Topic areas: original research articles describing single gene function studies and large scale forward genetics screens; characterisation of EST collections; full and partial genome annotation; protein-protein interaction mapping; inter-comparison of specific gene mutants within and between species; bioinformatics analysis; other databases on interactions and review articles.

2025

Berelson, M. et al, (2025). From air to insight: the evolution of airborne DNA sequencing technologies. Microbiology doi: 10.1099/mic.0.001564.

Chakraborty, A. et al, (2025). Deciphering the microbiome potential and metabolic profiling of animal waste co-composting reveals the co-occurrence network of non-microbial and microbial biostimulants to strengthen conservative practices in sustainable agriculture. Chem. Biol. Technol. Agric. doi: 10.1186/s40538-025-00765-3.

Chen, H. et al, (2025). Accumulation and translocation of antibiotic resistance genes in plants cultivated in hydroponic systems with nitrified biogas slurry. J. Hazard. Mater. doi: 10.1016/j.jhazmat.2025.140092.

Chen, M. et al, (2025). Particle size transfer of antibiotic resistance genes in typical processes of municipal wastewater treatment plant. Bioresourc. Technol. doi: 10.1016/j.biortech.2025.132288.

D'Angelo, D. et al, (2025). IMA GENOME-F20 A draft genome assembly of Agroathelia rolfsii, Ceratobasidium papillatum, Pyrenopeziza brassicae, Neopestalotiopsis macadamiae, Sphaerellopsis filum and genomic resources for Colletotrichum spaethianum and Colletotrichum fructicola. Ima Fungus doi: 10.3897/imafungus.16.141732.

De Maayer, P. et al, (2025). Pan-genome analysis of the Enterobacter hormaechei complex highlights its genomic flexibility and pertinence as a multidrug resistant pathogen. BMC Genomics doi: 10.1186/s12864-025-11590-1.

Deng, K. et al, (2025). Decoding pecan's fungal foe: A genomic insight into Colletotrichum plurivorum isolate w-6. Journal of Fungi doi: 10.3390/jof11030203.

Du, S. et al, (2025). Children's home environments as reservoirs of antimicrobial resistance: Divergent urban-rural risks from antibiotic resistance genes and pathogens. J. Hazard. Mater. doi: 10.1016/j.jhazmat.2025.139053.

Duan, G. et al, (2025). An emerging bacterial leaf disease in rice caused by Pantoea ananatis and Pantoea eucalypti in Northeast China. Microorganisms doi: 10.3390/microorganisms13061376.

Gardoul, M. et al, (2025). Comprehensive whole-genome analysis of Streptococcus infantarius strains from Moroccan farmhouse dairy products: Genomic insights into dairy adaptation, safety, and biotechnological potential. Int. J. Food Microbiol. doi: 10.1016/j.ijfoodmicro.2025.111358.

Gu, T. et al, (2025). Faucicola mancuniensis isolated from human respiratory tract and its genomic characteristicstics. BMC Microbiol. doi: 10.1186/s12866-025-04253-4.

Harrigian, F. et al, (2025). Uncovering the Fungus Responsible for Stem and Root Rot of False Indigo: Pathogen Identification, New Disease Description, and Genome Analyses. Plant Disease doi: 10.1094/pdis-07-24-1396-re.

Hearfield, N. et al, (2025). Establishment of an experimental system to analyse extracellular vesicles during apoplastic fungal pathogenesis. Journal of Extracellular Biology doi: 10.1002/jex2.70029.

Hill, R. et al, (2025). Evolutionary genomics reveals variation in structure and genetic content implicated in virulence and lifestyle in the genus Gaeumannomyces. BMC Genomics doi: 10.1186/s12864-025-11432-0.

Hill, R. et al, (2025). Starship giant transposable elements cluster by host taxonomy using k-mer-based phylogenetics. G3-Genes Genomes Genet. doi: 10.1093/g3journal/jkaf082.

Horiguchi, T. et al, (2025). Whole-genome sequencing and comparative genomic analysis of three clinical bloodstream infection isolates of Trichosporon austroamericanum. Journal of Fungi doi: 10.3390/jof11050401.

Hou, W. et al, (2025). As a reservoir of antibiotic resistance genes and pathogens, the hydrodynamic characteristics drive their distribution patterns in Lake Victoria. Environmental Pollution doi: 10.1016/j.envpol.2025.125903.

Hudson, O.J. Brawner, (2025). Using genome-wide associations and host-by-pathogen predictions to identify allelic interactions that control disease resistance. Plant Genome doi: 10.1002/tpg2.70006.

Ji, B. et al, (2025). Distributions of pathogenic bacteria, antibiotic resistance genes, and virulence factors in pig farms in China. Ecotox. Environ. Safe. doi: 10.1016/j.ecoenv.2025.118607.

Jin, W. et al, (2025). Polyethylene microplastic pollution drives quorum sensing-mediated enrichment of rhizosphere pathogens, resistance genes, and virulence factors genes. J. Hazard. Mater. doi: 10.1016/j.jhazmat.2025.139800.

Khan, A. et al, (2025). Host-pathogen interaction databases: Tools for rapid understanding of microbial pathogenesis. WIREs Mech. Dis. doi: 10.1002/wsbm.1654.

Kharte, S. et al, (2025). Whole genome sequencing and functional annotation of Fusarium oxysporum f. sp. lentis to unravel virulence and secondary metabolite biosynthesis gene clusters. Front. Genet. doi: 10.3389/fgene.2025.1585510.

Kleyn, M. et al, (2025). Draft genome sequence of Lysinibacillus capsici NAVL5D with potential for plant growth promotion. 3 Biotech doi: 10.1007/s13205-025-04488-y.

Kroll, E. et al, (2025). A conserved fungal Knr4/Smi1 protein is crucial for maintaining cell wall stress tolerance and host plant pathogenesis. PLoS Pathog. doi: 10.1371/journal.ppat.1012769.

Kyrkou, I. et al, (2025). Pseudomonas aeruginosa maintains an inducible array of novel and diverse prophages over lengthy persistence in cystic fibrosis lungs. FEMS Microbiol. Lett. doi: 10.1093/femsle/fnaf017.

LeBlanc, N. et al, (2025). Endophytic Agrobacterium sp. from Strawberry Roots Suppresses Host Plant Growth. Phytobiomes J. doi: 10.1094/pbiomes-01-25-0003-sc.

Li, H. et al, (2025). Eutrophication shifts microbial communities and life-history strategies in the Yangtze River Estuary. Front. Microbiol. doi: 10.3389/fmicb.2025.1650511.

Lin, P. et al, (2025). Zhengella sedimenti sp. nov. and Phycobacter sedimenti sp. nov., two novel bacteria isolated from coastal sediment with genomic and metabolic analysis. Antonie Van Leeuwenhoek doi: 10.1007/s10482-025-02120-w.

Liu, F. et al, (2025). Uneven distribution of prokaryote-derived horizontal gene transfer in fungi: a lifestyle-dependent phenomenon. Mbio doi: 10.1128/mbio.02855-24.

Liu, J. et al, (2025). Kexb gene correlates with Aspergillus flavus keratitis severity: A whole-genome analysis. Invest. Ophthalmol. Vis. Sci. doi: 10.1167/iovs.66.2.42.

Liu, K. et al, (2025). Identification and virulence factors prediction of Didymella segeticola causing leaf spot disease in Asarum heterotropoides in China. Sci. Rep. doi: 10.1038/s41598-025-94398-z.

Liu, W. et al, (2025). Transmission of antimicrobial resistance genes from the environment to human gut is more pronounced in colorectal cancer patients than in healthy subjects. Imeta doi: 10.1002/imt2.70008.

Liu, Y. et al, (2025). The whole genome sequence of Cordyceps cicadae - an edible and potential medicinal fungus. Mol. Genet. Genomics doi: 10.1007/s00438-025-02255-5.

