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Items: 14

1.

Algorithmic methods to infer the evolutionary trajectories in cancer progression.

Caravagna G, Graudenzi A, Ramazzotti D, Sanz-Pamplona R, De Sano L, Mauri G, Moreno V, Antoniotti M, Mishra B.

Proc Natl Acad Sci U S A. 2016 Jul 12;113(28):E4025-34. doi: 10.1073/pnas.1520213113. Epub 2016 Jun 28.

2.

Gene switching rate determines response to extrinsic perturbations in the self-activation transcriptional network motif.

de Franciscis S, Caravagna G, Mauri G, d'Onofrio A.

Sci Rep. 2016 Jun 3;6:26980. doi: 10.1038/srep26980.

3.

TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data.

De Sano L, Caravagna G, Ramazzotti D, Graudenzi A, Mauri G, Mishra B, Antoniotti M.

Bioinformatics. 2016 Jun 15;32(12):1911-3. doi: 10.1093/bioinformatics/btw035. Epub 2016 Feb 9.

PMID:
26861821
4.

CABeRNET: a Cytoscape app for augmented Boolean models of gene regulatory NETworks.

Paroni A, Graudenzi A, Caravagna G, Damiani C, Mauri G, Antoniotti M.

BMC Bioinformatics. 2016 Feb 4;17:64. doi: 10.1186/s12859-016-0914-z.

5.

CoGNaC: A Chaste Plugin for the Multiscale Simulation of Gene Regulatory Networks Driving the Spatial Dynamics of Tissues and Cancer.

Rubinacci S, Graudenzi A, Caravagna G, Mauri G, Osborne J, Pitt-Francis J, Antoniotti M.

Cancer Inform. 2015 Sep 1;14(Suppl 4):53-65. doi: 10.4137/CIN.S19965. eCollection 2015.

6.

Automatising the analysis of stochastic biochemical time-series.

Caravagna G, De Sano L, Antoniotti M.

BMC Bioinformatics. 2015;16 Suppl 9:S8. doi: 10.1186/1471-2105-16-S9-S8. Epub 2015 Jun 1.

7.

CAPRI: efficient inference of cancer progression models from cross-sectional data.

Ramazzotti D, Caravagna G, Olde Loohuis L, Graudenzi A, Korsunsky I, Mauri G, Antoniotti M, Mishra B.

Bioinformatics. 2015 Sep 15;31(18):3016-26. doi: 10.1093/bioinformatics/btv296. Epub 2015 May 13.

PMID:
25971740
8.

Inferring tree causal models of cancer progression with probability raising.

Olde Loohuis L, Caravagna G, Graudenzi A, Ramazzotti D, Mauri G, Antoniotti M, Mishra B.

PLoS One. 2014 Oct 9;9(10):e108358. doi: 10.1371/journal.pone.0108358. eCollection 2014. Erratum in: PLoS One. 2014;9(12):e115570. Loohuis, Loes Olde [corrected to Olde Loohuis, Loes].

9.

Investigating the relation between stochastic differentiation, homeostasis and clonal expansion in intestinal crypts via multiscale modeling.

Graudenzi A, Caravagna G, De Matteis G, Antoniotti M.

PLoS One. 2014 May 28;9(5):e97272. doi: 10.1371/journal.pone.0097272. eCollection 2014.

10.

The interplay of intrinsic and extrinsic bounded noises in biomolecular networks.

Caravagna G, Mauri G, d'Onofrio A.

PLoS One. 2013;8(2):e51174. doi: 10.1371/journal.pone.0051174. Epub 2013 Feb 21.

11.

Distributed delays in a hybrid model of tumor-immune system interplay.

Caravagna G, Graudenzi A, d'Onofrio A.

Math Biosci Eng. 2013 Feb;10(1):37-57. doi: 10.3934/mbe.2013.10.37.

PMID:
23311361
12.

GESTODIFFERENT: a Cytoscape plugin for the generation and the identification of gene regulatory networks describing a stochastic cell differentiation process.

Antoniotti M, Bader GD, Caravagna G, Crippa S, Graudenzi A, Mauri G.

Bioinformatics. 2013 Feb 15;29(4):513-4. doi: 10.1093/bioinformatics/bts726. Epub 2013 Jan 3.

13.

Fine-tuning anti-tumor immunotherapies via stochastic simulations.

Caravagna G, Barbuti R, d'Onofrio A.

BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:S8. doi: 10.1186/1471-2105-13-S4-S8.

14.

Tumour suppression by immune system through stochastic oscillations.

Caravagna G, d'Onofrio A, Milazzo P, Barbuti R.

J Theor Biol. 2010 Aug 7;265(3):336-45. doi: 10.1016/j.jtbi.2010.05.013. Epub 2010 May 16.

PMID:
20580640

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