Comparative Study of Pine Reference Genomes Reveals Transposable Element Interconnected Gene Networks

Long Tandem Arrays of Cassandra Retroelements and Their Role in Genome Dynamics in Plants

(2020) Ruslan Kalendar et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Miniature inverted-repeat transposable elements (MITEs), derived insertional polymorphism as a tool of marker systems for molecular plant breeding

(2020) Venkatesh et al.   MOLECULAR BIOLOGY REPORTS

Variation of gene expression in plants is influenced by gene architecture and structural properties of promoters

(2019) Sanjukta Das et al.   PLoS One

Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases

(2019) Ole K Tørresen et al.   NUCLEIC ACIDS RESEARCH

Long Noncoding RNAs and Repetitive Elements: Junk or Intimate Evolutionary Partners?

(2019) Hyunmin Lee et al.   TRENDS IN GENETICS

Exploring the loblolly pine ( Pinus taeda L.) genome by BAC sequencing and Cot analysis

(2018) Dinum Perera et al.   GENE

Proliferation of Regulatory DNA Elements Derived from Transposable Elements in the Maize Genome

(2018) Hainan Zhao et al.   PLANT PHYSIOLOGY

Protein Kinases and Phosphatases of the Plastid and Their Potential Role in Starch Metabolism

(2018) Chris White-Gloria et al.   Frontiers in Plant Science

Genome Size Diversity and Its Impact on the Evolution of Land Plants

(2018) et al.   Genes

The Role of Transposable Elements in Speciation

(2018) Antonio Serrato-Capuchina et al.   Genes

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

miRBase: from microRNA sequences to function

(2018) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

The Arabidopsis RRM domain protein EDM3 mediates race-specific disease resistance by controlling H3K9me2-dependent alternative polyadenylation of RPP7 immune receptor transcripts

(2018) Yan Lai et al.   PLANT JOURNAL

Global identification of Arabidopsis lncRNAs reveals the regulation of MAF4 by a natural antisense RNA

(2018) Xinyue Zhao et al.   Nature Communications

LTR-retrotransposons in plants: Engines of evolution

(2017) Leonardo Galindo-González et al.   GENE

Retrotransposon distribution and copy number variation in gymnosperm genomes

(2017) Angelika Voronova et al.   Tree Genetics & Genomes

Gene Deletion in Barley Mediated by LTR-retrotransposon BARE

(2017) Yi Shang et al.   Scientific Reports

From Pine Cones to Read Clouds: Rescaffolding the Megagenome of Sugar Pine ( Pinus lambertiana )

(2017) Marc W. Crepeau et al.   G3-Genes Genomes Genetics

Miniature Inverted Repeat Transposable Element Insertions Provide a Source of Intron Length Polymorphism Markers in the Carrot (Daucus carota L.)

(2017) Katarzyna Stelmach et al.   Frontiers in Plant Science

Chromosome Evolution in Connection with Repetitive Sequences and Epigenetics in Plants

(2017) Shu-Fen Li et al.   Genes

DyNet: visualization and analysis of dynamic molecular interaction networks

(2016) Ivan H. Goenawan et al.   BIOINFORMATICS

Exome genotyping, linkage disequilibrium and population structure in loblolly pine (Pinus taeda L.)

(2016) Mengmeng Lu et al.   BMC GENOMICS

How retrotransposons shape genome regulation

(2016) Paolo Mita et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Sequence of the Sugar Pine Megagenome

(2016) Kristian A. Stevens et al.   GENETICS

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Small RNA and degradome deep sequencing reveals drought-and tissue-specific micrornas and their important roles in drought-sensitive and drought-tolerant tomato genotypes

(2016) Bilgin Candar-Cakir et al.   PLANT BIOTECHNOLOGY JOURNAL

Assessing the Gene Content of the Megagenome: Sugar Pine ( Pinus lambertiana )

