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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