Fungal secondary metabolites in food and pharmaceuticals in the era of multi-omics

Fungal Endophytes: A Potential Source of Antibacterial Compounds

(2022) Sunil K. Deshmukh et al.   Journal of Fungi

Genome Assembly and Transcriptome Analysis of the Fungus Coniella diplodiella During Infection on Grapevine (Vitis vinifera L.)

(2021) Ruitao Liu et al.   Frontiers in Microbiology

Fungal Endophytes as Efficient Sources of Plant-Derived Bioactive Compounds and Their Prospective Applications in Natural Product Drug Discovery: Insights, Avenues, and Challenges

(2021) Archana Singh et al.   Microorganisms

Deep sequencing of the Sanghuangporus vaninii transcriptome reveals dynamic landscapes of candidate genes involved in the biosynthesis of active compounds

(2021) Qiumei Zhou et al.   ARCHIVES OF MICROBIOLOGY

Applications of CRISPR/Cas9 in the Synthesis of Secondary Metabolites in Filamentous Fungi

(2021) Chunmiao Jiang et al.   Frontiers in Microbiology

Gene Set Enrichment Analysis of Interaction Networks Weighted by Node Centrality

(2021) Alessandra Zito et al.   Frontiers in Genetics

Omics-Driven Biotechnology for Industrial Applications

(2021) Bashar Amer et al.   Frontiers in Bioengineering and Biotechnology

An interpreted atlas of biosynthetic gene clusters from 1,000 fungal genomes

(2021) Matthew T. Robey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assessing the nutritional quality of fungal treated wheat straw: Compounds formed after treatment with Ceriporiopsis subvermispora and Lentinula edodes

(2021) Lei Mao et al.   ANIMAL FEED SCIENCE AND TECHNOLOGY

In silico investigation on the inhibitory effect of fungal secondary metabolites on RNA dependent RNA polymerase of SARS-CoV-II: A docking and molecular dynamic simulation study

(2021) Kosar Sadat Ebrahimi et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Fungi Population Metabolomics and Molecular Network Study Reveals Novel Biomarkers for Early Detection of Aflatoxigenic Aspergillus species

(2021) Huali Xie et al.   JOURNAL OF HAZARDOUS MATERIALS

Native Structural and Functional Proteoform Characterization of the Prolyl-Alanyl-Specific Endoprotease EndoPro from Aspergillus niger

(2021) Guusje van Schaick et al.   JOURNAL OF PROTEOME RESEARCH

Secretome characterization of the lignocellulose-degrading fungi Pycnoporus sanguineus and Ganoderma resinaceum growing on Panicum prionitis biomass

(2021) Albertina Gauna et al.   MYCOLOGIA

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Pentacyclic triterpenoids, fuscotorunones A and B, with ε-caprolactone in ring E from Fuscoporia torulosa

(2021) Masaaki Noji et al.   PHYTOCHEMISTRY

Trends and Applications of Omics Technologies to Functional Characterisation of Enzymes and Protein Metabolites Produced by Fungi

(2021) Grace N. Ijoma et al.   Journal of Fungi

Classifying natural products from plants, fungi or bacteria using the COCONUT database and machine learning

(2021) Alice Capecchi et al.   Journal of Cheminformatics

Fruiting bodies of selected edible mushrooms as a potential source of lovastatin

(2020) Katarzyna Kała et al.   EUROPEAN FOOD RESEARCH AND TECHNOLOGY

Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC–MS/MS

(2020) Yangyang Bian et al.   Nature Communications

Evolutionary Histories of Type III Polyketide Synthases in Fungi

(2020) Jorge Carlos Navarro-Muñoz et al.   Frontiers in Microbiology

SELEX tool: a novel and convenient gel-based diffusion method for monitoring of aptamer-target binding

(2020) Qingxiu Liu et al.   Journal of Biological Engineering

Response of the wood-decay fungus Schizophyllum commune to co-occurring microorganisms

(2020) Katrin Krause et al.   PLoS One

Bioactive small secondary metabolites from the mushrooms Lentinula edodes and Flammulina velutipes

(2020) Emi Fukushima-Sakuno   JOURNAL OF ANTIBIOTICS

Cordycepin for Health and Wellbeing: A Potent Bioactive Metabolite of an Entomopathogenic Medicinal Fungus Cordyceps with Its Nutraceutical and Therapeutic Potential

