2025 []

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Calcolo Scientifico dell'Università di Parma</em>
<br><font size="5"> Scientific results  </font></font> </b></center><p><hr></html>


[[https://www.hpc.unipr.it/dokuwiki/doku.php?id=calcoloscientifico:userguide#acknowledgement |
The papers listed here describe results made possible in part by the support of the High Performance Computing facility of the University of Parma (HPC.unipr.it) ]]:

===  2025===

  * Marco Malatesta ,Carlo De Rito,Francesca Gasparinia, Giovanni Merici, Davide Dell’Accantera, Giacomo Quilici, Francesco Sansone,and Riccardo Percudani; C11orf54 catalyzes L- xylulose formation in human metabolism: PNAS, July 30, 2025122 (31) e2506597122 
  * Skonieczny, K.†; Di Maiolo, F.†; Venturi, S.†; Iagatti, A.; Ricci, A.; Bertocchi, F.; Gryko, D. T.*; Lapini, A.* How nitro group position determines the emission properties of diketopyrrolopyrroles, Phys. Chem. Chem. Phys., 2025,27, 5965-5972 †: these Authors contributed equally.

===  2024===

  * Matteo Dubbini, Federico Bonvini, Lorenzo Savi, and Francesco Di Maiolo; Turning on Organic Radical Emitters; The Journal of Physical Chemistry C; DOI: 10.1021/acs.jpcc.4c04362 
  * Andrea Landi, D. K. Andrea Phan Huu, and Anna Painelli; From the Fermi Golden Rule to Open Quantum Systems: Basic Concepts on Non-radiative Rates The Journal of Physical Chemistry C; DOI: 10.1021/acs.jpcc.4c05567 
  * Bedogni, M.; Di Maiolo, F. "Singlet–Triplet Inversion in Triangular Boron Carbon Nitrides" Journal of Chemical Theory and Computation DOI:10.1021/acs.jctc.4c00706 (2024)
  * Di Maiolo, F.; Phan Huu, D. K. A.; Giavazzi, D.; Landi, A.; Racchi, O.; Painelli A. "Shedding light on thermally-activated delayed fluorescence" Chemical Science 15, 5434-5450 (2024).
  * Perugino F, Pedroni L, Galaverna G, Dall'Asta C, Dellafiora L. Virtual display of targets: A new level to rise the current understanding of ochratoxin A toxicity from a molecular standpoint. Toxicology. Published online March 2, 2024. doi:10.1016/j.tox.2024.153765
  * Pedroni L, Perugino F, Magnaghi F, Dall’Asta C, Galaverna G, Dellafiora L. Free fatty acid receptors beyond fatty acids: A computational journey to explore peptides as possible binders of GPR120. Current Research in Food Science. Volume 8, 2024. doi:10.1016/j.crfs.2024.100710
  * Battiston, P., Gamba, S., Santoro, A. (2024). Machine learning and the optimization of prediction-based policies. Technological Forecasting and Social Change, 199, 123080
  * Bedini A, Elisi GM, Fanini F, Retini M, Scalvini L, Pasquini S, Contri C, Varani K, Spadoni G, Mor M, Vincenzi F, Rivara S. Binding and unbinding of potent melatonin receptor ligands: mechanistic simulations and experimental evidence. J. Pineal Res. 2024 76:e12941

===  2023 ===

  * Arafet K, Scalvini L, Galvani F, Martí S, Moliner V, Mor M, Lodola A. Mechanistic modeling of Lys745 sulfonylation in EGFR C797S reveals chemical determinants for inhibitor activity and discriminates reversible from irreversible agents. J. Chem. Inf. Model. 2023 63, 1301-1312.
  * Galvani F, Pala D, Cuzzolin A, Scalvini L, Lodola A, Mor M, Rizzi A. Unbinding kinetics of muscarinic M3 receptor antagonists explained by metadynamics simulations. J. Chem. Inf. Model. 2023 63, 2842-2856.
  * Guidetti L, Zappia A, Scalvini L, Ferrari FR, Giorgio C, Castelli R, Galvani F, Vacondio F, Rivara S, Mor M, Urbinati C, Rusnati M, Tognolini M, Lodola A. Molecular determinants of EphA2 and EphB2 antagonism enable the design of ligands with improved selectivity. J. Chem. Inf. Model. 2023 63, 6900-6911
  * Buoli Comani, V., De Bei, O., Cozzi, M., Marchesani, F., Marchetti, M., Paris, G., Ronda, L., Campanini, B., Luisi, B.F., Bettati, S., Faggiano, S. (2023). Solving the Cryo-EM structure of a complex between human hemoglobin and a bacterial receptor to model new protein-protein interaction inhibitors. In "XXII Giornata della Chimica dell’Emilia Romagna 2023"
  * Rabasco, M., & Battiston, P. (2023). Predicting the deterrence effect of tax audits. A machine learning approach. Metroeconomica, 1–XXX. https://onlinelibrary.wiley.com/doi/10.1111/meca.12420
  * Matteo Bedogni, Davide Giavazzi, Francesco Di Maiolo, Anna Painelli Shining Light on Inverted Singlet–Triplet Emitters J. Chem. Theory Comput. (2023) https://pubs.acs.org/doi/full/10.1021/acs.jctc.3c01112
  * Giavazzi, D.; Di Maiolo, F.; Painelli, A. The fate of molecular excited states: modeling donor-acceptor dyes Phys. Chem. Chem. Phys., 24, 5555-5563 (2022).
  * Giavazzi, D.; Saseendran, S.; Di Maiolo, F.; Painelli, A. A Comprehensive Approach to Exciton Delocalization and Energy Transfer J. Chem. Theory Comput., 19, 2, 436-447 (2023). (COVER PAPER).
  * Swathi, K.; Sujith, M.; Divya, P. S.; Varghese P, M.; Delledonne, A.; Phan Huu, D. K. A.; Di Maiolo, F.; Terenziani, F.; Lapini, A.; Painelli, A.; Sissa, C.; Thomas K. G. From symmetry breaking to symmetry swapping: is Kasha’s rule violated in multibranched phenyleneethynylenes? Chem. Sci., 14, 1986-1996 (2023).
  * Crovini, E.; Dhali, R.; Sun, D.; Matulaitis, T.; Comerford, T.; Slawin, A. M. Z.; Sissa, C.; Azzolin, F.; Di Maiolo, F.; Painelli, A.; Zysman-Colman, E. Molecular geometry and the photophysics of thermally activated delayed fluorescence: the strange case of DMAC-py-TRZ J. Mater. Chem. C, doi:10.1039/D2TC05213J (2023).
  * Giavazzi, D.; Schumacher, M.; Grisanti, L.; Anzola, M.; Di Maiolo, F.; Zablocki, J.; Lützen, A.; Schiek, M.; Painelli, A. A Marvel of Chiral Squaraine Aggregates: Chiroptical Spectra beyond the Exciton Model J. Mater. Chem. C, doi:10.1039/D2TC05555D (2023).
  * Bardi, B; Giavazzi, D.; Iagatti, A.; Ferrari, E.; Di Donato, M.; Phan Huu, D. K. A.; Di Maiolo, F.; Sissa, C.; Masino, M.; Lapini, A.*; Painelli, A.* Solid State Solvation: a fresh view Mater. Horiz., doi:10.1039/D3MH00988B (2023).
  * Pedroni L, Perugino F, Kurtaga A, Galaverna G, Dall'Asta C, Dellafiora L. The bitter side of toxicity: A big data analysis spotted the interaction between trichothecenes and bitter receptors. Food Research International. 2023. 173: 113284. doi: 10.1016/j.foodres.2023.113284
  * Pedroni L, Louisse J, Dorne JCM, Dall'Asta C, Dellafiora L. A computational study on the biotransformation of alkenylbenzenes by a selection of CYPs: Reflections on their possible bioactivation. Toxicology. 2023. 488:153471. doi: 10.1016/j.tox.2023.153471
  * Louisse J, Dellafiora L, van den Heuvel JJMW, Rijkers D, Leenders L, Dorne JCM, Punt A, Russel FGM, Koenderink JB. Perfluoroalkyl substances (PFASs) are substrates of the renal human organic anion transporter 4 (OAT4). Arch Toxicol. 2023. 97(3):685-696. doi: 10.1007/s00204-022-03428-6
  * Pedroni L, Louisse J, Punt A, Dorne JLCM, Dall'Asta C, Dellafiora L. A Computational Inter-Species Study on Safrole Phase I Metabolism-Dependent Bioactivation: A Mechanistic Insight into the Study of Possible Differences among Species. Toxins (Basel). 2023. 15(2):94. doi:10.3390/toxins15020094
  * Pedroni L, Perugino F, Galaverna G, Dall'Asta C, Dellafiora L. An In Silico Framework to Mine Bioactive Peptides from Annotated Proteomes: A Case Study on Pancreatic Alpha Amylase Inhibitory Peptides from Algae and Cyanobacteria. Nutrients. 2022. 14(21):4680. doi: 10.3390/nu14214680
  * Dadousis, C., M. Ablondi, C. Cipolat-Gotet, J.-T. van Kaam, R. Finocchiaro, M. Marusi, M. Cassandro, A. Sabbioni, and A. Summer. 2023. Genomic inbreeding coefficients using imputed genotypes: assessing differences among SNP panels in Holstein-Friesian dairy cows. Frontiers in Veterinary Science 10 https://www.frontiersin.org/articles/10.3389/fvets.2023.1142476/full
  * Dembech, E., Malatesta, M., De Rito, C., Mori, G., Cavazzini, D., Secchi, A., Morandin, F., Percudani, R. Identification of hidden associations among eukaryotic genes through statistical analysis of coevolutionary transitions. PNAS, April, 2023. https://doi.org/10.1073/pnas.2218329120

=== 2022 ===

  * Elisi GM, Scalvini L, Lodola A, Mor M, Rivara S. Free-energy simulations support a lipophilic binding route for melatonin receptors. J. Chem. Inf. Model. 2022 62, 210-222.
  * Galvani F, Scalvini L, Rivara S, Lodola A, Mor M. Mechanistic modeling of monoglyceride lipase covalent modification elucidates the role of leaving group expulsion and discriminates inhibitors with high and low potency. J. Chem. Inf. Model. 2022 62, 2771-2787.
  * Mari M, Elisi GM, Bedini A, Lucarini S, Retini M, Lucini V, Scaglione F, Vincenzi F, Varani K, Castelli R, Mor M, Rivara S, Spadoni G. 2-Arylmelatonin analogues: probing the 2-phenyl binding pocket of melatonin MT1 and MT2 receptors. Eur. J. Med. Chem. 2022 243:114762.
  * Gianmarco Lazzini, Luca Romoli, Francesco Fuso, Fluid-driven bacterial accumulation in proximity of laser-textured surfaces, Colloids and Surfaces B: Biointerfaces, Volume 217, 2022, 112654, ISSN 0927-7765, https://doi.org/10.1016/j.colsurfb.2022.112654
  * Lammi C, Boschin G, Bartolomei M, Arnoldi A, Galaverna G, Dellafiora L. Mechanistic Insights into Angiotensin I-Converting Enzyme Inhibitory Tripeptides to Decipher the Chemical Basis of Their Activity [published online ahead of print, 2022 Sep 8]. J Agric Food Chem. 2022;10.1021/acs.jafc.2c04755. doi:10.1021/acs.jafc.2c04755
  * Dellafiora L., Magnaghi F, Galaverna G, Dall'Asta C. A mechanistic investigation on kokumi-active γ-Glutamyl tripeptides – a computational study to understand molecular basis of their activity and to identify novel potential kokumi-tasting sequences. [published online ahead of print, 2022 Sep 14] Food Res Int 2022; doi:10.1016/j.foodres.2022.111932
  * Pedroni L, Dellafiora L, Varrà MO, Galaverna G, Ghidini S. In silico study on the Hepatitis E virus RNA Helicase and its inhibition by silvestrol, rocaglamide and other flavagline compounds. Sci Rep 2022, 12: 15512; doi:10.1038/s41598-022-19818-w
  * Dadousis C., M. Ablondi, C. Cipolat-Gotet, J.T. Van Kaam, M. Marusi, M. Cassandro, A. Sabbioni and A. Summer. Genomic inbreeding coefficients using imputed genotypes: assessing different estimators in Holstein-Friesian dairy cows. J Dairy Sci. doi: 10.3168/jds.2021-21125 [[https://doi.org/10.3168/jds.2021-21125]]
  * Battiston, P., Sacco, P., Stanca, L. (2022) Cover effects on citations uncovered: Evidence from Nature. Journal of Informetrics. 16(2), 101293. [[https://doi.org/10.1016/j.joi.2022.101293]]
  * De Bei O., Marchetti M., Ronda L., Gianquinto E., Lazzarato L., Chirgadze D.Y., Hardwick S.W., Cooper L.R., Spyrakis F., Luisi B.F., Campanini B., & Bettati S., Cryo-EM structures of staphylococcal IsdB bound to human hemoglobin reveal the process of heme extraction. Proceedings of the National Academy of Sciences. 2022 Apr 5;119(14):e2116708119. https://doi.org/10.1073/pnas.2116708119
  * Dazzi, S., Vacondio, R., Mignosa, P., & Aureli, F. (2022). Assessment of pre-simulated scenarios as a non-structural measure for flood management in case of levee-breach inundations. International Journal of Disaster Risk Reduction, 102926. https://doi.org/10.1016/j.ijdrr.2022.102926
  * Ferrari, A., & Vacondio, R. (2022). An augmented HLLEM ADER numerical model parallel on GPU for the porous Shallow Water Equations. Computers & Fluids, 105360. https://doi.org/10.1016/j.compfluid.2022.105360
  * Tessoni, V., Amoretti, M. (2022). Advanced statistical and machine learning methods for multi-step multivariate time series forecasting in predictive maintenance. 3rd International Conference on Industry 4.0 and Smart Manufacturing. Procedia Computer Science, vol. 200, pp. 748-757. DOI:10.1016/j.procs.2022.01.273 
  * Lombardo, G., Pellegrino, M., Tomaiuolo, M., Cagnoni, S., Mordonini, M., Giacobini, M., & Poggi, A. (2022). Fine-Grained Agent-Based Modeling to Predict Covid-19 Spreading and Effect of Policies in Large-Scale Scenarios. IEEE Journal of Biomedical and Health Informatics.
  * Pellegrino, M., Lombardo, G., Cagnoni, S., & Poggi, A. (2022). High-Performance Computing and ABMS for High-Resolution COVID-19 Spreading Simulation. Future Internet, 14(3), 83.
  * Dorne J.L.C.M., Cirlini M., Louisse J., Pedroni L., Galaverna G., Dellafiora L. A Computational Understanding of Inter-Individual Variability in CYP2D6 Activity to Investigate the Impact of Missense Mutations on Ochratoxin A Metabolism. 2022. Toxins. 14, 207. https://doi.org/10.3390/toxins14030207
  * Peracchi, A.; Polverini, E., Using Steady-State Kinetics to Quantitate Substrate Selectivity and Specificity: A Case Study with Two Human Transaminases. Molecules, 27, 1398 (2022).DOI: 10.3390/molecules27041398

