Paolo Magni

Summary

Affiliation: University of Pavia
Country: Italy

Publications

  1. ncbi request reprint Inferring gene expression networks via static and dynamic data integration
    Fulvia Ferrazzi
    Dipartimento di Informatica e Sistemistica, Universita degli Studi di Pavia, Italy
    Stud Health Technol Inform 124:119-24. 2006
  2. pmc A standard vector for the chromosomal integration and characterization of BioBrick™ parts in Escherichia coli
    Susanna Zucca
    Dipartimento di Ingegneria Industriale e dell Informazione, Universita degli Studi di Pavia, via Ferrata 3, Pavia, Italy
    J Biol Eng 7:12. 2013
  3. doi request reprint A minimal model of tumor growth inhibition in combination regimens under the hypothesis of no interaction between drugs
    P Magni
    Dipartimento di Ingegneria Industriale edell Informazione, Universita degli Studi di Pavia, Pavia, Italy
    IEEE Trans Biomed Eng 59:2161-70. 2012
  4. pmc The two tryptophans of β2-microglobulin have distinct roles in function and folding and might represent two independent responses to evolutionary pressure
    Sara Raimondi
    Department of Biochemistry, University of Pavia, via Taramelli 3b, 27100 Pavia, Italy
    BMC Evol Biol 11:159. 2011
  5. pmc A hierarchical Naïve Bayes Model for handling sample heterogeneity in classification problems: an application to tissue microarrays
    Francesca Demichelis
    Bionformatics, SRA, ITC irst and Dept of Information and Communication Technology, University of Trento, Trento, Italy
    BMC Bioinformatics 7:514. 2006
  6. doi request reprint A minimal model of tumor growth inhibition
    Paolo Magni
    Dipartimento di Informatica e Sistemistica, Universita degli Studi di Pavia, I 27100 Pavia, Italy
    IEEE Trans Biomed Eng 55:2683-90. 2008
  7. ncbi request reprint TimeClust: a clustering tool for gene expression time series
    Paolo Magni
    Dipartimento di Informatica e Sistemistica, Universita degli Studi di Pavia, Via Ferrata 1, Pavia, Italy
    Bioinformatics 24:430-2. 2008
  8. doi request reprint Summarizing probe intensities of affymetrix GeneChip 3' expression arrays taking into account day-to-day variability
    Paolo Magni
    Universita degli Studi di Pavia, Pavia
    IEEE/ACM Trans Comput Biol Bioinform 8:1425-30. 2011
  9. ncbi request reprint A stochastic model to assess the variability of blood glucose time series in diabetic patients self-monitoring
    Paolo Magni
    Dipartimento di Informatica e Sistemistica, Universita degli Studi di Pavia, Italy
    IEEE Trans Biomed Eng 53:977-85. 2006
  10. ncbi request reprint A mathematical model to study the effects of drugs administration on tumor growth dynamics
    P Magni
    Dipartimento di Informatica e Sistemistica, Universita degli Studi di Pavia, Via Ferrata 1, I 27100 Pavia, Italy
    Math Biosci 200:127-51. 2006

