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For: Land M, Hauser L, Jun SR, Nookaew I, Leuze MR, Ahn TH, Karpinets T, Lund O, Kora G, Wassenaar T, Poudel S, Ussery DW. Insights from 20 years of bacterial genome sequencing. Funct Integr Genomics 2015;15:141-61. [PMID: 25722247 DOI: 10.1007/s10142-015-0433-4] [Cited by in Crossref: 373] [Cited by in F6Publishing: 267] [Article Influence: 53.3] [Reference Citation Analysis]
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3 Wigginton SK, Brannon EQ, Kearns PJ, Lancellotti BV, Cox A, Moseman-valtierra S, Loomis GW, Amador JA. Nitrifying and Denitrifying Microbial Communities in Centralized and Decentralized Biological Nitrogen Removing Wastewater Treatment Systems. Water 2020;12:1688. [DOI: 10.3390/w12061688] [Cited by in Crossref: 3] [Cited by in F6Publishing: 1] [Article Influence: 1.5] [Reference Citation Analysis]
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7 Willms IM, Rudolph AY, Göschel I, Bolz SH, Schneider D, Penone C, Poehlein A, Schöning I, Nacke H. Globally Abundant "Candidatus Udaeobacter" Benefits from Release of Antibiotics in Soil and Potentially Performs Trace Gas Scavenging. mSphere 2020;5:e00186-20. [PMID: 32641424 DOI: 10.1128/mSphere.00186-20] [Cited by in Crossref: 4] [Cited by in F6Publishing: 1] [Article Influence: 2.0] [Reference Citation Analysis]
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9 Quainoo S, Coolen JPM, van Hijum SAFT, Huynen MA, Melchers WJG, van Schaik W, Wertheim HFL. Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis. Clin Microbiol Rev 2017;30:1015-63. [PMID: 28855266 DOI: 10.1128/CMR.00016-17] [Cited by in Crossref: 156] [Cited by in F6Publishing: 78] [Article Influence: 31.2] [Reference Citation Analysis]
10 Cheong JC, Lee JT, Lim JW, Song S, Tan JK, Chiam ZY, Yap KY, Lim EY, Zhang J, Tan HT, Tong YW. Closing the food waste loop: Food waste anaerobic digestate as fertilizer for the cultivation of the leafy vegetable, xiao bai cai (Brassica rapa). Science of The Total Environment 2020;715:136789. [DOI: 10.1016/j.scitotenv.2020.136789] [Cited by in Crossref: 23] [Cited by in F6Publishing: 17] [Article Influence: 11.5] [Reference Citation Analysis]
11 Koringa PG, Thakkar JR, Pandit RJ, Hinsu AT, Parekh MJ, Shah RK, Jakhesara SJ, Joshi CG. Metagenomic characterisation of ruminal bacterial diversity in buffaloes from birth to adulthood using 16S rRNA gene amplicon sequencing. Funct Integr Genomics 2019;19:237-47. [DOI: 10.1007/s10142-018-0640-x] [Cited by in Crossref: 7] [Cited by in F6Publishing: 7] [Article Influence: 1.8] [Reference Citation Analysis]
12 Tyml T, Date SV, Woyke T. A single-cell genome perspective on studying intracellular associations in unicellular eukaryotes. Philos Trans R Soc Lond B Biol Sci 2019;374:20190082. [PMID: 31587647 DOI: 10.1098/rstb.2019.0082] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 0.3] [Reference Citation Analysis]
13 Tuttle MJ, Buchan A. Lysogeny in the oceans: Lessons from cultivated model systems and a reanalysis of its prevalence. Environ Microbiol 2020;22:4919-33. [PMID: 32935433 DOI: 10.1111/1462-2920.15233] [Cited by in Crossref: 4] [Cited by in F6Publishing: 4] [Article Influence: 2.0] [Reference Citation Analysis]
