Bassetti F, Lagomarsino MC, Bassetti B, Jona P

Random networks tossing biased coins.

Phys Rev E Stat Nonlin Soft Matter Phys 2007; 056109. doi: 10.1103/PhysRevE.75.056109

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Fusco D, Bassetti B, Jona P, Lagomarsino MC

DIA-MCIS: an importance sampling network randomizer for network motif discovery and other topological observables in transcription networks.

Bioinformatics 2007; 3388-90. doi: 10.1093/bioinformatics/btm454

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Llopis I, Pagonabarraga I, Lagomarsino MC, Lowe CP

Sedimentation of pairs of hydrodynamically interacting semiflexible filaments.

Phys Rev E Stat Nonlin Soft Matter Phys 2007; 061901. doi: 10.1103/PhysRevE.76.061901

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van den Heuvel MG, Bondesan R, Lagomarsino MC, Dekker C

Single-molecule observation of anomalous electrohydrodynamic orientation of microtubules.

Phys Rev Lett 2008; 118301. doi: 10.1103/PhysRevLett.101.118301

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Lagomarsino MC, Bassetti B, Castellani G, Remondini D

Functional models for large-scale gene regulation networks: realism and fiction.

Mol Biosyst 2009; 335-44. doi: 10.1039/b816841p

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Bailey AG, Lowe CP, Pagonabarraga I, Lagomarsino MC

Accurate simulation dynamics of microscopic filaments using "caterpillar" Oseen hydrodynamics.

Phys Rev E Stat Nonlin Soft Matter Phys 2009; 046707. doi: 10.1103/PhysRevE.80.046707

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Kotar J, Leoni M, Bassetti B, Lagomarsino MC, Cicuta P

Hydrodynamic synchronization of colloidal oscillators.

Proc Natl Acad Sci U S A 2010; 7669-73. doi: 10.1073/pnas.0912455107

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Grassi L, Fusco D, Sellerio A, Corà D, Bassetti B, Caselle M, Lagomarsino MC

Identity and divergence of protein domain architectures after the yeast whole-genome duplication event.

Mol Biosyst 2010; 2305-15. doi: 10.1039/c003507f

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Scolari VF, Bassetti B, Sclavi B, Lagomarsino MC

Gene clusters reflecting macrodomain structure respond to nucleoid perturbations.

Mol Biosyst 2011; 878-88. doi: 10.1039/c0mb00213e

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Pierobon P, Miné-Hattab J, Cappello G, Viovy JL, Lagomarsino MC

Separation of time scales in one-dimensional directed nucleation-growth processes.

Phys Rev E Stat Nonlin Soft Matter Phys 2010; 061904. doi: 10.1103/PhysRevE.82.061904

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Bruot N, Damet L, Kotar J, Cicuta P, Lagomarsino MC

Noise and synchronization of a single active colloid.

Phys Rev Lett 2011; 094101. doi: 10.1103/PhysRevLett.107.094101

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Grassi L, Caselle M, Lercher MJ, Lagomarsino MC

Horizontal gene transfers as metagenomic gene duplications.

Mol Biosyst 2012; 790-5. doi: 10.1039/c2mb05330f

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Cicuta GM, Onofri E, Lagomarsino MC, Cicuta P

Patterns of synchronization in the hydrodynamic coupling of active colloids.

Phys Rev E Stat Nonlin Soft Matter Phys 2012; 016203. doi: 10.1103/PhysRevE.85.016203

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Scolari VF, Zarei M, Osella M, Lagomarsino MC

NuST: analysis of the interplay between nucleoid organization and gene expression.

Bioinformatics 2012; 1643-4. doi: 10.1093/bioinformatics/bts201

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Benza VG, Bassetti B, Dorfman KD, Scolari VF, Bromek K, Cicuta P, Lagomarsino MC

Physical descriptions of the bacterial nucleoid at large scales, and their biological implications.

Rep Prog Phys 2012; 076602. doi: 10.1088/0034-4885/75/7/076602

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Grassi L, Grilli J, Lagomarsino MC

Large-scale dynamics of horizontal transfers.

Mob Genet Elements 2012; 163-167. doi: 10.4161/mge.21112

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Bottinelli A, Bassetti B, Lagomarsino MC, Gherardi M

Influence of homology and node age on the growth of protein-protein interaction networks.

Phys Rev E Stat Nonlin Soft Matter Phys 2012; 041919. doi: 10.1103/PhysRevE.86.041919

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Osella M, Lagomarsino MC

Growth-rate-dependent dynamics of a bacterial genetic oscillator.

