Chromonomer: A Tool Set for Repairing and Enhancing Assembled Genomes Through Integration of Genetic Maps and Conserved Synteny
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[1] Russell E. Durrett,et al. Assembly and diploid architecture of an individual human genome via single-molecule technologies , 2015, Nature Methods.
[2] Elizabeth P. Murchison,et al. Rapid evolutionary response to a transmissible cancer in Tasmanian devils , 2016, Nature Communications.
[3] M. Snyder,et al. High-throughput sequencing technologies. , 2015, Molecular cell.
[4] I. Amit,et al. Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .
[5] Josh Goodman,et al. Polytene chromosomal maps of 11 Drosophila species: the order of genomic scaffolds inferred from genetic and physical maps. , 2008, Genetics.
[6] James G. Baldwin-Brown,et al. Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage , 2016, bioRxiv.
[7] Steven J. M. Jones,et al. Insights into Conifer Giga-Genomes1 , 2014, Plant Physiology.
[8] Catherine A. Wilson,et al. Cold Fusion: Massive Karyotype Evolution in the Antarctic Bullhead Notothen Notothenia coriiceps , 2017, G3: Genes, Genomes, Genetics.
[9] Jin-Wu Nam,et al. The present and future of de novo whole-genome assembly , 2016, Briefings Bioinform..
[10] A. Gnirke,et al. High-quality draft assemblies of mammalian genomes from massively parallel sequence data , 2010, Proceedings of the National Academy of Sciences.
[11] Gordon Luikart,et al. Population Genomics: Advancing Understanding of Nature , 2018 .
[12] Mihai Pop,et al. Genome assembly reborn: recent computational challenges , 2009, Briefings Bioinform..
[13] K. Reinhardt,et al. A Linkage Map and QTL Analysis for Pyrethroid Resistance in the Bed Bug Cimex lectularius , 2016, G3: Genes, Genomes, Genetics.
[14] Jonathan M D Wood,et al. Using optical mapping data for the improvement of vertebrate genome assemblies , 2015, GigaScience.
[15] Eugene W. Myers,et al. A whole-genome assembly of Drosophila. , 2000, Science.
[16] Isaac Y. Ho,et al. Meraculous: De Novo Genome Assembly with Short Paired-End Reads , 2011, PloS one.
[17] Ian T. Fiddes,et al. Resolving the full spectrum of human genome variation using Linked-Reads , 2019, Genome research.
[18] J. V. Moran,et al. Initial sequencing and analysis of the human genome. , 2001, Nature.
[19] Julian Michael Catchen,et al. Stacks 2: Analytical Methods for Paired-end Sequencing Improve RADseq-based Population Genomics , 2019, bioRxiv.
[20] L. Keller,et al. A Y-like social chromosome causes alternative colony organization in fire ants , 2013, Nature.
[21] J. Mallet,et al. Supergene Evolution Triggered by the Introgression of a Chromosomal Inversion , 2017, Current Biology.
[22] Michael Hiller,et al. Author Correction: The axolotl genome and the evolution of key tissue formation regulators , 2018, Nature.
[23] F. Collins,et al. The Human Genome Project: Lessons from Large-Scale Biology , 2003, Science.
[24] Pavel A Pevzner,et al. How to apply de Bruijn graphs to genome assembly. , 2011, Nature biotechnology.
[25] J. Postlethwait,et al. A new model army: Emerging fish models to study the genomics of vertebrate Evo-Devo. , 2015, Journal of experimental zoology. Part B, Molecular and developmental evolution.
[26] T. Zhao,et al. Network-based microsynteny analysis identifies major differences and genomic outliers in mammalian and angiosperm genomes , 2019, Proceedings of the National Academy of Sciences.
[27] N. Weisenfeld,et al. Direct determination of diploid genome sequences , 2016, bioRxiv.
[28] C. Peichel,et al. The genetic and molecular architecture of phenotypic diversity in sticklebacks , 2017, Philosophical Transactions of the Royal Society B: Biological Sciences.
[29] Heng Li,et al. Fast and accurate long-read assembly with wtdbg2 , 2019, Nature Methods.
[30] Shaobin Lin,et al. Comprehensive Genome Profiling of Single Sperm Cells by Multiple Annealing and Looping‐Based Amplification Cycles and Next‐Generation Sequencing from Carriers of Robertsonian Translocation , 2017, Annals of human genetics.
[31] O. Jaillon,et al. Gene loss and evolutionary rates following whole-genome duplication in teleost fishes. , 2006, Molecular biology and evolution.