14 Mindlin S, Petrenko A, Petrova M. Chromium resistance genetic element flanked by XerC/XerD recombination sites and its distribution in environmental and clinical Acinetobacter strains. FEMS Microbiol Lett 2018;365. [PMID: 29514194 DOI: 10.1093/femsle/fny047] [Cited by in Crossref: 7] [Cited by in F6Publishing: 6] [Article Influence: 2.3] [Reference Citation Analysis]
15 Altae-tran H, Gao L, Strecker J, Macrae RK, Zhang F. Computational Identification of Repeat-Containing Proteins and Systems. QRB Discovery 2020;1. [DOI: 10.1017/qrd.2020.14] [Reference Citation Analysis]
16 Criscuolo A. A fast alignment-free bioinformatics procedure to infer accurate distance-based phylogenetic trees from genome assemblies. RIO 2019;5:e36178. [DOI: 10.3897/rio.5.e36178] [Cited by in Crossref: 27] [Cited by in F6Publishing: 12] [Article Influence: 9.0] [Reference Citation Analysis]
17 Manzoor SS, Doedens A, Burns MB. The promise and challenge of cancer microbiome research. Genome Biol 2020;21:131. [PMID: 32487228 DOI: 10.1186/s13059-020-02037-9] [Cited by in Crossref: 8] [Cited by in F6Publishing: 6] [Article Influence: 4.0] [Reference Citation Analysis]
18 Schouw A, Vulcano F, Roalkvam I, Hocking WP, Reeves E, Stokke R, Bødtker G, Steen IH. Genome Analysis of Vallitalea guaymasensis Strain L81 Isolated from a Deep-Sea Hydrothermal Vent System. Microorganisms 2018;6:E63. [PMID: 29973550 DOI: 10.3390/microorganisms6030063] [Cited by in Crossref: 8] [Cited by in F6Publishing: 6] [Article Influence: 2.0] [Reference Citation Analysis]
19 López-Pérez M, Ramon-Marco N, Rodriguez-Valera F. Networking in microbes: conjugative elements and plasmids in the genus Alteromonas. BMC Genomics 2017;18:36. [PMID: 28056800 DOI: 10.1186/s12864-016-3461-0] [Cited by in Crossref: 10] [Cited by in F6Publishing: 9] [Article Influence: 2.0] [Reference Citation Analysis]
20 Lima ARJ, Siqueira AS, de Vasconcelos JM, Pereira JS, de Azevedo JSN, Moraes PHG, Aguiar DCF, de Lima CPS, Vianez-Júnior JLSG, Nunes MRT, Xavier LP, Dall'Agnol LT, Goncalves EC. Insights Into Limnothrix sp. Metabolism Based on Comparative Genomics. Front Microbiol 2018;9:2811. [PMID: 30515147 DOI: 10.3389/fmicb.2018.02811] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 0.3] [Reference Citation Analysis]
21 Chen J, Galván AE, Nadar VS, Yoshinaga M, Rosen BP. An ArsRC fusion protein enhances arsenate sensing and detoxification. Environ Microbiol 2022. [PMID: 35229439 DOI: 10.1111/1462-2920.15957] [Reference Citation Analysis]
22 Mier P, Andrade-Navarro MA. Toward completion of the Earth's proteome: an update a decade later. Brief Bioinform 2019;20:463-70. [PMID: 29040399 DOI: 10.1093/bib/bbx127] [Cited by in Crossref: 3] [Cited by in F6Publishing: 2] [Article Influence: 1.0] [Reference Citation Analysis]
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24 Acuña-Amador L, Primot A, Cadieu E, Roulet A, Barloy-Hubler F. Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains. BMC Genomics 2018;19:54. [PMID: 29338683 DOI: 10.1186/s12864-017-4429-4] [Cited by in Crossref: 17] [Cited by in F6Publishing: 9] [Article Influence: 4.3] [Reference Citation Analysis]