(2016) Daniel Gonzalez-Ibeas et al.   G3-Genes Genomes Genetics

Sequence of the Sugar Pine Megagenome

(2016) Kristian A. Stevens et al.   GENETICS

Comparative Analysis of GC Content Variations in Plant Genomes

(2016) Ratnesh Singh et al.   Tropical Plant Biology

Draft genome of the living fossil Ginkgo biloba

(2016) Rui Guan et al.   GigaScience

LTR retrotransposons, handy hitchhikers of plant regulation and stress response

(2015) Marie-Angèle Grandbastien   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Conifer genomics and adaptation: at the crossroads of genetic diversity and genome function

(2015) Julien Prunier et al.   NEW PHYTOLOGIST

Epigenetic regulation of intragenic transposable elements impacts gene transcription in Arabidopsis thaliana

(2015) Tu N. Le et al.   NUCLEIC ACIDS RESEARCH

DNA Methylation within Transcribed Regions

(2015) Taiko K. To et al.   PLANT PHYSIOLOGY

Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress

(2015) Irina Makarevitch et al.   PLoS Genetics

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Plant Transposable Elements and Their Application to Genetic Analysis via High-throughput Sequencing Platform

(2015) Yuki Monden et al.   Horticulture Journal

The Role of Transposable Elements in the Origin and Evolution of MicroRNAs in Human

(2015) Sheng Qin et al.   PLoS One

Unique Features of the Loblolly Pine (Pinus taeda L.) Megagenome Revealed Through Sequence Annotation

(2014) J. L. Wegrzyn et al.   GENETICS

Sequencing and Assembly of the 22-Gb Loblolly Pine Genome

(2014) A. Zimin et al.   GENETICS

Widespread contribution of transposable elements to the innovation of gene regulatory networks

(2014) Vasavi Sundaram et al.   GENOME RESEARCH

Genomic Distribution of H3K9me2 and DNA Methylation in a Maize Genome

(2014) Patrick T. West et al.   PLoS One

Stress-induced transcriptional activation of retrotransposon-like sequences in the Scots pine (Pinus sylvestris L.) genome

(2014) Angelika Voronova et al.   Tree Genetics & Genomes

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies

(2014) David B Neale et al.   GENOME BIOLOGY

The Intertwining of Transposable Elements and Non-Coding RNAs

(2013) Michael Hadjiargyrou et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

TARE1, a Mutated Copia-Like LTR Retrotransposon Followed by Recent Massive Amplification in Tomato

(2013) Hao Yin et al.   PLoS One

An alternative polyadenylation mechanism coopted to the Arabidopsis RPP7 gene through intronic retrotransposon domestication

(2013) T. Tsuchiya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic structure and association mapping of adaptive and selective traits in the east Texas loblolly pine (Pinus taeda L.) breeding populations

(2013) Vikram E. Chhatre et al.   Tree Genetics & Genomes

When epigenetics meets alternative splicing: the roles of DNA methylation and GC architecture

(2013) Sahar Gelfman et al.   Epigenomics

Transposable Elements: An Abundant and Natural Source of Regulatory Sequences for Host Genes

(2012) Rita Rebollo et al.   Annual Review of Genetics

Cytokinin Signaling Networks

(2012) Ildoo Hwang et al.   Annual Review of Plant Biology

BEDOPS: high-performance genomic feature operations

(2012) Shane Neph et al.   BIOINFORMATICS

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research--an update

(2012) R. Peakall et al.   BIOINFORMATICS

Photoperiod- and thermo-sensitive genic male sterility in rice are caused by a point mutation in a novel noncoding RNA that produces a small RNA

(2012) Hai Zhou et al.   CELL RESEARCH

Diversity, classification and function of the plant protein kinase superfamily

(2012) M. D. Lehti-Shiu et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Retrotransposons Control Fruit-Specific, Cold-Dependent Accumulation of Anthocyanins in Blood Oranges

(2012) E. Butelli et al.   PLANT CELL

Genetic Diversity and Ecosystem Functioning in the Face of Multiple Stressors

(2012) Fabian Roger et al.   PLoS One

Functional and Structural Divergence of an Unusual LTR Retrotransposon Family in Plants

