FLASH: fast length adjustment of short reads to improve genome assemblies

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1. Composition of the soil fungal community is more sensitive to phosphorus than nitrogen addition in the alpine meadow on the Qinghai-Tibetan Plateau
   Dan He, Xingjia Xiang, Jin-Sheng He, Chao Wang, Guangmin Cao, Jonathan M. Adams, Haiyan Chu · 2016 · Biology and Fertility of Soils
2. Tobacco bacterial wilt suppression with biochar soil addition associates to improved soil physiochemical properties and increased rhizosphere bacteria abundance
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3. Study of Microbiomes in Aseptically Collected Samples of Human Breast Tissue Using Needle Biopsy and the Potential Role of in situ Tissue Microbiomes for Promoting Malignancy
   Meng Shen, Bin Chen, Junjie Yang, Jingwen Wang, Dequan Zhu, Qingsong Meng, Lei Zhang · 2018 · Frontiers in Oncology
4. Gut dysbiosis and lack of short chain fatty acids in a Chinese cohort of patients with multiple sclerosis
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5. Iron Corrosion via Direct Metal-Microbe Electron Transfer
   Haiyan Tang, Dawn E. Holmes, Toshiyuki Ueki, Paola Andrea Palacios, Derek R. Lovley · 2019 · mBio
6. Effects of fortification of Daqu with various yeasts on microbial community structure and flavor metabolism
   Weiwei Li, Guangsen Fan, Zhilei Fu, Wenhua Wang, Youqiang Xu, Chao Teng, Chengnan Zhang, Ran Yang, Baoguo Sun, Xiuting Li · 2019 · Food Research International
7. Structural and functional responses of bacterial and fungal communities to multiple heavy metal exposure in arid loess
   Xiaoying Zeng, Shi-Weng Li, Yan Leng, Xiao-Hu Kang · 2020 · The Science of The Total Environment
8. Imprecision and DNA Break Repair Biased towards Incompatible End Joining in Leukemia
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9. Bacteriophages Isolated from Stunted Children Can Regulate Gut Bacterial Communities in an Age-Specific Manner
   Mohammadali Khan Mirzaei, Md Anik Ashfaq Khan, Prakash Ghosh, Zofia Ecaterina Taranu, Mariia Taguer, Jinlong Ru, Rajashree Chowdhury, Md. Mamun Kabir, Li Deng, Dinesh Mondal et al. · 2020 · Cell Host & Microbe
10. Antidiabetic Effects of Gegen Qinlian Decoction via the Gut Microbiota are Attributable to Its Key Ingredient Berberine
    Xizhan Xu, Zezheng Gao, Fuquan Yang, Yingying Yang, Liang Chen, Han Lin, Na Zhao, Jiayue Xu, Xinmiao Wang, Yue Ma et al. · 2020 · Genomics Proteomics & Bioinformatics
11. Phyllostomid bat microbiome composition is associated to host phylogeny and feeding strategies
    Mario Carrillo-Araujo, Neslihan Taş, Rocío Alcántara‐Hernández, Osiris Gaona, Jorge E. Schondube, Rodrigo A. Medellín, Janet K Jansson, Luisa I. Falcón · 2015 · Frontiers in Microbiology
12. Small RNAs derived from tRNAs and rRNAs are highly enriched in exosomes from both old and new world Leishmania providing evidence for conserved exosomal RNA Packaging
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13. Nitrifying moving bed biofilm reactor (MBBR) biofilm and biomass response to long term exposure to 1 °C
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14. An improved genome assembly uncovers prolific tandem repeats in Atlantic cod
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15. Community dynamics of free-living and particle-attached bacteria following a reservoir Microcystis bloom
    Min Liu, Lemian Liu, Huihuang Chen, Zheng Yu, Jun R. Yang, Yuanyuan Xue, Bangqin Huang, Jun Yang · 2018 · The Science of The Total Environment
16. Intratumor microbiome features reveal antitumor potentials of intrahepatic cholangiocarcinoma
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17. Microbial modulation of behavior and stress responses in zebrafish larvae
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18. Transcript, protein and metabolite temporal dynamics in the CAM plant Agave
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19. Long-term fertilization changes bacterial diversity and bacterial communities in the maize rhizosphere of Chinese Mollisols
    Qingfeng Wang, Xin Peng Jiang, Dawei Guan, Dan Wei, Baisuo Zhao, Mingchao Ma, Sanfeng Chen, Li Li, Fengming Cao, Xiangnan Li · 2017 · Applied Soil Ecology
20. The Gills of Reef Fish Support a Distinct Microbiome Influenced by Host-Specific Factors
    Zoe A. Pratte, Marc Besson, Rebecca D. Hollman, Frank J. Stewart · 2018 · Applied and Environmental Microbiology
21. Rapid microevolution of biofilm cells in response to antibiotics
    Anahit Penesyan, Stephanie S. Nagy, Staffan J. Kjelleberg, Michael Richard Gillings, Ian T. Paulsen · 2019 · npj Biofilms and Microbiomes
22. Bacteroides uniformis combined with fiber amplifies metabolic and immune benefits in obese mice
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23. One step closer to understanding the role of bacteria in diabetic foot ulcers: characterising the microbiome of ulcers
