Alberto de la Fuente

alf_beard.jpg

Email: ( alf@crs4.it ) (I am fairly happy with my spam filter)


Research interests

Central to my research is the concept of 'networks' as an abstract representation of complex biochemical systems. Reverse engineering Gene Networks from gene-expression data has been and still is my main research interest. My current focus is on developing methodology for integrative analysis of gene expression and genotyping data ('Systems Genetics') to elucidate gene networks and predicting complex (disease) phenotypes, and identification of dysfunctional gene networks from disease gene expression data ('Differential Networking').


NEWS: DREAM DREAM DREAM DREAM

NEWS: Paperpublished in Nature Biotechnology

NEWS (1, 2, 3): SysGenSIMsoftware to simulate Systems Genetics data released

NEWS (1, 2, 3, 4): Alberto and his group had an honorary mention at the DREAM5 competition.

NEWS: Alberto and his group contributed the Systems Genetics challenges to the DREAM5 competition.

NEWS: Alberto and his group had a winning submission to the DREAM4 competition.


Peer reviewed journal articles

(jp25) Meyer, P., Alexopoulos, L.G., Bonk, T., Califano, A., Cho, C.R., de la Fuente, A., de Graaf, D., Hartemink, A.J., Hoeng, J., Ivanov, N.V., Koeppl, H., Linding, R., Marbach, D., Norel, R., Peitsch, M.C., Rice, J.J., Royyuru, A., Schacherer, F., Sprengel, J., Stolle, K., Vitkup, D., and Stolovitzky, G. (2011) Verification of systems biology research in the age of collaborative competition. Nature Biotechnology, 29(9): 811-815

(jp24) Pinna, A., Soranzo, N., De Leo, V. and de la Fuente, A. (2011) Elucidating Transcriptional Regulatory Networks from Heterogeneous Gene-Expression Compendia. Invited for PLoS ONE DREAM5 special collection.

(jp23) Pinna, A., Soranzo, N.,Hoeschele, I. and de la Fuente, A. (2011) Simulating system genetics data with SysGenSIM. Bioinformatics. 27(17), 2459-2462

(jp22) de la Fuente, A.(2011) Structure, Dynamics and Function - Dynamical Properties of Large Bio-Molecular Networks, The Open Bioinformatics Journal 5 (Special Issue #001, Editor: Alberto de la Fuente), 1–3

(jp21) Tieri, P., de la Fuente, A., Termanini, A., Franceschi, C (2011). Integrating Omics data for signaling pathways, interactome reconstruction, and functional analysis. Methods Mol Biol. 2011;719:415-33 (Rating 8 "must read" by Faculty of 1000)

(jp20) Pflieger, D., Gonnet, F., de la Fuente van Bentem, S., Hirt, H. and de la Fuente, A. (2011) Linking the proteins - Elucidation of proteome-scale networks using mass spectrometry. Mass Spectrometry Reviews, 30(2):268-97

(jp19) Pinna, A., Soranzo, N. and de la Fuente, A. (2010) From Knockouts to Networks: Establishing Direct Cause-Effect Relationships through Graph Analysis, PLoS ONE 5(10), e12912 (DREAM4 Special Collection)

(jp18) de la Fuente, A. (2010) From ‘differential expression’ to ‘differential networking’ – identification of dysfunctional regulatory networks in diseases. Trends in Genetics, 26(7) 326– 333

(jp17) Mentzen, W., Floris, M., and de la Fuente, A. (2009) Dissecting the dynamics of dysregulation of cellular processes in mouse mammary gland tumor. BMC Genomics 10: 601

(jp16) Baralla, A., Mentzen, W., and de la Fuente, A. (2009) Inferring Gene Networks: Dream or nightmare? Part 1: Challenges 1 and 3. Annals of the New York Academy of Sciences 1158: 246256

(jp15) Scheinine, A., Mentzen, W., Pieroni E., Fotia, G., Maggio, F., Mancosu, G. and de la Fuente, A. (2009) Inferring Gene Networks: Dream or nightmare? Part 2: Challenges 4 and 5. Annals of the New York Academy of Sciences 1158: 287301

(jp14) de la Fuente van Bentem, Mentzen, W., de la Fuente, A. and Hirt, H. (2008) Towards functional phosphoproteomics by mapping differential phosphorylation events in signalling networks. Proteomics 8(21): 44534465

