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。Sphingolipids: towards an integrated view of metabolism during the plant stress response
Eloise Huby et al.
NEW PHYTOLOGIST (2020)
Changes in ambient temperature are the prevailing cue in determining Brachypodium distachyon diurnal gene regulation
Kirk J-M. MacKinnon et al.
NEW PHYTOLOGIST (2020)
Building near-complete plant genomes
Todd P. Michael et al.
CURRENT OPINION IN PLANT BIOLOGY (2020)
The NLR-Annotator Tool Enables Annotation of the Intracellular Immune Receptor Repertoire1[OPEN]
Burkhard Steuernagel et al.
PLANT PHYSIOLOGY (2020)
Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida
Camilla Ferrari et al.
NATURE COMMUNICATIONS (2019)
Circadian Rhythms in Plants
Nicky Creux et al.
COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2019)
Time of day and network reprogramming during drought induced CAM photosynthesis in Sedum album
Ching Man Wai et al.
PLOS GENETICS (2019)
Plant evolution and environmental adaptation unveiled by long-read whole-genome sequencing of Spirodela
Dong An et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)
Stronger When Together: Clustering of Plant NLR Disease resistance Genes
Solveig van Wersch et al.
TRENDS IN PLANT SCIENCE (2019)
One thousand plant transcriptomes and the phylogenomics of green plants
James H. Leebens-Mack et al.
NATURE (2019)
UniProt: a worldwide hub of protein knowledge
Alex Bateman et al.
NUCLEIC ACIDS RESEARCH (2019)
OrthoFinder: phylogenetic orthology inference for comparative genomics
David M. Emms et al.
GENOME BIOLOGY (2019)
Variation in genome size, cell and nucleus volume, chromosome number and rDNA loci among duckweeds
Phuong T. N. Hoang et al.
SCIENTIFIC REPORTS (2019)
PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics
Michiel Van Bel et al.
NUCLEIC ACIDS RESEARCH (2018)
Shining Light on the Function of NPH3/RPT2-Like Proteins in Phototropin Signaling
John M. Christie et al.
PLANT PHYSIOLOGY (2018)
Minimap2: pairwise alignment for nucleotide sequences
Heng Li
BIOINFORMATICS (2018)
The Circadian Clock Sets the Time of DNA Replication Licensing to Regulate Growth in Arabidopsis
Jorge Fung-Uceda et al.
DEVELOPMENTAL CELL (2018)
TANDEM ZINC-FINGER/PLUS3 Is a Key Component of Phytochrome A Signaling
Shaoman Zhang et al.
PLANT CELL (2018)
Footprints of parasitism in the genome of the parasitic flowering plant Cuscuta campestris
Alexander Vogel et al.
NATURE COMMUNICATIONS (2018)
Large-scale gene losses underlie the genome evolution of parasitic plant Cuscuta australis
Guiling Sun et al.
NATURE COMMUNICATIONS (2018)
FAR1-RELATED SEQUENCE (FRS) and FRS-RELATED FACTOR (FRF) Family Proteins in Arabidopsis Growth and Development
Lin Ma et al.
FRONTIERS IN PLANT SCIENCE (2018)
Generating a high-confidence reference genome map of the Greater Duckweed by integration of cytogenomic, optical mapping, and Oxford Nanopore technologies
Phuong N. T. Hoang et al.
PLANT JOURNAL (2018)
Fast and accurate de novo genome assembly from long uncorrected reads
Robert Vaser et al.
GENOME RESEARCH (2017)
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation
Sergey Koren et al.
GENOME RESEARCH (2017)
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper
Jaime Huerta-Cepas et al.
MOLECULAR BIOLOGY AND EVOLUTION (2017)
Dancing in the dark: darkness as a signal in plants
Adam Seluzicki et al.
PLANT CELL AND ENVIRONMENT (2017)
Comprehensive definition of genome features in Spirodela polyrhiza by high-depth physical mapping and short-read DNA sequencing strategies
Todd P. Michael et al.
PLANT JOURNAL (2017)
LAZY Genes Mediate the Effects of Gravity on Auxin Gradients and Plant Architecture
Takeshi Yoshihara et al.
PLANT PHYSIOLOGY (2017)
Evolution of Daily Gene Co-expression Patterns from Algae to Plants
Pedro de los Reyes et al.
FRONTIERS IN PLANT SCIENCE (2017)
The Arabidopsis thaliana Nuclear Factor Y Transcription Factors
Hang Zhao et al.
FRONTIERS IN PLANT SCIENCE (2017)
Transcription through the eye of a needle: daily and annual cyclic gene expression variation in Douglas-fir needles
Richard Cronn et al.
BMC GENOMICS (2017)
GenomeScope: fast reference-free genome profiling from short reads
Gregory W. Vurture et al.
BIOINFORMATICS (2017)
BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS
Katharina J. Hoff et al.
