Tandem repeats finder: a program to analyze DNA sequences

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1. Relapses ofPlasmodium vivaxInfection Usually Result from Activation of Heterologous Hypnozoites
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3. Flexible Pattern Matching in Strings
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4. Bioinformatics-Based Identification of Expanded Repeats: A Non-reference Intronic Pentamer Expansion in RFC1 Causes CANVAS
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7. TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools
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   Hyung‐Soon Yim, Yun Sung Cho, Xuanmin Guang, Sung Gyun Kang, Jae-Yeon Jeong, Sun‐Shin Cha, Hyun‐Myung Oh, Jae‐Hak Lee, Eun Chan Yang, Kae Kyoung Kwon et al. · 2013 · Nature Genetics
9. Draft Genome of the Pearl Oyster Pinctada fucata: A Platform for Understanding Bivalve Biology
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11. The high‐quality genome of Brassica napus cultivar ‘ ZS 11’ reveals the introgression history in semi‐winter morphotype
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12. High-Resolution Genome-Wide Dissection of the Two Rules of Speciation in Drosophila
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13. The DNA sequence and analysis of human chromosome 6
    Andrew J. J. Mungall, Sophie Palmer, Sarah K. Sims, Carol A. Edwards, Jennifer L. Ashurst, Laurens G. Wilming, M. C. Jones, R. Horton, Sarah E Hunt, Carol Scott et al. · 2003 · Nature
14. Complete MHC Haplotype Sequencing for Common Disease Gene Mapping
    C. Andrew Stewart, Roger Horton, Richard J.N. Allcock, Jennifer L. Ashurst, Alexey M. Atrazhev, Penny Coggill, Ian Dunham, Simon Forbes, Karen Halls, Joanna M.M. Howson et al. · 2004 · Genome Research
15. The Genome of Dendrobium officinale Illuminates the Biology of the Important Traditional Chinese Orchid Herb
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16. Inverted Repeat Structure of the Human Genome: The X-Chromosome Contains a Preponderance of Large, Highly Homologous Inverted Repeats That Contain Testes Genes
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17. Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED
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18. OUP accepted manuscript
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19. Long-read sequencing of 3,622 Icelanders provides insight into the role of structural variants in human diseases and other traits
    Doruk Beyter, Helga Ingimundardóttir, Ásmundur Oddsson, Hannes P. Eggertsson, Eyþór Björnsson, Hákon Jónsson, Bjarni A. Atlason, Snædís Kristmundsdóttir, Svenja Mehringer, Marteinn Thor Hardarson et al. · 2021 · Nature Genetics
20. Dual domestications and origin of traits in grapevine evolution
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21. Direct estimate of the rate of germline mutation in a bird
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22. Ascaris suum draft genome
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23. Genome of wild olive and the evolution of oil biosynthesis
    Turgay Ünver, Zhangyan Wu, Lieven Sterck, Mine Türktaş, Rolf Lohaus, Zhen Li, Ming Yu Yang, Lijuan He, Tianquan Deng, Francisco Javier Escalante et al. · 2017 · Proceedings of the National Academy of Sciences
24. Repetitive DNA in the pea (Pisum sativum L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula
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25. Genome assembly forensics: finding the elusive mis-assembly
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26. Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease
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27. Comparisons Among Two Fertile and Three Male-Sterile Mitochondrial Genomes of Maize
    James O. Allen, Christiane M.‐R. Fauron, Patrick J. Minx, Leah M Roark, Swetha Oddiraju, Guan Ning Lin, Louis J. Meyer, Hui Sun, Kyung Kim, Chunyan Wang et al. · 2007 · Genetics
28. Liriodendron genome sheds light on angiosperm phylogeny and species–pair differentiation
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29. Expressed Sequence Tag-Linked Microsatellites as a Source of Gene-Associated Polymorphisms for Detecting Signatures of Divergent Selection in Atlantic Salmon (Salmo salar L.)
