Dense sampling of bird diversity increases power of comparative genomics
暂无分享,去创建一个
Timothy B Sackton | Bette A. Loiselle | A. T. Vasconcelos | Rebecca B. Dikow | Matthew J. Fuxjager | Araxi O. Urrutia | Libby C. Megna | Adam M. Fudickar | Scott A. Taylor | D. Haussler | M. Diekhans | A. Clark | Huanming Yang | Jian Wang | T. Sicheritz-Pontén | J. Cracraft | M. Braun | Qiye Li | M. Cox | B. Paten | E. Jarvis | B. Faircloth | L. Eckhart | H. Mouritsen | Miriam Liedvogel | D. Burt | A. Vignal | C. Mello | O. Ryder | N. Gemmell | A. Franke | G. Graves | K. Jønsson | J. Fjeldså | C. Rahbek | J. Mudge | J. Fitzpatrick | J. Rozas | Bent Petersen | I. Jamieson | I. Lovette | T. Székely | A. Margaryan | Guojie Zhang | M. Bertelsen | B. Shapiro | J. McGuire | F. Sheldon | S. Edwards | S. Hackett | T. Ryder | M. Bunce | J. Armstrong | S. Mirarab | C. Witt | G. Borgia | P. Ryan | M. Carling | R. T. Brumfield | L. Christidis | E. Braun | R. D. da Fonseca | M. Hauber | L. Keller | Matthew I. M. Louder | F. Lei | R. van der Sluis | P. Njoroge | Josefin Stiller | Qi Zhou | M. Sinding | R. Bowman | B. Schlinger | E. Ketterson | A. Urrutia | Jason T. Howard | Morgan E. Wirthlin | M. G. Campana | A. Fidler | C. Visser | A. Vasconcelos | Nancy Chen | C. Balakrishnan | P. Battley | P. Houde | Alexander Suh | F. Prosdocimi | P. Frandsen | J. DaCosta | M. Gilbert | Peter A. Hosner | Alison Cloutier | J. Dumbacher | R. Fleischer | H. C. Lim | L. Dalén | Yang Liu | B. Milá | B. Loiselle | Guillermo Friis | J. Blake | A. Aleixo | L. Day | J. González‐Solís | B. Hansson | O. Krone | G. Song | Zongji Wang | D. T. Tietze | T. Parchman | Kim M Rutherford | A. Corvelo | J. Weir | S. Claramunt | V. Friesen | B. Robertson | M. Hoeppner | M. Riutort | Guanliang Meng | George Pacheco | A. H. Reeve | Mikkel-Holger S. Sinding | Kira E. Delmore | Anna Tigano | S. Cowen | J. Fuchs | N. C. B. Lima | Maude W. Baldwin | Biao Wang | Shaohong Feng | H. van der Zwan | Qi Fang | Duo Xie | Yuan Deng | Hanna Sigeman | M. Stervander | Suvi Ponnikas | S. Andreu-Sánchez | Chunxue Guo | Lara C. Puetz | G. Camenisch | N. Dussex | Guangji Chen | Wanjun Chen | Carole Parent | Emily Cavill | Â. M. Ribeiro | Dustin J Foote | Subir B Shakya | André E. R. Soares | Joan Ferrer-Obiol | N. Thiele | Á. M. Parody-Merino | M. Baldwin | Glaucia Del-Rio | Guojie Zhang | K. Delmore | N. C. Lima | D. Tietze | M. Liedvogel | Subir B. Shakya | P. Hosner | A. Cloutier | Lara C Puetz | Dustin J. Foote | E. Cavill | Â. Ribeiro | Matthew D. Carling | Jeffrey M. DaCosta | Emily L. Cavill | Ângela M. Ribeiro | A. Clark | Scott A. Taylor | Martin Stervander | Thomas Sicheritz-Pontén | A. Clark | J. Howard | Lara Puetz | S. Andreu‐Sánchez
[1] Voichita D. Marinescu,et al. Progressive Cactus is a multiple-genome aligner for the thousand-genome era , 2020, Nature.
