Related references
Note: Only part of the references are listed.ksrates: positioning whole-genome duplications relative to speciation events in KS distributions
Cecilia Sensalari et al.
BIOINFORMATICS (2022)
The flying spider-monkey tree fern genome provides insights into fern evolution and arborescence
Xiong Huang et al.
NATURE PLANTS (2022)
The nearly complete genome of Ginkgo biloba illuminates gymnosperm evolution
Hailin Liu et al.
NATURE PLANTS (2021)
Charting the genomic landscape of seed-free plants
Peter Szovenyi et al.
NATURE PLANTS (2021)
Recurrent genome duplication events likely contributed to both the ancient and recent rise of ferns
Chien-Hsun Huang et al.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY (2020)
Jasmonic Acid Signaling Pathway in Response to Abiotic Stresses in Plants
Md. Sarafat Ali et al.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)
GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes
T. Rhyker Ranallo-Benavidez et al.
NATURE COMMUNICATIONS (2020)
Gapless assembly of maize chromosomes using long-read technologies
Jianing Liu et al.
GENOME BIOLOGY (2020)
Genomes of Subaerial Zygnematophyceae Provide Insights into Land Plant Evolution
Shifeng Cheng et al.
CELL (2019)
Limonin: A Review of Its Pharmacology, Toxicity, and Pharmacokinetics
Shunming Fan et al.
MOLECULES (2019)
One thousand plant transcriptomes and the phylogenomics of green plants
James H. Leebens-Mack et al.
NATURE (2019)
Assembly of chromosome-scale contigs by efficiently resolving repetitive sequences with long reads
Huilong Du et al.
NATURE COMMUNICATIONS (2019)
EMS1 and BRI1 control separate biological processes via extracellular domain diversity and intracellular domain conservation
Bowen Zheng et al.
NATURE COMMUNICATIONS (2019)
wgd-simple command line tools for the analysis of ancient whole-genome duplications
Arthur Zwaenepoel et al.
BIOINFORMATICS (2019)
PubChem 2019 update: improved access to chemical data
Sunghwan Kim et al.
NUCLEIC ACIDS RESEARCH (2019)
The C-Fern (Ceratopteris richardit) genome: insights into plant genome evolution with the first partial homosporous fern genome assembly
D. Blaine Marchant et al.
SCIENTIFIC REPORTS (2019)
OrthoFinder: phylogenetic orthology inference for comparative genomics
David M. Emms et al.
GENOME BIOLOGY (2019)
Gene3D: Extensive prediction of globular domains in proteins
Tony E. Lewis et al.
NUCLEIC ACIDS RESEARCH (2018)
20 years of the SMART protein domain annotation resource
Ivica Letunic et al.
NUCLEIC ACIDS RESEARCH (2018)
LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons
Shujun Ou et al.
PLANT PHYSIOLOGY (2018)
fastp: an ultra-fast all-in-one FASTQ preprocessor
Shifu Chen et al.
BIOINFORMATICS (2018)
Ligand-receptor co-evolution shaped the jasmonate pathway in land plants
Isabel Monte et al.
NATURE CHEMICAL BIOLOGY (2018)
Jasmonic and salicylic acid response in the fern Azolla filiculoides and its cyanobiont
Sophie de Vries et al.
PLANT CELL AND ENVIRONMENT (2018)
LEA Proteins and the Evolution of the WHy Domain
Jasmin Mertens et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2018)
Fern genomes elucidate land plant evolution and cyanobacterial symbioses
Fay-Wei Li et al.
NATURE PLANTS (2018)
KEGG: new perspectives on genomes, pathways, diseases and drugs
Minoru Kanehisa et al.
NUCLEIC ACIDS RESEARCH (2017)
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation
Sergey Koren et al.
GENOME RESEARCH (2017)
Identification of Jasmonic Acid and Jasmonoyl-Isoleucine, and Characterization of AOS, AOC, OPR and JAR1 in the Model Lycophyte Selaginella moellendorffii
Putri Pratiwi et al.
PLANT AND CELL PHYSIOLOGY (2017)
LEC1 sequentially regulates the transcription of genes involved in diverse developmental processes during seed development
Julie M. Pelletier et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds
Olga Dudchenko et al.
SCIENCE (2017)
Large-scale phylogenomic analysis resolves a backbone phylogeny in ferns
Hui Shen et al.
GIGASCIENCE (2017)
Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome
John L. Bowman et al.
CELL (2017)
Field Guide to Plant Model Systems
Caren Chang et al.
