Regulatory remodeling in the allo-tetraploid frog Xenopus laevis

[1]  T. Kwon,et al.  Xenopus Hybrids Provide Insight Into Cell and Organism Size Control , 2018, bioRxiv.

[2]  I. Arkhipova,et al.  Transposable elements and polyploid evolution in animals. , 2018, Current opinion in genetics & development.

[3]  M. Huynen,et al.  Regulatory remodeling in the allo-tetraploid frog Xenopus laevis , 2017, Genome Biology.

[4]  M. Huynen,et al.  Heterochromatic histone modifications at transposons in Xenopus tropicalis embryos. , 2017, Developmental biology.

[5]  Kevin A. Burns,et al.  Genome evolution in the allotetraploid frog Xenopus laevis , 2016, Nature.

[6]  V. Tarabykin,et al.  Coordinately Co-opted Multiple Transposable Elements Constitute an Enhancer for wnt5a Expression in the Mammalian Secondary Palate , 2016, PLoS genetics.

[7]  M. Perino,et al.  Chromatin Control of Developmental Dynamics and Plasticity. , 2016, Developmental cell.

[8]  Simon J. van Heeringen,et al.  fluff: exploratory analysis and visualization of high-throughput sequencing data , 2016, bioRxiv.

[9]  Steven J. M. Jones,et al.  The Atlantic salmon genome provides insights into rediploidization , 2016, Nature.

[10]  Pamela S Soltis,et al.  Ancient WGD events as drivers of key innovations in angiosperms. , 2016, Current opinion in plant biology.

[11]  Matthew D. Schultz,et al.  Active DNA demethylation at enhancers during the vertebrate phylotypic period , 2016, Nature Genetics.

[12]  Xiaodong Cheng,et al.  Structural basis for human PRDM9 action at recombination hot spots , 2016, Genes & development.

[13]  S. Grant.  The molecular evolution of the vertebrate behavioural repertoire , 2016, Philosophical Transactions of the Royal Society B: Biological Sciences.

[14]  P. Donnelly,et al.  Re-engineering the zinc fingers of PRDM9 reverses hybrid sterility in mice , 2016, Nature.

[15]  S. V. van Heeringen,et al.  Embryonic transcription is controlled by maternally defined chromatin state , 2015, Nature Communications.

[16]  Jonathan F Wendel,et al.  The wondrous cycles of polyploidy in plants. , 2015, American journal of botany.

[17]  M. K. Rudd,et al.  Human Structural Variation: Mechanisms of Chromosome Rearrangements. , 2015, Trends in genetics : TIG.

[18]  Caleb Webber,et al.  Haploinsufficiency predictions without study bias , 2015, Nucleic acids research.

[19]  M. Schmid,et al.  A New Nomenclature of Xenopus laevis Chromosomes Based on the Phylogenetic Relationship to Silurana/Xenopus tropicalis , 2015, Cytogenetic and Genome Research.

[20]  Q. Song,et al.  Epigenetic and developmental regulation in plant polyploids. , 2015, Current opinion in plant biology.

[21]  Robert J. Schmitz,et al.  MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing , 2015, Nature Protocols.

[22]  J. T. Erichsen,et al.  Enhancer Evolution across 20 Mammalian Species , 2015, Cell.

[23]  Zhihai Ma,et al.  Widespread contribution of transposable elements to the innovation of gene regulatory networks , 2014, Genome research.

[24]  M. Lynch,et al.  Differential retention and divergent resolution of duplicate genes following whole-genome duplication , 2014, Genome research.

[25]  D. Odom,et al.  Evolution of transcription factor binding in metazoans — mechanisms and functional implications , 2014, Nature Reviews Genetics.

[26]  James C. Schnable,et al.  Two evolutionarily distinct classes of paleopolyploidy. , 2014, Molecular biology and evolution.

[27]  Tyler H. Garvin,et al.  A Reference Methylome Database and Analysis Pipeline to Facilitate Integrative and Comparative Epigenomics , 2013, PloS one.

[28]  Mauricio O. Carneiro,et al.  From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline , 2013, Current protocols in bioinformatics.

[29]  J. Tena,et al.  The developmental epigenomics toolbox: ChIP-seq and MethylCap-seq profiling of early zebrafish embryos. , 2013, Methods.

