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Group Leader

Biomedical Cybernetics

Machine learning and complex-network science for personalized and systems biomedicine

 Carlo Vittorio Cannistraci

The Biomedical Cybernetics Group adopts a transdisciplinary approach integrating information theory, machine learning and network science to investigate adaptive processes that characterize complex interacting systems at different scales, from molecules to organisms, in biology and medicine. This knowledge is leveraged to create novel and more efficient artificial intelligence algorithms; and to perform advanced analysis of patterns hidden in biomedical data, signals and images. Our theoretical effort is to translate advanced mathematical paradigms typically adopted in theoretical physics (like topology and manifold theory) to characterize many-body interactions in quantitative biology. We apply the theoretical frameworks we invent in the mission to develop computational tools for systems and network biology, personalized biomedicine and combinatorial drug therapy.

Research Scope

Plasticity phenomena - like remodelling, growth and evolution - modify the topology of complex systems, their internal state and their multidimensional representation in form of networks or high-dimensional datasets. Our theoretical mission is to elucidate the general rules and mechanisms that underlie this type of structural plasticity, which is at the basis of learning and memory processes in living organisms. In particular, we develop methods for topological analysis of self-adaptive and self-organizing learning systems such as protein interaction and epigenetic networks at the molecular level, and brain networks at the cellular level.

In neuroscience, we are interested in how the brain networks wire at synaptic and functional levels to modulate learning processes. And, on a molecular pathway scale, we seek to identify the network patterns that could suggest which broken functional-modules are responsible for memory aberrations in neurodegenerative diseases. Since general paradigms of regeneration and degeneration can be significantly inspired by developmental biology models, we study regulatory patterns of tissue differentiation in normal and cancer conditions. Lastly, as the cardiovascular system is a paradigmatic example of an adaptive complex system, we apply our pattern recognition algorithms to explore normal/pathological conditions in cardiovascular patients.

Finally, our mission in translation and network medicine is to adopt advanced machine learning and network science approaches to integrate molecular networks and genomic profiles for the definition of personalised therapeutical plans and individualised drug treatments.

Curriculum Vitae

February 2014 to present

Biotechnologisches Zentrum (BIOTEC), Technische Universität Dresden (TUD), Tatzberg 47/49, 01307 Dresden. Research Group Leader of the Biomedical Cybernetics Group.

 

 

August 2013  to January 2014

King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia

Researcher Scientist in intelligent systems and complex-network science for personalized biomedicine.

 

July 2010 to July 2013

King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia

Postdoctoral Researcher in information theory and machine learning applied in systems and network biology.

 

January 2009 to December 2009

University of California San Diego (UCSD), Department of Bioengineering, California, USA

Visiting Scholar, Trey Ideker Lab of Integrative Systems Biology, http://idekerlab.ucsd.edu/ Research Focus: Complex Systems Theory, Machine Learning and Information Theory applied in Systems Biology.

 

January 2007 to February 2010

Doctorate student in Biomedical Engineering of the Scuola Interpoltecnica di Dottorato (SIPD, http://sipd.polito.itwith specialization in Computational, Systems and Network Biology. A prestigious project organized by the three Italian Technical Universities, the Polytechnic School of Turin, Bari and Milan. The most talented candidates were selected in order to participate in international relations, cooperation programs, and high level research projects. Every selected candidate was granted €13.000 to spend within three years for personal research.

 

March 2006 to March 2010

Proteome Biochemistry Lab, San Raffaele Scientific Institute, Milan, Italy

Researcher, Project: Development of computational biology approaches for quantitative analysis, pattern recognition and classification of experimental biological data.

 

October 2005 to February 2006

Biomedical Engineering Institute of the Italian National Research Council (ISIB-CNR, Milan department) www.isib.cnr.it, Milan, Italy

Researcher, Project: Development of algorithms for quantitative analysis and classification of experimental data from proteomics studies in neuroplasticity and neurodegenerative diseases.

 

October 2005

Polytechnic School of Milan, Milan, Italy

Master’s Degree in Bioengineering

 

October 2004 to October 2005

Neurobiology of Learning Lab, San Raffaele Scientific Institute, Milan, Italy

Period of Internship. Project: Development of methods for detection and analysis of the electrical signals of synaptically connected neurons and advanced proteomic analysis of brain synapses.

