10.7717/peerj.10977 PubMed 33717701

February 12, 2021

RNA sequencing-based exploration of the effects of far-red light on lncRNAs involved in the shade-avoidance response of D. officinale

Hansheng Li, Wei Ye, Yaqian Wang, Xiaohui Chen, Yan Fang, Gang Sun

https://doi.org/10.7717/peerj.10769 PubMed 33614278

February 9, 2021

Transcriptome analysis reveals the mechanism of improving erect-plant-type peanut yield by single-seeding precision sowing

Sha Yang, Jialei Zhang, Yun Geng, Zhaohui Tang, Jianguo Wang, Feng Guo, Jingjing Meng, Quan Wang, Shubo Wan, Xinguo Li

https://doi.org/10.7717/peerj.10616 PubMed 33614263

January 21, 2021

Genome-wide identification and analysis of cystatin family genes in Sorghum (Sorghum bicolor (L.) Moench)

Jie Li, Xinhao Liu, Qingmei Wang, Junyan Sun, Dexian He

https://doi.org/10.7717/peerj.10617 PubMed 33552717

January 19, 2021

Genome-wide analysis of growth-regulating factors (GRFs) in Triticum aestivum

Wendi Huang, Yiqin He, Lei Yang, Chen Lu, Yongxing Zhu, Cai Sun, Dongfang Ma, Junliang Yin

https://doi.org/10.7717/peerj.10701 PubMed 33552727

October 30, 2020

Biases in genome reconstruction from metagenomic data

William C. Nelson, Benjamin J. Tully, Jennifer M. Mobberley

https://doi.org/10.7717/peerj.10119 PubMed 33194386

September 25, 2020

Global gene expression analyses of the alkamide-producing plant Heliopsis longipes supports a polyketide synthase-mediated biosynthesis pathway

Génesis V. Buitimea-Cantúa, Nayelli Marsch-Martinez, Patricia Ríos-Chavez, Alfonso Méndez-Bravo, Jorge Molina-Torres

https://doi.org/10.7717/peerj.10074 PubMed 33033663

May 6, 2020

Cloning, sequencing, and expression analysis of 32 NAC transcription factors (MdNAC) in apple

Huifeng Li, Kun Ran, Qinglong Dong, Qiang Zhao, Song Shi

https://doi.org/10.7717/peerj.8249 PubMed 32411503

April 29, 2020

Post-transcriptional regulation of several biological processes involved in latex production in Hevea brasiliensis

Julie Leclercq, Shuangyang Wu, Benoît Farinas, Stéphanie Pointet, Bénédicte Favreau, Hélène Vignes, Kuswanhadi Kuswanhadi, Enrique Ortega-Abboud, Jean-François Dufayard, Shenghan Gao, Gaëtan Droc, Songnian Hu, Chaorong Tang, Pascal Montoro

https://doi.org/10.7717/peerj.8932 PubMed 32391199

March 4, 2020

The complete chloroplast genomes of seventeen Aegilops tauschii: genome comparative analysis and phylogenetic inference

Qing Su, Luxian Liu, Mengyu Zhao, Cancan Zhang, Dale Zhang, Youyong Li, Suoping Li

https://doi.org/10.7717/peerj.8678 PubMed 32181055

February 11, 2020

Proteogenomic analysis of pitaya reveals cold stress-related molecular signature

Junliang Zhou, Zhuang Wang, Yongya Mao, Lijuan Wang, Tujian Xiao, Yang Hu, Yang Zhang, Yuhua Ma

https://doi.org/10.7717/peerj.8540 PubMed 32095361

January 22, 2020

Prehaustorial local resistance to coffee leaf rust in a Mexican cultivar involves expression of salicylic acid-responsive genes

Edgar Couttolenc-Brenis, Gloria L. Carrión, Luc Villain, Fernando Ortega-Escalona, Daniel Ramírez-Martínez, Martín Mata-Rosas, Alfonso Méndez-Bravo

https://doi.org/10.7717/peerj.8345 PubMed 32002327

January 21, 2020

Global transcriptome analysis of alfalfa reveals six key biological processes of senescent leaves

Jianbo Yuan, Xinbo Sun, Tao Guo, Yuehui Chao, Liebao Han

https://doi.org/10.7717/peerj.8426 PubMed 32002335

January 3, 2020

Identification of a genome-specific repetitive element in the Gossypium D genome

Hejun Lu, Xinglei Cui, Yanyan Zhao, Richard Odongo Magwanga, Pengcheng Li, Xiaoyan Cai, Zhongli Zhou, Xingxing Wang, Yuling Liu, Yanchao Xu, Yuqing Hou, Renhai Peng, Kunbo Wang, Fang Liu

https://doi.org/10.7717/peerj.8344 PubMed 31915591

December 13, 2019

consensusDE: an R package for assessing consensus of multiple RNA-seq algorithms with RUV correction

Ashley J. Waardenberg, Matthew A. Field

https://doi.org/10.7717/peerj.8206 PubMed 31844586

November 19, 2019

Genome-wide identification and transcriptional expression analysis of superoxide dismutase (SOD) family in wheat (Triticum aestivum)

Wenqiang Jiang, Lei Yang, Yiqin He, Haotian Zhang, Wei Li, Huaigu Chen, Dongfang Ma, Junliang Yin

https://doi.org/10.7717/peerj.8062 PubMed 31763072

October 11, 2019

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

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)

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)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.)

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

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

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

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

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

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

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)

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)

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

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

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

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

Véronique Geoffroy, Cécile Pizot, Claire Redin, Amélie Piton, Nasim Vasli, Corinne Stoetzel, André Blavier, Jocelyn Laporte, Jean Muller

https://doi.org/10.7717/peerj.796 PubMed 25780760

February 26, 2015

Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives

Susan R. Strickler, Aureliano Bombarely, Jesse D. Munkvold, Thomas York, Naama Menda, Gregory B. Martin, Lukas A. Mueller

https://doi.org/10.7717/peerj.793 PubMed 25780758

January 6, 2015

Intragenomic polymorphisms among high-copy loci: a genus-wide study of nuclear ribosomal DNA in Asclepias (Apocynaceae)

Kevin Weitemier, Shannon C.K. Straub, Mark Fishbein, Aaron Liston

https://doi.org/10.7717/peerj.718 PubMed 25653903

March 13, 2014

Integrative study of Arabidopsis thaliana metabolomic and transcriptomic data with the interactive MarVis-Graph software

Manuel Landesfeind, Alexander Kaever, Kirstin Feussner, Corinna Thurow, Christiane Gatz, Ivo Feussner, Peter Meinicke

https://doi.org/10.7717/peerj.239 PubMed 24688832

September 17, 2013

Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology

Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz, Leighton Pritchard

https://doi.org/10.7717/peerj.167 PubMed 24109552

July 23, 2013

Improving transcriptome assembly through error correction of high-throughput sequence reads

Matthew D. MacManes, Michael B. Eisen

https://doi.org/10.7717/peerj.113 PubMed 23904992

March 5, 2013

Virus-host co-evolution under a modified nuclear genetic code

Derek J. Taylor, Matthew J. Ballinger, Shaun M. Bowman, Jeremy A. Bruenn

https://doi.org/10.7717/peerj.50 PubMed 23638388