Publications

Publications from Jonas Cremer and the Cremer Lab. For a complete list, see ORCID.

2026
Quantifying the resource landscape that shapes the human gut microbiome
Jonas Cremer
bioRxiv
DOI
Order invariance of fitness makes evolution predictable despite strong history-dependent effects
Shaili Mathur, Clare I. Abreu, Olivia M. Ghosh, Jonas Cremer, and Dmitri A. Petrov
bioRxiv
DOI
Quantifying chemical fluxes underlying gut microbiota–host interactions
Jonas Cremer and Markus Arnoldini
bioRxiv
DOI
The proportional scaling of mRNA and ribosome concentrations controls eukaryotic cell growth
Xin Gao, Michael Lanz, Rosslyn Grosely, Jonas Cremer, Joseph Puglisi, and Jan M. Skotheim
Nature Cell Biology, 28, 9, p.1901
DOI
Abundance-weighted pathway mapping demonstrates family-level structure of butyrate and propionate production across the human gut microbiome
Rebecca Christensen, Yu Han Daisy Wang, Markus Arnoldini, and Jonas Cremer
ISME Communications, 6, 1, p.ycag075
DOI Preprint Code
Limits and frontiers of microbial phenotype measurements
Tristan A. Caro, George A. Schaible, Jonas Cremer, Shin Haruta, and Wenying Shou
Current Opinion in Microbiology, 94, p.102822
DOI
Community metabolism in dynamic redox landscapes
Alberto Scarampi, Jonas Cremer, and Orkun S. Soyer
Current Opinion in Microbiology, 93, p.102804
DOI Code Project
Interactive redox tower companion website (https://cremerlab.github.io/redox-tower/)
2025
Community coalescence reveals strong selection and coexistence within species in complex microbial communities
Sophie Jean Walton, Qing Xu, Richa Sharma, Hannah R. Gellert, Chih-Fu Yeh, Jonas Cremer, Katherine S. Xue, Dmitri A. Petrov, and Benjamin H. Good
bioRxiv
DOI
Diversity and prevalence of sulfate- and sulfite-reducing microorganisms in the human gut microbiome
Rebecca A. Christensen, Albert L. Müller, Alfred M. Spormann, Jonas Cremer, and Jessica A. Grembi
bioRxiv
DOI
A mismatch between slow protein synthesis and fast environmental fluctuations determines tradeoffs in bacterial proteome allocation strategies
Leron Perez and Jonas Cremer
bioRxiv
DOI
Maintenance of cytoplasmic and membrane densities shapes cellular geometry in Escherichia coli
Griffin Chure, Roshali de Silva, Richa Sharma, Michael C Lanz and Jonas Cremer
Nature Communications, 16, p.11557
DOI Preprint Code
Quantifying the varying harvest of fermentation products from the human gut microbiota
Markus Arnoldini, Richa Sharma, Claudia Moresi, Griffin Chure, Julien Chabbey, Emma Slack, and Jonas Cremer
Cell, 188, 19, p.5332
DOI Preprint Code Project
Diurnal Variations in Digestion and Flow Drive Microbial Dynamics in the Gut
Alinaghi Salari and Jonas Cremer
PRX Life, 3, p.023012
DOI Preprint Code
Featured in a Physics Viewpoint by Anne-Florence Bitbol (https://physics.aps.org/articles/v18/121)
2024
hplc-py: A Python Package For Rapid Peak Quantification in Complex Chromatograms
Griffin Chure and Jonas Cremer
Journal of Open Source Software, 9, (94), p.6270
DOI Preprint Code Project
2023
Conditionally unutilized proteins and their profound effects on growth and adaptation across microbial species
Rohan Balakrishnan and Jonas Cremer
Current Opinion in Microbiology, 75, p.102366
DOI Preprint
An optimal regulation of fluxes dictates microbial growth in and out of steady-state
Griffin Chure and Jonas Cremer
eLife
DOI Preprint Code Project
Featured as a Spotlight Article by Avi Flamholz and Akshit Goyal. Trends in Microbiology 2023 (https://doi.org/10.1016/j.tim.2023.06.003)
2022
Changing flows balance nutrient absorption and bacterial growth along the gut
Agnese Codutti, Jonas Cremer, and Karen Alim
PRL, 129
DOI Preprint
Editors suggestion; featured in Physics (https://physics.aps.org/articles/v15/146)
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)
DOI Preprint
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
DOI Preprint Code
A traveling-wave solution for bacterial chemotaxis with growth
Avaneesh V. Narla, Jonas Cremer, and Terrence Hwa
PNAS, 118, (48)
DOI
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
DOI
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
DOI
An evolutionarily stable strategy to colonize spatially extended habitats
Weirong Liu*, Jonas Cremer, Dengjin Li, Terence Hwa, and Chenli Liu.
Nature, 575
DOI
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
DOI
2018
Bacterial growth, flow, and mixing shape human gut microbiota density and composition
Markus Arnoldini, Jonas Cremer, and Terence Hwa.
Gut Microbes, 9, (6)
DOI
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)
DOI
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)
DOI
2015
The emergence of cooperation from a single mutant during microbial life cycles
Anna Melbinger, Jonas Cremer, and Erwin Frey.
Interface, 12, (108)
DOI
2013
Mobility, fitness collection, and the breakdown of cooperation
Anatolij Gelimson, Jonas Cremer, and Erwin Frey.
Physical Review E, 87
DOI
2012
Growth dynamics and the evolution of cooperation in microbial populations
Jonas Cremer, Anna Melbinger, and Erwin Frey.
Scientific Reports, 281
DOI
2011
Evolutionary and population dynamics: A coupled approach
Jonas Cremer, Anna Melbinger, and Erwin Frey.
Physical Review E, 84
DOI
2010
Evolutionary game theory in growing populations
Anna Melbinger, Jonas Cremer, and Erwin Frey
Physical Review Letters, 105
DOI
Entropy production of cyclic population dynamics
Benjamin Andrae, Jonas Cremer, Tobias Reichenbach, and Erwin Frey.
Physical Review Letters, 104
DOI
2009
The edge of neutral evolution in social dilemmas
Jonas Cremer, Tobias Reichenbach, and Erwin Frey.
New Journal of Physics, 11
DOI
2008
Anomalous finite-size effects in the battle of the sexes
Jonas Cremer, Tobias Reichenbach, and Erwin Frey.
European Physical Journal B, 63
DOI