{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T03:48:11Z","timestamp":1782272891686,"version":"3.54.5"},"reference-count":57,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T00:00:00Z","timestamp":1781568000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Pseudomonas aeruginosa (P. aeruginosa) is a multidrug-resistant opportunistic pathogen that causes both acute and chronic infections and is known for its ability to form biofilms. In the current study, we applied a hypothesis-generating framework primarily based on integrating four different datasets and applying batch correction. Weighted Gene Co-Expression Network Analysis (WGCNA) was performed in parallel with differential expression analysis using limma. Therefore, we aimed to identify potential biofilm-associated gene candidates. Significant candidate genes were subjected to functional analysis and gene ontology, followed by the construction of a protein\u2013protein interaction network using STRING. The Pseudomonas Genome Database was used to highlight the candidate genes. A total of 271, 687, 533, and 277 significantly up-regulated differentially expressed genes (DEGs), as well as 306, 985, 472, and 312 significantly down-regulated DEGs, resulted from the exploratory analysis. Through WGCNA\/limma integration, 223 common significantly up-regulated\/positively correlated gene candidates were identified. Functional analysis results showed significant enrichment in virulence-related pathways, such as biofilm formation (PA0083, PA0084, hcp1, hcpC, pilH, pilI, pilJ, vfr, pqsA, pqsB, pqsC, pqsE, PA1657, and PA1658). In addition, other virulence-related pathways, such as quorum sensing, phenazine biosynthesis, the bacterial secretion system, and secondary metabolite biosynthesis, were enriched. In conclusion, our hypothesis-generating integrative analysis identifies candidate genes and potential pathways associated with biofilm formation, virulence, and other processes in P. aeruginosa. In light of this, we point out that all candidate genes presented in this study remain hypothesis-generating. Further validation is recommended, including large-scale in silico analyses and in vitro experimental studies.<\/jats:p>","DOI":"10.3390\/ijms27125407","type":"journal-article","created":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T09:06:52Z","timestamp":1781600812000},"page":"5407","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Integrative Systems-Level Transcriptomic Network Analysis Identifies Candidate Genes Associated with Biofilm Formation and Virulence in Pseudomonas aeruginosa"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1379-6493","authenticated-orcid":false,"given":"Sara H.","family":"Mohamed","sequence":"first","affiliation":[{"name":"Department of Microbiology, Egyptian Drug Authority (EDA), Formerly National Organization for Drug Control and Research (NODCAR), Giza 12654, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3887-8196","authenticated-orcid":false,"given":"Asmaa","family":"Reda","sequence":"additional","affiliation":[{"name":"Computational Biology and Bioinformatics Division, Zoology Department, Faculty of Science, Benha University, Benha 13518, Egypt"},{"name":"Center of Nanotechnology, King Abdulaziz University, Jeddah 21589, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3039-7646","authenticated-orcid":false,"given":"Tarek A.","family":"Yousef","sequence":"additional","affiliation":[{"name":"Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mona G.","family":"Nada","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology and Immunology Department, Faculty of Medicine, Cairo University, Cairo 11956, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3540-2195","authenticated-orcid":false,"given":"Maha S. I.","family":"Wizrah","sequence":"additional","affiliation":[{"name":"Department of Biology, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2500-0480","authenticated-orcid":false,"given":"Sahar A.","family":"Mandour","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Faculty of Pharmacy, Deraya University, New Minia 61111, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,6,16]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Tuon, F.F., Dantas, L.R., Suss, P.H., and Tasca Ribeiro, V.S. (2022). Pathogenesis