A Deluge of Complex Repeats: The Solanum Genome

MicroRNA mediates DNA methylation of target genes

(2014) Wangxiong Hu et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Identification and characterization of miRNAome in root, stem, leaf and tuber developmental stages of potato (Solanum tuberosum L.) by high-throughput sequencing

(2014) Nisha Lakhotia et al.   BMC PLANT BIOLOGY

The Peculiar Landscape of Repetitive Sequences in the Olive (Olea europaea L.) Genome

(2014) Elena Barghini et al.   Genome Biology and Evolution

miRNAting control of DNA methylation

(2014) Ashwani Jha et al.   JOURNAL OF BIOSCIENCES

Chromosomal organizations of major repeat families on potato (Solanum tuberosum) and further exploring in its sequenced genome

(2014) Xiaomin Tang et al.   MOLECULAR GENETICS AND GENOMICS

RNA-directed DNA methylation: an epigenetic pathway of increasing complexity

(2014) Marjori A. Matzke et al.   NATURE REVIEWS GENETICS

Boom-Bust Turnovers of Megabase-Sized Centromeric DNA in Solanum Species: Rapid Evolution of DNA Sequences Associated with Centromeres

(2014) H. Zhang et al.   PLANT CELL

Genome-Wide Comparative Analysis of 20 Miniature Inverted-Repeat Transposable Element Families in Brassica rapa and B. oleracea

(2014) Perumal Sampath et al.   PLoS One

Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization

(2014) C. Qin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

siRNAs from an X-linked satellite repeat promote X-chromosome recognition inDrosophila melanogaster

(2014) Debashish U. Menon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenetic relationships in Solanaceae and related species based on cpDNA sequence from plastid trnE-trnT region

(2014) D.M. Melotto-Passarin et al.   Crop Breeding and Applied Biotechnology

A phylogenetic framework for evolutionary study of the nightshades (Solanaceae): a dated 1000-tip tree

(2013) Tiina Särkinen et al.   BMC EVOLUTIONARY BIOLOGY

Comparative transcriptome analysis of tomato (Solanum lycopersicum) in response to exogenous abscisic acid

(2013) Yan Wang et al.   BMC GENOMICS

Characterization of a new high copy Stowaway family MITE, BRAMI-1 in Brassica genome

(2013) Perumal Sampath et al.   BMC PLANT BIOLOGY

Transposable element-associated microRNA hairpins produce 21-nt sRNAs integrated into typical microRNA pathways in rice

(2013) Fangqian Ou-Yang et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

TamiR1123 originated from a family of miniature inverted-repeat transposable elements (MITE) including one inserted in the Vrn-A1a promoter in wheat

(2013) Ming Yu et al.   PLANT SCIENCE

Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato

(2013) D. Koenig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Construction of Reference Chromosome-Scale Pseudomolecules for Potato: Integrating the Potato Genome with Genetic and Physical Maps

(2013) Sanjeev Kumar Sharma et al.   G3-Genes Genomes Genetics

Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs

(2013) Aurélie Kapusta et al.   PLoS Genetics

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution

(2013) Daniël P Melters et al.   GENOME BIOLOGY

Molecular diversity among seven Solanum (eggplant and relatives) species assessed by simple sequence repeats (SSRs) markers

(2012) O. T. Adeniji et al.   AFRICAN JOURNAL OF BIOTECHNOLOGY

Mutator-Like Elements with Multiple Long Terminal Inverted Repeats in Plants

(2012) Ann A. Ferguson et al.   COMPARATIVE AND FUNCTIONAL GENOMICS

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Analysis of the bread wheat genome using whole-genome shotgun sequencing

(2012) Rachel Brenchley et al.   NATURE

Repeatless and Repeat-Based Centromeres in Potato: Implications for Centromere Evolution

(2012) Z. Gong et al.   PLANT CELL

The sunflower (Helianthus annuusL.) genome reflects a recent history of biased accumulation of transposable elements

(2012) S. Evan Staton et al.   PLANT JOURNAL

Ds transposon is biased towards providing splice donor sites for exonization in transgenic tobacco

(2012) Kuo-Chan Huang et al.   PLANT MOLECULAR BIOLOGY

Diverse correlation patterns between microRNAs and their targets during tomato fruit development indicates different modes of microRNA actions

(2012) Sara Lopez-Gomollon et al.   PLANTA

Transposable elements domesticated and neofunctionalized by eukaryotic genomes

(2012) Ahmed M. Alzohairy et al.   PLASMID

miR-BAG: Bagging Based Identification of MicroRNA Precursors

(2012) Ashwani Jha et al.   PLoS One

Single Nucleotide Polymorphism Discovery in Cultivated Tomato via Sequencing by Synthesis

(2012) John P. Hamilton et al.   Plant Genome

Microarray Analysis of LTR Retrotransposon Silencing Identifies Hdac1 as a Regulator of Retrotransposon Expression in Mouse Embryonic Stem Cells

