The little skate genome and the evolutionary emergence of wing-like fins

[1]  Brendan L. O’Connell,et al.  Deeply conserved synteny and the evolution of metazoan chromosomes , 2022, Science advances.

[2]  T. Gabaldón,et al.  PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies , 2021, Nucleic Acids Res..

[3]  K. Kawasaki,et al.  The bowfin genome illuminates the developmental evolution of ray-finned fishes , 2021, Nature Genetics.

[4]  B. Venkatesh,et al.  Reconstruction of proto-vertebrate, proto-cyclostome and proto-gnathostome genomes provides new insights into early vertebrate evolution , 2021, Nature Communications.

[5]  S. Kuraku.  Shark and ray genomics for disentangling their morphological diversity and vertebrate evolution. , 2021, Developmental biology.

[6]  Roy G van Heesbeen,et al.  3D genomics across the tree of life reveals condensin II as a determinant of architecture type , 2021, Science.

[7]  J. Gillis,et al.  Conserved and unique transcriptional features of pharyngeal arches in the skate (Leucoraja erinacea) and evolution of the jaw , 2021, bioRxiv.

[8]  Juan M. Vaquerizas,et al.  FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data , 2020, Genome Biology.

[9]  Yuan Jiang,et al.  The White-Spotted Bamboo Shark Genome Reveals Chromosome Rearrangements and Fast-Evolving Immune Genes of Cartilaginous Fish , 2020, iScience.

[10]  A. Meyer,et al.  The mole genome reveals regulatory rearrangements associated with adaptive intersexuality , 2020, Science.

[11]  Drew R. Schield,et al.  Microchromosomes Exhibit Distinct Features of Vertebrate Chromosome Structure and Function with Underappreciated Ramifications for Genome Evolution , 2020, Molecular biology and evolution.

[12]  J. Tena,et al.  CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression , 2020, Nature Communications.

[13]  J. Lopez-Rios,et al.  The Shh/Gli3 gene regulatory network precedes the origin of paired fins and reveals the deep homology between distal fins and digits , 2020, Proceedings of the National Academy of Sciences.

[14]  H. Philippe,et al.  Broccoli: combining phylogenetic and network analyses for orthology assignment. , 2020, Molecular biology and evolution.

[15]  Alexey M. Kozlov,et al.  GeneRax: A Tool for Species-Tree-Aware Maximum Likelihood-Based Gene Family Tree Inference under Gene Duplication, Transfer, and Loss , 2020, Molecular biology and evolution.

[16]  J. Tena,et al.  Ancient Genomic Regulatory Blocks Are a Source for Regulatory Gene Deserts in Vertebrates after Whole-Genome Duplications , 2020, Molecular biology and evolution.

[17]  Tetsuya Nakamura,et al.  Developmental constraints on fin diversity , 2020, Development, growth & differentiation.

[18]  Leszek P. Pryszcz,et al.  MetaPhOrs 2.0: integrative, phylogeny-based inference of orthology and paralogy across the tree of life , 2020, Nucleic Acids Res..

[19]  Nicholas H. Putnam,et al.  Deeply conserved synteny resolves early events in vertebrate evolution , 2020, Nature Ecology & Evolution.

[20]  M. Schatz,et al.  GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes , 2020, Nature Communications.

[21]  Rolf Backofen,et al.  Loop detection using Hi-C data with HiCExplorer , 2020, bioRxiv.

[22]  Philip A. Ewels,et al.  The nf-core framework for community-curated bioinformatics pipelines , 2020, Nature Biotechnology.

[23]  S. Mackem,et al.  The formation of the thumb requires direct modulation of Gli3 transcription by Hoxa13 , 2020, Proceedings of the National Academy of Sciences.

[24]  Ferhat Ay,et al.  Identification of significant chromatin contacts from HiChIP data by FitHiChIP , 2019, Nature Communications.

[25]  J. Grimwood,et al.  A chromosome-scale genome assembly and dense genetic map for Xenopus tropicalis. , 2019, Developmental biology.