=== 2021 ===

  * Dazzi, S., Shustikova, I., Domeneghetti, A., Castellarin, A., & Vacondio, R. (2021). Comparison of two modelling strategies for 2D large-scale flood simulations. Environmental Modelling & Software, 146, 105225 https://doi.org/10.1016/j.envsoft.2021.105225
  * Dazzi, S., Vacondio, R., & Mignosa, P. (2021). Flood Stage Forecasting Using Machine-Learning Methods: A Case Study on the Parma River (Italy). Water, 13, 1612. https://doi.org/10.3390/w13121612
  * Dazzi, S., Mignosa, P., Pianforini, M., Bertuzzi, F., & Vacondio, R. (2021). Assessment of flood hazard induced by levee breaches in the middle Po Valley. In Tecniche per la difesa del suolo e dall’inquinamento - Atti della 42^ Edizione (a cura di G. Frega e F. Macchione).
  * Aureli, F., Mignosa, P., Prost, F., & Dazzi, S. (2021). Hydrological and Hydraulic Flood Hazard Modeling in Poorly Gauged Catchments: An Analysis in Northern Italy. Hydrology, 8(4), 149, https://doi.org/10.3390/hydrology8040149 
  * Pellegrino, M., Lombardo, G., Mordonini, M., Tomaiuolo, M., Cagnoni, S., & Poggi, A. (2021). ActoDemic: A Distributed Framework for Fine-Grained Spreading Modeling and Simulation in Large Scale Scenarios. In " 22nd Workshop "From Objects to Agents", WOA 2021" (pp. 194-209).
  * Lammi C, Boschin G, Bollati C, Arnoldi A, Galaverna G, Dellafiora L., A heuristic, computer-driven and top-down approach to identify novel bioactive peptides: A proof-of-principle on angiotensin I converting enzyme inhibitory peptides. 2021. Food Res Int. 150(Pt A), 110753. doi: 10.1016/j.foodres.2021.110753
  * Del Favero G, Aichinger G, Hohenbichler J, Marko D, Dall'Asta C, Dellafiora L., A target fishing study to spot possible biological targets of fusaric acid: Inhibition of protein kinase-A and insights on the underpinning mechanisms. 2022. Food Chem Toxicol. 159:112663. doi: 10.1016/j.fct.2021.112663
  * Leo L.; Bridelli M. G.; Polverini E., Reversible processes in collagen dehydration: A molecular dynamics study. Archives of Biochemistry and Biophysics, 714: 109079 (2021). DOI: 10.1016/j.abb.2021.109079
  * Brunoni F., Rolli E., Polverini E., Spichal L., Ricci A., The adjuvant activity of two urea derivatives on cytokinins: an example of serendipitous dual effect. Plant Growth Regulation, 95: 169-190 (2021). DOI: 10.1007/s10725-021-00735-3
  * Fontana, F., Mancabelli, L., Lugli, G. A., Taracchini, C., Alessandri, G., Longhi, G., Anzalone, R., Viappiani, A., Famo, R., Brognan, M., Micondo, K. H., Turroni, F., Ventura, M., D’Alfonso, R., & Milani, C. (2021). Investigating the infant gut microbiota in developing countries: worldwide metagenomic meta‐analysis involving infants living in sub‐urban areas of Côte d’Ivoire. Environmental Microbiology Reports. https://doi.org/10.1111/1758-2229.12960
  * Lugli, G. A., Alessandri, G., Milani, C., Viappiani, A., Fontana, F., Tarracchini, C., Mancabelli, L., Argentini, C., Ruiz, L., Margolles, A., van Sinderen, D., Turroni, F., & Ventura, M. (2021). Genetic insights into the dark matter of the mammalian gut microbiota through targeted genome reconstruction. Environmental Microbiology, 23(6), 3294–3305. https://doi.org/10.1111/1462-2920.15559
  * Mancabelli, L., Mancino, W., Lugli, G. A., Argentini, C., Longhi, G., Milani, C., Viappiani, A., Anzalone, R., Bernasconi, S., van Sinderen, D., Ventura, M., & Turroni, F. (2021). Amoxicillin-Clavulanic Acid Resistance in the Genus Bifidobacterium. Applied and Environmental Microbiology, 87(7), 1–16. https://doi.org/10.1128/AEM.03137-20
  * Mancabelli, L., Mancino, W., Lugli, G. A., Milani, C., Viappiani, A., Anzalone, R., Longhi, G., van Sinderen, D., Ventura, M., & Turroni, F. (2021). Comparative genome analyses of Lactobacillus crispatus isolated from different ecological niches reveal an environmental adaptation of this species to the human vaginal environment. Applied and Environmental Microbiology, 87(8), 1–21. https://doi.org/10.1128/AEM.02899-20
  * Mancabelli, L., Milani, C., Anzalone, R., Alessandri, G., Lugli, G. A., Tarracchini, C., Fontana, F., Turroni, F., & Ventura, M. (2021). Free DNA and Metagenomics Analyses: Evaluation of Free DNA Inactivation Protocols for Shotgun Metagenomics Analysis of Human Biological Matrices. Frontiers in Microbiology, 12. https://doi.org/10.3389/FMICB.2021.749373