of the Pseudomonas aeruginosa Biofilm: A Review. Pathogens, 11.","DOI":"10.3390\/pathogens11030300"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1007\/s00284-025-04167-4","article-title":"Pathogen Partnerships or Power Struggles? Pseudomonas aeruginosa, and Staphylococcus aureus Dynamics in Cystic Fibrosis","volume":"82","author":"Saleh","year":"2025","journal-title":"Curr. Microbiol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1016\/S1473-3099(25)00118-5","article-title":"The WHO Bacterial Priority Pathogens List 2024: A Prioritisation Study to Guide Research, Development, and Public Health Strategies against Antimicrobial Resistance","volume":"25","author":"Sati","year":"2025","journal-title":"Lancet Infect. Dis."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Elfadadny, A., Ragab, R.F., AlHarbi, M., Badshah, F., Ib\u00e1\u00f1ez-Arancibia, E., Farag, A., Hendawy, A.O., De los R\u00edos-Escalante, P.R., Aboubakr, M., and Zakai, S.A. (2024). Antimicrobial resistance of Pseudomonas aeruginosa: Navigating clinical impacts, current resistance trends, and innovations in breaking therapies. Front. Microbiol., 15.","DOI":"10.3389\/fmicb.2024.1374466"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"11288","DOI":"10.1038\/s41598-025-90791-w","article-title":"Comparison of antimicrobial resistance in Pseudomonas aeruginosa from intensive care and non-intensive care units and its impact on treatment decisions","volume":"15","author":"Eid","year":"2025","journal-title":"Sci. Rep."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Vidal-Cort\u00e9s, P., Campos-Fern\u00e1ndez, S., Cuenca-Fito, E., del R\u00edo-Carbajo, L., Fern\u00e1ndez-Ugidos, P., L\u00f3pez-Ciudad, V.J., Nieto-del Olmo, J., Rodr\u00edguez-V\u00e1zquez, A., and Tiz\u00f3n-Varela, A.I. (2025). Difficult-to-Treat Pseudomonas aeruginosa Infections in Critically Ill Patients: A Comprehensive Review and Treatment Proposal. Antibiotics, 14.","DOI":"10.3390\/antibiotics14020178"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Abdulhak, A., Zedan, H.H., El-Mahallawy, H.A., Sayed, A.A., Mohamed, H.O., and Zafer, M.M. (2025). Multidrug-resistant Pseudomonas aeruginosa in immunocompromised cancer patients: Epidemiology, antimicrobial resistance, and virulence factors. BMC Infect. Dis., 25.","DOI":"10.1186\/s12879-025-11182-0"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Schwartz, B., Klamer, K., Zimmerman, J., Kale-Pradhan, P.B., and Bhargava, A. (2024). Multidrug Resistant Pseudomonas aeruginosa in Clinical Settings: A Review of Resistance Mechanisms and Treatment Strategies. Pathogens, 13.","DOI":"10.3390\/pathogens13110975"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Ciofu, O., and Tolker-Nielsen, T. (2019). Tolerance and Resistance of Pseudomonas aeruginosa Biofilms to Antimicrobial Agents\u2014How P. aeruginosa Can Escape Antibiotics. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.00913"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Hu, M., and Chua, S.L. (2025). Antibiotic-Resistant Pseudomonas aeruginosa: Current Challenges and Emerging Alternative Therapies. Microorganisms, 13.","DOI":"10.3390\/microorganisms13040913"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Hindieh, P., Yaghi, J., Assaf, J.C., Chokr, A., Atoui, A., Tzenios, N., Louka, N., and El Khoury, A. (2025). Emerging Multimodal Strategies for Bacterial Biofilm Eradication: A Comprehensive Review. Microorganisms, 13.","DOI":"10.3390\/microorganisms13122796"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1038\/s41392-022-01056-1","article-title":"Pseudomonas aeruginosa: Pathogenesis, virulence factors, antibiotic resistance, interaction with host, technology advances and emerging therapeutics","volume":"7","author":"Qin","year":"2022","journal-title":"Signal Transduct. Target. Ther."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"bbaf241","DOI":"10.1093\/bib\/bbaf241","article-title":"Multi-omics analysis of Helicobacter pylori-associated gastric cancer identifies hub genes as a novel therapeutic biomarker","volume":"26","author":"Mohamed","year":"2025","journal-title":"Brief. Bioinform."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.vetmic.2011.06.014","article-title":"Everything at Once: Comparative Analysis of the Genomes of Bacte-rial Pathogens","volume":"153","author":"Laing","year":"2011","journal-title":"Vet. Microbiol."