Liu, Y. et al, (2025). Whole-genome characterization and antibiotic resistance phenotype of Escherichia marmotae first isolated from Berylmys bowersi. Microbiology Spectrum doi: 10.1128/spectrum.02946-24.

Long, S. et al, (2025). Insights into the combined effect of ofloxacin and humic substances on sewage sludge anaerobic digestion. Environ. Res. doi: 10.1016/j.envres.2025.122493.

Lu, Y. et al, (2025). A complete genome analysis of toxic compound gene families in the genus Cordyceps. J. Food Biochem. doi: 10.1155/jfbc/9371774.

Matsumura, Y. et al, (2025). Integrating whole-genome sequencing into antimicrobial resistance surveillance: methodologies, challenges, and perspectives. Clin. Microbiol. Rev. doi: 10.1128/cmr.00140-22.

Matta, T. et al, (2025). Safety assessment of gaba-producing Levilactobacillus brevis LAB6 MTCC 25662 and its anti-inflammatory effects in murine macrophages. Probiotics Antimicrob. Proteins doi: 10.1007/s12602-025-10628-w.

Moses, A. et al, (2025). Inferring fungal cis-regulatory networks from genome sequences via unsupervised and interpretable representation learning. Genetics doi: 10.1093/genetics/iyaf209.

Mushynska, V. et al, (2025). Genome analysis and characterization of Enterococcus sp. SB12 isolated from carpathian artisanal cheese. Curr. Microbiol. doi: 10.1007/s00284-025-04337-4.

Narváez-Zapata, J. et al, (2025). Unveiling the molecular arsenal: genome sequencing and in silico secretome analysis of Fusarium verticillioides provide insights into maize root rot pathogenesis. Front. Plant Sci. doi: 10.3389/fpls.2025.1672761.

Navasca, A. et al, (2025). Dispensable genome and segmental duplications drive the genome plasticity in Fusarium solani. Front. Fung. Biol. doi: 10.3389/ffunb.2025.1432339.

Ninkuu, V. et al, (2025). Genome sequencing of a novel Verticillium dahliae strain (huangweibingjun). Sci. Rep. doi: 10.1038/s41598-025-99279-z.

Okoye, C. et al, (2025). Advances in tea processing and mycotoxin detection: Prospects of machine learning-assisted multi-omics for enhancing safety and quality. J. Food compos. Anal. doi: 10.1016/j.jfca.2025.108434.

Patricio-Hernández, A. et al, (2025). Comparison and analysis of the genomes of three strains of Botrytis cinerea isolated from pomegranate. Microorganisms doi: 10.3390/microorganisms13071605.

Qiu, M. et al, (2025). Screening, identification, and whole-genome sequencing of ferulic acid esterase-producing lactic acid bacteria from sheep rumen. Microorganisms doi: 10.3390/microorganisms13061295.

Que, T. et al, (2025). HPD-Kit: a comprehensive toolkit for pathogen detection and analysis. Front Cell Infect Mi doi: 10.3389/fcimb.2025.1580165.

Rehmani, M. et al, (2025). Computational design of an mRNA vaccine targeting antifungal-resistant Lomentospora prolificans. Sci. Rep. doi: 10.1038/s41598-025-14907-y.

Rivera-Lopez, E. et al, (2025). Regulatory Landscape and the Potential of Bacteriophage Applications in the United States' Food Industry. J. Food Protect. doi: 10.1016/j.jfp.2025.100510.

Rossi, L. et al, (2025). Genome characterization of Trichophyton mentagrophytes genotype VII strain PG12DES from Italy. Med. Mycol. doi: 10.1093/mmy/myaf054.

Salemi, A. et al, (2025). Proteome-wide reverse vaccinology to identify potential vaccine candidates against Staphylococcus aureus. Molecular Immunology doi: 10.1016/j.molimm.2025.05.016.

Samarskaya, V. et al, (2025). The emerging role of omics-based approaches in plant virology. Viruses-Basel doi: 10.3390/v17070986.

Sato, Y. et al, (2025). Starship giant transposons dominate plastic genomic regions in a fungal plant pathogen and drive virulence evolution. Nat. Commun. doi: 10.1038/s41467-025-61986-6.

Sheng, B. et al, (2025). Response of bacterial pathogens to process upgrades and floc sizes in a full-scale landfill leachate treatment plant. J. Environ. Manag. doi: 10.1016/j.jenvman.2025.127377.

Shi, X. et al, (2025). Comparative genome and transcriptome analysis of the endophytic fungus Epichloe sibirica reveals biological control mechanism in host Achnatherum sibiricum. Biol. Control doi: 10.1016/j.biocontrol.2025.105778.

Shukla, A. et al, (2025). Comprehensive Genomic Analysis of Bipolaris sorokiniana Strains: Insights Into Genetic Diversity and Pathogenicity. Plant Pathol. doi: 10.1111/ppa.70008.

Song, B. et al, (2025). Genomic analysis of alternaria alternata, the causal agent of black spot disease in Korla fragrant pears (pyrus sinkiangensis Yü) in China. Can. J. Plant Sci. doi: 10.1139/cjps-2024-0124.

Sutherland, C. et al, (2025). The resistance awakens: Diversity at the DNA, RNA, and protein levels informs engineering of plant immune receptors from Arabidopsis to crops. Plant Cell doi: 10.1093/plcell/koaf109.

Teli, B.B. Sarma, (2025). Identification of Magnaporthe oryzae candidate secretory effector proteins through standardizing the filtering process of the canonical parameters. Plant Pathol. doi: 10.1111/ppa.14003.

Thakur, S. et al, (2025). Turning susceptibility into strength: A new era of durable resistance in plants through genome editing. Plants doi: 10.3390/plants14193080.

Todd, J. et al, (2025). Proteomics-based prediction of candidate effectors in the interaction secretome of Trichoderma harzianum and Pseudocercospora fijiensis. Microbiol. Res. doi: 10.3390/microbiolres16080175.

Tu, Y. et al, (2025). Genomic and molecular characterization of a ceftazidime-avibactam resistant Klebsiella pneumoniae strain isolated from a Chinese tertiary hospital. BMC Microbiol. doi: 10.1186/s12866-025-03929-1.

Turco, S. et al, (2025). Harnessing genomics of Diaporthe amygdali for improved control of peach twig canker and shoot blight (tcsb). Plants doi: 10.3390/plants14192960.

Vasistha, P. et al, (2025). Effector proteins of Funneliformis mosseae BR221: unravelling plant-fungal interactions through reference-based transcriptome analysis, in vitro validation, and protein-protein docking studies. BMC Genomics doi: 10.1186/s12864-024-10918-7.

Wang, A. et al, (2025). Gwpd: A multifunctional platform to unravel biological risk factors in global engineered water systems. Engineering doi: 10.1016/j.eng.2024.04.022.

Wang, R. et al, (2025). Combining whole genome and transcriptome sequencing to analyze the pathogenic mechanism of Diplodia sapinea blight in Pinus sylvestris var. mongolica Litv. Virulence doi: 10.1080/21505594.2025.2490216.

Wang, Y. et al, (2025). Wastewater-based surveillance reveals distinct resistome profiles in younger and older populations. Environmental Pollution doi: 10.1016/j.envpol.2025.126950.

Wang, Y. et al, (2025). Presence of high-risk ARGs with greater diversity and abundance in the rare resistome in wastewater across China. J. Hazard. Mater. doi: 10.1016/j.jhazmat.2025.137435.

Wang, Y. et al, (2025). Emergence of highly virulent Aeromonas dhakensis in channel catfish aquaculture: Genomic insights into pathogenicity and antimicrobial resistance. Virulence doi: 10.1080/21505594.2025.2525933.

Wang, Y. et al, (2025). Whole- genome sequencing and comparative genomic analysis of Irpex lacteus isolated from the female reproductive tract. Microb. Genom. doi: 10.1099/mgen.0.001416.

Wang, Y. et al, (2025). Whole genome sequence data of Comamonas sediminis FS4_11, a fumonisin B1-transforming bacterium, using hybrid nanopore-illumina. Data Brief doi: 10.1016/j.dib.2025.111829.

Wendling, C. et al, (2025). Phage quest: a beginner's guide to explore viral diversity in the prokaryotic world. Brief. Bioinform. doi: 10.1093/bib/bbaf449.

Wu, F. et al, (2025). Rice grain storage reduces antibiotic resistance risks and pathogens through enrichment of antimicrobial metabolites. J. Food Qual. doi: 10.1155/jfq/9103608.

Wu, J. et al, (2025). Impact of human lifestyle on the pathogenic potential of urban wastewater. Environ. Res. doi: 10.1016/j.envres.2025.122591.

Xing, M. et al, (2025). Core effectorome of Fusarium oxysporum f. sp. conglutinans deciphered using a multiomics method exhibits diverse roles following infection in cabbage. Plant Stress doi: 10.1016/j.stress.2025.100899.

Xu, S. et al, (2025). Chromosome-level genome assembly of Fusarium tricinctum, a fungal pathogen associated with root rot in alfalfa. Sci. Data doi: 10.1038/s41597-025-05961-2.

Yan, S. et al, (2025). Endophytic strategies decoded by genome and transcriptome analysis of Fusarium nematophilum strain NQ8GII4. Front. Microbiol. doi: 10.3389/fmicb.2024.1487022.

Yan, Z. et al, (2025). Dietary microbiota-mediated shifts in gut microbial ecology and pathogen interactions in giant pandas (Ailuropoda melanoleuca). Communications Biology doi: 10.1038/s42003-025-08270-x.

Yeh, Z. et al, (2025). Genomic analyses of Purpureocillium lilacinum reveal unique DNA regions for developing isolate-specific molecular markers. BMC Genomics doi: 10.1186/s12864-025-12018-6.

Yu, H. et al, (2025). Dysbiosis and genomic plasticity in the oily scalp microbiome: a multi-omics analysis of dandruff pathogenesis. Front. Microbiol. doi: 10.3389/fmicb.2025.1595030.

Yuan, B. et al, (2025). Isolation and characterization of a highly pathogenic strain of vibrio harveyi EFL-2201 from pearl gentian grouper. Aquac. Rep. doi: 10.1016/j.aqrep.2025.102668.

Yuan, R. et al, (2025). Increased pathogens and reduced intestinal immune genes associated with fish diseases during the winter-spring transition. Internat. Microbiol. doi: 10.1007/s10123-025-00693-0.

Zhai, R. et al, (2025). Diets shape thermal responses in Chinese giant salamanders by altering liver metabolism. Front. Microbiol. doi: 10.3389/fmicb.2025.1546912.

Zhai, R. et al, (2025). The gut-liver axis plays a limited role in mediating the liver's heat susceptibility of Chinese giant salamander. BMC Genomics doi: 10.1186/s12864-025-11644-4.

Zhang, L. et al, (2025). Metagenomic insights to effective elimination of resistomes in food waste composting by lime addition. J. Hazard. Mater. doi: 10.1016/j.jhazmat.2025.140065.

Zhang, W. et al, (2025). Fungen: clustering and correcting long-read metatranscriptomic data for exploring eukaryotic microorganisms. Sci. China Life Sci. doi: 10.1007/s11427-024-2853-x.

Zhao, M. et al, (2025). Developing gut-healthy strains for pets: Probiotic potential and genomic insights of canine-derived Lactobacillus acidophilus GLA09. Microorganisms doi: 10.3390/microorganisms13020350.

Zhou, J. et al, (2025). Streptococcus lishijunsis sp. nov. isolated from feces of Apodemus chevrieri in western china and its genome function analysis. BMC Microbiol. doi: 10.1186/s12866-025-04353-1.

2024

Amezrou, R. et al, (2024). Quantitative pathogenicity and host adaptation in a fungal plant pathogen revealed by whole-genome sequencing. Nat Commun doi: 10.1038/s41467-024-46191-1.

Armer, V. J. et al, (2024). Navigating the Fusarium species complex: Host-range plasticity and genome variations. Fungal Biol. doi: 10.1016/j.funbio.2024.07.004.

Baranda, P. et al, (2024). Whole-genome sequencing of marine water-derived Curvularia verruculosa KHW-7: a pioneering study. Front Microbiol doi: 10.3389/fmicb.2024.1363879.

Baudin, M. et al, (2024). Pyricularia oryzae: Lab star and field scourge. Mol Plant Pathol doi: 10.1111/mpp.13449.

Bhagat, N. et al, (2024). Molecular warfare between pathogenic Fusarium oxysporum R1 and host Crocus sativus L. unraveled by dual transcriptomics. Plant Cell Rep doi: 10.1007/s00299-023-03101-x.

Bogdanova, E. A.V. N. Novoseletsky, (2024). ProBAN: Neural network algorithm for predicting binding affinity in protein-protein complexes. Proteins doi: 10.1002/prot.26700.

Cai, Y. et al, (2024). Mariculture waters as yet another hotbed for the creation and transfer of new antibiotic-resistant pathogenome. Environ Int doi: 10.1016/j.envint.2024.108704.

Calderon-Gonzalez, A. et al, (2024). Mapping an avirulence gene in the sunflower parasitic weed Orobanche cumana and characterization of host selection based on virulence alleles. BMC Plant Biol doi: 10.1186/s12870-024-05855-2.

Calia, G. et al, (2024). Definition of the effector landscape across 13 phytoplasma proteomes with LEAPH and EffectorComb. NAR Genom Bioinform doi: 10.1093/nargab/lqae087.

Cao, R. et al, (2024). Regulation of nitrogen transformation and microbial community by inoculation during livestock manure composting. Environ Microbiol Rep doi: 10.1111/1758-2229.13256.

Castillo-Ramirez, S., (2024). On the road to genomically defining bacterial intra-species units. mSystems doi: 10.1128/msystems.00584-24.

Chakraborty, S. et al, (2024). PBIT(V3) : A robust and comprehensive tool for screening pathogenic proteomes for drug targets and prioritizing vaccine candidates. Protein Sci doi: 10.1002/pro.4892.

Chen, J. et al, (2024). EV-COMM: A database of interspecies and intercellular interactions mediated by extracellular vesicles. J Extracell Vesicles doi: 10.1002/jev2.12442.

Chen, L. B. et al, (2024). Methylobacterium nigriterrae sp. nov., isolated from black soil. Antonie Van Leeuwenhoek doi: 10.1007/s10482-024-01981-x.

Cheng, Y. et al, (2024). Biochar reduced the risks of human bacterial pathogens in soil via disturbing quorum sensing mediated by persistent free radicals. Environ Sci Technol doi: 10.1021/acs.est.4c07668.

Christinaki, A. C.-.-M., A. I.-//-Kouvelis, V. N., (2024). Genomic insights into the evolution and adaptation of secondary metabolite gene clusters in fungicolous species Cladobotryum mycophilum ATHUM6906. G3 (Bethesda) doi: 10.1093/g3journal/jkae006.

Dapuliga, C. C. et al, (2024). First draft genome sequence of a Pectobacterium polaris strain isolated in South Africa from potato tuber affected by soft rot. Microbiol Resour Announc doi: 10.1128/mra.00691-24.

Darino, M. et al, (2024). Identification and functional characterisation of a locus for target site integration in Fusarium graminearum. Fungal Biol Biotechnol doi: 10.1186/s40694-024-00171-8.

Davis, K. P. et al, (2024). In vitro identification of underutilized beta-lactam combinations against methicillin-resistant Staphylococcus aureus bacteremia isolates. Microbiol Spectr doi: 10.1128/spectrum.00976-24.

Dobbs, J. T. et al, (2024). Genomic and transcriptomic comparisons of the twig blight pathogen, passalora sequoiae, with mycosphaerellaceae foliar and conifer pathogens. Phytopathology doi: 10.1094/PHYTO-08-23-0271-R.

