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

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KEGG: Kyoto Encyclopedia of Genes and Genomes

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

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Study Of Some Virulence Factors And Virulence Genes Produced By Gram (+Ve) And Gram (-Ve) Cocci Isolated From Clinical Samples In Al-Anbar Province/Iraq

Ghafoor, R. T. A., & Yassin, A. P. H. A. L. (2020) · European Journal of Molecular & Clinical Medicine

CASTLE: A database of synthetic lethal sets predicted from genome-scale metabolic networksPreprint

Senthamizhan, V., Subramaniam, S., Raghavan, A., & Raman, K. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.02.08.430024

Análise genômica comparativa de linhagens de Staphylococcus aureus isoladas de diferentes formas de mastite em ovinos

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Research Progress on the Correlation between Skin Microbiome and Pathogenesis of Psoriasis

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Peer Review #3 of "Genomic diversity of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated from a Children’s Hospital in México City in an eight-years survey (v0.2)"

(2019) · PeerJ · doi:10.7287/peerj.8068v0.2/reviews/3

Peer Review #1 of "Genome-wide comparison of four MRSA clinical isolates from Germany and Hungary (v0.2)"

(2021) · PeerJ · doi:10.7287/peerj.10185v0.2/reviews/1

Peer Review #2 of "Genomic diversity of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated from a Children’s Hospital in México City in an eight-years survey (v0.1)"

(2019) · PeerJ · doi:10.7287/peerj.8068v0.1/reviews/2

Peer Review #2 of "Genomic diversity of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated from a Children’s Hospital in México City in an eight-years survey (v0.2)"

(2019) · PeerJ · doi:10.7287/peerj.8068v0.2/reviews/2

Peer Review #2 of "Genome-wide comparison of four MRSA clinical isolates from Germany and Hungary (v0.1)"

(2021) · PeerJ · doi:10.7287/peerj.10185v0.1/reviews/2

Peer Review #3 of "Genomic diversity of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated from a Children’s Hospital in México City in an eight-years survey (v0.3)"

(2019) · PeerJ · doi:10.7287/peerj.8068v0.3/reviews/3

Peer Review #1 of "Genome-wide comparison of four MRSA clinical isolates from Germany and Hungary (v0.1)"

(2021) · PeerJ · doi:10.7287/peerj.10185v0.1/reviews/1

Peer Review #1 of "Genomic diversity of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated from a Children’s Hospital in México City in an eight-years survey (v0.1)"

(2019) · PeerJ · doi:10.7287/peerj.8068v0.1/reviews/1

Peer Review #3 of "Genomic diversity of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated from a Children’s Hospital in México City in an eight-years survey (v0.4)"

(2019) · PeerJ · doi:10.7287/peerj.8068v0.4/reviews/3

Peer Review #2 of "Genome-wide comparison of four MRSA clinical isolates from Germany and Hungary (v0.2)"

(2021) · PeerJ · doi:10.7287/peerj.10185v0.2/reviews/2

Interpreting roles of mutations associated with the emergence of S. aureus USA300 strains using transcriptional regulatory network reconstruction

(2023) · doi:10.1101/2023.07.26.550757

Staphylococcus aureus isolates from children with clinically differentiated osteomyelitis exhibit distinct transcriptomic signatures

Hachem, A. A., Filkins, L., Kidane, Y. H., Raj, P., Tareen, N. G., Arana, C. A., Muthukrishnan, G., & Copley, L. A. (2023) · PLoS ONE · doi:10.1371/journal.pone.0288758

Reviewer #2 (Public Review): Bactabolize is a tool for high-throughput generation of bacterial strain-specific metabolic models

(2023) · eLife · doi:10.7554/elife.87406.3.sa2

Interpreting roles of mutations associated with the emergence of S. aureus USA300 strains using transcriptional regulatory network reconstruction

Poudel, S., Hyun, J., Hefner, Y., Monk, J., Nizet, V., & Palsson, B. O. (2025) · eLife · doi:10.7554/elife.90668

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Carhuaricra, D. (2023) · doi:10.11606/d.95.2023.tde-07022024-204134

Reviewer #1 (Public Review): Interpreting roles of mutations associated with the emergence of S. aureus USA300 strains using transcriptional regulatory network reconstruction

