Archivio Istituzionale della RicercaPAGNANI, ANDREA
PAGNANI, ANDREA
Dipartimento Scienza Applicata e Tecnologia
030845
A common root for coevolution and substitution rate variability in protein sequence evolution
2019 Rizzato, F.; Zamuner, S.; Pagnani, A.; Laio, A.
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence
2008 Lourdes Peña, Castillo; Murat, Tasan; Chad L., Myers; Hyunju, Lee; Trupti, Joshi; Chao, Zhang; Yuanfang, Guan; Michele, Leone; Pagnani, Andrea; Wan, Kim; Chase, Krumpelman; Weidong, Tian; Guillaume, Obozinski; Yanjun, Qi; Sara, Mostafavi; Guan, Lin; Gabriel F., Berriz; Francis D., Gibbons; Gert, Lanckriet; Jian, Qiu; Charles, Grant; Zafer, Barutcuoglu; David P., Hill; David Warde, Farley; Chris, Grouios; Debajyoti, Ray; Judith A., Blake; Minghua, Deng; Michael I., Jordan; William S., Noble; Quaid, Morris; Judith Klein, Seetharaman; Ziv Bar, Joseph; Ting, Chen; Fengzhu, Sun; Olga G., Troyanskaya; Edward M., Marcotte; Dong, Xu; Timothy R., Hughes; Frederick P., Roth
A discrete model of water with two distinct glassy phases
2010 Pagnani, Andrea; Pretti, M.
A Stochastic Local Search Algorithm for Distance-Based Phylogeny Reconstruction
2010 F., Tria; E., Caglioti; V., Loreto; Pagnani, Andrea
A stochastic local search approach to language tree reconstruction
2010 Francesca, Tria; Emanuele, Caglioti; Vittorio, Loreto; Pagnani, Andrea
Against temperature chaos in naive Thouless-Anderson-Palmer equations
2001 R., Mulet; Pagnani, Andrea; G., Parisi
Aligning biological sequences by exploiting residue conservation and coevolution
2020 Muntoni, Anna Paola; Pagnani, Andrea; Weigt, Martin; Zamponi, Francesco
AMaLa: Analysis of Directed Evolution Experiments via Annealed Mutational Approximated Landscape
2021 Sesta, Luca; Uguzzoni, Guido; Fernandez-de-Cossio-Diaz, Jorge; Pagnani, Andrea
An analytic approximation of the feasible space of metabolic networks
2017 Braunstein, Alfredo; Muntoni, ANNA PAOLA; Pagnani, Andrea
Bridging the gaps in systems biology.
2014 Cvijovic, M; Almquist, J; Hagmar, J; Hohmann, S; Kaltenbach, Hm; Klipp, E; Krantz, M; Mendes, P; Nelander, S; Nielsen, J; Pagnani, Andrea; Przulj, N; Raue, A; Stelling, J; Stoma, S; Tobin, F; Wodke, Ja; Zecchina, Riccardo; Jirstrand, M.
CeRNA crosstalk stabilizes protein expression and affects the correlation pattern of interacting proteins
2017 Martirosyan, Araks; De Martino, Andrea; Pagnani, Andrea; Marinari, Enzo
Classification and sparse-signature extraction from gene-expression data
2009 Pagnani, Andrea; Francesca, Tria; Martin, Weigt
Clostridium cellulovorans metabolism of cellulose as studied by comparative proteomic approach
2020 Usai, G.; Cirrincione, S.; Re, A.; Manfredi, M.; Pagnani, A.; Pessione, E.; Mazzoli, R.
Coloring random graphs
2002 R., Mulet; Pagnani, Andrea; M., Weigt; Zecchina, Riccardo
Compressed sensing reconstruction using Expectation Propagation
2020 Braunstein, Alfredo; Muntoni, Anna Paola; Pagnani, Andrea; Pieropan, Mirko
Core percolation and onset of complexity in Boolean networks
2006 L., Correale; M., Leone; Pagnani, Andrea; M., Weigt; Zecchina, Riccardo
Critical exponents of the KPZ equation via multi-surface coding numerical simulations
2000 Enzo, Marinari; Pagnani, Andrea; Giorgio, Parisi
DCAlign v1.0: Aligning biological sequences using co-evolution models and informed priors
2023 Muntoni, Anna Paola; Pagnani, Andrea
Direct-coupling analysis of residue coevolution captures native contacts across many protein families
2011 Morcos, F.; Pagnani, Andrea; Lunt, B.; Bertolino, A.; Marks, D. S.; Sander, C.; Zecchina, Riccardo; Onuchic, J. N.; Hwa, T.; Weigt, M.