Publications

Selected Publications, Theory: information theory, machine learning and network topology

From link-prediction in brain connectomes and protein interactomes to the local-community-paradigm in complex networks
CV Cannistraci, G Alanis-Lobato, T Ravasi
Scientific reports 3, 2013

 

Minimum curvilinearity to enhance topological prediction of protein interactions by network embedding
CV Cannistraci, G Alanis-Lobato, T Ravasi
Bioinformatics 29 (13), i199-i209, 2013

 

Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes
CV Cannistraci, T Ravasi, FM Montevecchi, T Ideker, M Alessio
Bioinformatics 26 (18), i531-i539, 2010

 

Median‐modified Wiener filter provides efficient denoising, preserving spot edge and morphology in 2‐DE image processing
CV Cannistraci, FM Montevecchi, M Alessio
Proteomics 9 (21), 4908-4919, 2009

 

Selected Publications, Application: systems biology and personalized medicine

Questing for Circadian Dependence in ST-Segment–Elevation Acute Myocardial Infarction A Multicentric and Multiethnic Study
E Ammirati, N Cristell, D Cianflone, AC Vermi, G Marenzi,..., and CV Cannistraci

Circulation research 112 (10), e110-e114, 2013

 

Pivotal role of the muscle-contraction pathway in cryptorchidism and evidence for genomic connections with cardiomyopathy pathways in RASopathies
CV Cannistraci, J Ogorevc, M Zorc, T Ravasi, P Dovc, T Kunej
BMC medical genomics 6 (1), 5, 2013

 

Identification and Predictive Value of Interleukin-6+ Interleukin-10+ and Interleukin-6− Interleukin-10+ Cytokine Patterns in ST-Elevation Acute Myocardial Infarction
E Ammirati*, CV Cannistraci*, NA Cristell, V Vecchio, AG Palini, P Tornvall ...
Circulation Research 111 (10), 1336-1348, 2012

*first co-authorship

 

Ceruloplasmin oxidation, a feature of Parkinson's disease CSF, inhibits ferroxidase activity and promotes cellular iron retention
S Olivieri, A Conti, S Iannaccone, CV Cannistraci, A Campanella, M Barbariga ...
The Journal of Neuroscience 31 (50), 18568-18577, 2011

 

An atlas of combinatorial transcriptional regulation in mouse and man
T Ravasi*, H Suzuki*, CV Cannistraci*, et al.
Cell 140 (5), 744-752, 2010

*first co-authorship

 

 

For a complete list of publications
http://scholar.google.com/citations?user=b7xoXO0AAAAJ&hl=en

Awards

2013, ISMB/ECCB, Berlin, international travel Fellowship

2011ISMB/ECCB, Vienna, international travel  Fellowship

2010ECCB, Ghent, international travel Fellowship

2009, ISMB/ECCB, Stockholm, international travel Fellowship

2009, Growth factors and Signal Transduction (GFST) Conference, Iowa State University, international travel Fellowship

2007, Scuola Interpolitecnica di Dottorato (SIPD) PhD Research Scholarship

2005, Biomedical Engineering Institute of the Italian National Research Council (ISIB-CNR), Research Fellowship

Talks

2013: TBC/ISCB-Asia, Seoul, Korea, Selected Talk in Highlights track

2013: ISMB/ECCB, Berlin, Germany, Selected Talk in Highlights track

2013: ISMB/ECCB, Berlin, Germany, Selected talk in Proceedings track (and article publication in Bioinformatics)

2013: The 7th International Workshop on Machine Learning in Systems Biology (MLSB13), ISMB/ECCB Special Interest Group, Berlin, Germany, Contributed Talk

2013: KAUST-McGill Research Workshop, King Abdullah University of Science and Technology (KAUST), Saudi Arabia, Invited Speaker

2013: NetSci, satellite symposium "Complex Networks meet Machine Learning", Copenhagen, Denmark, Contributed Talk

2013: Bioinformatics Workshop for Health and Population Genomics Research, University of Philippines, Diliman, Invited Speaker

2013: Workshop in Network Theory and Paradigms in Complex Systems, King Abdullah University of Science and Technology (KAUST), Saudi Arabia, Invited Speaker

2012: ISMB/ECCB, Vienna, Austria, Selected talk in the Highlights track

2010: ECCB, Ghent, Belgium, Selected talk in Proceedings track (and article publication in Bioinformatics)

Open Positions (Join our Group)

Coming soon

Group Members

All current group members are listed on the Staff Page.

Teaching

Lecture materials can be downloaded here.

Contact

Dr. Ric. Ing. Carlo Vittorio Cannistraci

Head of the Biomedical Cybernetics Group

Biotechnology Center (BIOTEC)

Technische Universität Dresden

Tatzberg 47/49

01307 Dresden

Germany

Tel: +49 (0) 351 463-40080

Fax: +49 (0) 351 463-40087

Email: carlo.cannistraci[at]biotec.tu-dresden.de

 

Jana Fischer
Administration Assistant
Biotechnologisches Zentrum (BIOTEC)
Technische Universität Dresden
Tatzberg 47/49
01307 Dresden

Germany
Tel.: +49 (0) 351 463-40047
Fax.: +49 (0) 351 463-40038
Email: jana.fischer[at]biotec.tu-dresden.de

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