Corrado Priami

Corrado Priami

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Corrado Priami

Corrado Priami

Publications by authors named "Corrado Priami"

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Stochastic simulation algorithms for computational systems biology: Exact, approximate, and hybrid methods.

Wiley Interdiscip Rev Syst Biol Med 2019 Nov 1;11(6):e1459. Epub 2019 Jul 1.

The Microsoft Research-University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto, TN, Italy.

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http://dx.doi.org/10.1002/wsbm.1459DOI Listing
November 2019

A comparison of deterministic and stochastic approaches for sensitivity analysis in computational systems biology.

Brief Bioinform 2019 Feb 7. Epub 2019 Feb 7.

The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura, Rovereto (TN), Italy.

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http://dx.doi.org/10.1093/bib/bbz014DOI Listing
February 2019

Context-dependent prediction of protein complexes by SiComPre.

NPJ Syst Biol Appl 2018 17;4:37. Epub 2018 Sep 17.

4Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK.

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http://www.nature.com/articles/s41540-018-0073-0
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http://dx.doi.org/10.1038/s41540-018-0073-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6141528PMC
September 2018

Clinical and Vitamin Response to a Short-Term Multi-Micronutrient Intervention in Brazilian Children and Teens: From Population Data to Interindividual Responses.

Mol Nutr Food Res 2018 03 22;62(6):e1700613. Epub 2018 Feb 22.

Department of Pediatrics, Faculty of Medicine, Nutrition and Metabolism, University of São Paulo.

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http://doi.wiley.com/10.1002/mnfr.201700613
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http://dx.doi.org/10.1002/mnfr.201700613DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6120145PMC
March 2018

A closed-loop multi-level model of glucose homeostasis.

PLoS One 2018 8;13(2):e0190627. Epub 2018 Feb 8.

The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0190627PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5805234PMC
March 2018

Incorporating extrinsic noise into the stochastic simulation of biochemical reactions: A comparison of approaches.

J Chem Phys 2018 Feb;148(6):064111

The Microsoft Research-University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura 1, 38068 Rovereto (TN), Italy.

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http://dx.doi.org/10.1063/1.5016338DOI Listing
February 2018

Efficient Constant-Time Complexity Algorithm for Stochastic Simulation of Large Reaction Networks.

IEEE/ACM Trans Comput Biol Bioinform 2017 May-Jun;14(3):657-667. Epub 2016 Feb 15.

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http://dx.doi.org/10.1109/TCBB.2016.2530066DOI Listing
November 2017

Graphical Modeling Meets Systems Pharmacology.

Gene Regul Syst Bio 2017 10;11:1177625017691937. Epub 2017 Mar 10.

The Microsoft Research, University of Trento Centre for Computational and Systems Biology (COSBI), Trento, Italy.

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http://dx.doi.org/10.1177/1177625017691937DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5398309PMC
March 2017

Efficient stochastic simulation of biochemical reactions with noise and delays.

J Chem Phys 2017 Feb;146(8):084107

The Microsoft Research-University of Trento Centre for Computational and Systems Biology, Piazza Manifattura 1, Rovereto 38068, Italy and Department of Mathematics, University of Trento, Trento, Italy and Department of Computer Science, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1063/1.4976703DOI Listing
February 2017

Mechanistic interplay between ceramide and insulin resistance.

Sci Rep 2017 01 23;7:41231. Epub 2017 Jan 23.

The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Rovereto, Italy.

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http://dx.doi.org/10.1038/srep41231DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5253739PMC
January 2017

A Novel Insulin/Glucose Model after a Mixed-Meal Test in Patients with Type 1 Diabetes on Insulin Pump Therapy.

Sci Rep 2016 11 8;6:36029. Epub 2016 Nov 8.

The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy.

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http://dx.doi.org/10.1038/srep36029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5099899PMC
November 2016

Systems view of adipogenesis via novel omics-driven and tissue-specific activity scoring of network functional modules.

Sci Rep 2016 07 7;6:28851. Epub 2016 Jul 7.

The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza Manifattura 1, 38068 Rovereto, Italy.

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http://dx.doi.org/10.1038/srep28851DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4935943PMC
July 2016

Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease.

