Archivio Istituzionale della RicercaPAGNANI, ANDREA
PAGNANI, ANDREA
Dipartimento Scienza Applicata e Tecnologia
030845
DCAlign v1.0: Aligning biological sequences using co-evolution models and informed priors
2023 Muntoni, Anna Paola; Pagnani, Andrea
Generating Interacting Protein Sequences using Domain-to-Domain Translation
2023 Meynard-Piganeau, Barthelemy; Fabbri, Caterina; Weigt, Martin; Pagnani, Andrea; Feinauer, Christoph
Relationship between fitness and heterogeneity in exponentially growing microbial populations
2022 Muntoni, Anna Paola; Braunstein, Alfredo; Pagnani, Andrea; De Martino, Daniele; De Martino, Andrea
{LPTD}: a novel linear programming-based topology determination method for cryo-{EM} maps
2022 Behkamal, Bahareh; Naghibzadeh, Mahmoud; Pagnani, Andrea; Reza Saberi, Mohammad; Al Nasr, Kamal
AMaLa: Analysis of Directed Evolution Experiments via Annealed Mutational Approximated Landscape
2021 Sesta, Luca; Uguzzoni, Guido; Fernandez-de-Cossio-Diaz, Jorge; Pagnani, Andrea
Efficient generative modeling of protein sequences using simple autoregressive models
2021 Trinquier, Jeanne; Uguzzoni, Guido; Pagnani, Andrea; Zamponi, Francesco; Weigt, Martin
Expectation propagation on the diluted Bayesian classifier
2021 Braunstein, Alfredo; Gueudre, Thomas; Pagnani, Andrea; Pieropan, Mirko
Unsupervised inference of protein fitness landscape from deep mutational scan
2021 Fernandez-de-Cossio-Diaz, Jorge; Uguzzoni, Guido; Pagnani, Andrea
Aligning biological sequences by exploiting residue conservation and coevolution
2020 Muntoni, Anna Paola; Pagnani, Andrea; Weigt, Martin; Zamponi, Francesco
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.
Compressed sensing reconstruction using Expectation Propagation
2020 Braunstein, Alfredo; Muntoni, Anna Paola; Pagnani, Andrea; Pieropan, Mirko
A common root for coevolution and substitution rate variability in protein sequence evolution
2019 Rizzato, F.; Zamuner, S.; Pagnani, A.; Laio, A.
Nonconvex image reconstruction via expectation propagation
2019 Muntoni, ANNA PAOLA; Díaz Hernández Rojas, Rafael; Braunstein, Alfredo; Pagnani, Andrea; Pérez Castillo, Isaac
The intrinsic dimension of protein sequence evolution
2019 Facco, Elena; Pagnani, Andrea; Russo, Elena Tea; Laio, Alessandro
Somatic mutagenesis in satellite cells associates with human skeletal muscle aging
2018 Franco, Irene; Johansson, Anna; Olsson, Karl; Vrtačnik, Peter; Lundin, Pär; Helgadottir, Hafdis T.; Larsson, Malin; Revêchon, Gwladys; Bosia, Carla; Pagnani, Andrea; Provero, Paolo; Gustafsson, Thomas; Fischer, Helene; Eriksson, Maria
An analytic approximation of the feasible space of metabolic networks
2017 Braunstein, Alfredo; Muntoni, ANNA PAOLA; Pagnani, Andrea
CeRNA crosstalk stabilizes protein expression and affects the correlation pattern of interacting proteins
2017 Martirosyan, Araks; De Martino, Andrea; Pagnani, Andrea; Marinari, Enzo
Inverse problem for multi-body interaction of nonlinear waves
2017 Marruzzo, Alessia; Tyagi, Payal; Antenucci, Fabrizio; Pagnani, Andrea; Leuzzi, Luca
RNAs competing for microRNAs mutually influence their fluctuations in a highly non-linear microRNA-dependent manner in single cells
2017 Bosia, Carla; Sgrò, Francesco; Conti, Laura; Baldassi, Carlo; Cavallo, Federica; Di Cunto, Ferdinando; Turco, Emilia; Pagnani, Andrea; Zecchina, Riccardo
Inter-Protein Sequence Co-Evolution Predicts Known Physical Interactions in Bacterial Ribosomes and the Trp Operon
2016 Feinauer, Christoph; Szurmant, Hendrik; Weigt, Martin; Pagnani, Andrea
| Citazione | Data di pubblicazione | Autori | File |
|---|---|---|---|
| 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 |
| Generating Interacting Protein Sequences using Domain-to-Domain Translation / Meynard-Piganeau, Barthelemy; Fabbri, Caterina; Weigt, Martin; Pagnani, Andrea; Feinauer, Christoph. - In: BIOINFORMATICS. - ISSN 1367-4811. - 39:7(2023). [10.1093/bioinformatics/btad401] | 1-gen-2023 | Andrea PagnaniChristoph Feinauer + | btad401 (1).pdf |
