Preprints
- "Evolution of cell size control is canalized towards adders or sizers by cell cycle structure and selective pressures" Félix Proulx-Giraldeau, Jan M. Skotheim, Paul Francois. BiorXiv
2022
- "Universal antigen encoding of T cell activation from high-dimensional cytokine dynamics" Achar SR, Bourassa FXP, Rademaker TJ, Lee A, Kondo T, Salazar-Cavazos E, Davies JS, Taylor N, François P*, Altan-Bonnet G*, Science 2022. 376(6595):880-884
- "Arnold tongue entrainment reveals dynamical principles of the embryonic segmentation clock" Layague Sanchez PG, Mochulska V, Mauffette Denis C, Mönke G, Tomita T, Tsuchida-Straeten N, Petersen Y, Sonnen KF, François P*, Aulehla A* eLife (In Press)
- "Latent space of a small genetic network: Geometry of dynamics and information" Seyboldt R, Lavoie J, Henry A, Vanaret J, Petkova MD, Gregor T, François P* PNAS.2022. 119 (26) e2113651119
2021
- "Endocytic proteins with prion-like domains form viscoelastic condensates that enable membrane remodeling" Bergeron-Sandoval LP, Kumar S, Khadivi Heris H, Chang CLA, Hendricks AG, Cornell CE, Keller SL, François P, Hendricks AG, Ehrlicher AJ, Pappu RV, Michnick SW*. PNAS. 2021. 118 (50) e2113789118
- "Pre-existing chromatin accessibility and gene expression differences among naïve CD4+ T cells influence effector potential" Rogers D, Sood A, Wang H, van Beek JJP, Rademaker TJ, Artusa P, Schneider C, Shen C, Wong DC, Lebel M-E, Condotta SA, Richer MJ, Martins AJ, Tsang JS, Barreiro L, François P, Langlais D, Melichar HJ, Textor J, Mandl JN*. Cell Rep. 2021. 37(9):110064
2020
- "Geometric models for robust encoding of dynamical information into embryonic patterns" Jutras-Dubé L, El-Sherif E, François P, eLife 2020;9:e55778
- "Numerical Parameter Space Compression and Its Application to Biophysical Models" Hsu CT, Brouhard GJ, François P, Biophys J 118(6):1455-1465
2019
- "Successive Kinesin-5 Microtubule Crosslinking and Sliding Promote Fast, Irreversible Formation of a Stereotyped Bipolar Spindle" " Leary A, Sim S, Nazarova E, Shulist K ,Genthial R, Yang SK ,Bui KH , Francois P , Vogel J Curr Biol. 29(22):3825-3837.e3
- "Physical approaches to receptor sensing and ligand discrimination" François P, Zilman A, Curr. Op. Syst. Biol. 18,111-121
- "A High-Throughput Image Correlation Method for Rapid Analysis of Fluorophore Photoblinking and Photobleaching Rates" Sehayek S, Gidi Y, Glembockyte V, Brandão HB, François P, Cosa G, Wiseman PW, ACS Nano 13, 10, 11955-11966
- "Attack and Defense in Cellular decisions: lessons from machine learning" Rademaker T, Bengio E, François P, Physical Review X (In Press)
- "In Silico Evolution of Biochemical Log-Response" Hemery M, François P, J. Phys. Chem. B, 123,10, 2235-2243
2018
- “φ-evo: A program to evolve phenotypic models of biological networks" Henry A, Hemery M, François P. PLoS Comput Biol 14(6): e1006244.