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Li, J.X., Cao, X.J., Huang, Y.Y., Li, Y.P., Yu, Z.Y., Lin, M., Li, Q.Y., Chen, J.C., and Guo, X.G. (2021). Investigation of hub gene associated with the infection of Staphylococcus aureus via weighted gene co-expression network analysis. BMC Microbiol., 21.","DOI":"10.1186\/s12866-021-02392-y"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"105878","DOI":"10.1016\/j.micpath.2022.105878","article-title":"An integrated gene network analysis to decode the multi-drug resistance mechanism in Klebsiella pneumoniae","volume":"173","author":"Dey","year":"2022","journal-title":"Microb. Pathog."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"15342","DOI":"10.1038\/s41598-025-91269-5","article-title":"Analysis of stress response in multiple bacterial pathogens using a network biology approach","volume":"15","author":"Sharma","year":"2025","journal-title":"Sci. Rep."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"106770","DOI":"10.1016\/j.micpath.2024.106770","article-title":"Computational prediction of crucial genes involved in gonorrhea infection and neoplastic cell transformation: A multiomics approach","volume":"193","author":"Ravindranath","year":"2024","journal-title":"Microb. Pathog."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1038\/s41522-019-0113-6","article-title":"Parallel evolutionary paths to produce more than one Pseudomonas aeruginosa biofilm phenotype","volume":"6","author":"Tomasch","year":"2020","journal-title":"npj Biofilms Microbiomes"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"879","DOI":"10.1046\/j.1365-2958.2003.03338.x","article-title":"Microarray Expression Profiling: Capturing a Genome-wide Portrait of the Transcriptome","volume":"47","author":"Conway","year":"2003","journal-title":"Mol. Microbiol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1016\/B978-0-08-099387-4.00006-5","article-title":"Array-Based Approaches to Bacterial Transcriptome Analysis","volume":"Volume 39","author":"Harwood","year":"2012","journal-title":"Methods in Microbiology"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1016\/j.mib.2004.04.009","article-title":"Benefits and Pitfalls of Using Microarrays to Monitor Bacterial Gene Expression during Infection","volume":"7","author":"Hinton","year":"2004","journal-title":"Curr. Opin. Microbiol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"13504","DOI":"10.1038\/s41598-019-49967-4","article-title":"Multi-View Based Integrative Analysis of Gene Expression Data for Identifying Biomarkers","volume":"9","author":"Yang","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"7986","DOI":"10.1038\/s41467-023-43702-4","article-title":"Quorum-sensing synthase mutations re-calibrate autoinducer concentrations in clinical isolates of Pseudomonas aeruginosa to enhance pathogenesis","volume":"14","author":"Simanek","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Li, Q., Mao, S., Wang, H., and Ye, X. (2022). The Molecular Architecture of Pseudomonas aeruginosa Quorum-Sensing Inhibitors. Mar. Drugs, 20.","DOI":"10.3390\/md20080488"},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Yan, S., and Wu, G. (2019). Can Biofilm Be Reversed Through Quorum Sensing in Pseudomonas aeruginosa?. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.01582"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"e00339-24","DOI":"10.1128\/msystems.00339-24","article-title":"Secondary metabolite profiling of Pseudomonas aeruginosa isolates reveals rare genomic traits","volume":"9","author":"Neve","year":"2024","journal-title":"mSystems"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"102184","DOI":"10.1016\/j.genrep.2025.102184","article-title":"Biofilm formation, pigment production, and virulence gene profiles in Pseudomonas aeruginosa isolates from respiratory and urinary tract infections","volume":"39","author":"Sarkheili","year":"2025","journal-title":"Gene Rep."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1016\/j.molmed.2004.10.002","article-title":"The role of pyocyanin in Pseudomonas aeruginosa infection","volume":"10","author":"Lau","year":"2004","journal-title":"Trends Mol. Med."