Group of Clinical Genomic Networks - Publications

Department of  Combinatorics and Geometry - CAS-MPG Partner Institute for Computational Biology


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 ACM Copyright

APS Copyright


Peer-Reviewed Publications



Y. Xinyi, J. E. Dent, C. Nardini, An S-System Parameter Estimation Method for Biological Networks -SPEM, Journal of Computational Biology, 2012, 19(2): 175-187. doi:10.1089/cmb.2011.0269 [PDF]


R. Fronza, M. Tramonti, W. R Atchley and C. Nardini*, Brain Cancer Prognosis: Independent Validation of a Clinical Bioinformatics Approach, Journal of Clinical Bioinformatics 2012, 2:2 [PDF]


Zhu L., del Vecchio G., Liu Y. de Micheli G., Carrara S., Calza L., Nardini C*. Biochip for regenerative medicine: real time stem cell continuous monitoring as inferred by high-throughput Gene Analysis, Springer Bionanoscience Volume 1, Issue 4 (2011), Page 183-191 10.1007/s12668-011-0028-z [PDF]


D. Lai*, X. Wu, H Lu, C Nardini Learning overlapping communities in complex networks via non-negative matrix factorization, International Journal of Modern Physics C (IJMPC), Issue 2210), 2011


R. Fronza, M. Tramonti, W. R Atchley and C. Nardini, Joint Analysis of Transcriptional and post- Transcriptional Data: Searching Emergent Properties in Brain Tumor Samples, BMC Bioinformatics, 2011, 12:86doi:10.1186/1471-2105-12-86 HIGHLY ACCESSED [PDF]


D.Lai, C. Nardini, H. Lu,  Partitioning networks into communities by message passing, Physical Review E, 2011, 83 016115.[PDF]


D. Lai, X. Yang, G. Wu, Y. Liu, C. Nardini, Inference of Gene Networks - application to Bifidobacterium, Bioinformatics, 2010, doi: 10.1093/bioinformatics/btq629 [link


D.Lai*, H. Lu, and C. NardiniEnhanced modularity-based community detection by random walk network
   preprocessing, Physical Review E,
81(6 Pt 2):066118 [PDF]


D. Lai*, H. Lu, C. Nardini,  Extract weights from edge directions to find communities in directed networks, JSTAT, 2010, doi: 10.1088/1742-5468/2010/06/P06003  [PDF]  © copyright (2010) IOP Publishing Ltd


Y. Liu, C. Zhang, L, Zhao and C. Nardini*, Adapting Functional Genomic  Tools to Metagenomic Analyses: Investigating the Role of Gut Bacteria in the Onset of Obesity, Briefings in Functional Genomics and Proteomics, 2010, doi: 10.1093/bfgp/elq011[link]


G. Wu, L. Zhu, J. E. Dent, C. Nardini*, A Comprehensive Molecular Interaction Map for Rheumatoid Arthritis, PLoS ONE, 2010, 5(4): e10137. doi:10.1371/journal.pone.0010137 [link]


D. Lai*, H. Lu, C. Nardini, Finding Communities in Directed Networks by PageRank Random Walk Induced Network Embedding, Physica A, 2010, 389(12), p. 2443-2454, doi:10.1016/j.physa.2010.02.014 [PDF]


D. Lai, H. Lu, M. Lauria, D. di Bernardo, C. Nardini*, MANIA: A Gene Network Reverse Algorithm for Compounds Mode-of-Action and Genes Interactions Inference, Advances In Complex Systems (ACS), Vol 13, Issue1, 2010 [PDF] Electronic version of the article published  © copyright World Scientific Publishing Company



C. Nardini*, H. Peng, L. Wang, L. Benini, M.D. Kuo, MM-Correction: Meta-analysis-Based Multiple Hypotheses Correction in Omic StudiesSpringer CCIS, Vol 25, pp 242-255, 2008.


M. Diehn, C. Nardini, D.S. Wang, S. McGovern, M. Jayaraman, Y. Liang, K. Aldape, S. Cha, M. D. Kuo* Identification of non-invasive imaging surrogates for brain tumor gene expression modules, Proc. Natl. Acad. Sci., 2008, 105(13), p. 5213-5218. [PDF]


C. Guiducci*, C. Nardini*, High Parallelism, Portability and Broad Accessibility: Technologies for Genomics, ACM Journal on Emerging Technologies in Computing Systems, 2008, 4(1), Article 3. [PDF]


D. Masotti*, C. Nardini, S. Rossi, E. Bonora, G. Romeo, S. Volinia and L. Benini, TOM: enhancement and extension of a tool suite for in silico approaches to multigenic complex disorders, Bioinformatics, 2008, 24(3), p. 428-429, doi: 10.1093/bioinformatics/btm588.[link]


C. Nardini*, L. Benini and M. D. Kuo, Statistical Significance in omic data analyses, Proceedings of International Conference on bio-inspired systems and signal processing Biosignals2008, Portugal. [PDF]


C. Nardini*, L. Benini and G. de Micheli, Circuits and Systems for High-Throughput Biology, IEEE Circuits and Systems Magazine, 2006, 6(3), p.10-20. [PDF]


