Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity

KEGG: Kyoto Encyclopedia of Genes and Genomes

Kanehisa, M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.27 · Cited by 37,077

KEGG: Kyoto Encyclopedia of Genes and Genomes

Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., & Kanehisa, M. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.1.29 · Cited by 31,232

Construction of Escherichia coli K‐12 in‐frame, single‐gene knockout mutants: the Keio collection

Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K. A., Tomita, M., Wanner, B. L., & Mori, H. (2006) · Molecular Systems Biology · doi:10.1038/msb4100050 · Cited by 7,858

KEGG for integration and interpretation of large-scale molecular data sets

Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., & Tanabe, M. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr988 · Cited by 4,848

The COG database: an updated version includes eukaryotes

Tatusov, R. L., Fedorova, N. D., Jackson, J. D., Jacobs, A. R., Kiryutin, B., Koonin, E. V., Krylov, D. M., Mazumder, R., Mekhedov, S., Nikolskaya, A. N., et al. (2003) · BMC Bioinformatics · doi:10.1186/1471-2105-4-41 · Cited by 4,470

What is flux balance analysis?

Orth, J. D., Thiele, I., & Palsson, B. Ø. (2010) · Nature Biotechnology · doi:10.1038/nbt.1614 · Cited by 3,903

Invasive Methicillin-Resistant <EMPH TYPE="ITAL">Staphylococcus aureus</EMPH> Infections in the United States

Klevens, R. M. (2007) · JAMA · doi:10.1001/jama.298.15.1763 · Cited by 3,726

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

Caspi, R., Billington, R., Ferrer, L., Foerster, H., Fulcher, C. A., Keseler, I. M., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L. A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1164 · Cited by 3,395

Multiple Sequence Alignment Using ClustalW and ClustalX

Thompson, J., Gibson, T. J., & Higgins, D. G. (2002) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi0203s00 · Cited by 2,989

Waves of resistance: Staphylococcus aureus in the antibiotic era

Chambers, H. F., & DeLeo, F. R. (2009) · Nature Reviews Microbiology · doi:10.1038/nrmicro2200 · Cited by 2,718

Reconstruction and Validation of a Genome-Scale Metabolic Model of Streptococcus oralis (iCJ415), a Human Commensal and Opportunistic Pathogen

Jensen, C. S., Norsigian, C. J., Fang, X. D., Nielsen, X. C., Christensen, J. J., Palsson, B. Ø., & Monk, J. M. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.00116 · Cited by 20

Comparative genomic analyses of Lactobacillus rhamnosus isolated from Chinese subjects

Huang, D. Y., Yang, B. K., Chen, Y., Stanton, C., Ross, R. P., Zhao, J., Zhang, H., & Chen, W. (2020) · Food Bioscience · doi:10.1016/j.fbio.2020.100659 · Cited by 20

Comparative Genomic Analysis of a Panton–Valentine Leukocidin-Positive ST22 Community-Acquired Methicillin-Resistant Staphylococcus aureus from Pakistan

Ullah, N., Nasir, S., Ishaq, Z., Anwer, F., Raza, T., Rahman, M., Alshammari, A., Alharbi, M., Bae, T., Rahman, A., et al. (2022) · Antibiotics · doi:10.3390/antibiotics11040496 · Cited by 20

Pan-genome-scale metabolic modeling of Bacillus subtilis reveals functionally distinct groups

Neal, M., Brakewood, W., Betenbaugh, M. J., & Zengler, K. (2024) · mSystems · doi:10.1128/msystems.00923-24 · Cited by 19

Reconciling high-throughput gene essentiality data with metabolic network reconstructions

Blazier, A. S., & Papin, J. A. (2019) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006507 · Cited by 19

Association of Skin Microbiome with the Onset and Recurrence of Pressure Injury in Bedridden Elderly People

Okamoto, S., Ogai, K., Mukai, K., & Sugama, J. (2021) · Microorganisms · doi:10.3390/microorganisms9081603 · Cited by 19

Systems biology approach to functionally assess the Clostridioides difficile pangenome reveals genetic diversity with discriminatory power

Norsigian, C. J., Danhof, H. A., Ardis, C. K., Midani, F. S., Broddrick, J. T., Savidge, T., Britton, R. A., Palsson, B. Ø., Spinler, J. K., & Monk, J. M. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2119396119 · Cited by 18

Large-Scale CRISPRi and Transcriptomics of Staphylococcus epidermidis Identify Genetic Factors Implicated in Lifestyle Versatility

