GeM-Pro: a tool for genome functional mining and microbial profiling
Published 2019 View Full Article
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Title
GeM-Pro: a tool for genome functional mining and microbial profiling
Authors
Keywords
Bacterial profiling, Gene mining, Orthology, Phylogenomic analysis, Plant growth–promoting rhizobacteria, <em class="EmphasisTypeItalic ">Bacillus</em>
Journal
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
Volume 103, Issue 7, Pages 3123-3134
Publisher
Springer Nature
Online
2019-02-07
DOI
10.1007/s00253-019-09648-8
References
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Note: Only part of the references are listed.- Genomics-guided discovery and structure identification of cyclic lipopeptides from the Bacillus siamensis JFL15
- (2018) Ben-Hong Xu et al. PLoS One
- Frondibacter mangrovi sp. nov., a member of the family Flavobacteriaceae isolated from seawater by in situ cultivation, and emended description of Frondibacter aureus
- (2017) Jaewoo Yoon et al. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
- Comparative Genomics of Bacillus amyloliquefaciens Strains Reveals a Core Genome with Traits for Habitat Adaptation and a Secondary Metabolites Rich Accessory Genome
- (2017) Lassaad Belbahri et al. Frontiers in Microbiology
- Bacillus amyloliquefaciens, Bacillus velezensis, and Bacillus siamensis Form an “Operational Group B. amyloliquefaciens” within the B. subtilis Species Complex
- (2017) Ben Fan et al. Frontiers in Microbiology
- New Tools in Orthology Analysis: A Brief Review of Promising Perspectives
- (2017) Bruno T. L. Nichio et al. Frontiers in Genetics
- Ortholog-Finder: A Tool for Constructing an Ortholog Data Set
- (2016) Tokumasa Horiike et al. Genome Biology and Evolution
- OrthoANI: An improved algorithm and software for calculating average nucleotide identity
- (2016) Imchang Lee et al. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
- Taxonomic Identity Resolution of Highly Phylogenetically Related Strains and Selection of Phylogenetic Markers by Using Genome-Scale Methods: The Bacillus pumilus Group Case
- (2016) Martín Espariz et al. PLoS One
- WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning
- (2016) George L. Sutphin et al. PLoS Computational Biology
- AMAS: a fast tool for alignment manipulation and computing of summary statistics
- (2016) Marek L. Borowiec PeerJ
- Influence of root exudates on the extracellular proteome of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42
- (2015) Kinga Kierul et al. MICROBIOLOGY-SGM
- Induced systemic resistance responses in perennial ryegrass againstMagnaporthe oryzaeelicited by semi-purified surfactin lipopeptides and live cells ofBacillus amyloliquefaciens
- (2015) Alamgir Rahman et al. MOLECULAR PLANT PATHOLOGY
- Cyclic Lipopeptides ofBacillus amyloliquefacienssubsp.plantarumColonizing the Lettuce Rhizosphere Enhance Plant Defense Responses Toward the Bottom Rot PathogenRhizoctonia solani
- (2015) Soumitra Paul Chowdhury et al. MOLECULAR PLANT-MICROBE INTERACTIONS
- Difficidin and bacilysin from Bacillus amyloliquefaciens FZB42 have antibacterial activity against Xanthomonas oryzae rice pathogens
- (2015) Liming Wu et al. Scientific Reports
- Biocontrol mechanism by root-associated Bacillus amyloliquefaciens FZB42 – a review
- (2015) Soumitra Paul Chowdhury et al. Frontiers in Microbiology
- Genome mining: Prediction of lipopeptides and polyketides from Bacillus and related Firmicutes
- (2015) Gajender Aleti et al. Computational and Structural Biotechnology Journal
- Bacilysin from Bacillus amyloliquefaciens FZB42 Has Specific Bactericidal Activity against Harmful Algal Bloom Species
- (2014) Liming Wu et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Bacilysin overproduction in Bacillus amyloliquefaciens FZB42 markerless derivative strains FZBREP and FZBSPA enhances antibacterial activity
- (2014) Liming Wu et al. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
- RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
- (2014) Alexandros Stamatakis BIOINFORMATICS
- Amylocyclicin, a Novel Circular Bacteriocin Produced by Bacillus amyloliquefaciens FZB42
- (2014) R. Scholz et al. JOURNAL OF BACTERIOLOGY
- The highly modified microcin peptide plantazolicin is associated with nematicidal activity of Bacillus amyloliquefaciens FZB42
- (2013) Zhongzhong Liu et al. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
- eggNOG v4.0: nested orthology inference across 3686 organisms
- (2013) Sean Powell et al. NUCLEIC ACIDS RESEARCH
- TreeFam v9: a new website, more species and orthology-on-the-fly
- (2013) Fabian Schreiber et al. NUCLEIC ACIDS RESEARCH
- Effects of Bacillus amyloliquefaciens FZB42 on Lettuce Growth and Health under Pathogen Pressure and Its Impact on the Rhizosphere Bacterial Community
- (2013) Soumitra Paul Chowdhury et al. PLoS One
- PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees
- (2012) Huaiyu Mi et al. NUCLEIC ACIDS RESEARCH
- Easyfig: a genome comparison visualizer
- (2011) M. J. Sullivan et al. BIOINFORMATICS
- OrthoInspector: comprehensive orthology analysis and visual exploration
- (2011) Benjamin Linard et al. BMC BIOINFORMATICS
- Computational methods for Gene Orthology inference
- (2011) D. M. Kristensen et al. BRIEFINGS IN BIOINFORMATICS
- Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy
- (2011) I. Letunic et al. NUCLEIC ACIDS RESEARCH
- Prodigal: prokaryotic gene recognition and translation initiation site identification
- (2010) Doug Hyatt et al. BMC BIOINFORMATICS
- Plantazolicin, a Novel Microcin B17/Streptolysin S-Like Natural Product from Bacillus amyloliquefaciens FZB42
- (2010) R. Scholz et al. JOURNAL OF BACTERIOLOGY
- MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score
- (2010) Leszek P. Pryszcz et al. NUCLEIC ACIDS RESEARCH
- OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011
- (2010) Robert M. Waterhouse et al. NUCLEIC ACIDS RESEARCH
- Getting Started in Gene Orthology and Functional Analysis
- (2010) Gang Fang et al. PLoS Computational Biology
- How confident can we be that orthologs are similar, but paralogs differ?
- (2009) Romain A. Studer et al. TRENDS IN GENETICS
- Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods
- (2009) Adrian M. Altenhoff et al. PLoS Computational Biology
- EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
- (2008) A. J. Vilella et al. GENOME RESEARCH
- Genome analysis of Bacillus amyloliquefaciens FZB42 reveals its potential for biocontrol of plant pathogens
- (2008) X.H. Chen et al. JOURNAL OF BIOTECHNOLOGY
- Difficidin and bacilysin produced by plant-associated Bacillus amyloliquefaciens are efficient in controlling fire blight disease
- (2008) X.H. Chen et al. JOURNAL OF BIOTECHNOLOGY
- More than Anticipated – Production of Antibiotics and Other Secondary Metabolites by Bacillus amyloliquefaciens FZB42
- (2008) Xiao-Hua Chen et al. JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY
- NCBI BLAST: a better web interface
- (2008) M. Johnson et al. NUCLEIC ACIDS RESEARCH
- The quest for orthologs: finding the corresponding gene across genomes
- (2008) Arnold Kuzniar et al. TRENDS IN GENETICS
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