Research graph
References from Deciphering fungal-microbial interactions: From microscale experimental models to integrative systems biology. Local targets link to admitted publications; unresolved targets remain external evidence.
Co-cultivation of Saccharomyces cerevisiae strains combines advantages of different metabolic engineering strategies for improved ethanol yield
10.1016/j.ymben.2023.09.010 · 2023 · External reference
The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered
10.1093/nar/gkad1039 · 2024 · External reference
Accurate structure prediction of biomolecular interactions with AlphaFold 3
10.1038/s41586-024-07487-w · 2024 · External reference
Fungal dye-decolorizing peroxidase diversity: roles in either intra- or extracellular processes
10.1007/s00253-022-11923-0 · 2022 · External reference
Stepping out of the dark: how metabolomics shed light on fungal biology
10.1093/femsre/fuaf028 · 2025 · External reference
Branching out: towards a trait-based understanding of fungal ecology
10.1016/j.fbr.2015.03.001 · 2015 · External reference
Unresolved reference
2023 · External reference
Single-cell RNA sequencing defines developmental progression and reproductive transitions of Pneumocystis carinii
10.1128/spectrum.01277-25 · 2025 · External reference
Fungal foraging behaviour and hyphal space exploration in micro-structured soil chips
10.1038/s41396-020-00886-7 · 2021 · External reference
A review of methods for gene regulatory networks reconstruction and analysis
10.1007/s10462-025-11257-z · 2025 · External reference
Candida-bacteria interactions: their impact on human disease
10.1128/microbiolspec.vmbf-0030-2016 · 2016 · External reference
P456 Defungi: direct mycological examination of microscopic fungi images
10.1093/mmy/myac072.p456 · 2022 · External reference
Habitat geometry in artificial microstructure affects bacterial and fungal growth, interactions, and substrate degradation
10.1038/s42003-021-02736-4 · 2021 · External reference
Habitat complexity affects microbial growth in fractal maze
10.1016/j.cub.2023.02.064 · 2023 · External reference
Challenges in capturing the mycobiome from shotgun metagenome data: lack of software and databases
10.1186/s40168-025-02048-3 · 2025 · External reference
Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens
10.1038/ismej.2012.10 · 2012 · External reference
Dynamics of metabolite induction in fungal co-cultures by metabolomics at both volatile and non-volatile levels
10.3389/fmicb.2018.00072 · 2018 · External reference
Fungi as mediators linking organisms and ecosystems
10.1093/femsre/fuab058 · 2022 · External reference
Structure and function of the global topsoil microbiome
10.1038/s41586-018-0386-6 · 2018 · External reference
Increase of laccase activity during interspecific interactions of white-rot fungi
10.1016/j.femsec.2004.07.005 · 2004 · External reference
Forest microbiome: diversity, complexity and dynamics
10.1093/femsre/fuw040 · 2016 · External reference
Active and total microbial communities in forest soil are largely different and highly stratified during decomposition
10.1038/ismej.2011.95 · 2012 · External reference
SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing
10.1089/cmb.2012.0021 · 2012 · External reference
Microbial metabolomics in open microscale platforms
10.1038/ncomms10610 · 2016 · External reference
Role of quorum sensing and chemical communication in fungal biotechnology and pathogenesis
10.1093/femsre/fuy022 · 2018 · External reference
Mass spectrometry-based metabolomics in microbiome investigations
10.1038/s41579-021-00621-9 · 2022 · External reference
Metatranscriptomics reveals climate change effects on the rhizosphere microbiomes in European grassland
10.1016/j.soilbio.2019.107604 · 2019 · External reference
Transcriptomics reveals the regulation of the immune system of the mushroom-forming fungus Schizophyllum commune during interaction with four competitors
10.1016/j.micres.2024.127929 · 2024 · External reference
High-throughput screening of filamentous fungi using nanoliter-range droplet-based microfluidics
10.1038/srep27223 · 2016 · External reference
Polaramycin B, and not physical interaction, is the signal that rewires fungal metabolism in the Streptomyces-aspergillus interaction
10.1111/1462-2920.16118 · 2022 · External reference
Positive interactions between mycorrhizal fungi and bacteria are widespread and benefit plant growth
10.1016/j.cub.2023.06.010 · 2023 · External reference
De novo production of metabolites by fungal co-culture of Trichophyton rubrum and Bionectria ochroleuca
10.1021/np400258f · 2013 · External reference
Comparison of cosine, modified cosine, and neutral loss based spectrum alignment for discovery of structurally related molecules
10.1021/jasms.2c00153 · 2022 · External reference
antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation
10.1093/nar/gkad344 · 2023 · External reference
Unresolved reference
2024 · External reference
Fungal-bacterial endosymbiosis: recreating an ancient symbiotic relationship
10.1016/j.chom.2024.10.018 · 2024 · External reference
An ultra high-throughput, massively multiplexable, single-cell RNA-seq platform in yeasts
10.1002/yea.3927 · 2024 · External reference
The contribution of pelagic fungi to ocean biomass
10.1016/j.cell.2025.05.004 · 2025 · External reference
Label-free based comparative proteomic analysis of Morchella importuna development from the vegetative to the sexual reproductive stages
2022 · External reference
Compartmentalization of bacterial and fungal microbiomes in the gut of adult honeybees
10.1038/s41522-021-00212-9 · 2021 · External reference