Authors:
Genevera I Allen Nicola Amoroso Catalina Anghel Venkat Balagurusamy Christopher J Bare Derek Beaton Roberto Bellotti David A Bennett Kevin L Boehme Paul C Boutros Laura Caberlotto Cristian Caloian Frederick Campbell Elias Chaibub Neto Yu-Chuan Chang Beibei Chen Chien-Yu Chen Ting-Ying Chien Tim Clark Sudeshna Das Christos Davatzikos Jieyao Deng Donna Dillenberger Richard J B Dobson Qilin Dong Jimit Doshi Denise Duma Rosangela Errico Guray Erus Evan Everett David W Fardo Stephen H Friend Holger Fröhlich Jessica Gan Peter St George-Hyslop Satrajit S Ghosh Enrico Glaab Robert C Green Yuanfang Guan Ming-Yi Hong Chao Huang Jinseub Hwang Joseph Ibrahim Paolo Inglese Anandhi Iyappan Qijia Jiang Yuriko Katsumata John S K Kauwe Arno Klein Dehan Kong Roland Krause Emilie Lalonde Mario Lauria Eunjee Lee Xihui Lin Zhandong Liu Julie Livingstone Benjamin A Logsdon Simon Lovestone Tsung-Wei Ma Ashutosh Malhotra Lara M Mangravite Taylor J Maxwell Emily Merrill John Nagorski Aishwarya Namasivayam Manjari Narayan Mufassra Naz Stephen J Newhouse Thea C Norman Ramil N Nurtdinov Yen-Jen Oyang Yudi Pawitan Shengwen Peng Mette A Peters Stephen R Piccolo Paurush Praveen Corrado Priami Veronica Y Sabelnykova Philipp Senger Xia Shen Andrew Simmons Aristeidis Sotiras Gustavo Stolovitzky Sabina Tangaro Andrea Tateo Yi-An Tung Nicholas J Tustison Erdem Varol George Vradenburg Michael W Weiner Guanghua Xiao Lei Xie Yang Xie Jia Xu Hojin Yang Xiaowei Zhan Yunyun Zhou Fan Zhu Hongtu Zhu Shanfeng Zhu

Alzheimers Dement 2016 06 11;12(6):645-53. Epub 2016 Apr 11.

School of Computer Science, Fudan University, Shanghai, Shanghai, China; Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, Shanghai, China; Centre for Computational Systems Biology, Fudan University, Shanghai, China.

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http://dx.doi.org/10.1016/j.jalz.2016.02.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5474755PMC
June 2016

Accelerating rejection-based simulation of biochemical reactions with bounded acceptance probability.

J Chem Phys 2016 Jun;144(22):224108

Department of Mathematics, University of Trento, Trento, Italy.

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http://dx.doi.org/10.1063/1.4953559DOI Listing
June 2016

A network analysis of cofactor-protein interactions for analyzing associations between human nutrition and diseases.

Sci Rep 2016 Jan 18;6:19633. Epub 2016 Jan 18.

The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy.

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http://dx.doi.org/10.1038/srep19633DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4726080PMC
January 2016

Systems biology approaches to study the molecular effects of caloric restriction and polyphenols on aging processes.

Genes Nutr 2015 Nov 25;10(6):58. Epub 2015 Nov 25.

The Microsoft Research, University of Trento Centre for Computational Systems Biology (COSBI), Piazza Manifattura 1, 38068, Rovereto, Italy.

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http://dx.doi.org/10.1007/s12263-015-0508-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4659783PMC
November 2015

Qualitative and Quantitative Protein Complex Prediction Through Proteome-Wide Simulations.

PLoS Comput Biol 2015 Oct 22;11(10):e1004424. Epub 2015 Oct 22.

Department of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy; Randall Division of Cell and Molecular Biophysics and Institute for Mathematical and Molecular Biomedicine, King's College London, London, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.1004424DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4619657PMC
October 2015

Diversity of key players in the microbial ecosystems of the human body.

Sci Rep 2015 Oct 30;5:15920. Epub 2015 Oct 30.

The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza Manifattura 1, Rovereto, TN, 38068, Italy.

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http://dx.doi.org/10.1038/srep15920DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4626846PMC
October 2015

The role of breast-feeding in infant immune system: a systems perspective on the intestinal microbiome.

