The chromosome-level genome of Eucommia ulmoides provides insights into sex differentiation and α-linolenic acid biosynthesis

The pineapple MADS-box gene family and the evolution of early monocot flower

(2021) Juan Hu et al.   Scientific Reports

Transcriptomic analysis of α-linolenic acid content and biosynthesis in Paeonia ostii fruits and seeds

(2021) Shui-Yan Yu et al.   BMC GENOMICS

Identification and analysis of the FAD gene family in walnuts (Juglans regia L.) based on transcriptome data

(2020) Kai Liu et al.   BMC GENOMICS

RepeatModeler2 for automated genomic discovery of transposable element families

(2020) Jullien M. Flynn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MADS-Box and bHLH Transcription Factors Coordinate Transmitting Tract Development in Arabidopsis thaliana

(2020) Maurizio Di Marzo et al.   Frontiers in Plant Science

Molecular Sex Identification in the Hardy Rubber Tree (Eucommia ulmoides Oliver) via ddRAD Markers

(2020) Wencai Wang et al.   International Journal of Genomics

Quaternary land bridges have not been universal conduits of gene flow

(2020) Emilie Cros et al.   MOLECULAR ECOLOGY

Measuring and interpreting transposable element expression

(2020) Sophie Lanciano et al.   NATURE REVIEWS GENETICS

The genetic basis of sex determination in grapes

(2020) Mélanie Massonnet et al.   Nature Communications

Differential Activation of Partially Redundant Δ9 Stearoyl-ACP Desaturase Genes is Critical for Omega-9 Monounsaturated Fatty Acid Biosynthesis During Seed Development in Arabidopsis

(2020) Sami Kazaz et al.   PLANT CELL

Evolutionary Variation in MADS-box Dimerization Affects Floral Development and Protein Abundance in Maize

(2020) Maria Jazmin Abraham-Juarez et al.   PLANT CELL

Deciphering Hi-C: from 3D genome to function

(2019) Siyuan Kong et al.   CELL BIOLOGY AND TOXICOLOGY

Ethnobotany, Phytochemistry and Pharmacological Properties of Eucommia ulmoides: A Review

(2019) Chao-Yong Wang et al.   AMERICAN JOURNAL OF CHINESE MEDICINE

OsMADS18, a membrane-bound MADS-box transcription factor, modulates plant architecture and the abscisic acid response in rice

(2019) Xiaoming Yin et al.   JOURNAL OF EXPERIMENTAL BOTANY

Divergent Functional Diversification Patterns in the SEP/AGL6/AP1 MADS-Box Transcription Factor Superclade

(2019) Patrice Morel et al.   PLANT CELL

Dissecting the Function of MADS-Box Transcription Factors in Orchid Reproductive Development

(2019) Zhi Wei Norman Teo et al.   Frontiers in Plant Science

The water lily genome and the early evolution of flowering plants

(2019) Liangsheng Zhang et al.   NATURE

Transcriptomic analysis of Perilla frutescens seed to insight into the biosynthesis and metabolic of unsaturated fatty acids

(2018) BingNan Liao et al.   BMC GENOMICS

De novo transcriptome assembly of the eight major organs of Sacha Inchi (Plukenetia volubilis) and the identification of genes involved in α-linolenic acid metabolism

(2018) Xiao-Di Hu et al.   BMC GENOMICS

Contribution of transposable elements in the plant's genome

(2018) Mahbod Sahebi et al.   GENE

Eucommia ulmoides Oliver: A Potential Feedstock for Bioactive Products

(2018) Ming-Qiang Zhu et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Characterization of a New α-Linolenic Acid-Rich Oil: Eucommia ulmoides Seed Oil

(2018) Zhen-shan Zhang et al.   JOURNAL OF FOOD SCIENCE

The Hardy Rubber Tree Genome Provides Insights into the Evolution of Polyisoprene Biosynthesis

(2018) Ta-na Wuyun et al.   Molecular Plant

Whole-Genome Duplication and Plant Macroevolution

(2018) James W. Clark et al.   TRENDS IN PLANT SCIENCE

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Identification of the Sex-Biased Gene Expression and Putative Sex-Associated Genes in Eucommia ulmoides Oliver Using Comparative Transcriptome Analyses

(2017) Wencai Wang et al.   MOLECULES

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

Ancestors of modern plant crops

(2016) Jérôme Salse   CURRENT OPINION IN PLANT BIOLOGY

Ancient WGD events as drivers of key innovations in angiosperms

(2016) Pamela S Soltis et al.   CURRENT OPINION IN PLANT BIOLOGY

Characterization of Glycolytic Pathway Genes Using RNA-Seq in Developing Kernels of Eucommia ulmoides

(2016) Yanzhi Feng et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

(2016) Todd M. Lowe et al.   NUCLEIC ACIDS RESEARCH

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

(2016) Neva C. Durand et al.   Cell Systems

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Leaf oil bodies are subcellular factories producing antifungal oxylipins

(2015) Takashi L Shimada et al.   CURRENT OPINION IN PLANT BIOLOGY

Whole genome duplications in plants: an overview fromArabidopsis

(2015) Juan Carlos del Pozo et al.   JOURNAL OF EXPERIMENTAL BOTANY

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

α-Linolenic acid: Nutraceutical, pharmacological and toxicological evaluation

(2014) Kyu-Bong Kim et al.   FOOD AND CHEMICAL TOXICOLOGY

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary

(2014) Kevin Vanneste et al.   GENOME RESEARCH

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Sexual dimorphism in flowering plants

(2012) Spencer C.H. Barrett et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

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

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Jasmonate Biochemical Pathway

(2010) A. Gfeller et al.   Science Signaling

KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies

(2010) Dapeng Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Floral organ identity: 20 years of ABCs

(2009) Barry Causier et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY