Home

Publications CRS4

Modifier la recherche

Format imprimable

Votre sélection

47 publications Download the selection

Publications en 2015

Peer-reviewed publications in International Journals

[2-RJT15]

Transcriptomic profiles of aging in purified human immune cells

Lindsay M Reynolds, Ding J., Jackson R Taylor, Kurt Lohman, Nicola Soranzo, Alberto de la Fuente, Tie Fu Liu, Craig Johnson, R Graham Barr, Thomas C Register, Kathleen M Donohue, Monica V Talor, Daniela Cihakova, Charles Gu Charles, David Siscovick, Gregory Burke, Wendy Post, Steven Shea, David R Jacobs, Ina Hoeschele, David Herrington, Russell P Tracy, Yongmei Liu

BMC Genomics - 2015 doi: 10.1186/s12864-015-1522-4

[2-JRD15]

Alterations of a cellular cholesterol metabolism network is a molecular feature of obesity-related type 2 diabetes and cardiovascular disease

Ding J., Lindsay M Reynolds, Alberto de la Fuente, Nicola Soranzo, Ina Hoeschele, David Herrington, Charles E McCall, Yongmei Liu

Diabetes - 2015 doi: 10.2337/db14-1314

Publications en 2014

Peer-reviewed publications in International Journals

[2-MCC14]

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach

Pablo Meyer, Thomas Cokelaer, Deepak Chandran, Kyung Hyuk Kim, Po-Ru Loh, George Tucker, Mark Lipson, Bonnie Berger, Clemens Kreutz, Andreas Raue, Bernhard Steiert, Jens Timmer, Erhan Bilal, Alberto de la Fuente, Andrea Pinna, Nicola Soranzo, Herbert M. Sauro, Gustavo Stolovitzky, Julio Saez-Rodriguez

BMC Systems Biology pages 13 vol. 8 - 2014 doi: 10.1186/1752-0509-8-13

Publications en 2013

Books and Book Chapters

[1-PSD13]

Simulation of the Benchmark Datasets

Andrea Pinna, Nicola Soranzo, Alberto de la Fuente, Ina Hoeschele

Gene Network Inference, Springer Berlin Heidelberg de la Fuente, Alberto pages 1-8 chap. 1 - 2013

Peer-reviewed publications in International Journals

[2-PHF13]

Reconstruction of large-scale regulatory networks based on perturbation graphs and transitive reduction: improved methods and their evaluation

Andrea Pinna, Sandra Heise, Robert J Flassig, Alberto de la Fuente, Steffen Klamt

BMC Systems Biology BioMed Central vol. 7 num. 73 - 2013 doi: 10.1186/1752-0509-7-73

Various talks, works and publications

[6-PSH13]

Simulating Systems Genetics with SysGenSIM

Andrea Pinna, Nicola Soranzo, Ina Hoeschele, Alberto de la Fuente

Poster contribution at StatSeq meeting on Gene Network Inference with Systems Genetics data - - march 2013

Contractual reports

[7-PSH13]

SysGenSIM (release 1.1)

Andrea Pinna, Nicola Soranzo, Ina Hoeschele, Alberto de la Fuente

CRS4 Bioinformatica Research Note - 2013

Publications en 2012

Peer-reviewed publications in International Journals

[2-MCK12]

Wisdom of crowds for robust gene network inference

Daniel Marbach, James C. Costello, Robert Küffner, Nicole M. Vega, Robert J. Prill, Diogo M. Camacho, Kyle R. Allison, Alberto de la Fuente, Vincenzo De Leo, Andrea Pinna, Nicola Soranzo, Manolis Kellis, James J. Collins, Gustavo Stolovitzky

Nature Methods pages 796-804 vol. 9 num. 8 - 2012 doi: 10.1038/nmeth.2016

Various talks, works and publications

[5-DE 12]

Inferring Gene Networks from gene-expression data

Alberto de la Fuente

Collana seminari interni 2012 num. 20120502 - may 2012

Contractual reports

[7-PSH12]

StatSeq Systems Genetics Benchmark

Andrea Pinna, Nicola Soranzo, Ina Hoeschele, Alberto de la Fuente

CRS4 / StatSeq Description of published synthetic Systems Genetics datasets - 2012

