Preprints
- "Evolution of cell size control is canalized towards adders or sizers by cell cycle structure and selective pressures" F茅lix Proulx-Giraldeau, Jan M. Skotheim, Paul Francois.
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, Fran莽ois P*, Altan-Bonnet G*, 2022. 376(6595):880-884
- "Arnold tongue entrainment reveals dynamical principles of the embryonic segmentation clock" Layague Sanchez PG, Mochulska V, Mauffette Denis C, M枚nke G, Tomita T, Tsuchida-Straeten N, Petersen Y, Sonnen KF, Fran莽ois P*, Aulehla A* (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, Fran莽ois P* .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, Fran莽ois P, Hendricks AG, Ehrlicher AJ, Pappu RV, Michnick SW*. PNAS. 2021. 118 (50) e2113789118
- "Pre-existing chromatin accessibility and gene expression differences among na茂ve 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, Fran莽ois 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-Dub茅 L, El-Sherif E, Fran莽ois P,
- "Numerical Parameter Space Compression and Its Application to Biophysical Models" Hsu CT, Brouhard GJ, Fran莽ois P, 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
- "Physical approaches to receptor sensing and ligand discrimination" Fran莽ois P, Zilman A,
- "A High-Throughput Image Correlation Method for Rapid Analysis of Fluorophore Photoblinking and Photobleaching Rates" Sehayek S, Gidi Y, Glembockyte V, Brand茫o HB, Fran莽ois P, Cosa G, Wiseman PW,
- "Attack and Defense in Cellular decisions: lessons from machine learning" Rademaker T, Bengio E, Fran莽ois P,
- "In Silico Evolution of Biochemical Log-Response" Hemery M, Fran莽ois P,
2018
- 鈥溝�-evo: A program to evolve phenotypic models of biological networks" Henry A, Hemery M, Fran莽ois P.
- 鈥淟andscape, bifurcations, geometry for development" Fran莽ois P, Jutras-Dub茅 L.
- 鈥淔rom evolutionary computation to phenotypic spandrels Inverse problem for immune ligand recognition" Fran莽ois P, Hemery M. <
- 鈥淢odulation 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, Fran莽ois P, Merten CA, Aulehla A.
2017
- 鈥淯ntangling the hairball: fitness based asymptotic reduction of biological networks" Proulx-Giraldeau F, Rademaker TJ, Fran莽ois P )
- 鈥淪peed regulation of genetic cascades allows for evolvability in the body plan specification of insects" Zhua X, Rudolf H, Healey L, Fran莽ois P, Brown SJ, Klingler M, El-Sherif E,
- 鈥淢ultiscale 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, Fran莽ois P, Lansford R,
- "Sorting at embryonic boundaries requires high heterotypic interfacial tension" Canty L, Zarour E, Kashkooli L, Fran莽ois P, Fagotto F
2016
- 鈥淧henotypic spandrel: absolute discrimination and ligand antagonism" Fran莽ois P , Hemery M, Johnson KA, Saunders LN,
- 鈥淧ositional information from oscillatory phase shifts : insights from in silico evolution" Beaupeux M, Fran莽ois P
- 鈥淧redicting Ancestral Segmentation Phenotypes from Drosophila to Anopheles Using In Silico Evolution" Rothschild JB, Tsimiklis P, Siggia ED, Fran莽ois P
- 鈥淭he case for absolute ligand discrimination : modeling information processing and decision by immune T cells" Fran莽ois P and Altan-Bonnet G,
2015
- 鈥淐ritical Timing without a Timer for Embryonic Development" Tufcea DE and Fran莽ois P
- 鈥淒ynamics of the slowing segmentation clock reveal alternating two-segment periodicity" Shih NP, Fran莽ois P, Delaune E and Amacher SL
- 鈥淐hemodetection in fluctuating environments: Receptor coupling, buffering, and antagonism" Lalanne JB and Fran莽ois P
2014
- 鈥淓volving phenotypic networks in silico" Fran莽ois P S1084-9521(14)00185-2. (2014)
2013
- 鈥� Distinct roles for anti-parallel microtubule pairing and overlap during early spindle assembly." Nazarova E, O'Toole E, Kaitna S, Fran莽ois P, Winey M, Vogel J. Mol Biol Cell. 2013 Aug 21
- 鈥淧rinciples of Adaptive Sorting Revealed by In Silico Evolution鈥� Lalanne JB and Fran莽ois P, Physical Review Letters, vol. 110 no. 21 (2013),听
phys_rev_lett_2013_lalanne.pdf,听 supplements_v3.pdf
See 捆绑SM社区 press release, , , etc... - 鈥淎 phenotypic model for early T-cell activation displaying sensitivity, specificity and antagonism鈥� Fran莽ois P, Voisinne G, Siggia ED, Altan-Bonnet G, Vergassola M,
- 鈥淪caling of embryonic patterning based on phase-gradient encoding鈥�, Lauschke VM, Tsiairis CD, Fran莽ois P, Aulehla A, Nature 493, 101鈥�105 (2013)听 nature_2013_lauschke.pdf
See also associated Nature's . This paper has been covered by and 捆绑SM社区.