    Karen Smith, Andrew Collier, Eleanor R. Townsend, Lindsay E. O’Donnell, Abhijit M. Bal, John P. Butcher, William Gordon Mackay, Gordon Ramage, Craig Williams · 2016 · BMC Microbiology
24. Potent and broad HIV-neutralizing antibodies in memory B cells and plasma
    LaTonya D. Williams, Gilad Ofek, Sebastian Schätzle, Jonathan R. McDaniel, Xiaozhi Lu, Nathan I. Nicely, Liming Wu, C.S. Lougheed, Todd Bradley, Mark K. Louder et al. · 2017 · Science Immunology
25. Sequencing and de novo assembly of 150 genomes from Denmark as a population reference
    Lasse Maretty, Jacob Malte Jensen, Bent Petersen, Jonas A. Sibbesen, SiYang Maggie Liu, Palle Villesen, Laurits Skov, Kirstine Belling, Christian Theil Have, José M. G. Izarzugaza et al. · 2017 · Nature
26. Butyrate Producers as Potential Next-Generation Probiotics: Safety Assessment of the Administration of Butyricicoccus pullicaecorum to Healthy Volunteers
    Leen Boesmans, Mireia Valles‐Colomer, Jun Wang, Venessa Eeckhaut, Gwen Falony, Richard Ducatelle, Filip Van Immerseel, Jeroen Raes, Kristin Verbeke · 2018 · mSystems
27. Soil pH dominates elevational diversity pattern for bacteria in high elevation alkaline soils on the Tibetan Plateau
    Congcong Shen, Yu Shi, Kunkun Fan, Jin-Sheng He, Jonathan M. Adams, Yuan Ge, Haiyan Chu · 2019 · FEMS Microbiology Ecology
28. Bait input altered microbial community structure and increased greenhouse gases production in coastal wetland sediment
    Genmei Lin, Xianbiao Lin · 2022 · Water Research
29. Microhaplotypes provide increased power from short‐read DNA sequences for relationship inference
    Diana S. Baetscher, Anthony J. Clemento, Thomas C. Ng, Eric C. Anderson, John Carlos Garza · 2017 · Molecular Ecology Resources
30. A Coxiella mutualist symbiont is essential to the development of Rhipicephalus microplus
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31. Soil types influence the fate of antibiotic-resistant bacteria and antibiotic resistance genes following the land application of sludge composts
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32. Mitigating Anticipated Effects of Systematic Errors Supports Sister-Group Relationship between Xenacoelomorpha and Ambulacraria
    Philippe, Hervé, Poustka, Albert J., Chiodin, Marta, Hoff, Katharina J., Dessimoz, Christophe, Tomiczek, Bartlomiej, Schiffer, Philipp H., Müller, Steven, Domman, Daryl, Horn, Matthias et al. · 2019 · Current Biology
33. Staphylococcus epidermidis Contributes to Healthy Maturation of the Nasal Microbiome by Stimulating Antimicrobial Peptide Production
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34. A prospective longitudinal study on the microbiota composition in amyotrophic lateral sclerosis
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35. Multi-marker metabarcoding of coral skeletons reveals a rich microbiome and diverse evolutionary origins of endolithic algae
    Vanessa R. Marcelino, Heroen Verbruggen · 2016 · Scientific Reports
36. Environmental drivers of viral community composition in Antarctic soils identified by viromics
    Evelien M. Adriaenssens, Rolf Kramer, Marc W. Van Goethem, Thulani Peter Makhalanyane, Ian D. Hogg, Don Arthur Cowan · 2017 · Microbiome
37. Patterns and Processes in Marine Microeukaryotic Community Biogeography from Xiamen Coastal Waters and Intertidal Sediments, Southeast China
    Weidong Chen, Yongbo Pan, Lingyu Yu, Jun Yang, Wenjing Zhang · 2017 · Frontiers in Microbiology
38. Stratified Bacterial and Archaeal Community in Mangrove and Intertidal Wetland Mudflats Revealed by High Throughput 16S rRNA Gene Sequencing
    Zhichao Zhou, Han Meng, Yang Liu, Ji‐Dong Gu, Meng Li · 2017 · Frontiers in Microbiology
39. Host contributes to longitudinal diversity of fecal microbiota in swine selected for lean growth
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40. Genetic Modulation of RNA Splicing with a CRISPR-Guided Cytidine Deaminase
    Juanjuan Yuan, Yunqing Ma, Tao Huang, Yanhao Chen, Yuanzheng Peng, Bing Li, Jia Li, Yuchen Zhang, Bing Song, Xiaofang Sun et al. · 2018 · Molecular Cell
41. Heritable microbiome variation is correlated with source environment in locally adapted maize varieties
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42. Silage fermentation and bacterial community of bur clover, annual ryegrass and their mixtures prepared with microbial inoculant and chemical additive
    Li, Ping, Zhang, Yu, Gou, Wenlong, Cheng, Qiming, Bai, Shiqie, Cai, Yimin · 2019 · Animal Feed Science and Technology
43. MP3: A Software Tool for the Prediction of Pathogenic Proteins in Genomic and Metagenomic Data
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44. Competition drives the response of soil microbial diversity to increased grazing by vertebrate herbivores
