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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-CCG15]

NCBI BLAST+ integrated into Galaxy

Peter Cock, John Chilton, Bjorn Gruning, James Johnson, Nicola Soranzo

GigaScience pages 39 vol. 4 - 2015 doi: 10.1186/s13742-015-0080-7

[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

[2-COP14]

Orione, a web-based framework for NGS analysis in microbiology

Gianmauro Cuccuru, Massimiliano Orsini, Andrea Pinna, Andrea Sbardellati, Nicola Soranzo, Antonella Travaglione, Paolo Uva, Gianluigi Zanetti, Giorgio Fotia

Bioinformatics Oxford University Press pages 1928-1929 vol. 30 num. 13 - 2014 doi: 10.1093/bioinformatics/btu135

[2-LPC14]

BioBlend.objects: metacomputing with Galaxy

Simone Leo, Luca Pireddu, Gianmauro Cuccuru, Luca Lianas, Nicola Soranzo, Enis Afgan, Gianluigi Zanetti

Bioinformatics Oxford University Press pages 2816-2817 vol. 30 num. 19 - 2014 doi: 10.1093/bioinformatics/btu386

Peer-reviewed publications in international events

[4-PLS14]

A Hadoop-Galaxy adapter for user-friendly and scalable data-intensive bioinformatics in Galaxy

Luca Pireddu, Simone Leo, Nicola Soranzo, Gianluigi Zanetti

Proc. of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics ACM BCB '14 pages 184--191 New York, NY, USA - 2014
isbn: 978-1-4503-2894-4 doi: 10.1145/2649387.2649429

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 events

[4-CFL13]

Scalability, Reproducibility and Traceability in Large Scale NGS Facilities

Gianmauro Cuccuru, Giorgio Fotia, Simone Leo, Luca Lianas, Massimiliano Orsini, Andrea Pinna, Luca Pireddu, Andrea Sbardellati, Nicola Soranzo, Paolo Uva, Gianluigi Zanetti

Contributed presentation to Clinical Genomics & Informatics Europe, Lisbon, Portugal - 4, 6 December - 2013

Various talks, works and publications

[6-COS13]

Engaging Galaxy in Microbiology

Gianmauro Cuccuru, Massimiliano Orsini, Nicola Soranzo, Andrea Pinna, Andrea Sbardellati, Antonella Travaglione, Paolo Uva, Gianluigi Zanetti, Giorgio Fotia

Poster presentation at the Galaxy Community Conference 2013, Oslo,Norway - 30 June, 2 July - 2013

[6-SOC13]

Microbiome profiling on a Galaxy-based framework for Microbiology

Nicola Soranzo, Stefano Onano, Gianmauro Cuccuru, Massimiliano Orsini, Andrea Pinna, Andrea Sbardellati, Paolo Uva, Giorgio Fotia

Poster presentation at the Galaxy Community Conference 2013, Oslo,Norway - 30 June, 2 July - 2013

[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-SRI12]

Decompositions of large-scale biological systems based on dynamical properties

Nicola Soranzo, Fahimeh Ramezani, Giovanni Iacono, Claudio Altafini

Bioinformatics pages 76-83 vol. 28 num. 1 - 2012 doi: 10.1093/bioinformatics/btr620

[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

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-OCU12]

A course in Next Generation Sequencing data analysis using Galaxy

Massimiliano Orsini, Gianmauro Cuccuru, Paolo Uva, Vincenzo De Leo, Andrea Pinna, Andrea Sbardellati, Nicola Soranzo, Antonella Travaglione, Giorgio Fotia

CRS4 Course and praticals material, IZS G. Caporale, Teramo - november 2012

Publications en 2011

Books and Book Chapters

[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-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