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For: Shen W, Ren H. TaxonKit: A practical and efficient NCBI taxonomy toolkit. J Genet Genomics 2021:S1673-8527(21)00083-7. [PMID: 34001434 DOI: 10.1016/j.jgg.2021.03.006] [Cited by in Crossref: 47] [Cited by in F6Publishing: 53] [Article Influence: 23.5] [Reference Citation Analysis]
Number Citing Articles
1 Bell AG, Thornber K, Chaput DL, Hasan NA, Mehedi Alam M, Haque MM, Cable J, Temperton B, Tyler CR. Metagenomic assessment of the diversity and ubiquity of antimicrobial resistance genes in Bangladeshi aquaculture ponds. Aquaculture Reports 2023;29:101462. [DOI: 10.1016/j.aqrep.2023.101462] [Reference Citation Analysis]
2 Xin Y, Wang Y, Zhang H, Wu Y, Xia Y, Li H, Qu X. Cupriavidus pinatubonensis JMP134 Alleviates Sulfane Sulfur Toxicity after the Loss of Sulfane Dehydrogenase through Oxidation by Persulfide Dioxygenase and Hydrogen Sulfide Release. Metabolites 2023;13:218. [DOI: 10.3390/metabo13020218] [Reference Citation Analysis]
3 Nwosu EC, Brauer A, Monchamp ME, Pinkerneil S, Bartholomäus A, Theuerkauf M, Schmidt JP, Stoof-Leichsenring KR, Wietelmann T, Kaiser J, Wagner D, Liebner S. Early human impact on lake cyanobacteria revealed by a Holocene record of sedimentary ancient DNA. Commun Biol 2023;6:72. [PMID: 36653523 DOI: 10.1038/s42003-023-04430-z] [Reference Citation Analysis]
4 Yoshiba S, Nakagawa H, Kuwata H, Nabuchi A, Yaso A, Shirota T. Metagenomic analysis of oral plaques and aortic valve tissues reveals oral bacteria associated with aortic stenosis.. [DOI: 10.21203/rs.3.rs-2448726/v1] [Reference Citation Analysis]
5 Gill H, Sorensen JL, Collemare J. Lichen Fungal Secondary Metabolites: Progress in the Genomic Era Toward Ecological Roles in the Interaction. Plant Relationships 2023. [DOI: 10.1007/978-3-031-16503-0_7] [Reference Citation Analysis]
6 Shen W, Xiang H, Huang T, Tang H, Peng M, Cai D, Hu P, Ren H. KMCP: accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping. Bioinformatics 2023;39. [PMID: 36579886 DOI: 10.1093/bioinformatics/btac845] [Reference Citation Analysis]
7 Inwood SN, Harrop TWR, Dearden PK. The venom composition and parthenogenesis mechanism of the parasitoid wasp Microctonus hyperodae, a declining biocontrol agent. Insect Biochem Mol Biol 2022;153:103897. [PMID: 36584929 DOI: 10.1016/j.ibmb.2022.103897] [Reference Citation Analysis]
8 Zhao D, Zhang S, Kumar S, Zhou H, Xue Q, Sun W, Zhou J, Xiang H. Comparative Genomic Insights into the Evolution of Halobacteria-Associated "Candidatus Nanohaloarchaeota". mSystems 2022;7:e0066922. [PMID: 36259734 DOI: 10.1128/msystems.00669-22] [Reference Citation Analysis]
9 Patin NV, Goodwin KD. Long-Read Sequencing Improves Recovery of Picoeukaryotic Genomes and Zooplankton Marker Genes from Marine Metagenomes. mSystems 2022;7:e0059522. [PMID: 36448813 DOI: 10.1128/msystems.00595-22] [Reference Citation Analysis]
10 Masuda Y, Mise K, Xu Z, Zhang Z, Shiratori Y, Senoo K, Itoh H. Global soil metagenomics reveals ubiquitous yet previously-hidden predominance ofDeltaproteobacteriain nitrogen-fixing microbiome.. [DOI: 10.1101/2022.12.09.519847] [Reference Citation Analysis]
11 Tikhonenkov DV, Mikhailov KV, Gawryluk RMR, Belyaev AO, Mathur V, Karpov SA, Zagumyonnyi DG, Borodina AS, Prokina KI, Mylnikov AP, Aleoshin VV, Keeling PJ. Microbial predators form a new supergroup of eukaryotes. Nature 2022;612:714-9. [PMID: 36477531 DOI: 10.1038/s41586-022-05511-5] [Reference Citation Analysis]