(2012) Dongying Gao et al.   PLoS One

Two-Component Elements Mediate Interactions between Cytokinin and Salicylic Acid in Plant Immunity

(2012) Cristiana T. Argueso et al.   PLoS Genetics

Families of transposable elements, population structure and the origin of species

(2011) Jerzy Jurka et al.   Biology Direct

Association genetics of carbon isotope discrimination, height and foliar nitrogen in a natural population of Pinus taeda L

(2011) W P Cumbie et al.   HEREDITY

Miniature Inverted-Repeat Transposable Elements (MITEs) Have Been Accumulated through Amplification Bursts and Play Important Roles in Gene Expression and Species Diversity in Oryza sativa

(2011) C. Lu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Identification of a functional transposon insertion in the maize domestication gene tb1

(2011) Anthony Studer et al.   NATURE GENETICS

Repetitive DNA and next-generation sequencing: computational challenges and solutions

(2011) Todd J. Treangen et al.   NATURE REVIEWS GENETICS

Dissecting Plant Genomes with the PLAZA Comparative Genomics Platform

(2011) M. Van Bel et al.   PLANT PHYSIOLOGY

A Novel Retrotransposon Inserted in the Dominant Vrn-B1 Allele Confers Spring Growth Habit in Tetraploid Wheat ( Triticum turgidum L.)

(2011) C.-G. Chu et al.   G3-Genes Genomes Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences

(2010) Allen Kovach et al.   BMC GENOMICS

Patterns of Population Structure and Environmental Associations to Aridity Across the Range of Loblolly Pine (Pinus taeda L., Pinaceae)

(2010) A. J. Eckert et al.   GENETICS

Analysis of plant diversity with retrotransposon-based molecular markers

(2010) R Kalendar et al.   HEREDITY

NONEXPRESSOR OF PATHOGENESIS-RELATED PROTEINS1 (NPR1) and some NPR1-related proteins are sensitive to salicylic acid

(2010) FELIX MAIER et al.   MOLECULAR PLANT PATHOLOGY

LINE-1 retrotransposons: mediators of somatic variation in neuronal genomes?

(2010) Tatjana Singer et al.   TRENDS IN NEUROSCIENCES

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genic non-coding microsatellites in the rice genome: characterization, marker design and use in assessing genetic and evolutionary relationships among domesticated groups

(2009) Swarup KUMAR Parida et al.   BMC GENOMICS

Chromatin organization marks exon-intron structure

(2009) Schraga Schwartz et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Evolutionary History and Stress Regulation of Plant Receptor-Like Kinase/Pelle Genes

(2009) M. D. Lehti-Shiu et al.   PLANT PHYSIOLOGY

Evolution of Genome Size and Complexity in Pinus

(2009) Alison M. Morse et al.   PLoS One

Mutational Biases and Selective Forces Shaping the Structure of Arabidopsis Genes

(2009) Salvatore Camiolo et al.   PLoS One

QuickGO: a user tutorial for the web-based Gene Ontology browser

(2009) Rachael P. Huntley et al.   Database-The Journal of Biological Databases and Curation

Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome

(2009) Fusheng Wei et al.   PLoS Genetics

Population, quantitative and comparative genomics of adaptation in forest trees

(2008) David B Neale et al.   CURRENT OPINION IN PLANT BIOLOGY

Transposable elements and the evolution of regulatory networks

(2008) Cédric Feschotte   NATURE REVIEWS GENETICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

The Vienna RNA Websuite

(2008) A. R. Gruber et al.   NUCLEIC ACIDS RESEARCH

Intergenic and Genic Sequence Lengths Have Opposite Relationships with Respect to Gene Expression

(2008) Juliette Colinas et al.   PLoS One

A Retrotransposon-Mediated Gene Duplication Underlies Morphological Variation of Tomato Fruit

(2008) H. Xiao et al.   SCIENCE