Andrea Pagnani

Andrea Pagnani

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Andrea Pagnani

Andrea Pagnani

Publications by authors named "Andrea Pagnani"

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The intrinsic dimension of protein sequence evolution.

PLoS Comput Biol 2019 04 8;15(4):e1006767. Epub 2019 Apr 8.

SISSA, Trieste, Italy.

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http://dx.doi.org/10.1371/journal.pcbi.1006767DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6472826PMC
April 2019

Modelling Competing Endogenous RNA Networks.

PLoS One 2013 26;8(6):e66609. Epub 2013 Jun 26.

Human Genetics Foundation (HuGeF), Torino, Italy.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0066609PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694070PMC
October 2017

Inverse problem for multi-body interaction of nonlinear waves.

Sci Rep 2017 06 14;7(1):3463. Epub 2017 Jun 14.

NANOTEC-CNR, Institute of Nanotechnology, Soft and Living Matter Laboratory, Rome, Piazzale A. Moro 2, I-00185, Roma, Italy.

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http://dx.doi.org/10.1038/s41598-017-03163-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5471250PMC
June 2017

An analytic approximation of the feasible space of metabolic networks.

Nat Commun 2017 04 6;8:14915. Epub 2017 Apr 6.

DISAT, Politecnico di Torino, 10129 Torino, Italy.

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http://dx.doi.org/10.1038/ncomms14915DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5384209PMC
April 2017

ceRNA crosstalk stabilizes protein expression and affects the correlation pattern of interacting proteins.

Sci Rep 2017 03 7;7:43673. Epub 2017 Mar 7.

Dipartimento di Fisica, Sapienza Università di Roma, Rome, Italy.

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http://dx.doi.org/10.1038/srep43673DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5339858PMC
March 2017

Simultaneous identification of specifically interacting paralogs and interprotein contacts by direct coupling analysis.

Proc Natl Acad Sci U S A 2016 10 11;113(43):12186-12191. Epub 2016 Oct 11.

Department of Applied Science and Technology, Politecnico di Torino, 10129 Torino, Italy; Human Genetics Foundation, Molecular Biotechnology Center, 10126 Torino, Italy;

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http://www.pnas.org/lookup/doi/10.1073/pnas.1607570113
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http://dx.doi.org/10.1073/pnas.1607570113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5087065PMC
October 2016

Inter-Protein Sequence Co-Evolution Predicts Known Physical Interactions in Bacterial Ribosomes and the Trp Operon.

PLoS One 2016 16;11(2):e0149166. Epub 2016 Feb 16.

Department of Applied Science and Technology, and Center for Computational Sciences, Politecnico di Torino, Torino, Italy.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0149166PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4755613PMC
July 2016

Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity.

PLoS Comput Biol 2016 Apr 13;12(4):e1004870. Epub 2016 Apr 13.

Human Genetics Foundation, Molecular Biotechnology Center, Torino, Italy.

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http://dx.doi.org/10.1371/journal.pcbi.1004870DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4830580PMC
April 2016

Numerical estimate of the Kardar-Parisi-Zhang universality class in (2+1) dimensions.

Phys Rev E Stat Nonlin Soft Matter Phys 2015 Jul 2;92(1):010101. Epub 2015 Jul 2.

Dipartimento di Fisica, INFN-Sezione di Roma 1, CNR-IPCF UOS Roma, Università "La Sapienza", P.le Aldo Moro 2, I-00185 Roma, Italy.

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http://dx.doi.org/10.1103/PhysRevE.92.010101DOI Listing
July 2015

Identifying all moiety conservation laws in genome-scale metabolic networks.

PLoS One 2014 2;9(7):e100750. Epub 2014 Jul 2.

DISAT and Centre for Computational Sciences, Politecnico di Torino, Torino, Italy; Human Genetics Foundation, Torino, Italy.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0100750PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079565PMC
February 2015

Fast and accurate multivariate Gaussian modeling of protein families: predicting residue contacts and protein-interaction partners.

PLoS One 2014 24;9(3):e92721. Epub 2014 Mar 24.

Department of Applied Science and Technology and Center for Computational Sciences, Politecnico di Torino, Torino, Italy; Human Genetics Foundation-Torino, Torino, Italy.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0092721PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3963956PMC
January 2015

Bridging the gaps in systems biology.

Mol Genet Genomics 2014 Oct 13;289(5):727-34. Epub 2014 Apr 13.

Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Chalmers Tvärgata 3, 412 96, Göteborg, Sweden,

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http://dx.doi.org/10.1007/s00438-014-0843-3DOI Listing
October 2014

Improving contact prediction along three dimensions.

PLoS Comput Biol 2014 Oct 9;10(10):e1003847. Epub 2014 Oct 9.

Department of Information and Computer Science, Aalto University, Aalto, Finland; Aalto Science Institute (AScI), Aalto University, Aalto, Finland; Department of Computational Biology, Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden.

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http://dx.doi.org/10.1371/journal.pcbi.1003847DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4191875PMC
October 2014

Integrated transcriptional and competitive endogenous RNA networks are cross-regulated in permissive molecular environments.

Proc Natl Acad Sci U S A 2013 Apr 27;110(18):7154-9. Epub 2013 Mar 27.

Cancer Genetics Program, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.

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http://dx.doi.org/10.1073/pnas.1222509110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3645534PMC
April 2013

Multisurface coding simulations of the restricted solid-on-solid model in four dimensions.

Phys Rev E Stat Nonlin Soft Matter Phys 2013 Jan 14;87(1):010102. Epub 2013 Jan 14.

Human Genetics Foundation (HuGeF), Via Nizza 52, I-10126 Turin, Italy.

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http://dx.doi.org/10.1103/PhysRevE.87.010102DOI Listing
January 2013

Protein 3D structure computed from evolutionary sequence variation.

PLoS One 2011 7;6(12):e28766. Epub 2011 Dec 7.

Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0028766PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3233603PMC
July 2012

Direct-coupling analysis of residue coevolution captures native contacts across many protein families.

Proc Natl Acad Sci U S A 2011 Dec 21;108(49):E1293-301. Epub 2011 Nov 21.

Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093-0374, USA.

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http://dx.doi.org/10.1073/pnas.1111471108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3241805PMC
December 2011

A stochastic local search algorithm for distance-based phylogeny reconstruction.

Mol Biol Evol 2010 Nov 18;27(11):2587-95. Epub 2010 Jun 18.

Institute for Scientific Interchange, Torino, Italy.

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http://dx.doi.org/10.1093/molbev/msq154DOI Listing
November 2010

Inference of sparse combinatorial-control networks from gene-expression data: a message passing approach.

BMC Bioinformatics 2010 Jun 29;11:355. Epub 2010 Jun 29.

ISI Foundation Viale Settimio Severo 65, Villa Gualino, I-10133 Torino, Italy.

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http://dx.doi.org/10.1186/1471-2105-11-355DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2909222PMC
June 2010

Estimating the size of the solution space of metabolic networks.

BMC Bioinformatics 2008 May 19;9:240. Epub 2008 May 19.

Politecnico di Torino, Corso Duca degli Abruzzi 34, I-10129, Torino, Italy.

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http://dx.doi.org/10.1186/1471-2105-9-240DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2483728PMC
May 2008

Predicting protein functions with message passing algorithms.

Bioinformatics 2005 Jan 17;21(2):239-47. Epub 2004 Sep 17.

Institute for Scientific Interchange (ISI) Viale Settimio Severo 65, Turin, I-10133, Italy.

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http://bioinformatics.oxfordjournals.org/content/21/2/239.fu
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http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
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http://dx.doi.org/10.1093/bioinformatics/bth491DOI Listing
January 2005

Threshold values, stability analysis, and high-q asymptotics for the coloring problem on random graphs.

Phys Rev E Stat Nonlin Soft Matter Phys 2004 Oct 29;70(4 Pt 2):046705. Epub 2004 Oct 29.

Dipartimento di Fisica, INFM and SMC, Università di Roma La Sapienza, P. A. Moro 2, I-00185 Roma, Italy.

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http://dx.doi.org/10.1103/PhysRevE.70.046705DOI Listing
October 2004

Zero-temperature properties of RNA secondary structures.

Phys Rev E Stat Nonlin Soft Matter Phys 2002 Apr 8;65(4 Pt 1):041919. Epub 2002 Apr 8.

Dipartimento di Fisica, SMC and UdR1 of INFM, INFN, Università di Roma "La Sapienza," Piazzale Aldo Moro 2, I-00185 Rome, Italy.

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http://dx.doi.org/10.1103/PhysRevE.65.041919DOI Listing
April 2002