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
10.1093/nar/gkv1164 · 2016 · External reference
Microbial co-culturing strategies for fructo-oligosaccharide production
10.1016/j.nbt.2019.01.009 · 2019 · External reference
The aspergillus genome database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations
10.1093/nar/gkt1029 · 2014 · External reference
The effects of maternal care on the developmental transcriptome and metatranscriptome of a wild bee
10.1038/s42003-023-05275-2 · 2023 · External reference
A fungus–bacterium co-culture synergistically promoted nitrogen removal by enhancing enzyme activity and electron transfer
10.1016/j.scitotenv.2020.142109 · 2021 · External reference
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes
10.1093/nar/gky901 · 2019 · External reference
Dual RNA-seq profiling unveils mycoparasitic activities of Trichoderma atroviride against haploid Armillaria ostoyae in antagonistic interaction assays
2023 · External reference
Arbuscular mycorrhizal fungal community abundance, functions, and symbiotic interactions revealed by root metatranscriptomes
10.1002/imo2.70087 · 2026 · External reference
De novo biosynthesis of plant lignans by synthetic yeast consortia
2025 · External reference
MetaFlowTrain: a highly parallelized and modular fluidic system for studying exometabolite-mediated inter-organismal interactions
10.1038/s41467-025-58530-x · 2025 · External reference
Fungal secretome database: integrated platform for annotation of fungal secretomes
10.1186/1471-2164-11-105 · 2010 · External reference
Fungal-assisted microalgae flocculation and simultaneous lignocellulolytic enzyme production in wastewater treatment systems
10.1016/j.btre.2025.e00875 · 2025 · External reference
Synthetic biology of plants and microbes for agriculture, environment, and future applications
10.1021/acs.chemrev.4c00687 · 2026 · External reference
Quorum-driven microbial consortium for bioplastic production from agro-waste
10.1021/acssuschemeng.5c05453 · 2025 · External reference
Untangling the fungal niche: the trait-based approach
10.3389/fmicb.2014.00579 · 2014 · External reference
Fusarium species identification by means of digital signal processing
2019 · External reference
Transcriptomic responses of mixed cultures of ascomycete fungi to lignocellulose using dual RNA-seq reveal inter-species antagonism and limited beneficial effects on CAZyme expression
10.1016/j.fgb.2016.04.005 · 2017 · External reference
Applications of synthetic yeast consortia for the production of native and non-native chemicals
10.1080/07388551.2022.2118569 · 2024 · External reference
Surface frustration re-patterning underlies the structural landscape and evolvability of fungal orphan candidate effectors
10.1038/s41467-023-40949-9 · 2023 · External reference
Bacterial-fungal interactions: ecology, mechanisms and challenges
10.1093/femsre/fuy008 · 2018 · External reference
Trichoderma viride laccase plays a crucial role in defense mechanism against antagonistic organisms
10.3389/fmicb.2016.00741 · 2016 · External reference
The two-speed genomes of filamentous pathogens: waltz with plants
10.1016/j.gde.2015.09.001 · 2015 · External reference
Bacterial-fungal crosstalk is defined by a fungal lactone mycotoxin and its degradation by a bacterial lactonase
10.1128/aem.00299-24 · 2024 · External reference
Large-scale genomic analyses with machine learning uncover predictive patterns associated with fungal phytopathogenic lifestyles and traits
10.1038/s41598-023-44005-w · 2023 · External reference
SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information
10.1038/s41592-019-0344-8 · 2019 · External reference
Microbial interkingdom interactions in roots promote Arabidopsis survival
10.1016/j.cell.2018.10.020 · 2018 · External reference
Software survey: VOSviewer, a computer program for bibliometric mapping
10.1007/s11192-009-0146-3 · 2010 · External reference
Saccharomyces genome database: advances in genome annotation, expanded biochemical pathways, and other key enhancements
10.1093/genetics/iyae185 · 2025 · External reference
Reinforcement learning for efficient and robust multi-setpoint and multi-trajectory tracking in bioprocesses
10.1016/j.compchemeng.2025.109297 · 2025 · External reference
Unresolved reference
2025 · External reference
Developing filamentous fungal chassis for natural product production
10.1016/j.biortech.2024.131703 · 2025 · External reference
Microbial interactions: from networks to models
10.1038/nrmicro2832 · 2012 · External reference
Metagenome assembly of high-fidelity long reads with hifiasm-meta
10.1038/s41592-022-01478-3 · 2022 · External reference
Lower respiratory tract single-cell RNA sequencing and neutrophil extracellular trap profiling of COVID-19-associated pulmonary aspergillosis: a single Centre, retrospective, observational study
10.1016/s2666-5247(23)00368-3 · 2024 · External reference
From fungal secretomes to enzymes cocktails: the path forward to bioeconomy
10.1016/j.biotechadv.2021.107833 · 2021 · External reference
Chromatin mapping identifies BasR, a key regulator of bacteria-triggered production of fungal secondary metabolites
10.7554/elife.40969 · 2018 · External reference
Flow-FISH as a tool for studying bacteria, fungi and viruses
10.3390/biotech10040021 · 2021 · External reference
Tiberius: end-to-end deep learning with an HMM for gene prediction
10.1093/bioinformatics/btae685 · 2024 · External reference
Machine learning prediction of lignin content in poplar with Raman spectroscopy
10.1016/j.biortech.2022.126812 · 2022 · External reference
Machine learning for designing low-risk microbial consortia pesticides
