Nicola Soranzo

Nicola Soranzo, Ph.D.
Data Infrastructure & Algorithms group
The Genome Analysis Centre (TGAC)
Norwich Research Park, Norwich, NR4 7UH, UK
http://www.tgac.ac.uk/sequencing-informatics/

Email: <nicola.soranzo AT tgac DOT ac DOT uk>

Research interests

I am mainly interested in the bioinformatics web platform Galaxy and in systems biology (simulation and inference of gene regulatory networks, chemical reaction network theory, dynamical models in biology).

My CV.

Publications

Journal papers

  • J. Ding, L. M. Reynolds, T. Zeller, C. Müller, K. Lohman, B. J. Nicklas, S. B. Kritchevsky, Z. Huang, A. de la Fuente, N. Soranzo, R. E. Settlage, C.-C. Chuang, T. Howard, N. Xu, M. O. Goodarzi, Y.-D. I. Chen, J. I. Rotter, D. S. Siscovick, J. S. Parks, S. Murphy, D. R. Jacobs Jr., W. Post, R. P. Tracy, P. S. Wild, S. Blankenberg, I. Hoeschele, D. Herrington, C. E. McCall, Y. Liu
    "Alterations of a Cellular Cholesterol Metabolism Network Are a Molecular Feature of Obesity-Related Type 2 Diabetes and Cardiovascular Disease"
    Diabetes 64(10), pp. 3464-3474, 2015
    Article

  • P. J. A. Cock, J. M. Chilton, B. Grüning, J. E. Johnson, N. Soranzo
    "NCBI BLAST+ integrated into Galaxy"
    GigaScience, 4:39, 2015
    Article

  • L. M. Reynolds, J. Ding, J. R. Taylor, K. Lohman, N. Soranzo, A. de la Fuente, T. F. Liu, C. Johnson, R. G. Barr, T. C. Register, K. M. Donohue, M. V. Talor, D. Cihakova, C. Gu, J. Divers, D. Siscovick, G. Burke, W. Post, S. Shea, D. R. Jacobs Jr, I. Hoeschele, C. E. McCall, S. B. Kritchevsky, D. Herrington, R. P. Tracy, Y. Liu
    "Transcriptomic profiles of aging in purified human immune cells"
    BMC Genomics 16:333, 2015
    Article

  • S. Leo, L. Pireddu, G. Cuccuru, L. Lianas, N. Soranzo, E. Afgan, G. Zanetti
    "BioBlend.objects: metacomputing with Galaxy"
    Bioinformatics 30(19), pp. 2816-2817, 2014
    Article, Software

  • G. Cuccuru, M. Orsini, A. Pinna, A. Sbardellati, N. Soranzo, A. Travaglione, P. Uva, G. Zanetti, G. Fotia
    "Orione, a web-based framework for NGS analysis in microbiology"
    Bioinformatics 30(13), pp. 1928-1929, 2014
    Article

  • P. Meyer, T. Cokelaer, D. Chandran, K. H. Kim, P.-R. Loh, G. Tucker, M. Lipson, B. Berger, C. Kreutz, A. Raue, B. Steiert, J. Timmer, E. Bilal, DREAM 6&7 Parameter Estimation consortium (..., N. Soranzo, ...), H. Sauro, G. Stolovitzky, J. Saez-Rodriguez
    "Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach"
    BMC Syst. Biol. 8:13, 2014
    Article

  • D. Marbach, J. C. Costello, R. Küffner, N. M. Vega, R. J. Prill, D. M. Camacho, K. R. Allison, The DREAM5 Consortium (..., N. Soranzo, ...), 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

  • A. Pinna, N. Soranzo, A. de la Fuente, I. Hoeschele
    "Simulation of the Benchmark Datasets"
    In A. de la Fuente (ed.) Gene Network Inference, Springer, Berlin Heidelberg, Germany, pp. 1-8, 2013
    Chapter

  • 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

  • L. Pireddu, S. Leo, N. Soranzo, G. Zanetti
    "A Hadoop-Galaxy adapter for user-friendly and scalable data-intensive bioinformatics in Galaxy"
    Proc. of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, pp. 184-191, Newport Beach, CA, USA, September 2014
    Article

  • 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
    Article

  • M. Zampieri, N. Soranzo, C. Altafini
    "Modeling the genome-wide transient response to stimuli in yeast: adaptation through integral feedback"
    Proc. of the 47th 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, 7th IFAC Symposium on Nonlinear Control Systems, Pretoria, South Africa, 2007
    Article

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

  • "Scripting Galaxy using the API and BioBlend"
    Galaxy Community Conference 2015, Norwich, UK, 2015

  • "BioBlend and BioBlend.objects: high level API for scripting Galaxy"
    1st German Galaxy Developer workshop, Freiburg im Breisgau, Germany, October 2014

  • "Techniques for the inference of large-scale gene networks"
    Invited speaker at the 2nd 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 4th DREAM reverse engineering challenges, Cambridge, MA, USA, 2009

HowTos

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

Software patches

I publish here some patches I have developed for various software, 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 software

Patch description

Download link

GSCA 1.1.1 (R package)

Add NAMESPACE file

GSCA.patch

Netsim 1.5.1 (R package)

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

RMatlab 0.2-5 (R package)

Tons of bugfixes and Mac OS X experimental support, see NEWS file after applying the patch

RMatlab_20111026.patch

ROCR 1.0-5 (R package)

Patch adding a new performance measure: area under the precision/recall curve

ROCR_auprc.patch

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


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BioWiki: NicolaSoranzo (last edited 2016-03-31 19:13:49 by NicolaSoranzo)