(2020) Syed Amir Ashraf et al.   MOLECULES

CRISPR/Cas9-Based Genome Editing in the Filamentous Fungus Glarea lozoyensis and Its Application in Manipulating gloF

(2020) Teng-Yun Wei et al.   ACS Synthetic Biology

Agaricus brasiliensis Mushroom Protects Against Sepsis by Alleviating Oxidative and Inflammatory Response

(2020) Kely Campos Navegantes-Lima et al.   Frontiers in Immunology

Capillary electrophoresis electrospray ionization-mass spectrometry for peptidomics-based processing site determination

(2020) Takashi Tsuchiya et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Fun(gi)omics: Advanced and Diverse Technologies to Explore Emerging Fungal Pathogens and Define Mechanisms of Antifungal Resistance

(2020) B. Ball et al.   mBio

Use of the Versatility of Fungal Metabolism to Meet Modern Demands for Healthy Aging, Functional Foods, and Sustainability

(2020) Jacqueline A. Takahashi et al.   Journal of Fungi

Integrated proteomics and metabolomics analysis of tea leaves fermented by Aspergillus niger, Aspergillus tamarii and Aspergillus fumigatus

(2020) Yan Ma et al.   FOOD CHEMISTRY

Stabilization–destabilization and redox properties of laccases from medicinal mushroom Ganoderma lucidum and human pathogen Yersinia enterocolitica

(2020) Amit Kumar et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

SYN-View: A Phylogeny-Based Synteny Exploration Tool for the Identification of Gene Clusters Linked to Antibiotic Resistance

(2020) Jason Stahlecker et al.   MOLECULES

Transcriptome analysis of the brown rot fungus Gloeophyllum trabeum during lignocellulose degradation

(2020) Kiwamu Umezawa et al.   PLoS One

Phenolic profiles, antioxidant, and anticholinesterase activities of three Gloeophyllum species with chemometric approach

(2019) Gülsen Tel-Çayan   JOURNAL OF FOOD BIOCHEMISTRY

De novo transcriptome assembly and protein profiling of copper-induced lignocellulolytic fungus Ganoderma lucidum MDU-7 reveals genes involved in lignocellulose degradation and terpenoid biosynthetic pathways

(2019) Kavish Kumar Jain et al.   GENOMICS

The amazing potential of fungi: 50 ways we can exploit fungi industrially

(2019) Kevin D. Hyde et al.   FUNGAL DIVERSITY

EvoMining reveals the origin and fate of natural product biosynthetic enzymes

(2019) Nelly Sélem-Mojica et al.   Microbial Genomics

Phenylpropanoids and its derivatives: biological activities and its role in food, pharmaceutical and cosmetic industries

(2019) Anurag Khatkar et al.   CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION

Nutrient Properties and Nuclear Magnetic Resonance-Based Metabonomic Analysis of Macrofungi

(2019) Dan Liu et al.   Foods

Unearthing fungal chemodiversity and prospects for drug discovery

(2019) Claudio Greco et al.   CURRENT OPINION IN MICROBIOLOGY

A mechanistic and empirical review of antcins, a new class of phytosterols of formosan fungi origin

(2019) K.J. Senthil Kumar et al.   JOURNAL OF FOOD AND DRUG ANALYSIS

MIBiG 2.0: a repository for biosynthetic gene clusters of known function

(2019) Satria A Kautsar et al.   NUCLEIC ACIDS RESEARCH

Metabolic coupling in the co-cultured fungal-yeast suite of Trametes ljubarskyi and Rhodotorula mucilaginosa leads to hypersecretion of laccase isozymes

(2019) Amit Kumar et al.   Fungal Biology

Development of an eco-friendly deinking process for the production of bioethanol using diverse hazardous paper wastes

(2019) Sonu Saini et al.   RENEWABLE ENERGY

Omics and multi-omics approaches to study the biosynthesis of secondary metabolites in microorganisms

(2018) Emilia Palazzotto et al.   CURRENT OPINION IN MICROBIOLOGY

From correlation to causation: analysis of metabolomics data using systems biology approaches

(2018) Antonio Rosato et al.   Metabolomics

From genomics to metabolomics, moving toward an integrated strategy for the discovery of fungal secondary metabolites

(2018) T. Hautbergue et al.   NATURAL PRODUCT REPORTS

HMMER web server: 2018 update

(2018) Simon C Potter et al.   NUCLEIC ACIDS RESEARCH

Metabolomics Investigation of an Association of Induced Features and Corresponding Fungus during the Co-culture of Trametes versicolor and Ganoderma applanatum