12 Mise K, Iwasaki W. Unexpected absence of ribosomal protein genes from metagenome-assembled genomes. ISME COMMUN 2022;2:118. [DOI: 10.1038/s43705-022-00204-6] [Reference Citation Analysis]
13 Forni G, Mikheyev AS, Luchetti A, Mantovani B. Gene transcriptional profiles in gonads of Bacillus taxa (Phasmida) with different cytological mechanisms of automictic parthenogenesis. Zoological Lett 2022;8:14. [DOI: 10.1186/s40851-022-00197-z] [Reference Citation Analysis]
14 García-maldonado JQ, Latisnere-barragán H, Escobar-zepeda A, Cadena S, Ramírez-arenas PJ, Vázquez-juárez R, Maurilia R, López-cortés A. Revisiting microbial diversity in hypersaline microbial mats from Guerrero Negro for a better understanding of methanogenic archaeal communities.. [DOI: 10.21203/rs.3.rs-2281927/v1] [Reference Citation Analysis]
15 Camargo AP, Nayfach S, Chen IA, Palaniappan K, Ratner A, Chu K, Ritter SJ, Reddy TBK, Mukherjee S, Schulz F, Call L, Neches RY, Woyke T, Ivanova NN, Eloe-Fadrosh EA, Kyrpides NC, Roux S. IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata. Nucleic Acids Res 2023;51:D733-43. [PMID: 36399502 DOI: 10.1093/nar/gkac1037] [Cited by in Crossref: 1] [Article Influence: 1.0] [Reference Citation Analysis]
16 Song X, Li Y, Stirling E, Zhao K, Wang B, Zhu Y, Luo Y, Xu J, Ma B. AsgeneDB: a curated orthology arsenic metabolism gene database and computational tool for metagenome annotation. NAR Genom Bioinform 2022;4:lqac080. [PMID: 36330044 DOI: 10.1093/nargab/lqac080] [Reference Citation Analysis]
17 Zhou J, Ouyang J, Gao Z, Qin H, Jun W, Shi T. MagMD: database summarizing the Metabolic action of gut Microbiota to Drugs. Computational and Structural Biotechnology Journal 2022. [DOI: 10.1016/j.csbj.2022.11.021] [Reference Citation Analysis]
18 Limberg J, Egan CE, Mora HA, Putzel G, Stamatiou AT, Ullmann TM, Moore MD, Stefanova D, Thiesmeyer JW, Finnerty BM, Beninato T, McKenzie K, Robitsek RJ, Chan J, Zarnegar R, Fahey TJ 3rd. Metagenomic Sequencing of the Gallbladder Microbiome: Bacterial Diversity Does Not Vary by Surgical Pathology. J Gastrointest Surg 2022;26:2282-91. [PMID: 35915372 DOI: 10.1007/s11605-022-05418-6] [Reference Citation Analysis]
19 Manske F, Ogoniak L, Jürgens L, Grundmann N, Makałowski W, Wethmar K. The new uORFdb: integrating literature, sequence, and variation data in a central hub for uORF research. Nucleic Acids Res 2023;51:D328-36. [PMID: 36305828 DOI: 10.1093/nar/gkac899] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
20 Mahmoudabadi G, Consortium TS, Quake SR. Single Cell Transcriptomics Reveals the Hidden Microbiomes of Human Tissues.. [DOI: 10.1101/2022.10.11.511790] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
21 Vassallo CN, Doering CR, Littlehale ML, Teodoro GIC, Laub MT. A functional selection reveals previously undetected anti-phage defence systems in the E. coli pangenome. Nat Microbiol 2022. [PMID: 36123438 DOI: 10.1038/s41564-022-01219-4] [Cited by in F6Publishing: 3] [Reference Citation Analysis]
22 Jung J, Bugenyi AW, Lee M, Choi Y, Song K, Lee H, Son Y, Lee D, Lee S, Son Y, Heo J. High-quality metagenome-assembled genomes from proximal colonic microbiomes of synbiotic-treated korean native black pigs reveal changes in functional capacity. Sci Rep 2022;12. [DOI: 10.1038/s41598-022-18503-2] [Reference Citation Analysis]