CELL (2016)
iTAK: A Program for Genome-wide Prediction and Classification of Plant Transcription Factors, Transcriptional Regulators, and Protein Kinases
Yi Zheng et al.
MOLECULAR PLANT (2016)
Genome evolution of ferns: evidence for relative stasis of genome size across the fern phylogeny
James Clark et al.
NEW PHYTOLOGIST (2016)
Deciphering and modifying LAFL transcriptional regulatory network in seed for improving yield and quality of storage compounds
Abdelhak Fatihi et al.
PLANT SCIENCE (2016)
Chloroplast and nuclear photorelocation movements
Masamitsu Wada
PROCEEDINGS OF THE JAPAN ACADEMY SERIES B-PHYSICAL AND BIOLOGICAL SCIENCES (2016)
A community-derived classification for extant lycophytes and ferns
Eric Schuettpelz et al.
JOURNAL OF SYSTEMATICS AND EVOLUTION (2016)
Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments
Neva C. Durand et al.
CELL SYSTEMS (2016)
Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom
Neva C. Durand et al.
CELL SYSTEMS (2016)
The arabidopsis information resource: Making and mining the gold standard annotated reference plant genome
Tanya Z. Berardini et al.
GENESIS (2015)
An Exploration into Fern Genome Space
Paul G. Wolf et al.
GENOME BIOLOGY AND EVOLUTION (2015)
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)
Repbase Update, a database of repetitive elements in eukaryotic genomes
Weidong Bao et al.
MOBILE DNA (2015)
The Chromosome Counts Database (CCDB) - a community resource of plant chromosome numbers
Anna Rice et al.
NEW PHYTOLOGIST (2015)
InterProScan 5: genome-scale protein function classification
Philip Jones et al.
BIOINFORMATICS (2014)
On the Origin and Evolution of Plant Brassinosteroid Receptor Kinases
Hao Wang et al.
JOURNAL OF MOLECULAR EVOLUTION (2014)
iPfam: a database of protein family and domain interactions found in the Protein Data Bank
Robert D. Finn et al.
NUCLEIC ACIDS RESEARCH (2014)
Deciphering key features in protein structures with the new ENDscript server
Xavier Robert et al.
NUCLEIC ACIDS RESEARCH (2014)
Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation
Koichi Hori et al.
NATURE COMMUNICATIONS (2014)
Seed-Development Programs: A Systems Biology-Based Comparison Between Dicots and Monocots
Nese Sreenivasulu et al.
ANNUAL REVIEW OF PLANT BIOLOGY, VOL 64 (2013)
The Norway spruce genome sequence and conifer genome evolution
Bjorn Nystedt et al.
NATURE (2013)
LEAFY COTYLEDON1, a Key Regulator of Seed Development, Is Expressed in Vegetative and Sexual Propagules of Selaginella moellendorffii
Ryan C. Kirkbride et al.
PLOS ONE (2013)
The Amborella Genome and the Evolution of Flowering Plants
Victor A. Albert et al.
SCIENCE (2013)
Overview of the morphology, anatomy, and ontogeny of Adiantum capillus-veneris: An experimental system to study the development of ferns
Xia Li et al.
JOURNAL OF SYSTEMATICS AND EVOLUTION (2013)
Biosynthesis of allene oxides in Physcomitrella patens
Julia Scholz et al.
BMC PLANT BIOLOGY (2012)
i-ADHoRe 3.0-fast and sensitive detection of genomic homology in extremely large data sets
Sebastian Proost et al.
NUCLEIC ACIDS RESEARCH (2012)
MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity
Yupeng Wang et al.
NUCLEIC ACIDS RESEARCH (2012)
A fast, lock-free approach for efficient parallel counting of occurrences of k-mers
Guillaume Marcais et al.
BIOINFORMATICS (2011)
The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants
Jo Ann Banks et al.
SCIENCE (2011)
Late embryogenesis abundant proteins Versatile players in the plant adaptation to water limiting environments
Yadira Olvera-Carrillo et al.
PLANT SIGNALING & BEHAVIOR (2011)
EARLY RESPONSIVE to DEHYDRATION 15, a new transcription factor that integrates stress signaling pathways
Murilo S. Alves et al.
PLANT SIGNALING & BEHAVIOR (2011)
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
Mark D. Robinson et al.
BIOINFORMATICS (2010)
FastTree 2-Approximately Maximum-Likelihood Trees for Large Alignments
Morgan N. Price et al.
PLOS ONE (2010)
BLAST plus : architecture and applications
Christiam Camacho et al.