C. Nardini*, D. Masotti, S. Yoon, E. Macii, M.D. Kuo, G. de Micheli and L. Benini, Mining gene sets for measuring similarities, Proceedings of IEEE Symposium on Computers and Communications (ISCC), 2006.[PDF]


M. Diehn*, C. Nardini, D.S. Wang, A. Hsiao, S. Cha and M.D. Kuo Neuroimaging Characteristics Reflect Tumor Gene Expression Signatures and Predict Survival in Glioblastoma Multiforme, International Journal of Radiation Oncology Biology Physics, 2006, 66(3), p. S18.[link]


S. Rossi*-D. Masotti*, C. Nardini, E. Bonora, G. Romeo, E. Macii, L. Benini and S. Volinia, TOM: a web-based integrated approach for efficient identification of candidate disease genes, Nucleic Acids Res., 2006, 34, p. W285 - W292; doi:10.1093/nar/gkl340. [PDF]


S. Yoon*, C. Nardini, L. Benini and G. de Micheli, Discovering coherent biclusters from gene Expression Data Using Zero-Suppressed Binary Decision Diagrams, The IEEE/ACM Transaction on Computational Biology and Bioinformatics, 2005, 3(2), p.339-354.[PDF]


S. Yoon*, C. Nardini, L. Benini and G. de Micheli. Enhanced pClustering and its applications to gene expression data, In Proceedings of IEEE Symposium on BIBE (Bioinformatics and Bioengineering), 2004, p. 275-282.[PDF]


Bioinformatics-Related International Conferences:


M. Lauria, C. Nardini, D. di Bernardo, Simultaneous gene network and mode of action inference with mNIr, International Conference on Systems Biology (ICSB) 2007, Abstract for Poster.


S. Rossi, D. Masotti, C. Nardini, E. Bonora, E. Macii, S. Volinia, L. Benini, Integrated web-based approach to multigenic diseases, Consortium for Post Genome Science Conference, Manchester, 2006.


S. Volinia, S. Rossi, D. Valentini, G. Gamberoni, S. Storari, L. Benini, C. Nardini, D. Masotti, C. Camaschella, P. Gasperini, TOM: Transcriptomics of OMIM, Microarray Gene Expression Data Society Conference, 2005.


Medical Conferences:


DS Wang, C Nardini, M Diehn, S Cha, S McGovern, M D. Kuo, K Aldape, Integrative Radiogenomic Analysis of Glioblastoma Multiforme to Identify a MR Imaging Biomarker for EGFR Overexpression, Radiological Society of  Nord America, Book of Abstracts.


M.D. Kuo, M. Diehn, C. Nardini, D. Wang, S. Cha, Integrative Radiogenomic Analysis to Identify a Non-Invasive Imaging Phenotype Associated with EGFR Overexpression in Glioblastoma Multiforme, American Society Of Neuro Radiology, Book of Abstracts,  2006.


C. Nardini, M. Diehn, L Benini, M. D. Kuo, Degree of mass effect by MRI in glioblastoma multiforme can predict the gene expression level of a cell proliferation gene expression program, European Congress of Radiology, Book of Abstracts, Vol, 16, Suppl.1, pag. B-100, 2006.


C. Nardini, M. Diehn, L Benini, M. D. Kuo, A method for extracting sets of genes related to Magnetic Resonance Imaging (MRI) features significantly enriched for known biological function, International Oncology Symposium, Radiological Society of North America, 2005, p. 88.


M. D. Kuo, C. Nardini, D. Wang, L Benini, G De Micheli, S. Cha, M. Diehn, MRI Guided Feature Evaluation of Characteristic Gene Expression Signatures in Glioblastoma Multiforme, European Congress of Radiology, Book of Abstracts, Vol, 15, Suppl.1, pag. B-439, 2005.


C. Nardini, M. Diehn, B. K. Chan, G. De Micheli, L. Benini, M. D. Kuo, Imaging Correlation with Alterations in Global Gene Expression for Functional Radiogenomic Analysis, Radiological Society of  Nord America, Book of Abstracts, p. 403, 2004.


M. D. Kuo, D. S. Wang, C. Nardini, M. Diehn, B. K. Chan, Identification of Alterations in Global Gene Expression in Glioblastoma Multiforme with Magnetic Resonance Imaging, Radiological Society of  Nord America, Book of Abstracts, p. 533, 2004.


C. Nardini, S. Cha, D. Wang, M. Diehn, L. Benini, G. De Micheli, M. Kuo, A Non-Invasive Approach for Molecular Characterization of Glioblastoma Multiforme: Magnetic Resonance Imaging Correlation with cDNA Microarray Expression Profiles, American Association of Neurological Surgeons,  Article ID: 22678, 2004.


D. S. Wang, S. Cha, C. Nardini, M. Diehn, B. K. Chan, L. Benini, G. De Micheli, M. D. Kuo, Correlation between global gene expression patterns and magnetic resonance imaging findings in glioblastoma multiforme; Society for Neuro Oncology, Book of Abstracts,  p. 340, 2004.



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