23 Bell AG, Thornber K, Chaput DL, Hasan NA, Alam MM, Haque MM, Cable J, Temperton B, Tyler CR. The Diversity and Ubiquity of Antibiotic Resistance Genes in Finfish Culture Ponds in Bangladesh.. [DOI: 10.1101/2022.09.14.507951] [Reference Citation Analysis]
24 Inwood SN, Harrop TW, Dearden PK. The parthenogenesis mechanism and venom complement of the parasitoid wasp Microctonus hyperodae, a declining biocontrol agent.. [DOI: 10.1101/2022.09.11.507509] [Reference Citation Analysis]
25 Cheng D, Kolundžija S, Lauro FM. Global phylogenetic analysis of the RNA-dependent RNA polymerase with OrViT (OrthornaVirae Tree). Front Virol 2022;2. [DOI: 10.3389/fviro.2022.981177] [Reference Citation Analysis]
26 Li W, Wang L, Li X, Zheng X, Cohen MF, Liu Y. Sequence-based Functional Metagenomics Reveals Novel Natural Diversity of Functioning CopA in Environmental Microbiomes. Genomics, Proteomics & Bioinformatics 2022. [DOI: 10.1016/j.gpb.2022.08.006] [Reference Citation Analysis]
27 Jenckel M, Hall RN, Strive T. Pathogen profiling of Australian rabbits by metatranscriptomic sequencing. Transbound Emerg Dis 2022;69:e2629-40. [PMID: 35687756 DOI: 10.1111/tbed.14609] [Reference Citation Analysis]
28 Fan L, Peng W, Duan H, Lü F, Zhang H, He P. Presence and role of viruses in anaerobic digestion of food waste under environmental variability.. [DOI: 10.21203/rs.3.rs-1974582/v1] [Reference Citation Analysis]
29 Priest T, Appen WV, Oldenburg E, Popa O, Torres-valdés S, Bienhold C, Metfies K, Fuchs BM, Amann R, Boetius A, Wietz M. Variations in Atlantic water influx and sea-ice cover drive taxonomic and functional shifts in Arctic marine bacterial communities.. [DOI: 10.1101/2022.08.12.503524] [Reference Citation Analysis]
30 Baltrus DA, Carter ME. The 16S rRNA Gene Is Not a Precise Classifier for Luteibacter Species.. [DOI: 10.1101/2022.07.18.500475] [Reference Citation Analysis]
31 Saarenpää S, Shalev O, Ashkenazy H, de Oliveira-carlos V, Lundberg DS, Weigel D, Giacomello S. Spatially resolved host-bacteria-fungi interactomes via spatial metatranscriptomics.. [DOI: 10.1101/2022.07.18.496977] [Cited by in F6Publishing: 1] [Reference Citation Analysis]
32 Albrycht K, Rynkiewicz AA, Harasymczuk M, Barylski J, Zielezinski A. Daily Reports on Phage-Host Interactions. Front Microbiol 2022;13:946070. [DOI: 10.3389/fmicb.2022.946070] [Reference Citation Analysis]
33 Bhalla D, van Noort V. Molecular Evolution of Aryl Hydrocarbon Receptor Signaling Pathway Genes.. [DOI: 10.1101/2022.07.13.499904] [Reference Citation Analysis]
34 Shen M, Xiao N, Zhao Z, Guo N, Luo Z, Sun G, Li J. eDNA metabarcoding as a promising conservation tool to monitor fish diversity in Beijing water systems compared with ground cages. Sci Rep 2022;12:11113. [PMID: 35773335 DOI: 10.1038/s41598-022-15488-w] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
35 Oyserman BO, Flores SS, Griffioen T, Pan X, van der Wijk E, Pronk L, Lokhorst W, Nurfikari A, Paulson JN, Movassagh M, Stopnisek N, Kupczok A, Cordovez V, Carrión VJ, Ligterink W, Snoek BL, Medema MH, Raaijmakers JM. Disentangling the genetic basis of rhizosphere microbiome assembly in tomato. Nat Commun 2022;13:3228. [PMID: 35710629 DOI: 10.1038/s41467-022-30849-9] [Cited by in Crossref: 1] [Cited by in F6Publishing: 7] [Article Influence: 1.0] [Reference Citation Analysis]