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26 Vasdekis AE, Singh A. Microbial metabolic noise. Wiley Interdiscip Rev Syst Biol Med 2020;:e1512. [PMID: 33225608 DOI: 10.1002/wsbm.1512] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 1.0] [Reference Citation Analysis]
27 Shimada T, Tanaka K, Ishihama A. The whole set of the constitutive promoters recognized by four minor sigma subunits of Escherichia coli RNA polymerase. PLoS One 2017;12:e0179181. [PMID: 28666008 DOI: 10.1371/journal.pone.0179181] [Cited by in Crossref: 22] [Cited by in F6Publishing: 19] [Article Influence: 4.4] [Reference Citation Analysis]
28 Sun X, Hu Y, Wang J, Fang C, Li J, Han M, Wei X, Zheng H, Luo X, Jia Y, Gong M, Xiao L, Song Z. Efficient and stable metabarcoding sequencing data using a DNBSEQ-G400 sequencer validated by comprehensive community analyses. Gigabyte 2021;2021:1-15. [DOI: 10.46471/gigabyte.16] [Cited by in Crossref: 4] [Article Influence: 4.0] [Reference Citation Analysis]
29 Jenjaroenpun P, Wongsurawat T, Pereira R, Patumcharoenpol P, Ussery DW, Nielsen J, Nookaew I. Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D. Nucleic Acids Res 2018;46:e38. [PMID: 29346625 DOI: 10.1093/nar/gky014] [Cited by in Crossref: 76] [Cited by in F6Publishing: 64] [Article Influence: 25.3] [Reference Citation Analysis]
30 Doolittle WF, Brunet TD. What Is the Tree of Life? PLoS Genet 2016;12:e1005912. [PMID: 27078870 DOI: 10.1371/journal.pgen.1005912] [Cited by in Crossref: 25] [Cited by in F6Publishing: 19] [Article Influence: 4.2] [Reference Citation Analysis]
31 Law JN, Kale SD, Murali TM. Accurate and efficient gene function prediction using a multi-bacterial network. Bioinformatics 2021;37:800-6. [PMID: 33063084 DOI: 10.1093/bioinformatics/btaa885] [Reference Citation Analysis]
32 Gladkikh AS, Feranchuk SI, Ponomareva AS, Bochalgin NO, Mironova LV. Antibiotic resistance in Vibrio cholerae El Tor strains isolated during cholera complications in Siberia and the Far East of Russia. Infect Genet Evol 2020;78:104096. [PMID: 31689544 DOI: 10.1016/j.meegid.2019.104096] [Cited by in Crossref: 8] [Cited by in F6Publishing: 2] [Article Influence: 2.7] [Reference Citation Analysis]
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34 Afshari R, Pillidge CJ, Dias DA, Osborn AM, Gill H. Cheesomics: the future pathway to understanding cheese flavour and quality. Critical Reviews in Food Science and Nutrition 2020;60:33-47. [DOI: 10.1080/10408398.2018.1512471] [Cited by in Crossref: 21] [Cited by in F6Publishing: 17] [Article Influence: 5.3] [Reference Citation Analysis]
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36 Fels U, Gevaert K, Van Damme P. Bacterial Genetic Engineering by Means of Recombineering for Reverse Genetics. Front Microbiol 2020;11:548410. [PMID: 33013782 DOI: 10.3389/fmicb.2020.548410] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 0.5] [Reference Citation Analysis]
37 Castillo D, Christiansen RH, Dalsgaard I, Madsen L, Espejo R, Middelboe M. Comparative Genome Analysis Provides Insights into the Pathogenicity of Flavobacterium psychrophilum. PLoS One 2016;11:e0152515. [PMID: 27071075 DOI: 10.1371/journal.pone.0152515] [Cited by in Crossref: 25] [Cited by in F6Publishing: 21] [Article Influence: 4.2] [Reference Citation Analysis]
