Publications

• Soubrier C,  Foxall E,  Ciandrini L,  Dao Duc L, Optimal control of ribosome population for gene expression under periodic nutrient intake, submitted (2024) [arXiv:2401.06294]. 

• Calabrese L, Ciandrini L*, Cosentino Lagomarsino M*, How total mRNA influences cell growth (2024) [bioRxiv 2023.03.17.533181] .

• Ciandrini L, Crisostomo R L, Szavits-Nossan J, TASEPy: a Python-based package to iteratively solve the inhomogeneous exclusion process, SciPost Phys. Codebases 22 (2023). Codebase release 1.1 for TASEPy.  [arXiv:2308.00847]. 

• Eid J, Socol M, Naillon A, Feuillard J, Ciandrini L, Margeat E, Charlot B, Mougel M, Viro-fluidics: Real-time analysis of virus production kinetics at the single-cell level, Biophysical Reports 2 (3), 100068 (2022).

• Calabrese L, Grilli J,  Osella M, Kempes C P, Cosentino Lagomarsino M,* Ciandrini L*, Protein degradation sets the fraction of active ribosomes at vanishing growth, PLoS Comput Biol 18(5): e1010059. https://doi.org/10.1371/journal.pcbi.1010059  (2022) [bioRxiv 2021.03.25.436692] .

• Paloni M, Bailly R, Ciandrini L, Barducci A, Unraveling molecular interactions in a phase-separating protein by atomistic simulations  J. Phys. Chem. B (2020) [bioRxiv 099051].

• Zúñiga A, Guiziou S, Mayonove P, Zachary Ben Meriem, Camacho M, Moreau V, Ciandrini L, Hersen P, Bonnet J, Rational programming of history-dependent logic in cellular populations, Nature Communications volume 11, Article number: 4758 (2020)  [bioRxiv 617209]. 

• Szavits-Nossan J, Ciandrini L, Inferring efficiency of translation initiation and elongation from ribosome profiling, Nucleic Acids Research, gkaa678 (2020) [bioRxiv 719302].

• Rogalla P S, Rudge T J, Ciandrini L, An Equilibrium model for ribosome competition, Physical Biology, 17, 1 (2019) [arxiv:1907.09151].

• Rousset Y, Ciandrini L, Kern N, Exclusion process subject to conformational size changes, SciPost Phys. 6, 77 (2019) (2019) [arXiv:1902.03645].

• Fernandes L D, Ciandrini L, Driven transport on a flexible polymer with particle recycling: a model inspired by transcription and translation, Phys. Rev. E 99, 052409 (2019) [arXiv:1803.08110].

• Szavits-Nossan J, Romano M C, Ciandrini L, Power series solution of the inhomogeneous exclusion process, Phys Rev E 97, 052139 (2018) [arXiv:1803.00887].

• Szavits-Nossan J, Ciandrini L*, Romano M C*, Deciphering mRNA Sequence Determinants of Protein Production Rate, Phys. Rev. Lett. 120, 128101  (2018) [arXiv:1708.07678].

• Fernandes L D, de Moura A PS, Ciandrini L, Gene length as a regulator for ribosome recruitment and protein synthesis: theoretical insights, Scientific Reports 7: 17409 (2017) [bioRxiv 105296, arXiv:1702.00632] doi:10.1038/s41598-017-17618-1

• Gorgoni B, Ciandrini L, McFarland M R, Romano M C, Stansfield I, Identification of the mRNA targets of tRNA-specific regulation using genome-wide simulation of translation, Nucleic Acids Research (2016) doi: 10.1093/nar/gkw630

• Ciandrini L, Molecular motors with a stepping cycle: from theory to experiments.  Proceedings of Traffic and Granular Flow '13, pp 619-627, Springer (2015).

• Ciandrini L*, Neri I*, Walter J-C*, Dauloudet O, Parmeggiani A,  Motor protein traffic regulation by supply-demand balance of resources. FEATURED ARTICLE Physical Biology 11(5) 056006 (2014) [arXiv:1408.2945].

• Ciandrini L, Romano M C, Parmeggiani A,  Stepping and crowding of molecular motors: statistical kinetics from an exclusion process perspective. Biophysical Journal 107(5), p1176–1184 (2014) [arXiv:1312.1911].

• Ciandrini L, Stansfield I, Romano M C, Ribosome traffic on mRNAs maps to gene ontology: genome-wide quantification of translation initiation rates and polysome size regulation. PLoS Comput Biol 9(1), e1002866 (2013).

• Kemp A J, Betney R, Ciandrini L, Romano M C, Stansfield I, A yeast tRNA mutant that causes pseudohyphal growth exhibiths reduced rates of CAG codon translation. Molecular Microbiology 87 (2), 284-300 (2013).

• Turci F*, Parmeggiani A, Pitard E, Romano M C, Ciandrini L*, Exclusion process on a lattice with dynamical defects, Phys Rev E 87, 012705 (2013) [arXiv:1207.1804].

• Brackley C A, Ciandrini L, Romano M C, Multiple phase transitions in a system of exclusion processes with limited reservoir of particles and fuel carriers, J Stat Mech P03002 (2012). [arXiv:1201.2855]

• Greulich P*, Ciandrini L*, Allen R J †, Romano M C †, A mixed population of competing TASEPs with a shared reservoir of particles. Phys Rev E 85, 011142 (2012).  Selected for the Feb 1, 2012 issue of the Virtual Journal of Biological Physics Research [arXiv:1111.1775].

• Ciandrini L, Stansfield I, Romano M C, Role of the particle's stepping cycle in an asymmetric exclusion process: A model of mRNA translation, Phys Rev E 81, 051904 (2010). Selected for the May 15, 2010 issue of the Virtual Journal of Biological Physics Research [arXiv:0912.3482]

• Ciandrini L, Maffi C, Motta A, Bassetti B, Cosentino Lagomarsino M, Feedback topology and XOR-dynamics in Boolean networks with varying input structure, Phys Rev E 80, 026122 (2009). Selected for the September 15, 2009 issue of the Virtual Journal of Biological Physics Research [arXiv:0809.1526]

*denotes equal contribution, † also denotes equal contribution.

...and hopefully others soon...