Dong, B. et al, (2024). Genome sequencing and comparative genomic analysis of attenuated strain Gibellulopsis nigrescens GnVn.1 causing mild wilt in sunflower. J. Fungi doi: 10.3390/jof10120838.

Dong, Y. H. et al, (2024). Genome sequence of Fusarium oxysporum f. sp. malus HS2 causing apple replant disease. Phytofrontiers doi: 10.1094/Phytofr-03-23-0036-A.

Dou, S. et al, (2023). Preliminary exploratory research on the application value of oral and intestinal meta-genomics in predicting subjects' occupations-A case study of the distinction between students and migrant workers. Front Microbiol doi: 10.3389/fmicb.2023.1330603.

Du, Y. et al, (2024). Pathogenicity analysis and comparative genomics reveal the different infection strategies between the generalist Metarhizium anisopliae and the specialist Metarhizium acridum. Pest Manag Sci doi: 10.1002/ps.7812.

Du, Y. et al, (2024). Unveiling intraspecific diversity and evolutionary dynamics of the foodborne pathogen Bacillus paranthracis through high-quality pan-genome analysis. Curr Res Food Sci doi: 10.1016/j.crfs.2024.100867.

Dyer, S. C. et al, (2025). Ensembl 2025. Nucleic Acids Res doi: 10.1093/nar/gkae1071.

Fan, C. et al, (2024). Genomic and proteomic analyses of extracellular products reveal major virulence factors likely accounting for differences in pathogenicity to bivalves between vibrio mediterranei strains. Animals (Basel) doi: 10.3390/ani14050692.

Fang, X. M. et al, (2024). Metagenomics uncovers microbiome and resistome in soil and reindeer faeces from Ny-Alesund (Svalbard, High Arctic). Environ. Res. doi: 10.1016/j.envres.2024.119788.

Felix, C. et al, (2024). How temperature modulates the expression of pathogenesis-related molecules of the cross-kingdom pathogen Lasiodiplodia hormozganensis. Sci Total Environ doi: 10.1016/j.scitotenv.2024.171917.

Fernandes, A. S. et al, (2024). Investigating the impact of insertion sequences and transposons in the genomes of the most significant phytopathogenic bacteria. Microb Genom doi: 10.1099/mgen.0.001219.

Fu, X. et al, (2024). Two different types of hydrolases co-degrade ochratoxin A in a highly efficient degradation strain Lysobacter sp. CW239. J Hazard Mater doi: 10.1016/j.jhazmat.2024.134716.

Fu, Z. et al, (2024). Unveiling biosynthetic potential of an Arctic marine-derived strain Aspergillus sydowii MNP-2. BMC Genomics doi: 10.1186/s12864-024-10501-0.

Giolai, M. et al, (2024). Measuring air metagenomic diversity in an agricultural ecosystem. Curr Biol doi: 10.1016/j.cub.2024.07.030.

Godbold, G. D.M. B. Scholz, (2024). Annotation of functions of sequences of concern and its relevance to the new biosecurity regulatory framework in the United States. Appl Biosaf doi: 10.1089/apb.2023.0030.

Gourgues, G. et al, (2024). A toolbox for manipulating the genome of the major goat pathogen, Mycoplasma capricolum subsp. capripneumoniae. Microbiology (Reading) doi: 10.1099/mic.0.001423.

Granados-Casas, A. O. et al, (2024). Genomic sequencing and functional analysis of the ex-type strain of Malbranchea zuffiana. J. Fungi doi: 10.3390/jof10090600.

Gu, Y. et al, (2024). Genomic insights into bamboo witches' broom disease: pathogenicity and phytohormone biosynthesis in Aciculosporium take. Front Microbiol doi: 10.3389/fmicb.2024.1432979.

Guerrero-Egido, G. et al, (2024). BacLIFE: A user-friendly computational workflow for genome analysis and prediction of lifestyle-associated genes in bacteria. Nat Commun doi: 10.1038/s41467-024-46302-y.

Guo, X. et al, (2024). MOI is a comprehensive database collecting processed multi-omics data associated with viral infection. Sci Rep doi: 10.1038/s41598-024-65629-6.

Han, Z.R. Schneiter, (2024). Dual functionality of pathogenesis-related proteins: defensive role in plants versus immunosuppressive role in pathogens. Front Plant Sci doi: 10.3389/fpls.2024.1368467.

Harrison et al, (2024). Ensembl 2024. Nucleic Acids Res doi: 10.1093/nar/gkad1049.

He, L. et al, (2024). Discovery and characterization of a novel pathogen Erwinia pyri sp. nov. associated with pear dieback: taxonomic insights and genomic analysis. Front Microbiol doi: 10.3389/fmicb.2024.1365685.

Hu, B. et al, (2024). Whole-genome sequencing and pathogenicity analysis of Rhodococcus equi isolated in horses. Bmc Vet Res doi: 10.1186/s12917-024-04167-9.

Huang, H. et al, (2024). First complete genome sequence of: A fundamental resource for studying the plant pathogenic fungus. Phytofrontiers doi: 10.1094/Phytofr-12-23-0159-A.

Hughes, S. E. et al, (2024). A transcriptomics-based RNAi screen for regulators of meiosis and early stages of oocyte development in Drosophila melanogaster. G3 (Bethesda) doi: 10.1093/g3journal/jkae028.

Ji, W. et al, (2024). Algae blooms with resistance in fresh water: Potential interplay between Microcystis and antibiotic resistance genes. Sci Total Environ doi: 10.1016/j.scitotenv.2024.173528.

Jian, J. et al, (2024). Two high-quality Prototheca zopfii genomes provide new insights into their evolution as obligate algal heterotrophs and their pathogenicity. Microbiol Spectr doi: 10.1128/spectrum.04148-23.

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2023

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Yang, Y. et al, (2022). Draft genome sequence of Diaporthe batatatis causing dry rot disease in sweetpotato. Plant Dis doi: 10.1094/PDIS-07-21-1530-A.

Yao, B. et al, (2022). Seed-borne Erwinia persicina affects the growth and physiology of alfalfa (Medicago sativa L.). Front Microbiol doi: 10.3389/fmicb.2022.891188.

Yemelin, A. et al, (2021). Two novel dimorphism-related virulence factors of Zymoseptoria tritici identified using agrobacterium-mediated insertional mutagenesis. Int. J. Mol. Sci. doi: 10.3390/ijms23010400.

Zhang, G. et al, (2022). Time-series gene expression patterns and their characteristics of Beauveria bassiana in the process of infecting pest insects. J Basic Microbiol doi: 10.1002/jobm.202200155.

Zhang, H. et al, (2022). Screening for broad-spectrum antimicrobial endophytes from Rosa roxburghii and multi-omic analyses of biosynthetic capacity. Front Plant Sci doi: 10.3389/fpls.2022.1060478.

Zhang, L. L. et al, (2022). Identification of functional genes associated with the biotransformation of limonene to trans-dihydrocarvone in Klebsiella sp. O852. J Sci Food Agric doi: 10.1002/jsfa.11675.

Zhang, X. et al, (2022). Genome resource for Elsinoe batatas, the causal agent of stem and foliage scab disease of sweet potato. Phytopathology doi: 10.1094/PHYTO-08-21-0344-A.

Zheng, F. et al, (2022). Whole-genome sequence and comparative analysis of Trichoderma asperellum ND-1 reveal its unique enzymatic system for efficient biomass degradation. Catalysts doi: 10.3390/catal12040437.

Zhou, Y. et al, (2022). Complete genome analysis of highly pathogenic Non-O1/O139 Vibrio cholerae isolated from Macrobrachium rosenbergii reveals pathogenicity and antibiotic resistance-related genes. Front Vet Sci doi: 10.3389/fvets.2022.882885.

