• 2025
  Iacopo Ruolo, Sara Napolitano, Lorena Postiglione, Gennaro Napolitano, Andrea Ballabio, Diego Di Bernardo, Investigation of dynamic regulation of TFEB nuclear shuttling by microfluidics and quantitative modelling, Communications Biology, 2025, 8 (1), pp.443. ⟨10.1038/s42003-025-07870-x⟩.
• 2025
  Angelica Frusteri Chiacchiera, Michela Casanova, Massimo Bellato, Aurora Piazza, Roberta Migliavacca, Grégory Batt, Paolo Magni, Lorenzo Pasotti, Harnessing CRISPR interference to resensitize laboratory strains and clinical isolates to last resort antibiotics, Scientific Reports, 2025, 15, pp.261. .
• 2024
  Davide de Marchi, Roman Shaposhnikov, Samy Gobaa, Daniele Pastorelli, Gregory Batt, Paolo Magni, Lorenzo Pasotti, Design and model-driven analysis of synthetic circuits with the Staphylococcus aureus dead-Cas9 (sadCas9) as a programmable transcriptional regulator in bacteria, ACS Synthetic Biology, 2024, 13 (3), pp.763-780. .
• 2023
  Fox ZR, Batt G, Ruess J, Bayesian filtering for model predictive control of stochastic gene expression in single cells, Phys Biol 2023 Jul 12; 20(5):055003 .
• 2023
  Sosa-Carrillo S, Galez H, Napolitano S, Bertaux F, Batt G, Maximizing protein production by keeping cells at optimal secretory stress levels using real-time control approaches, Nat Commun. 2023 May 25;14(1):3028.
• 2023
  Lunz D, Bonnans JF, Ruess J, Optimal control of bioproduction in the presence of population heterogeneity, J Math Biol 2023 Feb 02; 86(3):43.
• 2023
  Vidal L, Lebrun E, Park YK, Mottet G, Nicaud JM, Bidirectional hybrid erythritol-inducible promoter for synthetic biology in Yarrowia lipolytica., Microb Cell Fact 2023 Jan; 22(1): 7.
• 2022
  Bertaux F, Sosa-Carrillo S, Gross V, Fraisse A, Aditya C, Furstenheim M, Batt G, Enhancing bioreactor arrays for automated measurements and reactive control with ReacSight, Nat Commun 2022 Jun; 13(1): 3363.
• 2022
  Fox Z, Fletcher S, Fraisse A, Aditya C, Sosa-Carrillo S, Petit J, Gilles S, Bertaux F, Ruess J, Batt B, Enabling reactive microscopy with MicroMator, Nat Commun. 2022 Apr22;13(1): 2199.
• 2022
  Aditya C, Bertaux F, Batt G, Ruess J, Using single-cell models to predict the functionality of synthetic circuits at the population scale, PNAS 2022; 119(11):e2114438119.
• 2022
  Davidović A, Chait R, Batt G, Ruess J, Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level, PLoS Comput Biol 2022 Mar; 18(3): e1009950.
• 2021
  Bertaux F, Ruess J, Batt G, External control of microbial populations for bioproduction: A modeling and optimization viewpoint, Current Opinion in Systems Biology. 2021 Dec 1;28:100394.
• 2021
  Aditya C, Bertaux F, Batt G, Ruess J, A light tunable differentiation system for the creation and control of consortia in yeast, Nat Commun. 2021 Oct 5;12(1):5829.
• 2021
  Andreani V, You L, Glaser P, Batt G, A model-based approach to characterize enzyme-mediated response to antibiotic treatments: going beyond the SIR classification, bioRxiv. 2021.07.16.452741.
• 2021
  Lunz D, Batt G, Ruess J, Bonnans JF, Beyond the chemical master equation: Stochastic chemical kinetics coupled with auxiliary processes, PLoS Comput Biol 2021 Jul 28; 17(7): e1009214.
• 2021
  Napolitano F, Rapakoulia T, Annunziata P, Hasegawa A, Cardon M, Napolitano S, Vaccaro L, Iuliano A, Wanderlingh LG, Kasukawa T, Medina DL, Cacchiarelli D, Gao X, di Bernardo D, Arner E, Automatic identification of small molecules that promote cell conversion and reprogramming., Stem Cell Reports 2021 May; 16(5): 1381-1390.
• 2021
  Perrino G, Napolitano S, Galdi F, La Regina A, Fiore D, Giuliano T, di Bernardo M, di Bernardo D, Automatic synchronisation of the cell cycle in budding yeast through closed-loop feedback control., Nat Commun 2021 Apr; 12(1): 2452.
