Nicola Soranzo

Nicola Soranzo, Ph.D.
CRS4 Bioinformatics Program
Loc. Piscina Manna
09010 Pula (CA), Italy

Email: <soranzo AT crs4 DOT it>

Tel.: +39 070 9250 430
Fax: +39 070 9243 3200

Research interests

I am mainly interested in systems biology (simulation and inference of gene regulatory networks, chemical reaction network theory, dynamical models in biology), bioinformatics (analysis of microarray data and pathway databases) and systems genetics.

My CV.

Publications

Journal papers

D. Marbach, J. C. Costello, R. Küffner, N. M. Vega, R. J. Prill, D. M. Camacho, K. R. Allison, The DREAM5 Consortium, M. Kellis, J. J. Collins, G. Stolovitzky
"Wisdom of crowds for robust gene network inference"
Nat. Methods 9(8), pp. 796-804, 2012
Article
N. Soranzo, F. Ramezani, G. Iacono, C. Altafini
"Decompositions of large-scale biological systems based on dynamical properties"
Bioinformatics 28(1), pp. 76-83, 2012
Article
A. Pinna, N. Soranzo, I. Hoeschele, A. de la Fuente
"Simulating systems genetics data with SysGenSIM"
Bioinformatics 27(17), pp. 2459-2462, 2011
Article, Software
A. Pinna, N. Soranzo, A. de la Fuente
"From Knockouts to Networks: Establishing Direct Cause-Effect Relationships through Graph Analysis"
PLoS ONE 5(10), e12912, 2010
Article
G. Iacono, F. Ramezani, N. Soranzo, C. Altafini
"Determining the distance to monotonicity of a biological network: a graph-theoretical approach"
IET Syst. Biol. 4(3), pp. 223-235, 2010
Article, Supplements
N. Soranzo, C. Altafini
"ERNEST: a toolbox for chemical reaction network theory"
Bioinformatics 25(21), pp. 2853-2854, 2009
Article, Software and supplements
N. Soranzo, M. Zampieri, L. Farina, C. Altafini
"mRNA stability and the unfolding of gene expression in the long-period yeast metabolic cycle"
BMC Syst. Biol. 3:18, 2009
Article
M. Zampieri, N. Soranzo, D. Bianchini, C. Altafini
"Origin of Co-Expression Patterns in E.coli and S.cerevisiae Emerging from Reverse Engineering Algorithms"
PLoS ONE 3(8), e2981, 2008
Article
M. Zampieri, N. Soranzo, C. Altafini
"Discerning static and causal interactions in genome-wide reverse engineering problems"
Bioinformatics 24(13), pp. 1510-1515, 2008
Article
N. Soranzo, G. Bianconi, C. Altafini
"Comparing association network algorithms for reverse engineering of large-scale gene regulatory networks: synthetic versus real data"
Bioinformatics 23(13), pp. 1640-1647, 2007
Article, Software and supplements

Book chapters

V. de Leo, F. Ricci, N. Soranzo, A. Chessa, A. de la Fuente
"Disentangling the Proteome: Re-Evaluations of Topological Insights from Yeast Protein Interaction Networks"
In L. V. Berhardt (ed.) Advances in Medicine and Biology, vol. 16, Nova Science, Hauppauge, NY, USA, pp. 141-166, 2011
Chapter

Conference papers

F. Ramezani, G. Iacono, N. Soranzo, C. Altafini
"On the distance to monotonicity of a biological network: a graph-theoretical approach"
Proc. of the European Control Conference 2009, Budapest, Hungary, August 2009
M. Zampieri, N. Soranzo, C. Altafini
"Modeling the genome-wide transient response to stimuli in yeast: adaptation through integral feedback"
Proc. of the 47^th IEEE Conference on Decision and Control, Cancun, Mexico, December 2008
N. Soranzo, M. Zampieri, D. Bianchini, C. Altafini
"Network inference from gene expression profiles: what “physical” network are we seeing?"
Proc. of FOSBE 2007, Stuttgart, Germany, 2007
N. Soranzo, G. Bianconi, C. Altafini
"Linear and nonlinear methods for gene regulatory network inference"
Proc. of NOLCOS 2007, 7^th IFAC Symposium on Nonlinear Control Systems, Pretoria, South Africa, 2007

PhD thesis

"Systems biology approaches to the dynamics of gene expression and chemical reactions"
Ph.D in Functional and Structural Genomics, SISSA
Supervisor: C. Altafini

Presentations

"Techniques for the inference of large-scale gene networks"
Invited speaker at the 2^nd Joint Summer School on Biology, Computation and Information, Udine, Italy, 2012
"From Knockouts to Networks - Establishing Direct Cause-effect Relationships Through Graph Analysis"
Invited speaker at the 4^th DREAM reverse engineering challenges, Cambridge, MA, USA, 2009

HowTos

How to export scientific (Media)Wiki pages to PDF with mwlib.rl

Patches for R packages

I publish here some patches I have developed for various R packages, which may be useful for other people. I have already submitted them to the relative maintainers, but they have not been accepted upstream yet.

Original R package	Description	Download link
GSCA 1.1.1	Add NAMESPACE file	GSCA.patch
hdf5 1.6.9	Patch to fix the linking to the hdf5 library when it is installed in a non-standard path	hdf5_linking.patch
RMatlab 0.2-5	Tons of bugfixes and Mac OS X experimental support, see NEWS file after applying the patch	RMatlab_20111026.patch
ROCR 1.0-5	Patch adding a new performance measure: area under the precision/recall curve	ROCR_auprc.patch
Netsim 1.5.1	Better packaging, unbundled muParser library, updated FindGLIB2.cmake, added FindmuParser.cmake, made compatible with both muParser 1.x and 2.x, miscellaneous bugfixes	netsim.gui_1.5.3.tar.gz

To update one of these R packages with the relative patch, you need to download the patch and the original package source tarball, then execute in a shell:

# tar xzf PACKAGE_VERSION.tar.gz
# patch -d PACKAGE/ -p1 < PATCHFILE
# tar czf PACKAGE_VERSION.tar.gz PACKAGE/
# rm -rf PACKAGE/

Finally, you can install the updated package as usual, for example with:

# R CMD INSTALL PACKAGE_VERSION.tar.gz

CategoryHomepage