Archivio Istituzionale della RicercaPAGNANI, ANDREA
PAGNANI, ANDREA
Dipartimento Scienza Applicata e Tecnologia
030845
Mammography classification with multi-view deep learning techniques: investigating graph and transformer-based architectures
2025 Manigrasso, Francesco; Milazzo, Rosario; Russo, Alessandro; Lamberti, Fabrizio; Strand, Fredrik; Pagnani, Andrea; Morra, Lia
Inference of annealed protein fitness landscapes with AnnealDCA
2024 Sesta, Luca; Pagnani, Andrea; Fernandez-de-Cossio-Diaz, Jorge; Uguzzoni, Guido
Unsupervised modeling of mutational landscapes of adeno-associated viruses viability
2024 DE LEONARDIS, Matteo; Fernandez-de-Cossio-Diaz, Jorge; Uguzzoni, Guido; Pagnani, Andrea
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
Small-coupling expansion for multiple sequence alignment
2023 Budzynski, Louise; Pagnani, Andrea
Relationship between fitness and heterogeneity in exponentially growing microbial populations
2022 Muntoni, Anna Paola; Braunstein, Alfredo; Pagnani, Andrea; De Martino, Daniele; De Martino, Andrea
Statistical-physics approaches to RNA molecules, families and networks
2022 Cocco, Simona; DE MARTINO, Andrea; Pagnani, Andrea; Weigt, Martin
{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
adabmDCA: adaptive Boltzmann machine learning for biological sequences
2021 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
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
Solving the α-helix correspondence problem at medium-resolution Cryo-EM maps through modeling and 3D matching
2021 Behkamal, Bahareh; Naghibzadeh, Mahmoud; Pagnani, Andrea; Saberi, Mohammad Reza; Al Nasr, Kamal
Three-Dimensional Graph Matching to Identify Secondary Structure Correspondence of Medium-Resolution Cryo-EM Density Maps
2021 Behkamal, Bahareh; Naghibzadeh, Mahmoud; Saberi, Mohammad Reza; Tehranizadeh, Zeinab Amiri; Pagnani, Andrea; Al Nasr, Kamal
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
Predicting interacting protein pairs by coevolutionary paralog matching
2020 Gueudre, T.; Baldassi, C.; Pagnani, A.; Weigt, M.
| Citazione | Data di pubblicazione | Autori | File |
|---|---|---|---|
| Mammography classification with multi-view deep learning techniques: investigating graph and transformer-based architectures / Manigrasso, Francesco; Milazzo, Rosario; Russo, Alessandro; Lamberti, Fabrizio; Strand, Fredrik; Pagnani, Andrea; Morra, Lia. - In: MEDICAL IMAGE ANALYSIS. - ISSN 1361-8415. - 99:(2025). [10.1016/j.media.2024.103320] | 1-gen-2025 | Francesco ManigrassoRosario MilazzoAlessandro RussoFabrizio LambertiAndrea PagnaniLia Morra + | 1-s2.0-S1361841524002457-main.pdf |
| Inference of annealed protein fitness landscapes with AnnealDCA / Sesta, Luca; Pagnani, Andrea; Fernandez-de-Cossio-Diaz, Jorge; Uguzzoni, Guido. - In: PLOS COMPUTATIONAL BIOLOGY. - ISSN 1553-7358. - ELETTRONICO. - 20:2(2024). [10.1371/journal.pcbi.1011812] | 1-gen-2024 | Sesta, LucaPagnani, AndreaFernandez-de-Cossio-Diaz, JorgeUguzzoni, Guido | journal.pcbi.1011812.pdf |
| Unsupervised modeling of mutational landscapes of adeno-associated viruses viability / DE LEONARDIS, Matteo; Fernandez-de-Cossio-Diaz, Jorge; Uguzzoni, Guido; Pagnani, Andrea. - In: BMC BIOINFORMATICS. - ISSN 1471-2105. - 25:(2024). [10.1186/s12859-024-05823-5] | 1-gen-2024 | Matteo De LeonardisJorge Fernandez-de-Cossio-DiazGuido UguzzoniAndrea Pagnani | s12859-024-05823-5-1.pdf |
| 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 | Barthelemy Meynard-PiganeauAndrea PagnaniChristoph Feinauer + | btad401 (1).pdf |
| Small-coupling expansion for multiple sequence alignment / Budzynski, Louise; Pagnani, Andrea. - In: PHYSICAL REVIEW. E. - ISSN 2470-0045. - ELETTRONICO. - 107:4(2023). [10.1103/physreve.107.044125] | 1-gen-2023 | Budzynski, LouisePagnani, Andrea | PhysRevE.107.044125.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 |
| Statistical-physics approaches to RNA molecules, families and networks / Cocco, Simona; DE MARTINO, Andrea; Pagnani, Andrea; Weigt, Martin. - (2022). | 1-gen-2022 | Andrea De MartinoAndrea Pagnani + | - |
| {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 + | - |
| adabmDCA: adaptive Boltzmann machine learning for biological sequences / Muntoni, Anna Paola; Pagnani, Andrea; Weigt, Martin; Zamponi, Francesco. - In: BMC BIOINFORMATICS. - ISSN 1471-2105. - 22:1(2021), pp. 1-19. [10.1186/s12859-021-04441-9] | 1-gen-2021 | Muntoni, Anna PaolaPagnani, AndreaZamponi, Francesco + | s12859-021-04441-9.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 |
| 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 |
| Solving the α-helix correspondence problem at medium-resolution Cryo-EM maps through modeling and 3D matching / Behkamal, Bahareh; Naghibzadeh, Mahmoud; Pagnani, Andrea; Saberi, Mohammad Reza; Al Nasr, Kamal. - In: JOURNAL OF MOLECULAR GRAPHICS & MODELLING. - ISSN 1093-3263. - 103:(2021). [10.1016/j.jmgm.2020.107815] | 1-gen-2021 | Pagnani, Andrea + | 1-s2.0-S1093326320306045-main.pdf |
| Three-Dimensional Graph Matching to Identify Secondary Structure Correspondence of Medium-Resolution Cryo-EM Density Maps / Behkamal, Bahareh; Naghibzadeh, Mahmoud; Saberi, Mohammad Reza; Tehranizadeh, Zeinab Amiri; Pagnani, Andrea; Al Nasr, Kamal. - In: BIOMOLECULES. - ISSN 2218-273X. - ELETTRONICO. - 11:12(2021). [10.3390/biom11121773] | 1-gen-2021 | Pagnani, Andrea + | biomolecules-11-01773-v2.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 |
| Predicting interacting protein pairs by coevolutionary paralog matching / Gueudre, T.; Baldassi, C.; Pagnani, A.; Weigt, M. (METHODS IN MOLECULAR BIOLOGY). - In: Protein-Protein Interaction Networks[s.l] : Humana Press Inc., 2020. - ISBN 978-1-4939-9872-2. - pp. 57-65 [10.1007/978-1-4939-9873-9_5] | 1-gen-2020 | Pagnani A. + | capitolo_protein_interaction.pdf |