Phys Rev E Stat Nonlin Soft Matter Phys 2013; 012726. doi: 10.1103/PhysRevE.87.012726

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Thacker VV, Bromek K, Meijer B, Kotar J, Sclavi B, Lagomarsino MC, Keyser UF, Cicuta P

Bacterial nucleoid structure probed by active drag and resistive pulse sensing.

Integr Biol (Camb) 2014; 184-91. doi: 10.1039/c3ib40147b

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Javer A, Kuwada NJ, Long Z, Benza VG, Dorfman KD, Wiggins PA, Cicuta P, Lagomarsino MC

Persistent super-diffusive motion of Escherichia coli chromosomal loci.

Nat Commun 2014; 3854. doi: 10.1038/ncomms4854

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Long Z, Olliver A, Brambilla E, Sclavi B, Lagomarsino MC, Dorfman KD

Measuring bacterial adaptation dynamics at the single-cell level using a microfluidic chemostat and time-lapse fluorescence microscopy.

Analyst 2014; 5254-62. doi: 10.1039/c4an00877d

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Mandrà S, Lagomarsino MC, Gherardi M

Soft bounds on diffusion produce skewed distributions and Gompertz growth.

Phys Rev E Stat Nonlin Soft Matter Phys 2014; 032805. doi: 10.1103/PhysRevE.90.032805

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Srinivasan R, Scolari VF, Lagomarsino MC, Seshasayee AS

The genome-scale interplay amongst xenogene silencing, stress response and chromosome architecture in Escherichia coli.

Nucleic Acids Res 2015; 295-308. doi: 10.1093/nar/gku1229

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Gherardi M, Lagomarsino MC

Characterizing the size and shape of sea ice floes.

Sci Rep 2015; 10226. doi: 10.1038/srep10226

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Lagomarsino MC, Espéli O, Junier I

From structure to function of bacterial chromosomes: Evolutionary perspectives and ideas for new experiments.

FEBS Lett 2015; 2996-3004. doi: 10.1016/j.febslet.2015.07.002

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Javer A, Lagomarsino MC, Cicuta P

Bacterial Chromosome Dynamics by Locus Tracking in Fluorescence Microscopy.

Methods Mol Biol 2016; 161-73. doi: 10.1007/978-1-4939-3631-1_13

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Russo M, Crisafulli G, Sogari A, Reilly NM, Arena S, Lamba S, Bartolini A, Amodio V, Magrì A, Novara L, Sarotto I, Nagel ZD, Piett CG, Amatu A, Sartore-Bianchi A, Siena S, Bertotti A, Trusolino L, Corigliano M, Gherardi M, Lagomarsino MC, Di Nicolantonio F, Bardelli A

Adaptive mutability of colorectal cancers in response to targeted therapies.

Science 2019; 1473-1480. doi: 10.1126/science.aav4474

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Russo M, Pompei S, Sogari A, Corigliano M, Crisafulli G, Puliafito A, Lamba S, Erriquez J, Bertotti A, Gherardi M, Di Nicolantonio F, Bardelli A, Cosentino Lagomarsino M

A modified fluctuation-test framework characterizes the population dynamics and mutation rate of colorectal cancer persister cells.

Nat Genet 2022; 976-984. doi: 10.1038/s41588-022-01105-z

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Pavani M, Bonaiuti P, Chiroli E, Gross F, Natali F, Macaluso F, Póti Á, Pasqualato S, Farkas Z, Pompei S, Cosentino Lagomarsino M, Rancati G, Szüts D, Ciliberto A

Epistasis, aneuploidy, and functional mutations underlie evolution of resistance to induced microtubule depolymerization.

EMBO J 2021; e108225. doi: 10.15252/embj.2021108225

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Cosentino Lagomarsino M, Jona P, Bassetti B

Metachronal waves for deterministic switching two-state oscillators with hydrodynamic interaction.

Phys Rev E Stat Nonlin Soft Matter Phys 2003; 021908. doi: 10.1103/PhysRevE.68.021908

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Cosentino Lagomarsino M, Pagonabarraga I, Lowe CP

Hydrodynamic induced deformation and orientation of a microscopic elastic filament.

Phys Rev Lett 2005; 148104. doi: 10.1103/PhysRevLett.94.148104

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Cosentino Lagomarsino M, Jona P, Bassetti B

Logic backbone of a transcription network.

Phys Rev Lett 2005; 158701. doi: 10.1103/PhysRevLett.95.158701

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Zumdieck A, Cosentino Lagomarsino M, Tanase C, Kruse K, Mulder B, Dogterom M, Jülicher F

Continuum description of the cytoskeleton: ring formation in the cell cortex.