Collaborators

Detail Information

Publications35

  1. ncbi request reprint Inferring gene expression networks via static and dynamic data integration
    Fulvia Ferrazzi
    Dipartimento di Informatica e Sistemistica, Universita degli Studi di Pavia, Italy
    Stud Health Technol Inform 124:119-24. 2006
    ..The proposed approach was able to reconstruct known relationships among genes and to provide meaningful biological results...
  2. pmc A standard vector for the chromosomal integration and characterization of BioBrick™ parts in Escherichia coli
    Susanna Zucca
    Dipartimento di Ingegneria Industriale e dell Informazione, Universita degli Studi di Pavia, via Ferrata 3, Pavia, Italy
    J Biol Eng 7:12. 2013
    ..Synthetic biology concepts can contribute to the development of standardized and user friendly solutions to easily produce engineered strains and to rapidly characterize the desired genetic parts in single-copy context...
  3. doi request reprint A minimal model of tumor growth inhibition in combination regimens under the hypothesis of no interaction between drugs
    P Magni
    Dipartimento di Ingegneria Industriale edell Informazione, Universita degli Studi di Pavia, Pavia, Italy
    IEEE Trans Biomed Eng 59:2161-70. 2012
    ..Under suitable assumptions on the cell death process, the model reduces to a lumped parameter model that represents the extension of the very popular Simeoni TGI model to the combined administration of noninteracting drugs...
  4. pmc The two tryptophans of β2-microglobulin have distinct roles in function and folding and might represent two independent responses to evolutionary pressure
    Sara Raimondi
    Department of Biochemistry, University of Pavia, via Taramelli 3b, 27100 Pavia, Italy
    BMC Evol Biol 11:159. 2011
    ..Therefore, based on the peculiar differences of the two tryptophans, we have analysed the evolution of β2-microglobulin with respect to these residues...
  5. pmc A hierarchical Naïve Bayes Model for handling sample heterogeneity in classification problems: an application to tissue microarrays
    Francesca Demichelis
    Bionformatics, SRA, ITC irst and Dept of Information and Communication Technology, University of Trento, Trento, Italy
    BMC Bioinformatics 7:514. 2006
    ..The aim of this paper is to provide and validate a classification model taking into consideration the uncertainty associated with measuring replicate samples...
  6. doi request reprint A minimal model of tumor growth inhibition
    Paolo Magni
    Dipartimento di Informatica e Sistemistica, Universita degli Studi di Pavia, I 27100 Pavia, Italy
    IEEE Trans Biomed Eng 55:2683-90. 2008
    ..The tumor growth inhibition model, which is a lumped parameter model that in the last few years has been successfully applied to several antitumor drugs, is shown to be a special case of the minimal model presented here...
  7. ncbi request reprint TimeClust: a clustering tool for gene expression time series
    Paolo Magni
    Dipartimento di Informatica e Sistemistica, Universita degli Studi di Pavia, Via Ferrata 1, Pavia, Italy
    Bioinformatics 24:430-2. 2008
    ..AVAILABILITY: TimeClust executable files for Windows and LINUX platforms can be downloaded free of charge for non-profit institutions from the following web site: http://aimed11.unipv.it/TimeClust...
  8. doi request reprint Summarizing probe intensities of affymetrix GeneChip 3' expression arrays taking into account day-to-day variability
    Paolo Magni
    Universita degli Studi di Pavia, Pavia
    IEEE/ACM Trans Comput Biol Bioinform 8:1425-30. 2011
    ....
  9. ncbi request reprint A stochastic model to assess the variability of blood glucose time series in diabetic patients self-monitoring
    Paolo Magni
    Dipartimento di Informatica e Sistemistica, Universita degli Studi di Pavia, Italy
    IEEE Trans Biomed Eng 53:977-85. 2006
    ..The method here proposed has been validated on two simulated data sets and tested with success in the retrospective analysis of three patients' data sets...
  10. ncbi request reprint A mathematical model to study the effects of drugs administration on tumor growth dynamics
    P Magni
    Dipartimento di Informatica e Sistemistica, Universita degli Studi di Pavia, Via Ferrata 1, I 27100 Pavia, Italy
    Math Biosci 200:127-51. 2006
    ..The model has already been employed in several drug discovery projects. Its application on a data set coming from one of these projects is discussed in this paper...
  11. pmc Characterization of a synthetic bacterial self-destruction device for programmed cell death and for recombinant proteins release
    Lorenzo Pasotti
    Dipartimento di Informatica e Sistemistica, Universita degli Studi di Pavia, Via Ferrata 1, Pavia, Italy
    J Biol Eng 5:8. 2011
    ..abstract:..
  12. ncbi request reprint TA-clustering: cluster analysis of gene expression profiles through Temporal Abstractions
    Lucia Sacchi
    Dipartimento di Informatica e Sistemistica, Universita di Pavia, Via Ferrata 1, 27100 Pavia, Italy
    Int J Med Inform 74:505-17. 2005
    ..We demonstrate the utility of the proposed algorithm on a set of two simulated data sets and on a study of gene expression data from S. cerevisiae...