10.1016/j.tibtech.2025.12.027 · 2026 · External reference
In vitro analysis of postbiotic antimicrobial activity against Candida species in a minimal synthetic model simulating the gut mycobiota in obesity
10.1038/s41598-024-66806-3 · 2024 · External reference
Evaluating the assembly strategy of a fungal genome from metagenomic data: Solorina crocea (Peltigerales, Ascomycota) as a case study
2025 · External reference
The importance of fungal biotechnology for sustainable applications
10.1016/j.tibtech.2025.06.010 · 2026 · External reference
Current advancements in fungal engineering technologies for sustainable development goals
10.1016/j.tim.2024.11.001 · 2025 · External reference
Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress
10.1371/journal.pbio.2004050 · 2017 · External reference
Discovering the hidden function in fungal genomes
10.1038/s41467-024-52568-z · 2024 · External reference
Sreening novel basidiomycete and ascomycete fungi for co-production of enzymes and antioxidants from agro-industrial wastes using solid-state fermentation
2025 · External reference
Inducing novel endosymbioses by implanting bacteria in fungi
10.1038/s41586-024-08010-x · 2024 · External reference
A versatile microfluidic platform measures hyphal interactions between Fusarium graminearum and Clonostachys rosea in real-time
10.1038/s42003-021-01767-1 · 2021 · External reference
Proteomic insights into the physiology and metabolism of oleaginous yeasts and filamentous fungi
10.3389/fmicb.2025.1637123 · 2025 · External reference
Genomic evidence of symbiotic adaptations in fungus-associated bacteria
10.1016/j.isci.2025.112253 · 2025 · External reference
MycoCosm portal: gearing up for 1000 fungal genomes
10.1093/nar/gkt1183 · 2014 · External reference
Synthetic microbial communities
10.1016/j.mib.2014.02.002 · 2014 · External reference
CYGD: the comprehensive yeast genome database
10.1093/nar/gki053 · 2004 · External reference
Machine learning for predicting phenotype from genotype and environment
10.1016/j.copbio.2022.102853 · 2023 · External reference
Mixed culture solid substrate fermentation of Trichoderma reesei with aspergillus Niger on sugar cane bagasse
10.1016/s0960-8524(98)00139-4 · 1999 · External reference
Hyphal exploration strategies and habitat modification of an arbuscular mycorrhizal fungus in microengineered soil chips
10.1016/j.funeco.2023.101302 · 2024 · External reference
A deep learning genome-mining strategy for biosynthetic gene cluster prediction
10.1093/nar/gkz654 · 2019 · External reference
Automatic detection of fungi in microscopic leucorrhea images based on convolutional neural network and morphological method
2019 · External reference
101 Dothideomycetes genomes: a test case for predicting lifestyles and emergence of pathogens
10.1016/j.simyco.2020.01.003 · 2020 · External reference
Pseudomonas strains induce transcriptional and morphological changes and reduce root colonization of Verticillium spp
10.3389/fmicb.2021.652468 · 2021 · External reference
Simulating 500 million years of evolution with a language model
10.1126/science.ads0018 · 2025 · External reference
Genome-scale phylogeny and comparative genomics of the fungal order Sordariales
10.1016/j.ympev.2023.107938 · 2023 · External reference
Missing data and technical variability in single-cell RNA-sequencing experiments
10.1093/biostatistics/kxx053 · 2018 · External reference
Automation in the life science research laboratory
10.3389/fbioe.2020.571777 · 2020 · External reference
10.1016/j.jpi.2026.100683 · 2026 · Admitted local publication
Widespread fungal-bacterial competition for magnesium lowers bacterial susceptibility to polymyxin antibiotics
10.1371/journal.pbio.3002694 · 2024 · External reference
Rhizosphere interactions: root exudates, microbes, and microbial communities
10.1139/cjb-2013-0225 · 2014 · External reference
Spec2Vec: improved mass spectral similarity scoring through learning of structural relationships
10.1371/journal.pcbi.1008724 · 2021 · External reference
MS2DeepScore: a novel deep learning similarity measure to compare tandem mass spectra
10.1186/s13321-021-00558-4 · 2021 · External reference
The emerging world of the fungal microbiome
10.1016/j.tim.2013.04.002 · 2013 · External reference
In it together: Candida-bacterial oral biofilms and therapeutic strategies
10.1111/1758-2229.13053 · 2022 · External reference
Interactions between commensal fungi and the C-type lectin receptor dectin-1 influence colitis
2012 · External reference
Advances and challenges in single-cell RNA-seq of microbial communities
10.1016/j.mib.2020.10.001 · 2020 · External reference
Construction of stable microbial consortia for effective biochemical synthesis
10.1016/j.tibtech.2023.05.008 · 2023 · External reference
High-efficiency flocculation of Leptosphaerulina australis J-22 to Chlorella vulgaris: characteristics, optimal parameters and mechanisms
10.1016/j.seppur.2024.129162 · 2025 · External reference
An automated and combinative method for the predictive ranking of candidate effector proteins of fungal plant pathogens
2021 · External reference
InterProScan 5: genome-scale protein function classification
10.1093/bioinformatics/btu031 · 2014 · External reference
Highly accurate protein structure prediction with AlphaFold
10.1038/s41586-021-03819-2 · 2021 · External reference
Democratization of fungal highway columns as a tool to investigate bacteria associated with soil fungi
10.1093/femsec/fiab003 · 2021 · External reference
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
10.7717/peerj.1165 · 2015 · External reference
Co-culturing microbial consortia: approaches for applications in biomanufacturing and bioprocessing