[7-CDO12]

Case Studies in Bioinformatics

Gianmauro Cuccuru, Alberto de la Fuente, Massimiliano Orsini, Antonella Travaglione, Paolo Uva, Giorgio Fotia

CRS4 Course and practical session, Master in Bioinformatica, Università di Cagliari, 2012 - october 2012

Publications en 2011

Books and Book Chapters

[1-TDT11]

Integrating omics data for signaling pathways, interactome reconstruction, and functional analysis

Paolo Tieri, Alberto de la Fuente, Alberto Termanini, Claudio Franceschi

Bioinformatics for Omics Data, Humana Press Mayer, Bernd pages 415-433 vol. 719 Methods in Molecular Biology - 2011

[1-DRS11]

Disentangling the proteome: re-evaluations of topological insights from yeast protein interaction networks

Vincenzo De Leo, Francesco Ricci, Nicola Soranzo, Alessandro Chessa, Alberto de la Fuente

Advances in Medicine and Biology, Nova Science Berhardt, Leon V. pages 141-166 vol. 16 chap. 4 Hauppauge, NY, USA - 2011

Peer-reviewed publications in International Journals

[2-PGD11]

Linking the proteins - Elucidation of proteome-scale networks using mass spectrometry

Delphine Pflieger, Florence Gonnet, Sergio de la Fuente van Bentem, Heribert Hirt, Alberto de la Fuente

Mass Spectrometry Reviews pages 268-297 vol. 30 num. 2 - 2011 doi: 10.1002/mas.20278

[2-DE 11]

Structure, dynamics and function - dynamical properties of large bio-molecular networks

Alberto de la Fuente

The Open Bioinformatics Journal pages 1-3 vol. 5 - 2011 doi: 10.2174/1875036201105010001

[2-MAB11]

Verification of systems biology research in the age of collaborative competition

Pablo Meyer, Leonidas G Alexopoulos, Thomas Bonk, Andrea Califano, Carolyn R Cho, Alberto de la Fuente, David de Graaf, Alexander J. Hartemink, Julia Hoeng, Nikolai V. Ivanov, Heinz Koeppl, Rune Linding, Daniel Marbach, Raquel Norel, Manuel C. Peitsch, J. Jeremy Rice, Ajay Royyuru, Frank Schacherer, Joerg Sprengel, Katrin Stolle, Dennis Vitkup, Gustavo Stolovitzky

Nature Biotechnology pages 811-815 vol. 29 num. 9 - 2011 doi: 10.1038/nbt.1968

[2-PSH11]

Simulating system genetics data with SysGenSIM

Andrea Pinna, Nicola Soranzo, Ina Hoeschele, Alberto de la Fuente

Bioinformatics pages 2459-2462 vol. 27 num. 17 - 2011 doi: 10.1093/bioinformatics/btr407

Various talks, works and publications

[6-PSH11]

Simulating Large Systems Genetics Datasets for the Evaluation of Analysis Methods

Andrea Pinna, Nicola Soranzo, Ina Hoeschele, Alberto de la Fuente

Poster contribution at RECOMB 2011 Systems Biology Conference - - 2011

[6-PSS11]

Structural Identification of Gene Regulatory Networks from Gene Expression Datasets

Andrea Pinna, Nicola Soranzo, Carla Seatzu, Alberto de la Fuente

Poster contribution at DISC 2011 PhD Summer School - - 2011

[6-OD11]

Quars: A pipeline for transcript discovery from RNAseq data

Massimiliano Orsini, Alberto de la Fuente

Invited talk at the DREAM6 competition AlternativeSplicing. DREAM6 Conference, Oct 14 2011, Barcelona. Spain - october 2011

Publications en 2010

Books and Book Chapters

[1-DDH10]

Integrative approaches to elucidate and analyze protein interaction and signaling networks

Sergio de la Fuente van Bentem, Alberto de la Fuente, Heribert Hirt

Plant Stress Biology, Wiley-VCH Verlag GmbH & Co. KGaA Hirt, Heribert pages 227-248 - 2010

Peer-reviewed publications in International Journals

[2-PSD10]

From knockouts to networks: establishing direct cause-effect relationships through graph analysis