(2018) Xiao-Yan Xu et al.   Frontiers in Microbiology

XCMS-MRM and METLIN-MRM: a cloud library and public resource for targeted analysis of small molecules

(2018) Xavier Domingo-Almenara et al.   NATURE METHODS

GOnet: a tool for interactive Gene Ontology analysis

(2018) Mikhail Pomaznoy et al.   BMC BIOINFORMATICS

Study on chemical constituents of an edible mushroom Volvariella volvacea and their antitumor activity in vitro

(2018) Ping Chen et al.   NATURAL PRODUCT RESEARCH

Fungal secondary metabolism: regulation, function and drug discovery

(2018) Nancy P. Keller   NATURE REVIEWS MICROBIOLOGY

Characterization of Dye Decolorization in Cell-Free Culture Broth of Trametes versicolor CBR43

(2017) Hyun Ryu et al.   JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY

Cinnabarinic acid and xanthurenic acid: Two kynurenine metabolites that interact with metabotropic glutamate receptors

(2017) Francesco Fazio et al.   NEUROPHARMACOLOGY

PRISM 3: expanded prediction of natural product chemical structures from microbial genomes

(2017) Michael A. Skinnider et al.   NUCLEIC ACIDS RESEARCH

Bioinformatic Approaches for Fungal Omics

(2017) Guohua Xiao et al.   Biomed Research International

Gel-Based Purification and Biochemical Study of Laccase Isozymes from Ganoderma sp. and Its Role in Enhanced Cotton Callogenesis

(2017) Amit Kumar et al.   Frontiers in Microbiology

Emerging Roles of Ganoderma Lucidum in Anti-Aging

(2017) Jue Wang et al.   Aging and Disease

Discovery of pentangular polyphenols hexaricins A–C from marine Streptosporangium sp. CGMCC 4.7309 by genome mining

(2016) Jun Tian et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

A non-linear model for temperature-dependent sporulation and T-2 and HT-2 production of Fusarium langsethiae and Fusarium sporotrichioides

(2016) Leyla Nazari et al.   Fungal Biology

Comprehensive curation and analysis of fungal biosynthetic gene clusters of published natural products

(2016) Yong Fuga Li et al.   FUNGAL GENETICS AND BIOLOGY

Phylogenomic Analysis of Natural Products Biosynthetic Gene Clusters Allows Discovery of Arseno-Organic Metabolites in Model Streptomycetes

(2016) Pablo Cruz-Morales et al.   Genome Biology and Evolution

Agarol, an ergosterol derivative from Agaricus blazei, induces caspase-independent apoptosis in human cancer cells

(2016) TAKAMITSU SHIMIZU et al.   INTERNATIONAL JOURNAL OF ONCOLOGY

IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes

(2016) Michalis Hadjithomas et al.   NUCLEIC ACIDS RESEARCH

Precision Nutrition 4.0: A Big Data and Ethics Foresight Analysis—Convergence of Agrigenomics, Nutrigenomics, Nutriproteomics, and Nutrimetabolomics

(2016) Vural Özdemir et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Targeted absolute quantitative proteomics with SILAC internal standards and unlabeled full-length protein calibrators (TAQSI)

(2016) Xinwen Wang et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

Fungal genome sequencing: basic biology to biotechnology

(2015) Krishna Kant Sharma   CRITICAL REVIEWS IN BIOTECHNOLOGY

Antimicrobial Activity of Extracts of the Oyster Culinary Medicinal Mushroom Pleurotus ostreatus (Higher Basidiomycetes) and Identification of a New Antimicrobial Compound

(2015) Ahmed M. Younis et al.   INTERNATIONAL JOURNAL OF MEDICINAL MUSHROOMS

Genome sequence of a laccase producing fungus Trametes sp. AH28-2

(2015) Jingjing Wang et al.   JOURNAL OF BIOTECHNOLOGY

Laccase isozymes from Ganoderma lucidum MDU-7: Isolation, characterization, catalytic properties and differential role during oxidative stress

(2015) Amit Kumar et al.   JOURNAL OF MOLECULAR CATALYSIS B-ENZYMATIC

Personalized medicine beyond genomics: alternative futures in big data—proteomics, environtome and the social proteome