Microbiome 2015 Sep 24;3:41. Epub 2015 Sep 24.

The Microsoft Research-University of Trento Centre for Computational and Systems Biology, 38068, Rovereto, Italy.

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http://dx.doi.org/10.1186/s40168-015-0104-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4581423PMC
September 2015

Simulation of biochemical reactions with time-dependent rates by the rejection-based algorithm.

J Chem Phys 2015 Aug;143(5):054104

The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza Manifattura 1, Rovereto 38068, Italy.

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http://dx.doi.org/10.1063/1.4927916DOI Listing
August 2015

SCUDO: a tool for signature-based clustering of expression profiles.

Nucleic Acids Res 2015 Jul 9;43(W1):W188-92. Epub 2015 May 9.

The Microsoft Research-University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura 1, 38068 Rovereto (TN), Italy Department of Mathematics, University of Trento, via Sommarive, 14, 38123 Povo (TN), Italy.

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http://dx.doi.org/10.1093/nar/gkv449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489218PMC
July 2015

Novel drug target identification for the treatment of dementia using multi-relational association mining.

Sci Rep 2015 Jul 8;5:11104. Epub 2015 Jul 8.

The Microsoft Research, University of Trento Centre for Computational Systems Biology (COSBI), Piazza Manifattura 1, 38068, Rovereto, Italy.

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http://dx.doi.org/10.1038/srep11104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4495601PMC
July 2015

On the rejection-based algorithm for simulation and analysis of large-scale reaction networks.

J Chem Phys 2015 Jun;142(24):244106

The Microsoft Research-University of Trento Centre for Computational and Systems Biology, Piazza Manifattura 1, Rovereto 38068, Italy.

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http://dx.doi.org/10.1063/1.4922923DOI Listing
June 2015

Efficient rejection-based simulation of biochemical reactions with stochastic noise and delays.

J Chem Phys 2014 Oct;141(13):134116

Department of Mathematics, University of Trento, Italy.

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http://dx.doi.org/10.1063/1.4896985DOI Listing
October 2014

Network analysis of neurodegenerative disease highlights a role of Toll-like receptor signaling.

Biomed Res Int 2014 16;2014:686505. Epub 2014 Jan 16.

The Microsoft Research, University of Trento Centre for Computational Systems Biology (COSBI), Piazza Manifattura 1, 38068 Rovereto, Italy ; Department of Mathematics, University of Trento, Via Sommarive, 14-38123 Povo, Italy.

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http://dx.doi.org/10.1155/2014/686505DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3914352PMC
September 2014

Algorithmic modeling quantifies the complementary contribution of metabolic inhibitions to gemcitabine efficacy.

PLoS One 2012 11;7(12):e50176. Epub 2012 Dec 11.

The Microsoft Research-University of Trento Centre for Computational and Systems Biology, Rovereto (Trento), Italy.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0050176PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3519828PMC
May 2013

Biological network inference for drug discovery.

Drug Discov Today 2013 Mar 10;18(5-6):256-64. Epub 2012 Nov 10.

The Microsoft Research, University of Trento, Centre for Computational and Systems Biology, Piazza Manifattura 1 - 38068 Rovereto, Italy.

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http://dx.doi.org/10.1016/j.drudis.2012.11.001DOI Listing
March 2013

Inferring biochemical reaction pathways: the case of the gemcitabine pharmacokinetics.

BMC Syst Biol 2012 May 28;6:51. Epub 2012 May 28.

The Microsoft Research - University of Trento Centre for Computational and Systems Biology, 38068 Rovereto, Italy.

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http://dx.doi.org/10.1186/1752-0509-6-51DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3536593PMC
May 2012

Model-based clustering reveals vitamin D dependent multi-centrality hubs in a network of vitamin-related proteins.

BMC Syst Biol 2011 Dec 2;5:195. Epub 2011 Dec 2.

The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura 1, 38068 Rovereto (Trento), Italy.

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http://dx.doi.org/10.1186/1752-0509-5-195DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3264545PMC
December 2011

Network inference from time-dependent Omics data.

Methods Mol Biol 2011 ;719:435-55

The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Povo, Trento, Italy.