    Anti Vasemägi, Jan Åke Nilsson, Craig Robert Primmer · 2005 · Molecular Biology and Evolution
30. Development of a Comprehensive Genotype-to-Fitness Map of Adaptation-Driving Mutations in Yeast
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31. A tandem repeats database for bacterial genomes: application to the genotyping of Yersinia pestis and Bacillus anthracis
    Philippe Le Flèche, Yolande Hauck, Lucie Onteniente, Agnès Prieur, France Denœud, Vincent Ramisse, Patricia Sylvestre, Gary Benson, Françoise Ramisse, Gilles Vergnaud · 2001 · BMC Microbiology
32. Profiling the genome-wide landscape of tandem repeat expansions
    2019
33. Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential
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34. Mutation of TBCE causes hypoparathyroidism– retardation–dysmorphism and autosomal recessive Kenny–Caffey syndrome
    Ruti Parvari, Eli Hershkovitz, Rafael Gorodischer, Nili Grossman, Bart Loeys, Geert R. Mortier, Alexandra Zecic, Simon G. Gregory, Reuven Sharony, Marios Kambouris et al. · 2002 · Nature Genetics
35. The genome-wide determinants of human and chimpanzee microsatellite evolution
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36. The common marmoset genome provides insight into primate biology and evolution
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37. The Penium margaritaceum Genome: Hallmarks of the Origins of Land Plants
    Chen Jiao, Iben Sørensen, Xuepeng Sun, Honghe Sun, Hila Behar, Saleh Alseekh, Glenn Philippe, Kattia Palacio‐López, Li Sun, Reagan Reed et al. · 2020 · Cell
38. Gene family innovation, conservation and loss on the animal stem lineage
    2018
39. Complete Chloroplast Genome Sequence of a Major Invasive Species, Crofton Weed (Ageratina adenophora)
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40. Whole-Genome Comparison Reveals Novel Genetic Elements That Characterize the Genome of Industrial Strains of Saccharomyces cerevisiae
    Anthony R. Borneman, Brian A. Desany, David Riches, Jason P. Affourtit, Angus H. Forgan, Isak S. Pretorius, Michael Egholm, Paul J. Chambers · 2011 · PLoS Genetics
41. The sea cucumber genome provides insights into morphological evolution and visceral regeneration
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42. Genomic diversity and evolution of the head crest in the rock pigeon
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43. Worldwide Genetic Relationships among Francisella tularensis Isolates Determined by Multiple-Locus Variable-Number Tandem Repeat Analysis
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44. The Genome Sequence ofMycoplasma hyopneumoniaeStrain 232, the Agent of Swine Mycoplasmosis
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45. GinkgoandWelwitschiaMitogenomes Reveal Extreme Contrasts in Gymnosperm Mitochondrial Evolution
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46. Live visualization of chromatin dynamics with fluorescent TALEs
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47. Dothideomycete–Plant Interactions Illuminated by Genome Sequencing and EST Analysis of the Wheat Pathogen Stagonospora nodorum
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48. Adaptation and conservation insights from the koala genome
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49. A reference-grade wild soybean genome
    Min Xie, Claire Chung, Man‐Wah Li, Fuk‐Ling Wong, Xin Wang, Ailin Liu, Zhili Wang, Alden King-Yung Leung, Tin-Hang Wong, S.-W. Tong et al. · 2019 · Nature Communications
50. A specific missense mutation in GTF2I occurs at high frequency in thymic epithelial tumors
    Iacopo Petrini, Paul S. Meltzer, In‐Kyu Kim, Marco Lucchi, Kang-Seo Park, Gabriella Fontanini, James Gao, Paolo Andrea Zucali, Fiorella Calabrese, Adolfo Gino Favaretto et al. · 2014 · Nature Genetics
51. The complete reference genome for grapevine ( Vitis vinifera L.) genetics and breeding
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52. Discovering and detecting transposable elements in genome sequences
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53. Mining microsatellites in eukaryotic genomes
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54. Mutation spectrum revealed by breakpoint sequencing of human germline CNVs
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55. On the origin of new genes in Drosophila
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56. Bias of Selection on Human Copy-Number Variants
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57. Estimation of divergence times in cnidarian evolution based on mitochondrial protein-coding genes and the fossil record
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58. MicroRNA Gene Evolution in Arabidopsis lyrata and Arabidopsis thaliana
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59. Microstructural Changes in Noncoding Chloroplast DNA: Interpretation, Evolution, and Utility of Indels and Inversions in Basal Angiosperm Phylogenetic Inference
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60. Complete Genome Sequence of Yersinia pestis Strain 91001, an Isolate Avirulent to Humans
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61. Genome-Wide Analysis of DNA Methylation Dynamics during Early Human Development
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62. A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies
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63. Use of a Novel Panel of Nine Short Tandem Repeats for Exact and High-Resolution Fingerprinting of Aspergillus fumigatus Isolates