[2] Phillip A. Richmond,et al. JASPAR 2020: update of the open-access database of transcription factor binding profiles , 2019, Nucleic Acids Res..
[3] C. Lalueza-Fox,et al. Evolutionary History, Genomic Adaptation to Toxic Diet, and Extinction of the Carolina Parakeet , 2019, Current Biology.
[4] V. Fellman,et al. A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye and inhibitor-resistant high-fidelity DNA polymerase , 2019, bioRxiv.
[5] David Haussler,et al. Progressive alignment with Cactus: a multiple-genome aligner for the thousand-genome era , 2019, bioRxiv.
[6] Berend Snel,et al. Measuring the impact of gene prediction on gene loss estimates in Eukaryotes by quantifying falsely inferred absences , 2019, PLoS Comput. Biol..
[7] Qiye Li,et al. Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits , 2019, Science.
[8] Yiyuan Li,et al. MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization , 2019, Nucleic acids research.
[9] Joel Armstrong,et al. Whole-Genome Alignment and Comparative Annotation. , 2019, Annual review of animal biosciences.
[10] Martin Kuhlwilm,et al. The Genomic Footprints of the Fall and Recovery of the Crested Ibis , 2019, Current Biology.
[11] David Haussler,et al. The UCSC Genome Browser database: 2019 update , 2018, Nucleic Acids Res..
[12] J. Armstrong. Enabling comparative genomics at the scale of hundreds of species , 2019 .
[13] Leucopsar rothschildi: BirdLife International , 2018, IUCN Red List of Threatened Species.
[14] Juan Carlos Castilla-Rubio,et al. Earth BioGenome Project: Sequencing life for the future of life , 2018, Proceedings of the National Academy of Sciences.
[15] Xun Xu,et al. 10KP: A phylodiverse genome sequencing plan , 2018, GigaScience.
[16] Sheng Chen,et al. Efficient generation of complete sequences of MDR-encoding plasmids by rapid assembly of MinION barcoding sequencing data , 2018, GigaScience.
[17] Michael Q. Zhang,et al. NONCODEV5: a comprehensive annotation database for long non-coding RNAs , 2017, Nucleic Acids Res..
[18] Ning Wang,et al. The development of scientific consensus: Analyzing conflict and concordance among avian phylogenies. , 2017, Molecular phylogenetics and evolution.
[19] L. Keller,et al. The Global Ant Genomics Alliance (GAGA) , 2017 .
[20] Patrick Mardulyn,et al. NOVOPlasty: de novo assembly of organelle genomes from whole genome data. , 2016, Nucleic acids research.
[21] SH Song,et al. The BIG Data Center: from deposition to integration to translation , 2016, Nucleic Acids Res..
[22] Brant C. Faircloth,et al. PHYLUCE is a software package for the analysis of conserved genomic loci , 2015, bioRxiv.
[23] J. Townsend,et al. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing , 2015, Nature.
[24] Evgeny M. Zdobnov,et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..
[25] Guojie Zhang,et al. Genomics: Bird sequencing project takes off , 2015, Nature.
[26] O. Kohany,et al. Repbase Update, a database of repetitive elements in eukaryotic genomes , 2015, Mobile DNA.
[27] Alexey M. Kozlov,et al. ExaML version 3: a tool for phylogenomic analyses on supercomputers , 2015, Bioinform..
[28] A. von Haeseler,et al. IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies , 2014, Molecular biology and evolution.
[29] Md. Shamsuzzoha Bayzid,et al. Whole-genome analyses resolve early branches in the tree of life of modern birds , 2014, Science.
[30] E. Jarvis,et al. Evidence for a single loss of mineralized teeth in the common avian ancestor , 2014, Science.
[31] Andreas R. Pfenning,et al. Comparative genomics reveals insights into avian genome evolution and adaptation , 2014, Science.
