BioModels' model of the year 2024.

Malik Sheriff RS, Asari H, Geris L, Hermjakob H, Raman K, Shtylla B, Zimmermann-Kogadeeva M

Frontiers in systems biology, 2026

doi:10.3389/fsysb.2026.1829848.

Gut microbiota restricts intestinal lipid uptake via modulation of bile phosphatidylcholine metabolism in mice.

Brunner S, Plagge J, Zimmermann-Kogadeeva M, Höring M, Liebisch G, Basic M, Bolsega S, Janssen KP, Slack E, von Gamm S, Viehof-Beckmann A, Clavel T, Zimmermann M, Heeren J, Giansanti P, Weiss AS, Hermeling S, Dupont A, Ullrich AL, Jokisch F, Seeliger C, Bleich A, Hidrobo M, Stecher B, Coleman OI, Moresi C, Greter G, Arnoldini M, Scheiber J, Matysik S, Klingenspor M, Küster B, Haller D, Burkhardt R, Kuipers F, Ecker J

Nature microbiology, 2026

doi:10.1038/s41564-026-02434-z.

13 C flux ratio analysis with FRAPPPE reveals differences in metabolic fluxes between gut Bacteroidota and Escherichia coli.

Torka D, Bartmanski BJ, Spiegelhalter A, Herrera-Gomez I, Barcenas M, Drotleff B, Zimmermann M, Zimmermann-Kogadeeva M

bioRxiv, 2026

doi:10.64898/2026.05.29.728648.

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

Matveishina EK, Bartmanski BJ, Benito-Vaquerizo S, Zimmermann-Kogadeeva M

mSystems, 2025

doi:10.1128/msystems.00574-25.

Multi-omics profiling of cross-resistance between ceftazidime-avibactam and meropenem identifies common and strain-specific mechanisms in Pseudomonas aeruginosa clinical isolates.

Bartmanski BJ, Bösch A, Schmitt S, Ireddy NR, Ren Q, Findlay J, Egli A, Zimmermann-Kogadeeva M, Babouee Flury B

mBio, 2025

doi:10.1128/mbio.03896-24.

GEMsembler: cross-tool structural comparison and ensemble modeling improve metabolic model performance.

Matveishina EK, Bartmanski BJ, Benito-Vaquerizo S, Zimmermann-Kogadeeva M

bioRxiv, 2025

doi:10.1101/2025.04.09.647174.

Comparative assessment of protein large language models for enzyme commission number prediction.

Capela J, Zimmermann-Kogadeeva M, Dijk ADJV, de Ridder D, Dias O, Rocha M

BMC bioinformatics, 2025

doi:10.1186/s12859-025-06081-9.

Pervasive sublethal effects of agrochemicals on insects at environmentally relevant concentrations.

Gandara L, Jacoby R, Laurent F, Spatuzzi M, Vlachopoulos N, Borst NO, Ekmen G, Potel CM, Garrido-Rodriguez M, Böhmert AL, Misunou N, Bartmanski BJ, Li XC, Kutra D, Hériché JK, Tischer C, Zimmermann-Kogadeeva M, Ingham VA, Savitski MM, Masson JB, Zimmermann M, Crocker J

Science (New York, N.Y.), 2024

doi:10.1126/science.ado0251.

Consistency across multi-omics layers in a drug-perturbed gut microbial community.

Wuyts S, Alves R, Zimmermann-Kogadeeva M, Nishijima S, Blasche S, Driessen M, Geyer PE, Hercog R, Kartal E, Maier L, Müller JB, Garcia Santamarina S, Schmidt TSB, Sevin DC, Telzerow A, Treit PV, Wenzel T, Typas A, Patil KR, Mann M, Kuhn M, Bork P

Molecular systems biology, 2023

doi:10.15252/msb.202311525.

Recent advances in data- and knowledge-driven approaches to explore primary microbial metabolism.

Bartmanski BJ, Rocha M, Zimmermann-Kogadeeva M

Current opinion in chemical biology, 2023

doi:10.1016/j.cbpa.2023.102324.

Publisher Correction: visualizing translation dynamics at atomic detail inside a bacterial cell.

Xue L, Lenz S, Zimmermann-Kogadeeva M, Tegunov D, Cramer P, Bork P, Rappsilber J, Mahamid J

Nature, 2022

doi:10.1038/s41586-022-05455-w.

Visualizing translation dynamics at atomic detail inside a bacterial cell.

Xue L, Lenz S, Zimmermann-Kogadeeva M, Tegunov D, Cramer P, Bork P, Rappsilber J, Mahamid J

Nature, 2022

doi:10.1038/s41586-022-05255-2.

Microbiome and metabolome features of the cardiometabolic disease spectrum.

Fromentin S, Forslund SK, Chechi K, Aron-Wisnewsky J, Chakaroun R, Nielsen T, Tremaroli V, Ji B, Prifti E, Myridakis A, Chilloux J, Andrikopoulos P, Fan Y, Olanipekun MT, Alves R, Adiouch S, Bar N, Talmor-Barkan Y, Belda E, Caesar R, Coelho LP, Falony G, Fellahi S, Galan P, Galleron N, Helft G, Hoyles L, Isnard R, Le Chatelier E, Julienne H, Olsson L, Pedersen HK, Pons N, Quinquis B, Rouault C, Roume H, Salem JE, Schmidt TSB, Vieira-Silva S, Li P, Zimmermann-Kogadeeva M, Lewinter C, Søndertoft NB, Hansen TH, Gauguier D, Gøtze JP, Køber L, Kornowski R, Vestergaard H, Hansen T, Zucker JD, Hercberg S, Letunic I, Bäckhed F, Oppert JM, Nielsen J, Raes J, Bork P, Stumvoll M, Segal E, Clément K, Dumas ME, Ehrlich SD, Pedersen O

Nature medicine, 2022

doi:10.1038/s41591-022-01688-4.