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http://dx.doi.org/10.1007/978-1-61779-027-0_20DOI Listing
June 2011

Stochastic simulation of the spatio-temporal dynamics of reaction-diffusion systems: the case for the bicoid gradient.

J Integr Bioinform 2010 Nov 23;7(1):150. Epub 2010 Nov 23.

The Microsoft Research - University of Trento, Centre for Computational and Systems Biology, Povo (Trento), Italy.

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http://dx.doi.org/10.2390/biecoll-jib-2010-150DOI Listing
November 2010

Calibration of dynamic models of biological systems with KInfer.

Eur Biophys J 2010 May 11;39(6):1019-39. Epub 2009 Aug 11.

The Microsoft Research-University of Trento, Centre for Computational and Systems Biology, Piazza Manci 17, Povo, Trento, Italy.

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http://dx.doi.org/10.1007/s00249-009-0520-3DOI Listing
May 2010

Snazer: the simulations and networks analyzer.

BMC Syst Biol 2010 Jan 7;4. Epub 2010 Jan 7.

The Microsoft Research University of Trento, CoSBi, Trento, Italy.

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http://dx.doi.org/10.1186/1752-0509-4-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2880970PMC
January 2010

Elucidation of functional consequences of signalling pathway interactions.

BMC Bioinformatics 2009 Nov 6;10:370. Epub 2009 Nov 6.

The Microsoft Research-University of Trento, Centre for Computational Systems Biology, Povo (Trento), Italy.

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http://dx.doi.org/10.1186/1471-2105-10-370DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2778660PMC
November 2009

Narrative-based computational modelling of the Gp130/JAK/STAT signalling pathway.

BMC Syst Biol 2009 Apr 15;3:40. Epub 2009 Apr 15.

Laboratory for Foundations of Computer Science, School of Informatics, University of Edinburgh, Informatics Forum, 10 Crichton Street, EH8 9AB, Edinburgh, UK.

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http://dx.doi.org/10.1186/1752-0509-3-40DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2678071PMC
April 2009

The Beta Workbench: a computational tool to study the dynamics of biological systems.

Brief Bioinform 2008 Sep 7;9(5):437-49. Epub 2008 May 7.

ICT International Doctorate School at University of Trento and Microsoft Research, University of Trento, Centre for Computational and Systems Biology, Povo, TN, Italy.

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http://dx.doi.org/10.1093/bib/bbn023DOI Listing
September 2008

An automatic translation of SBML into Beta-binders.

IEEE/ACM Trans Comput Biol Bioinform 2008 Jan-Mar;5(1):80-90

University of Edinburgh, Scotland, UK.

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http://dx.doi.org/10.1109/TCBB.2007.70219DOI Listing
May 2008

Towards the integration of computational systems biology and high-throughput data: supporting differential analysis of microarray gene expression data.

J Integr Bioinform 2008 Jan 28;5(1). Epub 2008 Jan 28.

Dipartimento di Ingegneria e Scienza dell'Informazione, University of Trento, Italy.

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http://dx.doi.org/10.2390/biecoll-jib-2008-87DOI Listing
January 2008

Design and implementation of a tool for translating SBML into the biochemical stochastic pi-calculus.

Bioinformatics 2006 Dec 17;22(24):3075-81. Epub 2006 Oct 17.

DIT-University of Trento Trento, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btl516DOI Listing
December 2006

A formal language for computational systems biology.

OMICS 2004 ;8(4):370-80

Department of Information and Telecommunication, University of Trento, Povo, Italy.

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http://dx.doi.org/10.1089/omi.2004.8.370DOI Listing
June 2005

Modelling the dynamics of biosystems.

Brief Bioinform 2004 Sep;5(3):259-69

Department of Computer Science and Telecommunications, University of Trento, Italy.

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http://dx.doi.org/10.1093/bib/5.3.259DOI Listing
September 2004

Concurrency in leukocyte vascular recognition: developing the tools for a predictive computer model.

Trends Immunol 2004 Aug;25(8):411-6

BioXell S.p.A., Via Olgettina 58, 20132 Milan, Italy.

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http://dx.doi.org/10.1016/j.it.2004.05.010DOI Listing
August 2004