MIDDAS-M: motif-independent de novo detection of secondary metabolite gene clusters through the integration of genome sequencing and transcriptome data

scientific article

MIDDAS-M: motif-independent de novo detection of secondary metabolite gene clusters through the integration of genome sequencing and transcriptome data is …
instance of (P31):
scholarly articleQ13442814

External links are
P819ADS bibcode2013PLoSO...884028U
P356DOI10.1371/JOURNAL.PONE.0084028
P8608Fatcat IDrelease_z2qegg3c3bcidf44o6utavlxym
P932PMC publication ID3877130
P698PubMed publication ID24391870
P5875ResearchGate publication ID259589406

P50authorJoan W. BennettQ6205526
Kazuo Shin-yaQ56642617
Nozomi NaganoQ57048222
Myco UmemuraQ59689351
Masayuki MachidaQ107418357
P2093author name stringKiyoshi Asai
Katsuhisa Horimoto
Hideaki Koike
Tomoko Ishii
Noriko Yamane
Jiujiang Yu
Ikuko Kozone
Jin Kawano
P2860cites workClustered genes involved in cyclopiazonic acid production are next to the aflatoxin biosynthesis gene cluster in Aspergillus flavusQ46225516
Repeated-batch production of kojic acid in a cell-retention fermenter using Aspergillus oryzae M3B9.Q46491694
Sequence breakpoints in the aflatoxin biosynthesis gene cluster and flanking regions in nonaflatoxigenic Aspergillus flavus isolatesQ46696723
Kojic acid production in an airlift bioreactor using partially hydrolyzed raw corn starchQ46759522
CLUSEAN: a computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clustersQ48070728
Transcriptional regulation of genes on the non-syntenic blocks of Aspergillus oryzae and its functional relationship to solid-state cultivation.Q50876228
Co-expression of 15 contiguous genes delineates a fumonisin biosynthetic gene cluster in Gibberella moniliformis.Q52549674
Directed deletions in the aflatoxin biosynthesis gene homolog cluster of Aspergillus oryzaeQ62791968
Kojic acid biosynthesis in Aspergillus oryzae is regulated by a Zn(II)(2)Cys(6) transcriptional activator and induced by kojic acid at the transcriptional levelQ62843319
Isolation and structure of an antimitotic cyclic peptide, ustiloxin F: chemical interrelation with a homologous peptide, ustiloxin BQ74662915
The COG database: an updated version includes eukaryotesQ21284294
Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatusQ21972844
Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzaeQ22122464
Genome sequencing and analysis of Aspergillus oryzaeQ22122467
The Pfam protein families databaseQ24619716
Basic local alignment search toolQ25938991
Advances in Aspergillus secondary metabolite research in the post-genomic eraQ26823169
A genomic perspective on protein familiesQ27860913
Reorganizing the protein space at the Universal Protein Resource (UniProt)Q29547338
Biosynthesis of the red pigment bikaverin in Fusarium fujikuroi: genes, their function and regulationQ33435988
Efflux in fungi: la pièce de résistanceQ33474798
Fungal secondary metabolism - from biochemistry to genomicsQ34472162
Accurate prediction of secondary metabolite gene clusters in filamentous fungiQ34646585
Kojic acid, a cosmetic skin whitening agent, is a slow-binding inhibitor of catecholase activity of tyrosinaseQ34721978
Aflatoxin biosynthesis.Q35162341
Comparative genome analysis between Aspergillus oryzae strains reveals close relationship between sites of mutation localization and regions of highly divergent genes among Aspergillus speciesQ36323668
From miso, saké and shoyu to cosmetics: a century of science for kojic acidQ36660374
Ustiloxins, antimitotic cyclic peptides from false smut balls on rice panicles caused by Ustilaginoidea virensQ36738364
Transcriptional regulatory elements in fungal secondary metabolismQ37021208
Genetic regulation of aflatoxin biosynthesis: from gene to genomeQ37325993
Identification of two aflatrem biosynthesis gene loci in Aspergillus flavus and metabolic engineering of Penicillium paxilli to elucidate their functionQ37450906
Oxylipins in fungi.Q37833673
Current understanding on aflatoxin biosynthesis and future perspective in reducing aflatoxin contaminationQ38064273
antiSMASH 2.0--a versatile platform for genome mining of secondary metabolite producersQ41978369
Beyond aflatoxin: four distinct expression patterns and functional roles associated with Aspergillus flavus secondary metabolism gene clustersQ41991820
SMURF: Genomic mapping of fungal secondary metabolite clustersQ42573739
Identification of gene clusters associated with fusaric acid, fusarin, and perithecial pigment production in Fusarium verticillioidesQ42717743
antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequencesQ42779012
Identification and characterization of genes responsible for biosynthesis of kojic acid, an industrially important compound from Aspergillus oryzae.Q45595123
Genomics of industrial Aspergilli and comparison with toxigenic relativesQ46142543
P275copyright licenseCreative Commons CC0 LicenseQ6938433
P6216copyright statuscopyrighted, dedicated to the public domain by copyright holderQ88088423
P433issue12
P407language of work or nameEnglishQ1860
P921main subjecttranscriptomeQ252857
secondary metaboliteQ522244
P304page(s)e84028
P577publication date2013-12-31
P1433published inPLOS OneQ564954
P1476titleMIDDAS-M: motif-independent de novo detection of secondary metabolite gene clusters through the integration of genome sequencing and transcriptome data
P478volume8