10.1080/07388551.2021.1921691 · 2022 · External reference
Co-cultivation of Trichoderma asperellum GDFS1009 and Bacillus amyloliquefaciens 1841 causes differential gene expression and improvement in the wheat growth and biocontrol activity
10.3389/fmicb.2019.01068 · 2019 · External reference
Fungal secondary metabolism: regulation, function and drug discovery
10.1038/s41579-018-0121-1 · 2019 · External reference
Smart culture medium optimization for recombinant protein production: experimental, modeling, and AI/ML-driven strategies
10.1016/j.biotechadv.2025.108738 · 2026 · External reference
Recent advances in fungal xenobiotic metabolism: enzymes and applications
10.1007/s11274-023-03737-7 · 2023 · External reference
Candida albicans stimulates Streptococcus mutans microcolony development via cross-kingdom biofilm-derived metabolites
2017 · External reference
Design and application of synthetic human gut microbial communities
10.1080/19490976.2025.2575923 · 2025 · External reference
Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species
10.1073/pnas.1715954115 · 2018 · External reference
A comparative genomics study of 23 Aspergillus species from section Flavi
10.1038/s41467-019-14051-y · 2020 · External reference
Fungal–fungal co-culture: a primer for generating chemical diversity
10.1039/d1np00070e · 2022 · External reference
Taking the fungal highway: mobilization of pollutant-degrading bacteria by fungi
10.1021/es047979z · 2005 · External reference
Assembly of long, error-prone reads using repeat graphs
10.1038/s41587-019-0072-8 · 2019 · External reference
Designing microbial consortia with defined social interactions
10.1038/s41589-018-0091-7 · 2018 · External reference
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation
10.1101/gr.215087.116 · 2017 · External reference
Metabolic modeling of the international Space Station microbiome reveals key microbial interactions
10.1186/s40168-022-01279-y · 2022 · External reference
Genome-scale community modeling for deciphering the inter-microbial metabolic interactions in fungus-farming termite gut microbiome
10.1016/j.compbiomed.2023.106600 · 2023 · External reference
Machine learning for the advancement of genome-scale metabolic modeling
10.1016/j.biotechadv.2024.108400 · 2024 · External reference
10.1186/s13059-020-1926-6
10.1186/s13059-020-1926-6 · External reference
Lipid metabolic changes in an early divergent fungus govern the establishment of a mutualistic symbiosis with endobacteria
10.1073/pnas.1615148113 · 2016 · External reference
Common principles and best practices for engineering microbiomes
10.1038/s41579-019-0255-9 · 2019 · External reference
DIA-PASEF proteomic profiling of Aspergillus nidulans under MpkA-dependent iron stress
10.1021/acs.jproteome.5c01210 · 2026 · External reference
Synthetic microbial communities (SynComs) of the human gut: design, assembly, and applications
2023 · External reference
Genomic features of bacterial adaptation to plants
10.1038/s41588-017-0012-9 · 2018 · External reference
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
10.1093/bioinformatics/btv033 · 2015 · External reference
The multifaceted physiological roles of fungal laccases
10.1038/s42003-026-10224-w · 2026 · External reference
Multifaceted effects of volatile organic compounds released by Fusarium oxysporum on Trichoderma biocontrol agents
10.1016/j.biocontrol.2024.105473 · 2024 · External reference
Morphological regulation of filamentous fungi improves industrial production
10.1016/j.biotechadv.2025.108793 · 2026 · External reference
Revealing differences in flavor compounds during plum wine fermentation using single and mixed yeast strains through metabolomic analysis
10.1016/j.fochx.2024.102100 · 2025 · External reference
Large language model for knowledge synthesis and AI-enhanced biomanufacturing
10.1016/j.tibtech.2025.02.008 · 2025 · External reference
Metabolic division of labor and quorum sensing restructuring drive humification by a synthetic cross-kingdom consortium in high-lipid food waste
2026 · External reference
Tetracycline degradation by a mixed culture of halotolerant fungi-bacteria under static magnetic field: mechanism and antibiotic resistance genes transfer
10.1016/j.jhazmat.2025.138181 · 2025 · External reference
NPASS database update 2026: comprehensive quantitative composition, bioactivity, and ADME-tox data of natural products for biomedical research
10.1093/nar/gkaf1196 · 2026 · External reference
Evolutionary-scale prediction of atomic-level protein structure with a language model
2023 · External reference
Fungal community analysis by high-throughput sequencing of amplified markers - a user's guide
10.1111/nph.12243 · 2013 · External reference
Discerning promotion mechanisms of fungi Clonostachys rosea on growth of freshwater microalga Chlorella sp. by non-contact culture
10.1016/j.algal.2025.103967 · 2025 · External reference
Multi-kingdom microbiota analyses identify bacterial–fungal interactions and biomarkers of colorectal cancer across cohorts
10.1038/s41564-021-01030-7 · 2022 · External reference
Rational construction of synthetic consortia: key considerations and model-based methods for guiding the development of a novel biosynthesis platform
10.1016/j.biotechadv.2024.108348 · 2024 · External reference
Function and functional redundancy in microbial systems
10.1038/s41559-018-0519-1 · 2018 · External reference
FunSecKB: the fungal secretome knowledgebase
10.1093/database/bar001 · 2011 · External reference
Response of Bacillus velezensis 83 to interaction with Colletotrichum gloeosporioides resembles a Greek phalanx-style formation: a stress resistant phenotype with antibiosis capacity