- “Landscape, bifurcations, geometry for development" François P, Jutras-Dubé L. Curr. Op. Syst. Biol. (In Press)
- “From evolutionary computation to phenotypic spandrels Inverse problem for immune ligand recognition" François P, Hemery M. Systems Immunology <
- “Modulation of Phase Shift between Wnt and Notch Signaling Oscillations Controls Mesoderm Segmentation" Sonnen KF, Lauschke VM, Uraji J, Falk HJ, Petersen Y, Funk MC, Beaupeux M, François P, Merten CA, Aulehla A. Cell, 172(5):1079-1090
2017
- “Untangling the hairball: fitness based asymptotic reduction of biological networks" Proulx-Giraldeau F, Rademaker TJ, François P Biophys. J.,113(8):1893-1906 (2017) (see also a simple summary)
- “Speed regulation of genetic cascades allows for evolvability in the body plan specification of insects" Zhua X, Rudolf H, Healey L, François P, Brown SJ, Klingler M, El-Sherif E, PNAS 114(41):E8646-E8655 (2017)
- “Multiscale quantification of tissue behavior during amniote embryo axis elongation" Benazeraf B, Beaupeux M, Tchernookov M, Wallingford A, Salisbury T, Shirtz A, Shirtz A, Huss D, Pourquie O, François P, Lansford R, Development, 144: 4462-4472 (2017)
- "Sorting at embryonic boundaries requires high heterotypic interfacial tension" Canty L, Zarour E, Kashkooli L, François P, Fagotto F Nature Communications, 8(1):157 (2017)
2016
- “Phenotypic spandrel: absolute discrimination and ligand antagonism" François P , Hemery M, Johnson KA, Saunders LN, Phys. Biol., in Press
- “Positional information from oscillatory phase shifts : insights from in silico evolution" Beaupeux M, François P Phys. Biol. 13 : 036009 (2016)
- “Predicting Ancestral Segmentation Phenotypes from Drosophila to Anopheles Using In Silico Evolution" Rothschild JB, Tsimiklis P, Siggia ED, François P PLoS Genet 12(5): e1006052 (2016)
- “The case for absolute ligand discrimination : modeling information processing and decision by immune T cells" François P and Altan-Bonnet G, Journal of Statistical Physics, 162 (5):1130–1152 (2016)
2015
- “Critical Timing without a Timer for Embryonic Development" Tufcea DE and François P Biophysical J, 109 (8):1724-1734 (2015)
- “Dynamics of the slowing segmentation clock reveal alternating two-segment periodicity" Shih NP, François P, Delaune E and Amacher SL Development, 142, 1785-1793. (2015)
- “Chemodetection in fluctuating environments: Receptor coupling, buffering, and antagonism" Lalanne JB and François P Proc. Natl. Acad. Sci. U S A. 112(6):1898-903 (2015)
2014
- “Evolving phenotypic networks in silico" François P Seminars in Cell & Developmental Biology S1084-9521(14)00185-2. (2014)
2013
- “ Distinct roles for anti-parallel microtubule pairing and overlap during early spindle assembly." Nazarova E, O'Toole E, Kaitna S, François P, Winey M, Vogel J. Mol Biol Cell. 2013 Aug 21
- “Principles of Adaptive Sorting Revealed by In Silico Evolution” Lalanne JB and François P, Physical Review Letters, vol. 110 no. 21 (2013),
phys_rev_lett_2013_lalanne.pdf, supplements_v3.pdf
See McGill press release, Futurity , Science Daily , etc... - “A phenotypic model for early T-cell activation displaying sensitivity, specificity and antagonism” François P, Voisinne G, Siggia ED, Altan-Bonnet G, Vergassola M, Proc. Natl. Acad. Sci. U S A, vol. 110 no. 10 E888-E897 (2013)
- “Scaling of embryonic patterning based on phase-gradient encoding”, Lauschke VM, Tsiairis CD, François P, Aulehla A, Nature 493, 101–105 (2013) nature_2013_lauschke.pdf
See also associated Nature's "News and Views". This paper has been covered by Science Daily and McGill.