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"762","DOI":"10.1038\/s41467-019-08733-w","article-title":"Phenazine production promotes antibiotic tolerance and metabolic heterogeneity in Pseudomonas aeruginosa biofilms","volume":"10","author":"Schiessl","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Touati, A., Ibrahim, N.A., Tighilt, L., and Idres, T. (2025). Anti-QS Strategies Against Pseudomonas aeruginosa Infections. Microorganisms, 13.","DOI":"10.3390\/microorganisms13081838"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"3606","DOI":"10.1128\/JB.00396-11","article-title":"Phenazine-1-Carboxylic Acid Promotes Bacterial Biofilm Development via Ferrous Iron Acquisition","volume":"193","author":"Wang","year":"2011","journal-title":"J. Bacteriol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"e991","DOI":"10.1002\/mbo3.991","article-title":"Type VI secretion system of Pseudomonas aeruginosa is associated with biofilm formation but not environmental adaptation","volume":"9","author":"Chen","year":"2020","journal-title":"Microbiologyopen"},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Higgins, S., Heeb, S., Rampioni, G., Fletcher, M.P., Williams, P., and C\u00e1mara, M. (2018). Differential Regulation of the Phenazine Biosynthetic Operons by Quorum Sensing in Pseudomonas aeruginosa PAO1-N. Front. Cell. Infect. Microbiol., 8.","DOI":"10.3389\/fcimb.2018.00252"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"e00118-24","DOI":"10.1128\/aac.00118-24","article-title":"Quorum-sensing regulation of phenazine production heightens Pseudomonas aeruginosa resistance to ciprofloxacin","volume":"68","author":"Xia","year":"2024","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Li, Y., Chen, L., Zhang, P., Bhagirath, A.Y., and Duan, K. (2020). ClpV3 of the H3-Type VI Secretion System (H3-T6SS) Affects Multiple Virulence Factors in Pseudomonas aeruginosa. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.01096"},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Gholami Aghamahali, R., Pahlavanian, M., and Goli, H.R. (2025). Prevalence of Quorum-Sensing Genes (LasI, LasR, RhlI and RhlR) in Biofilm-Producing Pseudomonas Aeruginosa Clinical Isolates in Northern Iran. BMC Infect. Dis., 26.","DOI":"10.1186\/s12879-025-12406-z"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1016\/j.procbio.2020.06.001","article-title":"Biofilm and Quorum sensing mediated pathogenicity in Pseudomonas aeruginosa","volume":"96","author":"Brindhadevi","year":"2020","journal-title":"Process Biochem."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"100578","DOI":"10.1016\/j.microb.2025.100578","article-title":"Biofilm, resistance, and quorum sensing: The triple threat in bacterial pathogenesis","volume":"9","author":"Bhuiyan","year":"2025","journal-title":"Microbe"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"2511","DOI":"10.1038\/s41564-025-02087-4","article-title":"Pseudomonas aeruginosa senses exopolysaccharide trails using type IV pili and adhesins during biofilm formation","volume":"10","author":"Schmidt","year":"2025","journal-title":"Nat. Microbiol."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Liu, Q., Wu, Q., Liu, J., Xu, T., Liu, J., Wu, Q., Malakar, P.K., Zhu, Y., Zhao, Y., and Zhang, Z. (2025). New Insights into the Mediation of Biofilm Formation by Three Core Extracellular Polysaccharide Biosynthesis Pathways in Pseudomonas aeruginosa. Int. J. Mol. Sci., 26.","DOI":"10.3390\/ijms26083780"},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Chung, J., Eisha, S., Park, S., Morris, A.J., and Martin, I. (2023). How Three Self-Secreted Biofilm Exopolysaccharides of Pseudomonas aeruginosa, Psl, Pel, and Alginate, Can Each Be Exploited for Antibiotic Adjuvant Effects in Cystic Fibrosis Lung Infection. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms24108709"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"9497","DOI":"10.1038\/s41467-025-64557-x","article-title":"Stress-hardening behaviour of biofilm streamers","volume":"16","author":"Savorana","year":"2025","journal-title":"Nat. Commun."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"e00821-25","DOI":"10.1128\/aem.00821-25","article-title":"Flagellum-driven motility enhances Pseudomonas aeruginosa biofilm formation by altering cell orientation","volume":"91","author":"Wei","year":"2025","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1016\/j.celrep.2019.08.094","article-title":"The Pseudomonas aeruginosa T6SS Delivers a Periplasmic Toxin that Disrupts Bacterial Cell Morphology","volume":"29","author":"Wood","year":"2019","journal-title":"Cell Rep."