10.1016/j.micres.2023.127592 · 2024 · External reference
Diversity of fungal microbiome obtained from plant rhizoplanes
10.1016/j.scitotenv.2023.164506 · 2023 · External reference
Effect of imputation on gene network reconstruction from single-cell RNA-seq data
10.1016/j.patter.2021.100414 · 2022 · External reference
Advances in CRISPR/Cas9-based gene editing in filamentous fungi
10.3390/jof11050350 · 2025 · External reference
Production of a lignocellulolytic enzyme system for simultaneous bio-delignification and saccharification of corn Stover employing co-culture of fungi
10.1016/j.biortech.2014.10.161 · 2015 · External reference
Root exudates contribute to belowground ecosystem hotspots: a review
10.3389/fmicb.2022.937940 · 2022 · External reference
Exposure to polystyrene nanoplastics reduces bacterial and fungal biomass in microfabricated soil models
10.1016/j.scitotenv.2023.166503 · 2023 · External reference
Environmental fungi target thiol homeostasis to compete with Mycobacterium tuberculosis
10.1371/journal.pbio.3002852 · 2024 · External reference
Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences
10.1038/s41467-019-10927-1 · 2019 · External reference
Automatic classification of fungal-fungal interactions using deep leaning models
10.1016/j.csbj.2024.11.027 · 2024 · External reference
Advances in ultrahigh-throughput screening for directed enzyme evolution
10.1039/c8cs00981c · 2020 · External reference
Navigating complexity: key considerations for studying fungal-bacterial interactions
10.1128/msystems.01728-25 · 2026 · External reference
Complete, high-quality genomes from long-read metagenomic sequencing of two wolf lichen thalli reveals enigmatic genome architecture
10.1016/j.ygeno.2020.06.006 · 2020 · External reference
Inferring metabolic mechanisms of interaction within a defined gut microbiota
10.1016/j.cels.2018.08.003 · 2018 · External reference
Syntrophic exchange in synthetic microbial communities
10.1073/pnas.1405641111 · 2014 · External reference
FunSecKB2: a fungal protein subcellular location knowledgebase
10.5376/cmb.2014.04.0007 · 2014 · External reference
Syncytia in fungi
10.3390/cells9102255 · 2020 · External reference
Alkalinity role in recovery of disintegrated halophilic aerobic granular sludge treating high salt-alkali wastewater: insights into community ecology of fungi and bacteria
10.1016/j.cej.2025.164554 · 2025 · External reference
ScRAPdb: an integrated pan-omics database for the Saccharomyces cerevisiae reference assembly panel
10.1093/nar/gkae955 · 2025 · External reference
Metabolic modeling predicts specific gut bacteria as key determinants for Candida albicans colonization levels
10.1038/s41396-020-00848-z · 2021 · External reference
Genome-scale metabolic modeling of Aspergillus fumigatus strains reveals growth dependencies on the lung microbiome
10.1038/s41467-023-39982-5 · 2023 · External reference
Pfam: the protein families database in 2021
10.1093/nar/gkaa913 · 2021 · External reference
A genomic perspective on fungal diversity and evolution
10.1038/s41579-025-01195-6 · 2025 · External reference
Bacterial endosymbionts influence host sexuality and reveal reproductive genes of early divergent fungi
10.1038/s41467-017-02052-8 · 2017 · External reference
Advances and challenges in fluorescence in situ hybridization for visualizing fungal endobacteria
10.3389/fmicb.2022.892227 · 2022 · External reference
Interkingdom metabolic transformations captured by microbial imaging mass spectrometry
10.1073/pnas.1206855109 · 2012 · External reference
The black queen hypothesis: evolution of dependencies through adaptive gene loss
10.1128/mbio.00036-12 · 2012 · External reference
Learning representations of microbe–metabolite interactions
10.1038/s41592-019-0616-3 · 2019 · External reference
Mycoparasitism as a mechanism of Trichoderma-mediated suppression of plant diseases
10.1016/j.fbr.2021.11.004 · 2022 · External reference
Coordinated host-pathogen transcriptional dynamics revealed using sorted subpopulations and single macrophages infected with Candida albicans
10.1038/s41467-019-09599-8 · 2019 · External reference
Sensitive high-throughput single-cell RNA-seq reveals within-clonal transcript correlations in yeast populations
10.1038/s41564-018-0346-9 · 2019 · External reference
Spatial structure, cooperation and competition in biofilms
10.1038/nrmicro.2016.84 · 2016 · External reference
FUN-PROSE: a deep learning approach to predict condition-specific gene expression in fungi
10.1371/journal.pcbi.1011563 · 2023 · External reference
CRISPR/Cas9-mediated gene editing in filamentous fungi, focusing on mushrooms and plant-pathogenic fungi
10.1016/j.fbr.2025.100446 · 2025 · External reference
Classification of fungi images using different convolutional neural networks
2023 · External reference
Pervasive associations between dark septate endophytic fungi with tree root and soil microbiomes across Europe
10.1038/s41467-023-44172-4 · 2024 · External reference
Microbial communication leading to the activation of silent fungal secondary metabolite gene clusters
10.3389/fmicb.2015.00299 · 2015 · External reference
FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild
10.1016/j.funeco.2015.06.006 · 2016 · External reference
Mycobiome diversity: high-throughput sequencing and identification of fungi
10.1038/s41579-018-0116-y · 2019 · External reference
MIMOSA2: a metabolic network-based tool for inferring mechanism-supported relationships in microbiome-metabolome data
10.1093/bioinformatics/btac003 · 2022 · External reference
Breaking the reproducibility barrier with standardized protocols for plant-microbiome research