Phys Rev Lett 2005; 258103. doi: 10.1103/PhysRevLett.95.258103

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Cosentino Lagomarsino M, Tanase C, Vos JW, Emons AM, Mulder BM, Dogterom M

Microtubule organization in three-dimensional confined geometries: evaluating the role of elasticity through a combined in vitro and modeling approach.

Biophys J 2007; 1046-57. doi: 10.1529/biophysj.105.076893

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Cosentino Lagomarsino M, Jona P, Bassetti B, Isambert H

Hierarchy and feedback in the evolution of the Escherichia coli transcription network.

Proc Natl Acad Sci U S A 2007; 5516-20. doi: 10.1073/pnas.0609023104

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Sellerio AL, Bassetti B, Isambert H, Cosentino Lagomarsino M

A comparative evolutionary study of transcription networks. The global role of feedback and hierachical structures.

Mol Biosyst 2009; 170-9. doi: 10.1039/b815339f

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Cosentino Lagomarsino M, Sellerio AL, Heijning PD, Bassetti B

Universal features in the genome-level evolution of protein domains.

Genome Biol 2009; R12. doi: 10.1186/gb-2009-10-1-r12

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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 Stat Nonlin Soft Matter Phys 2009; 026122. doi: 10.1103/PhysRevE.80.026122

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Bassetti B, Zarei M, Cosentino Lagomarsino M, Bianconi G

Statistical mechanics of the "Chinese restaurant process": lack of self-averaging, anomalous finite-size effects, and condensation.

Phys Rev E Stat Nonlin Soft Matter Phys 2009; 066118. doi: 10.1103/PhysRevE.80.066118

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Angelini A, Amato A, Bianconi G, Bassetti B, Cosentino Lagomarsino M

Mean-field methods in evolutionary duplication-innovation-loss models for the genome-level repertoire of protein domains.

Phys Rev E Stat Nonlin Soft Matter Phys 2010; 021919. doi: 10.1103/PhysRevE.81.021919

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Leoni M, Bassetti B, Kotar J, Cicuta P, Cosentino Lagomarsino M

Minimal two-sphere model of the generation of fluid flow at low Reynolds numbers.

Phys Rev E Stat Nonlin Soft Matter Phys 2010; 036304. doi: 10.1103/PhysRevE.81.036304

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Fusco D, Grassi L, Bassetti B, Caselle M, Cosentino Lagomarsino M

Ordered structure of the transcription network inherited from the yeast whole-genome duplication.

BMC Syst Biol 2010; 77. doi: 10.1186/1752-0509-4-77

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Grilli J, Bassetti B, Maslov S, Cosentino Lagomarsino M

Joint scaling laws in functional and evolutionary categories in prokaryotic genomes.

Nucleic Acids Res 2012; 530-40. doi: 10.1093/nar/gkr711

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Grant MA, Saggioro C, Ferrari U, Bassetti B, Sclavi B, Cosentino Lagomarsino M

DnaA and the timing of chromosome replication in Escherichia coli as a function of growth rate.

BMC Syst Biol 2011; 201. doi: 10.1186/1752-0509-5-201

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Bruot N, Kotar J, de Lillo F, Cosentino Lagomarsino M, Cicuta P

Driving potential and noise level determine the synchronization state of hydrodynamically coupled oscillators.

Phys Rev Lett 2012; 164103. doi: 10.1103/PhysRevLett.109.164103

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Long Z, Nugent E, Javer A, Cicuta P, Sclavi B, Cosentino Lagomarsino M, Dorfman KD

Microfluidic chemostat for measuring single cell dynamics in bacteria.

Lab Chip 2013; 947-54. doi: 10.1039/c2lc41196b

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Agier N, Romano OM, Touzain F, Cosentino Lagomarsino M, Fischer G

The spatiotemporal program of replication in the genome of Lachancea kluyveri.

Genome Biol Evol 2013; 370-88. doi: 10.1093/gbe/evt014

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Zarei M, Sclavi B, Cosentino Lagomarsino M

Gene silencing and large-scale domain structure of the E. coli genome.

Mol Biosyst 2013; 758-67. doi: 10.1039/c3mb25364c

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Javer A, Long Z, Nugent E, Grisi M, Siriwatwetchakul K, Dorfman KD, Cicuta P, Cosentino Lagomarsino M

Short-time movement of E. coli chromosomal loci depends on coordinate and subcellular localization.

Nat Commun 2013; 3003. doi: 10.1038/ncomms3003

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Gherardi M, Mandrà S, Bassetti B, Cosentino Lagomarsino M

Evidence for soft bounds in Ubuntu package sizes and mammalian body masses.

Proc Natl Acad Sci U S A 2013; 21054-8. doi: 10.1073/pnas.1311124110

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