2012
- 鈥淪ingle-Cell-Resolution Imaging of the Impact of Notch Signaling and Mitosis on Segmentation Clock Dynamics鈥�, Delaune E, Fran莽ois P, Shih NP, Amacher SL,
See also associated Dev Cell's . This paper has been covered by and 捆绑SM社区. - 鈥淧henotypic Models of Evolution and Development: Geometry as Destiny鈥�, Fran莽ois P, Siggia ED,
- 鈥淧areto Evolution of Gene Networks鈥�, Warmflash A, Fran莽ois P, Siggia ED,听
This paper has been selected for the of Physical Biology. - 鈥淎daptive Temperature Compensation in Circadian Oscillations鈥� Fran莽ois P, Despierre N, Siggia ED
- 鈥淓volution in silico : from network structure to bifurcation theory鈥�, Fran莽ois P, Adv Exp Med Biol.751:157-82, in "Evolutionary Systems Biology", Springer (2012) O. Soyer Editor听 adv._exp._med._biol._2012_francois.pdf
2010 and before
- 鈥淧redicting embryonic patterning using mutual entropy fitness and in silico evolution鈥� Fran莽ois P, Siggia E, (2010)
This paper has been reviewed by - 鈥淎 random cell motility gradient downstream of FGF controls elongation of an amniote embryo.鈥�, Benazeraf B, Fran莽ois P, Baker R, Denans N, Little C, Pourqui茅 O, (2010)
This paper has been reviewed by, covered by and by the famous blog about evolution - 鈥淪caling of BMP gradients in Xenopus embryos鈥�, Fran莽ois P , Vonica A , Brivanlou AH, Siggia, E, Brief communication arising, Nature, 461(7260):E1; discussion E2 (2009)听 nature_2009_francois.pdf
- 鈥淎 case study of evolutionary computation of biochemical adaptation鈥�, Fran莽ois P, Siggia E, Physical Biology, 5 : 026009 (2008)听 phys_biol_2008_francois.pdf
This paper has been covered by - 鈥淒eriving structure from evolution : metazoan segmentation鈥�, Fran莽ois P, Hakim V, Siggia E, (2007)
This paper has been reviewed by. - 鈥� Core genetic module: the Mixed Feedback Loop 鈥�, Fran莽ois P, Hakim V,
- 鈥� A model for the Neurospora circadian clock 鈥�, Fran莽ois P,
- 鈥� Design of genetic networks with specified functions by evolution in silico 鈥�, Fran莽ois P, Hakim V,
This paper has been reviewed by and by the most famous popular Science Magazine in France, Science et Vie. - 鈥淎 matrix ansatz for the diffusion of an impurity in the asymmetric exclusion process鈥�, Boutillier C, Fran莽ois P, Mallick K, Mallick S, J. Phys. A, Math. Gen, 35 (46): 9703-9730 (2002)听 journal_of_physics_a_mathematical_and_general_2002_boutillier.pdf
- 听鈥淎daptation d鈥櫭ヽhelle et gradient de phase dans un mod猫le ex vivo de somitogen猫se鈥�, Fran莽ois P. Med Sci (Paris).2013 Aug-Sep;29(8-9):696-8.
- 听鈥淯ne avanc茅e technique pour comprendre la dynamique de l鈥� horloge de segmentation鈥�, Delaune E, Fran莽ois P, Shih NP, Amacher SL. Med Sci (Paris). 2013 Apr;29(4):355-8.
- 鈥淎 non directional cell migration gradient in the presomitic mesoderm contributes to axis elongation in chicken embryos鈥� Benazeraf B, Fran莽ois P, Baker R, Denans N, Little C, Pourqui茅 O, Biologie Aujourd'hui 205(2):95-103. (2011) doi: 10.1051/jbio/2011014
- Review on 鈥淎 Cell Biologist鈥檚 Guide to Modeling and Bioinformatics鈥�, Fran莽ois P,The Quaterly Review of Biology 83 (3):311-312(2008)
- 鈥� Genetic networks: design in silico and applications鈥�, Fran莽ois P, Physicalia Magazine (journal of the Belgian Physical Society) (2005)
- 鈥淐es gaz qui soufflent le chaud鈥�, Fran莽ois P, Science et vie hors s茅rie 脡nergie (2001)