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45. Intestinal microbiota profiles associated with low and high residual feed intake in chickens across two geographical locations
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46. The effect of several activated biochars on Cd immobilization and microbial community composition during in-situ remediation of heavy metal contaminated sediment
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47. Evolution and Global Transmission of a Multidrug-Resistant, Community-Associated Methicillin-Resistant Staphylococcus aureus Lineage from the Indian Subcontinent
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48. Effects of microplastics and nitrogen deposition on soil multifunctionality, particularly C and N cycling
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49. Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.
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50. Getting Started with Microbiome Analysis: Sample Acquisition to Bioinformatics
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51. Microbial community analysis in rice paddy soils irrigated by acid mine drainage contaminated water
    Min Ho Sun, Tangfu Xiao, Zengping Ning, Enzong Xiao, Weimin Sun · 2014 · Applied Microbiology and Biotechnology
52. Contrasting Soil Bacterial Community, Diversity, and Function in Two Forests in China
    Hua Wei, C. H. Peng, Bin Yang, Hanxiong Song, Quan Li, Lin Jiang, Gang Wei, Kefeng Wang, Hui Wang, Shirong Liu et al. · 2018 · Frontiers in Microbiology
53. Differential effects of monensin and a blend of essential oils on rumen microbiota composition of transition dairy cows
    Schären, M., Drong, C., Kiri, K., Riede, S., Gardener, M., Meyer, U., Hummel, J., Urich, T., Breves, G., Dänicke, S. · 2017 · Journal of Dairy Science
54. Highlighting the microbial diversity of 12 French cheese varieties
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55. Population genomics reveals that an anthropophilic population of Aedes aegypti mosquitoes in West Africa recently gave rise to American and Asian populations of this major disease vector
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56. Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean
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57. Exposure to heat-stress environment affects the physiology, circulation levels of cytokines, and microbiome in dairy cows
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58. Comparison of Healthy and Dandruff Scalp Microbiome Reveals the Role of Commensals in Scalp Health
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59. Climate warming accelerates temporal scaling of grassland soil microbial biodiversity
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60. Decoupled diversity patterns in bacteria and fungi across continental forest ecosystems
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61. Soil microbial community and network changes after long-term use of plastic mulch and nitrogen fertilization on semiarid farmland
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62. Microhomologies are prevalent at Cas9-induced larger deletions
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63. A preliminary investigation on the relationship between gut microbiota and gene expressions in peripheral mononuclear cells of infants with autism spectrum disorders
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64. Urbanization drives riverine bacterial antibiotic resistome more than taxonomic community at watershed scale
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65. Associations Between Endometriosis and Gut Microbiota
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66. Exon capture phylogenomics: efficacy across scales of divergence
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67. The Probiotic Butyricicoccus pullicaecorum Reduces Feed Conversion and Protects from Potentially Harmful Intestinal Microorganisms and Necrotic Enteritis in Broilers
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68. Metagenomic Analysis of Hot Springs in Central India Reveals Hydrocarbon Degrading Thermophiles and Pathways Essential for Survival in Extreme Environments
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69. Reduced genetic potential for butyrate fermentation in the gut microbiome of infants who develop allergic sensitization
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70. Dietary encapsulated essential oils and organic acids mixture improves gut health in broiler chickens challenged with necrotic enteritis
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71. CuO Nanoparticles Alter the Rhizospheric Bacterial Community and Local Nitrogen Cycling for Wheat Grown in a Calcareous Soil
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72. Soil microbiota manipulation and its role in suppressing soil-borne plant pathogens in organic farming systems under the light of microbiome-assisted strategies