  13. ncbi request reprint Inferring gene regulatory networks by integrating static and dynamic data
    Fulvia Ferrazzi
    Dipartimento di Informatica e Sistemistica, Universita degli Studi di Pavia, Via Ferrata 1, 27100 Pavia, Italy
    Int J Med Inform 76:S462-75. 2007
    ..We exploited data from deletion mutant experiments (static data), gene expression time series (dynamic data) and the knowledge encoded in the Gene Ontology...
  14. ncbi request reprint Precedence Temporal Networks to represent temporal relationships in gene expression data
    Lucia Sacchi
    Dipartimento di Informatica e Sistemistica, University of Pavia, Via Ferrata n o 1, 27100 Pavia, Italy
    J Biomed Inform 40:761-74. 2007
    ..The extracted networks reflect the capability of the algorithm to clearly reconstruct the timing of the considered gene sets, highlighting different stages in Dictyostelium development and in the cell cycle, respectively...
  15. ncbi request reprint Predictive pharmacokinetic-pharmacodynamic modeling of tumor growth kinetics in xenograft models after administration of anticancer agents
    Monica Simeoni
    Dipartimento di Informatica e Sistemistica, University of Pavia, Pavia, and Pharmacia Italia S p A, Nerviano Milan, Italy
    Cancer Res 64:1094-101. 2004
    ..It is, thus, possible to use the model prospectively, optimizing the design of new experiments...
  16. pmc Bottom-up engineering of biological systems through standard bricks: a modularity study on basic parts and devices
    Lorenzo Pasotti
    Dipartimento di Ingegneria Industriale e dell Informazione, Universita degli Studi di Pavia, Pavia, Italy
    PLoS ONE 7:e39407. 2012
    ..The success of the bottom-up approach strictly depends on the clear definition of the limits in which biological functions can be predictable...
  17. pmc Characterization of an inducible promoter in different DNA copy number conditions
    Susanna Zucca
    Dipartimento di Informatica e Sistemistica, Universita degli Studi di Pavia, Via Ferrata 1, I 27100 Pavia, Italy
    BMC Bioinformatics 13:S11. 2012
    ..It is important to disclose the linearity working boundaries of engineered biological systems when dealing with such phenomena...
  18. doi request reprint TGI-Simulator: a visual tool to support the preclinical phase of the drug discovery process by assessing in silico the effect of an anticancer drug
    Nadia Terranova
    Dipartimento di Informatica e Sistemistica, Universita degli Studi di Pavia, Via Ferrata 1, I 27100 Pavia, Italy
    Comput Methods Programs Biomed 105:162-74. 2012
    ..The availability of a movie with a temporal varying 2-D iconographic representation is an original instrument to communicate results and learn Simeoni TGI model and its potential application in preclinical studies...
  19. pmc Accurate peak list extraction from proteomic mass spectra for identification and profiling studies
    Nicola Barbarini
    Dipartimento di Informatica e Sistemistica, Universita degli Studi di Pavia, Pavia, Italy
    BMC Bioinformatics 11:518. 2010
    ..The main steps of the peak list extraction procedure are usually preprocessing, peak detection, peak selection, charge determination and monoisotoping operation...
  20. pmc A Perl procedure for protein identification by Peptide Mass Fingerprinting
    Alessandra Tiengo
    Dipartimento di Informatica e Sistemistica, Universita degli Studi di Pavia, Via Ferrata 1, Pavia, Italy
    BMC Bioinformatics 10:S11. 2009
    ..To this aim, several algorithms and software tools have been proposed. However, the scoring methods and mainly the statistical evaluation of the results can be significantly improved...
  21. ncbi request reprint Insulin minimal model indexes and secretion: proper handling of uncertainty by a Bayesian approach
    Paolo Magni
    Dipartimento di Informatica e Sistemistica, Università degli Studi di Pavia via Ferrata, Pavia, Italy
    Ann Biomed Eng 32:1027-37. 2004
    ....
  22. ncbi request reprint Temporal data mining for the quality assessment of hemodialysis services
    Riccardo Bellazzi
    Dipartimento di Informatica e Sistemistica, Universita di Pavia, Via Ferrata 1, 27100 Pavia, Italy
    Artif Intell Med 34:25-39. 2005
    ....
  23. pmc A predictive pharmacokinetic-pharmacodynamic model of tumor growth kinetics in xenograft mice after administration of anticancer agents given in combination
    Nadia Terranova
    Dipartimento di Ingegneria Industriale e dell Informazione, Universita degli Studi di Pavia, via Ferrata 3, Pavia, Italy
    Cancer Chemother Pharmacol 72:471-82. 2013
    ..To this aim, preclinical studies are routinely performed, even if they are only qualitatively analyzed due to the lack of generally applicable mathematical models...
  24. doi request reprint Multiplexing and demultiplexing logic functions for computing signal processing tasks in synthetic biology
    Lorenzo Pasotti
    Dipartimento di Informatica e Sistemistica, Universita degli Studi di Pavia, Pavia, Italy
    Biotechnol J 6:784-95. 2011
    ..According to both the experimental and simulated results, guidelines for future finalization of mux and demux are provided...