Reverse relations

cites work (P2860)
Q26781517Are Some Fungal Volatile Organic Compounds (VOCs) Mycotoxins?
Q39234336Bioinformatics tools for the identification of gene clusters that biosynthesize specialized metabolites
Q95514837Biosynthesis: bioinformatics bolster a renaissance
Q90303408Comparative genome analysis of Aspergillus flavus clinically isolated in Japan
Q64074144Complete biosynthetic pathways of ascofuranone and ascochlorin in
Q38615264Dereplication, sequencing and identification of peptidic natural products: from genome mining to peptidogenomics to spectral networks
Q46809688Development of fungal cell factories for the production of secondary metabolites: Linking genomics and metabolism
Q34731071Enhancing microbial metabolite and enzyme production: current strategies and challenges
Q36541427Expression of ustR and the Golgi protease KexB are required for ustiloxin B biosynthesis in Aspergillus oryzae.
Q52568340Heterologous Production of a Novel Cyclic Peptide Compound, KK-1, in Aspergillus oryzae.
Q93107369Linking biosynthetic and chemical space to accelerate microbial secondary metabolite discovery
Q26829521Motif-independent de novo detection of secondary metabolite gene clusters-toward identification from filamentous fungi
Q28081722Next-generation sequencing approach for connecting secondary metabolites to biosynthetic gene clusters in fungi
Q64944023Omics based approach for biodiscovery of microbial natural products in antibiotic resistance era.
Q48506941On being an honorary member of Arny's army: some musings about fungal fermentations, secondary metabolism, and scientific communities
Q98513710Post-translational formation of strained cyclophanes in bacteria
Q64250479Recent Advances in the Discovery and Biosynthetic Study of Eukaryotic RiPP Natural Products
Q57183197Safety of the fungal workhorses of industrial biotechnology: update on the mycotoxin and secondary metabolite potential of Aspergillus niger, Aspergillus oryzae, and Trichoderma reesei
Q61014545Taxonomy of section and their production of aflatoxins, ochratoxins and other mycotoxins
Q33653082Temperature during conidiation affects stress tolerance, pigmentation, and trypacidin accumulation in the conidia of the airborne pathogen Aspergillus fumigatus
Q38858040The evolution of genome mining in microbes - a review.
Q47104996The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production.
Q47707995Ustiloxins, fungal cyclic peptides, are ribosomally synthesized in Ustilaginoidea virens.