Spoto, M., Puma, J. P. R., Fleming, E. S., Guan, C., Ondouah-Nzutchi, Y., Kim, D., & Oh, J. (2022) · mBio · doi:10.1128/mbio.02632-22 · Cited by 18

The Comparative Analysis of Genomic Diversity and Genes Involved in Carbohydrate Metabolism of Eighty-Eight Bifidobacterium pseudocatenulatum Isolates from Different Niches of China

Lin, G., Liu, Q., Wang, L., Li, H., Zhao, J., Zhang, H., Wang, G., & Chen, W. (2022) · Nutrients · doi:10.3390/nu14112347 · Cited by 17

Genomic diversity of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated from a Children’s Hospital in México City in an eight-years survey

Cabrera-Contreras, R., Santamaría, R. I., Bustos, P., Martínez‐Flores, I., Meléndez-Herrada, E., Morelos-Ramírez, R., Barbosa-Amezcua, M., González-Covarrubias, V., Silva‐Herzog, E., Soberón, X., et al. (2019) · PeerJ · doi:10.7717/peerj.8068 · Cited by 17

Pan-Genome of Novel Pantoea stewartii subsp. indologenes Reveals Genes Involved in Onion Pathogenicity and Evidence of Lateral Gene Transfer

Agarwal, G., Gitaitis, R. D., & Dutta, B. (2021) · Microorganisms · doi:10.3390/microorganisms9081761 · Cited by 17

Pangenome Flux Balance Analysis Toward Panphenomes

Norsigian, C. J., Fang, X. D., Palsson, B. Ø., & Monk, J. M. (2020) · Springer eBooks · doi:10.1007/978-3-030-38281-0_10 · Cited by 17

Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes

Hafner, L., Gadin, E., Huang, L., Frouin, A., Laporte, F., Gaultier, C., Vieira, A., Maudet, C., Varet, H., Moura, A., et al. (2024) · Nature Microbiology · doi:10.1038/s41564-024-01859-8 · Cited by 19

Synthesized Geopolymers Adsorb Bacterial Proteins, Toxins, and Cells

Popovich, J., Chen, S., Iannuzo, N., Ganser, C., Seo, D., & Haydel, S. E. (2020) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2020.00527 · Cited by 16

Analysis of Piscirickettsia salmonis Metabolism Using Genome-Scale Reconstruction, Modeling, and Testing

Cortés, M. P., Mendoza, S. N., Travisany, D., Gaete, A., Siegel, A., Cambiazo, V., & Maass, A. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.02462 · Cited by 16

Biofilm-mediated antibiotic tolerance in Staphylococcus aureus from spinal cord stimulation device-related infections

Sivori, F., Cavallo, I., Truglio, M., Pelagalli, L., Mariani, V., Fabrizio, G., Abril, E., Santino, I., Fradiani, P. A., Solmone, M., et al. (2024) · Microbiology Spectrum · doi:10.1128/spectrum.01683-24 · Cited by 15

Pan-Genome Analyses of Geobacillus spp. Reveal Genetic Characteristics and Composting Potential

Wang, M., Zhu, H., Kong, Z., Tuo, L., Ma, L., Liu, D., & Shen, Q. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21093393 · Cited by 15

Genomic Analysis of Staphylococcus aureus Isolates Associated With Peracute Non-gangrenous or Gangrenous Mastitis and Comparison With Other Mastitis-Associated Staphylococcus aureus Isolates

Åvall-Jääskeläinen, S., Koort, J. M. K., Simojoki, H., & Taponen, S. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.688819 · Cited by 15

The Resistome and Mobilome of Multidrug-Resistant Staphylococcus sciuri C2865 Unveil a Transferable Trimethoprim Resistance Gene, Designated dfrE , Spread Unnoticed

Gómez-Sanz, E., Haro-Moreno, J. M., Jensen, S. O., Roda‐Garcia, J. J., & López‐Pérez, M. (2021) · mSystems · doi:10.1128/msystems.00511-21 · Cited by 15

Non-Canonical Host Intracellular Niche Links to New Antimicrobial Resistance Mechanism

Kember, M., Grandy, S. L., Raudonis, R., & Cheng, Z. (2022) · Pathogens · doi:10.3390/pathogens11020220 · Cited by 17

Forecasting Staphylococcus aureus Infections Using Genome-Wide Association Studies, Machine Learning, and Transcriptomic Approaches

Sassi, M., Bronsard, J., Pascreau, G., Emily, M., Donnio, P.-Y., Revest, M., Felden, B., Wirth, T., & Augagneur, Y. (2022) · mSystems · doi:10.1128/msystems.00378-22 · Cited by 14

