Mah J, Lohmueller K, Garud N, Garud N
Mol Biol Evol. 2025; 42(2).
PMID: 39838923
PMC: 11824422.
DOI: 10.1093/molbev/msaf010.
Conrad R, Brink C, Viver T, Rodriguez-R L, Aldeguer-Riquelme B, Hatt J
Nat Commun. 2024; 15(1):9906.
PMID: 39548060
PMC: 11568254.
DOI: 10.1038/s41467-024-53787-0.
Versluis D, Schoemaker R, Looijesteijn E, Geurts J, Merks R
iScience. 2024; 27(3):109085.
PMID: 38380251
PMC: 10877688.
DOI: 10.1016/j.isci.2024.109085.
Rodriguez-R L, Conrad R, Viver T, Feistel D, Lindner B, Venter S
mBio. 2023; 15(1):e0269623.
PMID: 38085031
PMC: 10790751.
DOI: 10.1128/mbio.02696-23.
Mah J, Lohmueller K, Garud N
bioRxiv. 2023; .
PMID: 38014007
PMC: 10680615.
DOI: 10.1101/2023.11.09.566454.
A Multiscale Spatiotemporal Model Including a Switch from Aerobic to Anaerobic Metabolism Reproduces Succession in the Early Infant Gut Microbiota.
Versluis D, Schoemaker R, Looijesteijn E, Muysken D, Jeurink P, Paques M
mSystems. 2022; 7(5):e0044622.
PMID: 36047700
PMC: 9600552.
DOI: 10.1128/msystems.00446-22.
Emergent evolutionary forces in spatial models of luminal growth and their application to the human gut microbiota.
Ghosh O, Good B
Proc Natl Acad Sci U S A. 2022; 119(28):e2114931119.
PMID: 35787046
PMC: 9282425.
DOI: 10.1073/pnas.2114931119.
Competition for nutrients increases invasion resistance during assembly of microbial communities.
Wagner A
Mol Ecol. 2022; 31(15):4188-4203.
PMID: 35713370
PMC: 9542400.
DOI: 10.1111/mec.16565.
Selective culture enrichment and sequencing of feces to enhance detection of antimicrobial resistance genes in third-generation cephalosporin resistant Enterobacteriaceae.
Peto L, Fawcett N, Crook D, Peto T, Llewelyn M, Walker A
PLoS One. 2019; 14(11):e0222831.
PMID: 31703058
PMC: 6839868.
DOI: 10.1371/journal.pone.0222831.
The distribution of bacterial doubling times in the wild.
Gibson B, Wilson D, Feil E, Eyre-Walker A
Proc Biol Sci. 2018; 285(1880).
PMID: 29899074
PMC: 6015860.
DOI: 10.1098/rspb.2018.0789.
Multicopy plasmids allow bacteria to escape from fitness trade-offs during evolutionary innovation.
Rodriguez-Beltran J, Hernandez-Beltran J, DelaFuente J, Escudero J, Fuentes-Hernandez A, MacLean R
Nat Ecol Evol. 2018; 2(5):873-881.
PMID: 29632354
PMC: 6055991.
DOI: 10.1038/s41559-018-0529-z.
SteadyCom: Predicting microbial abundances while ensuring community stability.
Chan S, Simons M, Maranas C
PLoS Comput Biol. 2017; 13(5):e1005539.
PMID: 28505184
PMC: 5448816.
DOI: 10.1371/journal.pcbi.1005539.
Carriage of λ Latent Virus Is Costly for Its Bacterial Host due to Frequent Reactivation in Monoxenic Mouse Intestine.
De Paepe M, Tournier L, Moncaut E, Son O, Langella P, Petit M
PLoS Genet. 2016; 12(2):e1005861.
PMID: 26871586
PMC: 4752277.
DOI: 10.1371/journal.pgen.1005861.
Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires.
Bauer E, Laczny C, Magnusdottir S, Wilmes P, Thiele I
Microbiome. 2015; 3:55.
PMID: 26617277
PMC: 4663747.
DOI: 10.1186/s40168-015-0121-6.
Allometry of animal-microbe interactions and global census of animal-associated microbes.
Kieft T, Simmons K
Proc Biol Sci. 2015; 282(1810).
PMID: 26108631
PMC: 4590480.
DOI: 10.1098/rspb.2015.0702.
Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework.
Heinken A, Thiele I
Gut Microbes. 2015; 6(2):120-30.
PMID: 25901891
PMC: 4615372.
DOI: 10.1080/19490976.2015.1023494.
Factors that affect transfer of the IncI1 β-lactam resistance plasmid pESBL-283 between E. coli strains.
Handel N, Otte S, Jonker M, Brul S, Ter Kuile B
PLoS One. 2015; 10(4):e0123039.
PMID: 25830294
PMC: 4382111.
DOI: 10.1371/journal.pone.0123039.
Selection for bacteriophage latent period length by bacterial density: A theoretical examination.
Abedon S
Microb Ecol. 2013; 18(2):79-88.
PMID: 24196124
DOI: 10.1007/BF02030117.
Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut.
Heinken A, Sahoo S, Fleming R, Thiele I
Gut Microbes. 2012; 4(1):28-40.
PMID: 23022739
PMC: 3555882.
DOI: 10.4161/gmic.22370.
Estimating the fitness effect of an insertion sequence.
Bichsel M, Barbour A, Wagner A
J Math Biol. 2012; 66(1-2):95-114.
PMID: 22252506
DOI: 10.1007/s00285-012-0504-2.