BIOINFORMATICS (2016)
Identification of Evening Complex Associated Proteins in Arabidopsis by Affinity Purification and Mass Spectrometry
He Huang et al.
MOLECULAR & CELLULAR PROTEOMICS (2016)
Simultaneous gene finding in multiple genomes
Stefanie Koenig et al.
BIOINFORMATICS (2016)
A simple method to control over-alignment in the MAFFT multiple sequence alignment program
Kazutaka Katoh et al.
BIOINFORMATICS (2016)
Comparative analysis of plant immune receptor architectures uncovers host proteins likely targeted by pathogens
Panagiotis F. Sarris et al.
BMC BIOLOGY (2016)
Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions
Taiji Kawakatsu et al.
CELL (2016)
How fast can angiosperms grow? Species and clonal diversity of growth rates in the genus Wolffia (Lemnaceae)
K. Sowjanya Sree et al.
ACTA PHYSIOLOGIAE PLANTARUM (2015)
Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.
Ryan R. Wick et al.
BIOINFORMATICS (2015)
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
Felipe A. Simao et al.
BIOINFORMATICS (2015)
Organizer-Derived WOX5 Signal Maintains Root Columella Stem Cells through Chromatin-Mediated Repression of CDF4 Expression
Limin Pi et al.
DEVELOPMENTAL CELL (2015)
The duckweed Wolffia microscopica: A unique aquatic monocot
K. Sowjanya Sree et al.
FLORA (2015)
Genetic characterization and barcoding of taxa in the genera Landoltia and Spirodela (Lemnaceae) by three plastidic markers and amplified fragment length polymorphism (AFLP)
Manuela Bog et al.
HYDROBIOLOGIA (2015)
HISAT: a fast spliced aligner with low memory requirements
Daehwan Kim et al.
NATURE METHODS (2015)
Fast and sensitive protein alignment using DIAMOND
Benjamin Buchfink et al.
NATURE METHODS (2015)
Assessment, validation and deployment strategy of a two-barcode protocol for facile genotyping of duckweed species
N. Borisjuk et al.
PLANT BIOLOGY (2015)
Relative in vitro growth rates of duckweeds (Lemnaceae) - the most rapidly growing higher plants
P. Ziegler et al.
PLANT BIOLOGY (2015)
Plant terpenes: defense responses, phylogenetic analysis, regulation and clinical applications
Bharat Singh et al.
3 BIOTECH (2015)
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy
David M. Emms et al.
GENOME BIOLOGY (2015)
InterProScan 5: genome-scale protein function classification
Philip Jones et al.
BIOINFORMATICS (2014)
Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads
Hongshan Jiang et al.
BMC BIOINFORMATICS (2014)
Duckweed in bloom: the 2nd International Conference on Duckweed Research and Applications heralds the return of a plant model for plant biology
Eric Lam et al.
PLANT MOLECULAR BIOLOGY (2014)
MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations
Michael S. Campbell et al.
PLANT PHYSIOLOGY (2014)
Functional and Evolutionary Analysis of the CASPARIAN STRIP MEMBRANE DOMAIN PROTEIN Family
Daniele Roppolo et al.
PLANT PHYSIOLOGY (2014)
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
Bruce J. Walker et al.
PLOS ONE (2014)
The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle
W. Wang et al.
NATURE COMMUNICATIONS (2014)
Light and gravity signals synergize in modulating plant development
Joshua P. Vandenbrink et al.
FRONTIERS IN PLANT SCIENCE (2014)
Architecture and evolution of a minute plant genome
Enrique Ibarra-Laclette et al.
NATURE (2013)
Oil palm genome sequence reveals divergence of interfertile species in Old and New Worlds
Rajinder Singh et al.
NATURE (2013)
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
Brian J. Haas et al.
NATURE PROTOCOLS (2013)
Hd16, a gene for casein kinase I, is involved in the control of rice flowering time by modulating the day-length response
Kiyosumi Hori et al.
PLANT JOURNAL (2013)
Fiji: an open-source platform for biological-image analysis
Johannes Schindelin et al.
NATURE METHODS (2012)
Fast gapped-read alignment with Bowtie 2
Ben Langmead et al.
NATURE METHODS (2012)
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
Cole Trapnell et al.
NATURE PROTOCOLS (2012)
Phytozome: a comparative platform for green plant genomics
David M. Goodstein et al.
NUCLEIC ACIDS RESEARCH (2012)
Preferential Retention of Circadian Clock Genes during Diploidization following Whole Genome Triplication in Brassica rapa
Ping Lou et al.
PLANT CELL (2012)
MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects
Carson Holt et al.
BMC BIOINFORMATICS (2011)
Isolation and analysis of high quality nuclear DNA with reduced organellar DNA for plant genome sequencing and resequencing
Kerry A. Lutz et al.
BMC BIOTECHNOLOGY (2011)
Cactus: Algorithms for genome multiple sequence alignment
Benedict Paten et al.