Revisiting pangenome openness with k-mers

Parmigiani, L., Wittler, R., & Stoye, J. (2024) · Peer Community Journal · doi:10.24072/pcjournal.415 · Cited by 14

PanKB: An interactive microbial pangenome knowledgebase for research, biotechnological innovation, and knowledge mining

Boying, S., Pashkova, L., Pieters, P. A., Panche, A. N., Mohite, O. S., Santos, A., Zielinski, D. C., Palsson, B. Ø., & Phaneuf, P. V. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae1042 · Cited by 14

Early-Stage Staphylococcus aureus Bloodstream Infection Causes Changes in the Concentrations of Lipoproteins and Acute-Phase Proteins and Is Associated with Low Antibody Titers against Bacterial Virulence Factors

Michalik, S., Sundaramoorthy, N., Murr, A., Depke, M., Völker, U., Bröker, B. M., Aamot, H. V., & Schmidt, F. (2020) · mSystems · doi:10.1128/msystems.00632-19 · Cited by 16

Genome-wide comparison of four MRSA clinical isolates from Germany and Hungary

Naorem, R. S., Blom, J., & Fekete, C. (2021) · PeerJ · doi:10.7717/peerj.10185 · Cited by 14

Evolutionary Divergence of the Novel Staphylococcal Species Staphylococcus argenteus

Wu, S., Pang, R., Huang, J., Zhang, F., Cai, Z., Zhang, J., Chen, M., Xue, L., Gu, Q., Wang, J., et al. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.769642 · Cited by 14

Genome-Scale Metabolic Modelling Approach to Understand the Metabolism of the Opportunistic Human Pathogen Staphylococcus epidermidis RP62A

Calvo, T. D., Tejera, N., McNamara, I., Langridge, G. C., Wain, J. R., Poolman, M. G., & Singh, D. (2022) · Metabolites · doi:10.3390/metabo12020136 · Cited by 14

Leveraging genome-scale metabolic models for human health applications

Chowdhury, S., & Fong, S. S. (2020) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2020.08.017 · Cited by 14

Bactericidal efficacy of low dose gaseous ozone against clinically relevant multidrug-resistant bacteria

Banerjee, B., Thompson, C., Nizet, V., & Bjånes, E. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1480433 · Cited by 15

Genome-scale metabolic modeling and in silico analysis of opportunistic skin pathogen Cutibacterium acnes

Kim, S.-K., Lee, M., Lee, Y. Q., Lee, H. J., Rho, M., Kim, Y., Seo, J. Y., Youn, S. H., Hwang, S. J., Kang, N. G., et al. (2023) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2023.1099314 · Cited by 14

Genomic epidemiology of methicillin-susceptible Staphylococcus aureus across colonisation and skin and soft tissue infection

Grinberg, A., Biggs, P. J., Zhang, J., Ritchie, S. R., Oneroa, Z., O'Neill, C., Karkaba, A., Velathanthiri, N., & Coombs, G. W. (2017) · Journal of Infection · doi:10.1016/j.jinf.2017.07.010 · Cited by 13

Analyses of Livestock-Associated Staphylococcus aureus Pan-Genomes Suggest Virulence Is Not Primary Interest in Evolution of Its Genome

Rao, R. T., Sivakumar, N., & Jayakumar, K. (2019) · OMICS A Journal of Integrative Biology · doi:10.1089/omi.2019.0005 · Cited by 13

Pan-genome analysis of Riemerella anatipestifer reveals its genomic diversity and acquired antibiotic resistance associated with genomic islands

Zhu, D., Yang, Z., Xu, J., Wang, M., Jia, R., Chen, S., Liu, M., Zhao, X., Yang, Q., Wu, Y., et al. (2019) · Functional & Integrative Genomics · doi:10.1007/s10142-019-00715-x · Cited by 13

Comparative Genomics of Plasmid-Bearing Staphylococcus aureus Strains Isolated From Various Retail Meats

Karki, A. B., Neyaz, L. A., & Fakhr, M. K. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.574923 · Cited by 13

A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentialityPreprint

Hawkey, J., Vezina, B., Monk, J. M., Judd, L. M., Harshegyi, T., López-Fernández, S., Rodrigues, C., Brisse, S., Holt, K. E., & Wyres, K. L. (2022) · Genome Research · doi:10.1101/gr.276289.121 · Cited by 13

A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism and capacity for intra-species co-operation