(jp13) Liu, B., de la Fuente, A. and Hoeschele, I. (2008) Gene Network Inference via Structural Equation Modeling in Genetical Genomics Experiments. Genetics 178: 1763-1776

(jp12) Pieroni, E., de la Fuente van Bentem, S., Mancosu, G., Capobianco, E., Hirt, H., and de la Fuente, A. (2008) Protein networking: insights into global functional organization of proteomes. Proteomics 8(4): 799-816

(jp11) de la Fuente, A., Fotia, G., Maggio, F., Mancosu, G. and Pieroni E. (2008) Insights into Biological Information Processing: Structural and Dynamical Analysis of a Human Protein Signalling Network. Journal of Physics A: Mathematical and Theoretical 41: 224013

(jp10) Veiga, D.F., da Rocha Vicente, F.F., Grivet, M, de la Fuente, A., Ribeiro de Vasconcelos, A.T. (2007) Genome-wide Partial Correlation Analysis of Escherichia coli Microarray Data. Genetics and Molecular Research 6(4): 730-742

(jp9) de la Fuente, A. and Makhecha, D. P. (2006) Unravelling gene networks from noisy under-determined experimental perturbation data. IEE Proceedings Systems Biology 153(4): 257-262

(jp8) Mendes, P., Camacho, D., de la Fuente, A. (2005) Modelling and simulation for metabolomics data analysis. Biochem Soc Trans. Dec; 33(Pt 6): 1427-1429

(jp7) Camacho D., de la Fuente A., Mendes P. (2005) The origin of correlations in metabolomic data. Metabolomics 1(1): 53-63

(jp6) de la Fuente, A., Bing, N., Hoeschele, I. and Mendes, P. (2004) Discovery of meaningful associations in genomic data using partial correlation coefficients. Bioinformatics, 20(18):3565-3574 (supp info)(ParCorA executables for Windows, Linux, Solaris)

(jp5) de la Fuente, A. and Mendes, P. (2003) Integrative modelling of gene expression and cell metabolism. Applied Bioinformatics 2: 79-90

(jp4) Brazhnik, P., de la Fuente, A. and Mendes, P. (2002) Gene networks: how to put the function in genomics. Trends Biotechnology Nov; 20(11):467-472>

(jp3) de la Fuente, A., Snoep, J. L., Westerhoff H. V. and Mendes, P. (2002) Metabolic control in integrated biochemical systems. European Journal of Biochemistry, Sep; 269 (18): 4399-4408

(jp2) de la Fuente, A. and Mendes, P. (2002) Quantifying gene networks with regulatory strengths. Molecular Biology Reports 29 (1): 73-77

(jp1) de la Fuente, A., Brazhnik, P. and Mendes, P. (2002) Linking the genes: Inferring quantitative gene networks from microarray data. Trends in Genetics, Aug; 18(8): 395-398

Book chapters

(bc5) de la Fuente van Bentem, de la Fuente, A. and Hirt, H. (2010) Integrative Approaches to Elucidate and Analyze Protein Interaction and Signaling Networks, in Plant Stress Biology. Editor: Heribert Hirt, Wiley-VCH Verlag GmbH & Co. KGaA, 227-248

(bc4) de la Fuente A. (2009) What are Gene Regulatory Networks?, in Computational Methodologies in Gene Regulatory Networks. Editors: Sanjoy Das, Doina Caragea, W. H. Hsu, Stephen M. Welch, IGI Global, 1-17

(bc3) Liu, B., Hoeschele, I., de la Fuente A. (2009) Inferring Gene Regulatory Networks from Genetical Genomics Data, in Computational Methodologies in Gene Regulatory Networks. Editors: Sanjoy Das, Doina Caragea, W. H. Hsu, Stephen M. Welch, IGI Global, 79-107

(bc2) de la Fuente A., Brazhnik, P. and Mendes, P. (2004) Regulatory Strength Analysis for Inferring Gene Networks, in Metabolic Engineering in the Post Genomic Era, Chapter 5 pp107-137. Editors: Boris N. Kholodenko and Hans V. Westerhoff, Horizon Bioscience, January 2004.

(bc1) Mendes, P., de la Fuente, A. and Hoops, S. (2002) Bioinformatics and computational Biology for Plant Functional Genomics. Advances in Phytochemistry 36: 1-13

Conference papers and technical reports

(cp8) Baralla, A., de la Fuente, A., Cavaliere, M. (2008) Modeling and parameter estimation of the SOS response network in E. coli, Tecnical Report 01-2008, Microsoft Research - University of Trento Centre for Computational and Systems Biology.