  * Mancabelli, L., Tarracchini, C., Milani, C., Lugli, G. A., Fontana, F., Turroni, F., van Sinderen, D., & Ventura, M. (2021). Vaginotypes of the human vaginal microbiome. Environmental Microbiology, 23(3), 1780–1792. https://doi.org/10.1111/1462-2920.15441
  * Milani, C., Lugli, G. A., Fontana, F., Mancabelli, L., Alessandri, G., Longhi, G., Anzalone, R., Viappiani, A., Turroni, F., van Sinderen, D., & Ventura, M. (2021). METAnnotatorX2: a Comprehensive Tool for Deep and Shallow Metagenomic Data Set Analyses. MSystems, 6(3). https://doi.org/10.1128/msystems.00583-21
  * Tarracchini, C., Milani, C., Longhi, G., Fontana, F., Mancabelli, L., Pintus, R., Lugli, G. A., Alessandri, G., Anzalone, R., Viappiani, A., Turroni, F., Mussap, M., Dessì, A., Cesare Marincola, F., Noto, A., De Magistris, A., Vincent, M., Bernasconi, S., Picaud, J.-C., … Ventura, M. (2021). Unraveling the Microbiome of Necrotizing Enterocolitis: Insights in Novel Microbial and Metabolomic Biomarkers. Microbiology Spectrum, 9(2). https://doi.org/10.1128/SPECTRUM.01176-21
  * Tarracchini, C., Milani, C., Lugli, G. A., Mancabelli, L., Fontana, F., Alessandri, G., Longhi, G., Anzalone, R., Viappiani, A., Turroni, F., van Sinderen, D., & Ventura, M. (2021). Phylogenomic disentangling of the Bifidobacterium longum subsp. infantis taxon. Microbial Genomics, 7(7). https://doi.org/10.1099/MGEN.0.000609
  * Turroni, F., Milani, C., Ventura, M., & van Sinderen, D. (2021). The human gut microbiota during the initial stages of life: insights from bifidobacteria. Current Opinion in Biotechnology, 73, 81–87. https://doi.org/10.1016/J.COPBIO.2021.07.012
  * DI LAZZARO, P., ATKINSON, A.C., IACOMUSSI, P., RIANI, M., RICCI, M., WADHAMS, P. (2020). Statistical and Proactive Analysis of an Inter-Laboratory Comparison: The Radiocarbon Dating of the Shroud of Turin. Entropy, 22, 926.  https://www.mdpi.com/1099-4300/22/9/926
  * ATKINSON A.C., RIANI M., CORBELLINI A. (2021). The Box-Cox Transformation: Review and Extensions, Statistical Science, 36, p. 239-255, DOI: 10.1214/20-STS778
  * TORTI F., RIANI M., MORELLI G. (2021). Semiautomatic robust regression clustering of international trade data, Statistical Methods and Applications, (open access) https://link.springer.com/content/pdf/10.1007/s10260-021-00569-3.pdf
  * RIANI M., HUBERT G. (2021). Special issue in robust statistics, Editorial, (open access) https://link.springer.com/article/10.1007/s40300-021-00213-w  
  * SALINI S., LAURINI F., MORELLI G., RIANI M. AND CERIOLI A. (2021). Covariance matrices of S robust regression estimators, Journal of Statistical Computation and Simulation, DOI:10.1080/00949655.2021.1972300 https://doi.org/10.1080/00949655.2021.1972300 
  * ATKINSON A.C., RIANI M., CORBELLINI A. MORELLI G. (2021), ACE,AVAS and Robust Data Transformations: Performance of Investment Funds”, in Statistical Learning and Modeling in Data Analysis - Methods and Applications, Balzano S., Porzio G.C., Salvatore R., Vistocco D., Vichi M. (eds.). Series in Studies in Classiﬁcation, Data Analysis, and Knowledge Organization, Springer, pp. 1-8
  * D. Ferrari, I. Tavernelli, M. Amoretti. Deterministic algorithms for compiling quantum circuits with recurrent patterns. Quantum Information Processing, vol. 20, no. 6, 2021. https://doi.org/10.1007/s11128-021-03150-9
  * Levante, A.; Lazzi, C.; Vatsellas, G.; Chatzopoulos, D.; Dionellis, V.S.; Makrythanasis, P.; Neviani, E.; Folli, C. Genome Sequencing of five Lacticaseibacillus Strains and Analysis of Type I and II Toxin-Antitoxin System Distribution. Microorganisms 2021, 9, 648. https://doi.org/10.3390/microorganisms9030648
  * Fabio Baroni, Mariana Gallo, Luigia Pazzagli, Simone Luti, Ivan Baccelli, Alberto Spisni, Thelma A. Pertinhez, A mechanistic model may explain the dissimilar biological efficiency of the fungal elicitors cerato-platanin and cerato-populin, Biochimica et Biophysica Acta (BBA) - General Subjects, Volume 1865, Issue 5, 2021, 129843, ISSN 0304-4165, https://doi.org/10.1016/j.bbagen.2021.129843 (http://www.sciencedirect.com/science/article/pii/S0304416521000027)
  * D. Ferrari, A.S. Cacciapuoti, M. Amoretti, M. Caleffi, Compiler Design for Distributed Quantum Computing, IEEE Trans. on Quantum Engineering, vol. 2, no. 4100720, 2021, https://doi:10.1109/TQE.2021.3053921
  * G. Lazzini, A.H.A. Lutey, L. Romoli, F. Fuso, Molecular dynamics model for the antibactericity of textured surfaces, Colloids and Surfaces B: Biointerfaces Volume 199, March 2021 https://www.sciencedirect.com/science/article/abs/pii/S0927776520308602

