Publications

This list might be neither exhaustive nor up-to-date: you can also find me on google scholar.

[preprint] Gervais T, Kscheschinski B, Mell M, Goepfert N, Nimwegen E van & Julou T (2025) E. coli prepares for starvation by dramatically remodeling its proteome in the first hours after loss of nutrients. 2024.02.29.582700.
doi:10.1101/2024.02.29.582700
Julou T, Gervais T, de Groot D & van Nimwegen E (2025) Growth rate controls the sensitivity of gene regulatory circuits. Sci Adv 11, eadu9279.
doi:10.1126/sciadv.adu9279
Galbusera L, Bellement-Theroue G, Julou T & van Nimwegen E (2025) Rapid transcription factor fluctuations drive nonequilibrium gene regulatory dynamics in bacteria. PRX Life 3, 033006.
doi:10.1103/nvk3-jsvm
Jacquel B et al. (2025) A trade-off between stress resistance and tolerance underlies the adaptive response to hydrogen peroxide. Cell Systems 16, 101320.
doi:10.1016/j.cels.2025.101320
Kolter R, Balaban N & Julou T (2022) Bacteria grow swiftly and live thriftily. Current Biology 32, R599–R605.
doi:10.1016/j.cub.2022.05.005
Sobota M et al. (2022) The expression of virulence genes increases membrane permeability and sensitivity to envelope stress in Salmonella Typhimurium. PLoS Biology 20, e3001608.
doi:10.1371/journal.pbio.3001608
Urchueguía A, Galbusera L, Chauvin D, Bellement G, Julou T & van Nimwegen E (2021) Genome-wide gene expression noise in Escherichia coli is condition-dependent and determined by propagation of noise through the regulatory network. PLoS Biology 19, e3001491.
doi:10.1371/journal.pbio.3001491
Julou T, Zweifel L, Blank D, Fiori A & van Nimwegen E (2020) Subpopulations of sensorless bacteria drive fitness in fluctuating environments. PLoS Biology 18, e3000952.
doi:10.1371/journal.pbio.3000952
Images (raw and preprocessed datasets), raw data and analysis scripts.
Galbusera L, Bellement-Theroue G, Urchueguia A, Julou T & van Nimwegen E (2020) Using fluorescence flow cytometry data for single-cell gene expression analysis in bacteria. PLoS One 15, e0240233.
doi:10.1371/journal.pone.0240233
Witz G, van Nimwegen E & Julou T (2019) Initiation of chromosome replication controls both division and replication cycles in E. coli through a double-adder mechanism. eLife 8, e48063. doi:10.7554/eLife.48063
Images and raw data with analysis scripts.
Our rebuttal to a comment of this work by the Jun's lab.
Kaiser M, Jug F, Julou T, Deshpande S, Pfohl T, Silander OK, Myers G & Nimwegen E van (2018) Monitoring single-cell gene regulation under dynamically controllable conditions with integrated microfluidics and software. Nature Communications 9, 212.
doi:10.1038/s41467-017-02505-0
Images and raw data.
Denoth Lippuner A, Julou T & Barral Y (2014) Budding yeast as a model organism to study the effects of age. FEMS Microbiol. Rev. 38, 300–325.
doi:10.1111/1574-6976.12060
Julou T, Mora T, Guillon L, Croquette V, Schalk IJ, Bensimon D & Desprat N (2013) Cell-cell contacts confine public goods diffusion inside Pseudomonas aeruginosa clonal microcolonies. Proc. Natl. Acad. Sci. U.S.A. 110, 12577–12582.
doi:10.1073/pnas.1301428110
Coquel A-S, Jacob J-P, Primet M, Demarez A, Dimiccoli M, Julou T, Moisan L, Lindner AB & Berry H (2013) Localization of protein aggregation in Escherichia coli is governed by diffusion and nucleoid macromolecular crowding effect. PLoS Comput. Biol. 9, e1003038.
doi:10.1371/journal.pcbi.1003038
Julou T, Desprat N, Bensimon D & Croquette V (2012) Monitoring microbial population dynamics at low densities. Rev Sci Instrum 83, 074301.
doi:10.1063/1.4729796
Flutre T, Julou T, Riboli-Sasco L & Ribrault C (2011) Research community: Pilot scheme for misconduct database. Nature 478, 37.
doi:10.1038/478037c
Julou T (2011) Evolution, competition and cooperation in bacterial populations. PhD thesis, Ecole Normale Supérieure (Paris).
link
Flutre T, Julou T, Riboli-Sasco L & Ribrault C (2010) Scientific Red Cards: a collaborative website for better communication between scientists and institutions about misconduct. European Science Editing 36, 49.
link
Mosconi F, Julou T, Desprat N, Sinha DK, Allemand J-F, Croquette V & Bensimon D (2008) Some nonlinear challenges in biology. Nonlinearity 21, T131.
doi:10.1088/0951-7715/21/8/T03
Julou T, Burghardt B, Gebauer G, Berveiller D, Damesin C & Selosse M-A (2005) Mixotrophy in orchids: insights from a comparative study of green individuals and nonphotosynthetic individuals of Cephalanthera damasonium. The New phytologist 166, 639–653.
doi:10.1111/j.1469-8137.2005.01364.x