[26]  R. Lister,et al.  Retention of paternal DNA methylome in the developing zebrafish germline , 2019, Nature Communications.

[27]  J. Gómez-Skarmeta,et al.  Reprogramming Nuclear Architecture: Just a TAD. , 2019, Cell stem cell.

[28]  Daniel S. Rokhsar,et al.  A New Spiralian Phylogeny Places the Enigmatic Arrow Worms among Gnathiferans , 2019, Current Biology.

[29]  Anthony R. Borneman,et al.  Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies , 2018, BMC Bioinformatics.

[30]  R. Fisher,et al.  How the Devil Ray Got Its Horns: The Evolution and Development of Cephalic Lobes in Myliobatid Stingrays (Batoidea: Myliobatidae) , 2018, Front. Ecol. Evol..

[31]  Piotr J. Balwierz,et al.  Amphioxus functional genomics and the origins of vertebrate gene regulation , 2018, Nature.

[32]  V. Corces,et al.  Organizational principles of 3D genome architecture , 2018, Nature Reviews Genetics.

[33]  M. Kadota,et al.  Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates , 2018, Nature Ecology & Evolution.

[34]  A. Visel,et al.  Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis , 2018, Nature Genetics.

[35]  Jacob M. Luber,et al.  HiGlass: web-based visual exploration and analysis of genome interaction maps , 2017, Genome Biology.

[36]  Jonas Ibn-Salem,et al.  Evolutionary stability of topologically associating domains is associated with conserved gene regulation , 2017, BMC Biology.

[37]  D. Menke,et al.  PITX1 promotes chondrogenesis and myogenesis in mouse hindlimbs through conserved regulatory targets. , 2017, Developmental biology.

[38]  K. Crow,et al.  The role of HoxA11 and HoxA13 in the evolution of novel fin morphologies in a representative batoid (Leucoraja erinacea) , 2017, EvoDevo.

[39]  D. Swarbreck,et al.  Efficient and accurate detection of splice junctions from RNA-seq with Portcullis , 2017, bioRxiv.

[40]  Shabhonam Caim,et al.  Leveraging multiple transcriptome assembly methods for improved gene structure annotation , 2017, bioRxiv.

[41]  Johannes Söding,et al.  MMseqs2: sensitive protein sequence searching for the analysis of massive data sets , 2017, bioRxiv.

[42]  Yijun Ruan,et al.  Evolutionarily Conserved Principles Predict 3D Chromatin Organization. , 2017, Molecular cell.

[43]  Heng Li,et al.  Minimap2: pairwise alignment for nucleotide sequences , 2017, Bioinform..

[44]  Frédéric Delsuc,et al.  Phylotranscriptomic consolidation of the jawed vertebrate timetree , 2017, Nature Ecology & Evolution.

[45]  Job Dekker,et al.  Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation. , 2017, Methods.

[46]  Marc A. Martí-Renom,et al.  Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors , 2017, PLoS Comput. Biol..

[47]  Hernando G. Suarez Duran,et al.  chainCleaner improves genome alignment specificity and sensitivity , 2017, Bioinform..

[48]  T. Hore,et al.  The elephant shark methylome reveals conservation of epigenetic regulation across jawed vertebrates , 2017, F1000Research.

[49]  Paolo Di Tommaso,et al.  Nextflow enables reproducible computational workflows , 2017, Nature Biotechnology.

[50]  A. Visel,et al.  Distal Limb Patterning Requires Modulation of cis-Regulatory Activities by HOX13 , 2016, Cell reports.

[51]  Ting Chen,et al.  WALT: fast and accurate read mapping for bisulfite sequencing , 2016, Bioinform..

[52]  M. Cohn,et al.  Loss and Re-emergence of Legs in Snakes by Modular Evolution of Sonic hedgehog and HOXD Enhancers , 2016, Current Biology.