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2021

Achari, S. R. et al, (2021). Investigating the effector suite profile of Australian Fusarium oxysporum isolates from agricultural and natural ecosystems. Plant Pathol doi: 10.1111/ppa.13303.

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Bakula, Z. et al, (2021). A first insight into the genome of Prototheca wickerhamii, a major causative agent of human protothecosis. Bmc Genomics doi: 10.1186/s12864-021-07491-8.

Barber, A. E. et al, (2021). Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection. Nat Microbiol doi: 10.1038/s41564-021-00993-x.

Bertazzoni, S. et al, (2021). Chromosome-level genome assembly and manually-curated proteome of model necrotroph Parastagonospora nodorum Sn15 reveals a genome-wide trove of candidate effector homologs, and redundancy of virulence-related functions within an accessory chromosome. Bmc Genomics doi: 10.1186/s12864-021-07699-8.

Bian, D.-r. et al, (2021). Affinibrenneria salicis gen. nov. sp. nov. isolated from Salix matsudana bark canker. Archives of Microbiology doi: 10.1007/s00203-021-02323-5.

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Chandra, A. et al, (2021). A highly contiguous reference genome assembly for Colletotrichum falcatum pathotype Cf08 causing red rot disease in sugarcane. 3 Biotech doi: 10.1007/s13205-021-02695-x.

Chen, J.-Y. et al, (2021). Dynamics of Verticillium dahliae race 1 population under managed agricultural ecosystems. Bmc Biology doi: 10.1186/s12915-021-01061-w.

Chen, Y. F.Y. Xia, (2021). Structural profiling of bacterial effectors reveals enrichment of host-interacting domains and motifs. Front Mol Biosci doi: 10.3389/fmolb.2021.626600.

Chen, Z.-Y. et al, (2021). Genome sequencing and functional annotation of Bacillus sp. strain BS-Z15 isolated from cotton rhizosphere soil having antagonistic activity against Verticillium dahliae. Archives of Microbiology doi: 10.1007/s00203-020-02149-7.

Cui, Y. et al, (2021). The genome of banana leaf blight pathogen fusarium sacchari str. fs66 harbors widespread gene transfer from Fusarium oxysporum. Front Plant Sci doi: 10.3389/fpls.2021.629859.

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Feng, H. et al, (2021). Vm-milR37 contributes to pathogenicity by regulating glutathione peroxidase gene VmGP in Valsa mali. Mol. Plant Pathol. doi: 10.1111/mpp.13023.

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Johns, L. E. et al, (2021). Nutrient sensing and acquisition in fungi: mechanisms promoting pathogenesis in plant and human hosts. Fungal Biology Reviews doi: 10.1016/j.fbr.2021.01.002.

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Karabulut, O. C. et al, (2021). ML-AdVInfect: a machine-learning based adenoviral infection predictor. Front Mol Biosci doi: 10.3389/fmolb.2021.647424.

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Kumar, A. et al, (2021). De novo genome sequencing of mycoparasite Mycogone perniciosa strain MgR1 sheds new light on its biological complexity. Brazilian Journal of Microbiology doi: 10.1007/s42770-021-00535-x.

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Li, Y. et al, (2021). Pseudomonas quercus sp. nov, associated with leaf spot disease of Quercus mongolica. Int J Syst Evol Microbiol doi: 10.1099/ijsem.0.004800.

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Liu, X. et al, (2021). The first in-depth exploration of the genome of the engineered bacterium, Gluconobacter thailandicus. Biotechnol Appl Biochem doi: 10.1002/bab.2195.

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Marcet-Houben, M. et al, (2021). Comparative genomics used to predict virulence factors and metabolic genes among monilinia species. Journal of Fungi doi: 10.3390/jof7060464.

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Wu, Y. T. et al, (2021). Long-term nitrogen and sulfur deposition increased root-associated pathogen diversity and changed mutualistic fungal diversity in a boreal forest. Soil Biol Biochem doi: ARTN 108163 10.1016/j.soilbio.2021.108163.

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2020

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Gao, Z. X. et al, (2020). ORF I of mycovirus SsNSRV-1 is associated with debilitating symptoms of Sclerotinia sclerotiorum. Viruses-Basel doi: 10.3390/v12040456.

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Santos, S. A. et al, (2020). Comparative genomic and transcriptomic analyses reveal different pathogenicity-related genes among three eucalyptus fungal pathogens. Fungal Genet. Biol. doi: 10.1016/j.fgb.2019.103332.

Shah, R. M. et al, (2020). Reference genome assembly for australian Ascochyta rabiei isolate ArME14. G3-Genes Genomes Genet. doi: 10.1534/g3.120.401265.

Shanmugam, G. et al, (2020). Draft genome sequences of elsinoe fawcettii and elsinoe australis causing scab diseases on Citrus. Mol. Plant-Microbe Interact. doi: 10.1094/mpmi-06-19-0169-a.

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Sun, J. Y. et al, (2020). Whole-genome sequencing and bioinformatics analysis of Apiotrichum mycotoxinivorans: predicting putative zearalenone-degradation enzymes. Front. Microbiol. doi: 10.3389/fmicb.2020.01866.

Tang, L. T. et al, (2020). Co-occurrence of the bla(KPC-2) and Mcr-3.3 gene in Aeromonas caviae SCAc2001 isolated from patients with diarrheal disease. Infect. Drug Resistance doi: 10.2147/idr.S245553.

Thomas, G. et al, (2020). Identifying Candida albicans gene networks involved in pathogenicity. Front. Genet. doi: 10.3389/fgene.2020.00375.

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Valdes, I. D. et al, (2020). The sino-nasal war zone: transcriptomic and genomic studies on sino-nasal aspergillosis in dogs. npj Biofilms Microbomes doi: 10.1038/s41522-020-00163-7.

Vasquez-Montano, E. et al, (2020). Defects in the ferroxidase that participates in the reductive iron assimilation system results in hypervirulence in Botrytis Cinerea. mBio doi: 10.1128/mBio.01379-20.

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Wang, C. et al, (2020). FunEffector-Pred: identification of fungi effector by activate learning and genetic algorithm sampling of imbalanced data. IEEE Access doi: 10.1109/access.2020.2982410.

Wang, M. et al, (2020). Complete genome sequence of zearalenone degrading bacteria Bacillus velezensis A2. Curr. Microbiol. doi: 10.1007/s00284-020-02234-6.

Wang, X. X. et al, (2020). Genome sequencing of Paecilomyces penicillatus provides insights into its phylogenetic placement and mycoparasitism mechanisms on morel mushrooms. Pathogens doi: 10.3390/pathogens9100834.

Will, I. et al, (2020). Genetic underpinnings of host manipulation by Ophiocordyceps as revealed by comparative transcriptomics. G3-Genes Genomes Genet. doi: 10.1534/g3.120.401290.

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Xu, M. et al, (2020). Adaptive regulation of virulence genes by microRNA-like RNAs in Valsa mali. New Phytol. doi: 10.1111/nph.16561.

Xu, P. et al, (2020). Comparative genomics analysis provides new strategies for bacteriostatic ability of Bacillus velezensis HAB-2. Front. Microbiol. doi: 10.3389/fmicb.2020.594079.

Xu, R. et al, (2020). Genomic features of Cladobotryum dendroides, which causes cobweb disease in edible mushrooms, and identification of genes related to pathogenicity and mycoparasitism. Pathogens doi: 10.3390/pathogens9030232.

Zhang, H.-L. et al, (2020). Complete genome sequence reveals evolutionary and comparative genomic features of Xanthomonas albilineans causing sugarcane leaf scald. Microorganisms doi: 10.3390/microorganisms8020182.

Zhang, M. et al, (2020). Variation of antibiotic resistome during commercial livestock manure composting. Environ. Int. doi: 10.1016/j.envint.2020.105458.