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73. Succession of the microbial communities and function prediction during short-term peach sawdust-based composting
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74. High‐throughput monitoring of wild bee diversity and abundance via mitogenomics
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75. Diversity and distribution patterns of acidobacterial communities in the black soil zone of northeast China
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76. Scale-dependent effects of climate and geographic distance on bacterial diversity patterns across northern China's grasslands
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77. Circular linkages between soil biodiversity, fertility and plant productivity are limited to topsoil at the continental scale
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78. A longitudinal study of the diabetic skin and wound microbiome
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79. Saturated long-chain fatty acid-producing bacteria contribute to enhanced colonic motility in rats
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81. Comparison of the Vaginal Microbiomes of Premenopausal and Postmenopausal Women
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82. Biochar Induces Changes to Basic Soil Properties and Bacterial Communities of Different Soils to Varying Degrees at 25 mm Rainfall: More Effective on Acidic Soils
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83. The diversity and biogeography of abundant and rare intertidal marine microeukaryotes explained by environment and dispersal limitation
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84. Long-term combined application of manure and chemical fertilizer sustained higher nutrient status and rhizospheric bacterial diversity in reddish paddy soil of Central South China
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85. Microbial production and consumption of dissolved organic matter in glacial ecosystems on the Tibetan Plateau
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86. Dynamic change of bacterial community during dairy manure composting process revealed by high-throughput sequencing and advanced bioinformatics tools
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87. Warming-induced permafrost thaw exacerbates tundra soil carbon decomposition mediated by microbial community
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88. Missense mutations in TENM4 , a regulator of axon guidance and central myelination, cause essential tremor
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89. Detection of Antibiotic Resistance Genes in Source and Drinking Water Samples from a First Nations Community in Canada
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90. Massively parallel sequencing of short tandem repeats—Population data and mixture analysis results for the PowerSeq™ system
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91. The Underlying Ecological Processes of Gut Microbiota Among Cohabitating Retarded, Overgrown and Normal Shrimp
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92. Soil microbial community structure and diversity are largely influenced by soil pH and nutrient quality in 78-year-old tree plantations
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93. Interplay between the gut microbiota and immune responses of ayu (Plecoglossus altivelis) during Vibrio anguillarum infection
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94. Pathogen invasion changes the intestinal microbiota composition and induces innate immune responses in the zebrafish intestine
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95. Ontogeny of human mucosal-associated invariant T cells and related T cell subsets
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96. Influenza infection elicits an expansion of gut population of endogenous Bifidobacterium animalis which protects mice against infection
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97. Beneficial effect of the short-chain fatty acid propionate on vascular calcification through intestinal microbiota remodelling
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98. Glycoursodeoxycholic acid regulates bile acids level and alters gut microbiota and glycolipid metabolism to attenuate diabetes
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99. Exogenous addition of H 2 for an in situ biogas upgrading through biological reduction of carbon dioxide into methane
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100. Biodiversity of fungi on Vitis vinifera L. revealed by traditional and high-resolution culture-independent approaches
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