Andrea Pagnani

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Riccardo Zecchinaprofessor, theoretical physics, Bocconi UniversityVerified email at unibocconi.it
Martin WeigtSorbonne Université Paris (former Université Pierre & Marie Curie)Verified email at upmc.fr
Alfredo BraunsteinDISAT, Politecnico di TorinoVerified email at polito.it
Chris SanderHarvard Medical School, Broad Institute, MGH, Dana-Farber Cancer Institute, Memorial Sloan KetteringVerified email at sanderlab.org
Giorgio ParisiProfessor of Theoretical Physics, Rome I University "La Sapienza"Verified email at roma1.infn.it
Debora MarksSystems Biology, Harvard Medical School, Broad Institute of Harvard and MITVerified email at hms.harvard.edu
Roberto MuletFacultad de Fisica, Universidad de la HabanaVerified email at fisica.uh.cu
Enzo MarinariProfessor of Theoretical Physics, Sapienza Università di RomaVerified email at uniroma1.it
Carlo BaldassiBocconi University; ELLIS scholarVerified email at unibocconi.it
Thomas A. HopfScientific ConsultantVerified email at thomashopf.com
Christoph FeinauerIsomorphic LabsVerified email at isomorphiclabs.com
Bryan J. LuntPhD Candidate, University of Illinois as Urbana-ChampaignVerified email at illinois.edu
Faruck MorcosUniversity of Texas at Dallas - Dept. Biological SciencesVerified email at utdallas.edu
Jose OnuchicCTBP Rice UniversityVerified email at rice.edu
Paolo ProveroProfessor, University of TurinVerified email at unito.it
Marco ZamparoUniversità del Piemonte OrientaleVerified email at uniupo.it
Federico Ricci-TersenghiProfessor of Theoretical Physics, "La Sapienza" University, RomaVerified email at roma1.infn.it
Pier Paolo PandolfiDirector, Cancer Center and Cancer Research Institute, Beth Israel Deaconess Medical CenterVerified email at bidmc.harvard.edu
Florian KarrethH. Lee Moffitt Cancer CenterVerified email at moffitt.org
Riccardo TaulliUniversity of TorinoVerified email at unito.it

Andrea Pagnani

Professor at DISAT - Politecnico di Torino, and PI at the IIGM

Verified email at polito.it - Homepage

Statistical physics combinatorial optimization bioinformatics biological modeling statistical inference


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Direct-coupling analysis of residue coevolution captures native contacts across many protein families F Morcos, A Pagnani, B Lunt, A Bertolino, DS Marks, C Sander, ... Proceedings of the National Academy of Sciences 108 (49), E1293-E1301, 2011	1590	2011
Protein 3D structure computed from evolutionary sequence variation DS Marks, LJ Colwell, R Sheridan, TA Hopf, A Pagnani, R Zecchina, ... PLoS One 6 (12), e28766, 2011	1286	2011
Integrated transcriptional and competitive endogenous RNA networks are cross-regulated in permissive molecular environments U Ala, FA Karreth, C Bosia, A Pagnani, R Taulli, V Léopold, Y Tay, ... Proceedings of the National Academy of Sciences 110 (18), 7154-7159, 2013	347	2013
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence L Peña-Castillo, M Tasan, CL Myers, H Lee, T Joshi, C Zhang, Y Guan, ... Genome biology 9 (1), 1-19, 2008	300	2008
Coloring random graphs R Mulet, A Pagnani, M Weigt, R Zecchina Physical review letters 89 (26), 268701, 2002	251	2002
Genome-wide analysis identifies a functional association of Tet1 and Polycomb repressive complex 2 in mouse embryonic stem cells F Neri, D Incarnato, A Krepelova, S Rapelli, A Pagnani, R Zecchina, ... Genome biology 14 (8), R91, 2013	205	2013
Fast and accurate multivariate Gaussian modeling of protein families: Predicting residue contacts and protein-interaction partners C Baldassi, M Zamparo, C Feinauer, A Procaccini, R Zecchina, M Weigt, ... PloS one 9 (3), e92721, 2014	179	2014
Critical exponents of the KPZ equation via multi-surface coding numerical simulations E Marinari, A Pagnani, G Parisi Journal of Physics A: Mathematical and General 33 (46), 8181, 2000	176	2000
Perturbation biology: inferring signaling networks in cellular systems EJ Molinelli, A Korkut, W Wang, ML Miller, NP Gauthier, X Jing, P Kaushik, ... PLoS computational biology 9 (12), e1003290, 2013	173	2013
Modelling competing endogenous RNA networks C Bosia, A Pagnani, R Zecchina PloS one 8 (6), e66609, 2013	145	2013
Somatic mutagenesis in satellite cells associates with human skeletal muscle aging I Franco, A Johansson, K Olsson, P Vrtačnik, P Lundin, HT Helgadottir, ... Nature communications 9 (1), 1-12, 2018	139	2018
Simultaneous identification of specifically interacting paralogs and interprotein contacts by direct coupling analysis T Gueudré, C Baldassi, M Zamparo, M Weigt, A Pagnani Proceedings of the National Academy of Sciences 113 (43), 12186-12191, 2016	134	2016
Simultaneous reconstruction of multiple signaling pathways via the prize-collecting Steiner forest problem N Tuncbag, A Braunstein, A Pagnani, SSC Huang, J Chayes, C Borgs, ... Journal of computational biology 20 (2), 124-136, 2013	134	2013
Width distributions and the upper critical dimension of Kardar-Parisi-Zhang interfaces E Marinari, A Pagnani, G Parisi, Z Rácz Physical review E 65 (2), 026136, 2002	134	2002
Polynomial iterative algorithms for coloring and analyzing random graphs A Braunstein, R Mulet, A Pagnani, M Weigt, R Zecchina Physical Review E 68 (3), 036702, 2003	122	2003
Glassy transition in a disordered model for the RNA secondary structure A Pagnani, G Parisi, F Ricci-Tersenghi Physical review letters 84 (9), 2026, 2000	93	2000
Improving contact prediction along three dimensions C Feinauer, MJ Skwark, A Pagnani, E Aurell PLoS computational biology 10 (10), e1003847, 2014	88	2014
Numerical estimate of the Kardar-Parisi-Zhang universality class in (2+ 1) dimensions A Pagnani, G Parisi Physical Review E 92 (1), 010101, 2015	86	2015
Efficient generative modeling of protein sequences using simple autoregressive models J Trinquier, G Uguzzoni, A Pagnani, F Zamponi, M Weigt Nature Communications 12, 2021	84	2021
Threshold values, stability analysis, and high-q asymptotics for the coloring problem on random graphs F Krząkała, A Pagnani, M Weigt Physical Review E 70 (4), 046705, 2004	75	2004

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