* indicates equal contribution
2024
Quantifying the daily harvest of fermentation products from the human gut microbiota
Markus Arnoldini, Richa Sharma, Claudia Moresi, Griffin Chure, Julien Chabbey, Emma Slack, and Jonas Cremer
bioRxiv (2024) doi: 10.1101/2024.01.05.573977
GitHub Repository Additional Paper Website
2023
Stringent Control Over Cytoplasmic and Membrane Densities Defines Cell Geometry in Escherichia coli
Griffin Chure, Roshali de Silva, Richa Sharma, Michael C Lanz and Jonas Cremer
bioRxiv (2023) doi: 10.1101/2023.10.28.564462
GitHub Repository
The differing prevalences of propionate and butyrate-producing bacteria in the human gut microbiota
Rebecca Christensen, Yu Han Daisy Wang, Markus Arnoldini, and Jonas Cremer
bioRxiv (2023) doi: 10.1101/2023.11.27.568948
GitHub Repository
hplc-py: A Python Package For Rapid Peak Quantification in Complex Chromatograms
Griffin Chure and Jonas Cremer
Journal of Open Source Software 9(94) (2023) doi: 10.21105/joss.06270
GitHub Repository Additional Paper Website
Conditionally unutilized proteins and their profound effects on growth and adaptation across microbial species
Rohan Balakrishnan and Jonas Cremer
Current Opinion in Microbiology 75 (2023) doi: 10.1016/j.mib.2023.102366
An optimal regulation of fluxes dictates microbial growth in and out of steady-state
Griffin Chure and Jonas Cremer
eLife (2023) doi: 10.7554/eLife.84878
GitHub Repository Additional Paper Website Featured as a Spotlight Article by Avi Flamholz and Akshit Goyal: Matching metabolic supply to demand optimizes microbial growth. Trends in Microbiology, 2023
2022
Changing flows balance nutrient absorption and bacterial growth along the gut
Agnese Codutti, Jonas Cremer, and Karen Alim
PRL 129 (2022) doi: 10.1103/PhysRevLett.129.138101
Editors suggestion and featured in Physics
Coordination of gene expression with cell size enables Escherichia coli to efficiently maintain motility across conditions
Tomoya Honda, Jonas Cremer, Leonardo Mancini, Zhongge Zhang, Teuta Pilizota, and Terence Hwa
PNAS 119(37) (2022) doi: 10.1073/pnas.2110342119
2021
Suboptimal resource allocation during changing environments constrains bacterial response and growth recovery
Rohan Balakrishnan, Roshali T. de Silva, Terrence Hwa, and Jonas Cremer
Molecular Systems Biology 17 (2021) doi: 10.15252/msb.202110597
GitHub Repository
A traveling-wave solution for bacterial chemotaxis with growth
Avaneesh V. Narla, Jonas Cremer, and Terrence Hwa
PNAS 118(48) (2021) doi: 10.1073/pnas.2105138118
2019
Cooperation in microbial populations: Theory and experimental model systems
Jonas Cremer, Anna Melbinger, Karl Wienand, Tania Henriquez, Heinrich Jung, and Erwin Frey.
Journal of Molecular Biology 431 (2019) doi: 10.1016/j.jmb.2019.09.023
Chemotaxis as a navigation strategy to boost range expansion
Jonas Cremer*, Tomoya Honda *, Ying Tang, Jerome Wong-Ng, Massimo Vergassola, and Terrence Hwa
Nature 575 (2019) doi: 10.1038/s41586-019-1733-y
An evolutionarily stable strategy to colonize spatially extended habitats
Weirong Liu*, Jonas Cremer, Dengjin Li, Terence Hwa, and Chenli Liu.
Nature 575 (2019) doi: 10.1038/s41586-019-1734-x
Spatiotemporal establishment of dense bacterial colonies growing on hard agar
Mya R. Warren, Hui Sun, Yue Yan, Jonas Cremer, Bo Li, and Terence Hwa.
eLife (2019) doi: 10.7554/eLife.41093
2018
Bacterial growth, flow, and mixing shape human gut microbiota density and composition
Markus Arnoldini, Jonas Cremer, and Terence Hwa.
Gut Microbes 9(6) (2018) doi: 10.1080/19490976.2018.1448741
2017
Effect of water flow and chemical environment on microbiota growth and composition in the human colon
Jonas Cremer, Markus Arnoldini, and Terence Hwa.
PNAS 114(25) (2017) doi: 10.1073/pnas.1619598114
2016
Effect of flow and peristaltic mixing on bacterial growth in a gut-like channel
Jonas Cremer, Igor Segota, Chih-yu Yang, Markus Arnoldini, John T. Sauls, Zhongge Zhang, Edgar Guitierrez, Alex Groisman, and Terence Hwa.
PNAS 113(41) (2016) doi: 10.1073/pnas.1601306113
2015
The emergence of cooperation from a single mutant during microbial life cycles
Anna Melbinger, Jonas Cremer, and Erwin Frey.
Interface 12(108) (2015) doi: 10.1098/rsif.2015.0171
2013
Mobility, fitness collection, and the breakdown of cooperation
Anatolij Gelimson, Jonas Cremer, and Erwin Frey.
Physical Review E 87 (2013) doi: 10.1103/PhysRevE.87.042711
2012
Growth dynamics and the evolution of cooperation in microbial populations
Jonas Cremer, Anna Melbinger, and Erwin Frey.
Scientific Reports 281 (2012) doi: 10.1038/srep00281
2011
Evolutionary and population dynamics: A coupled approach
Jonas Cremer, Anna Melbinger, and Erwin Frey.
Physical Review E 84 (2011) doi: 10.1103/PhysRevE.84.051921
2010
Evolutionary game theory in growting populations
Anna Melbinger, Jonas Cremer, and Erwin Frey
Physical Review Letters 105 (2010) doi: 10.1103/PhysRevLett.105.178101
Entropy production of cyclic population dynamics
Benjamin Andrae, Jonas Cremer, Tobias Reichenbach, and Erwin Frey.
Physical Review Letters 104 (2010) doi: 10.1103/PhysRevLett.104.218102
2009
The edge of neutral evolution in social dilemmas
Jonas Cremer, Tobial Reichenbach, and Erwin Frey.
New Journal of Physics 11 (2009) doi: 10.1088/1367-2630/11/9/093029
2008
Anomalous finite-size effects in the battle of the sexes
Jonas Cremer, Tobias Reichenbach, and Erwin Frey.
European Physical Journal B 63 (2008) doi: 10.1140/epjb/e2008-00036-x