The genome of the largest bony fish, ocean sunfish (Mola mola), provides insights into its fast growth rate

[1]  S. Koren,et al.  The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts , 2016, Nature Communications.

[2]  Bronwen L. Aken,et al.  The spotted gar genome illuminates vertebrate evolution and facilitates human-to-teleost comparisons , 2016, Nature Genetics.

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

[4]  O. Kohany,et al.  Repbase Update, a database of repetitive elements in eukaryotic genomes , 2015, Mobile DNA.

[5]  H. Ellegren,et al.  Temporal Dynamics of Avian Populations during Pleistocene Revealed by Whole-Genome Sequences , 2015, Current Biology.

[6]  G. Ortí,et al.  An evaluation of fossil tip-dating versus node-age calibrations in tetraodontiform fishes (Teleostei: Percomorphaceae). , 2015, Molecular phylogenetics and evolution.

[7]  Ying Sun,et al.  Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes , 2014, Nature Communications.

[8]  Ting Wang,et al.  The draft genome of the large yellow croaker reveals well-developed innate immunity , 2014, Nature Communications.

[9]  Marco Biasini,et al.  SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information , 2014, Nucleic Acids Res..

[10]  N. Longo,et al.  Sequencing analysis of insulin receptor defects and detection of two novel mutations in INSR gene☆ , 2014, Molecular genetics and metabolism reports.

[11]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

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

[13]  Fabian Sievers,et al.  Clustal Omega, accurate alignment of very large numbers of sequences. , 2014, Methods in molecular biology.

[14]  Ari Löytynoja,et al.  Phylogeny-aware alignment with PRANK. , 2014, Methods in molecular biology.

[15]  D. Mortlock,et al.  Hox11 genes are required for regional patterning and integration of muscle, tendon and bone , 2013, Development.

[16]  B. Björnsson,et al.  Regulation of skeletal muscle growth in fish by the growth hormone--insulin-like growth factor system. , 2013, General and comparative endocrinology.

[17]  Jianying Yuan,et al.  Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects , 2013, 1308.2012.

[18]  P. Wainwright,et al.  Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes , 2013, Proceedings of the National Academy of Sciences.

[19]  Laurent Gil,et al.  Ensembl 2013 , 2012, Nucleic Acids Res..

[20]  Jian Wang,et al.  SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler , 2012, GigaScience.

[21]  Huanming Yang,et al.  Single-cell sequencing analysis characterizes common and cell-lineage-specific mutations in a muscle-invasive bladder cancer , 2012, GigaScience.

[22]  S. Anker,et al.  Growth hormone, insulin-like growth factor 1, and insulin signaling—a pharmacological target in body wasting and cachexia , 2011, Journal of cachexia, sarcopenia and muscle.

[23]  R. Durbin,et al.  Inference of human population history from individual whole-genome sequences. , 2011, Nature.

[24]  Syed Haider,et al.  Ensembl BioMarts: a hub for data retrieval across taxonomic space , 2011, Database J. Biol. Databases Curation.

[25]  Christine Ortiz,et al.  Nanomechanics of the Cartilage Extracellular Matrix. , 2011, Annual review of materials research.

[26]  K. Kawasaki The SCPP Gene Family and the Complexity of Hard Tissues in Vertebrates , 2011, Cells Tissues Organs.

[27]  M. S. Barash Environmental changes in the neogene and the biotic response , 2011 .

[28]  Jianzhi Zhang,et al.  Pseudogenization of the umami taste receptor gene Tas1r1 in the giant panda coincided with its dietary switch to bamboo. , 2010, Molecular biology and evolution.

[29]  M. Waters,et al.  The growth hormone receptor: mechanism of activation and clinical implications , 2010, Nature Reviews Endocrinology.

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

[31]  Tal Pupko,et al.  GUIDANCE: a web server for assessing alignment confidence scores , 2010, Nucleic Acids Res..

[32]  R. Krumlauf,et al.  Hox genes and segmentation of the hindbrain and axial skeleton. , 2009, Annual review of cell and developmental biology.

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

[34]  György Abrusán,et al.  TEclass - a tool for automated classification of unknown eukaryotic transposable elements , 2009, Bioinform..

[35]  K. Kawasaki The SCPP gene repertoire in bony vertebrates and graded differences in mineralized tissues , 2009, Development Genes and Evolution.

[36]  G. Hays,et al.  The biology and ecology of the ocean sunfish Mola mola: a review of current knowledge and future research perspectives , 2009, Reviews in Fish Biology and Fisheries.

[37]  Katsufumi Sato,et al.  Functional Dorsoventral Symmetry in Relation to Lift-Based Swimming in the Ocean Sunfish Mola mola , 2008, PloS one.

[38]  T. Nakatsubo,et al.  Growth of Captive Ocean Sunfish, Mola mola , 2007 .

[39]  Axel Meyer,et al.  Comparative phylogenomic analyses of teleost fish Hox gene clusters: lessons from the cichlid fish Astatotilapia burtoni , 2007, BMC Genomics.