2012
- “Single-Cell-Resolution Imaging of the Impact of Notch Signaling and Mitosis on Segmentation Clock Dynamics”, Delaune E, François P, Shih NP, Amacher SL, Developmental Cell, Volume 23, Issue 5, 995-1005 (2012)
See also associated Dev Cell's "Preview". This paper has been covered by Science Daily and McGill University. - “Phenotypic Models of Evolution and Development: Geometry as Destiny”, François P, Siggia ED, Current Opinion in Genetics and Development, 22 (2012)
- “Pareto Evolution of Gene Networks”, Warmflash A, François P, Siggia ED, Phys. Biol. 9 056001 (2012)
This paper has been selected for the "Highlights of 2012" of Physical Biology. - “Adaptive Temperature Compensation in Circadian Oscillations” François P, Despierre N, Siggia ED PLoS Comput Biol 8(7): e1002585. (2012)
- “Evolution in silico : from network structure to bifurcation theory”, François P, Adv Exp Med Biol.751:157-82, in "Evolutionary Systems Biology", Springer (2012) O. Soyer Editor adv._exp._med._biol._2012_francois.pdf
2010 and before
- “Predicting embryonic patterning using mutual entropy fitness and in silico evolution” François P, Siggia E, Development 137, 2385-2395. (2010)
This paper has been reviewed by Faculty of 1000 - “A random cell motility gradient downstream of FGF controls elongation of an amniote embryo.”, Benazeraf B, François P, Baker R, Denans N, Little C, Pourquié O, Nature. Jul 8;466(7303):248-52. (2010)
This paper has been reviewed by Faculty of 1000, covered by CNRS and by the famous blog about evolution "Panda's Thumb". - “Scaling of BMP gradients in Xenopus embryos”, François P , Vonica A , Brivanlou AH, Siggia, E, Brief communication arising, Nature, 461(7260):E1; discussion E2 (2009) nature_2009_francois.pdf
- “A case study of evolutionary computation of biochemical adaptation”, François P, Siggia E, Physical Biology, 5 : 026009 (2008) phys_biol_2008_francois.pdf
This paper has been covered by ScienceDaily - “Deriving structure from evolution : metazoan segmentation”, François P, Hakim V, Siggia E, Mol. Syst. Biol., 3:154 (2007)
This paper has been reviewed by Faculty of 1000. - “ Core genetic module: the Mixed Feedback Loop ”, François P, Hakim V, Phys. Rev. E., 72:031908 (2005)
- “ A model for the Neurospora circadian clock ”, François P, Biophys. J., 88 (4): 2369-2383 (2005)
- “ Design of genetic networks with specified functions by evolution in silico ”, François P, Hakim V, Proc. Natl. Acad. Sci. U S A, 101(2):580-5 (2004)
This paper has been reviewed by Trends in Biotechnology and by the most famous popular Science Magazine in France, Science et Vie. - “A matrix ansatz for the diffusion of an impurity in the asymmetric exclusion process”, Boutillier C, François P, Mallick K, Mallick S, J. Phys. A, Math. Gen, 35 (46): 9703-9730 (2002) journal_of_physics_a_mathematical_and_general_2002_boutillier.pdf
- “Adaptation d’échelle et gradient de phase dans un modèle ex vivo de somitogenèse”, François P. Med Sci (Paris).2013 Aug-Sep;29(8-9):696-8.
- “Une avancée technique pour comprendre la dynamique de l’ horloge de segmentation”, Delaune E, François P, Shih NP, Amacher SL. Med Sci (Paris). 2013 Apr;29(4):355-8.
- “A non directional cell migration gradient in the presomitic mesoderm contributes to axis elongation in chicken embryos” Benazeraf B, François P, Baker R, Denans N, Little C, Pourquié O, Biologie Aujourd'hui 205(2):95-103. (2011) doi: 10.1051/jbio/2011014
- Review on “A Cell Biologist’s Guide to Modeling and Bioinformatics”, François P,The Quaterly Review of Biology 83 (3):311-312(2008)
- “ Genetic networks: design in silico and applications”, François P, Physicalia Magazine (journal of the Belgian Physical Society) (2005)
- “Ces gaz qui soufflent le chaud”, François P, Science et vie hors série Énergie (2001)