BMC BIOINFORMATICS (2009)
The genome of the cucumber, Cucumis sativus L.
Sanwen Huang et al.
NATURE GENETICS (2009)
Seed Dehydration and the Establishment of Desiccation Tolerance During Seed Maturation is Altered in the Arabidopsis thaliana Mutant atem6-1
Alicia J. Manfre et al.
PLANT AND CELL PHYSIOLOGY (2009)
VH1/BRL2 receptor-like kinase interacts with vascular-specific adaptor proteins VIT and VIK to influence leaf venation
Teresa Ceserani et al.
PLANT JOURNAL (2009)
A rapid wound signal activates the systemic synthesis of bioactive jasmonates in Arabidopsis
Abraham J. K. Koo et al.
PLANT JOURNAL (2009)
WGCNA: an R package for weighted correlation network analysis
Peter Langfelder et al.
BMC BIOINFORMATICS (2008)
LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons
David Ellinghaus et al.
BMC BIOINFORMATICS (2008)
Duplication and functional diversification of HAP3 genes leading to the origin of the seed-developmental regulatory gene, LEAFY COTYLEDON1 (LEC1), in nonseed plant genomes
Zengyan Xie et al.
MOLECULAR BIOLOGY AND EVOLUTION (2008)
LECs go crazy in embryo development
Siobhan A. Braybrook et al.
TRENDS IN PLANT SCIENCE (2008)
The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants
Stefan A. Rensing et al.
SCIENCE (2008)
The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
Olivier Jaillon et al.
NATURE (2007)
PAML 4: Phylogenetic analysis by maximum likelihood
Ziheng Yang
MOLECULAR BIOLOGY AND EVOLUTION (2007)
LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons
Zhao Xu et al.
NUCLEIC ACIDS RESEARCH (2007)
KAAS: an automatic genome annotation and pathway reconstruction server
Yuki Moriya et al.
NUCLEIC ACIDS RESEARCH (2007)
Advantages of combined transmembrane topology and signal peptide prediction -: the Phobius web server
Lukas Kaell et al.
NUCLEIC ACIDS RESEARCH (2007)
Phototropins and neochrome1 mediate nuclear movement in the fern Adiantum capillus-veneris
Hidenori Tsuboi et al.
PLANT AND CELL PHYSIOLOGY (2007)
Evaluation of fern and moss protein-based defenses against phytophagous insects
K Markham et al.
INTERNATIONAL JOURNAL OF PLANT SCIENCES (2006)
LEAFY COTYLEDON1 controls seed storage protein genes through its regulation of FUSCA3 and ABSCISIC ACID INSENSITIVE3
Y Kagaya et al.
PLANT AND CELL PHYSIOLOGY (2005)
The Genomes of Oryza sativa:: A history of duplications
J Yu et al.
PLOS BIOLOGY (2005)
Coronalon:: a powerful tool in plant stress physiology
G Schüler et al.
FEBS LETTERS (2004)
MUSCLE: multiple sequence alignment with high accuracy and high throughput
RC Edgar
NUCLEIC ACIDS RESEARCH (2004)
BRL1 and BRL3 are novel brassinosteroid receptors that function in vascular differentiation in Arabidopsis
A Caño-Delgado et al.
DEVELOPMENT (2004)
Comparative analysis of the receptor-like kinase family in Arabidopsis and rice
SH Shiu et al.
PLANT CELL (2004)
Mechanism of toxicity in rotenone models of Parkinson's disease
TB Sherer et al.
JOURNAL OF NEUROSCIENCE (2003)
Cytoscape: A software environment for integrated models of biomolecular interaction networks
P Shannon et al.
GENOME RESEARCH (2003)
An efficient algorithm for large-scale detection of protein families
AJ Enright et al.
NUCLEIC ACIDS RESEARCH (2002)
Effects of desiccation on photosynthesis pigments and the ELIP-like dsp 22 protein complexes in the resurrection plant Craterostigma plantagineum
JM Alamillo et al.
PLANT SCIENCE (2001)
Horsetails and ferns are a monophyletic group and the closest living relatives to seed plants
KM Pryer et al.
NATURE (2001)
Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
A Krogh et al.
JOURNAL OF MOLECULAR BIOLOGY (2001)
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
S Kaul et al.
NATURE (2000)
Differential gene expression in response to mechanical wounding and insect feeding in Arabidopsis
P Reymond et al.
PLANT CELL (2000)
The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
A Bairoch et al.
NUCLEIC ACIDS RESEARCH (2000)