Research graph
References from Traces of transposable elements in genome dark matter co-opted by flowering gene regulation networks. Local targets link to admitted publications; unresolved targets remain external evidence.
Evolution of a Polymorphic Regulatory Element in Interferon-γ Through Transposition and Mutation
10.1093/oxfordjournals.molbev.a004145 · 2002 · External reference
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
10.1093/nar/25.17.3389 · 1997 · External reference
MEME SUITE: tools for motif discovery and searching
10.1093/nar/gkp335 · 2009 · External reference
Repbase Update, a database of repetitive elements in eukaryotic genomes
10.1186/s13100-015-0041-9 · 2015 · External reference
Network biology: understanding the cell's functional organization
10.1038/nrg1272 · 2004 · External reference
Transcriptional regulatory networks inArabidopsis thalianaduring single and combined stresses
10.1093/nar/gkv1463 · 2016 · External reference
A distal enhancer and an ultraconserved exon are derived from a novel retroposon
10.1038/nature04696 · 2006 · External reference
Geminivirus AL2 and L2 Proteins Suppress Transcriptional Gene Silencing and Cause Genome-Wide Reductions in Cytosine Methylation
10.1128/jvi.01771-08 · 2009 · External reference
Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets
10.1016/j.ygeno.2008.01.005 · 2008 · External reference
An Arabidopsis hAT-like transposase is essential for plant development
10.1038/nature03667 · 2005 · External reference
Architecture of gene regulatory networks controlling flower development in Arabidopsis thaliana
10.1038/s41467-018-06772-3 · 2018 · External reference
Birth of a chimeric primate gene by capture of the transposase gene from a mobile element
10.1073/pnas.0601161103 · 2006 · External reference
Darwin's abominable mystery: Insights from a supertree of the angiosperms
10.1073/pnas.0308127100 · 2004 · External reference
Accelerated Profile HMM Searches
10.1371/journal.pcbi.1002195 · 2011 · External reference
Unresolved reference
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The Pfam protein families database in 2019
10.1093/nar/gky995 · 2018 · External reference
Plant transposable elements: where genetics meets genomics
10.1038/nrg793 · 2002 · External reference
Considering Transposable Element Diversification in De Novo Annotation Approaches
10.1371/journal.pone.0016526 · 2011 · External reference
Stress activation and genomic impact of Tnt1 retrotransposons in Solanaceae
10.1159/000084957 · 2005 · External reference
An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions
10.1038/ng.2684 · 2013 · External reference
A Functional and Evolutionary Perspective on Transcription Factor Binding in Arabidopsis thaliana
10.1105/tpc.114.130591 · 2014 · External reference
PASTEC: An Automatic Transposable Element Classification Tool
10.1371/journal.pone.0091929 · 2014 · External reference
A Time-Calibrated Road Map of Brassicaceae Species Radiation and Evolutionary History
10.1105/tpc.15.00482 · 2015 · External reference
Cross species selection scans identify components of C4 photosynthesis in the grasses
10.1093/jxb/erw256 · 2017 · External reference
Resolution of Brassicaceae Phylogeny Using Nuclear Genes Uncovers Nested Radiations and Supports Convergent Morphological Evolution
10.1093/molbev/msv226 · 2016 · External reference
An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress
10.1038/nature09861 · 2011 · External reference
Regulation of heterochromatic DNA replication by histone H3 lysine 27 methyltransferases
10.1038/nature09290 · 2010 · External reference
De Novo Annotation of Transposable Elements: Tackling the Fat Genome Issue
10.1109/jproc.2016.2590833 · 2017 · External reference
Censor—a program for identification and elimination of repetitive elements from DNA sequences
10.1016/s0097-8485(96)80013-1 · 1996 · External reference
10.1023/a:1016072014259
10.1023/a:1016072014259 · 2002 · External reference
Control of FWA gene silencing in Arabidopsis thaliana by SINE-related direct repeats
10.1111/j.1365-313x.2006.02936.x · 2007 · External reference
Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor
10.1186/1471-2105-7-474 · 2006 · External reference
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
10.1101/gr.1224503 · 2003 · External reference
How important are transposons for plant evolution?
10.1038/nrg3374 · 2013 · External reference
Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis
10.1016/j.cell.2008.03.029 · 2008 · External reference
siRNAs targeting an intronic transposon in the regulation of natural flowering behavior in Arabidopsis
10.1101/gad.1217304 · 2004 · External reference
Thousands of human mobile element fragments undergo strong purifying selection near developmental genes
10.1073/pnas.0611223104 · 2007 · External reference
Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for natural antisense transcript production
10.1111/tpj.12017 · 2013 · External reference
MEME-ChIP: motif analysis of large DNA datasets
10.1093/bioinformatics/btr189 · 2011 · External reference
Angiosperm diversification through time
10.3732/ajb.0800060 · 2009 · External reference
Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana
10.1038/ncomms5104 · 2014 · External reference
10.1023/a:1005727132202
10.1023/a:1005727132202 · 1997 · External reference
Database indexing for production MegaBLAST searches
10.1093/bioinformatics/btn322 · 2008 · External reference
Unexpected consequences of a sudden and massive transposon amplification on rice gene expression
10.1038/nature08479 · 2009 · External reference
Genic and Global Functions for Paf1C in Chromatin Modification and Gene Expression in Arabidopsis
10.1371/journal.pgen.1000077 · 2008 · External reference
Combined Evidence Annotation of Transposable Elements in Genome Sequences
10.1371/journal.pcbi.0010022 · 2005 · External reference
Detection of New Transposable Element Families in Drosophila melanogaster and Anopheles gambiae Genomes
10.1007/s00239-003-0007-2 · 2003 · External reference
EMBOSS: The European Molecular Biology Open Software Suite
10.1016/s0168-9525(00)02024-2 · 2000 · External reference
The B73 Maize Genome: Complexity, Diversity, and Dynamics
10.1126/science.1178534 · 2009 · External reference
Unresolved reference
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Major-Effect Alleles at Relatively Few Loci Underlie Distinct Vernalization and Flowering Variation in Arabidopsis Accessions
10.1371/journal.pone.0019949 · 2011 · External reference
Inhibition of RNA polymerase II allows controlled mobilisation of retrotransposons for plant breeding
10.1186/s13059-017-1265-4 · 2017 · External reference
Arabidopsis TFL2/LHP1 Specifically Associates with Genes Marked by Trimethylation of Histone H3 Lysine 27
10.1371/journal.pgen.0030086 · 2007 · External reference
Inference of Transcriptional Networks in Arabidopsis through Conserved Noncoding Sequence Analysis
10.1105/tpc.114.127001 · 2014 · External reference
Effect of Divergence Time and Recombination Rate on Molecular Evolution of Drosophila INE-1 Transposable Elements and Other Candidates for Neutrally Evolving Sites
10.1007/s00239-007-9028-6 · 2007 · External reference
High-Resolution Chromatin Dynamics during a Yeast Stress Response
10.1016/j.molcel.2015.02.002 · 2015 · External reference
Impact of transposable elements on genome structure and evolution in bread wheat
10.1186/s13059-018-1479-0 · 2018 · External reference
Whole-Genome Analysis of Histone H3 Lysine 27 Trimethylation in Arabidopsis
10.1371/journal.pbio.0050129 · 2007 · External reference
S-MART, A Software Toolbox to Aid RNA-seq Data Analysis
10.1371/journal.pone.0025988 · 2011 · External reference