(2012) Judith Reichmann et al.   PLoS Computational Biology

Transposable elements reveal a stem cell-specific class of long noncoding RNAs

(2012) David Kelley et al.   GENOME BIOLOGY

Exonization of transposed elements: A challenge and opportunity for evolution

(2011) Jürgen Schmitz et al.   BIOCHIMIE

The regulatory epicenter of miRNAs

(2011) Ashwani Jha et al.   JOURNAL OF BIOSCIENCES

LigPlot+: Multiple Ligand–Protein Interaction Diagrams for Drug Discovery

(2011) Roman A. Laskowski et al.   Journal of Chemical Information and Modeling

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

Targeted Identification of Short Interspersed Nuclear Element Families Shows Their Widespread Existence and Extreme Heterogeneity in Plant Genomes

(2011) Torsten Wenke et al.   PLANT CELL

Profiling of short RNAs during fleshy fruit development reveals stage-specific sRNAome expression patterns

(2011) Irina Mohorianu et al.   PLANT JOURNAL

Gene Expression Changes in Phosphorus Deficient Potato (Solanum tuberosum L.) Leaves and the Potential for Diagnostic Gene Expression Markers

(2011) John P. Hammond et al.   PLoS One

Raptorx: Exploiting structure information for protein alignment by statistical inference

(2011) Jian Peng et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Organization and Evolution of Subtelomeric Satellite Repeats in the Potato Genome

(2011) Giovana A. Torres et al.   G3-Genes Genomes Genetics

Vive la différence: biogenesis and evolution of microRNAs in plants and animals

(2011) Michael J Axtell et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Assessment of genetic variation among commercial tomato (Solanum lycopersicum L) varieties using SSR markers and morphological characteristics

(2010) Yong-Sham Kwon et al.   Genes & Genomics

Miniature Inverted-Repeat Transposable Elements of Stowaway Are Active in Potato

(2010) Masaki Momose et al.   GENETICS

DNA Methylation Mediated by a MicroRNA Pathway

(2010) Liang Wu et al.   MOLECULAR CELL

The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl

(2010) A. Bombarely et al.   NUCLEIC ACIDS RESEARCH

miRBase: integrating microRNA annotation and deep-sequencing data

(2010) A. Kozomara et al.   NUCLEIC ACIDS RESEARCH

Characteristics of Transposable Element Exonization within Human and Mouse

(2010) Noa Sela et al.   PLoS One

Transposable elements and an epigenetic basis for punctuated equilibria

(2009) David W. Zeh et al.   BIOESSAYS

Evolution of ribosomal DNA-derived satellite repeat in tomato genome

(2009) Sung-Hwan Jo et al.   BMC PLANT BIOLOGY

Small RNAs as Guardians of the Genome

(2009) Colin D. Malone et al.   CELL

Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen

(2009) R. Keith Slotkin et al.   CELL

Retroelements and their impact on genome evolution and functioning

(2009) Elena Gogvadze et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

The Contribution of Transposable Elements to Expressed Coding Sequence in Arabidopsis thaliana

(2009) Steven Lockton et al.   JOURNAL OF MOLECULAR EVOLUTION

Many roads to maturity: microRNA biogenesis pathways and their regulation

(2009) Julia Winter et al.   NATURE CELL BIOLOGY

PlnTFDB: updated content and new features of the plant transcription factor database

(2009) Paulino Pérez-Rodríguez et al.   NUCLEIC ACIDS RESEARCH

Genome organization of the tomatosunlocus and characterization of the unusual retrotransposonRider

(2009) Ning Jiang et al.   PLANT JOURNAL

Characterization and distribution of retrotransposons and simple sequence repeats in the bovine genome

(2009) D. L. Adelson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

The Take and Give Between Retrotransposable Elements and their Hosts

(2008) Arthur Beauregard et al.   Annual Review of Genetics

The SGN comparative map viewer

(2008) L. A. Mueller et al.   BIOINFORMATICS

Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition

(2008) Wei Zhu et al.   BMC GENOMICS

FISH mapping and molecular organization of the major repetitive sequences of tomato

(2008) Song-Bin Chang et al.   CHROMOSOME RESEARCH

Transposable elements as drivers of genomic and biological diversity in vertebrates

(2008) Astrid Böhne et al.   CHROMOSOME RESEARCH

Different Strategies to Persist: The pogo-Like Lemi1 Transposon Produces Miniature Inverted-Repeat Transposable Elements or Typical Defective Elements in Different Plant Genomes

(2008) H. Guermonprez et al.   GENETICS

Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: New functional implications for MITEs

(2008) H. Kuang et al.   GENOME RESEARCH

Transposable elements and the evolution of regulatory networks

(2008) Cédric Feschotte   NATURE REVIEWS GENETICS

Dual coding of siRNAs and miRNAs by plant transposable elements

(2008) J. Piriyapongsa et al.   RNA

Drosophila telomeres: an exception providing new insights

(2007) James M. Mason et al.   BIOESSAYS