10.1371/journal.pbio.3003358 · 2025 · External reference
metaSPAdes: a new versatile metagenomic assembler
10.1101/gr.213959.116 · 2017 · External reference
Bacteria-induced natural product formation in the fungus Aspergillus nidulans requires Saga/Ada-mediated histone acetylation
10.1073/pnas.1103523108 · 2011 · External reference
Distinct amino acids of histone H3 control secondary metabolism in aspergillus nidulans
10.1128/aem.01578-13 · 2013 · External reference
Current concepts, advances, and challenges in deciphering the human microbiota with metatranscriptomics
10.1016/j.tig.2023.05.004 · 2023 · External reference
Understanding human health through metatranscriptomics
10.1016/j.molmed.2023.02.002 · 2023 · External reference
Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms
10.1038/nrmicro3033 · 2013 · External reference
Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts
10.1126/science.adj4503 · 2024 · External reference
Biosynthesis of biobased products from lignocellulose using filamentous fungi-integrated microbial consortia
10.1186/s13068-025-02715-5 · 2025 · External reference
Engineered cross-feeding creates inter- and intra-species synthetic yeast communities with enhanced bioproduction
10.1038/s41467-024-53117-4 · 2024 · External reference
Pathogenic fungus harbours endosymbiotic bacteria for toxin production
10.1038/nature03997 · 2005 · External reference
Boltz-2: towards accurate and efficient binding affinity prediction
2025 · External reference
Dimensions of biodiversity in the earth mycobiome
10.1038/nrmicro.2016.59 · 2016 · External reference
Flocculation performance and mechanism of fungal pellets on harvesting of microalgal biomass
10.1016/j.biortech.2020.124463 · 2021 · External reference
When FLOW-FISH met FACS: combining multiparametric, dynamic approaches for microbial single-cell research in the total environment
10.1016/j.scitotenv.2021.150682 · 2022 · External reference
Comparative genomic study of the Penicillium genus elucidates a diverse pangenome and 15 lateral gene transfer events
10.1186/s43008-023-00108-7 · 2023 · External reference
Probing mutual interactions between Pseudomonas aeruginosa and Candida albicans in a biofabricated membrane-based microfluidic platform
10.1039/d2lc00728b · 2022 · External reference
Sequencing-based analysis of microbiomes
10.1038/s41576-024-00746-6 · 2024 · External reference
FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles
10.1007/s13225-020-00466-2 · 2020 · External reference
Genome evolution in filamentous plant pathogens: why bigger can be better
10.1038/nrmicro2790 · 2012 · External reference
Designing synthetic microbial communities with the capacity to upcycle fermentation byproducts to increase production yields
10.1016/j.tibtech.2024.10.015 · 2025 · External reference
Classification of fungal genera from microscopic images using artificial intelligence
10.1016/j.jpi.2023.100314 · 2023 · External reference
Living together: the role of Candida albicans in the formation of polymicrobial biofilms in the oral cavity
10.1002/yea.3855 · 2023 · External reference
Artificial intelligence and machine learning applications in biopharmaceutical manufacturing
10.1016/j.tibtech.2022.08.007 · 2023 · External reference
MeFunX: a novel meta-learning-based deep learning architecture to detect fungal infection directly from microscopic images
10.1016/j.fraope.2023.100069 · 2024 · External reference
The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database
10.1093/nar/gkx1134 · 2018 · External reference
MGnify: the microbiome sequence data analysis resource in 2023
10.1093/nar/gkac1080 · 2023 · External reference
Fungi-on-a-Chip: microfluidic platforms for single-cell studies on fungi
10.1093/femsre/fuac039 · 2022 · External reference
Transcription activator-like effectors from endosymbiotic bacteria control the reproduction of their fungal host
10.1128/mbio.01824-23 · 2023 · External reference
Transcription activator-like effector protects bacterial endosymbionts from entrapment within fungal hyphae
10.1016/j.cub.2023.05.028 · 2023 · External reference
Deazaflavin metabolite produced by endosymbiotic bacteria controls fungal host reproduction
10.1093/ismejo/wrae074 · 2024 · External reference
Endofungal bacteria as hidden facilitators of biotic interactions
10.1093/ismejo/wraf128 · 2025 · External reference
A centralized resource for bacterial–fungal interactions research
10.1016/j.funbio.2023.04.002 · 2023 · External reference
A new flavor of synthetic yeast communities sees the light
10.1128/mbio.02008-23 · 2025 · External reference
Biosynthetic gene clusters and the evolution of fungal chemodiversity
10.1039/c9np00045c · 2020 · External reference
Fungal-bacterial mutualism: species and strain-dependent simultaneous modulation of branched-chain esters and indole derivatives in fermented sausages through metabolite cross-feeding
10.1021/acs.jafc.3c08616 · 2024 · External reference
Overcoming genetic heterogeneity in industrial fermentations
10.1038/s41587-019-0171-6 · 2019 · External reference
Spatial metatranscriptomics resolves host–bacteria–fungi interactomes
10.1038/s41587-023-01979-2 · 2024 · External reference
Single-cell imaging and RNA sequencing reveal patterns of gene expression heterogeneity during fission yeast growth and adaptation
10.1038/s41564-018-0330-4 · 2019 · External reference
Toward merging bottom-up and top-down model-based designing of synthetic microbial communities
10.1016/j.mib.2022.102169 · 2022 · External reference
Activity assays for flavoprotein oxidases: an overview
10.1007/s00253-025-13494-2 · 2025 · External reference