Talks & Posters

“Quantitative Microbial Physiology & Ecology” conference (2025; Invited Talk) at SIAT, Shenzhen (China).
Microbiology Department Seminar (2025) at Pasteur Institute, Paris (France).
Seminar Day: “Quantitative Approaches to Biology” (2023) at IST (Austria).
Qbio Seminar (2023) at ENS, Paris (France).
PoLS Seminar (2023) at EPFL, Lausanne (Switzerland).
Program “Quantitative Biology of Non-growing Microbes” (2022; Program Organizer) at KITP, Santa Barbara (USA).
4th International Workshop on Microbial Life under Exteme Energy Limitation (2022) at Sandbjerg Manor, Denmark.
Workshop “Major ideas in quantitative microbial physiology: Past, Present and Future” (2022) at Copenhagen (Denmark).
Cell Size and Growth Seminar (2022) online (hosted by Stanford).
Institute Seminar (2021) online (hosted by MPI Plön, Germany).
BIRS workshop “Advances in Theoretical and Experimental Methods for Analyzing Complex Regulatory Networks” (2020; Invited Talk) at BIRS (Banff, Canada). (video)
Séminaire du LiPhy (2019) at Univ. Grenoble Alpes (France).
q-bio Conference (2019) at San Francisco (USA).
Workshop “Information Processing in Single Cells” (2019) at Aspen Center for Physics (USA).
2nd SPP1617 International Conference "Phenotypic heterogeneity and sociobiology of bacterial populations" (2019; Invited Talk), at Schloss Hohenkammer (Germany).
EMBO workshop "Bacterial Persistence & Antimicrobial Therapy" (2018; Poster), at Ascona (Switzerland).
IS2M Annual Meetings: Microfluidics in Upper Rhine Valley (2018), at Université de Haute Alsace (France).
Institute Seminar (2018) at Institute of Cell Biology & SynthSys, University of Edinburgh (UK).
FriSBi seminar (2018) at IST (Austria).
Principles of microbial adaptation (2018; Poster) at Lorentz Center, Leiden (NL).
EMBO workshop “Optimizations and trade-offs in cellular growth and survival” (2018) at Weizmann Institute (Israel).
Quantitative Methods in Gene Regulation IV (2017) at Cambridge (UK).
Basel Computational Biology Conference [BC]2 (2017) at Basel (Switzerland).
Eco-Evolutionary Dynamics in Nature and the Lab (2017) at KITP, Santa Barbara (USA). (video)
New Approaches and Concepts in Microbiology (2017; Poster) at EMBL, Heidelberg (Germany).
Biozentrum Symposium (2017; Poster) at Basel (Switzerland).
Quantitative Laws Summer School (2016) at Como (Italy).
Microbiology Department Seminar (2016) at UNIGE, Genève (Switzerland).
Rigi Workshop (2016; Poster) at Luzern (Switzerland).
Biozentrum Symposium (2016; Poster) at Basel (Switzerland).
New Approaches and Concepts in Microbiology (2015; Poster) at EMBL, Heidelberg (Germany).
Experimental Approaches to Evolution & Ecology (2014; Poster) at EMBL, Heidelberg (Germany).
Computational Biology Seminar (2014) at ETH Zürich (Switzerland).
Institute Seminar (2013) at IGBMC, Strasbourg (France).
New Approaches and Concepts in Microbiology (2013; 2 Posters!!) at EMBL, Heidelberg (Germany).
Experimental Approaches to Evolution & Ecology (2012; Poster) at EMBL, Heidelberg (Germany).
Seminaire du LiPhy (2011) at Univ. Joseph Fourier, Grenoble (France).
Paris-Zürich Young Scientists Symposium in Applied Microscopy (2011) at ETH Zürich (Switzerland).
MMEMS conference “Evolution of Microbial Cooperation” (2011; Poster) at University of Bath (UK).
Between unicellularity and multicellularity: microbes in interaction (2010) at Institut des Systèmes Complexes, Paris (France).
The Evolution of Cooperation: Paradoxes of Collectivity & Individuality (2010) at Indiana University, Bloomington (USA).
102nd Statistical Mechanics Conference (2009) at Rutgers University (USA).
Journées du LPS (2008) at ENS, Paris (France).
New perspectives on the systematics & ecology of Orchids (2004) at Univ. P. Sabatier, Toulouse (France).
5ème Rencontres de Mycopathologie J. Chevaugeon (2004) at Aussois (France).

Tools

  • MoMA a.k.a. the Mother Machine Analyzer, written by Florian Jug in collaboration with our lab: a state-of-the-art image analysis software to track bacteria growing in microfluidics channels.
  • DIMM a.k.a the Dual Input Mother Machine: a microfluidics design for long-term growth and monitoring in precisely controlled environmental conditions.
  • a collection of scripts and configuration files for quantitative light microscopy using Micro-Manager.
  • a minimalist R package to tweak ggplot2 to my taste.
  • a lightweight, responsive website template based on the Skeleton boilerplate (no javascript — except for media lightbox, no jQuery dependency, no Bootstrap dependency: loading a page transfers less than 200kb!). You’re currently looking at it ;)

Data