The population genomics of structural variation in a songbird genus
暂无分享,去创建一个
Fritz J. Sedlazeck | Alexander Suh | Ignas Bunikis | Ulrich Knief | F. Sedlazeck | A. Catalán | Kees-Jan Françoijs | Vera M. Warmuth | Alexander Suh | J. Wolf | Matthias H. Weissensteiner | I. Bunikis | U. Knief | Ana Catalán | Kees-Jan Francoijs | Wieland Heim | Valentina Peona | Saurabh D. Pophaly | Jochen B.W. Wolf | V. Peona | W. Heim | S. Pophaly
[1] ZhengXiuwen,et al. A high-performance computing toolset for relatedness and principal component analysis of SNP data , 2012 .
[2] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[3] Kevin P. Johnson,et al. Introgression of regulatory alleles and a missense coding mutation drive plumage pattern diversity in the rock pigeon , 2018, eLife.
[4] M. Quail,et al. The industrial melanism mutation in British peppered moths is a transposable element , 2016, Nature.
[5] Ryan L. Collins,et al. Multi-platform discovery of haplotype-resolved structural variation in human genomes , 2017, bioRxiv.
[6] M. Schatz,et al. Phased diploid genome assembly with single-molecule real-time sequencing , 2016, Nature Methods.
[7] Thomas Zichner,et al. DELLY: structural variant discovery by integrated paired-end and split-read analysis , 2012, Bioinform..
[8] J. Wingfield,et al. A supergene determines highly divergent male reproductive morphs in the ruff , 2015, Nature Genetics.
[9] Xiaoyu Chen,et al. Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications , 2016, Bioinform..
[10] I. Amit,et al. Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .
[11] Pall I. Olason,et al. A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution , 2014, Molecular ecology.
[12] Ryan M. Layer,et al. LUMPY: a probabilistic framework for structural variant discovery , 2012, Genome Biology.
[13] D. Bates,et al. Linear Mixed-Effects Models using 'Eigen' and S4 , 2015 .
[14] A. Pang,et al. Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications , 2017, Genome research.
[15] B. Weir,et al. ESTIMATING F‐STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE , 1984, Evolution; international journal of organic evolution.
[16] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[17] Yuanda Lv,et al. The population genetics of structural variants in grapevine domestication , 2019, Nature Plants.
[18] M. Wikelski,et al. The genomic landscape underlying phenotypic integrity in the face of gene flow in crows , 2014, Science.
[19] M. Schatz,et al. Phased diploid genome assembly with single-molecule real-time sequencing , 2016, Nature Methods.
[20] Robert S. Harris,et al. Improved pairwise alignment of genomic dna , 2007 .
[21] Pui-Yan Kwok,et al. Genome maps across 26 human populations reveal population-specific patterns of structural variation , 2019, Nature Communications.
[22] Evgeny M. Zdobnov,et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..
[23] I. Kaj,et al. Polymorphism Data Assist Estimation of the Nonsynonymous over Synonymous Fixation Rate Ratio ω for Closely Related Species , 2019, Molecular biology and evolution.
[24] N. Saino,et al. Epistatic mutations under divergent selection govern phenotypic variation in the crow hybrid zone , 2019, Nature Ecology & Evolution.
[25] Michael C. Schatz,et al. Assemblytics: a web analytics tool for the detection of variants from an assembly , 2016, Bioinform..
[26] N. Vijay,et al. Transcriptomics of colour patterning and coloration shifts in crows , 2015, Molecular ecology.
[27] J. Korlach,et al. A High-Quality, Long-Read De Novo Genome Assembly to Aid Conservation of Hawaiiʻs Last Remaining Crow Species , 2018, bioRxiv.
[28] Richard Durbin,et al. Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..
[29] H. Innan,et al. On the estimation of the insertion time of LTR retrotransposable elements. , 2010, Molecular biology and evolution.
[30] Natural Selection Constrains Neutral Diversity Across a Wide Range of Species , 2014 .
[31] A. Long,et al. Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits , 2019, Nature Communications.
