Genome-wide analysis of autophagy-related genes (ARGs) in grapevine and plant tolerance to copper stress

RNA-Sequencing Reveals Biological Networks during Table Grapevine (‘Fujiminori’) Fruit Development

(2017) Lingfei Shangguan et al.   PLoS One

Genome-wide analysis of autophagy-associated genes in foxtail millet (Setaria italica L.) and characterization of the function of SiATG8a in conferring tolerance to nitrogen starvation in rice

(2016) Weiwei Li et al.   BMC GENOMICS

Ectopic expression of an autophagy-associated MdATG7b gene from apple alters growth and tolerance to nutrient stress in Arabidopsis thaliana

(2016) Ping Wang et al.   PLANT CELL TISSUE AND ORGAN CULTURE

Identification of Barley (Hordeum vulgare L.) Autophagy Genes and Their Expression Levels during Leaf Senescence, Chronic Nitrogen Limitation and in Response to Dark Exposure

(2016) Liliana Avila-Ospina et al.   Agronomy-Basel

Endocytic and autophagic pathways crosstalk in plants

(2015) Xiaohong Zhuang et al.   CURRENT OPINION IN PLANT BIOLOGY

A comprehensive, genome-wide analysis of autophagy-related genes identified in tobacco suggests a central role of autophagy in plant response to various environmental cues

(2015) Xue-mei Zhou et al.   DNA RESEARCH

Transporters, chaperones, and P-type ATPases controlling grapevine copper homeostasis

(2015) Xiangpeng Leng et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Autophagic Recycling Plays a Central Role in Maize Nitrogen Remobilization

(2015) Faqiang Li et al.   PLANT CELL

GSDS 2.0: an upgraded gene feature visualization server

(2014) Bo Hu et al.   BIOINFORMATICS

AUTOPHAGY-RELATED11 Plays a Critical Role in General Autophagy- and Senescence-Induced Mitophagy in Arabidopsis

(2014) F. Li et al.   PLANT CELL

Identification of autophagy-related genes ATG4 and ATG8 from wheat (Triticum aestivum L.) and profiling of their expression patterns responding to biotic and abiotic stresses

(2014) Dan Pei et al.   PLANT CELL REPORTS

NBR1-Mediated Selective Autophagy Targets Insoluble Ubiquitinated Protein Aggregates in Plant Stress Responses

(2013) Jie Zhou et al.   PLoS Genetics

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

microRNA30Apromotes autophagy in response to cancer therapy

(2012) Yan Yu et al.   Autophagy

ParaAT: A parallel tool for constructing multiple protein-coding DNA alignments

(2012) Zhang Zhang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Proteomic analysis of copper stress responses in the roots of two rice (Oryza sativa L.) varieties differing in Cu tolerance

(2012) Yufeng Song et al.   PLANT AND SOIL

Excess copper induced oxidative stress and response of antioxidants in rice

(2012) Thorny Chanu Thounaojam et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Autophagy-related gene, TdAtg8, in wild emmer wheat plays a role in drought and osmotic stress response

(2012) Duygu Kuzuoglu-Ozturk et al.   PLANTA

Silencing of MicroRNA-21 Confers Radio-Sensitivity through Inhibition of the PI3K/AKT Pathway and Enhancing Autophagy in Malignant Glioma Cell Lines

(2012) Ho-Shin Gwak et al.   PLoS One

microRNA-101 is a potent inhibitor of autophagy

(2011) Lisa B Frankel et al.   EMBO JOURNAL

Protein dynamics during seed germination under copper stress in Arabidopsis over-expressing Potentilla superoxide dismutase

(2011) Tejpal Gill et al.   JOURNAL OF PLANT RESEARCH

The ATG1/ATG13 Protein Kinase Complex Is Both a Regulator and a Target of Autophagic Recycling in Arabidopsis

(2011) A. Suttangkakul et al.   PLANT CELL

A critical role of autophagy in plant resistance to necrotrophic fungal pathogens

(2011) Zhibing Lai et al.   PLANT JOURNAL

Autophagy in plants and phytopathogens

(2010) Kohki Yoshimoto et al.   FEBS LETTERS

A DREB gene from Limonium bicolor mediates molecular and physiological responses to copper stress in transgenic tobacco

(2010) Qiaoying Ban et al.   JOURNAL OF PLANT PHYSIOLOGY

Autophagy is required for tolerance of drought and salt stress in plants

(2009) Yimo Liu et al.   Autophagy

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Autophagy in plants

(2009) Soon Il Kwon et al.   JOURNAL OF PLANT BIOLOGY

OsATG10b, an autophagosome component, is needed for cell survival against oxidative stresses in rice

(2009) Jun-Hye Shin et al.   MOLECULES AND CELLS

An autophagy-associated Atg8 protein is involved in the responses of Arabidopsis seedlings to hormonal controls and abiotic stresses

(2008) Silvia Slavikova et al.   JOURNAL OF EXPERIMENTAL BOTANY

A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells

(2008) Ken Cadwell et al.   NATURE