(2025) · eLife · doi:10.7554/elife.90668.3.sa1

Implications of virtual screening for South African natural compounds against Plesiomonas shigelloides, a pathogen with zoonotic potential

Wei, C. R., Basharat, Z., & Adhikari, P. (2025) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2025.110882

Unraveling the Genomic Landscape of Staphylococcus aureus in Hospital Settings of East AfricaPreprint

Olweny, G., Mboowa, G., Kayongo, A., Kidenya, B. R., & Kateete, D. P. (2025) · Research Square · doi:10.21203/rs.3.rs-6846109/v1

Gempipe: a tool for drafting, curating, and analyzing pan and multi-strain genome-scale metabolic models

Lazzari, G., Felis, G. E., Salvetti, E., Calgaro, M., Cesare, F. D., Teusink, B., & Vitulo, N. (2025) · mSystems · doi:10.1128/msystems.01007-25

Additional file 2 of Genomic epidemiology of methicillin-resistant and -susceptible Staphylococcus aureus from bloodstream infections

Smith, J. T., Eckhardt, E. M., Hansel, N. B., Eliato, T. R., Martin, I. W., & Andam, C. P. (2021) · Figshare · doi:10.6084/m9.figshare.14821181

Additional file 5 of 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) · Figshare · doi:10.6084/m9.figshare.13719106

Additional file 10 of 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) · Figshare · doi:10.6084/m9.figshare.13719076

Additional file 9 of High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917

Hof, M. V. ‘., Mohite, O. S., Monk, J. M., Weber, T., Palsson, B. O., & Sommer, M. O. A. (2024) · Figshare · doi:10.6084/m9.figshare.26558360

Additional file 3 of High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917

Hof, M. V. ‘., Mohite, O. S., Monk, J. M., Weber, T., Palsson, B. O., & Sommer, M. O. A. (2024) · Figshare · doi:10.6084/m9.figshare.26558342

Additional file 8 of Genomic epidemiology of methicillin-resistant and -susceptible Staphylococcus aureus from bloodstream infections

Smith, J. T., Eckhardt, E. M., Hansel, N. B., Eliato, T. R., Martin, I. W., & Andam, C. P. (2021) · Figshare · doi:10.6084/m9.figshare.14821202

Additional file 6 of High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917

Hof, M. V. ‘., Mohite, O. S., Monk, J. M., Weber, T., Palsson, B. O., & Sommer, M. O. A. (2024) · Figshare · doi:10.6084/m9.figshare.26558351

Additional file 7 of 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) · Figshare · doi:10.6084/m9.figshare.13719112

Additional file 11 of High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917

Hof, M. V. ‘., Mohite, O. S., Monk, J. M., Weber, T., Palsson, B. O., & Sommer, M. O. A. (2024) · Figshare · doi:10.6084/m9.figshare.26558366

Additional file 6 of Genomic epidemiology of methicillin-resistant and -susceptible Staphylococcus aureus from bloodstream infections

Smith, J. T., Eckhardt, E. M., Hansel, N. B., Eliato, T. R., Martin, I. W., & Andam, C. P. (2021) · Figshare · doi:10.6084/m9.figshare.14821196

Additional file 1 of High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917

Hof, M. V. ‘., Mohite, O. S., Monk, J. M., Weber, T., Palsson, B. Ø., & Sommer, M. O. A. (2024) · Figshare · doi:10.6084/m9.figshare.26558336

Additional file 7 of High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917

Hof, M. V. ‘., Mohite, O. S., Monk, J. M., Weber, T., Palsson, B. O., & Sommer, M. O. A. (2024) · Figshare · doi:10.6084/m9.figshare.26558354

Additional file 10 of High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917

Hof, M. V. ‘., Mohite, O. S., Monk, J. M., Weber, T., Palsson, B. O., & Sommer, M. O. A. (2024) · Figshare · doi:10.6084/m9.figshare.26558363

Additional file 8 of 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) · Figshare · doi:10.6084/m9.figshare.13719115

Additional file 5 of High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917

Hof, M. V. ‘., Mohite, O. S., Monk, J. M., Weber, T., Palsson, B. O., & Sommer, M. O. A. (2024) · Figshare · doi:10.6084/m9.figshare.26558348

Additional file 11 of 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) · Figshare · doi:10.6084/m9.figshare.13719079

Additional file 12 of 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) · Figshare · doi:10.6084/m9.figshare.13719085