[32] L. Eckhart,et al. Trichohyalin-like proteins have evolutionarily conserved roles in the morphogenesis of skin appendages. , 2014, The Journal of investigative dermatology.
[33] Daniel R. Zerbino,et al. WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis , 2013, Bioinform..
[34] R Core Team,et al. R: A language and environment for statistical computing. , 2014 .
[35] Susan J. Brown,et al. The i5K Initiative: advancing arthropod genomics for knowledge, human health, agriculture, and the environment. , 2013, The Journal of heredity.
[36] M. Albà,et al. Accelerated evolution after gene duplication: a time-dependent process affecting just one copy. , 2013, Molecular biology and evolution.
[37] A. Azem,et al. Methylation-controlled J-protein MCJ acts in the import of proteins into human mitochondria. , 2013, Human molecular genetics.
[38] K. Katoh,et al. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.
[39] Jian Wang,et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler , 2012, GigaScience.
[40] Travis C Glenn,et al. Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. , 2012, Systematic biology.
[41] Liam J. Revell,et al. phytools: an R package for phylogenetic comparative biology (and other things) , 2012 .
[42] F. Peñagaricano,et al. Differential expression of heat shock protein genes and their splice variants in bovine preimplantation embryos. , 2011, Journal of dairy science.
[43] Colin N. Dewey. Positional orthology: putting genomic evolutionary relationships into context , 2011, Briefings Bioinform..
[44] Alex A. Pollen,et al. Human-specific loss of regulatory DNA and the evolution of human-specific traits , 2011, Nature.
[45] Adam C. Siepel,et al. PHAST and RPHAST: phylogenetic analysis with space/time models , 2011, Briefings Bioinform..
[46] J. Plotkin,et al. Synonymous but not the same: the causes and consequences of codon bias , 2011, Nature Reviews Genetics.
[47] A. Gnirke,et al. High-quality draft assemblies of mammalian genomes from massively parallel sequence data , 2010, Proceedings of the National Academy of Sciences.
[48] K. Pollard,et al. Detection of nonneutral substitution rates on mammalian phylogenies. , 2010, Genome research.
[49] Joshua M. Stuart,et al. Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. , 2009, The Journal of heredity.
[50] M. Braun,et al. Duplication of accelerated evolution and growth hormone gene in passerine birds. , 2008, Molecular biology and evolution.
[51] J. Mank,et al. Fast-X on the Z: rapid evolution of sex-linked genes in birds. , 2007, Genome research.
[52] N. Fletcher,et al. Songbirds tune their vocal tract to the fundamental frequency of their song. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[53] Laurent Excoffier,et al. Conserved noncoding sequences are selectively constrained and not mutation cold spots , 2006, Nature Genetics.
[54] D. Burt,et al. Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes. , 2005, Genome research.
[55] Ewan Birney,et al. Automated generation of heuristics for biological sequence comparison , 2005, BMC Bioinformatics.
[56] D. Haussler,et al. Aligning multiple genomic sequences with the threaded blockset aligner. , 2004, Genome research.
[57] S. Batzoglou,et al. Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes. , 2003, Genome research.
[58] E C Dickinson,et al. THE HOWARD AND MOORE COMPLETE CHECKLIST OF THE BIRDS OF THE WORLD. 4 th EDITION VOLUME 2 (2014) , 2003 .
[59] W. Fitch. Homology a personal view on some of the problems. , 2000, Trends in genetics : TIG.
[60] G. Benson,et al. Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.
[61] Y. Benjamini,et al. Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .
[62] F. Wright. The 'effective number of codons' used in a gene. , 1990, Gene.
[63] Nicholas H. Barton,et al. The Relative Rates of Evolution of Sex Chromosomes and Autosomes , 1987, The American Naturalist.
[64] R. Clarke,et al. Theory and Applications of Correspondence Analysis , 1985 .
[65] W. Fitch. Distinguishing homologous from analogous proteins. , 1970, Systematic zoology.