Machine learning aided experimental approach for evaluating the growth kinetics of Candida antarctica for lipase production
10.1016/j.biortech.2022.127087 · 2022 · External reference
A state of the art review on the co-cultivation of microalgae-fungi in wastewater for biofuel production
10.1016/j.scitotenv.2023.161828 · 2023 · External reference
Intimate bacterial-fungal interaction triggers biosynthesis of archetypal polyketides in Aspergillus nidulans
10.1073/pnas.0901870106 · 2009 · External reference
Variation in root exudate composition influences soil microbiome membership and function
10.1128/aem.00226-22 · 2022 · External reference
Prediction of effector protein structures from fungal phytopathogens enables evolutionary analyses
10.1038/s41564-022-01287-6 · 2023 · External reference
Spatial co-transcriptomics reveals discrete stages of the arbuscular mycorrhizal symbiosis
10.1038/s41477-024-01666-3 · 2024 · External reference
An alternative diagnostic method for C. neoformans: preliminary results of deep-learning based detection model
10.3390/diagnostics13010081 · 2022 · External reference
Fungi as Sources of Industrial Enzymes: Sources, Production, Properties, Structure and Applications
2025 · External reference
Dissecting the mechanism of synergistic interactions between aspergillus fumigatus and the microalgae Synechocystis sp. PCC6803 under cd(II) exposure: insights from untargeted metabolomics
10.1016/j.jhazmat.2024.135354 · 2024 · External reference
Tempo and mode of genome evolution in the budding yeast subphylum
10.1016/j.cell.2018.10.023 · 2018 · External reference
Recent advances of integrated microfluidic systems for fungal and bacterial analysis
2023 · External reference
Exploiting the fungal highway: development of a novel tool for the in situ isolation of bacteria migrating along fungal mycelium
10.1093/femsec/fiv116 · 2015 · External reference
The Candida genome database (CGD): incorporation of assembly 22, systematic identifiers and visualization of high throughput sequencing data
10.1093/nar/gkw924 · 2017 · External reference
Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0
10.1111/mpp.12682 · 2018 · External reference
FungiDB: an integrated functional genomics database for fungi
10.1093/nar/gkr918 · 2012 · External reference
Probing bacterial-fungal interactions at the single cell level
10.1039/c4ib00154k · 2014 · External reference
Democratizing protein language model training, sharing and collaboration
10.1038/s41587-025-02859-7 · 2025 · External reference
High-throughput 96-well bioelectrochemical platform for screening of electroactive microbial consortia
10.1016/j.cej.2021.131692 · 2022 · External reference
A fungus spores dataset and a convolutional neural network based approach for fungus detection
10.1109/tnb.2018.2839585 · 2018 · External reference
Discovery of fungal onoceroid triterpenoids through domainless enzyme-targeted global genome mining
10.1038/s41467-024-48771-7 · 2024 · External reference
Imprint desorption electrospray ionization mass spectrometry imaging for monitoring secondary metabolites production during antagonistic interaction of fungi
10.1021/acs.analchem.5b03614 · 2015 · External reference
Applications of AI to single-cell and spatial transcriptomics: current state-of-the-art and challenges
10.3389/fbinf.2025.1715821 · 2026 · External reference
White rot fungi as tools for the bioremediation of xenobiotics: a review
10.3390/jof10030167 · 2024 · External reference
Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants
10.1038/ismej.2013.119 · 2013 · External reference
Microfluidics and metabolomics reveal symbiotic bacterial–fungal interactions between Mortierella elongata and Burkholderia include metabolite exchange
10.3389/fmicb.2019.02163 · 2019 · External reference
Filamentous fungi as emerging cell factories for the production of aromatic compounds
10.1186/s40694-024-00188-z · 2024 · External reference
PHI-base: the pathogen-host interactions database
10.1093/nar/gkz904 · 2019 · External reference
Genotype-by-genotype interkingdom cross-talk between symbiotic nitrogen fixing Sinorhizobium meliloti strains and Trichoderma species
10.1016/j.micres.2024.127768 · 2024 · External reference
Toward deciphering the molecular dialogue in the rhizomicrobiota: transcriptomic profiling of Trichoderma in rhizobia interaction
10.1016/j.micres.2025.128180 · 2025 · External reference
Genome-resolved metatranscriptomics reveals conserved root colonization determinants in a synthetic microbiota
10.1038/s41467-023-43688-z · 2023 · External reference
Mass spectrometry imaging of natural carbonyl products directly from agar-based microbial interactions using 4-APEBA derivatization
10.1128/msystems.00803-23 · 2024 · External reference
Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri
10.1038/s41588-018-0246-1 · 2018 · External reference
GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies
2020 · External reference
Automation and artificial intelligence in filamentous fungi-based bioprocesses: a review
10.1016/j.biortech.2022.128421 · 2023 · External reference
Comparative study of fluid dynamic stress on aspergillus Niger and model systems
10.1002/cite.202300193 · 2024 · External reference
Endofungal bacteria: emerging paradigms and future directions
10.1016/j.micres.2025.128361 · 2026 · External reference
Discovery of alkaline laccases from basidiomycete fungi through machine learning-based approach
10.1186/s13068-024-02566-6 · 2024 · External reference
Fungal-fungal cocultivation leads to widespread secondary metabolite alteration requiring the partial loss-of-function VeA1 protein
2022 · External reference
