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- Marco Cosentino Lagomarsino, Fabrizio Capuani, Christopher P. Lowe
- Journal of theoretical biology
- 2003

We describe a method, based on techniques used in molecular dynamics, for simulating the inertialess dynamics of an elastic filament immersed in a fluid. The model is used to study the "one-armed swimmer". That is, a flexible appendage externally perturbed at one extremity. For small-amplitude motion our simulations confirm theoretical predictions that, for… (More)

- Matthew A. A. Grant, Chiara Saggioro, Ulisse Ferrari, Bruno Bassetti, Bianca Sclavi, Marco Cosentino Lagomarsino
- BMC Systems Biology
- 2011

In Escherichia coli, overlapping rounds of DNA replication allow the bacteria to double in faster times than the time required to copy the genome. The precise timing of initiation of DNA replication is determined by a regulatory circuit that depends on the binding of a critical number of ATP-bound DnaA proteins at the origin of replication, resulting in the… (More)

- Diana Fusco, Bruno Bassetti, P. Jona, Marco Cosentino Lagomarsino
- Bioinformatics
- 2007

MOTIVATION
Transcription networks, and other directed networks can be characterized by some topological observables (e.g. network motifs), that require a suitable randomized network ensemble, typically with the same degree sequences of the original ones. The commonly used algorithms sometimes have long convergence times, and sampling problems. We present… (More)

- Federico Bassetti, Marco Cosentino Lagomarsino, Bruno Bassetti, P. Jona
- Physical review. E, Statistical, nonlinear, and…
- 2007

In statistical mechanical investigations of complex networks, it is useful to employ random graph ensembles as null models to compare with experimental realizations. Motivated by transcription networks, we present here a simple way to generate an ensemble of random directed graphs with asymptotically, scale-free out-degree and compact in-degree. Entries in… (More)

- Vincenzo G Benza, Bruno Bassetti, +4 authors Marco Cosentino Lagomarsino
- Reports on progress in physics. Physical Society
- 2012

Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex and dynamic protein-rich state, which is highly organized at various length scales. This has implications for modulating… (More)

- Matteo Osella, Marco Cosentino Lagomarsino
- Physical review. E, Statistical, nonlinear, and…
- 2013

Gene networks exhibiting oscillatory dynamics are widespread in biology. The minimal regulatory designs giving rise to oscillations have been implemented synthetically and studied by mathematical modeling. However, most of the available analyses generally neglect the coupling of regulatory circuits with the cellular "chassis" in which the circuits are… (More)

*Correspondence to: Marco Cosentino Lagomarsino; Email: marco.cosentino-lagomarsino@upmc.fr The widespread exchange of genes between bacteria must have consequences on the global architecture of their genomes, which are being found in the abundant genomic data available today. Most of the expansion of bacterial protein families can be attributed to transfer… (More)

- Jurij Kotar, Marco Leoni, Bruno Bassetti, Marco Cosentino Lagomarsino, Pietro Cicuta
- Proceedings of the National Academy of Sciences…
- 2010

Two colloidal spheres are maintained in oscillation by switching the position of an optical trap when a sphere reaches a limit position, leading to oscillations that are bounded in amplitude but free in phase and period. The interaction between the oscillators is only through the hydrodynamic flow induced by their motion. We prove that in the absence of… (More)

- Vittore F. Scolari, Bruno Bassetti, Bianca Sclavi, Marco Cosentino Lagomarsino
- Molecular bioSystems
- 2011

Focusing on the DNA-bridging nucleoid proteins Fis and H-NS, and integrating several independent experimental and bioinformatic data sources, we investigate the links between chromosomal spatial organization and global transcriptional regulation. By means of a novel multi-scale spatial aggregation analysis, we uncover the existence of contiguous clusters of… (More)

- Marco Cosentino Lagomarsino, Olivier Espéli, Ivan Junier
- FEBS letters
- 2015

The link between chromosome structure and function is a challenging open question because chromosomes in vivo are highly dynamic and arduous to manipulate. Here, we examine several promising approaches to tackle this question specifically in bacteria, by integrating knowledge from different sources. Toward this end, we first provide a brief overview of… (More)