• 2021
  Lunz D, On rapid oscillations driving biological processes at disparate timescales, Phys Biol. 2021 Mar 15;18(3):036002.
• 2021
  de Cesare I, Zamora-Chimal CG, Postiglione L, Khazim M, Pedone E, Shannon B, Fiore G, Perrino G, Napolitano S, di Bernardo D, Savery NJ, Grierson C, di Bernardo M, Marucci L, ChipSeg: An Automatic Tool to Segment Bacterial and Mammalian Cells Cultured in Microfluidic Devices., ACS Omega 2021 Feb; 6(4): 2473-2476.
• 2020
  Lunz D, Batt G, Ruess J, To quarantine, or not to quarantine: A theoretical framework for disease control via contact tracing, Epidemics, 2020, 34.
• 2020
  Jashnsaz H, Fox ZR, Hughes JJ, Li G, Munsky B, Neuert G, Diverse cell stimulation kinetics identify predictive signal transduction models, iScience 2020 Oct; 23(10): 101565.
• 2020
  Lunz D, Optimal feedback control in first-passage resetting, J. Phys. A: Math. Theor. 2020; 53:44LT01.
• 2020
  Bertaux F, von Kügelgen J, Marguerat S, Shahrezaei V, A bacterial size law revealed by a coarse-grained model of cell physiology, PLoS Comput Biol 2020 09; 16(9): e1008245.
• 2020
  Banderas A, Carcano A, Sia E, Li S, Lindner AB, Ratiometric quorum sensing governs the trade-off between bacterial vertical and horizontal antibiotic resistance propagation, PLoS Biol 2020 08; 18(8): e3000814.
• 2020
  Fox ZR, Neuert G, Munsky B, Optimal design of single-cell experiments within temporally fluctuating environments, Complexity 2020 .
• 2019
  Cepeda-Humerez SA, Ruess J, Tkačik G, Estimating information in time-varying signals, PLoS Comput. Biol. 2019 09;15(9):e1007290.
• 2019
  Ruess J, Pleška M, Guet CC, Tkačik G, Molecular noise of innate immunity shapes bacteria-phage ecologies, PLoS Comput. Biol. 2019 07;15(7):e1007168.
• 2019
  Bäuerl C, Abitayeva G, Sosa-Carrillo S, Mencher-Beltrán A, Navarro-Lleó N, Coll-Marqués JM, Zúñiga-Cabrera M, Shaikhin S, Pérez-Martinez G, P40 and P75 Are Singular Functional Muramidases Present in the Taxon, Front Microbiol 2019;10:1420.
• 2019
  Kryukov M, Carcano A, Batt G, Ruess J, Can optimal experimental design serve as a tool to characterize highly non-linear synthetic circuits?, ECC 2019, pp. 1176-1181.
• 2019
  Weill E, Andréani V, Aditya C, Martinon P, Ruess J, Batt G, Bonnans JF, Optimal control of an artificial microbial differentiation system for protein bioproduction, ECC 2019, pp. 2663-2668.
• 2018
  Meredith HR, Andreani V, Ma HR, Lopatkin AJ, Lee AJ, Anderson DJ, Batt G, You L, Applying ecological resistance and resilience to dissect bacterial antibiotic responses, Sci Adv 2018 Dec; 4(12): eaau1873.
• 2018
  Postiglione L, Napolitano S, Pedone E, Rocca DL, Aulicino F, Santorelli M, Tumaini B, Marucci L, di Bernardo D, Regulation of Gene Expression and Signaling Pathway Activity in Mammalian Cells by Automated Microfluidics Feedback Control., ACS Synth Biol 2018 Nov; 7(11): 2558-2565.
• 2018
  Lugagne JB, Jain S, Ivanovitch P, Ben Meriem Z, Vulin C, Fracassi C, Batt G, Hersen P, Identification of individual cells from z-stacks of bright-field microscopy images, Sci Rep 2018 Jul; 8(1): 11455.
• 2017
  Lugagne JB, Sosa Carrillo S, Kirch M, Köhler A, Batt G, Hersen P, Balancing a genetic toggle switch by real-time feedback control and periodic forcing, Nat Commun. 2017 Nov 17;8(1):1671.
• 2017
  Chait R, Ruess J, Bergmiller T, Tkačik G, Guet CC, Shaping bacterial population behavior through computer-interfaced control of individual cells, Nat Commun. 2017 Nov 16;8(1):1535.