=== 2020 ===

  * Aureli, F., Prost, F., Vacondio, R., Dazzi, S., & Ferrari, A. (2020). A GPU-accelerated Shallow Water scheme for surface runoff simulations. Water, 12, 637, https://doi.org/10.3390/w12030637 
  * Ferrari, A., & Viero, D. P. (2020). Floodwater pathways in urban areas: A method to compute porosity fields for anisotropic subgrid models in differential form. Journal of Hydrology, 589, 125193. https://doi.org/10.1016/j.jhydrol.2020.125193
  * Mignosa, P., Ferrari, A., Dazzi, S., & Vacondio, R. (2020). Scenari di allagamento causati da dam-break/ dam-breach a valle di casse di espansione. In Tecniche per la difesa del suolo e dall’inquinamento - Atti della 41^ Edizione (a cura di G. Frega e F. Macchione).
  * Lombardo, G., & Poggi, A. (2020, September). A preliminary experimentation for large scale epidemic forecasting simulations. In WOA (Vol. 1613, p. 28).
  * Polverini E., Schackert F.K., Losi, A., Interplay among the “flipping” glutamine, a conserved phenylalanine, water and hydrogen bonds within a blue-light sensing LOV domain. Photochem. Photobiol. Sci., 19: 892-904 (2020). DOI: 10.1039/d0pp00082e
  * Alessandri, G., Argentini, C., Milani, C., Turroni, F., Cristina Ossiprandi, M., van Sinderen, D., & Ventura, M. (2020). Catching a glimpse of the bacterial gut community of companion animals: a canine and feline perspective. Microbial Biotechnology, 13(6), 1708–1732. https://doi.org/10.1111/1751-7915.13656
  * Alessandri, G., Milani, C., Mancabelli, L., Longhi, G., Anzalone, R., Lugli, G. A., Duranti, S., Turroni, F., Ossiprandi, M. C., van Sinderen, D., & Ventura, M. (2020). Deciphering the Bifidobacterial Populations within the Canine and Feline Gut Microbiota. Applied and Environmental Microbiology, 86(7). https://doi.org/10.1128/AEM.02875-19
  * Lugli, G. A., Duranti, S., Milani, C., Mancabelli, L., Turroni, F., Alessandri, G., Longhi, G., Anzalone, R., Viappinai, A., Tarracchini, C., Bernasconi, S., Yonemitsu, C., Bode, L., Goran, M. I., Ossiprandi, M. C., van Sinderen, D., & Ventura, M. (2020). Investigating bifidobacteria and human milk oligosaccharide composition of lactating mothers. FEMS Microbiology Ecology, 96(5). https://doi.org/10.1093/femsec/fiaa049
  * Duranti, S., Lugli, G. A., Viappiani, A., Mancabelli, L., Alessandri, G., Anzalone, R., Longhi, G., Milani, C., Ossiprandi, M. C., Turroni, F., & Ventura, M. (2020). Characterization of the phylogenetic diversity of two novel species belonging to the genus Bifidobacterium: Bifidobacterium cebidarum sp. nov. and Bifidobacterium leontopitheci sp. nov. International Journal of Systematic and Evolutionary Microbiology, 70(4), 2288–2297. https://doi.org/10.1099/IJSEM.0.004032
  * Duranti, S., Ruiz, L., Lugli, G. A., Tames, H., Milani, C., Mancabelli, L., Mancino, W., Longhi, G., Carnevali, L., Sgoifo, A., Margolles, A., Ventura, M., Ruas-Madiedo, P., & Turroni, F. (2020). Bifidobacterium adolescentis as a key member of the human gut microbiota in the production of GABA. Scientific Reports, 10(1). https://doi.org/10.1038/S41598-020-70986-Z
  * Fontana, F., Alessandri, G., Lugli, G. A., Mancabelli, L., Longhi, G., Anzalone, R., Viappiani, A., Ventura, M., Turroni, F., & Milani, C. (2020). Probiogenomics Analysis of 97 Lactobacillus crispatus Strains as a Tool for the Identification of Promising Next-Generation Probiotics. Microorganisms, 9(1), 1–14. https://doi.org/10.3390/MICROORGANISMS9010073
  * Lugli, G. A., Alessandri, G., Milani, C., Mancabelli, L., Ruiz, L., Fontana, F., Borragán, S., González, A., Turroni, F., Ossiprandi, M. C., Margolles, A., Sinderen, D., & Ventura, M. (2020). Evolutionary development and co‐phylogeny of primate‐associated bifidobacteria. Environmental Microbiology, 22(8), 1462-2920.15108. https://doi.org/10.1111/1462-2920.15108
  * Lugli, G. A., Tarracchini, C., Alessandri, G., Milani, C., Mancabelli, L., Turroni, F., Neuzil-Bunesova, V., Ruiz, L., Margolles, A., & Ventura, M. (2020). Decoding the Genomic Variability among Members of the Bifidobacterium dentium Species. Microorganisms, 8(11), 1–18. https://doi.org/10.3390/MICROORGANISMS8111720
  * Mancabelli, L., Milani, C., Lugli, G. A., Fontana, F., Turroni, F., van Sinderen, D., & Ventura, M. (2020). The impact of primer design on amplicon-based metagenomic profiling accuracy: Detailed insights into bifidobacterial community structure. Microorganisms, 8(1). https://doi.org/10.3390/microorganisms8010131
  * Mancabelli, L., Tarracchini, C., Milani, C., Lugli, G. A., Fontana, F., Turroni, F., van Sinderen, D., & Ventura, M. (2020). Multi-population cohort meta-analysis of human intestinal microbiota in early life reveals the existence of infant community state types (ICSTs). Computational and Structural Biotechnology Journal, 18, 2480–2493. https://doi.org/10.1016/j.csbj.2020.08.028
  * Milani, C., Alessandri, G., Mancabelli, L., Mangifesta, M., Lugli, G. A., Viappiani, A., Longhi, G., Anzalone, R., Duranti, S., Turroni, F., Ossiprandi, M. C., Sinderen, D. van, & Ventura, M. (2020). Multi-omics Approaches To Decipher the Impact of Diet and Host Physiology on the Mammalian Gut Microbiome. Applied and Environmental Microbiology, 86(23). https://doi.org/10.1128/AEM.01864-20
  * Milani, C., Alessandri, G., Mangifesta, M., Mancabelli, L., Lugli, G. A., Fontana, F., Longhi, G., Anzalone, R., Viappiani, A., Duranti, S., Turroni, F., Costi, R., Annicchiarico, A., Morini, A., Sarli, L., Ossiprandi, M. C., van Sinderen, D., & Ventura, M. (2020). Untangling Species-Level Composition of Complex Bacterial Communities through a Novel Metagenomic Approach. MSystems, 5(4). https://doi.org/10.1128/msystems.00404-20
  * Milani, C., Fontana, F., Alessandri, G., Mancabelli, L., Lugli, G. A., Longhi, G., Anzalone, R., Viappiani, A., Duranti, S., Turroni, F., Ossiprandi, M. C., van Sinderen, D., & Ventura, M. (2020). Ecology of lactobacilli present in italian cheeses produced from raw milk. Applied and Environmental Microbiology, 86(12). https://doi.org/10.1128/AEM.00139-20
  * Tarracchini, C., Lugli, G. A., Mancabelli, L., Milani, C., Turroni, F., & Ventura, M. (2020). Assessing the Genomic Variability of Gardnerella vaginalis through Comparative Genomic Analyses: Evolutionary and Ecological Implications. Applied and Environmental Microbiology, 87(1), 1–16. https://doi.org/10.1128/AEM.02188-20
  * Ticinesi, A., Mancabelli, L., Tagliaferri, S., Nouvenne, A., Milani, C., Del Rio, D., Lauretani, F., Maggio, M. G., Ventura, M., & Meschi, T. (2020). The Gut-Muscle Axis in Older Subjects with Low Muscle Mass and Performance: A Proof of Concept Study Exploring Fecal Microbiota Composition and Function with Shotgun Metagenomics Sequencing. International Journal of Molecular Sciences, 21(23), 1–16. https://doi.org/10.3390/IJMS21238946
  * Turroni, F., Milani, C., Duranti, S., Lugli, G. A., Bernasconi, S., Margolles, A., Di Pierro, F., Van Sinderen, D., & Ventura, M. (2020). The infant gut microbiome as a microbial organ influencing host well-being. In Italian Journal of Pediatrics (Vol. 46, Issue 1). BioMed Central Ltd. https://doi.org/10.1186/s13052-020-0781-0
  * Lombardo, G., & Poggi, A. (2020, September). A preliminary experimentation for large scale epidemic forecasting simulations. In " 21st Workshop From Objects to Agents", WOA 2020, pp. 28-36
  * L. Gaudio, M. Kobayashi, G. Caire and G. Colavolpe, "Joint Radar Target Detection and Parameter Estimation with MIMO OTFS," 2020 IEEE Radar Conference (RadarConf20), Florence, Italy, 2020, pp. 1-6, doi: 10.1109/RadarConf2043947.2020.9266546.
  * L. Gaudio, M. Kobayashi, G. Caire and G. Colavolpe, "On the Effectiveness of OTFS for Joint Radar Parameter Estimation and Communication," in IEEE Transactions on Wireless Communications, vol. 19, no. 9, pp. 5951-5965, Sept. 2020, doi: 10.1109/TWC.2020.2998583.