Multimodal interactions of drugs, natural compounds and pollutants with the gut microbiota.

Lindell AE, Zimmermann-Kogadeeva M, Patil KR

Nature reviews. Microbiology, 2022

doi:10.1038/s41579-022-00681-5.

AmpC hyperproduction in a Cedecea davisae implant-associated bone infection during treatment: a case report and therapeutic implications.

Notter J, Seiffert SN, Zimmermann-Kogadeeva M, Bösch A, Wenger R, Strahm C, Frischknecht M, Livermore DM, Babouee Flury B

BMC infectious diseases, 2022

doi:10.1186/s12879-021-07000-y.

Combinatorial, additive and dose-dependent drug-microbiome associations.

Forslund SK, Chakaroun R, Zimmermann-Kogadeeva M, Markó L, Aron-Wisnewsky J, Nielsen T, Moitinho-Silva L, Schmidt TSB, Falony G, Vieira-Silva S, Adriouch S, Alves RJ, Assmann K, Bastard JP, Birkner T, Caesar R, Chilloux J, Coelho LP, Fezeu L, Galleron N, Helft G, Isnard R, Ji B, Kuhn M, Le Chatelier E, Myridakis A, Olsson L, Pons N, Prifti E, Quinquis B, Roume H, Salem JE, Sokolovska N, Tremaroli V, Valles-Colomer M, Lewinter C, Søndertoft NB, Pedersen HK, Hansen TH, MetaCardis Consortium*, Gøtze JP, Køber L, Vestergaard H, Hansen T, Zucker JD, Hercberg S, Oppert JM, Letunic I, Nielsen J, Bäckhed F, Ehrlich SD, Dumas ME, Raes J, Pedersen O, Clément K, Stumvoll M, Bork P

Nature, 2021

doi:10.1038/s41586-021-04177-9.

Insights from pharmacokinetic models of host-microbiome drug metabolism.

Zimmermann-Kogadeeva M, Zimmermann M, Goodman AL

2020

doi:10.1080/19490976.2019.1667724.

Mapping human microbiome drug metabolism by gut bacteria and their genes.

Zimmermann M, Zimmermann-Kogadeeva M, Wegmann R, Goodman AL

Nature, 2019

doi:10.1038/s41586-019-1291-3.

Separating host and microbiome contributions to drug pharmacokinetics and toxicity.

Zimmermann M, Zimmermann-Kogadeeva M, Wegmann R, Goodman AL

Science (New York, N.Y.), 2019

doi:10.1126/science.aat9931.

The Stringent Response Determines the Ability of a Commensal Bacterium to Survive Starvation and to Persist in the Gut.

Schofield WB, Zimmermann-Kogadeeva M, Zimmermann M, Barry NA, Goodman AL

Cell host & microbe, 2018

doi:10.1016/j.chom.2018.06.002.

Integration of Metabolomics and Transcriptomics Reveals a Complex Diet of Mycobacterium tuberculosis during Early Macrophage Infection.

Zimmermann M, Kogadeeva M, Gengenbacher M, McEwen G, Mollenkopf HJ, Zamboni N, Kaufmann SHE, Sauer U

mSystems, 2017

doi:10.1128/mSystems.00057-17.

L-arginine modulates T cell metabolism and enhances survival and anti-tumor activity.

Geiger R, Rieckmann JC, Wolf T, Basso C, Feng YH, Fuhrer T, Kogadeeva M, Picotti P, Meissner F, Mann M, Zamboni N, Sallusto F, Lanzavecchia A

CELL, 2016

doi:10.1016/j.cell.2016.09.031.

High coverage metabolomics analysis reveals phage-specific alterations to Pseudomonas aeruginosa physiology during infection.

De Smet J, Zimmermann M, Kogadeeva M, Ceyssens PJ, Vermaelen W, Blasdel B, Bin Jang H, Sauer U, Lavigne R

The ISME journal, 2016

doi:10.1038/ismej.2016.3.

SUMOFLUX: A Generalized Method for Targeted C-13 Metabolic Flux Ratio Analysis.

Kogadeeva M, Zamboni N

PLOS COMPUTATIONAL BIOLOGY, 2016

doi:10.1371/journal.pcbi.1005109.

Next-generation "-omics" approaches reveal a massive alteration of host RNA metabolism during bacteriophage infection of Pseudomonas aeruginosa.

Chevallereau A, Blasdel BG, De Smet J, Monot M, Zimmermann M, Kogadeeva M, Sauer U, Jorth P, Whiteley M, Debarbieux L, Lavigne R

PLOS GENETICS, 2016

doi:10.1371/journal.pgen.1006134.

Absolute Proteome Composition and Dynamics during Dormancy and Resuscitation of Mycobacterium tuberculosis.

Schubert OT, Ludwig C, Kogadeeva M, Zimmermann M, Rosenberger G, Gengenbacher M, Gillet LC, Collins BC, Röst HL, Kaufmann SH, Sauer U, Aebersold R

Cell host & microbe, 2015

doi:10.1016/j.chom.2015.06.001.

Regulation of yeast central metabolism by enzyme phosphorylation.

Oliveira AP, Ludwig C, Picotti P, Kogadeeva M, Aebersold R, Sauer U

MOLECULAR SYSTEMS BIOLOGY, 2012

doi:10.1038/msb.2012.55.