Efficient generative modeling of protein sequences using simple autoregressive models
2021 Trinquier, Jeanne; Uguzzoni, Guido; Pagnani, Andrea; Zamponi, Francesco; Weigt, Martin
| Citazione | Data di pubblicazione | Autori | File |
|---|---|---|---|
| A common root for coevolution and substitution rate variability in protein sequence evolution / Rizzato, F.; Zamuner, S.; Pagnani, A.; Laio, A.. - In: SCIENTIFIC REPORTS. - ISSN 2045-2322. - 9:1(2019), p. 18032. [10.1038/s41598-019-53958-w] | 1-gen-2019 | Pagnani A. + | s41598-019-53958-w.pdf |
| A critical assessment of Mus musculus gene function prediction using integrated genomic evidence / Lourdes Peña, Castillo; Murat, Tasan; Chad L., Myers; Hyunju, Lee; Trupti, Joshi; Chao, Zhang; Yuanfang, Guan; Michele, Leone; Pagnani, Andrea; Wan, Kim; Chase, Krumpelman; Weidong, Tian; Guillaume, Obozinski; Yanjun, Qi; Sara, Mostafavi; Guan, Lin; Gabriel F., Berriz; Francis D., Gibbons; Gert, Lanckriet; Jian, Qiu; Charles, Grant; Zafer, Barutcuoglu; David P., Hill; David Warde, Farley; Chris, Grouios; Debajyoti, Ray; Judith A., Blake; Minghua, Deng; Michael I., Jordan; William S., Noble; Quaid, Morris; Judith Klein, Seetharaman; Ziv Bar, Joseph; Ting, Chen; Fengzhu, Sun; Olga G., Troyanskaya; Edward M., Marcotte; Dong, Xu; Timothy R., Hughes; Frederick P., Roth. - In: GENOME BIOLOGY. - ISSN 1474-760X. - 9:(2008), p. S2. [10.1186/gb-2008-9-s1-s2] | 1-gen-2008 | PAGNANI, ANDREA + | - |
| A discrete model of water with two distinct glassy phases / Pagnani, Andrea; Pretti, M.. - In: EUROPHYSICS LETTERS. - ISSN 0295-5075. - 92:(2010), p. 46008. [10.1209/0295-5075/92/46008] | 1-gen-2010 | PAGNANI, ANDREAM. Pretti | - |
| A Stochastic Local Search Algorithm for Distance-Based Phylogeny Reconstruction / F., Tria; E., Caglioti; V., Loreto; Pagnani, Andrea. - In: MOLECULAR BIOLOGY AND EVOLUTION. - ISSN 0737-4038. - 27:(2010), pp. 2587-2595. [10.1093/molbev/msq154] | 1-gen-2010 | PAGNANI, ANDREA + | - |
| A stochastic local search approach to language tree reconstruction / Francesca, Tria; Emanuele, Caglioti; Vittorio, Loreto; Pagnani, Andrea. - In: DIACHRONICA. - ISSN 0176-4225. - 27:(2010), pp. 341-358. [10.1075/dia.27.2.09tri] | 1-gen-2010 | PAGNANI, ANDREA + | - |
| Against temperature chaos in naive Thouless-Anderson-Palmer equations / R., Mulet; Pagnani, Andrea; G., Parisi. - In: PHYSICAL REVIEW. B, CONDENSED MATTER AND MATERIALS PHYSICS. - ISSN 1098-0121. - 63:(2001). [10.1103/PhysRevB.63.184438] | 1-gen-2001 | PAGNANI, ANDREA + | - |
| Aligning biological sequences by exploiting residue conservation and coevolution / Muntoni, Anna Paola; Pagnani, Andrea; Weigt, Martin; Zamponi, Francesco. - In: PHYSICAL REVIEW. E. - ISSN 2470-0045. - 102:6(2020), p. 062409. [10.1103/PhysRevE.102.062409] | 1-gen-2020 | Muntoni, Anna PaolaPagnani, Andrea + | PhysRevE.102.062409.pdf |
| AMaLa: Analysis of Directed Evolution Experiments via Annealed Mutational Approximated Landscape / Sesta, Luca; Uguzzoni, Guido; Fernandez-de-Cossio-Diaz, Jorge; Pagnani, Andrea. - In: INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES. - ISSN 1422-0067. - ELETTRONICO. - 22:20(2021), p. 10908. [10.3390/ijms222010908] | 1-gen-2021 | Luca SestaGuido UguzzoniAndrea Pagnani + | ijms-22-10908.pdf |
| An analytic approximation of the feasible space of metabolic networks / Braunstein, Alfredo; Muntoni, ANNA PAOLA; Pagnani, Andrea. - In: NATURE COMMUNICATIONS. - ISSN 2041-1723. - ELETTRONICO. - 8:(2017), p. 14915. [10.1038/ncomms14915] | 1-gen-2017 | BRAUNSTEIN, ALFREDOMUNTONI, ANNA PAOLAPAGNANI, ANDREA | ncomms14915.pdf |
