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About me

PROFESSIONAL EXPERIENCES

2017-now Associate Karolinska Institute, Division of Chemical Chemistry
2016-now Associate CNR IAC Rome
2015-now Systems Biology Coordinator at Personal Genomics spin-off University of Bologna and Verona, Italy;
2008-2014. Principal Investigator and Full Professor at Max Planck Institute- Chinese Academy of Science - Partner Institute for Computational Biology CAS-MPG PICB, Shanghai, China.
2007 Collaborator at the Telethon Institute for Genetics and Medicine (TIGEM) in Naples, Project on gene-network reverse-engineering.
2006- 2007. Research Assistant at the Department of Electronic Informatics and Systems (DEIS) at the University of Bologna. Research on complex diseases (Funded by PRIN 2004, Italian National Grant); Research on synthetic biology (Genetic Schmitt Trigger in E. coli, Funded by SYNBIOCOM, European Grant).
2005 Visiting Researcher at The Center for Translational Medical Systems at University of California San Diego (UCSD, USA), with Michael D. Kuo, MD, development of Radiogenomics.
2003-2004 – Visiting researcher at the Computer Science Department at Stanford University (CA, USA), with Prof Giovanni de Micheli. Development of data mining approaches applied to microarrays for gene expression analyses.
1999 - 2002. Field Engineer in the Cardiac Rhythm Management Division at Medtronic S.p.A. Assistance during implant and follow-up of patients with implantable devices for brady/tachy arrhythmias. Education activity on brady/tachy arrhythmias and cardiac stimulation for nurses and medical doctors in hospitals in  Emilia Romagna and Marche (Italy).

 

KNOWN LANGUAGES

Italian: mother tongue;
French: mother-tongue;
English: fluent;
German: intermediate level;
Chinese: beginner-intermediate (spoken).

Education

2002-2006 PhD in Electronics and Informatics at the University of Bologna. Thesis Title: “Statistical-Computational Techniques for Extraction of Functional Genomic Units from Microarray Experiments”.
1999 National Habilitation to Engineers Professional Activity.
1998 a.a EE Master Degree in Electrical Engineering – Biomedical specialization at the University of Bologna (90/100). Thesis title: “Identification of non-linear dynamics through space and time dependent neural networks”.
1992 – BS Degree at Istituto N. Copernico in Bologna (60/60).

Research description

My main interest is in the discovery, analysis and control of the regenerative and healing mechanisms that can be triggered to control autoimmune, chronic and degenerative diseases.
I am expert in the development, application and integration of methods from high-throughput data mining and network modeling to biological hypotheses validation on animal models and to the design of human clinical studies to take maximum advantage from the systems biology pipeline “from desk-to bench-to bed “.
To date I have focused on rheumatoid arthritis as a notable model disease with special attention to the variations occurring in blood and in the gut intestinal microbiome

Specialties: Translational Research; High throughput biological data mining; multi-omic data integration. Computational biology, biostatistics.

Teaching portfolio

February 23rd 2016, lecturer Winter School of Bologna on Biomarkers for Precision Medicine, “Biomarkers for Nanobiochips”.
2015 Lecturer for Advanced teaching at the International Master of Bioinformatics at the University of Bologna. Course title: “Omics & Multi-omics”
February 2015, lecturer Bologna Winter School on Bioinformatics and New Molecular Scenarios, “Are clustering and association rules enough for inferring causation”
February 2014, lecturer Bologna Winter School on complexity in Biology, “The added complexity of the gut intestinal microbiome”
2012 Lecturer for a module of the “Bioinformatics Algorithms” 1st year PICB course
2011 Lecturer for a module of the “Bioinformatics Algorithms” 1st year PICB course.
2011 Lecturer for the school Advanced Computational Biology
2009 Lecturer for a module of the “Bioinformatics Algorithms” 1st year PICB course.
2006 –Faculty for the refresher course ‘Integrating Cancer Genomics and Radiological Imaging: Practical Answers to Complex Problems (How-to Workshop)’, Conference RSNA Radiological Society of North America,
2007-2008 – Lecturer for the course ‘Biosensors’ at the University of Bologna for the Bioinformatics Degree in the Faculty of Mathematics Physics and Natural Sciences.
2006-2007 – Lecturer for the course ‘Biosensors’ at the University of Bologna for the Bioinformatics Degree in the Faculty of Mathematics Physics and Natural Sciences.