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39 Ferrandis-Vila M, Tiwari SK, Mamerow S, Semmler T, Menge C, Berens C; HECTOR consortium. Using unique ORFan genes as strain-specific identifiers for Escherichia coli. BMC Microbiol 2022;22:135. [PMID: 35585491 DOI: 10.1186/s12866-022-02508-y] [Reference Citation Analysis]
40 Maeda M, Shimada T, Ishihama A. Strength and Regulation of Seven rRNA Promoters in Escherichia coli. PLoS One 2015;10:e0144697. [PMID: 26717514 DOI: 10.1371/journal.pone.0144697] [Cited by in Crossref: 25] [Cited by in F6Publishing: 17] [Article Influence: 3.6] [Reference Citation Analysis]
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43 Guthrie JL, Gardy JL. A brief primer on genomic epidemiology: lessons learned from Mycobacterium tuberculosis. Ann N Y Acad Sci 2017;1388:59-77. [PMID: 28009051 DOI: 10.1111/nyas.13273] [Cited by in Crossref: 15] [Cited by in F6Publishing: 14] [Article Influence: 2.5] [Reference Citation Analysis]
44 Salazar AN, Nobrega FL, Anyansi C, Aparicio-Maldonado C, Costa AR, Haagsma AC, Hiralal A, Mahfouz A, McKenzie RE, van Rossum T, Brouns SJJ, Abeel T. An educational guide for nanopore sequencing in the classroom. PLoS Comput Biol 2020;16:e1007314. [PMID: 31971941 DOI: 10.1371/journal.pcbi.1007314] [Cited by in Crossref: 10] [Cited by in F6Publishing: 7] [Article Influence: 5.0] [Reference Citation Analysis]
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46 Bouso JM, Planet PJ. Complete nontuberculous mycobacteria whole genomes using an optimized DNA extraction protocol for long-read sequencing. BMC Genomics 2019;20:793. [PMID: 31666009 DOI: 10.1186/s12864-019-6134-y] [Cited by in Crossref: 4] [Cited by in F6Publishing: 3] [Article Influence: 1.3] [Reference Citation Analysis]
47 Yokoyama E, Hirai S, Ishige T, Murakami S. Single-Nucleotide Polymorphisms in the Whole-Genome Sequence Data of Shiga Toxin-Producing Escherichia coli O157:H7/H- Strains by Cultivation. Curr Microbiol 2017;74:425-30. [PMID: 28197720 DOI: 10.1007/s00284-017-1208-z] [Cited by in Crossref: 4] [Cited by in F6Publishing: 4] [Article Influence: 0.8] [Reference Citation Analysis]
48 Luo G, Li B, Yang C, Wang Y, Bian X, Li W, Liu F, Huo G. Major Traditional Probiotics: Comparative Genomic Analyses and Roles in Gut Microbiome of Eight Cohorts. Front Microbiol 2019;10:712. [PMID: 31024492 DOI: 10.3389/fmicb.2019.00712] [Cited by in Crossref: 4] [Cited by in F6Publishing: 2] [Article Influence: 1.3] [Reference Citation Analysis]
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51 Wick RR, Holt KE. Benchmarking of long-read assemblers for prokaryote whole genome sequencing. F1000Res 2019;8:2138. [PMID: 31984131 DOI: 10.12688/f1000research.21782.4] [Cited by in Crossref: 36] [Cited by in F6Publishing: 3] [Article Influence: 12.0] [Reference Citation Analysis]
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60 Asaf S, Khan A, Khan AL, Al-Harrasi A, Al-Rawahi A. Complete Chloroplast Genomes of Vachellia nilotica and Senegalia senegal: Comparative Genomics and Phylogenomic Placement in a New Generic System. PLoS One 2019;14:e0225469. [PMID: 31765416 DOI: 10.1371/journal.pone.0225469] [Cited by in Crossref: 6] [Cited by in F6Publishing: 5] [Article Influence: 2.0] [Reference Citation Analysis]
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