| Bridging the gaps in systems biology / Cvijovic, M; Almquist, J; Hagmar, J; Hohmann, S; Kaltenbach, Hm; Klipp, E; Krantz, M; Mendes, P; Nelander, S; Nielsen, J; Pagnani, Andrea; Przulj, N; Raue, A; Stelling, J; Stoma, S; Tobin, F; Wodke, Ja; Zecchina, Riccardo; Jirstrand, M.. - In: MOLECULAR GENETICS AND GENOMICS. - ISSN 1617-4615. - ELETTRONICO. - 189:5(2014), pp. 727-734. [10.1007/s00438-014-0843-3] | 1-gen-2014 | PAGNANI, ANDREAZECCHINA, RICCARDO + | - |
| CeRNA crosstalk stabilizes protein expression and affects the correlation pattern of interacting proteins / Martirosyan, Araks; De Martino, Andrea; Pagnani, Andrea; Marinari, Enzo. - In: SCIENTIFIC REPORTS. - ISSN 2045-2322. - 7:(2017), p. 43673. [10.1038/srep43673] | 1-gen-2017 | De Martino, AndreaPAGNANI, ANDREA + | srep43673.pdf |
| Classification and sparse-signature extraction from gene-expression data / Pagnani, Andrea; Francesca, Tria; Martin, Weigt. - In: JOURNAL OF STATISTICAL MECHANICS: THEORY AND EXPERIMENT. - ISSN 1742-5468. - 2009:(2009), p. P05001. [10.1088/1742-5468/2009/05/P05001] | 1-gen-2009 | PAGNANI, ANDREA + | - |
| Clostridium cellulovorans metabolism of cellulose as studied by comparative proteomic approach / Usai, G.; Cirrincione, S.; Re, A.; Manfredi, M.; Pagnani, A.; Pessione, E.; Mazzoli, R.. - In: JOURNAL OF PROTEOMICS. - ISSN 1874-3919. - ELETTRONICO. - 216:(2020), p. 103667. [10.1016/j.jprot.2020.103667] | 1-gen-2020 | Usai G.Re A.Pagnani A. + | 1-s2.0-S187439192030035X_main.pdf; 1-s2.0-S187439192030035X-mmc1.pptx; 1-s2.0-S187439192030035X-mmc2.pptx; 1-s2.0-S187439192030035X-mmc3.xlsx |
| Coloring random graphs / R., Mulet; Pagnani, Andrea; M., Weigt; Zecchina, Riccardo. - In: PHYSICAL REVIEW LETTERS. - ISSN 0031-9007. - 89:(2002), p. 268701. [10.1103/PhysRevLett.89.268701] | 1-gen-2002 | PAGNANI, ANDREAZECCHINA, RICCARDO + | - |
| Compressed sensing reconstruction using Expectation Propagation / Braunstein, Alfredo; Muntoni, Anna Paola; Pagnani, Andrea; Pieropan, Mirko. - In: JOURNAL OF PHYSICS. A, MATHEMATICAL AND THEORETICAL. - ISSN 1751-8113. - 53:18(2020), p. 184001. [10.1088/1751-8121/ab3065] | 1-gen-2020 | Braunstein, AlfredoMuntoni, Anna PaolaPagnani, AndreaPieropan, Mirko | Braunstein+et+al_2019_J._Phys._A:_Math._Theor._10.1088_1751-8121_ab3065.pdf; Braunstein_2020_J._Phys._A__Math._Theor._53_184001.pdf |
| Core percolation and onset of complexity in Boolean networks / L., Correale; M., Leone; Pagnani, Andrea; M., Weigt; Zecchina, Riccardo. - In: PHYSICAL REVIEW LETTERS. - ISSN 0031-9007. - 96:(2006), p. 018101. [10.1103/PhysRevLett.96.018101] | 1-gen-2006 | PAGNANI, ANDREAZECCHINA, RICCARDO + | - |
| Critical exponents of the KPZ equation via multi-surface coding numerical simulations / Enzo, Marinari; Pagnani, Andrea; Giorgio, Parisi. - In: JOURNAL OF PHYSICS. A, MATHEMATICAL AND GENERAL. - ISSN 0305-4470. - 33:(2000), pp. 8181-8192. [10.1088/0305-4470/33/46/303] | 1-gen-2000 | PAGNANI, ANDREA + | - |
| DCAlign v1.0: Aligning biological sequences using co-evolution models and informed priors / Muntoni, Anna Paola; Pagnani, Andrea. - In: BIOINFORMATICS. - ISSN 1367-4811. - 39:9(2023). [10.1093/bioinformatics/btad537] | 1-gen-2023 | Muntoni, Anna PaolaPagnani, Andrea | btad537.pdf |
| Direct-coupling analysis of residue coevolution captures native contacts across many protein families / Morcos, F.; Pagnani, Andrea; Lunt, B.; Bertolino, A.; Marks, D. S.; Sander, C.; Zecchina, Riccardo; Onuchic, J. N.; Hwa, T.; Weigt, M.. - In: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. - ISSN 0027-8424. - STAMPA. - 108:(2011), pp. 1293-1301. [10.1073/pnas.1111471108] | 1-gen-2011 | PAGNANI, ANDREAZECCHINA, RICCARDO + | - |
| Efficient generative modeling of protein sequences using simple autoregressive models / Trinquier, Jeanne; Uguzzoni, Guido; Pagnani, Andrea; Zamponi, Francesco; Weigt, Martin. - In: NATURE COMMUNICATIONS. - ISSN 2041-1723. - ELETTRONICO. - 12:(2021). [10.1038/s41467-021-25756-4] | 1-gen-2021 | Guido UguzzoniAndrea Pagnani + | s41467-021-25756-4.pdf |