[30]  Robert Gentleman,et al.  Software for Computing and Annotating Genomic Ranges , 2013, PLoS Comput. Biol..

[31]  Anushya Muruganujan,et al.  Large-scale gene function analysis with the PANTHER classification system , 2013, Nature Protocols.

[32]  H. Hakonarson,et al.  Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing , 2013, Genome Medicine.

[33]  M. Rubinstein,et al.  Exaptation of Transposable Elements into Novel Cis-Regulatory Elements: Is the Evidence Always Strong? , 2013, Molecular biology and evolution.

[34]  L. Pachter,et al.  Streaming fragment assignment for real-time analysis of sequencing experiments , 2012, Nature Methods.

[35]  Adi Doron-Faigenboim,et al.  FastML: a web server for probabilistic reconstruction of ancestral sequences , 2012, Nucleic Acids Res..

[36]  J. Gurdon,et al.  Deficient Induction Response in a Xenopus Nucleocytoplasmic Hybrid , 2011, PLoS biology.

[37]  Frédéric Delsuc,et al.  MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons , 2011, PloS one.

[38]  M. DePristo,et al.  A framework for variation discovery and genotyping using next-generation DNA sequencing data , 2011, Nature Genetics.

[39]  R. Stewart,et al.  Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells , 2011, Nature.

[40]  James C. Schnable,et al.  Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss , 2011, Proceedings of the National Academy of Sciences.

[41]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[42]  M. Gerstein,et al.  Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates , 2010, Genome Biology.

[43]  Mariko Sasaki,et al.  Genome destabilization by homologous recombination in the germ line , 2010, Nature Reviews Molecular Cell Biology.

[44]  Aaron R. Quinlan,et al.  Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .

[45]  Lee E. Edsall,et al.  Human DNA methylomes at base resolution show widespread epigenomic differences , 2009, Nature.

[46]  Robert Gentleman,et al.  rtracklayer: an R package for interfacing with genome browsers , 2009, Bioinform..

[47]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[48]  J. Stamatoyannopoulos,et al.  Human mutation rate associated with DNA replication timing , 2009, Nature Genetics.

[49]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[50]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[51]  S. Carroll.  Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution , 2008, Cell.

[52]  A. Shilatifard,et al.  Covalent modifications of histones during development and disease pathogenesis , 2007, Nature Structural &Molecular Biology.

[53]  Hans-Werner Mewes,et al.  CORUM: the comprehensive resource of mammalian protein complexes , 2007, Nucleic Acids Res..

[54]  Octave Noubibou Doudieu,et al.  CORUM: the comprehensive resource of mammalian protein complexes , 2007, Nucleic Acids Res..

[55]  R. Martienssen,et al.  Transposable elements and the epigenetic regulation of the genome , 2007, Nature Reviews Genetics.

[56]  Ewan Birney,et al.  Automated generation of heuristics for biological sequence comparison , 2005, BMC Bioinformatics.

[57]  D. Kelley,et al.  A mitochondrial DNA phylogeny of African clawed frogs: phylogeography and implications for polyploid evolution. , 2004, Molecular phylogenetics and evolution.

[58]  Sudhir Kumar,et al.  Neutral substitutions occur at a faster rate in exons than in noncoding DNA in primate genomes. , 2003, Genome research.

[59]  S. Ohno,et al.  Gene duplication and the uniqueness of vertebrate genomes circa 1970-1999. , 1999, Seminars in cell & developmental biology.

[60]  P. Holland,et al.  Hox genes and chordate evolution. , 1996, Developmental biology.

[61]  B. Charlesworth,et al.  The effect of deleterious mutations on neutral molecular variation. , 1993, Genetics.

[62]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[63]  Takeo Watanabe,et al.  Advances in visual perceptual learning and plasticity , 2010, Nature Reviews Neuroscience.

[64]  J. R. Lobry,et al.  SeqinR 1.0-2: A Contributed Package to the R Project for Statistical Computing Devoted to Biological Sequences Retrieval and Analysis , 2007 .

[65]  U. Bastolla,et al.  Structural approaches to sequence evolution : molecules, networks, populations , 2007 .