Documents

Links

Publications

Molecular Aging of Human Liver: An Epigenetic/Transcriptomic Signature
Bacalini Mg, Franceschi C, Gentilini D, Ravaioli F, Zhou X, Remondini D, et al
The journals of gerontology. Series A, Biological sciences and medical sciences 2018;():-

Aberrant methylation patterns in colorectal cancer: a meta-analysis
Durso Df, Bacalini Mg, Do Valle If, Pirazzini C, Bonafe M, Castellani G, et al
ONCOTARGET 2017;8(8):12820-12830

Acceleration of leukocytes' epigenetic age as an early tumor and sex-specific marker of breast and colorectal cancer
Durso Df, Bacalini Mg, Sala C, Pirazzini C, Marasco E, Bonafé M, et al
Oncotarget 2017;8(14):23237-23245

Dissection of the module network implementation "LemonTree": enhancements towards applications in metagenomics and translation in autoimmune maladies
Lu Yt, Zhou Xy, Nardini C
MOLECULAR BIOSYSTEMS 2017;13(10):2083-2091

Link prediction in complex networks via modularity-based belief propagation
Lai Dr, Shu X, Nardini C
CHINESE PHYSICS B 2017;26(3):-

Systemic evaluation of cellular reprogramming processes exploiting a novel R-tool: eegc
Zhou Xy, Meng Gf, Nardini C, Mei Hk
BIOINFORMATICS 2017;33(16):2532-2538

Systemic Wound Healing Associated with local subCutaneous Mechanical Stimulation (vol 6, 39043, 2017)
Nardini C, Devescovi V, Liu Yh, Zhou Xy, Lu Yt, Dent Je
SCIENTIFIC REPORTS 2017;:46118-

The emerging role of ECM crosslinking in T cell mobility as a hallmark of immunosenescence in humans
Moreau Jf, Pradeu T, Grignolio A, Nardini C, Castiglione F, Tieri P, et al
AGEING RESEARCH REVIEWS 2017;:322-335

The methylation of nuclear and mitochondrial DNA in ageing phenotypes and longevity
Bacalini Mg, D'aquila P, Marasco E, Nardini C, Montesanto A, Franceschi C, et al
MECHANISMS OF AGEING AND DEVELOPMENT 2017;:156-161

A corrected normalized mutual information for performance evaluation of community detection
Lai Dr, Nardini C
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT 2016;:-

A method for automated pathogenic content estimation with application to rheumatoid arthritis
Zhou Xy, Nardini C
BMC SYSTEMS BIOLOGY 2016;:107-

Correlation enhanced modularity-based belief propagation method for community detection in networks
Lai Dr, Shu X, Nardini C
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT 2016;:-

Systemic Wound Healing Associated with local sub-Cutaneous Mechanical Stimulation
Nardini C, Devescovi V, Liu Yh, Zhou Xy, Lu Yt, Dent Je
SCIENTIFIC REPORTS 2016;:39043-

Editorial: Multi-omic data integration
Nardini C, Dent J, Tieri P
Frontiers in cell and developmental biology 2015;3():46-

Mechanotransduction map: simulation model, molecular pathway, gene set
Dent Je, Devescovi V, Li H, Di Lena P, Lu Yt, Liu Yh, et al
BIOINFORMATICS 2015;31(7):1053-9

Exploring the molecular causes of hepatitis B virus vaccination response: an approach with epigenomic and transcriptomic data
Lu Yt, Cheng Y, Yan Wl, Nardini C
BMC MEDICAL GENOMICS 2014;:12-

i-Needle: Detecting the biological mechanisms of acupuncture
Nardini C, Carrara S, Liu Yh, Devescovi V, Lu Yt, Zhou Xy
SCIENCE 2014;346(6216):S21-S22

Multi-omic landscape of rheumatoid arthritis: re-evaluation of drug adverse effects
Tieri P, Zhou X, Zhu L, Nardini C
Frontiers in cell and developmental biology 2014;2():59-

From desk to bed: Computational simulations provide indication for rheumatoid arthritis clinical trials
Dent Je, Nardini C
BMC SYSTEMS BIOLOGY 2013;:10-

MIMO: an efficient tool for molecular interaction maps overlap
Di Lena P, Wu G, Martelli Pl, Casadio R, Nardini C
BMC BIOINFORMATICS 2013;:159-