  * M. Morini, A. Ugolini and G. Colavolpe, "Detection of Variable Length PLH Codes for the DVB-S2X System," 2020 10th Advanced Satellite Multimedia Systems Conference and the 16th Signal Processing for Space Communications Workshop (ASMS/SPSC), Graz, Austria, 2020, pp. 1-7, doi: 10.1109/ASMS/SPSC48805.2020.9268824.
  * Morandin, F., Amato, G., Fantozzi, M., ...Metta, C., Parton, M. SAI: A sensible artificial intelligence that plays with handicap and targets high scores in 9.Frontiers in Artificial Intelligence and Applications, 2020, 325, pp. 403–410
  * Dhali, R., Phan Huu, F., Sissa, F., Terenziani, F., Painelli, A.Understanding TADF: a joint experimental and theoretical study of DMAC-TRZ Phys. Chem. Chem. Phys., 2021, 23, 378
  * Anzola, M., Sissa, C., Painelli, A., Hassanali, A. A., Grisanti, L. Understanding Forster Energy Transfer through the Lens of Molecular Dynamics Journal of Chemical Theory and Computation 2020 16 (12), 7281
  * Phan Huu, D.K.A., Bertocchi, F., Sissa, F., Terenziani, F., Painelli, A. PCCP Hot Article Optical spectra of organic dyes in condensed phases: the role of the medium polarizability Phys. Chem. Chem. Phys., 2020, 22, 25483
  * Swathi, K., Sissa, C., Painelli, A., Thomas, K.G. Supramolecular chirality: a caveat in assigning the handedness of chiral aggregates (2020) Chemical Communications, 56 (59), pp. 8281.
  * Phan Huu, D.K.A., Dhali, R., Pieroni, C., Di Maiolo, F., Sissa, C., Terenziani, F., Painelli, A. Antiadiabatic View of Fast Environmental Effects on Optical Spectra (2020) Physical Review Letters, 124 (10), 107401. 
  * Di Maiolo, F., Painelli, A. PCCP Hot Paper Dynamical disorder and resonance energy transfer: A novel quantum-classical approach (2020) Physical Chemistry Chemical Physics, 22, 1061.
  * N-Acylethanolamine Acid Amidase (NAAA): Mechanism of Palmitoylethanolamide Hydrolysis Revealed by Mechanistic Simulations, Laura Scalvini, Andrea Ghidini, Alessio Lodola, Donatella Callegari, Silvia Rivara, Daniele Piomelli, and Marco Mor, ACS Catalysis 2020 10 (20), 11797-11813 DOI: 10.1021/acscatal.0c02903
  * Malatesta, M., Mori, G., Acquotti, D. et al. Birth of a pathway for sulfur metabolism in early amniote evolution. Nat Ecol Evol 4, 1239–1246 (2020). https://doi.org/10.1038/s41559-020-1232-4
  * Corbellini, Aldo, Marco Magnani, and Gianluca Morelli. "Labour market analysis through transformations and robust multivariate models." Socio-Economic Planning Sciences (2020): 100826.
  * G. Lamura, I. J. Onuorah, P. Bonfà, S. Sanna, Z. Shermadini, R. Khasanov, J.-C. Orain, C. Baines, F. Gastaldo, M. Giovannini, I. Čurlík, A. Dzubinska, G. Pristas, M. Reiffers, A. Martinelli, C. Ritter, B. Joseph, E. Bauer, R. De Renzi, and T. Shiroka, ‘Pressure-induced antiferromagnetic dome in the heavy-fermion Yb2Pd2In1−xSnx system’ Phys. Rev. B 101, 054410 , (2020)
  * Dellafiora L., Dorne, C.M.J.L, Galaverna G., Dall'Asta C. Preventing the Interaction between Coronaviruses Spike Protein and Angiotensin I Converting Enzyme 2: An In Silico Mechanistic Case Study on Emodin as a Potential Model Compound. Appl. Sci., 2020, 10 (18), 6358; https://doi.org/10.3390/app1018635
  *  Dellafiora L, Milioli M, Falco A, et al. A Hybrid In Silico/In Vitro Target Fishing Study to Mine Novel Targets of Urolithin A and B: A Step Towards a Better Comprehension of their Estrogenicity. Molecular Nutrition & Food Research. 2020;e2000289. doi:10.1002/mnfr.202000289
  * ATKINSON A.C., RIANI M., CORBELLINI A. (2020). The analysis of transformations for profit-and-loss data, Journal of the Royal Statistical Society, Series C, Applied Statistics, https://doi.org/10.1111/rssc.12389
  * ATKINSON A.C., RIANI M., CORBELLINI A. (2020). The Box-Cox Transformation: Review and Extensions, Statistical Science,https://imstat.org/journals-and-publications/statistical-science/statistical-science-future-papers/  
  * RIANI M., ATKINSON A.C.,, CORBELLINI A., PERROTTA D. (2020). Robust Regression with Density Power Divergence: Theory, Comparisons, and Data Analysis, Entropy, 22, 399. https://www.mdpi.com/1099-4300/22/4/399
  * GARCÍA-ESCUDERO L.A., MAYO-ISCAR A., RIANI M . (2020). Model-based clustering with determinant-and-shape constraint, Statistics and Computing, https://link.springer.com/article/10.1007/s11222-020-09950-w 
  * Del Favero G, Mayer RM, Dellafiora L, Janker L, Niederstaetter L, Dall'Asta C, Gerner C, Marko D. Structural Similarity with Cholesterol Reveals Crucial Insights into Mechanisms Sustaining the Immunomodulatory Activity of the Mycotoxin Alternariol. Cells. 2020 Mar 31;9(4). pii: E847. doi:10.3390/cells9040847
  *  Lammi C, Aiello G, Dellafiora L, Bollati C, Boschin G, Ranaldi G, Ferruzza S, Sambuy Y, Galaverna G, Arnoldi A. Assessment of the Multifunctional Behavior of Lupin Peptide P7 and Its Metabolite Using an Integrated Strategy. J Agric Food Chem. 2020 Apr 3. doi: 10.1021/acs.jafc.0c00130
  * Dellafiora L, Gonaus C, Streit B, Galaverna G, Moll W-D, Vogtentanz G, Schatzmayr G, Dall'Asta C, Prasad S. An In Silico Target Fishing Approach to Identify Novel Ochratoxin A Hydrolyzing Enzyme. Toxins. 2020, 12 (4). 258. doi: 10.3390/toxins12040258  
  * [[ https://www.nature.com/articles/s41598-020-60298-7 | A comparative analysis of link removal strategies in real complex weighted networks]], M. Bellingeri, D. Bevacqua, F. Scotognella, R. Alfieri & D. Cassi, Scientific Reports volume 10, Article number: 3911 (2020) 
  * Antiadiabatic View of Fast Environmental Effects on Optical Spectra, D. K. Andrea Phan Huu, Rama Dhali, Carlotta Pieroni, Francesco Di Maiolo , Cristina Sissa , Francesca Terenziani, Anna Painelli, Phys. Rev. Lett. 124, 107401 (2020) DOI: 10.1103/PhysRevLett.124.107401 Open Access
  * About the origin of the large Stokes shift in aminoalkyl substituted heptamethine cyanine dyes, Cristina Sissa,  Anna Painelli, Roberta Ragni, Francesca Terenziani, Massimo Trotta, Phys. Chem. Chem. Phys., 2020,22, 129-135, : DOI: 10.1039/c9cp05473a Open Access
  *Dazzi, S., Vacondio, R., and Mignosa, P. (2020). "Internal boundary conditions for a GPU-accelerated 2D shallow water model: implementation and applications." Advances in Water Resources, https://doi.org/10.1016/j.advwatres.2020.103525
  *Ferrari, A., Dazzi, S., Vacondio, R., and Mignosa, P. (2020). "Enhancing the resilience to flooding induced by levee breaches in lowland areas: a methodology based on numerical modelling." Natural Hazards and Earth System Sciences, 20, 59–72. https://doi.org/10.5194/nhess-20-59-2020
  *Dynamical disorder and resonance energy transfer: a novel quantum-classical approach Francesco Di Maiolo and Anna Painelli, Phys. Chem. Chem. Phys. 2020, DOI: 10.1039/C9CP06038C
  *Dellafiora Luca, Virginia Filipello, Chiara Dall'Asta, Guido Finazzi, Gianni Galaverna, Marina Nadia Losio. A Structural Study on the Listeria Monocytogenes Internalin A—Human E-cadherin Interaction: A Molecular Tool to Investigate the Effects of Missense Mutations. Toxins 2020. 12 (1), 60.  https://doi.org/10.3390/toxins12010060
  *Dellafiora L, Pugliese R, Bollati C, Gelain F, Galaverna G, Arnoldi A, Lammi C. "Bottom-Up" Strategy for the Identification of Novel Soybean Peptides with Angiotensin-Converting Enzyme Inhibitory Activity. J Agric Food Chem. 2020 Feb 19;68(7):2082-2090. doi: 10.1021/acs.jafc.9b07361
  *Dellafiora L, Oswald IP, Dorne JL, Galaverna G, Battilani P, Dall'Asta C. An in silico structural approach to characterize human and rainbow trout estrogenicity of mycotoxins: Proof of concept study using zearalenone and alternariol. Food Chem. 2020 May 15;312:126088. doi: 10.1016/j.foodchem.2019.126088

