Recurrent evolution of heat-responsiveness in Brassicaceae COPIA elements

[1]  Sudhir Kumar,et al.  MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. , 2016, Molecular biology and evolution.

[2]  P. Dear,et al.  Comparative Genome Analysis Reveals Divergent Genome Size Evolution in a Carnivorous Plant Genus , 2015, The plant genome.

[3]  Detlef Weigel,et al.  Improving the Annotation of Arabidopsis lyrata Using RNA-Seq Data , 2015, PloS one.

[4]  T. Baubec,et al.  Repair of DNA Damage Induced by the Cytidine Analog Zebularine Requires ATR and ATM in Arabidopsis[OPEN] , 2015, Plant Cell.

[5]  K. Fal,et al.  HISTONE DEACETYLASE6 Controls Gene Expression Patterning and DNA Methylation-Independent Euchromatic Silencing1[OPEN] , 2015, Plant Physiology.

[6]  M. Grandbastien LTR retrotransposons, handy hitchhikers of plant regulation and stress response. , 2015, Biochimica et biophysica acta.

[7]  M. Zytnicki,et al.  Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation , 2015, Nature Plants.

[8]  K. Fal,et al.  HISTONE DEACETYLASE 6 Controls Gene Expression Patterning and DNA Methylation-Independent Euchromatic Silencing 1 , 2015 .

[9]  D. Weigel,et al.  Evolution of DNA Methylation Patterns in the Brassicaceae is Driven by Differences in Genome Organization , 2014, PLoS genetics.

[10]  M. Matzke,et al.  RNA-directed DNA methylation: an epigenetic pathway of increasing complexity , 2014, Nature Reviews Genetics.

[11]  T. Korves,et al.  Lagging adaptation to warming climate in Arabidopsis thaliana , 2014, Proceedings of the National Academy of Sciences.

[12]  T. Baubec,et al.  Meristem‐specific expression of epigenetic regulators safeguards transposon silencing in Arabidopsis , 2014, EMBO reports.

[13]  Chun-Hsin Liu,et al.  Drugs for Plant Chromosome and Chromatin Research , 2014, Cytogenetic and Genome Research.

[14]  Nicole Lettner,et al.  How a Retrotransposon Exploits the Plant's Heat Stress Response for Its Activation , 2014, PLoS genetics.

[15]  A. Marchais,et al.  Reconstructing de novo silencing of an active plant retrotransposon , 2013, Nature Genetics.

[16]  Mathieu Blanchette,et al.  The Capsella rubella genome and the genomic consequences of rapid mating system evolution , 2013, Nature Genetics.

[17]  S. Tsukahara,et al.  Evolution of the ONSEN retrotransposon family activated upon heat stress in Brassicaceae. , 2013, Gene.

[18]  D. Coleman-Derr,et al.  The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin , 2013, Cell.

[19]  Simon Prochnik,et al.  The Reference Genome of the Halophytic Plant Eutrema salsugineum , 2013, Front. Plant Sci..

[20]  Cole Trapnell,et al.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.

[21]  O. Mittelsten Scheid,et al.  Epigenetic responses to stress: triple defense? , 2012, Current opinion in plant biology.

[22]  M. P. Guerreiro,et al.  What makes transposable elements move in the Drosophila genome? , 2011, Heredity.

[23]  David M. Goodstein,et al.  Phytozome: a comparative platform for green plant genomics , 2011, Nucleic Acids Res..

[24]  Damon Lisch,et al.  How important are transposons for plant evolution? , 2012, Nature Reviews Genetics.

[25]  Huy Q. Dinh,et al.  Genetic Rearrangements Can Modify Chromatin Features at Epialleles , 2011, PLoS genetics.

[26]  H. Sakurai,et al.  Diversity in DNA recognition by heat shock transcription factors (HSFs) from model organisms , 2011, FEBS letters.

[27]  E. Bucher,et al.  An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress , 2011, Nature.

[28]  Richard M. Clark,et al.  The Arabidopsis lyrata genome sequence and the basis of rapid genome size change , 2011, Nature Genetics.