[53]  A. Chinnaiyan,et al.  TACO produces robust multi-sample transcriptome assemblies from RNA-seq , 2016, Nature Methods.

[54]  Axel Visel,et al.  Progressive Loss of Function in a Limb Enhancer during Snake Evolution , 2016, Cell.

[55]  Howard Y. Chang,et al.  HiChIP: efficient and sensitive analysis of protein-directed genome architecture , 2016, Nature Methods.

[56]  Andrew R. Gehrke,et al.  Digits and Fin Rays Share Common Developmental Histories , 2016, Nature.

[57]  Neva C. Durand,et al.  Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. , 2016, Cell systems.

[58]  Daisy E. Pagete.  An end-to-end assembly of the Aedes aegypti genome , 2016, 1605.04619.

[59]  Mikiko Tanaka.  Fins into limbs: Autopod acquisition and anterior elements reduction by modifying gene networks involving 5'Hox, Gli3, and Shh. , 2016, Developmental biology.

[60]  C. Borchiellini,et al.  Retracing the path of planar cell polarity , 2016, BMC Evolutionary Biology.

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

[62]  P. Holland,et al.  A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation , 2016, Nature Genetics.

[63]  Andrew R. Gehrke,et al.  Molecular mechanisms underlying the exceptional adaptations of batoid fins , 2015, Proceedings of the National Academy of Sciences.

[64]  Evgeny M. Zdobnov,et al.  BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..

[65]  A. Visel,et al.  Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions , 2015, Cell.

[66]  J. Dekker,et al.  Condensin-Driven Remodeling of X-Chromosome Topology during Dosage Compensation , 2015, Nature.

[67]  Matthieu Muffato,et al.  The 3D organization of chromatin explains evolutionary fragile genomic regions. , 2015, Cell reports.

[68]  Brendan L. O’Connell,et al.  Chromosome-scale shotgun assembly using an in vitro method for long-range linkage , 2015, Genome research.

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

[70]  S. Salzberg,et al.  StringTie enables improved reconstruction of a transcriptome from RNA-seq reads , 2015, Nature Biotechnology.

[71]  M. Rattray,et al.  Hoxa2 Selectively Enhances Meis Binding to Change a Branchial Arch Ground State , 2015, Developmental cell.

[72]  Andrew R. Gehrke,et al.  Deep conservation of wrist and digit enhancers in fish , 2014, Proceedings of the National Academy of Sciences.

[73]  Neva C. Durand,et al.  A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping , 2014, Cell.

[74]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[75]  A. von Haeseler,et al.  IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies , 2014, Molecular biology and evolution.

[76]  Chengxi Ye,et al.  DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies , 2014, Scientific Reports.

[77]  Benoit Robert,et al.  Attenuated sensing of SHH by Ptch1 underlies evolution of bovine limbs , 2014, Nature.

[78]  Fidel Ramírez,et al.  deepTools: a flexible platform for exploring deep-sequencing data , 2014, Nucleic Acids Res..

[79]  Brian J. Raney,et al.  Elephant shark genome provides unique insights into gnathostome evolution , 2014, Nature.

[80]  Salvador Capella-Gutiérrez,et al.  PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome , 2013, Nucleic Acids Res..

[81]  G. Hon,et al.  Adult tissue methylomes harbor epigenetic memory at embryonic enhancers , 2013, Nature Genetics.

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

[83]  Michael Hiller,et al.  Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish , 2013, Nucleic acids research.

[84]  F. Casares,et al.  Hoxd13 contribution to the evolution of vertebrate appendages. , 2012, Developmental cell.

[85]  Hunter B. Fraser,et al.  Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints , 2012, Genome research.

[86]  R. Gibbs,et al.  Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology , 2012, PloS one.

[87]  Guangchuang Yu,et al.  clusterProfiler: an R package for comparing biological themes among gene clusters. , 2012, Omics : a journal of integrative biology.