},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Wu, Y., Huang, S., Zhang, K., Shen, Y., Zhang, S., Xia, H., Pu, J., Shen, C., Chen, C., and Zeng, J. (2025). Transcriptomic profiling reveals RetS-mediated regulation of type VI secretion system and host cell responses in Pseudomonas aeruginosa infections. Front. Cell. Infect. Microbiol., 15.","DOI":"10.3389\/fcimb.2025.1582339"},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Jurado-Mart\u00edn, I., Sainz-Mej\u00edas, M., and McClean, S. (2021). Pseudomonas aeruginosa: An audacious pathogen with an adaptable arsenal of virulence factors. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms22063128"},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Rudzite, M., Subramoni, S., Endres, R.G., and Filloux, A. (2023). Effectiveness of Pseudomonas aeruginosa type VI secretion system relies on toxin potency and type IV pili-dependent interaction. PLoS Pathog., 19.","DOI":"10.1371\/journal.ppat.1011428"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"7536","DOI":"10.1074\/jbc.M112.439273","article-title":"The HsiB1C1 (TssB-TssC) Complex of the Pseudomonas aeruginosa Type VI Secretion System Forms a Bacteriophage Tail Sheathlike Structure","volume":"288","author":"Lossi","year":"2013","journal-title":"J. Biol. Chem."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"5510","DOI":"10.1128\/JB.00268-11","article-title":"Pseudomonas aeruginosa tssC1 Links Type VI Secretion and Biofilm-Specific Antibiotic Resistance","volume":"193","author":"Zhang","year":"2011","journal-title":"J. Bacteriol."},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"Yarrington, K.D., Shendruk, T.N., and Limoli, D.H. (2024). The type IV pilus chemoreceptor PilJ controls chemotaxis of one bacterial species towards another. PLoS Biol., 22.","DOI":"10.1371\/journal.pbio.3002488"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"3553","DOI":"10.1128\/JB.00363-10","article-title":"The Pseudomonas aeruginosa Vfr Regulator Controls Global Virulence Factor Expression through Cyclic AMP-Dependent and -Independent Mechanisms","volume":"192","author":"Fuchs","year":"2010","journal-title":"J. Bacteriol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1016\/j.chembiol.2015.04.012","article-title":"PqsE of Pseudomonas aeruginosa Acts as Pathway-Specific Thioesterase in the Biosynthesis of Alkylquinolone Signaling Molecules","volume":"22","author":"Drees","year":"2015","journal-title":"Chem. Biol."},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Hanes, R., Zhang, F., and Huang, Z. (2023). Protein Interaction Network Analysis to Investigate Stress Response, Virulence, and Antibiotic Resistance Mechanisms in Listeria monocytogenes. Microorganisms, 11.","DOI":"10.3390\/microorganisms11040930"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"21025","DOI":"10.1038\/s41598-025-07334-6","article-title":"Integrating Multi-Omic Data to Identify Key Genes and Pathways Involved in Rice Bacterial Leaf Streak Disease","volume":"15","author":"Saeed","year":"2025","journal-title":"Sci. Rep."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1093\/nar\/gkn861","article-title":"Pseudomonas Genome Database: Facilitating user-friendly, comprehensive comparisons of microbial genomes","volume":"37","author":"Winsor","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"D646","DOI":"10.1093\/nar\/gkv1227","article-title":"Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database","volume":"44","author":"Winsor","year":"2016","journal-title":"Nucleic Acids Res."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/12\/5407\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T03:13:12Z","timestamp":1782270792000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/12\/5407"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,16]]},"references-count":57,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2026,6]]}},"alternative-id":["ijms27125407"],"URL":"https:\/\/doi.org\/10.3390\/ijms27125407","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,16]]}}}