Vezina, B., Cooper, H. B., Barlow, C. K., Rethoret-Pasty, M., Brisse, S., Monk, J. M., Holt, K. E., & Wyres, K. L. (2025) · PLoS Biology · doi:10.1371/journal.pbio.3003559 · Cited by 15

Comparative genomics study reveals Red Sea Bacillus with characteristics associated with potential microbial cell factories (MCFs)

Othoum, G., Prigent, S., Derouiche, A., Shi, L., Bokhari, A., Alamoudi, S. A., Bougouffa, S., Gao, X., Hoehndorf, R., Arold, S. T., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-55726-2 · Cited by 12

Characterization of two novel psychrophilic and piezotolerant strains, Shewanella psychropiezotolerans sp. nov. and Shewanella eurypsychrophilus sp. nov, adapted to an extreme deep-sea environment

Yu, L., Jian, H., Gai, Y., Yi, Z., Feng, Y., Xu, Q., Shao, Z., & Tang, X. (2021) · Systematic and Applied Microbiology · doi:10.1016/j.syapm.2021.126266 · Cited by 12

Interrogation of Essentiality in the Reconstructed Haemophilus influenzae Metabolic Network Identifies Lipid Metabolism Antimicrobial Targets: Preclinical Evaluation of a FabH β-Ketoacyl-ACP Synthase Inhibitor

López-López, N., León, D. S., de Castro, S., Díez‐Martínez, R., Iglesias-Bexiga, M., Camarasa, M., Menéndez, M., Nogales, J., & Garmendia, J. (2022) · mSystems · doi:10.1128/msystems.01459-21 · Cited by 12

Insights into genome evolution, pan-genome, and phylogenetic implication through mitochondrial genome sequence of Naegleria fowleri species

Aurongzeb, M., Rashid, Y., Naqvi, S. H. A., Malik, H. M. T., Azim, M. K., Hassan, S. S., Yasir, M., & Karim, A. M. (2022) · Scientific Reports · doi:10.1038/s41598-022-17006-4 · Cited by 12

Genomic investigation of emerging zoonotic pathogen Shewanella xiamenensis

Tung, K., Wang, J.-H., & Tseng, S. (2019) · Tzu Chi Medical Journal · doi:10.4103/tcmj.tcmj_69_19 · Cited by 12

Bacterial metabolism and pathogenesis intimate intertwining: time for metabolic modelling to come into action

Nogales, J., & Garmendia, J. (2021) · Microbial Biotechnology · doi:10.1111/1751-7915.13942 · Cited by 12

Ratio of Histamine-Producing/Non-Histamine-Producing Subgroups of Tetragenococcus halophilus Determines the Histamine Accumulation during Spontaneous Fermentation of Soy Sauce

Ma, J., Nie, Y., Zhang, L., & Xu, Y. (2023) · Applied and Environmental Microbiology · doi:10.1128/aem.01884-22 · Cited by 11

Comparative genome‐scale modelling of the pathogenic Flavobacteriaceae species Riemerella anatipestifer in China

Liu, J., Zeng, Q., Wang, M., Cheng, A., Liu, M., Zhu, D., Chen, S., Jia, R., Zhao, X., Wu, Y., et al. (2019) · Environmental Microbiology · doi:10.1111/1462-2920.14635 · Cited by 11

Complex effects of macrolide venturicidins on bacterial F-ATPases likely contribute to their action as antibiotic adjuvants

Milgrom, Y. M., & Duncan, T. M. (2021) · Scientific Reports · doi:10.1038/s41598-021-93098-8 · Cited by 11

Risk-Based Bioengineering Strategies for Reliable Bacterial Vaccine Production

Kamminga, T., Slagman, S., dos Santos, V. A. P. M., Bijlsma, J. J. E., & Schaap, P. J. (2019) · Trends in biotechnology · doi:10.1016/j.tibtech.2019.03.005 · Cited by 11

Evolutionary dynamics of the accessory genomes of Staphylococcus aureus

Piper, K. R., Ikhimiukor, O. O., Souza, S. S. R., Garcia-Aroca, T., & Andam, C. P. (2024) · mSphere · doi:10.1128/msphere.00751-23 · Cited by 10

Iron-associated protein interaction networks reveal the key functional modules related to survival and virulence of Pasteurella multocida

Jatuponwiphat, T., Chumnanpuen, P., Othman, S. S., E-kobon, T., & Vongsangnak, W. (2018) · Microbial Pathogenesis · doi:10.1016/j.micpath.2018.12.013 · Cited by 10