Andrea Pinna, Nicola Soranzo, Alberto de la Fuente

PLoS ONE pages e12912 vol. 10 num. 5 - 2010 doi: 10.1371/journal.pone.0012912

[2-DE 10]

From 'differential expression' to 'differential networking' - identification of dysfunctional regulatory networks in diseases

Alberto de la Fuente

Trends in Genetics pages 326-333 vol. 26 num. 7 - 2010 doi: 10.1016/j.tig.2010.05.001

Various talks, works and publications

[6-PSD10]

Elucidating Transcriptional Regulatory Networks from heterogeneous gene-expression compendia

Andrea Pinna, Nicola Soranzo, Vincenzo De Leo, Alberto de la Fuente

Poster contribution at DREAM5 2010 Conference and at FEBSX-SYSBIO 2011 Meeting - - 2010

[6-SPD10]

Differential networking studies of microRNA regulation

Nicola Soranzo, Andrea Pinna, Alberto de la Fuente

Poster contribution at 11th International Conference on Systems Biology and at FEBSX-SYSBIO 2011 Meeting - - 2010

[6-PSH10]

SysGenSIM: simulating large Systems Genetics datasets for the evaluation of analysis methods

Andrea Pinna, Nicola Soranzo, Ina Hoeschele, Alberto de la Fuente

Poster contribution at RECOMB 2010 Conference and at CMSB 2010 Conference - - 2010

Publications en 2009

Books and Book Chapters

[1-DE 09]

What are gene regulatory networks?

Alberto de la Fuente

Handbook of Research on Computational Methodologies in Gene Regulatory Networks, IGI Global Das, Sanjoy and Caragea, Doina and Welch, Stephen and Hsu, William H. pages 1-27 chap. 1 Hershey, PA, USA - 2009

[1-DE 09]

Inferring gene regulatory networks from genetical genomics data

Alberto de la Fuente

Handbook of Research on Computational Methodologies in Gene Regulatory Networks, IGI Global Das, Sanjoy and Caragea, Doina and Welch, Stephen and Hsu, William H. pages 79-107 chap. 4 Hershey, PA, USA - 2009

Peer-reviewed publications in International Journals

[2-MFD09]

Dissecting the dynamics of dysregulation of cellular processes in mouse mammary gland tumor

Wieslawa Mentzen, Matteo Floris, Alberto de la Fuente

BMC Genomics vol. 10 num. 601 - 2009 doi: 10.1186/1471-2164-10-601

[2-SMP09]

Inferring gene networks: dream or nightmare? Part 2: challenges 4 and 5

Alan Louis Scheinine, Wieslawa Mentzen, Enrico Pieroni, Giorgio Fotia, Fabio Maggio, Gianmaria Mancosu, Alberto de la Fuente

Annals of the New York Academy of Sciences pages 287-301 vol. 1158 - march 2009 doi: 10.1111/j.1749-6632.2008.04100.x

[2-BMD09]

Inferring gene networks: dream or nightmare? Part 1: challenges 1 and 3

Angela Baralla, Wieslawa Mentzen, Alberto de la Fuente

Annals of the New York Academy of Sciences pages 246-256 vol. 1158 - march 2009 doi: 10.1111/j.1749-6632.2008.04099.x

Various talks, works and publications

[6-PHD09]

Sysgensim: simulating large systems genetics datasets for the evaluation of analysis methods

Andrea Pinna, Ina Hoeschele, Alberto de la Fuente

Contributed poster at the 1st Symposium on Systems Genetics, Groningen (NL), October 2009 - 2009

[6-MFD09]

Dissecting the dynamics of dysregulation of cellular processes in mouse mammary gland tumor

Wieslawa Mentzen, Matteo Floris, Alberto de la Fuente

Poster presented at Intelligent Systems for Molecular Biology (ISMB) - Stockholm, Sweden - june 2009

Publications en 2008

Peer-reviewed publications in International Journals

[2-DFM08]

Insights into biological information processing: structural and dynamical analysis of a human protein signalling network

Alberto de la Fuente, Giorgio Fotia, Fabio Maggio, Gianmaria Mancosu, Enrico Pieroni