Key metabolites and regulatory network mechanisms in co-culture of fungi and microalgae based on metabolomics analysis
10.1016/j.biortech.2023.129718 · 2023 · External reference
Metabolomics-based analysis of the interaction effects and stress response mechanisms in the co-culture system of fungi and microalgae under cadmium stress
10.1016/j.jclepro.2024.141473 · 2024 · External reference
Recent advances in enzyme activity assay methods: a systematic review of emerging technologies and applications
10.1021/acs.analchem.5c04502 · 2026 · External reference
A predator-prey interaction between myxobacteria and fungi mediated by outer membrane vesicles
2025 · External reference
Dual RNA sequencing reveals the interactions mechanism between Aspergillus fumigatus and Synechocystis sp. PCC6803 under Cd(II) exposure
2025 · External reference
Combined transcriptomics and metabolomics analysis reveals the antifungal activity and mechanism of enterococcus faecium cell-free supernatant against Alternaria alternata
10.1016/j.fbio.2023.103442 · 2024 · External reference
Sharing and community curation of mass spectrometry data with global natural products social molecular networking
10.1038/nbt.3597 · 2016 · External reference
Ecological design of high-performance synthetic microbial communities: from theoretical foundations to functional optimization
10.1093/ismeco/ycaf133 · 2025 · External reference
Metagenomics and plant-microbe symbioses: microbial community dynamics, functional roles in carbon sequestration, nitrogen transformation, sulfur and phosphorus mobilization for sustainable soil health
10.1016/j.biotechadv.2025.108580 · 2025 · External reference
Mass spectral molecular networking of living microbial colonies
10.1073/pnas.1203689109 · 2012 · External reference
Single-cell transcriptomic analysis highlights specific cell types manipulated by Fusarium head blight fungus leading to wheat susceptibility
10.1016/j.devcel.2025.07.022 · 2025 · External reference
Two's company: studying interspecies relationships with dual RNA-seq
10.1016/j.mib.2017.09.001 · 2018 · External reference
Design and construction of novel biocatalyst for bioprocessing: recent advances and future outlook
10.1016/j.biortech.2021.125071 · 2021 · External reference
Ensembl genomes 2022: an expanding genome resource for non-vertebrates
10.1093/nar/gkab1007 · 2022 · External reference
FunARTS, the fungal bioactive compound resistant target seeker, an exploration engine for target-directed genome mining in fungi
10.1093/nar/gkad386 · 2023 · External reference
Enhanced bioremediation performance of diesel-contaminated soil by immobilized composite fungi on rice husk biochar
10.1016/j.envres.2023.115663 · 2023 · External reference
Candida albicans as an essential “keystone” component within polymicrobial oral biofilm models?
10.3390/microorganisms9010059 · 2020 · External reference
Studies on the behavior of nutrients in the rhizosphere I: establishment of a new rhizobox system to study nutrient status in the rhizosphere
10.1080/01904168709363646 · 1987 · External reference
Engineering a gut synthetic microbial community to enhance protein bioconversion from organic wastes by black soldier fly larvae
10.1016/j.biortech.2026.134927 · 2026 · External reference
The dynamics of fungal genome organization and its impact on host adaptation and antifungal resistance
10.1016/j.jgg.2024.10.010 · 2025 · External reference
Fungal functional ecology: bringing a trait-based approach to plant-associated fungi
10.1111/brv.12570 · 2020 · External reference
NPASS: natural product activity and species source database for natural product research, discovery and tool development
10.1093/nar/gkx1026 · 2018 · External reference
Dynamical changes of tea metabolites fermented by aspergillus cristatus, Aspergillus neoniger and mixed fungi: a temporal clustering strategy for untargeted metabolomics
10.1016/j.foodres.2023.112992 · 2023 · External reference
EcoFABs: advancing microbiome science through standardized fabricated ecosystems
10.1038/s41592-019-0465-0 · 2019 · External reference
dbCAN2: a meta server for automated carbohydrate-active enzyme annotation
10.1093/nar/gky418 · 2018 · External reference
Advancing functional and translational microbiome research using meta-omics approaches
10.1186/s40168-019-0767-6 · 2019 · External reference
Principles for rigorous design and application of synthetic microbial communities
2026 · External reference
Unresolved reference
2026 · External reference
dbCAN3: automated carbohydrate-active enzyme and substrate annotation
10.1093/nar/gkad328 · 2023 · External reference
Mechanisms of single and mixed microbial fermentation to improve summer-autumn green tea
10.1016/j.fbio.2024.104830 · 2024 · External reference
Distributing a metabolic pathway among a microbial consortium enhances production of natural products
10.1038/nbt.3095 · 2015 · External reference
Recent advances in microfluidic devices for bacteria and fungus research
10.1016/j.trac.2018.12.024 · 2019 · External reference
Cross-kingdom synthetic microbiota supports tomato suppression of Fusarium wilt disease
10.1038/s41467-022-35452-6 · 2022 · External reference
Comparative proteomic analysis reveals differential protein expression of Hypsizygus marmoreus in response to different light qualities
10.1016/j.ijbiomac.2022.11.037 · 2022 · External reference
Interkingdom sensing of fungal tyrosol promotes bacterial antifungal T6SS activity in the murine gut
10.1038/s41564-025-02208-z · 2025 · External reference
Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities
10.1038/s41467-017-01407-5 · 2017 · External reference