Genomic profile of Brazilian methicillin-resistant Staphylococcus aureus resembles clones dispersed worldwide

de Carvalho, S. P., de Almeida, J. B., de Freitas, L. M., Guimarães, A. M. S., do Nascimento, N. C., dos Santos, A. P., Campos, G. B., Messick, J. B., Timenetsky, J., & Marques, L. M. (2019) · Journal of Medical Microbiology · doi:10.1099/jmm.0.000956 · Cited by 10

Reduced Production of Bacterial Membrane Vesicles Predicts Mortality in ST45/USA600 Methicillin-Resistant Staphylococcus aureus Bacteremia

Dey, S., Gudipati, S., Giuliano, C. A., Zervos, M., Monk, J. M., Szubin, R., Jorgensen, S. C. J., Sakoulas, G., & Berti, A. D. (2019) · Antibiotics · doi:10.3390/antibiotics9010002 · Cited by 10

Proliferation and benevolence—A framework for dissecting the mechanisms of microbial virulence and health promotion

Waldetoft, K. W., Råberg, L., & Lood, R. (2020) · Evolutionary Applications · doi:10.1111/eva.12952 · Cited by 10

Comparative genomics of dairy-associated Staphylococcus aureus from selected sub-Saharan African regions reveals milk as reservoir for human-and animal-derived strains and identifies a putative animal-related clade with presumptive novel siderophore

Jans, C., Wambui, J., Stevens, M. J. A., & Tasara, T. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.923080 · Cited by 10

Phenotype and multi-omics comparison of Staphylococcus and Streptococcus uncovers pathogenic traits and predicts zoonotic potential

Zondervan, N. A., dos Santos, V. A. P. M., Diez, M. S., & Saccenti, E. (2021) · BMC Genomics · doi:10.1186/s12864-021-07388-6 · Cited by 10

Scaling metabolic model reconstruction up to the pan-genome level: A systematic review and prospective applications to photosynthetic organisms

Arend, M., Paulitz, E., Hsieh, Y. E., & Nikoloski, Z. (2025) · Metabolic Engineering · doi:10.1016/j.ymben.2025.02.015 · Cited by 9

Yeast adapts to diverse ecological niches driven by genomics and metabolic reprogramming

Wang, H., Nielsen, J., Zhou, Y. J., & Lu, H. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2502044122 · Cited by 12

sRNA-mediated crosstalk between cell wall stress and galactose metabolism in Staphylococcus aureus

Germain, M., Robin, H., Huyen, K. B. L., Massier, S., Nalpas, N., Hardouin, J., Bouloc, P., Rouillon, A., & Chabelskaya, S. V. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf616 · Cited by 8

Modeling of stringent-response reflects nutrient stress induced growth impairment and essential amino acids in different Staphylococcus aureus mutants

Audretsch, C. K., Gratani, F. L., Wolz, C., & Dandekar, T. (2021) · Scientific Reports · doi:10.1038/s41598-021-88646-1 · Cited by 8

Facemask acne attenuation through modulation of indirect microbiome interactions

Na, H.-H., Kim, S., Kim, J., Lee, S., Kim, Y.-S., Kim, S., Lee, C.-H., Kim, D., Yoon, S. H., Jeong, H., et al. (2024) · npj Biofilms and Microbiomes · doi:10.1038/s41522-024-00512-w · Cited by 9

Computational Systems Biology of Metabolism in Infection

Cesur, M. F., Abdi̇k, E., gülhan, Ü. G., Durmuş, S., & Çakır, T. (2018) · Experientia supplementum · doi:10.1007/978-3-319-74932-7_6 · Cited by 8

Integrating Omics Data to Prioritize Target Genes in Pathogenic Bacteria

Nicolás, M., Costa, M. D. O. C. E., Ramos, P. I. P., dos Santos, M. T., Pérez‐Rueda, E., Marti, M. A., Porto, D. F. D., & Turjanski, A. G. (2020) · Computational biology · doi:10.1007/978-3-030-51862-2_10 · Cited by 8

Using genome-scale metabolic models to compare serovars of the foodborne pathogen Listeria monocytogenes

Metz, Z. P., Ding, T., & Baumler, D. J. (2018) · PLoS ONE · doi:10.1371/journal.pone.0198584 · Cited by 8

The mobilome of Staphylococcus aureus from wild ungulates reveals epidemiological links at the animal-human interface

Ramos, B., & Cunha, M. V. (2024) · Environmental Pollution · doi:10.1016/j.envpol.2024.124241 · Cited by 7

Comprehensive genome analysis of Burkholderia contaminans SK875, a quorum-sensing strain isolated from the swine