=== 2019 ===

  * Alessandri, G., Milani, C., Mancabelli, L., Mangifesta, M., Lugli, G. A., Viappiani, A., Duranti, S., Turroni, F., Ossiprandi, M. C., van Sinderen, D., & Ventura, M. (2019). Metagenomic dissection of the canine gut microbiota: insights into taxonomic, metabolic and nutritional features. Environmental Microbiology, 21(4), 1331–1343. https://doi.org/10.1111/1462-2920.14540
  * Alessandri, G., Milani, C., Mancabelli, L., Mangifesta, M., Lugli, G. A., Viappiani, A., Duranti, S., Turroni, F., Ossiprandi, M. C., Van Sinderen, D., & Ventura, M. (2019). The impact of human-facilitated selection on the gut microbiota of domesticated mammals. FEMS Microbiology Ecology, 95(9). https://doi.org/10.1093/FEMSEC/FIZ121
  * Duranti, S., Lugli, G. A., Milani, C., James, K., Mancabelli, L., Turroni, F., Alessandri, G., Mangifesta, M., Mancino, W., Ossiprandi, M. C., Iori, A., Rota, C., Gargano, G., Bernasconi, S., Di Pierro, F., van Sinderen, D., & Ventura, M. (2019). Bifidobacterium bifidum and the infant gut microbiota: an intriguing case of microbe-host co-evolution. Environmental Microbiology, 21(10), 3683–3695. https://doi.org/10.1111/1462-2920.14705
  * Duranti, S., Lugli, G. A., Napoli, S., Anzalone, R., Milani, C., Mancabelli, L., Alessandri, G., Turroni, F., Ossiprandi, M. C., Van Sinderen, D., & Ventura, M. (2019). Characterization of the phylogenetic diversity of five novel species belonging to the genus Bifidobacterium: Bifidobacterium castoris sp. nov., Bifidobacterium callimiconis sp. nov., Bifidobacterium goeldii sp. nov., Bifidobacterium samirii sp. nov. and Bifidobacterium dolichotidis sp. nov. International Journal of Systematic and Evolutionary Microbiology, 69(5), 1288–1298. https://doi.org/10.1099/IJSEM.0.003306
  * Lugli, G. A., Duranti, S., Albert, K., Mancabelli, L., Napoli, S., Viappiani, A., Anzalone, R., Longhi, G., Milani, C., Turroni, F., Alessandri, G., Sela, D. A., Van Sinderen, D., & Ventura, M. (2019). Unveiling Genomic Diversity among Members of the Species Bifidobacterium pseudolongum, a Widely Distributed Gut Commensal of the Animal Kingdom. https://doi.org/10.1128/AEM
  * Lugli, G. A., Duranti, S., Milani, C., Mancabelli, L., Turroni, F., van Sinderen, D., & Ventura, M. (2019). Uncovering Bifidobacteria via Targeted Sequencing of the Mammalian Gut Microbiota. Microorganisms, 7(11). https://doi.org/10.3390/MICROORGANISMS7110535
  * Lugli, G. A., Mancino, W., Milani, C., Duranti, S., Mancabelli, L., Napoli, S., Mangifesta, M., Viappiani, A., Anzalone, R., Longhi, G., Van Sinderen, D., Ventura, M., & Turroni, F. (2019). Dissecting the Evolutionary Development of the Species Bifidobacterium animalis through Comparative Genomics Analyses. http://aem.asm.org/
  * Alessandri, G., Milani, C., Duranti, S., Mancabelli, L., Ranjanoro, T., Modica, S., Carnevali, L., Statello, R., Bottacini, F., Turroni, F., Cristina Ossiprandi, M., Sgoifo, A., Van Sinderen, D., & Ventura, M. (2019). Ability of bifidobacteria to metabolize chitin-glucan and its impact on the gut microbiota. https://doi.org/10.1038/s41598-019-42257-z
  * Lugli, G. A., Mangifesta, M., Mancabelli, L., Milani, C., Turroni, F., Viappiani, A., van Sinderen, D., & Ventura, M. (2019). Compositional assessment of bacterial communities in probiotic supplements by means of metagenomic techniques. International Journal of Food Microbiology, 294, 1–9. https://doi.org/10.1016/J.IJFOODMICRO.2019.01.011
  * Lugli, G. A., Milani, C., Duranti, S., Alessandri, G., Turroni, F., Mancabelli, L., Tatoni, D., Ossiprandi, M. C., Van Sinderen, D., & Ventura, M. (2019). Isolation of novel gut bifidobacteria using a combination of metagenomic and cultivation approaches. Genome Biology, 20(1). https://doi.org/10.1186/S13059-019-1711-6
  * Lugli, G. A., Milani, C., Mancabelli, L., Turroni, F., van Sinderen, D., & Ventura, M. (2019). A microbiome reality check: limitations of in silico-based metagenomic approaches to study complex bacterial communities. Environmental Microbiology Reports, 11(6), 840–847. https://doi.org/10.1111/1758-2229.12805
  * Mancino, W., Duranti, S., Mancabelli, L., Longhi, G., Anzalone, R., Milani, C., Lugli, G. A., Carnevali, L., Statello, R., Sgoifo, A., Sinderen, D. van, Ventura, M., & Turroni, F. (2019). Bifidobacterial Transfer from Mother to Child as Examined by an Animal Model. Microorganisms, 7(9). https://doi.org/10.3390/MICROORGANISMS7090293
  * Milani, C., Alessandri, G., Mancabelli, L., Lugli, G. A., Longhi, G., Anzalone, R., Viappiani, A., Duranti, S., Turroni, F., Ossiprandi, M. C., van Sinderen, D., & Ventura, M. (2019). Bifidobacterial Distribution Across Italian Cheeses Produced from Raw Milk. Microorganisms, 7(12). https://doi.org/10.3390/MICROORGANISMS7120599
  * Milani, C., Duranti, S., Napoli, S., Alessandri, G., Mancabelli, L., Anzalone, R., Longhi, G., Viappiani, A., Mangifesta, M., Lugli, G. A., Bernasconi, S., Ossiprandi, M. C., van Sinderen, D., Ventura, M., & Turroni, F. (2019). Colonization of the human gut by bovine bacteria present in Parmesan cheese. Nature Communications, 10(1), 1–12. https://doi.org/10.1038/s41467-019-09303-w
  * Turroni, F., Duranti, S., Milani, C., Lugli, G. A., van Sinderen, D., & Ventura, M. (2019). Bifidobacterium bifidum: A key member of the early human gut microbiota. Microorganisms, 7(11). https://doi.org/10.3390/microorganisms7110544
  * RIANI M., ATKINSON A.C., CERIOLI A., CORBELLINI A. (2019). Efficient robust methods via monitoring for clustering and multivariate data analysis, Pattern Recognition, 88, p. 246–260. https://doi.org/10.1016/j.patcog.2018.11.016
  * Ifeanyi John Onuorah, Pietro Bonfà, Roberto De Renzi, Lorenzo Monacelli, Francesco Mauri, Matteo Calandra, and Ion Errea, ‘Quantum effects in muon spin spectroscopy within the stochastic self-consistent harmonic approximation’, Phys. Rev. Materials 3, 073804, (2019)
  *Excited-State Symmetry Breaking in an Aza-nanographene Dye, Brunella Bardi, Maciej Krzeszewski, Daniel T. Gryko, Anna Painelli, Francesca Terenziani, Chem. Europ. J, 25, 13930 (2019)  DOI: 10.1002/chem.201902554 Hot paper Open Access
  *Addressing Charge-Transfer and Locally-Excited States in a Twisted Biphenyl Push-Pull Chromophore, Elisa Campioli, Somananda Sanyal, Agnese Marcelli, Mariangela Di Donato, Mireille Blanchard-Desce, Olivier Mongin, Anna Painelli, Francesca Terenziani , ChemPhysChem 2019, 20, 2860 – 2873, DOI: 10.1002/cphc.201900703
  *Optical spectra of molecular aggregates and crystals: testing approximation schemes, M. Anzola, F. Di Maiolo, A. Painelli, Phys. Chem. Chem. Phys. 21, 19816 (2019) DOI: 10.1039/c9cp03122g Hot paper 
  *Ferrari, A., Viero, D. P., Vacondio, R., Defina, A., & Mignosa, P. (2019). Flood inundation modeling in urbanized areas: A mesh-independent porosity approach with anisotropic friction. Advances in water resources, 125, 98-113. https://doi.org/10.1016/j.advwatres.2019.01.010
  *Dazzi, S., A. Ferrari, Vacondio, R., and Mignosa, P. (2019). "Esondazioni provocate dall'apertura di brecce arginali" In Tecniche per la difesa del suolo e dall’inquinamento - Atti della 40^ Edizione (a cura di Giuseppe Frega e Francesco Macchione), Guardia Piemontese (CS) 19-22 Giugno 2019
  *Leo L.; Bridelli M. G.; Polverini E., Insight on collagen self-assembly mechanisms by coupling molecular dynamics and UV spectroscopy techniques, Biophysical Chemistry, 253: 106224-106237 (2019). DOI: 10.1016/j.bpc.2019.106224
  *G.Lazzini L.Romoli A.H.A.Lutey F.Fuso (2019). Modelling the interaction between bacterial cells and laser-textured surfaces. Sciencedirect. https://doi.org/10.1016/j.surfcoat.2019.06.078
  *Dellafiora L, Galaverna G, Cruciani G, Dall’Asta C. (2019) A computational study toward the“personalized”activity of alternariol–Does it matter for safe food at individual level?. Food Chem Toxicol 130. 199-206
  *Dazzi, S., Vacondio, R., & Mignosa, P. (2019). Integration of a levee breach erosion model in a GPU-accelerated 2D shallow water equations code. Water Resources Research, 55. https://doi.org/10.1029/2018WR023826
  *Gaia Bertani, Alessia Levante, Camilla Lazzi, Benedetta Bottari, Monica Gatti, Erasmo Neviani (2019) Dynamics of a natural bacterial community under technological and environmental pressures: the case of natural whey starter for Parmigiano Reggiano cheese, Food Research International, https://doi.org/10.1016/j.foodres.2019.108860
  *Simone Benatti, Alessandro Tasora, Dario Fusai,Dario Mangoni; ICACR 2019: Proceedings of the 2019 3rd International Conference on Automation, Control and Robots October 2019 Pages 7–11 https://doi.org/10.1145/3365265.3365274