Zhang, P. P. et al, (2020). Identification of a mobilizable, multidrug-resistant genomic island in Myroides odoratimimus isolated from Tibetan pasture. Sci. Total Environ. doi: 10.1016/j.scitotenv.2020.137970.

Zhang, R. Z. et al, (2020). Traditional chinese medicine and gut microbiome: their respective and concert effects on healthcare. Front. Pharmacol. doi: 10.3389/fphar.2020.00538.

Zhang, W. et al, (2020). Comparative genome and transcriptome analysis of the nematode-trapping fungus Duddingtonia flagrans reveals high pathogenicity during nematode infection. Biol. Control doi: 10.1016/j.biocontrol.2019.104159.

Zhang, X. X. et al, (2020). Source of hemolymph microbiota and their roles in the immune system of mud crab. Dev. Comp. Immunol. doi: 10.1016/j.dci.2019.103470.

Zhang, X. et al, (2020). Shifts in microbial community, pathogenicity-related genes and antibiotic resistance genes during dairy manure piled up. Microb. Biotechnol. doi: 10.1111/1751-7915.13551.

Zhao, J. et al, (2020). Genome sequencing and transcriptome analysis of Geotrichum citri-aurantii on citrus reveal the potential pathogenic- and guazatine-resistance related genes. Genomics doi: 10.1016/j.ygeno.2020.07.013.

Zhao, Q. et al, (2020). Genome-scale analyses and characteristics of putative pathogenicity genes of Stagonosporopsis cucurbitacearum, a pumpkin gummy stem blight fungus. Sci Rep doi: 10.1038/s41598-020-75235-x.

Zong, G. et al, (2020). The carbapenem resistance gene bla(OXA-23) is disseminated by a conjugative plasmid containing the novel transposon Tn6681 in Acinetobacter johnsonii M19. Antimicrobial Resistance and Infection Control doi: 10.1186/s13756-020-00832-4.

dos Santos, R. A. C. et al, (2020). Genomic and phenotypic heterogeneity of clinical isolates of the human pathogens Aspergillus fumigatus, Aspergillus lentulus, and Aspergillus fumigatiaffinis. Front. Genet. doi: 10.3389/fgene.2020.00459.

2019

Argemi, X. et al, (2019). Coagulase-negative Staphylococci pathogenomics. International Journal of Molecular Sciences doi: 10.3390/ijms20051215.

Bai, P. et al, (2019). Decreased metabolism and increased tolerance to extreme environments in Staphylococcus warneri during long-term spaceflight. Microbiologyopen doi: 10.1002/mbo3.917.

Burgos-Canul, Y. Y. et al, (2019). The cell wall proteome from two strains of Pseudocercospora fijiensis with differences in virulence. World Journal of Microbiology & Biotechnology doi: 10.1007/s11274-019-2681-2.

Chakdar, H. et al, (2019). noxB-based marker for Alternaria spp.: a new diagnostic marker for specific and early detection in crop plants. 3 Biotech doi: 10.1007/s13205-019-1779-4.

Dilks, T. et al, (2019). Non-canonical fungal G-protein coupled receptors promote Fusarium head blight on wheat. PLoS Pathog. doi: 10.1371/journal.ppat.1007666.

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Fabre, F. et al, (2019). Time-resolved dissection of the molecular crosstalk driving Fusarium head blight in wheat provides new insights into host susceptibility determinism. Plant Cell and Environment doi: 10.1111/pce.13549.

Fonseca, N. R. et al, (2019). Transcriptome analysis of a powdery mildew pathogen (Podosphaera pannosa) infecting Eucalyptus urophylla: De novo assembly, expression profiling and secretome prediction. Forest Pathology doi: 10.1111/efp.12508.

Fourie, A. et al, (2019). QTL mapping of mycelial growth and aggressiveness to distinct hosts in Ceratocystis pathogens. Fungal Genet. Biol. doi: 10.1016/j.fgb.2019.103242.

Gabaldon, T. et al, (2019). Recent trends in molecular diagnostics of yeast infections: from PCR to NGS. Fems Microbiol. Rev. doi: 10.1093/femsre/fuz015.

Ghosh, S. et al, (2019). Genome analysis provides insight about pathogenesis of Indian strains of Rhizoctonia solani in rice. Functional & Integrative Genomics doi: 10.1007/s10142-019-00687-y.

Gurjar, M. S. et al, (2019). De novo genome sequencing and secretome analysis of Tilletia indica inciting Karnal bunt of wheat provides pathogenesis-related genes. 3 Biotech doi: 10.1007/s13205-019-1743-3.

Hawkins, N. J. et al, (2019). The evolutionary origins of pesticide resistance. Biol. Rev. doi: 10.1111/brv.12440.

Jabeen, S. et al, (2019). Complete genome sequence analysis and characterization of selected iron regulation genes of Pasteurella multocida serotype A strain PMTB2.1. Genes doi: 10.3390/genes10020081.

Janowska-Sejda, E. I. et al, (2019). PHI-Nets: A Network Resource for Ascomycete Fungal Pathogens to Annotate and Identify Putative Virulence Interacting Proteins and siRNA Targets. Front. Microbiol. doi: 10.3389/fmicb.2019.02721.

Jones, D. A. B. et al, (2019). A specific fungal transcription factor controls effector gene expression and orchestrates the establishment of the necrotrophic pathogen lifestyle on wheat. Sci Rep doi: 10.1038/s41598-019-52444-7.

Kosesoy, I. et al, (2019). A new sequence based encoding for prediction of host-pathogen protein interactions. Computational Biology and Chemistry doi: 10.1016/j.compbiolchem.2018.12.001.

Lelwala, R. V. et al, (2019). Comparative genome analysis indicates high evolutionary potential of pathogenicity genes in Colletotrichum tanaceti. Plos One doi: 10.1371/journal.pone.0212248.

Levin, E. et al, (2019). Identification of pathogenicity-related genes and the role of a subtilisin-related peptidase S8 (PePRT) in authophagy and virulence of Penicillium expansum on apples. Postharvest Biology and Technology doi: 10.1016/j.postharvbio.2018.10.011.

Li, D. et al, (2019). Genome analysis of Hypomyces perniciosus, the causal agent of wet bubble disease of button mushroom (Agaricus bisporus). Genes doi: 10.3390/genes10060417.

Liu, X. et al, (2020). A time-resolved dual transcriptome analysis reveals the molecular regulating network underlying the compatible/incompatible interactions between cabbage (Brassica oleracea) and Fusarium oxysporum f. sp. conglutinans. Plant Soil doi: 10.1007/s11104-020-04437-z.

Ma, S. W. et al, (2019). Prediction of protein-protein interactions between fungus (Magnaporthe grisea) and rice (Oryza sativa L.). Briefings in Bioinformatics doi: 10.1093/bib/bbx132.

Malar, C. M. et al, (2019). Haplotype-phased genome assembly of virulent Phytophthora ramorum isolate ND886 facilitated by long-read sequencing reveals effector polymorphisms and copy number variation. Molecular Plant-Microbe Interactions doi: 10.1094/mpmi-08-18-0222-r.

Martin-Galiano, A. J.M. J. McConnell, (2019). Using Omics Technologies and Systems Biology to Identify Epitope Targets for the Development of Monoclonal Antibodies Against Antibiotic-Resistant Bacteria. Front. Immunol. doi: 10.3389/fimmu.2019.02841.

Messal, M. et al, (2019). Active Fungal Communities in Asymptomatic Eucalyptus grandis Stems Differ between a Susceptible and Resistant Clone. Microorganisms doi: 10.3390/microorganisms7100375.

Mitchell, A. L. et al, (2019). InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Res. doi: 10.1093/nar/gky1100.

Mousavi-Derazmahalleh, M. et al, (2019). Prediction of pathogenicity genes involved in adaptation to a lupin host in the fungal pathogens Botrytis cinerea and Sclerotinia sclerotiorum via comparative genomics. BMC Genomics doi: 10.1186/s12864-019-5774-2.