Kim, E., Jung, H.-I., Park, S. H., Kim, H., & Kim, S. (2023) · AMB Express · doi:10.1186/s13568-023-01537-8 · Cited by 6

Leveraging big data bioinformatics approaches to extract knowledge from Staphylococcus aureus public omics data

Subramanian, D., & Natarajan, J. (2022) · Critical Reviews in Microbiology · doi:10.1080/1040841x.2022.2065905 · Cited by 7

Genome-scale metabolic modelling in antimicrobial pharmacology: Present and future

Tao, J., Lin, Y.-W., Zhong, L., Zhu, Y., Yao, X., Aichem, M., Schreiber, F., Zhao, J., & Li, J. (2025) · Advanced Drug Delivery Reviews · doi:10.1016/j.addr.2025.115672 · Cited by 5

Extraction of High-Quality RNA from S. aureus Internalized by Endothelial Cells

Maurer, M., Klassert, T. E., Löffler, B., Slevogt, H., & Tuchscherr, L. P. N. (2023) · Microorganisms · doi:10.3390/microorganisms11041020 · Cited by 6

Genomic epidemiology of Staphylococcus aureus from the Iberian Peninsula highlights the expansion of livestock associated-CC398 towards wildlife

Ramos, B., & Cunha, M. V. (2024) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2024.173027 · Cited by 5

Model-driven characterization of functional diversity of Pseudomonas aeruginosa clinical isolates with broadly representative phenotypes

Islam, M. M., Kolling, G. L., Glass, E. M., Goldberg, J. B., & Papin, J. A. (2024) · Microbial Genomics · doi:10.1099/mgen.0.001259 · Cited by 5

Integration of Comparative Genomics with Genome-Scale Metabolic Modeling to Investigate Strain-Specific Phenotypical Differences

Monk, J. M., & Bosi, E. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-7528-0_7 · Cited by 5

Mikrobiom & NASH – enge Komplizen in der Progression von Fettlebererkrankungen

Wree, A., Geisler, L. J., & Tacke, F. (2019) · Zeitschrift für Gastroenterologie · doi:10.1055/a-0755-2595 · Cited by 5

Genome Sequence of a Highly Virulent pvl-positive Vancomycin intermediate- resistant Staphylococcus aureus Sequence Type 30

Chamon, R. C., Marques, L. M., Timenetsky, J., Rachid, C. T. C. D. C., Ferreira, R. B. R., de Oliveira, T. L. R., Glatthardt, T., Moreira, L. D. O., & dos Santos, K. R. N. (2020) · Current Genomics · doi:10.2174/1389202921666200327105756 · Cited by 5

Comparative Genomic Analyses of the Genus Photobacterium Illuminate Biosynthetic Gene Clusters Associated with Antagonism

Lau, N., Heng, W. L., Miswan, N., Azami, N. A., & Furusawa, G. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23179712 · Cited by 4

Comparative genomic analysis of ovine and other host associated isolates of Staphylococcus aureus exhibit the important role of mobile genetic elements and virulence factors in host adaptation

da Silva, A. L., Caetano, A. C. B., Castillo, R. H., dos Santos, R. G., Rodrigues, D. L. N., Sousa, T. J., Kato, R. B., Viana, M. V. C., Gomide, A. C. P., Aburjaile, F. F., et al. (2022) · Gene · doi:10.1016/j.gene.2022.147131 · Cited by 4

Large-scale CRISPRi and transcriptomics of Staphylococcus epidermidis identify genetic factors implicated in commensal-pathogen lifestyle versatilityPreprint

Spoto, M., Fleming, E. S., Ondouah-Nzutchi, Y., Guan, C., & Oh, J. (2021) · Research Square · doi:10.21203/rs.3.rs-484119/v1 · Cited by 4

Mass Spectrometry-Based Analysis of Surface Proteins in Staphylococcus aureus Clinical Strains: Identification of Promising k-mer Targets for Diagnostics

Svetličić, E., Alarcón, L. A., Karlsson, R., Jers, C., & Mijakovic̀, I. (2025) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5c00321 · Cited by 3

GEMsembler: consensus model assembly and structural comparison of genome-scale metabolic models across tools improve functional performance

Matveishina, E., Bartmanski, B. J., Benito-Vaquerizo, S., & Zimmermann‐Kogadeeva, M. (2025) · mSystems · doi:10.1128/msystems.00574-25 · Cited by 3