(2015) Vural Özdemir et al.   JOURNAL OF NEURAL TRANSMISSION

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

PubChem Substance and Compound databases

(2015) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

Secondary metabolites from Ganoderma

(2015) Sabulal Baby et al.   PHYTOCHEMISTRY

Proteome Exploration to Provide a Resource for the Investigation of Ganoderma lucidum

(2015) Guo-Jun Yu et al.   PLoS One

Next-generation sequencing approach for connecting secondary metabolites to biosynthetic gene clusters in fungi

(2015) Ralph A. Cacho et al.   Frontiers in Microbiology

Qualitative analysis of an ethanolic extract from Trametes versicolor and biological screening against Leishmania amazonensis.

(2015) Vivian LeliebreLara et al.   Emirates Journal of Food and Agriculture

Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future

(2015) Georgios A. Pavlopoulos et al.   GigaScience

Aggressive dereplication using UHPLC–DAD–QTOF: screening extracts for up to 3000 fungal secondary metabolites

(2014) Andreas Klitgaard et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Crux: Rapid Open Source Protein Tandem Mass Spectrometry Analysis

(2014) Sean McIlwain et al.   JOURNAL OF PROTEOME RESEARCH

A Proteomic Approach to Investigating Gene Cluster Expression and Secondary Metabolite Functionality in Aspergillus fumigatus

(2014) Rebecca A. Owens et al.   PLoS One

High-Resolution MS, MS/MS, and UV Database of Fungal Secondary Metabolites as a Dereplication Protocol for Bioactive Natural Products

(2013) Tamam El-Elimat et al.   JOURNAL OF NATURAL PRODUCTS

Differential in Gel Electrophoresis (DIGE) Comparative Proteomic Analysis of Macrophages Cell Cultures in Response to Perthamide C Treatment

(2013) Annalisa Vilasi et al.   Marine Drugs

INMEX—a web-based tool for integrative meta-analysis of expression data

(2013) Jianguo Xia et al.   NUCLEIC ACIDS RESEARCH

antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers

(2013) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

ReliefSeq: A Gene-Wise Adaptive-K Nearest-Neighbor Feature Selection Tool for Finding Gene-Gene Interactions and Main Effects in mRNA-Seq Gene Expression Data

(2013) Brett A. McKinney et al.   PLoS One

Foodomics: a new comprehensive approach to food and nutrition

(2012) Francesco Capozzi et al.   Genes and Nutrition

Submerged Fermentation of the Edible Mushroom Pleurotus ostreatus in a Batch Stirred Tank Bioreactor as a Promising Alternative for the Effective Production of Bioactive Metabolites

(2012) Lefki-Maria Papaspyridi et al.   MOLECULES

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Clarifying Omics Concepts, Challenges, and Opportunities for Prunus Breeding in the Postgenomic Era

(2012) Pedro Martínez-Gómez et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

RIKEN tandem mass spectral database (ReSpect) for phytochemicals: A plant-specific MS/MS-based data resource and database

(2012) Yuji Sawada et al.   PHYTOCHEMISTRY

The Natural Product Domain Seeker NaPDoS: A Phylogeny Based Bioinformatic Tool to Classify Secondary Metabolite Gene Diversity

(2012) Nadine Ziemert et al.   PLoS One

Biotransformation of three pharmaceutical active compounds by the fungus Phanerochaete chrysosporium in a fed batch stirred reactor under air and oxygen supply

(2011) A. I. Rodarte-Morales et al.   BIODEGRADATION

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

SMURF: Genomic mapping of fungal secondary metabolite clusters

(2010) Nora Khaldi et al.   FUNGAL GENETICS AND BIOLOGY

MassBank: a public repository for sharing mass spectral data for life sciences

(2010) Hisayuki Horai et al.   JOURNAL OF MASS SPECTROMETRY

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

Simultaneous Clustering of Multiple Gene Expression and Physical Interaction Datasets

(2010) Manikandan Narayanan et al.   PLoS Computational Biology

emPAI Calc—for the estimation of protein abundance from large-scale identification data by liquid chromatography-tandem mass spectrometry

(2009) Kosaku Shinoda et al.   BIOINFORMATICS

The lifespan-promoting effect of acetic acid and Reishi polysaccharide

(2009) Ming-Hong Chuang et al.   BIOORGANIC & MEDICINAL CHEMISTRY

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(2009)   NATURE REVIEWS MICROBIOLOGY