Additional file 8 of High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917

Hof, M. V. ‘., Mohite, O. S., Monk, J. M., Weber, T., Palsson, B. O., & Sommer, M. O. A. (2024) · Figshare · doi:10.6084/m9.figshare.26558357

Additional file 1 of 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.-Y., & Kim, S. (2024) · Figshare · doi:10.6084/m9.figshare.26574412

Additional file 9 of 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) · Figshare · doi:10.6084/m9.figshare.13719118

Additional file 13 of 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) · Figshare · doi:10.6084/m9.figshare.13719088

Additional file 6 of 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) · Figshare · doi:10.6084/m9.figshare.13719109

Additional file 4 of Genomic epidemiology of methicillin-resistant and -susceptible Staphylococcus aureus from bloodstream infections

Smith, J. T., Eckhardt, E. M., Hansel, N. B., Eliato, T. R., Martin, I. W., & Andam, C. P. (2021) · Figshare · doi:10.6084/m9.figshare.14821190

Additional file 4 of High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917

Hof, M. V. ‘., Mohite, O. S., Monk, J. M., Weber, T., Palsson, B. O., & Sommer, M. O. A. (2024) · Figshare · doi:10.6084/m9.figshare.26558345

Additional file 17 of Orally administered Odoribacter laneus improves glucose control and inflammatory profile in obese mice by depleting circulating succinate

Huber‐Ruano, I., Calvo, E., Mayneris‐Perxachs, J., Rodríguez-Peña, M.-M., Ceperuelo‐Mallafré, V., Cedó, L., Núñez‐Roa, C., Miró, J., Arnoriaga‐Rodríguez, M., Balvay, A., et al. (2022) · Figshare · doi:10.6084/m9.figshare.20624955

Additional file 2 of High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917

Hof, M. V. ‘., Mohite, O. S., Monk, J. M., Weber, T., Palsson, B. O., & Sommer, M. O. A. (2024) · Figshare · doi:10.6084/m9.figshare.26558339

Distinct genetic programs drive antibiotic resistance and intracellular invasion in emerging MRSA strains

Kim, S. J., Shin, Y., Lee, S., Kim, J., Jang, J., Kim, J., & Lee, W. (2026) · mSystems · doi:10.1128/msystems.01396-25

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Brielle, R. (2016) · theses.fr (ABES) · doi:10.70675/1ace3dadzbebdz43c2z80e4z0762009040ee

Real-time genomics to decipher atypical bacteria in clinical microbiology

Mlaga, K. D. (2017) · theses.fr (ABES) · doi:10.70675/c62b198fz520bz433az8b20zd67be9ef537c

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Ivain, L. (2017) · theses.fr (ABES) · doi:10.70675/b3195b95z47b9z4717za271zd067f4768cb2

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Mauro, T. (2017) · doi:10.70675/3184c264z9323z4e70zbc7dz88d55fc49c11

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Liu, W. (2018) · theses.fr (ABES) · doi:10.70675/1ab43e4bz428bz410ez90c9z8b5f463c1e38

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Riffaud, C. (2019) · theses.fr (ABES) · doi:10.70675/96c9ff69zc5b6z487cz96afz0191edf32242

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Bronsard, J. (2019) · theses.fr (ABES) · doi:10.70675/c72ac3f5z499dz49f7zb3cez33d73c5197bb

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Morgene, M. F. (2018) · theses.fr (ABES) · doi:10.70675/b0196800za02fz441eza108z5f55bfa12952

Caractéristiques toxiniques et diversité génétique des souches de Clostridium perfringens impliquées dans des toxi-infections alimentaires collectives en Ile-de-France

Abdelrahim, A. M. (2019) · theses.fr (ABES) · doi:10.70675/528aacdaz1fe8z44bez8abczbab466f56cfa

Décryptage des interactions bactériennes entre Pseudomonas aeruginosa et Staphylococcus aureus dans un contexte d'infection pulmonaire

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Hurel, J. (2020) · doi:10.70675/76336b00zeab1z454cz8541zb6bba562b646

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Cross Kingdom Metabolic Engineering Paradigm Elevating Sustainable Protein Production

Du, Y., Pi, C., Hong, K., Gao, L., & Wu, X. (2026) · Advanced Science · doi:10.1002/advs.202517703

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