| Relationship between fitness and heterogeneity in exponentially growing microbial populations / Muntoni, Anna Paola; Braunstein, Alfredo; Pagnani, Andrea; De Martino, Daniele; De Martino, Andrea. - In: BIOPHYSICAL JOURNAL. - ISSN 0006-3495. - ELETTRONICO. - 121:10(2022), pp. 1919-1930. [10.1016/j.bpj.2022.04.012] | 1-gen-2022 | Muntoni, Anna PaolaBraunstein, AlfredoPagnani, AndreaDe Martino, Andrea + | mmc2.pdf |
| {LPTD}: a novel linear programming-based topology determination method for cryo-{EM} maps / Behkamal, Bahareh; Naghibzadeh, Mahmoud; Pagnani, Andrea; Reza Saberi, Mohammad; Al Nasr, Kamal. - In: BIOINFORMATICS. - ISSN 1367-4803. - ELETTRONICO. - (2022). [10.1093/bioinformatics/btac170] | 1-gen-2022 | Andrea Pagnani + | - |
| 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 |
| 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 |
| Expectation propagation on the diluted Bayesian classifier / Braunstein, Alfredo; Gueudre, Thomas; Pagnani, Andrea; Pieropan, Mirko. - In: PHYSICAL REVIEW. E. - ISSN 2470-0045. - ELETTRONICO. - 103:4(2021). [10.1103/PhysRevE.103.043301] | 1-gen-2021 | Alfredo BraunsteinThomas GueudréAndrea PagnaniMirko Pieropan | PhysRevE.103.043301.pdf |
| Unsupervised inference of protein fitness landscape from deep mutational scan / Fernandez-de-Cossio-Diaz, Jorge; Uguzzoni, Guido; Pagnani, Andrea. - In: MOLECULAR BIOLOGY AND EVOLUTION. - ISSN 0737-4038. - ELETTRONICO. - 38:1(2021), pp. 318-328. [10.1093/molbev/msaa204] | 1-gen-2021 | Uguzzoni, GuidoPagnani, Andrea + | 2020.03.18.996595v1.full (1).pdf; msaa204.pdf; msaa204.pdf |
| 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 |
| 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 |
| 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 |
| 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 |
| Nonconvex image reconstruction via expectation propagation / Muntoni, ANNA PAOLA; Díaz Hernández Rojas, Rafael; Braunstein, Alfredo; Pagnani, Andrea; Pérez Castillo, Isaac. - In: PHYSICAL REVIEW. E. - ISSN 2470-0053. - ELETTRONICO. - 100:(2019), p. 032134. [10.1103/PhysRevE.100.032134] | 1-gen-2019 | Anna Paola MuntoniAlfredo BraunsteinAndrea Pagnani + | PhysRevE.100.032134.pdf |
| The intrinsic dimension of protein sequence evolution / Facco, Elena; Pagnani, Andrea; Russo, Elena Tea; Laio, Alessandro. - In: PLOS COMPUTATIONAL BIOLOGY. - ISSN 1553-734X. - ELETTRONICO. - 15:4(2019), p. e1006767. [10.1371/journal.pcbi.1006767] | 1-gen-2019 | Pagnani, AndreaLAIO, ALESSANDRO + | journal.pcbi.1006767.pdf |
| Somatic mutagenesis in satellite cells associates with human skeletal muscle aging / Franco, Irene; Johansson, Anna; Olsson, Karl; Vrtačnik, Peter; Lundin, Pär; Helgadottir, Hafdis T.; Larsson, Malin; Revêchon, Gwladys; Bosia, Carla; Pagnani, Andrea; Provero, Paolo; Gustafsson, Thomas; Fischer, Helene; Eriksson, Maria. - In: NATURE COMMUNICATIONS. - ISSN 2041-1723. - ELETTRONICO. - 9:1(2018), p. 800. [10.1038/s41467-018-03244-6] | 1-gen-2018 | BOSIA, CARLAPagnani, Andrea + | s41467-018-03244-6.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 |
| 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 |
| Inverse problem for multi-body interaction of nonlinear waves / Marruzzo, Alessia; Tyagi, Payal; Antenucci, Fabrizio; Pagnani, Andrea; Leuzzi, Luca. - In: SCIENTIFIC REPORTS. - ISSN 2045-2322. - ELETTRONICO. - 7:1(2017), p. 3463. [10.1038/s41598-017-03163-4] | 1-gen-2017 | PAGNANI, ANDREA + | 41598_2017_Article_3163.pdf |
| RNAs competing for microRNAs mutually influence their fluctuations in a highly non-linear microRNA-dependent manner in single cells / Bosia, Carla; Sgrò, Francesco; Conti, Laura; Baldassi, Carlo; Cavallo, Federica; Di Cunto, Ferdinando; Turco, Emilia; Pagnani, Andrea; Zecchina, Riccardo. - In: GENOME BIOLOGY. - ISSN 1474-760X. - ELETTRONICO. - 18:(2017), pp. 17-30. [10.1186/s13059-017-1162-x] | 1-gen-2017 | BOSIA, CARLABALDASSI, CARLOPAGNANI, ANDREA + | s13059-017-1162-x.pdf |
| Inter-Protein Sequence Co-Evolution Predicts Known Physical Interactions in Bacterial Ribosomes and the Trp Operon / Feinauer, Christoph; Szurmant, Hendrik; Weigt, Martin; Pagnani, Andrea. - In: PLOS ONE. - ISSN 1932-6203. - ELETTRONICO. - 11:2(2016), pp. 1-18. [10.1371/journal.pone.0149166] | 1-gen-2016 | FEINAUER, CHRISTOPHPAGNANI, ANDREA + | journal.pone.0149166 (1).PDF |