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64. The genome and transcriptome of Japanese flounder provide insights into flatfish asymmetry
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65. A burst of segmental duplications in the genome of the African great ape ancestor
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66. Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (Arachis hypogaea)
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67. Evidence for a Global Wolbachia Replacement in Drosophila melanogaster
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68. The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non‐structural polyphenols
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69. Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale
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70. A graph-based genome and pan-genome variation of the model plant Setaria
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71. Reconstructing the Genomic Architecture of Ancestral Mammals: Lessons From Human, Mouse, and Rat Genomes
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72. Earl Grey: A Fully Automated User-Friendly Transposable Element Annotation and Analysis Pipeline
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73. Comparative Analysis of the Complete Chloroplast Genomes of Five Quercus Species
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74. The allotetraploid origin and asymmetrical genome evolution of the common carp Cyprinus carpio
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75. Genome-wide detection of tandem DNA repeats that are expanded in autism
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76. Sweet Sorghum Genetic Diversity and Association Mapping for Brix and Height
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77. Genomic analysis of the causative agents of coccidiosis in domestic chickens
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78. The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming
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79. A physical and genetic map of Cannabis sativa identifies extensive rearrangements at the THC/CBD acid synthase loci
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80. SSR Locator: Tool for Simple Sequence Repeat Discovery Integrated with Primer Design and PCR Simulation
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81. The Nephila clavipes genome highlights the diversity of spider silk genes and their complex expression
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82. Genetic structure and insecticide resistance characteristics of fall armyworm populations invading China
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83. Parameters for accurate genome alignment
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84. A Comprehensive Survey of Human Y-Chromosomal Microsatellites
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85. Sequence, Chromatin and Evolution of Satellite DNA
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86. Computational detection of genomic cis- regulatory modules applied to body patterning in the early Drosophila embryo
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87. Truvari: refined structural variant comparison preserves allelic diversity
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88. The Cycas genome and the early evolution of seed plants
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89. Targeted long-read sequencing identifies missing disease-causing variation
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90. Evolution and Diversity in Human Herpes Simplex Virus Genomes
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91. Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs
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92. Sequencing of the smallest Apicomplexan genome from the human pathogen Babesia microti†
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93. Epigenomic consequences of immortalized plant cell suspension culture
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94. Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments
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95. IMEx: Imperfect Microsatellite Extractor
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96. CRISPR-Mediated Programmable 3D Genome Positioning and Nuclear Organization
    Haifeng Wang, Xiaoshu Xu, Cindy M. Nguyen, Yanxia Liu, Yuchen Gao, Xueqiu Lin, Timothy Daley, Nathan H. Kipniss, Marie F. La Russa, Lei S. Qi · 2018 · Cell
97. Genome assembly of wild tea tree DASZ reveals pedigree and selection history of tea varieties
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98. Genome sequence and genetic diversity of European ash trees
    Elizabeth Sollars, Andrea L. Harper, Laura J. Kelly, Christine Sambles, Ricardo Humberto Ramirez-Gonzalez, David Swarbreck, Gemy Kaithakottil, Endymion D. Cooper, Cristóbal Uauy, Lenka Havlíčková et al. · 2016 · Nature
99. Stout camphor tree genome fills gaps in understanding of flowering plant genome evolution
    Shu‐Miaw Chaw, Yu-Ching Liu, Yu‐Wei Wu, Han-Yu Wang, Chan‐Yi Ivy Lin, Chung‐Shien Wu, Huei‐Mien Ke, Lo‐Yu Chang, Chih-Yao Hsu, Hui-Ting Yang et al. · 2019 · Nature Plants
100. Pathogenomic Sequence Analysis of Bacillus cereus and Bacillus thuringiensis Isolates Closely Related to Bacillus anthracis
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