Genome-scale metabolic modeling of Aspergillus fumigatus strains reveals growth dependencies on the lung microbiome

[1]  Ronan M. T. Fleming,et al.  Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine , 2023, Nature Biotechnology.

[2]  L. Segal,et al.  The dynamic lung microbiome in health and disease , 2022, Nature Reviews Microbiology.

[3]  G. Walther,et al.  Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection , 2021, Nature Microbiology.

[4]  M. Kostrzewa,et al.  Aspergillus fumigatus and aspergillosis: From basics to clinics , 2021, Studies in mycology.

[5]  B. Tümmler,et al.  Identification of core and rare species in metagenome samples based on shotgun metagenomic sequencing, Fourier transforms and spectral comparisons , 2021, ISME Communications.

[6]  A. Beauvais,et al.  Aspergillus fumigatus tryptophan metabolic route differently affects host immunity , 2021, Cell reports.

[7]  S. Brunke,et al.  Metabolic modeling predicts specific gut bacteria as key determinants for Candida albicans colonization levels , 2020, The ISME Journal.

[8]  B. Tümmler,et al.  The human respiratory tract microbial community structures in healthy and cystic fibrosis infants , 2020, NPJ biofilms and microbiomes.

[9]  A. D. da Cunha,et al.  The Lung Microbiome of Three Young Brazilian Patients With Cystic Fibrosis Colonized by Fungi , 2020, Frontiers in Cellular and Infection Microbiology.

[10]  K. Pollard,et al.  Accurate and sensitive detection of microbial eukaryotes from metagenomic shotgun sequencing , 2020, bioRxiv.

[11]  S. Krappmann,et al.  The Essential Thioredoxin Reductase of the Human Pathogenic Mold Aspergillus fumigatus Is a Promising Antifungal Target , 2020, Frontiers in Microbiology.

[12]  M. Uhlén,et al.  Genome-Scale Metabolic Modeling of Glioblastoma Reveals Promising Targets for Drug Development , 2020, Frontiers in Genetics.

[13]  J. Vestbo,et al.  The global impact of Aspergillus infection on COPD , 2020, BMC Pulmonary Medicine.

[14]  Bernhard O. Palsson,et al.  A workflow for generating multi-strain genome-scale metabolic models of prokaryotes , 2019, Nature Protocols.

[15]  Adam M. Feist,et al.  High‐quality genome‐scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities , 2019, Environmental microbiology.

[16]  Nikolaus Sonnenschein,et al.  A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism , 2019, Nature Communications.

[17]  E. Halperin,et al.  FEAST: fast expectation-maximization for microbial source tracking , 2019, Nature Methods.

[18]  Shishir K. Gupta,et al.  Aspergillus fumigatus Challenged by Human Dendritic Cells: Metabolic and Regulatory Pathway Responses Testify a Tight Battle , 2019, Front. Cell. Infect. Microbiol..

[19]  Daniel N. Baker,et al.  KrakenUniq: confident and fast metagenomics classification using unique k-mer counts , 2018, Genome Biology.

[20]  Bernhard O. Palsson,et al.  Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits , 2018, Nature Communications.

[21]  Zohar Meir,et al.  Riboflavin and pantothenic acid biosynthesis are crucial for iron homeostasis and virulence in the pathogenic mold Aspergillus fumigatus , 2018, Virulence.

[22]  B. Mao,et al.  Sputum signatures for invasive pulmonary aspergillosis in patients with underlying respiratory diseases (SPARED): study protocol for a prospective diagnostic trial , 2018, BMC Infectious Diseases.

[23]  Bas E Dutilh,et al.  Towards predicting the environmental metabolome from metagenomics with a mechanistic model , 2018, Nature Microbiology.

[24]  C. Castellani,et al.  ECFS best practice guidelines: the 2018 revision. , 2018, Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society.

[25]  D. Machado,et al.  Fast automated reconstruction of genome-scale metabolic models for microbial species and communities , 2018, bioRxiv.

[26]  Sergio Bordel,et al.  Genome scale metabolic models as tools for drug design and personalized medicine , 2018, PloS one.

[27]  J. Banfield,et al.  Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome , 2017, Nature Communications.

[28]  Markus Krummenacker,et al.  The MetaCyc database of metabolic pathways and enzymes , 2017, Nucleic acids research.

[29]  C. Cunha,et al.  The microbiome-metabolome crosstalk in the pathogenesis of respiratory fungal diseases , 2017, Virulence.

[30]  R. Bro,et al.  Gas chromatography - mass spectrometry data processing made easy. , 2017, Journal of chromatography. A.

[31]  Martin J. Lercher,et al.  Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal , 2017, PLoS Comput. Biol..

[32]  C. von Mering,et al.  Sputum DNA sequencing in cystic fibrosis: non-invasive access to the lung microbiome and to pathogen details , 2017, Microbiome.

[33]  Margaret Rosenfeld,et al.  Diagnosis of Cystic Fibrosis: Consensus Guidelines from the Cystic Fibrosis Foundation , 2017, The Journal of pediatrics.

[34]  Mikko Arvas,et al.  Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction , 2016, Biotechnology for Biofuels.

[35]  Antje Chang,et al.  BRENDA in 2017: new perspectives and new tools in BRENDA , 2016, Nucleic Acids Res..

[36]  Marco Fondi,et al.  Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity , 2016, Proceedings of the National Academy of Sciences.

[37]  S. Salzberg,et al.  Centrifuge: rapid and sensitive classification of metagenomic sequences , 2016, bioRxiv.