36 Mastriani E, Bienes KM, Wong G, Berthet N. PIMGAVir and Vir-MinION: Two Viral Metagenomic Pipelines for Complete Baseline Analysis of 2nd and 3rd Generation Data. Viruses 2022;14:1260. [PMID: 35746732 DOI: 10.3390/v14061260] [Reference Citation Analysis]
37 Zajkowski T, Lee MD, Sharma S, Vallota-eastman A, Kuska M, Malczewska M, Rothschild LJ. Universal functions of prion candidates across all three domains of life suggest a primeval role of protein self-templating.. [DOI: 10.1101/2022.05.30.493841] [Reference Citation Analysis]
38 Zhao D, Zhang S, Kumar S, Zhou H, Xue Q, Sun W, Zhou J, Xiang H. Comparative genomic insights into the evolution of Halobacteria-associated “Candidatus Nanohaloarchaeota”.. [DOI: 10.1101/2022.05.20.492899] [Reference Citation Analysis]
39 Roach M, Beecroft S, Mihindukulasuriya KA, Wang L, Oliveira Lima LF, Dinsdale EA, Edwards RA, Handley SA. Hecatomb: An End-to-End Research Platform for Viral Metagenomics.. [DOI: 10.1101/2022.05.15.492003] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
40 Scanlan J, Guillonneau R, Cunningham MR, Najmin S, Mausz MA, Murphy A, Murray LL, Zhang L, Kumaresan D, Chen Y. The Proteobacterial Methanotroph Methylosinus trichosporium OB3b Remodels Membrane Lipids in Response to Phosphate Limitation. mBio 2022;:e0024722. [PMID: 35575546 DOI: 10.1128/mbio.00247-22] [Reference Citation Analysis]
41 Vassallo C, Doering C, Littlehale ML, Teodoro G, Laub MT. Mapping the landscape of anti-phage defense mechanisms in the E. coli pangenome.. [DOI: 10.1101/2022.05.12.491691] [Cited by in Crossref: 7] [Cited by in F6Publishing: 7] [Article Influence: 7.0] [Reference Citation Analysis]
42 Veldsman WP, Campli G, Dind S, de Laval VR, Drage HB, Waterhouse RM, Robinson-rechavi M. Taxonbridge: an R package to create custom taxonomies based on the NCBI and GBIF taxonomies.. [DOI: 10.1101/2022.05.02.490269] [Reference Citation Analysis]
43 Wu H, Fu P, Fu Q, Zhang Z, Zheng H, Mao L, Li X, Yu F, Peng Y. Plant Virus Database: a resource for exploring the diversity of plant viruses and their interactions with hosts.. [DOI: 10.1101/2022.03.20.485054] [Reference Citation Analysis]
44 He R, Zhang J, Shao Y, Gu S, Yin W, Li Z. Non-ribosomal peptide synthetase domain boundary identification and new motifs discovery based on motif-intermotifs standardized architecture.. [DOI: 10.1101/2022.03.14.484258] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
45 Shen W, Xiang H, Huang T, Tang H, Peng M, Cai D, Hu P, Ren H. KMCP: accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping.. [DOI: 10.1101/2022.03.07.482835] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
46 Charon J, Buchmann JP, Sadiq S, Holmes EC. RdRp-scan: A Bioinformatic Resource to Identify and Annotate Divergent RNA Viruses in Metagenomic Sequence Data.. [DOI: 10.1101/2022.02.28.482397] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
47 Wu WH, Kim M, Chang LC, Assie A, Saldana-Morales FB, Zegarra-Ruiz DF, Norwood K, Samuel BS, Diehl GE. Interleukin-1β secretion induced by mucosa-associated gut commensal bacteria promotes intestinal barrier repair. Gut Microbes 2022;14:2014772. [PMID: 34989321 DOI: 10.1080/19490976.2021.2014772] [Cited by in Crossref: 4] [Cited by in F6Publishing: 3] [Article Influence: 4.0] [Reference Citation Analysis]