Journal of Physics A: Mathematical and Theoretical pages 224013 vol. 41 num. 22 - 2008 doi: 10.1088/1751-8113/41/22/224013

[2-LDH08]

Gene network inference via structural equation modeling in genetical genomics experiments

Bing Liu, Alberto de la Fuente, Ina Hoeschele

Genetics pages 1763-1776 vol. 178 num. 3 - 2008 doi: 10.1534/genetics.107.080069

[2-DMD08]

Towards functional phosphoproteomics by mapping differential phosphorylation events in signaling networks

Sergio de la Fuente van Bentem, Wieslawa Mentzen, Alberto de la Fuente, Heribert Hirt

Proteomics pages 4453-4465 vol. 8 num. 21 - november 2008 doi: 10.1002/pmic.200800175

[2-PDM08]

Protein networking: insights into global functional organization of proteomes

Enrico Pieroni, Sergio de la Fuente van Bentem, Gianmaria Mancosu, Enrico Capobianco, Heribert Hirt, Alberto de la Fuente

Proteomics pages 799-816 vol. 8 num. 4 - february 2008 doi: 10.1002/pmic.200700767

Various talks, works and publications

[6-MFD08]

Network oncology: analysis of cancer gene expression in the context of protein interaction networks and mirna target motifs

Wieslawa Mentzen, Matteo Floris, Alberto de la Fuente

Poster presented at ECCB 2008, Cagliari, Italy, September 22-25 - 2008

[6-MFD08]

Network oncology: analysis of cancer gene expression in the context of protein interaction networks and mirna target motifs

Wieslawa Mentzen, Matteo Floris, Alberto de la Fuente

Poster presented at the International Conference on Systems Biology (ISMB), 2008, Goteborg, Sweden - 2008

Publications en 2007

Peer-reviewed publications in International Journals

[2-VVG07]

Genome-wide partial correlation analysis of Escherichia coli microarray data

Diogo F. T. Veiga, Fábio F. R. Vicente, Marco Grivet, Alberto de la Fuente, Ana Tereza R. Vasconcelos

Genetics and Molecular Research pages 730-742 vol. 6 num. 4 - 2007

Various talks, works and publications

[6-MFP07]

A web of genes: inference and structural analysis of a yeast gene network

Gianmaria Mancosu, Giorgio Fotia, Enrico Pieroni, Fabio Maggio, Alberto de la Fuente

Poster presented at COMPLEX NETWORKS, from Biology to Information Technology Conference, July 2-6 2007 Pula (Italy) - 2007

[6-BSM07]

A set of approaches to infer gene networks

A. Battaglia, Alan Louis Scheinine, Fabio Maggio, Giorgio Fotia, Wieslawa Mentzen, Alberto de la Fuente

Poster presented at the DREAM2 Conference -- New York Academy of Science, New York, NY (USA) - december 2007

[6-PMD07]

Growing a yeast gene network.

Enrico Pieroni, Gianmaria Mancosu, Alberto de la Fuente

Poster presented at STATPHYS23 -- COMPLEX NETWORKS, from Biology to Information Technology - Pula (Italy) - july 2007

[6-MFP07]

Inference and structural analysis of a yeast gene network

Gianmaria Mancosu, Giorgio Fotia, Enrico Pieroni, Fabio Maggio, Alberto de la Fuente

Poster presented at the 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB) - july 2007

[6-MPF07]

Dynamics on `signed motifs' in a yeast gene network

Fabio Maggio, Enrico Pieroni, Giorgio Fotia, Gianmaria Mancosu, Alberto de la Fuente

Poster presented at STATPHYS23 -- COMPLEX NETWORKS, from Biology to Information Technology -- Pula (Italy) - july 2007

[6-DE 07]

Exploring a web of genes: structure and dynamics of a yeast gene network

Alberto de la Fuente

Presentation at STATPHYS23 -- COMPLEX NETWORKS, from Biology to Information Technology Conference, Pula (Italy) - july 2007

[6-MFM07]

Dynamics on `signed motifs' in a yeast gene network

Fabio Maggio, Giorgio Fotia, Gianmaria Mancosu, Enrico Pieroni, Alberto de la Fuente

Poster presented at 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), Vienna (Austria) - july 2007

47 publications Download the selection