[88]  Jernej Ule,et al.  Psip1/Ledgf p52 Binds Methylated Histone H3K36 and Splicing Factors and Contributes to the Regulation of Alternative Splicing , 2012, PLoS genetics.

[89]  Rolf Zeller,et al.  GLI3 constrains digit number by controlling both progenitor proliferation and BMP-dependent exit to chondrogenesis. , 2012, Developmental cell.

[90]  J. Sedat,et al.  Spatial partitioning of the regulatory landscape of the X-inactivation centre , 2012, Nature.

[91]  M. Heithaus,et al.  Biology of Sharks and Their Relatives, Second Edition , 2012 .

[92]  Jesse R. Dixon,et al.  Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions , 2012, Nature.

[93]  K. Kawakami,et al.  Transposon-mediated BAC transgenesis in zebrafish , 2011, Nature Protocols.

[94]  Sean R. Eddy,et al.  Accelerated Profile HMM Searches , 2011, PLoS Comput. Biol..

[95]  N. Friedman,et al.  Trinity : reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2016 .

[96]  William Stafford Noble,et al.  FIMO: scanning for occurrences of a given motif , 2011, Bioinform..

[97]  Albert J. Vilella,et al.  Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis , 2010, PLoS biology.

[98]  Alexis Criscuolo,et al.  BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments , 2010, BMC Evolutionary Biology.

[99]  Davis J. McCarthy,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[100]  Nicolas Lartillot,et al.  PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating , 2009, Bioinform..

[101]  Laurent Duret,et al.  Biased gene conversion and the evolution of mammalian genomic landscapes. , 2009, Annual review of genomics and human genetics.

[102]  Gaston H. Gonnet,et al.  Algorithm of OMA for large-scale orthology inference , 2009, BMC Bioinform..

[103]  Toni Gabaldón,et al.  trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses , 2009, Bioinform..

[104]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

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

[106]  E. Maxwell,et al.  Variability and Conservation in Late Chondrichthyan Development: Ontogeny of the Winter Skate (Leucoraja ocellata) , 2008, Anatomical record.

[107]  Oliver Eulenstein,et al.  DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony , 2008, Bioinform..

[108]  Jonathan E. Allen,et al.  Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments , 2007, Genome Biology.

[109]  Y. Kohara,et al.  Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates. , 2007, Genome research.

[110]  N. Shubin,et al.  Sonic hedgehog function in chondrichthyan fins and the evolution of appendage patterning , 2007, Nature.

[111]  R. Schweitzer,et al.  Pitx1 determines the morphology of muscle, tendon, and bones of the hindlimb. , 2006, Developmental biology.

[112]  Burkhard Morgenstern,et al.  AUGUSTUS: ab initio prediction of alternative transcripts , 2006, Nucleic Acids Res..

[113]  Iain M. Wallace,et al.  M-Coffee: combining multiple sequence alignment methods with T-Coffee , 2006, Nucleic acids research.

[114]  Erik L. L. Sonnhammer,et al.  Kalign – an accurate and fast multiple sequence alignment algorithm , 2005, BMC Bioinformatics.

[115]  K. Katoh,et al.  MAFFT version 5: improvement in accuracy of multiple sequence alignment , 2005, Nucleic acids research.

[116]  Z. Weng,et al.  Detection of functional DNA motifs via statistical over-representation. , 2004, Nucleic acids research.

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

[118]  D. Haussler,et al.  Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[119]  K. Katoh,et al.  MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. , 2002, Nucleic acids research.

[120]  P. Holland,et al.  Vertebrate innovations. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[121]  P Chambon,et al.  Hoxa-13 and Hoxd-13 play a crucial role in the patterning of the limb autopod. , 1996, Development.

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

[123]  Ira M. Hall,et al.  BEDTools: a flexible suite of utilities for comparing genomic features , 2010, Bioinform..

[124]  Claude-Alain H. Roten,et al.  Fast and accurate short read alignment with Burrows–Wheeler transform , 2009, Bioinform..