[38]  D. Amador-Noguez,et al.  TrpE feedback mutants reveal roadblocks and conduits toward increasing secondary metabolism in Aspergillus fumigatus. , 2016, Fungal genetics and biology : FG & B.

[39]  S. Krappmann,et al.  Mutant characterization and in vivo conditional repression identify aromatic amino acid biosynthesis to be essential for Aspergillus fumigatus virulence , 2016, Virulence.

[40]  Bin Zhang,et al.  Multiscale Embedded Gene Co-expression Network Analysis , 2015, PLoS Comput. Biol..

[41]  Philip Miller,et al.  BiGG Models: A platform for integrating, standardizing and sharing genome-scale models , 2015, Nucleic Acids Res..

[42]  M. Whiteley,et al.  Essential genome of Pseudomonas aeruginosa in cystic fibrosis sputum , 2015, Proceedings of the National Academy of Sciences.

[43]  D. Hagiwara,et al.  The role of AtfA and HOG MAPK pathway in stress tolerance in conidia of Aspergillus fumigatus. , 2014, Fungal genetics and biology : FG & B.

[44]  Chao Xie,et al.  Fast and sensitive protein alignment using DIAMOND , 2014, Nature Methods.

[45]  D. Denning,et al.  Multi-Country Estimate of Different Manifestations of Aspergillosis in Cystic Fibrosis , 2014, PloS one.

[46]  Zachary A. King,et al.  Constraint-based models predict metabolic and associated cellular functions , 2014, Nature Reviews Genetics.

[47]  Joshua A. Lerman,et al.  Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments , 2013, Proceedings of the National Academy of Sciences.

[48]  Joshua A. Lerman,et al.  COBRApy: COnstraints-Based Reconstruction and Analysis for Python , 2013, BMC Systems Biology.

[49]  Nikos Vlassis,et al.  Fast Reconstruction of Compact Context-Specific Metabolic Network Models , 2013, PLoS Comput. Biol..

[50]  I. Jacobsen,et al.  Murine infection models for Aspergillus terreus pulmonary aspergillosis reveal long-term persistence of conidia and liver degeneration. , 2012, The Journal of infectious diseases.

[51]  J. Brownstein,et al.  Emerging fungal threats to animal, plant and ecosystem health , 2012, Nature.

[52]  Aurélien Mazurie,et al.  Transcriptomic and proteomic analyses of the Aspergillus fumigatus hypoxia response using an oxygen-controlled fermenter , 2012, BMC Genomics.

[53]  M. Schaller,et al.  Persistence versus Escape: Aspergillus terreus and Aspergillus fumigatus Employ Different Strategies during Interactions with Macrophages , 2012, PloS one.

[54]  Olga Genilloud,et al.  A New Approach to Drug Discovery , 2012, Journal of biomolecular screening.

[55]  Hubertus Haas,et al.  HapX-Mediated Adaption to Iron Starvation Is Crucial for Virulence of Aspergillus fumigatus , 2010, PLoS pathogens.

[56]  S. Villas-Bôas,et al.  Analytical platform for metabolome analysis of microbial cells using methyl chloroformate derivatization followed by gas chromatography–mass spectrometry , 2010, Nature Protocols.

[57]  P. Sobrado,et al.  Aspergillus fumigatus SidA is a highly specific ornithine hydroxylase with bound flavin cofactor. , 2010, Biochemistry.

[58]  Adam M. Feist,et al.  The biomass objective function. , 2010, Current opinion in microbiology.

[59]  J. Latgé,et al.  Functional analysis of the superoxide dismutase family in Aspergillus fumigatus , 2010, Molecular microbiology.

[60]  J. Nielsen,et al.  Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger , 2008, Molecular systems biology.

[61]  J. Grimalt,et al.  Ergosterol biosynthesis pathway in Aspergillus fumigatus , 2008, Steroids.

[62]  C. J. Adams-Collier,et al.  WoLF PSORT: protein localization predictor , 2007, Nucleic Acids Res..

[63]  Terry Roemer,et al.  Essential Gene Identification and Drug Target Prioritization in Aspergillus fumigatus , 2007, PLoS pathogens.

[64]  A. Beauvais,et al.  AGS3, an α(1-3)glucan synthase gene family member of Aspergillus fumigatus, modulates mycelium growth in the lung of experimentally infected mice , 2006 .

[65]  Thomas W. Mühleisen,et al.  Deletion of the Aspergillus fumigatus lysine biosynthesis gene lysF encoding homoaconitase leads to attenuated virulence in a low-dose mouse infection model of invasive aspergillosis , 2004, Archives of Microbiology.

[66]  Steffen Klamt,et al.  Minimal cut sets in biochemical reaction networks , 2004, Bioinform..

[67]  R. Mahadevan,et al.  The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. , 2003, Metabolic engineering.

[68]  H. Arst,et al.  Signature‐tagged and directed mutagenesis identify PABA synthetase as essential for Aspergillus fumigatus pathogenicity , 2000, Molecular microbiology.

[69]  C. d’Enfert,et al.  Development of a homologous transformation system for the human pathogenic fungus Aspergillus fumigatus based on the pyrG gene encoding orotidine 5′′-monophosphate decarboxylase , 1998, Current Genetics.

[70]  T. Tsukahara Changes in Chemical Composition of Conidia of Aspergillus fumigatus during Maturation and Germination , 1980, Microbiology and immunology.