Neu, E.T. Debener, (2019). Prediction of the Diplocarpon rosae secretome reveals candidate genes for effectors and virulence factors. Fungal Biol-Uk doi: 10.1016/j.funbio.2018.12.003.

Pedro, H. et al, (2019). Collaborative Annotation Redefines Gene Sets for Crucial Phytopathogens. Front. Microbiol. doi: 10.3389/fmicb.2019.02477.

Petrasch, S. et al, (2019). Infection strategies deployed by Botrytis cinerea, Fusarium acuminatum, and Rhizopus stolonifer as a function of tomato fruit ripening stage. Frontiers in Plant Science doi: 10.3389/fpls.2019.00223.

Priyann, A. et al, (2019). Sequenceserver: A Modern Graphical User Interface for Custom BLAST Databases. Mol. Biol. Evol. doi: 10.1093/molbev/msz185.

Rendueles, O.G. J. Velicer, (2020). Hidden paths to endless forms most wonderful: Complexity of bacterial motility shapes diversification of latent phenotypes. BMC Evol. Biol. doi: 10.1186/s12862-020-01707-3.

Rodrigues, C. M. et al, (2019). Comparative genome analysis of Phyllosticta citricarpa and Phyllosticta capitalensis, two fungi species that share the same host. Bmc Genomics doi: 10.1186/s12864-019-5911-y.

Rodriguez-Romero, J. et al, (2019). Virulence- and signaling-associated genes display a preference for long 3 ' UTRs during rice infection and metabolic stress in the rice blast fungus. New Phytologist doi: 10.1111/nph.15405.

Sayers, S. et al, (2019). Victors: a web-based knowledge base of virulence factors in human and animal pathogens. Nucleic Acids Research doi: 10.1093/nar/gky999.

Sossah, F. L. et al, (2019). Genome sequencing of Cladobotryum protrusum provides insights into the evolution and pathogenic mechanisms of the cobweb disease pathogen on cultivated mushroom. Genes doi: 10.3390/genes10020124.

Vieira, A. et al, (2019). Genome-wide signatures of selection in Colletotrichum kahawae reveal candidate genes potentially Involved in pathogenicity and aggressiveness. Frontiers in Microbiology doi: 10.3389/fmicb.2019.01374.

Vinatzer, B. A. et al, (2019). Cyberbiosecurity challenges of pathogen genome databases. Frontiers in Bioengineering and Biotechnology doi: 10.3389/fbioe.2019.00106.

Xu, M. et al, (2020). Adaptive regulation of virulence genes by microRNA-like RNAs in Valsa mali. New Phytol. doi: 10.1111/nph.16561.

Xu, P. D. et al, (2020). Comparative Genomics Analysis Provides New Strategies for Bacteriostatic Ability of Bacillus velezensis HAB-2. Front. Microbiol. doi: 10.3389/fmicb.2020.594079.

Yamamoto, N. et al, (2019). Integrative transcriptome analysis discloses the molecular basis of a heterogeneous fungal phytopathogen complex, Rhizoctonia solani AG-1 subgroups. Sci Rep doi: 10.1038/s41598-019-55734-2.

Yang, S. P. et al, (2019). Critical assessment and performance improvement of plant-pathogen protein-protein interaction prediction methods. Briefings in Bioinformatics doi: 10.1093/bib/bbx123.

Yang, Y. H. et al, (2019). Integrated transcriptomic and secretomic approaches reveal critical pathogenicity factors in Pseudofabraea citricarpa inciting citrus target spot. Microb. Biotechnol. doi: 10.1111/1751-7915.13440.

Yu, B. B. et al, Parasitism by Cuscuta australis affects the rhizhospheric soil bacterial communities of Trifolium repens L. Acta Agriculturae Scandinavica Section B-Soil and Plant Science doi: 10.1080/09064710.2019.1637016.

Zhang, H. et al, (2019). Global Screening of Genomic and Transcriptomic Factors Associated with Phenotype Differences between Multidrug-Resistant and -Susceptible Candida haemulonii Strains. mSystems doi: 10.1128/mSystems.00459-19.

Zhao, X. et al, (2019). MADS-box transcription factor Mcm1 controls cell cycle, fungal development, cell integrity and virulence in the filamentous insect pathogenic fungus Beauveria bassiana. Environ. Microbiol. doi: 10.1111/1462-2920.14629.

Zumaquero, A. et al, (2019). Transcriptome analysis of the fungal pathogen Rosellinia necatrix during infection of a susceptible avocado rootstock identifies potential mechanisms of pathogenesis. BMC Genomics doi: 10.1186/s12864-019-6387-5.

de Queiroz, C. B.M. F. Santana, (2020). Prediction of the secretomes of endophytic and nonendophytic fungi reveals similarities in host plant infection and colonization strategies. Mycologia doi: 10.1080/00275514.2020.1716566.

van der Nest, M. A. et al, (2019). Genomic analysis of the aggressive tree pathogen Ceratocystis albifundus. Fungal Biol. doi: 10.1016/j.funbio.2019.02.002.

2018

Armitage, A. D. et al, (2018). Bioinformatic characterisation of the effector repertoire of the strawberry pathogen Phytophthora cactorum. PLoS One doi: 10.1371/journal.pone.0202305.

Baldwin, T. T. et al, (2018). Sharing mutants and experimental information prepublication using FgMutantDb (https://scabusa.org/FgMutantDb). Fungal Genet Biol doi: 10.1016/j.fgb.2018.01.002.

Chagas, F. O. et al, (2018). Chemical signaling involved in plant-microbe interactions. Chem Soc Rev doi: 10.1039/c7cs00343a.

Chen, J. Y. et al, (2018). Comparative genomics reveals cotton-specific virulence factors in flexible genomic regions in Verticillium dahliae and evidence of horizontal gene transfer from Fusarium. The New phytologist doi: 10.1111/nph.14861.

Figueroa, M. et al, (2018). A review of wheat diseases-a field perspective. Mol Plant Pathol doi: 10.1111/mpp.12618.

Ghosh, S. et al, (2018). Identification of candidate pathogenicity determinants of Rhizoctonia solani AG1-IA, which causes sheath blight disease in rice. Current Genetics doi: 10.1007/s00294-017-0791-7.

He, Z. J. et al, (2018). Comparative transcriptome and gene co-expression network analysis reveal genes and signaling pathways adaptively responsive to varied adverse stresses in the insect fungal pathogen, Beauveria bassiana. Journal of Invertebrate Pathology doi: 10.1016/j.jip.2017.12.002.

Jones, D. A. B. et al, (2018). Bioinformatic prediction of plant-pathogenicity effector proteins of fungi. Current Opinion in Microbiology doi: 10.1016/j.mib.2018.01.017.

Kersey, P. J. et al, (2018). Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species. Nucleic Acids Res doi: 10.1093/nar/gkx1011.

King, R. et al, (2018). Inter-genome comparison of the Quorn fungus Fusarium venenatum and the closely related plant infecting pathogen Fusarium graminearum. BMC Genomics doi: 10.1186/s12864-018-4612-2.

Lacasta, J. et al, (2018). Agricultural recommendation system for crop protection. Comput Electron Agr doi: 10.1016/j.compag.2018.06.049.

Li, S. et al, (2018). The interactomic analysis reveals pathogenic protein networks in Phomopsis longicolla underlying seed decay of soybean. Front Genet doi: 10.3389/fgene.2018.00104.

Liang, P. et al, (2018). Powdery mildews are characterized by contracted carbohydrate metabolism and diverse effectors to adapt to obligate biotrophic lifestyle. Frontiers in Microbiology doi: 10.3389/fmicb.2018.03160.

Liu, F. et al, (2018). Whole-genome sequence and genome annotation of Xanthomonas citri pv. mangiferaeindicae, causal agent of bacterial black spot on Mangifera indica. Arch Microbiol doi: 10.1007/s00203-018-1513-3.