GENOME RESEARCH (2011)
Full-length transcriptome assembly from RNA-Seq data without a reference genome
Manfred G. Grabherr et al.
NATURE BIOTECHNOLOGY (2011)
The Mediator Complex in Plants: Structure, Phylogeny, and Expression Profiling of Representative Genes in a Dicot (Arabidopsis) and a Monocot (Rice) during Reproduction and Abiotic Stress
Saloni Mathur et al.
PLANT PHYSIOLOGY (2011)
Global Profiling of Rice and Poplar Transcriptomes Highlights Key Conserved Circadian-Controlled Pathways and cis-Regulatory Modules
Sergei A. Filichkin et al.
PLOS ONE (2011)
A Fasciclin-Like Arabinogalactan-Protein (FLA) Mutant of Arabidopsis thaliana, fla1, Shows Defects in Shoot Regeneration
Kim L. Johnson et al.
PLOS ONE (2011)
REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms
Fran Supek et al.
PLOS ONE (2011)
Orchestrated transcription of biological processes in the marine picoeukaryote Ostreococcus exposed to light/dark cycles
Annabelle Monnier et al.
BMC GENOMICS (2010)
JTK_CYCLE: An Efficient Nonparametric Algorithm for Detecting Rhythmic Components in Genome-Scale Data Sets
Michael E. Hughes et al.
JOURNAL OF BIOLOGICAL RHYTHMS (2010)
The CURLY LEAF Interacting Protein BLISTER Controls Expression of Polycomb-Group Target Genes and Cellular Differentiation of Arabidopsis thaliana
Nicole Schatlowski et al.
PLANT CELL (2010)
Comprehensive Analysis of CLE Polypeptide Signaling Gene Expression and Overexpression Activity in Arabidopsis
JiHyung Jun et al.
PLANT PHYSIOLOGY (2010)
The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program
Michel Schneider et al.
JOURNAL OF PROTEOMICS (2009)
MEME SUITE: tools for motif discovery and searching
Timothy L. Bailey et al.
NUCLEIC ACIDS RESEARCH (2009)
Using native and syntenically mapped cDNA alignments to improve de novo gene finding
Mario Stanke et al.
BIOINFORMATICS (2008)
The NAC Domain Transcription Factors FEZ and SOMBRERO Control the Orientation of Cell Division Plane in Arabidopsis Root Stem Cells
Viola Willemsen et al.
DEVELOPMENTAL CELL (2008)
Vein patterning screens and the defectively organized tributaries mutants in Arabidopsis thaliana
Jalean Joyanne Petricka et al.
PLANT JOURNAL (2008)
Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules
Todd P. Michael et al.
PLOS GENETICS (2008)
A zinc knuckle protein that negatively controls morning-specific growth in Arabidopsis thaliana
Olivier Loudet et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
A morning-specific phytohormone gene expression program underlying rhythmic plant growth
Todd P. Michael et al.
PLOS BIOLOGY (2008)
Conserved Daily Transcriptional Programs in Carica papaya
Anna Zdepski et al.
Tropical Plant Biology (2008)
Conserved factors regulate signalling in Arabidopsis thaliana shoot and root stem cell organizers
Ananda K. Sarkar et al.
NATURE (2007)
Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources
M Stanke et al.
BMC BIOINFORMATICS (2006)
Genome sequencing in microfabricated high-density picolitre reactors
M Margulies et al.
NATURE (2005)
Plant circadian clocks increase photosynthesis, growth, survival, and competitive advantage
AN Dodd et al.
SCIENCE (2005)
Enhanced fitness conferred by naturally occurring variation in the circadian clock
TP Michael et al.
SCIENCE (2003)
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
BJ Haas et al.
NUCLEIC ACIDS RESEARCH (2003)
Enhancer trapping reveals widespread circadian clock transcriptional control in Arabidopsis
TP Michael et al.
PLANT PHYSIOLOGY (2003)
Phase-specific circadian clock regulatory elements in Arabidopsis
TP Michael et al.
PLANT PHYSIOLOGY (2002)
Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis
KM Devos et al.
GENOME RESEARCH (2002)
The APRR3 component of the clock-associated APRR1/TOC1 quintet is phosphorylated by a novel protein kinase belonging to the WNK family, the gene for which is also transcribed rhythmically in Arabidopsis thaliana
M Murakami-Kojima et al.
PLANT AND CELL PHYSIOLOGY (2002)
Circadian rhythms confer a higher level of fitness to Arabidopsis plants
RM Green et al.
PLANT PHYSIOLOGY (2002)
Orchestrated transcription of key pathways in Arabidopsis by the circadian clock
SL Harmer et al.
SCIENCE (2000)
Comparative shoot development and evolution in the Lemnaceae
GD Lemon et al.
INTERNATIONAL JOURNAL OF PLANT SCIENCES (2000)