相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。Wide-ranging transcriptome remodelling mediated by alternative polyadenylation in response to abiotic stresses in Sorghum
Manohar Chakrabarti et al.
PLANT JOURNAL (2020)
The Dynamic Kaleidoscope of RNA Biology in Plants
Julia Bailey-Serres et al.
PLANT PHYSIOLOGY (2020)
Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies
Anireddy S. N. Reddy et al.
BIOCHEMICAL SOCIETY TRANSACTIONS (2020)
Single-Molecule Real-Time (SMRT) Isoform Sequencing (Iso-Seq) in Plants: The Status of the Bioinformatics Tools to Unravel the Transcriptome Complexity
Yubang Gao et al.
CURRENT BIOINFORMATICS (2019)
Analysis of Transcriptome and Epitranscriptome in Plants Using PacBio Iso-Seq and Nanopore-Based Direct RNA Sequencing
Liangzhen Zhao et al.
FRONTIERS IN GENETICS (2019)
Sequenceserver: A Modern Graphical User Interface for Custom BLAST Databases
Anurag Priyann et al.
MOLECULAR BIOLOGY AND EVOLUTION (2019)
Genome-wide alternative polyadenylation dynamics in response to biotic and abiotic stresses in rice
Congting Ye et al.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY (2019)
The AREB1 Transcription Factor Influences Histone Acetylation to Regulate Drought Responses and Tolerance in Populus trichocarpa
Shuang Li et al.
PLANT CELL (2019)
PacBio full-length cDNA sequencing integrated with RNA-seq reads drastically improves the discovery of splicing transcripts in rice
Guoqiang Zhang et al.
PLANT JOURNAL (2019)
MCENet: A database for maize conditional co-expression network and network characterization collaborated with multi-dimensional omics levels
Tian Tian et al.
JOURNAL OF GENETICS AND GENOMICS (2018)
HMMER web server: 2018 update
Simon C. Potter et al.
NUCLEIC ACIDS RESEARCH (2018)
Abiotic Stresses Modulate Landscape of Poplar Transcriptome via Alternative Splicing, Differential Intron Retention, and Isoform Ratio Switching
Sergei A. Filichkin et al.
FRONTIERS IN PLANT SCIENCE (2018)
PRAPI: post-transcriptional regulation analysis pipeline for Iso-Seq
Yubang Gao et al.
BIOINFORMATICS (2018)
Light Regulation of Alternative Pre-mRNA Splicing in Plants
Hangxiao Zhang et al.
PHOTOCHEMISTRY AND PHOTOBIOLOGY (2017)
Comprehensive profiling of rhizome-associated alternative splicing and alternative polyadenylation in moso bamboo (Phyllostachys edulis)
Taotao Wang et al.
PLANT JOURNAL (2017)
Tissue and cell-type co-expression networks of transcription factors and wood component genes in Populus trichocarpa
Rui Shi et al.
PLANTA (2017)
Reciprocal cross-regulation of VND and SND multigene TF families for wood formation in Populus trichocarpa
Ying-Chung Jimmy Lin et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)
ALCOdb: Gene Coexpression Database for Microalgae
Yuichi Aoki et al.
PLANT AND CELL PHYSIOLOGY (2016)
Genome-wide dynamics of alternative polyadenylation in rice
Haihui Fu et al.
GENOME RESEARCH (2016)
Co-expression network analyses identify functional modules associated with development and stress response in Gossypium arboreum
Qi You et al.
SCIENTIFIC REPORTS (2016)
JBrowse: a dynamic web platform for genome visualization and analysis
Robert Buels et al.
GENOME BIOLOGY (2016)
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
Mihaela Pertea et al.
NATURE BIOTECHNOLOGY (2015)
HISAT: a fast spliced aligner with low memory requirements
Daehwan Kim et al.
NATURE METHODS (2015)
A resource for characterizing genome-wide binding and putative target genes of transcription factors expressed during secondary growth and wood formation in Populus
Lijun Liu et al.
PLANT JOURNAL (2015)
DroughtDB: an expert-curated compilation of plant drought stress genes and their homologs in nine species
Svenja Alter et al.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2015)
The Populus ARBORKNOX1 homeodomain transcription factor regulates woody growth through binding to evolutionarily conserved target genes of diverse function
Lijun Liu et al.
NEW PHYTOLOGIST (2015)
Analysis of the Drought Stress-Responsive Transcriptome of Black Cottonwood (Populus trichocarpa) Using Deep RNA Sequencing
Sha Tang et al.
PLANT MOLECULAR BIOLOGY REPORTER (2015)
Alternative Transcription Initiation and the AUG Context Configuration Control Dual-Organellar Targeting and Functional Competence of Arabidopsis Lon1 Protease
Gerasimos Daras et al.
MOLECULAR PLANT (2014)
A robust chromatin immunoprecipitation protocol for studying transcription factor-DNA interactions and histone modifications in wood-forming tissue
Wei Li et al.