Liu, J. Y. et al, (2018). Complete genomic analysis of multidrug-resistance Pseudomonas aeruginosa Guangzhou-Pae617, the host of megaplasmid pBM413. Microbial Pathogenesis doi: 10.1016/j.micpath.2018.02.049.

Munoz, J. F. et al, (2018). Genome analysis reveals evolutionary mechanisms of adaptation in systemic dimorphic fungi. Sci Rep doi: 10.1038/s41598-018-22816-6.

Ramos-Garcia, A. A. et al, (2018). Draft genome sequence of the 1,4-dioxane-degrading bacterium Pseudonocardia dioxanivorans BERK-1. Microbiology Resource Announcements doi: 10.1128/genomeA.00207-18.

Ravet, K. et al, (2018). The power and potential of genomics in weed biology and management. Pest Manag Sci doi: 10.1002/ps.5048.

Rivera, Y. et al, (2018). Genome analysis of the ubiquitous boxwood pathogen Pseudonectria foliicola. PeerJ doi: 10.7717/peerj.5401.

Ruocco, M. et al, (2018). Polyketide synthases of Diaporthe helianthi and involvement of DhPKS1 in virulence on sunflower. BMC Genomics doi: 10.1186/s12864-017-4405-z.

Sanchez-Rangel, D. et al, (2018). Environmental pH modulates transcriptomic responses in the fungus Fusarium sp. associated with KSHB Euwallacea sp. near fornicatus. BMC Genomics doi: 10.1186/s12864-018-5083-1.

Sieber, P. et al, (2018). Comparative study on alternative splicing in human fungal pathogens suggests its involvement during host invasion. Front Microbiol doi: 10.3389/fmicb.2018.02313.

Sperschneider, J. et al, (2018). Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0. Mol Plant Pathol doi: 10.1111/mpp.12682.

Wang, A. J. et al, (2018). The pathogenic mechanisms of Tilletia horrida as revealed by comparative and functional genomics. Scientific Reports doi: 10.1038/s41598-018-33752-w.

Wang, J. H. et al, (2018). Transcriptomic insight into pathogenicity-associated factors of Conidiobolus obscurus, an obligate aphid-pathogenic fungus belonging to Entomopthoromycota. Pest Management Science doi: 10.1002/ps.4861.

Wang, J. et al, (2018). SNARE-Encoding genes VdSec22 and VdSso1 mediate protein secretion required for full virulence in Verticillium dahliae. Mol Plant Microbe Interact doi: 10.1094/MPMI-12-17-0289-R.

Wang, R. et al, (2018). Comparative genomic analyses reveal the features for adaptation to nematodes in fungi. DNA Res doi: 10.1093/dnares/dsx053.

Wang, Y. et al, (2018). Comparative genomics reveals the core gene toolbox for the fungus-insect symbiosis. MBio doi: 10.1128/mBio.00636-18.

Zeng, R. et al, (2018). Prediction of pathogenesis-related secreted proteins from Stemphylium lycopersici. BMC Microbiology doi: 10.1186/s12866-018-1329-y.

Zeng, Z. et al, (2018). Intraspecific comparative genomics of isolates of the Norway spruce pathogen (Heterobasidion parviporum) and identification of its potential virulence factors. BMC Genomics doi: 10.1186/s12864-018-4610-4.

Zhang, W. Q. et al, (2018). Verticillium dahliae transcription factor VdFTF1 regulates the expression of multiple secreted virulence factors and is required for full virulence in cotton. Mol Plant Pathol doi: 10.1111/mpp.12569.

Zheng, H. K. et al, (2018). Comparative genomic analysis revealed rapid differentiation in the pathogenicity-related gene repertoires between Pyricularia oryzae and Pyricularia penniseti isolated from a Pennisetum grass. Bmc Genomics doi: 10.1186/s12864-018-5222-8.

Zhu, J. et al, (2018). Breast cancer in postmenopausal women is associated with an altered gut metagenome. Microbiome doi: 10.1186/s40168-018-0515-3.

2017

Aylward, J. et al, (2017). A plant pathology perspective of fungal genome sequencing. IMA Fungus doi: 10.5598/imafungus.2017.08.01.01.

Bashyal, B. M. et al, (2017). whole genome sequencing of Fusarium fujikuroi provides insight into the role of secretory proteins and cell wall degrading enzymes in causing bakanae disease of rice. Front Plant Sci doi: 10.3389/fpls.2017.02013.

Basim, E. et al, (2017). Identification and characterization of Alternaria alternata causing leaf spot of olive tree (Olea europaea) in Turkey. Crop Prot doi: 10.1016/j.cropro.2016.10.013.

Buiate, E. A. et al, (2017). A comparative genomic analysis of putative pathogenicity genes in the host-specific sibling species Colletotrichum graminicola and Colletotrichum sublineola. BMC Genomics doi: 10.1186/s12864-016-3457-9.

Galperin, M. Y. et al, (2017). The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. Nucleic Acids Res doi: 10.1093/nar/gkx021.

Kumar, A. et al, (2017). Draft genome sequence of Karnal bunt pathogen (Tilletia indica) of wheat provides insights into the pathogenic mechanisms of quarantined fungus. PLoS One doi: 10.1371/journal.pone.0171323.

Min, B. et al, (2017). Genome analysis of a zygomycete fungus Choanephora cucurbitarum elucidates necrotrophic features including bacterial genes related to plant colonization. Sci Rep doi: 10.1038/srep40432.

Castiblanco, V. et al, (2017). Candidate gene based association mapping in Fusarium culmorum for field quantitative pathogenicity and mycotoxin production in wheat. BMC genetics doi: 10.1186/s12863-017-0511-9.

Deng, C. H. et al, (2017). Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range. BMC Genomics doi: 10.1186/s12864-017-3699-1.

Derbyshire, M. et al, (2017). The complete genome sequence of the phytopathogenic fungus Sclerotinia sclerotiorum reveals insights into the genome architecture of broad host range pathogens. Genome Biol Evol doi: 10.1093/gbe/evx030.

Dong, W. X. et al, (2017). Transcriptomic insights into the alternative splicing-mediated adaptation of the entomopathogenic fungus Beauveria bassiana to host niches: autophagy-related gene 8 as an example. Environ Microbiol doi: 10.1111/1462-2920.13862.

Ferrareze, P. A. G. et al, (2017). Transcriptional analysis allows genome reannotation and reveals that Cryptococcus gattii VGII undergoes nutrient restriction during infection. Microorganisms doi: 10.3390/microorganisms5030049.

Finn, R. D. et al, (2017). InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res doi: 10.1093/nar/gkw1107.

Iquebal, M. A. et al, (2017). Draft whole genome sequence of groundnut stem rot fungus Athelia rolfsii revealing genetic architect of its pathogenicity and virulence. Sci Rep doi: 10.1038/s41598-017-05478-8.

Kim, H. et al, (2017). Characterization of the Rosellinia necatrix Transcriptome and Genes Related to Pathogenesis by Single-Molecule mRNA Sequencing. Plant Pathol J doi: 10.5423/PPJ.OA.03.2017.0046.

Lara-Marquez, A. et al, (2017). Evolutionary analysis of pectin lyases of the genus Colletotrichum. J Mol Evol doi: 10.1007/s00239-017-9812-x.

Liu, J. Y. et al, (2017). Complete genome sequence and bioinformatics analyses of Bacillus thuringiensis strain BM-BT15426. Microbial Pathogenesis doi: 10.1016/j.micpath.2017.05.006.

Lu, Y. et al, (2017). Omics data reveal the unusual asexual-fruiting nature and secondary metabolic potentials of the medicinal fungus Cordyceps cicadae. BMC Genomics doi: 10.1186/s12864-017-4060-4.

Luo, X. et al, (2017). Genome sequencing and comparative genomics reveal the potential pathogenic mechanism of Cercospora sojina Hara on soybean. DNA Res doi: 10.1093/dnares/dsx035.

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2014

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