Multilevel omic data integration in cancer cell lines: advanced annotation and emergent properties
Liu Yh, Devescovi V, Chen Sn, Nardini C
BMC SYSTEMS BIOLOGY 2013;:14-

Signalling pathway database usability: lessons learned
Tieri P, Nardini C
MOLECULAR BIOSYSTEMS 2013;9(10):2401-7

SPNConverter: a new link between static and dynamic complex network analysis
Dent Je, Yang Xy, Nardini C
BIOINFORMATICS 2013;29(19):2507-8

Understanding human diseases with high-throughput quantitative measurement and analysis of molecular signatures
Yang L, Wei G, Tang K, Nardini C, Han Jdj
SCIENCE CHINA-LIFE SCIENCES 2013;56(3):213-9

An S-System Parameter Estimation Method (SPEM) for Biological Networks
Yang Xy, Dent Je, Nardini C
JOURNAL OF COMPUTATIONAL BIOLOGY 2012;19(2):175-87

Brain cancer prognosis: independent validation of a clinical bioinformatics approach
Fronza R, Tramonti M, Atchley Wr, Nardini C
Journal of clinical bioinformatics 2012;2():2-

Inference of gene networks-application to Bifidobacterium
Lai Dr, Yang Xy, Wu G, Liu Yh, Nardini C
BIOINFORMATICS 2011;27(2):232-7

Joint analysis of transcriptional and post-transcriptional brain tumor data: searching for emergent properties of cellular systems
Fronza R, Tramonti M, Atchley Wr, Nardini C
BMC BIOINFORMATICS 2011;:86-

LEARNING OVERLAPPING COMMUNITIES IN COMPLEX NETWORKS VIA NON-NEGATIVE MATRIX FACTORIZATION
Lai Dr, Wu Xj, Lu Ht, Nardini C
INTERNATIONAL JOURNAL OF MODERN PHYSICS C 2011;22(10):1173-1190

Partitioning networks into communities by message passing
Lai Dr, Nardini C, Lu Ht
PHYSICAL REVIEW E 2011;83(1):016115-

A Comprehensive Molecular Interaction Map for Rheumatoid Arthritis
Wu G, Zhu Ls, Dent Je, Nardini C
PLOS ONE 2010;5(4):e10137-

Adapting functional genomic tools to metagenomic analyses: investigating the role of gut bacteria in relation to obesity
Liu Yh, Zhang Ch, Zhao Lp, Nardini C
BRIEFINGS IN FUNCTIONAL GENOMICS 2010;9(5-6):355-61

Enhanced modularity-based community detection by random walk network preprocessing
Lai Dr, Lu Ht, Nardini C
PHYSICAL REVIEW E 2010;81(6):066118-

Extracting weights from edge directions to find communities in directed networks
Lai Dr, Lu Ht, Nardini C
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT 2010;:-

Finding communities in directed networks by PageRank random walk induced network embedding
Lai Dr, Lu Ht, Nardini C
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS 2010;389(12):2443-2454

MANIA: A GENE NETWORK REVERSE ALGORITHM FOR COMPOUNDS MODE-OF-ACTION AND GENES INTERACTIONS INFERENCE
Lai Dr, Lu Ht, Lauria M, Di Bernardo D, Nardini C
ADVANCES IN COMPLEX SYSTEMS 2010;13(1):83-94

High Parallelism, Portability, and Broad Accessibility: Technologies for Genomics
Guiducci C, Nardini C
ACM JOURNAL ON EMERGING TECHNOLOGIES IN COMPUTING SYSTEMS 2008;4(1):-

Identification of noninvasive imaging surrogates for brain tumor gene-expression modules
Diehn M, Nardini C, Wang Ds, Mcgovern S, Jayaraman M, Liang Y, et al
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2008;105(13):5213-8

TOM: enhancement and extension of a tool suite for in silico approaches to multigenic hereditary disorders
Masotti D, Nardini C, Rossi S, Bonora E, Romeo G, Volinia S, et al
BIOINFORMATICS 2008;24(3):428-9

TOM: a web-based integrated approach for identification of candidate disease genes
Rossi S, Masotti D, Nardini C, Bonora E, Romeo G, Macii E, et al
NUCLEIC ACIDS RESEARCH 2006;:W285-92

Discovering coherent biclusters from gene expression data using zero-suppressed binary decision diagrams
Yoon S, Nardini C, Benini L, De Micheli G
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2005;2(4):339-54

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