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1

An Intermediate Language for the Simulation of Biological Systems

Roberto Barbuti, Giulio Caravagna, Andrea Maggiolo–Schettini, Paolo Milazzo

Journal:

Electronic Notes in Theoretical Computer Science

Year:

2008

Language:

english

File:

PDF, 333 KB

english, 2008

2

[Lecture Notes in Computer Science] Computational Intelligence Methods for Bioinformatics and Biostatistics Volume 10477 || A Problem-Driven Approach for Building a Bioinformatics GraphDB

Bracciali, Andrea, Caravagna, Giulio, Gilbert, David, Tagliaferri, Roberto

Year:

2017

Language:

english

File:

PDF, 1.06 MB

english, 2017

3

Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data

Chkhaidze, Ketevan, Heide, Timon, Werner, Benjamin, Williams, Marc J., Huang, Weini, Caravagna, Giulio, Graham, Trevor A., Sottoriva, Andrea, Reiter, Johannes

Journal:

PLoS Computational Biology

Year:

2019

Language:

english

File:

PDF, 8.14 MB

english, 2019

4

Tumour suppression by immune system through stochastic oscillations

Giulio Caravagna, Alberto d’Onofrio, Paolo Milazzo, Roberto Barbuti

Journal:

Journal of Theoretical Biology

Year:

2010

Language:

english

File:

PDF, 422 KB

english, 2010

5

An intermediate language for the stochastic simulation of biological systems

Roberto Barbuti, Giulio Caravagna, Andrea Maggiolo-Schettini, Paolo Milazzo

Journal:

Theoretical Computer Science

Year:

2009

Language:

english

File:

PDF, 1.75 MB

english, 2009

6

Bio-PEPAd: A non-Markovian extension of Bio-PEPA

Giulio Caravagna, Jane Hillston

Journal:

Theoretical Computer Science

Year:

2012

Language:

english

File:

PDF, 539 KB

english, 2012

7

Foundational aspects of multiscale modeling of biological systems with process algebras

Roberto Barbuti, Giulio Caravagna, Andrea Maggiolo-Schettini, Paolo Milazzo, Simone Tini

Journal:

Theoretical Computer Science

Year:

2012

Language:

english

File:

PDF, 322 KB

english, 2012

8

Anandamide centrally depresses the respiratory rhythm generator of neonatal mice

K. Tree, C. Caravagna, G. Hilaire, J. Peyronnet, F. Cayetanot

Journal:

Year:

2010

Language:

english

File:

PDF, 4.61 MB

english, 2010

9

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

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

Journal:

Year:

2013

Language:

english

File:

PDF, 1023 KB

english, 2013

10

Fine-tuning anti-tumor immunotherapies via stochastic simulations

Giulio Caravagna, Roberto Barbuti, Alberto d’Onofrio

Journal:

BMC Bioinformatics

Year:

2012

Language:

english

File:

PDF, 488 KB

english, 2012

11

Brain-derived neurotrophic factor interacts with astrocytes and neurons to control respiration

Caravagna, Céline, Soliz, Jorge, Seaborn, Tommy

Journal:

European Journal of Neuroscience

Year:

2013

Language:

english

File:

PDF, 679 KB

english, 2013

12

MORE HERESY

Caravagna, Giulio, d'Onofrio, Alberto, Antoniotti, Marco, Mauri, Giancarlo

Journal:

Year:

1952

Language:

english

File:

PDF, 209 KB

english, 1952

13

Stochastic Hybrid Automata with delayed transitions to model biochemical systems with delays

Caravagna, Giulio, d'Onofrio, Alberto, Antoniotti, Marco, Mauri, Giancarlo

Journal:

Information and Computation

Year:

2014

Language:

english

File:

PDF, 1.36 MB

english, 2014

14

Bounded noises as a natural tool to model extrinsic fluctuations in biomolecular networks

de Franciscis, Sebastiano, Caravagna, Giulio, d’Onofrio, Alberto

Journal:

Natural Computing

Year:

2014

Language:

english

File:

PDF, 513 KB

english, 2014

15

Preface

Alex Graudenzi,Giulio Caravagna,Giancarlo Mauri

Journal:

Natural Computing

Year:

2014

Language:

english

File:

PDF, 114 KB

english, 2014

16

PI3K and MEK1/2 molecular pathways are involved in the erythropoietin-mediated regulation of the central respiratory command

Caravagna, Céline, Soliz, Jorge

Journal:

Respiratory Physiology & Neurobiology

Year:

2015

Language:

english

File:

PDF, 789 KB

english, 2015

17

[IEEE 2012 Sixth International Conference on Innovative Mobile and Internet Services in Ubiquitous Computing (IMIS) - Palermo, Italy (2012.07.4-2012.07.6)] 2012 Sixth International Conference on Innovative Mobile and Internet Services in Ubiquitous Computing - Lazy Monitoring for Distributed Computing Environments

Caravagna, Giulio, Costa, Gabriele, Wiegand, Luca, Pardini, Giovanni

Year:

2012

Language:

english

File:

PDF, 292 KB

english, 2012

18

Gestational Stress Promotes Pathological Apneas and Sex-Specific Disruption of Respiratory Control Development in Newborn Rat

Fournier, S., Steele, S., Julien, C., Fournier, S., Gulemetova, R., Caravagna, C., Soliz, J., Bairam, A., Kinkead, R.