(cp7) Hoeschele, I., Chetia, C., de la Fuente, A., Gao, G., Liu, B., Mao, Y., Stock, K.F. (2006) Genetic Architecture of Quantitative Traits, Annual Report of the Virginia Bioinformatics Institute

(cp6) Hoeschele, I., Gao, G., de la Fuente, A., Li, H., Mao, Y., Bing, N., Liu, B., Chetia, C. (2005) Genetic Architecture of Quantitative Traits, Annual Report of the Virginia Bioinformatics Institute

(cp5) Mendes, P., Camacho, D., de la Fuente, A., Hoops, S., Kamal, A., Lee, C., Li X. J., Martins, A. Mehrotra, B., Sha, W., Shibru, H., Singh, G., Srivastava, A., Tupe, S. (2005) Developing Strategies for Systems Biology, Annual Report of the Virginia Bioinformatics Institute

(cp4) Hoops, S., de la Fuente, A. and Mendes, P. (2003) Partial estimation of the Jacobian from time course data, in Proceedings of the 3rd workshop on Computation of Biochemical Pathways and Genetic Networks, Logos Verlag Berlin, 93-98

(cp3) de la Fuente, A., Brazhnik, P. and Mendes, P. (2001) A quantitative method for reverse engineering genetic regulatory networks from microarray experiments using regulatory strengths, in Proceedings of the 2nd International Conference for Systems Biology, Omnipress, 213-221

(cp2) de la Fuente, A., Brazhnik, P. and Mendes, P. (2001) Two complimentary methods for reverse engineering gene networks, in Proceedings of the 2nd workshop on Computation of Biochemical Pathways and Genetic Networks, Logos Verlag Berlin, 45-53

(cp1) de la Fuente, A., Mendes, P., Westerhoff, H.V. and Snoep, J.L. (2000) Can metabolic control analysis be applied to hierarchical regulated metabolism? MCA versus HCA, in BTK2000: Animating the cellular map, Stellenbosch University Press, 191-198

Presentations

(p11) Speaker at the joint conference: 5th Annual DREAM reverse engineering challenges, the 6th Annual RECOMB Satellite on Systems Biology, and the 7th Annual RECOMB Satellite on Regulatory Genomics , Columbia University, November 16-20, 2010. Title: The DREAM5 Systems Genetics challenges

(p10) Invited speaker at the seminar series of Instituto Dermopatico dell’Immacolata, Rome, Italy, May 19 2009. Title: Network oncology - identifying dysregulated regulatory networks in cancers

(p9) Invited speaker at the workshop Networks: Theory and Practice in Biology at ECCB08 22 September, 2008 - Title: Linking the genes

(p8) Invited speaker at Genopole seminar series, Evry, France, February 22, 2008 - Title: Deciphering bio-molecular networks

(p7) Speaker at StatPhys23 Satelite, Complex Networks: from Biology to Information Technology, Pula (Cagliari), Italy, July 2-6, 2007 - Title: Exploring a Web of Genes - Structure and Dynamics of a Yeast Gene Network

(p6) Invited speaker at Alliance fro the Advancement of Biomedical Research Execellence (AABRE) Seminar Tour, San Juan, Puerto Rico, February 14-16, 2006. Title: Linking the Genes - Strategies for inferring regulatory networks from data

(p5) Invited speaker at Systems Biology Seminar Series, Virginia Bioinformatics Institute, Virginia Tech, November 09, 2004, Title: Linking the Genes - two strategies for inferring gene networks

(p4) Invited speaker at Cambridge Healthtech Institute’s Annual Integrated Bioinformatics: High-throughput Interpretation of Pathways and Biology, Zurich, Switzerland, January 18, 2002, Title: A Quantitative Method to Reverse Engineer Gene Networks from Microarray Data

(p3) Speaker at 10th International BioThermoKineticsMeeting, Bordeaux, France, 2002

(p2) Speaker at 9th International BioThermoKinetics Meeting, Stellenbosch, South Africa, 2000

(p1) Poster presentations: ECCB/ICSB 2007, StatPhys23 Satelite 2007, FEBS SysBio 2005, ICSB 2001, 2004, BioThermoKinetics 2002, Recomb 2001, 2003, 2010


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