A phylotranscriptomic dataset of angiosperm species under cold stress

[1]  Yirong Shen,et al.  Innovations and Stepwise Evolution of CBFs/DREB1s and Their Regulatory Networks in Angiosperms. , 2022, Journal of integrative plant biology.

[2]  Yirong Shen,et al.  Convergent evolution of AP2/ERF III and IX subfamilies through recurrent polyploidization and tandem duplication during eudicot adaptation to paleoenvironmental changes , 2022, Plant communications.

[3]  Yirong Shen,et al.  Innovation and Emerging Roles of Populus trichocarpa TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR Transcription Factors in Abiotic Stresses by Whole-Genome Duplication , 2022, Frontiers in Plant Science.

[4]  Shuhua Yang.  Cold responses in rice: From physiology to molecular biology , 2022, Journal of Plant Physiology.

[5]  Yirong Shen,et al.  The SR Splicing Factors: Providing Perspectives on Their Evolution, Expression, Alternative Splicing, and Function in Populus trichocarpa , 2021, International journal of molecular sciences.

[6]  Xiaoshuang Li,et al.  Transcriptome profiling of Malus sieversii under freezing stress after being cold-acclimated , 2021, BMC Genomics.

[7]  Jon S. Robertson,et al.  Genome sequence and evolution of Betula platyphylla , 2021, Horticulture research.

[8]  P. Jameson,et al.  Transcription-associated metabolomic adjustments in maize occur during combined drought and cold stress. , 2021, Plant physiology.

[9]  Hong Luo,et al.  Transcriptome profiling reveals the crucial biological pathways involved in cold response in Moso bamboo (Phyllostachys edulis). , 2019, Tree physiology.

[10]  Yiting Shi,et al.  Advances and challenges in uncovering cold tolerance regulatory mechanisms in plants. , 2019, The New phytologist.

[11]  Yiting Shi,et al.  Molecular Regulation of CBF Signaling in Cold Acclimation. , 2018, Trends in plant science.

[12]  Peijian Cao,et al.  Integrated transcriptomics and metabolomics analysis to characterize cold stress responses in Nicotiana tabacum , 2017, BMC Genomics.

[13]  Jian‐Kang Zhu.  Abiotic Stress Signaling and Responses in Plants , 2016, Cell.

[14]  Jian‐Kang Zhu,et al.  De novo assembly and analysis of the transcriptome of Ocimum americanum var. pilosum under cold stress , 2016, BMC Genomics.

[15]  Evgeny M. Zdobnov,et al.  BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..

[16]  Steven L Salzberg,et al.  HISAT: a fast spliced aligner with low memory requirements , 2015, Nature Methods.

[17]  Alyssa C. Frazee,et al.  Ballgown bridges the gap between transcriptome assembly and expression analysis , 2015, Nature Biotechnology.

[18]  S. Salzberg,et al.  StringTie enables improved reconstruction of a transcriptome from RNA-seq reads , 2015, Nature Biotechnology.

[19]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[20]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[21]  Colin N. Dewey,et al.  De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis , 2013, Nature Protocols.

[22]  Peter Li,et al.  GigaDB: announcing the GigaScience database , 2012, GigaScience.

[23]  David M. Goodstein,et al.  Phytozome: a comparative platform for green plant genomics , 2011, Nucleic Acids Res..

[24]  Davis J. McCarthy,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[25]  Kazuo Shinozaki,et al.  Metabolic Pathways Involved in Cold Acclimation Identified by Integrated Analysis of Metabolites and Transcripts Regulated by DREB1A and DREB2A1[W][OA] , 2009, Plant Physiology.

[26]  Jianhua Zhu,et al.  Cold stress regulation of gene expression in plants. , 2007, Trends in plant science.

[27]  Matthew A Hannah,et al.  A Global Survey of Gene Regulation during Cold Acclimation in Arabidopsis thaliana , 2005, PLoS genetics.

[28]  Tatiana A. Tatusova,et al.  NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..

[29]  Oliver Fiehn,et al.  A prominent role for the CBF cold response pathway in configuring the low-temperature metabolome of Arabidopsis. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[30]  Michael F. Thomashow,et al.  PLANT COLD ACCLIMATION: Freezing Tolerance Genes and Regulatory Mechanisms. , 1999, Annual review of plant physiology and plant molecular biology.

[31]  P. Kersey,et al.  Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomic Data. , 2017, Methods in molecular biology.

[32]  Wen Huang,et al.  The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant , 2001, Nucleic Acids Res..