NATURE PROTOCOLS (2014)
Intron-Mediated Alternative Splicing of WOOD-ASSOCIATED NAC TRANSCRIPTION FACTOR1B Regulates Cell Wall Thickening during Fiber Development in Populus Species
Yunjun Zhao et al.
PLANT PHYSIOLOGY (2014)
rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data
Shihao Shen et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
HTQC: a fast quality control toolkit for Illumina sequencing data
Xi Yang et al.
BMC BIOINFORMATICS (2013)
The developing xylem transcriptome and genome-wide analysis of alternative splicing in Populus trichocarpa (black cottonwood) populations
Hua Bao et al.
BMC GENOMICS (2013)
Structure, Function and Networks of Transcription Factors Involved in Abiotic Stress Responses
Soren Lindemose et al.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2013)
Assessment of transcript reconstruction methods for RNA-seq
Tamara Steijger et al.
NATURE METHODS (2013)
SND1 Transcription Factor-Directed Quantitative Functional Hierarchical Genetic Regulatory Network in Wood Formation in Populus trichocarpa
Ying-Chung Lin et al.
PLANT CELL (2013)
Histone Deacetylase Complex1 Expression Level Titrates Plant Growth and Abscisic Acid Sensitivity in Arabidopsis
Giorgio Perrella et al.
PLANT CELL (2013)
Alternative Splicing at the Intersection of Biological Timing, Development, and Stress Responses
Dorothee Staiger et al.
PLANT CELL (2013)
Complexity of the Alternative Splicing Landscape in Plants
Anireddy S. N. Reddy et al.
PLANT CELL (2013)
Genomic era analyses of RNA secondary structure and RNA-binding proteins reveal their significance to post-transcriptional regulation in plants
Ian M. Silverman et al.
PLANT SCIENCE (2013)
Alternative splicing of transcription factors in plant responses to low temperature stress: mechanisms and functions
Pil Joon Seo et al.
PLANTA (2013)
diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates
Li Shen et al.
PLOS ONE (2013)
Ptr-miR397a is a negative regulator of laccase genes affecting lignin content in Populus trichocarpa
Shanfa Lu et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis
Yamile Marquez et al.
GENOME RESEARCH (2012)
Fast gapped-read alignment with Bowtie 2
Ben Langmead et al.
NATURE METHODS (2012)
Phytozome: a comparative platform for green plant genomics
David M. Goodstein et al.
NUCLEIC ACIDS RESEARCH (2012)
Transition of Chromatin Status During the Process of Recovery from Drought Stress in Arabidopsis thaliana
Jong-Myong Kim et al.
PLANT AND CELL PHYSIOLOGY (2012)
Improving PacBio Long Read Accuracy by Short Read Alignment
Kin Fai Au et al.
PLOS ONE (2012)
Splice variant of the SND1 transcription factor is a dominant negative of SND1 members and their regulation in Populus trichocarpa
Quanzi Li et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
The Sequence Read Archive
Rasko Leinonen et al.
NUCLEIC ACIDS RESEARCH (2011)
Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation
Xiaohui Wu et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
Alternative polyadenylation and gene expression regulation in plants
Denghui Xing et al.
WILEY INTERDISCIPLINARY REVIEWS-RNA (2011)
A role for SR proteins in plant stress responses
Paula Duque
PLANT SIGNALING & BEHAVIOR (2011)
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
Mark D. Robinson et al.
BIOINFORMATICS (2010)
Genome-wide mapping of alternative splicing in Arabidopsis thaliana
Sergei A. Filichkin et al.
GENOME RESEARCH (2010)
Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome
Guojie Zhang et al.
GENOME RESEARCH (2010)
Secondary Cell Wall Deposition in Developing Secondary Xylem of Poplar
Minako Kaneda et al.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY (2010)
The Sequence Alignment/Map format and SAMtools
Heng Li et al.
BIOINFORMATICS (2009)
Rank of Correlation Coefficient as a Comparable Measure for Biological Significance of Gene Coexpression
Takeshi Obayashi et al.
DNA RESEARCH (2009)
Histone occupancy-dependent and -independent removal of H3K27 trimethylation at cold-responsive genes in Arabidopsis
Chang Seob Kwon et al.
PLANT JOURNAL (2009)
Alternative Splicing Studies of the Reactive Oxygen Species Gene Network in Populus Reveal Two Isoforms of High-Isoelectric-Point Superoxide Dismutase
Vaibhav Srivastava et al.
PLANT PHYSIOLOGY (2009)
Characterization and comparison of intron structure and alternative splicing between Medicago truncatula, Populus trichocarpa, Arabidopsis and rice
Jong-Min Baek et al.
PLANT MOLECULAR BIOLOGY (2008)
Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang et al.
GENOME BIOLOGY (2008)
The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)
G. A. Tuskan et al.
SCIENCE (2006)
Progress in the study of molecular genetic improvements of poplar in China
Shan-Zhi Lin et al.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY (2006)
Genome analysis:: RNA recognition motif (RRM) and K homology (KH) domain RNA-binding proteins from the flowering plant Arabidopsis thaliana
ZJ Lorkovic et al.
NUCLEIC ACIDS RESEARCH (2002)