The Host R‐M Systems Change the Host Range of Staphylococcus Phage EBHT

Tuomala, H., Holtel, J., Markkanen, M. A., Patpatia, S., Kaansalo, K., Rolland, C., Bayfield, O. W., Ranta, K., Skurnik, M., Wittmann, J., et al. (2025) · MicrobiologyOpen · doi:10.1002/mbo3.70165 · Cited by 3

Machine–learning and gene–synergy networks reveal interpretable drivers of antibiotic resistance in Staphylococcus aureus

Xu, J., Li, Y., Wang, Y., Liu, F., Long, J., Zhu, J., Jin, Y., Chen, S., Duan, G., & Yang, H. (2025) · International Journal of Antimicrobial Agents · doi:10.1016/j.ijantimicag.2025.107690 · Cited by 3

AntiPan: a genome-informed in silico pipeline for advancing subunit vaccine discovery against Staphylococcus aureus

Ibrahim, M. S., Fahmy, J. A., Helal, M. A., Hakem, F. T., Sidarous, L. R., Attallah, N. E., Abouelhadid, S., Elhadidy, M., & Badr, E. (2026) · Scientific Reports · doi:10.1038/s41598-025-33445-1 · Cited by 3

Bacterial defense systems and host ecology drive the evolution of intra-species lineages

Gorzynski, J., Harling-Lee, J. D., Figueroa, W., Alves, J., Yebra, G., Freeman, T., Penadés, J. R., & Fitzgerald, J. R. (2026) · Cell Reports · doi:10.1016/j.celrep.2026.116957 · Cited by 3

Analysis of Genome Sequences of Coagulase-Negative Staphylococci Isolates from South Africa and Nigeria Highlighted Environmentally Driven Heterogeneity

Maguvu, T. E., Oladipo, A. O., & Bezuidenhout, C. C. (2021) · Journal of Genomics · doi:10.7150/jgen.53019 · Cited by 3

Characterisation of key genotypic and phenotypic traits of clinical cystic fibrosis Staphylococcus aureus isolates

Mossop, M., Robinson, L. A., Jiang, J., Peleg, A. Y., Blakeway, L. V., Maćešić, N., Perry, A., Bourke, S., Ulhuq, F. R., & Palmer, T. (2023) · Journal of Medical Microbiology · doi:10.1099/jmm.0.001703 · Cited by 3

Whole genome sequencing of methicillin-resistant and methicillin-sensitive Staphylococcus aureus isolated from 4 horses in a veterinary teaching hospital and its ambulatory service.

Morice, P., Allano, M., Provost, C., Fairbrother, J., Gagnon, C. A., & Sauvé, F. (2021) · PubMed Central · Cited by 3

Molecular characteristics and antimicrobial resistance profiles of Staphylococcus aureus isolates from burns

Kadhum, D. A., Hamad, E. M., & Fahad, M. A. (2024) · Molecular Biology Reports · doi:10.1007/s11033-024-09837-3 · Cited by 3

Bioinformatics approaches applied in pan-genomics and their challenges

Pantoja, Y., Pinheiro, K. D. C., Araújo, F. A., Silva, A., & Ramos, R. T. J. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-817076-2.00002-0 · Cited by 3

New antimicrobials to target gut and food pathogens

García-Gutiérrez, E. (2019) · UEA Digital Repository (University of East Anglia) · doi:10.13140/rg.2.2.20637.26082 · Cited by 3

From Single Organisms to Communities: Modeling Methanotrophs and Their Satellites

Esembaeva, M. A., Melikhova, E. V., Kachnov, V. A., & Kulyashov, M. A. (2025) · Microorganisms · doi:10.3390/microorganisms14010003 · Cited by 2

High-throughput generation and comparison of genome-scale metabolic models reveal strain-specific metabolic diversity in 439 Lactococcus strains

Bras, J. E., Sánchez, B. J., Sonnenschein, N., & Zeidan, A. A. (2026) · mSystems · doi:10.1128/msystems.01517-25 · Cited by 2

Multi-strain analysis of Pseudomonas putida reveals the metabolic and genetic diversity of the species

Mueller, J., Krishnan, J., Wei, Q., Hefner, Y., Monk, J. M., Verkler, H., Tibocha‐Bonilla, J. D., Ayala, A., Palsson, B. Ø., Feist, A. M., et al. (2026) · mSystems · doi:10.1128/msystems.01594-25 · Cited by 2

The Cutaneous Barrier and Skin Infections

Rawal, S., Gupta, P., Bachhuka, A., & Yadav, T. C. (2023) · Royal Society of Chemistry eBooks · doi:10.1039/9781837671540-00017 · Cited by 3