[32] David Haussler,et al. High-resolution comparative analysis of great ape genomes , 2018, Science.
[33] L. Feuk,et al. Structural variation in the human genome , 2006, Nature Reviews Genetics.
[34] C. Feschotte,et al. Regulatory activities of transposable elements: from conflicts to benefits , 2016, Nature Reviews Genetics.
[35] H. Ellegren. Microsatellite mutations in the germline: implications for evolutionary inference. , 2000, Trends in genetics : TIG.
[36] F. Sedlazeck,et al. Ancestral Admixture Is the Main Determinant of Global Biodiversity in Fission Yeast , 2019, Molecular biology and evolution.
[37] M. K. Rudd,et al. Human Structural Variation: Mechanisms of Chromosome Rearrangements. , 2015, Trends in genetics : TIG.
[38] Michael C. Schatz,et al. Accurate detection of complex structural variations using single molecule sequencing , 2017, Nature Methods.
[39] Brendan L. O’Connell,et al. Chromosome-scale shotgun assembly using an in vitro method for long-range linkage , 2015, Genome research.
[40] J. McPherson,et al. Coming of age: ten years of next-generation sequencing technologies , 2016, Nature Reviews Genetics.
[41] David Levine,et al. A high-performance computing toolset for relatedness and principal component analysis of SNP data , 2012, Bioinform..
[42] J. Bennetzen,et al. A unified classification system for eukaryotic transposable elements , 2007, Nature Reviews Genetics.
[43] S. Salzberg,et al. Versatile and open software for comparing large genomes , 2004, Genome Biology.
[44] Nicholas W. VanKuren,et al. Hidden genetic variation shapes the structure of functional elements in Drosophila , 2017, Nature Genetics.
[45] Alexander Suh,et al. Abundant recent activity of retrovirus‐like retrotransposons within and among flycatcher species implies a rich source of structural variation in songbird genomes , 2018, Molecular ecology.
[46] J. Jurka,et al. Repbase Update, a database of eukaryotic repetitive elements , 2005, Cytogenetic and Genome Research.
[47] D. Bates,et al. Fitting Linear Mixed-Effects Models Using lme4 , 2014, 1406.5823.
[48] Ben G. Holt,et al. A supermatrix phylogeny of corvoid passerine birds (Aves: Corvides). , 2016, Molecular phylogenetics and evolution.
[49] Petr Danecek,et al. BCFtools/csq: haplotype-aware variant consequences , 2016, bioRxiv.
[50] K. van Oers,et al. Gene and transposable element methylation in great tit (Parus major) brain and blood , 2016, BMC Genomics.
[51] Evan E. Eichler,et al. Genetic variation and the de novo assembly of human genomes , 2015, Nature Reviews Genetics.
[52] Timothy B Sackton,et al. Natural Selection Constrains Neutral Diversity across A Wide Range of Species , 2014, bioRxiv.
[53] Fritz J Sedlazeck,et al. Piercing the dark matter: bioinformatics of long-range sequencing and mapping , 2018, Nature Reviews Genetics.
[54] Kazutaka Katoh,et al. Recent developments in the MAFFT multiple sequence alignment program , 2008, Briefings Bioinform..
[55] Wolfgang Stephan,et al. The evolutionary dynamics of repetitive DNA in eukaryotes , 1994, Nature.
[56] Gonçalo R. Abecasis,et al. The variant call format and VCFtools , 2011, Bioinform..
[57] Todd J. Vision,et al. The Standing Pool of Genomic Structural Variation in a Natural Population of Mimulus guttatus , 2013, Genome biology and evolution.
[58] H. Ellegren,et al. Making sense of genomic islands of differentiation in light of speciation , 2016, Nature Reviews Genetics.
[59] F. Balloux,et al. Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast , 2016, Nature Communications.
[60] Alexander Suh,et al. Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex , 2016, Nature Communications.
[61] John Huddleston,et al. An Incomplete Understanding of Human Genetic Variation , 2016, Genetics.
[62] Melissa Gymrek,et al. A genomic view of short tandem repeats. , 2017, Current opinion in genetics & development.