[29]  H. Sakurai,et al.  Novel aspects of heat shock factors: DNA recognition, chromatin modulation and gene expression , 2010, The FEBS journal.

[30]  O. Mathieu,et al.  Stress-Induced Activation of Heterochromatic Transcription , 2010, PLoS genetics.

[31]  Huy Q. Dinh,et al.  Epigenetic Regulation of Repetitive Elements Is Attenuated by Prolonged Heat Stress in Arabidopsis[W][OA] , 2010, Plant Cell.

[32]  Martin Krzywinski,et al.  Fast Diploidization in Close Mesopolyploid Relatives of Arabidopsis[W][OA] , 2010, Plant Cell.

[33]  W. Huber,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .

[34]  Julie A. Law,et al.  Establishing, maintaining and modifying DNA methylation patterns in plants and animals , 2010, Nature Reviews Genetics.

[35]  Aaron R. Quinlan,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2022 .

[36]  E. Bucher,et al.  MOM1 and Pol‐IV/V interactions regulate the intensity and specificity of transcriptional gene silencing , 2010, The EMBO journal.

[37]  Peter Dalgaard,et al.  R Development Core Team (2010): R: A language and environment for statistical computing , 2010 .

[38]  D. Weigel,et al.  Selective epigenetic control of retrotransposition in Arabidopsis , 2009, Nature.

[39]  Heribert Hirt,et al.  Transgenerational Stress Memory Is Not a General Response in Arabidopsis , 2009, PloS one.

[40]  K. Yamaguchi-Shinozaki,et al.  Transcriptional Regulatory Networks in Response to Abiotic Stresses in Arabidopsis and Grasses1 , 2009, Plant Physiology.

[41]  T. Baubec,et al.  Effective, homogeneous and transient interference with cytosine methylation in plant genomic DNA by zebularine , 2008, The Plant journal : for cell and molecular biology.

[42]  J. Bennetzen,et al.  A unified classification system for eukaryotic transposable elements , 2007, Nature Reviews Genetics.

[43]  Zhao Xu,et al.  LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons , 2007, Nucleic Acids Res..

[44]  D. Huson,et al.  Application of phylogenetic networks in evolutionary studies. , 2006, Molecular biology and evolution.

[45]  J. Filkowski,et al.  Homologous recombination in plants is temperature and day-length dependent. , 2005, Mutation research.

[46]  Andreas Krause,et al.  A standard curve based method for relative real time PCR data processing , 2005, BMC Bioinformatics.

[47]  Lior Pachter,et al.  VISTA: computational tools for comparative genomics , 2004, Nucleic Acids Res..

[48]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[49]  Mikael Thollesson,et al.  LDDist: a Perl module for calculating LogDet pair-wise distances for protein and nucleotide sequences , 2004, Bioinform..

[50]  V. Moulton,et al.  Neighbor-net: an agglomerative method for the construction of phylogenetic networks. , 2002, Molecular biology and evolution.

[51]  Nicholas L. Bray,et al.  AVID: A global alignment program. , 2003, Genome research.

[52]  S. Ivashuta,et al.  Genotype-dependent transcriptional activation of novel repetitive elements during cold acclimation of alfalfa (Medicago sativa). , 2002, The Plant journal : for cell and molecular biology.

[53]  James K. M. Brown,et al.  Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. , 2002, Genome research.

[54]  T. Kakutani,et al.  Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis , 2001, Nature.

[55]  Lior Pachter,et al.  VISTA : visualizing global DNA sequence alignments of arbitrary length , 2000, Bioinform..

[56]  T. A. Hall,et al.  BIOEDIT: A USER-FRIENDLY BIOLOGICAL SEQUENCE ALIGNMENT EDITOR AND ANALYSIS PROGRAM FOR WINDOWS 95/98/ NT , 1999 .

[57]  Daniel H. Huson,et al.  SplitsTree: analyzing and visualizing evolutionary data , 1998, Bioinform..

[58]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[59]  B. Mcclintock,et al.  The significance of responses of the genome to challenge. , 1984, Science.