[32] Etsuko N. Moriyama,et al. Evolution of a Large, Conserved, and Syntenic Gene Family in Insects , 2012, G3: Genes | Genomes | Genetics.
[33] Marius Roesti,et al. Recombination in the threespine stickleback genome—patterns and consequences , 2013, Molecular ecology.
[34] Mihai Pop,et al. Modern technologies and algorithms for scaffolding assembled genomes , 2019, PLoS Comput. Biol..
[35] J. Bednar,et al. Alpha-trimmed means and their relationship to median filters , 1984 .
[36] Jordan S. Ramsdell,et al. A Male-Specific Genetic Map of the Microcrustacean Daphnia pulex Based on Single-Sperm Whole-Genome Sequencing , 2015, Genetics.
[37] The genome sequence of the Antarctic bullhead notothen reveals evolutionary adaptations to a cold environment , 2014, Genome Biology.
[38] Morgan Wirthlin,et al. Conserved syntenic clusters of protein coding genes are missing in birds , 2014, Genome Biology.
[39] A. Amores,et al. The genome of the Gulf pipefish enables understanding of evolutionary innovations , 2016, Genome Biology.
[40] Akihiro Shima,et al. A medaka gene map: the trace of ancestral vertebrate proto-chromosomes revealed by comparative gene mapping. , 2004, Genome research.
[41] R. Gibbs,et al. Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology , 2012, PloS one.
[42] D. Ebert,et al. A high-density genetic map reveals variation in recombination rate across the genome of Daphnia magna , 2016, BMC Genetics.
[43] Kin Fai Au,et al. A comparative evaluation of hybrid error correction methods for error-prone long reads , 2019, Genome Biology.
[44] P. Phillips,et al. Using Population Genomics to Detect Selection in Natural Populations: Key Concepts and Methodological Considerations , 2010, International Journal of Plant Sciences.
[45] D. Kleinjan,et al. Long-range control of gene expression: emerging mechanisms and disruption in disease. , 2005, American journal of human genetics.
[46] R. Wilson,et al. Modernizing Reference Genome Assemblies , 2011, PLoS biology.
[47] J. Catchen,et al. Genomic Resources for Darters (Percidae: Etheostominae) Provide Insight into Postzygotic Barriers Implicated in Speciation , 2019, Molecular biology and evolution.
[48] L. Bernatchez,et al. Salmonid Chromosome Evolution as Revealed by a Novel Method for Comparing RADseq Linkage Maps , 2016, bioRxiv.
[49] Yu Lin,et al. Assembly of long, error-prone reads using repeat graphs , 2018, Nature Biotechnology.
[50] Iris Tzafrir,et al. A Sequence-Based Map of Arabidopsis Genes with Mutant Phenotypes1,212 , 2003, Plant Physiology.
[51] M. Blaxter,et al. Genome-wide genetic marker discovery and genotyping using next-generation sequencing , 2011, Nature Reviews Genetics.
[52] Han-Woo Kim,et al. Antarctic blackfin icefish genome reveals adaptations to extreme environments , 2019, Nature Ecology & Evolution.
[53] P. Etter,et al. Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers , 2008, PloS one.
[54] Michael Hiller,et al. The axolotl genome and the evolution of key tissue formation regulators , 2018, Nature.
[55] Charles E. Chapple,et al. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype , 2004, Nature.
[56] M. Perry,et al. A transposable element insertion is associated with an alternative life history strategy , 2019, Nature Communications.
[57] Jian Wang,et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler , 2012, GigaScience.
[58] Alberto Policriti,et al. GapFiller: a de novo assembly approach to fill the gap within paired reads , 2012, BMC Bioinformatics.
[59] G. Luikart,et al. Harnessing the power of RADseq for ecological and evolutionary genomics , 2016, Nature Reviews Genetics.
[60] A. Perkins,et al. Evolution of gene function and regulatory control after whole-genome duplication: comparative analyses in vertebrates. , 2009, Genome research.
[61] International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome , 2001, Nature.
[62] A. Amores,et al. A RAD-Tag Genetic Map for the Platyfish (Xiphophorus maculatus) Reveals Mechanisms of Karyotype Evolution Among Teleost Fish , 2014, Genetics.
[63] T. S. Painter,et al. A NEW METHOD FOR THE STUDY OF CHROMOSOME REARRANGEMENTS AND THE PLOTTING OF CHROMOSOME MAPS. , 1933, Science.
[64] C. Hutchison. DNA sequencing: bench to bedside and beyond , 2007, Nucleic acids research.