MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

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1. Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies
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2. The genome of Chenopodium quinoa
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3. Case Study: Prolonged Infectious SARS-CoV-2 Shedding from an Asymptomatic Immunocompromised Individual with Cancer
   Victoria A. Avanzato, M. Jeremiah Matson, Stephanie N. Seifert, Rhys Pryce, Brandi N. Williamson, Sarah L. Anzick, Kent Barbian, Seth David Judson, Elizabeth R. Fischer, Craig Martens et al. · 2020 · Cell
4. Comparative protein structure modeling using MODELLER
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5. Taxonomic classification of cyanoprokaryotes (cyanobacterial genera) 2014, using a polyphasic approach
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6. ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference
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7. Renewing Felsenstein’s phylogenetic bootstrap in the era of big data
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8. SARS-CoV-2 infection in farmed minks, the Netherlands, April and May 2020
   Nadia Oreshkova, Robert Jan Molenaar, Sandra Vreman, Frank Harders, Bas B. Oude Munnink, Renate W. Hakze‐van der Honing, Nora M. Gerhards, Paulien Tolsma, Ruth Bouwstra, Reina S. Sikkema et al. · 2020 · Eurosurveillance
9. Haplotype-resolved diverse human genomes and integrated analysis of structural variation
   Ebert, Peter, Audano, Peter A., Zhu, Qihui, Rodriguez-Martin, Bernardo, Porubsky, David, Bonder, Marc Jan, Sulovari, Arvis, Ebler, Jana, Zhou, Weichen, Serra Mari, Rebecca et al. · 2021 · Science
10. Origin and evolution of the octoploid strawberry genome
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11. Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts
    Gallone, Brigida, Steensels, Jan, Prahl, Troels, Soriaga, Leah, Saels, Veerle, Herrera-Malaver, Beatriz, Merlevede, Adriaan, Roncoroni, Miguel, Voordeckers, Karin, Miraglia, Loren et al. · 2016 · Cell
12. Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals
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13. Crystal Structure of the Human Cannabinoid Receptor CB1
    Tian Hua, Kiran V. Vemuri, Mengchen Pu, Lu Qu, Gye Won Han, Yiran Wu, Suwen Zhao, Wenqing Shui, Shanshan Li, Anisha Korde et al. · 2016 · Cell
14. A thermostable mRNA vaccine against COVID-19
    Zhang, Na-Na, Li, Xiao-Feng, Deng, Yong-Qiang, Zhao, Hui, Huang, Yi-Jiao, Yang, Guan, Huang, Wei-Jin, Gao, Peng, Zhou, Chao, Zhang, Rong-Rong et al. · 2020 · Cell
15. Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities
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16. Corrigendum: Powdery Mildews Are Characterized by Contracted Carbohydrate Metabolism and Diverse Effectors to Adapt to Obligate Biotrophic Lifestyle
    Peng Liang, Songyu Liu, Feng Xu, Shuqin Jiang, Jun Yan, Qiguang He, Wenbo Liu, Chunhua Lin, Fucong Zheng, Xiangfeng Wang et al. · 2019 · Frontiers in Microbiology
17. Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes
    Alexandra Moura, Alexis Criscuolo, Hannes Pouseele, Mylène M. Maury, Alexandre Leclercq, Cheryl L. Tarr, Johanna Björkman, Timothy J. Dallman, Aleisha R. Reimer, Vincent Enouf et al. · 2016 · Nature Microbiology
18. Improved metagenome binning and assembly using deep variational autoencoders
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19. eggNOG v4.0: nested orthology inference across 3686 organisms
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20. Root traits are multidimensional: specific root length is independent from root tissue density and the plant economic spectrum
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21. Classification of Aspergillus, Penicillium, Talaromyces and related genera (Eurotiales): An overview of families, genera, subgenera, sections, series and species
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22. Revisiting the taxonomy and evolution of pathogenicity of the genus Leptospira through the prism of genomics
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23. Isolation of an archaeon at the prokaryote–eukaryote interface
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24. KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks
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25. Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum
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26. Innovations to culturing the uncultured microbial majority
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27. Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation
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28. 16S rRNA Gene Analysis with QIIME2
    Michael Hall, Robert Gerald Beiko · 2018 · Methods in molecular biology
29. Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins
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30. The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies
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31. Neutralizing antibodies correlate with protection from SARS-CoV-2 in humans during a fishery vessel outbreak with a high attack rate
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32. A simple method to control over-alignment in the MAFFT multiple sequence alignment program
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33. Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades
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34. Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines
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35. Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants
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36. A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals
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37. SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity
    Motozono, Chihiro, Toyoda, Mako, Zahradnik, Jiri, Saito, Akatsuki, Nasser, Hesham, Tan, Toong Seng, Ngare, Isaac, Kimura, Izumi, Uriu, Keiya, Kosugi, Yusuke et al. · 2021 · Cell Host & Microbe
38. New CRISPR–Cas systems from uncultivated microbes
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39. Hydrogen peroxide sensor HPCA1 is an LRR receptor kinase in Arabidopsis
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40. A human gut bacterial genome and culture collection for improved metagenomic analyses
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41. DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work
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42. Taxonomy ofAspergillussectionFlaviand their production of aflatoxins, ochratoxins and other mycotoxins
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43. Basidiomycete yeasts in the cortex of ascomycete macrolichens
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44. The industrial melanism mutation in British peppered moths is a transposable element
    Arjèn E. van’t Hof, Pascal Campagne, Daniel John Rigden, Carl J. Yung, Jessica K. Lingley, Michael Andrew Quail, Neil Hall, Alistair C. Darby, Ilik J. Saccheri · 2016 · Nature
45. Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