A Journey Beyond Resistance: Discovering the Promise of Non-Antibiotic Therapies

Singh, N. K., Singh, A., & Dubey, R. (2024) · Springer eBooks · doi:10.1007/978-981-97-5272-0_11 · Cited by 2

Genetic Diversity in Staphylococcus aureus and Its Relation to Biofilm Production

Awan, F., Ali, M. M., Mushtaq, M. H., & Ijaz, M. (2021) · Infectious diseases · doi:10.5772/intechopen.99967 · Cited by 2

AR Mechanism‐Based Drug Design

Zloh, M. (2019) · Wiley eBooks · doi:10.1002/9781119282549.ch13 · Cited by 2

Conserved Virulence-Linked Metabolic Reprogramming in Clostridioides Difficile Identified Through Genome-Scale Metabolic Network AnalysisPreprint

Jenior, M. L., Leslie, J. L., Powers, D. A., Garrett, E. M., Walker, K. A., Dickenson, M. E., Petri, W. A., Tamayo, R., & Papin, J. A. (2021) · SSRN Electronic Journal · doi:10.2139/ssrn.3773788 · Cited by 2

Detection and expression of SapS, a class C nonspecific acid phosphatase with O-phospho-Ltyrosine- phosphatase activity, in Staphylococcus aureus isolates from patients with chronic osteomyelitis

Martínez-Canseco, C. J., Franco-Bourland, R. E., González‐Huerta, N. C., Paredes-Espinosa, M. A., Giono-Cerezo, S., Sánchez‐Chapul, L., Paniagua‐Pérez, R., Valdez-Mijares, R., & Hernández-Flores, C. (2023) · Biomédica · doi:10.7705/biomedica.6604 · Cited by 1

Bioactive environments to combat antimicrobial resistance: artificial intelligence and model-driven microbial biocontrol for living materials

Furtado, K. L., Gilbert, J. A., & Neal, M. J. (2026) · Journal of Applied Microbiology · doi:10.1093/jambio/lxag161 · Cited by 1

Pan-genomics of model bacteria and their outcomes

Naz, K., Ullah, N., Zaheer, T., Shehroz, M., Naz, A., & Ali, A. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-817076-2.00009-3 · Cited by 1

Large-scale CRISPRi and transcriptomics of Staphylococcus epidermidis identify genetic factors implicated in commensal-pathogen lifestyle versatilityPreprint

Spoto, M., Puma, J. P. R., Fleming, E. S., Guan, C., Ondouah-Nzutchi, Y., Kim, D. Y., & Oh, J. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.29.442003 · Cited by 1

Pan-Genome Analysis with Virulence Factors: Charting the Genomic Landscape of Uropathogenic Escherichia coli (UPEC)Preprint

Salian, L. S., Sajeevan, A., K, K. P. S., Suma Mohan, S., & Solomon, A. P. (2024) · Research Square · doi:10.21203/rs.3.rs-3982260/v1 · Cited by 1

The grammar of the pangenome: terms, concepts, methods, and emerging patterns—a general framework for comparative genomics and genome biology

Chasapi, A., Michailidis, A., Schriml, L. M., Donati, C., Kyrpides, N. C., & Ouzounis, C. A. (2026) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00403-25

Curating and comparing 114 strain-specific genome-scale metabolic models of Staphylococcus aureus

Renz, A., & Dräger, A. (2021) · npj Systems Biology and Applications · doi:10.1038/s41540-021-00188-4 · Cited by 21

Genome-scale metabolic model atlas of the zoonotic pathogen Streptococcus suisPreprint

Kochanowski, K., LIU, C., Obregón-Gutierrez, P., Murray, G. G. R., Dresen, M., Lefranc, I., Wells, H., Perez-Falcon, A., Munnoch, J., Hoskisson, P. A., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.06.17.732996

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

Monk, J. M., Charusanti, P., Aziz, R. K., Lerman, J. A., Premyodhin, N., Orth, J. D., Feist, A. M., & Palsson, B. Ø. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1307797110 · Cited by 284

A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types

Seif, Y., Monk, J. M., Mih, N., Tsunemoto, H., Poudel, S., Zúñiga, C., Broddrick, J. T., Zengler, K., & Palsson, B. Ø. (2019) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006644 · Cited by 53

An integrated computational and experimental study to elucidate Staphylococcus aureus metabolismPreprint

Islam, M. M., Thomas, V. C., Beek, M. V., Ahn, J., Alqarzaee, A. A., Zhou, C., Fey, P. D., Bayles, K. W., & Saha, R. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/703884