48 Jenckel M, Hall R, Strive T. Pathogen profiling of Australian rabbits by metatranscriptomic sequencing.. [DOI: 10.1101/2022.02.15.480619] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
49 Li W, Wang L, Li X, Zheng X, Cohen MF, Liu Y. Sequence-based Functional Metagenomics Reveals Novel Natural Diversity of Functioning CopA in Environmental Microbiomes.. [DOI: 10.1101/2022.02.12.480192] [Reference Citation Analysis]
50 Wei W, Koslicki D. Using the UniFrac metric on Whole Genome Shotgun data.. [DOI: 10.1101/2022.01.17.476629] [Reference Citation Analysis]
51 Rodríguez-pérez H, Ciuffreda L, Flores C. NanoRTax, a real-time pipeline for taxonomic and diversity analysis of nanopore 16S rRNA amplicon sequencing data. Computational and Structural Biotechnology Journal 2022;20:5350-4. [DOI: 10.1016/j.csbj.2022.09.024] [Reference Citation Analysis]
52 Palatini U, Pischedda E, Bonizzoni M. Computational Methods for the Discovery and Annotation of Viral Integrations. Methods in Molecular Biology 2022. [DOI: 10.1007/978-1-0716-2380-0_18] [Cited by in Crossref: 1] [Article Influence: 1.0] [Reference Citation Analysis]
53 Oyserman BO, Flores SS, Griffioen T, Pan X, van der Wijk E, Pronk L, Lokhorst W, Nurfikari A, Stopnisek N, Kupczok A, Cordovez V, Carrión VJ, Ligterink W, Snoek BL, Medema MH, Raaijmakers JM. Disentangling the genetic basis of rhizosphere microbiome assembly in tomato.. [DOI: 10.1101/2021.12.20.473370] [Reference Citation Analysis]
54 Mise K, Masuda Y, Senoo K, Itoh H. Undervalued Pseudo-nifH Sequences in Public Databases Distort Metagenomic Insights into Biological Nitrogen Fixers. mSphere 2021;:e0078521. [PMID: 34787447 DOI: 10.1128/msphere.00785-21] [Cited by in Crossref: 5] [Cited by in F6Publishing: 5] [Article Influence: 2.5] [Reference Citation Analysis]
55 Hou S, Cheng S, Chen T, Fuhrman JA, Sun F. DeepMicrobeFinder sorts metagenomes into prokaryotes, eukaryotes and viruses, with marine applications.. [DOI: 10.1101/2021.10.26.466018] [Reference Citation Analysis]
56 Sakamoto T, Ortega JM. Taxallnomy: an extension of NCBI Taxonomy that produces a hierarchically complete taxonomic tree. BMC Bioinformatics 2021;22:388. [PMID: 34325658 DOI: 10.1186/s12859-021-04304-3] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 1.0] [Reference Citation Analysis]
57 Porter LL, Kim AK, Rimal S, Looger LL, Majumdar A, Mensh BD, Starich M. Many dissimilar protein domains switch between α-helix and β-sheet folds.. [DOI: 10.1101/2021.06.10.447921] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 1.0] [Reference Citation Analysis]
58 Burke GR, Hines HM, Sharanowski BJ. The Presence of Ancient Core Genes Reveals Endogenization from Diverse Viral Ancestors in Parasitoid Wasps. Genome Biol Evol 2021;13:evab105. [PMID: 33988720 DOI: 10.1093/gbe/evab105] [Cited by in Crossref: 6] [Cited by in F6Publishing: 7] [Article Influence: 3.0] [Reference Citation Analysis]
59 Sulit AK, Kolisnik T, Frizelle FA, Purcell R, Schmeier S. MetaFunc: Taxonomic and Functional Analyses of High Throughput Sequencing for Microbiomes.. [DOI: 10.1101/2020.09.02.271098] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 0.7] [Reference Citation Analysis]