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46. Plant cell-surface GIPC sphingolipids sense salt to trigger Ca2+ influx
    Zhonghao Jiang, Xiaoping Zhou, Ming Tao, Fang Yuan, Lulu Liu, Fei-Hua Wu, Xiaomei Wu, Yun Xiang, Yue Niu, Feng Liu et al. · 2019 · Nature
47. KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-Coding Sequences
    Zhang Zhang · 2022 · Genomics Proteomics & Bioinformatics
48. A mitochondrial genome sequence of a hominin from Sima de los Huesos
    Meyer, Matthias, Fu, Qiaomei, Aximu-Petri, Ayinuer, Glocke, Isabelle, Nickel, Birgit, Arsuaga, Juan-Luis, Martínez, Ignacio, Gracia, Ana, de Castro, José María Bermúdez, Carbonell, Eudald et al. · 2014 · Nature
49. An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons
    Jacobs, Frank M. J., Greenberg, David, Nguyen, Ngan, Haeussler, Maximilian, Ewing, Adam D., Katzman, Sol, Paten, Benedict, Salama, Sofie R., Haussler, David · 2014 · Nature
50. Predicting multiple conformations via sequence clustering and AlphaFold2
    Wayment-Steele, Hannah K., Ojoawo, Adedolapo, Otten, Renee, Apitz, Julia M., Pitsawong, Warintra, Hömberger, Marc, Ovchinnikov, Sergey, Colwell, Lucy, Kern, Dorothee · 2024 · Nature
51. Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant
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52. Lineages of ectomycorrhizal fungi revisited: Foraging strategies and novel lineages revealed by sequences from belowground
    Leho Tedersoo, Matthew E. Smith · 2013 · Fungal Biology Reviews
53. Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX
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54. The ORF8 protein of SARS-CoV-2 mediates immune evasion through down-regulating MHC-Ι
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55. Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape
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56. Bayesian Evolutionary Analysis with BEAST
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57. Recent introduction of a chytrid fungus endangers Western Palearctic salamanders
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58. Genomes of Subaerial Zygnematophyceae Provide Insights into Land Plant Evolution
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59. The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization
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60. The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations
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61. A single bacterial genus maintains root growth in a complex microbiome
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62. Phylogenomics reveals the evolutionary timing and pattern of butterflies and moths
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63. Outline of Fungi and fungus-like taxa – 2021
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64. Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016
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65. SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape
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66. CATH: increased structural coverage of functional space
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67. The spider tree of life: phylogeny of Araneae based on target‐gene analyses from an extensive taxon sampling
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68. Clades of huge phages from across Earth’s ecosystems
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69. Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits
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70. Miniaturized mitogenome of the parasitic plant Viscum scurruloideum is extremely divergent and dynamic and has lost all nad genes
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71. Development of CRISPR as an Antiviral Strategy to Combat SARS-CoV-2 and Influenza
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72. Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information
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73. Molecular signatures and phylogenomic analysis of the genus Burkholderia: proposal for division of this genus into the emended genus Burkholderia containing pathogenic organisms and a new genus Paraburkholderia gen. nov. harboring environmental species
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74. Spillover of highly pathogenic avian influenza H5N1 virus to dairy cattle
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75. Phylogenetic Analysis and Structural Modeling of SARS-CoV-2 Spike Protein Reveals an Evolutionary Distinct and Proteolytically Sensitive Activation Loop
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76. A standardized archaeal taxonomy for the Genome Taxonomy Database
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77. Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus
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78. Antibody 10-1074 suppresses viremia in HIV-1-infected individuals
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79. Slow Delivery Immunization Enhances HIV Neutralizing Antibody and Germinal Center Responses via Modulation of Immunodominance
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80. The complete sequence of a human Y chromosome
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81. S1 gene-based phylogeny of infectious bronchitis virus: An attempt to harmonize virus classification
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82. Dense sampling of bird diversity increases power of comparative genomics
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83. AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential
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84. Structure of the activated ROQ1 resistosome directly recognizing the pathogen effector XopQ
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85. Neandertal and Denisovan DNA from Pleistocene sediments
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86. Mutations Strengthened SARS-CoV-2 Infectivity
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87. A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification
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88. SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern
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89. Cas13d Is a Compact RNA-Targeting Type VI CRISPR Effector Positively Modulated by a WYL-Domain-Containing Accessory Protein
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90. Generic concepts in Nectriaceae
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91. COVID-19 in Amazonas, Brazil, was driven by the persistence of endemic lineages and P.1 emergence
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92. A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour
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93. The genetic and epigenetic landscape of the Arabidopsis centromeres
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94. Efficient evolution of human antibodies from general protein language models
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95. Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis
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