Journal:

Journal of Neuroscience

Year:

2013

Language:

english

File:

PDF, 1.47 MB

english, 2013

19

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.

Journal:

Year:

2015

Language:

english

File:

PDF, 2.98 MB

english, 2015

20

Chronic overexpression of cerebral Epo improves the ventilatory response to acute hypoxia during the postnatal development

Caravagna, Céline, Gasser, Edith M.Schneider, Ballot, Orlane, Joseph, Vincent, Soliz, Jorge

Journal:

International Journal of Developmental Neuroscience

Year:

2015

Language:

english

File:

PDF, 350 KB

english, 2015

21

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

De Sano, Luca, Caravagna, Giulio, Ramazzotti, Daniele, Graudenzi, Alex, Mauri, Giancarlo, Mishra, Bud, Antoniotti, Marco

Journal:

Year:

2016

Language:

english

File:

PDF, 862 KB

english, 2016

22

Ordering cancer mutational profiles of cross-sectional copy number alterations

Graudenzi, Alex, Caravagna, Giulio, Bocicor, Iuliana M., Cava, Claudia, Antoniotti, Marco, Mauri, Giancarlo

Journal:

International Journal of Data Mining and Bioinformatics

Year:

2016

Language:

english

File:

PDF, 2.17 MB

english, 2016

23

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

Paroni, Andrea, Graudenzi, Alex, Caravagna, Giulio, Damiani, Chiara, Mauri, Giancarlo, Antoniotti, Marco

Journal:

BMC Bioinformatics

Year:

2016

Language:

english

File:

PDF, 2.41 MB

english, 2016

24

Automatising the analysis of stochastic biochemical time-series

Caravagna, Giulio, De Sano, Luca, Antoniotti, Marco

Journal:

BMC Bioinformatics

Year:

2015

Language:

english

File:

PDF, 2.26 MB

english, 2015

25

Oxygen Sensing in Early Life

Caravagna, Céline, Seaborn, Tommy

Journal:

Year:

2016

Language:

english

File:

PDF, 652 KB

english, 2016

26

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

de Franciscis, Sebastiano, Caravagna, Giulio, Mauri, Giancarlo, d’Onofrio, Alberto

Journal:

Scientific Reports

Year:

2016

Language:

english

File:

PDF, 2.55 MB

english, 2016

27

[Lecture Notes in Computer Science] Computational Intelligence Methods for Bioinformatics and Biostatistics Volume 10477 || A Novel Algorithm for CpG Island Detection in Human Genome Based on Clustering and Chaotic Particle Swarm Optimization

Bracciali, Andrea, Caravagna, Giulio, Gilbert, David, Tagliaferri, Roberto

Year:

2017

Language:

english

File:

PDF, 593 KB

english, 2017

28

[Lecture Notes in Computer Science] Computational Intelligence Methods for Bioinformatics and Biostatistics Volume 10477 || COSYS: A Computational Infrastructure for Systems Biology

Bracciali, Andrea, Caravagna, Giulio, Gilbert, David, Tagliaferri, Roberto

Year:

2017

Language:

english

File:

PDF, 1.56 MB

english, 2017

29

[Lecture Notes in Computer Science] Computational Intelligence Methods for Bioinformatics and Biostatistics Volume 10477 || Constraining Mechanism Based Simulations to Identify Ensembles of Parametrizations to Characterize Metabolic Features

Bracciali, Andrea, Caravagna, Giulio, Gilbert, David, Tagliaferri, Roberto

Year:

2017

Language:

english

File:

PDF, 2.18 MB

english, 2017

30

[Lecture Notes in Computer Science] Computational Intelligence Methods for Bioinformatics and Biostatistics Volume 10477 || Inference in a Partial Differential Equations Model of Pulmonary Arterial and Venous Blood Circulation Using Statistical Emulation

Bracciali, Andrea, Caravagna, Giulio, Gilbert, David, Tagliaferri, Roberto

Year:

2017

Language:

english

File:

PDF, 4.33 MB

english, 2017

31

Bounded noise induced first-order phase transitions in a baseline non-spatial model of gene transcription

d’Onofrio, Alberto, Caravagna, Giulio, de Franciscis, Sebastiano

Journal:

Physica A: Statistical Mechanics and its Applications

Year:

2017

Language:

english

File:

PDF, 1.19 MB

english, 2017

32

[IEEE 2017 IEEE International Conference on Robotics and Automation (ICRA) - Singapore, Singapore (2017.5.29-2017.6.3)] 2017 IEEE International Conference on Robotics and Automation (ICRA) - Overlap-based ICP tuning for robust localization of a humanoid robot

Nobili, Simona, Scona, Raluca, Caravagna, Marco, Fallon, Maurice

Year:

2017

Language:

english

File:

PDF, 1.97 MB

english, 2017

33

Electrophysiology on Isolated Brainstem-spinal Cord Preparations from Newborn Rodents Allows Neural Respiratory Network Output Recording

Rousseau, Jean-Philippe, Caravagna, Céline

Journal:

Journal of Visualized Experiments

Year:

2015

Language:

english

File:

PDF, 301 KB

english, 2015

34

Diversity of innate immune cell subsets across spatial and temporal scales in an EAE mouse model

Caravagna, Céline, Jaouën, Alexandre, Desplat-Jégo, Sophie, Fenrich, Keith K., Bergot, Elise, Luche, Hervé, Grenot, Pierre, Rougon, Geneviève, Malissen, Marie, Debarbieux, Franck

Journal:

Scientific Reports

Year:

2018

Language:

english

File:

PDF, 4.71 MB

english, 2018

35

The Interplay of Intrinsic and Extrinsic Bounded Noises in Biomolecular Networks

Caravagna, Giulio, Mauri, Giancarlo, d'Onofrio, Alberto, Xue, Bin

Journal:

Year:

2013

Language:

english

File:

PDF, 11.77 MB

english, 2013

36

Investigating the Relation between Stochastic Differentiation, Homeostasis and Clonal Expansion in Intestinal Crypts via Multiscale Modeling

Graudenzi, Alex, Caravagna, Giulio, De Matteis, Giovanni, Antoniotti, Marco, Garcia-Ojalvo, Jordi

Journal:

Year:

2014

Language:

english

File:

PDF, 7.59 MB

english, 2014

37

Inferring Tree Causal Models of Cancer Progression with Probability Raising

Loohuis, Loes Olde, Caravagna, Giulio, Graudenzi, Alex, Ramazzotti, Daniele, Mauri, Giancarlo, Antoniotti, Marco, Mishra, Bud, Kaderali, Lars

Journal:

Year:

2014

Language:

english

File:

PDF, 1018 KB

english, 2014

38

Detecting repeated cancer evolution from multi-region tumor sequencing data

Caravagna, Giulio, Giarratano, Ylenia, Ramazzotti, Daniele, Tomlinson, Ian, Graham, Trevor A., Sanguinetti, Guido, Sottoriva, Andrea

Journal:

Year:

2018

Language:

english

File:

PDF, 3.19 MB

english, 2018

39

Reply to ‘Neutral tumor evolution?’

Heide, Timon, Zapata, Luis, Williams, Marc J., Werner, Benjamin, Caravagna, Giulio, Barnes, Chris P., Graham, Trevor A., Sottoriva, Andrea

Journal:

Nature Genetics

Year:

2018

Language:

english

File:

PDF, 1.25 MB

english, 2018

40

Evolutionary dynamics of residual disease in human glioblastoma

Spiteri, I, Caravagna, G, Cresswell, G D, Vatsiou, A, Nichol, D, Acar, A, Ermini, L, Chkhaidze, K, Werner, B, Mair, R, Brognaro, E, Verhaak, R G W, Sanguinetti, G, Piccirillo, S G M, Watts, C, Sottori

Journal:

Annals of Oncology

Year:

2018

Language:

english

File:

PDF, 1.65 MB

english, 2018

41

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

Rubinacci, Simone, Graudenzi, Alex, Caravagna, Giulio, Mauri, Giancarlo, Osborne, James, Pitt-Francis, Joe, Antoniotti, Marco

Journal:

Cancer Informatics

Year:

2015

File:

PDF, 3.38 MB

2015

42

Learning mutational graphs of individual tumour evolution from single-cell and multi-region sequencing data

Ramazzotti, Daniele, Graudenzi, Alex, De Sano, Luca, Antoniotti, Marco, Caravagna, Giulio

Journal:

BMC Bioinformatics

Year:

2019

Language:

english

File:

PDF, 2.14 MB

english, 2019

43

The Influence of Nutrients Diffusion on a Metabolism-driven Model of a Multi-cellular System

Maspero, Davide, Damiani, Chiara, Antoniotti, Marco, Graudenzi, Alex, Di Filippo, Marzia, Vanoni, Marco, Caravagna, Giulio, Colombo, Riccardo, Ramazzotti, Daniele, Pescini, Dario, Dennunzio, Alberto,

Journal:

Fundamenta Informaticae

Year:

2019

File:

PDF, 8.91 MB

2019

44

Subclonal reconstruction of tumors by using machine learning and population genetics

Caravagna, Giulio, Heide, Timon, Williams, Marc J., Zapata, Luis, Nichol, Daniel, Chkhaidze, Ketevan, Cross, William, Cresswell, George D., Werner, Benjamin, Acar, Ahmet, Chesler, Louis, Barnes, Chris

Journal:

Nature Genetics

Year:

2020

File:

PDF, 11.81 MB

2020

45

The MOBSTER R package for tumour subclonal deconvolution from bulk DNA whole-genome sequencing data

Caravagna, Giulio, Sanguinetti, Guido, Graham, Trevor A., Sottoriva, Andrea

Journal:

BMC Bioinformatics

Year:

2020

File:

PDF, 1.79 MB

2020