  25. doi request reprint Mouse embryonic stem cells that survive γ-rays exposure maintain pluripotent differentiation potential and genome stability
    Paola Rebuzzini
    Laboratorio di Biologia dello Sviluppo, Dipartimento di Biologia Animale, Universita degli Studi di Pavia, Pavia, Italy
    J Cell Physiol 227:1242-9. 2012
    ..Overall, these results indicate a commitment of mESCs to maintain pluripotency and genome stability...
  26. ncbi request reprint Analysing Italian voluntary abortion data using a Bayesian approach to the time series decomposition
    Paolo Magni
    Dipartimento di Informatica e Sistemistica, Universita degli Studi di Pavia, Via Ferrata 1, Pavia, Italy
    Stat Med 23:105-23. 2004
    ..Finally, at the local level this analysis allows us to find similarities/differences between different areas in trends and/or in seasonal preferences...
  27. ncbi request reprint Reduced sampling schedule for the glucose minimal model: importance of Bayesian estimation
    Paolo Magni
    Dipartimento di Informatica e Sistemica, Universita degli Studi di Padova, I 35131 Padua, Italy
    Am J Physiol Endocrinol Metab 290:E177-E184. 2006
    ..g., excluding negative values) are obtained. They can be crucial for a subsequent use of the estimated MM parameters, such as in classification, clustering, regression, or risk analysis...
  28. ncbi request reprint Cholinergic regulation of neuropeptide Y synthesis and release in human neuroblastoma cells
    Elena Dozio
    Istituto di Endocrinologia, Center of Excellence on Neurodegenerative Diseases and Center for Endocrinological Oncology, University of Milan, Milano, Italy
    Peptides 29:491-5. 2008
    ..In conclusion, the present observations support the hypothesis that muscarinic receptor activation regulates the biosynthesis and secretion of NPY...
  29. ncbi request reprint Modulatory actions of neuropeptide Y on prostate cancer growth: role of MAP kinase/ERK 1/2 activation
    Massimiliano Ruscica
    Center for Endocrinological Oncology, Department of Endocrinology, University of Milan, Milan, Italy
    Adv Exp Med Biol 604:96-100. 2007
    ..The diagnostic and therapeutical value of targeting the NPY system in PCa will be evaluated in future studies...
  30. ncbi request reprint Leukemia inhibitory factor induces the chemomigration of immortalized gonadotropin-releasing hormone neurons through the independent activation of the Janus kinase/signal transducer and activator of transcription 3, mitogen-activated protein kinase/extrac
    Paolo Magni
    Department of Endocrinology, Center of Excellence on Neurodegenerative Diseases, University of Milan, via G Balzaretti, 9, 20133 Milano, Italy
    Mol Endocrinol 21:1163-74. 2007
    ..The present data, together with the observation that LIF and LIFRbeta are expressed prenatally in the mouse nasal compartment, would suggest that LIF might participate in the migration of GnRH neurons...
  31. ncbi request reprint Activation of the Y1 receptor by neuropeptide Y regulates the growth of prostate cancer cells
    Massimiliano Ruscica
    Istituto di Endocrinologia, via G Balzaretti, 9 20133 Milano, Italy
    Endocrinology 147:1466-73. 2006
    ..transient, and to the clone-specific involvement of other intracellular signals. These findings suggest that NPY-related mechanisms might play a relevant role in the progression of PCa, at both androgen dependent and independent stages...
  32. ncbi request reprint Comprehensive two-dimensional gas chromatography using large sample volume injection for the determination of polynuclear aromatic hydrocarbons in complex matrices
    Daniela Cavagnino
    Thermo Finnigan Italia S p A, Strada Rivoltana, Rodano, Milan 20090, Italy
    J Chromatogr A 1019:211-20. 2003
    ..A dedicated data system is presented for acquiring and managing GC x GC data: three-dimensional and color plot visualization, peaks integration, identification and quantitation are functions available with the software...
  33. ncbi request reprint Integrating model-based decision support in a multi-modal reasoning system for managing type 1 diabetic patients
    Stefania Montani
    DiSTA, Universita del Piemonte Orientale A Avogadro, Alessandria, Italy
    Artif Intell Med 29:131-51. 2003
    ..The system has been tested both on simulated and on real patients' data...
  34. ncbi request reprint In vitro cell growth pharmacodynamic studies: a new nonparametric approach to determining the relative importance of drug concentration and treatment time
    Massimiliano Germani
    Global Drug Metabolism, Pharmacia, Via Pasteur 10, 20014, Nerviano MI, Italy
    Cancer Chemother Pharmacol 52:507-13. 2003
    ..Therefore, a new, general, nonparametric approach was developed...
  35. ncbi request reprint Minimal model S(I)=0 problem in NIDDM subjects: nonzero Bayesian estimates with credible confidence intervals
    Gianluigi Pillonetto
    Dipartimento di Elettronica e Informatica, Universita degli Studi di Padova, 35131 Padova, Italy
    Am J Physiol Endocrinol Metab 282:E564-73. 2002
    ..This Bayesian approach should prove useful in reanalyzing large databases of epidemiological studies...