[40]  B. Hayward,et al.  Last global extinction in the deep sea during the mid-Pleistocene climate transition , 2007 .

[41]  Wei-Min Huang,et al.  Bone growth in zebrafish fins occurs via multiple pulses of cell proliferation , 2007, Developmental dynamics : an official publication of the American Association of Anatomists.

[42]  Denis Duboule,et al.  The role of Hox genes during vertebrate limb development. , 2007, Current opinion in genetics & development.

[43]  Keith Bradnam,et al.  CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes , 2007, Bioinform..

[44]  M. Benton,et al.  Paleontological evidence to date the tree of life. , 2006, Molecular biology and evolution.

[45]  Robert S. Harris,et al.  Improved pairwise alignment of genomic dna , 2007 .

[46]  G. Weinstock,et al.  Creating a honey bee consensus gene set , 2007, Genome Biology.

[47]  M. Nakae,et al.  Peripheral nervous system of the ocean sunfish Mola mola (Tetraodontiformes: Molidae) , 2006, Ichthyological Research.

[48]  R. Tuan,et al.  Technology Insight: adult stem cells in cartilage regeneration and tissue engineering , 2006, Nature Clinical Practice Rheumatology.

[49]  Peer Bork,et al.  PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments , 2006, Nucleic Acids Res..

[50]  Tao Liu,et al.  TreeFam: a curated database of phylogenetic trees of animal gene families , 2005, Nucleic Acids Res..

[51]  Ziheng Yang,et al.  Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. , 2006, Molecular biology and evolution.

[52]  Thomas J Naughton,et al.  Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified , 2006, BMC Evolutionary Biology.

[53]  A. Amores,et al.  Developmental genetic basis for the evolution of pelvic fin loss in the pufferfish Takifugu rubripes. , 2005, Developmental biology.

[54]  H. Bern,et al.  Insulin-like growth factor signaling in fish. , 2005, International review of cytology.

[55]  Nansheng Chen,et al.  Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences , 2009, Current protocols in bioinformatics.

[56]  C. Lautier,et al.  IGF-I receptor mutations resulting in intrauterine and postnatal growth retardation. , 2003, The New England journal of medicine.

[57]  Mario Stanke,et al.  Gene prediction with a hidden Markov model and a new intron submodel , 2003, ECCB.

[58]  Stephen L. Johnson,et al.  Saltatory control of isometric growth in the zebrafish caudal fin is disrupted in long fin and rapunzel mutants. , 2003, Developmental biology.

[59]  B. Hayward LATE PLIOCENE TO MIDDLE PLEISTOCENE EXTINCTIONS OF DEEP-SEA BENTHIC FORAMINIFERA (“STILOSTOMELLA EXTINCTION”) IN THE SOUTHWEST PACIFIC , 2002 .

[60]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[61]  Christian E. V. Storm,et al.  Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. , 2001, Journal of molecular biology.

[62]  T. Mommsen Paradigms of growth in fish. , 2001, Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology.

[63]  D. Powell A Fascination for Fish: Adventures of an Underwater Pioneer , 2001 .

[64]  S. Velleman The role of the extracellular matrix in skeletal development. , 2000, Poultry science.

[65]  Wei Qian,et al.  Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. , 2000, Molecular biology and evolution.

[66]  G. Benson,et al.  Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.

[67]  N. Mckern,et al.  Crystal structure of the first three domains of the type-1 insulin-like growth factor receptor , 1998, Nature.

[68]  C. Ohlsson,et al.  Growth hormone and bone. , 1998, Endocrine reviews.

[69]  Ziheng Yang,et al.  PAML: a program package for phylogenetic analysis by maximum likelihood , 1997, Comput. Appl. Biosci..

[70]  Makoto Sato,et al.  Targeted Disruption of Cbfa1 Results in a Complete Lack of Bone Formation owing to Maturational Arrest of Osteoblasts , 1997, Cell.

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

[72]  V. Radha,et al.  Association of Lyn tyrosine kinase with the nuclear matrix and cell-cycle-dependent changes in matrix-associated tyrosine kinase activity. , 1996, European journal of biochemistry.

[73]  T. Clackson,et al.  A hot spot of binding energy in a hormone-receptor interface , 1995, Science.

[74]  J. T. Thomas,et al.  Cartilage collagens: strategies for the study of their organisation and expression in the extracellular matrix. , 1994, Annals of the rheumatic diseases.

[75]  P. Pilch,et al.  The insulin receptor: structure, function, and signaling. , 1994, The American journal of physiology.

[76]  B. Shilo,et al.  Interallelic complementation among DER/flb alleles: implications for the mechanism of signal transduction by receptor-tyrosine kinases. , 1991, Genetics.

[77]  J. Wells,et al.  A systematic mutational analysis of hormone-binding determinants in the human growth hormone receptor. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[78]  A. Fraser‐Brunner The Ocean Sunfishes (Family Molidae) , 1952 .