=== 2018 ===

  * CERIOLI A., FARCOMENI A., RIANI M. (2018). Wild adaptive trimming for robust estimation and cluster analysis. Scandinavian Journal of Statistics, p. 1–22. https://onlinelibrary.wiley.com/doi/abs/10.1111/sjos.12349
  *Ifeanyi John Onuorah, Pietro Bonfà, Roberto De Renzi, “Muon contact hyperfine field in metals: A DFT calculation”, Phy. Rev. B 97, 174414, (2018)
  *Martínez N, Luque R, Milani C, Ventura M, Bañuelos O, Margolles A. A Gene Homologous to rRNA Methylase Genes Confers Erythromycin and Clindamycin Resistance in Bifidobacterium breve. Appl Environ Microbiol. 2018 May 1;84(10). pii: e02888-17. doi: 10.1128/AEM.02888-17. Print 2018 May 15. PMID: 29500262 https://www.ncbi.nlm.nih.gov/pubmed/29500262
  *Ticinesi A, Milani C, Guerra A, Allegri F, Lauretani F, Nouvenne A, Mancabelli L, Lugli GA, Turroni F, Duranti S, Mangifesta M, Viappiani A, Ferrario C, Dodi R, Dall'Asta M, Del Rio D, Ventura M, Meschi T. Understanding the gut-kidney axis in nephrolithiasis: an analysis of the gut microbiota composition and functionality of stone formers. Gut. 2018 Dec;67(12):2097-2106. doi: 10.1136/gutjnl-2017-315734. Epub 2018 Apr 28. PMID: 29705728 https://www.ncbi.nlm.nih.gov/pubmed/29705728
  *Milani C, Duranti S, Mangifesta M, Lugli GA, Turroni F, Mancabelli L, Viappiani A, Anzalone R, Alessandri G, Ossiprandi MC, van Sinderen D, Ventura M. Phylotype-Level Profiling of Lactobacilli in Highly Complex Environments by Means of an Internal Transcribed Spacer-Based Metagenomic Approach. Appl Environ Microbiol. 2018 Jul 2;84(14). pii: e00706-18. doi: 10.1128/AEM.00706-18. Print 2018 Jul 15. PMID: 29728382 https://www.ncbi.nlm.nih.gov/pubmed/29728382 
  *Lugli GA, Mancino W, Milani C, Duranti S, Turroni F, van Sinderen D, Ventura M. Reconstruction of the bifidobacterial pan-secretome reveals the network of extracellular interactions between bifidobacteria and the infant gut. Appl Environ Microbiol. 2018 Jun 8. pii: AEM.00796-18. doi: 10.1128/AEM.00796-18. [Epub ahead of print] PMID: 29884754 https://www.ncbi.nlm.nih.gov/pubmed/29884754
  *Milani C, Casey E, Lugli GA, Moore R, Kaczorowska J, Feehily C, Mangifesta M, Mancabelli L, Duranti S, Turroni F, Bottacini F, Mahony J, Cotter PD, McAuliffe FM, van Sinderen D, Ventura M. Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorX. Microbiome. 2018 Aug 20;6(1):145. doi: 10.1186/s40168-018-0527-z. PMID: 30126456 https://www.ncbi.nlm.nih.gov/pubmed/30126456
  *Duranti S, Vivo V, Zini I, Milani C, Mangifesta M, Anzalone R, Mancabelli L, Viappiani A, Cantoni AM, Barocelli E, van Sinderen D, Bertoni S, Turroni F. Bifidobacterium bifidum PRL2010 alleviates intestinal ischemia/reperfusion injury. PLoS One. 2018 Aug 30;13(8):e0202670. doi: 10.1371/journal.pone.0202670. eCollection 2018. PMID: 30161157 https://www.ncbi.nlm.nih.gov/pubmed/30161157
  *Mangifesta M, Mancabelli L, Milani C, Gaiani F, de'Angelis N, de'Angelis GL, van Sinderen D, Ventura M, Turroni F. Mucosal microbiota of intestinal polyps reveals putative biomarkers of colorectal cancer. Sci Rep. 2018 Sep 18;8(1):13974. doi: 10.1038/s41598-018-32413-2. PMID: 30228361 https://www.ncbi.nlm.nih.gov/pubmed/30228361
  *Dellafiora L, Galaverna G, Cruciani G, Dall'Asta C, Bruni R. On the Mechanism of Action of Anti-Inflammatory Activity of Hypericin: An In  Silico Study Pointing to the Relevance of Janus Kinases Inhibition. Molecules. 2018 Nov 22;23(12). pii: E3058
  * CERIOLI A., RIANI M., ATKINSON A.C., CORBELLINI A., (2018). The power of monitoring: how to make the most of a contaminated multivariate sample, Statistical Methods and Applications (with discussion), DOI https://doi.org/10.1007/s10260-017-0409-8 
  * ATKINSON A.C., RIANI M., CERIOLI A., (2018). Cluster Detection and Clustering with Random Start Forward Searches Journal of Applied Statistics, n. 45, p. 777-798 http://dx.doi.org/10.1080/02664763.2017.1310806
  * RIANI M., CORBELLINI A., ATKINSON A.C. (2018). The Use of Prior Information in Very Robust Regression for Fraud Detection. International Statistical Review, Vol. 86, p. 205-218. http://dx.doi.org/10.1111/insr.12247   
  * TORTI F. PERROTTA D., RIANI M. CERIOLI A (2018). Assessing Trimming Methodologies for Clustering Linear Regression Data, Advances in Data Analysis and Classification, https://doi.org/10.1007/s11634-018-0331-4 .
  * RIANI M., ATKINSON A.C., CERIOLI A., CORBELLINI A. (2019). Efficient robust methods via monitoring for clustering and multivariate data analysis, Pattern Recognition, 88, p. 246–260. https://doi.org/10.1016/j.patcog.2018.11.016
  * Riccardo Castelli, Nicole Bozza, Andrea Cavazzoni, Mara Bonelli, Federica Vacondio, Francesca Ferlenghi, Donatella Callegari, Claudia Silva, Silvia Rivara, Alessio Lodola, Graziana Digiacomo, Claudia Fumarola, Roberta Alfieri, Pier Giorgio Petronini, Marco Mor, "Balancing reactivity and antitumor activity: heteroarylthioacetamide derivatives as potent and time-dependent inhibitors of EGFR" European Journal of Medicinal Chemistry, Pub Date : 2018-11-13 , DOI: 10.1016/j.ejmech.2018.11.029  
  * Menozzi I., Polverini E., Berni R., Deciphering protein dynamics changes along the pathway of retinol uptake by cellular retinol-binding proteins 1 and 2, Archives of Biochemistry and Biophysics, 645: 107-116 (2018). DOI: 10.1016/j.abb.2018.03.020
  *Ferrari, A., D'Oria, M., Vacondio, R., Dal Palù, A., Mignosa, P., & Tanda, M. G. (2018). Discharge hydrograph estimation at upstream-ungauged sections by coupling a Bayesian methodology and a 2-D GPU shallow water model. Hydrology and Earth System Sciences, 22(10), 5299-5316
  *Ferrari, A., D'Oria, M., Vacondio, R., Mignosa, P., & Tanda, M. G. (2018). Hydrograph estimation at upstream ungauged sections on the Secchia River (Italy) by means of a parallel Bayesian inverse methodology. In E3S Web of Conferences (Vol. 40), River Flow 2018, Lyon, 5-8 September 2018.
  * Intermolecular Energy Transfer in Real Time Francesco Di Maiolo and Anna Painelli Journal of Chemical Theory and Computation 2018 14 (10), 5339-5349 DOI: 10.1021/acs.jctc.8b0054
  * Marco Villani, Laura Sani, Riccardo Pecori, Michele Amoretti,Andrea Roli, Monica Mordonini, Roberto Serra, and Stefano Cagnoni "An iterative information-theoretic approach to the detection of structures in complex systems" Complexity, Volume 2018, article ID 3687839.
  * F. Magliani, T. Fontanini, A Prati, “Efficient Nearest Neighbors Search for Large-Scale Landmark Recognition”, in Proceedings of 13th International Symposium on Visual Computing (ISVC) 2018, Las Vegas, Nevada (USA) 
  *  F. Magliani, T. Fontanini, A Prati, “A Dense-Depth Representation for VLAD descriptors in Content-Based Image Retrieval”, in Proceedings of 13th International Symposium on Visual Computing (ISVC) 2018, Las Vegas, Nevada (USA)
  * F. Magliani, A Prati, “An accurate retrieval through R-MAC+ descriptors for landmark recognition”, in Proceedings of ACM International Conference on Distributed Smart Cameras (ICDSC 2018), Eindhoven (The Netherlands)
  * L. Donani, E. Iotti, A. Prati, “Computer Vision and Deep Learning for Fashion Creative Workflows”, in Atti del Convegno del gruppo Computer Vision, Pattern Recognition and Machine Learning (CVPL), 2018.
  * F. Magliani, T. Fontanini, A. Prati, “Approximate Nearest Neighbor Search for Large-Scale Content-Based Image Retrieval”, in Atti del Convegno del gruppo Computer Vision, Pattern Recognition and Machine Learning (CVPL), 2018.
  * F. Magliani, T. Fontanini, A. Prati, “Landmark Recognition: From Small-Scale to Large-Scale Retrieval”, book chapter in the book “Recent Advances in Computer Vision: Theories and Applications”, edito da M. Hassaballah, K.M. Hosny, Publisher: Springer 2018
  * F. Magliani, NM Bidgoli, A Prati, “A  location-aware embedding technique for accurate landmark recognition”, in Proceedings of ACM International Conference on Distributed Smart Cameras (ICDSC 2017), Stanford, CA (USA) 
  * G. Pietrini, A. Soldati, C. Concari and N. Bianchi, "General Magnetic Model for the Analysis and Optimization of Multiple Barrier Rotors," 2018 IEEE Energy Conversion Congress and Exposition (ECCE), Portland, OR, 2018, accepted.
  * G. Pietrini, A. Soldati, C. Concari and N. Bianchi, "Saliency-enhanced Spoke-type Rotor Geometry for Permanent Magnet Volume Reduction in Hybrid and Electric Vehicle Motors," 2018 IEEE Energy Conversion Congress and Exposition (ECCE), Portland, OR, 2018, accepted.
  * G. Pietrini, M. Dalboni, D. Mangoni, A. Soldati and C. Concari, "Discussion on the Mechanical Design Methods of the Rotor Ribs in Electric Vehicle Motors," in IEEE Transactions on Transportation Electrification, 2018, under review.
  * Peter Rousseeuw, Domenico Perrotta, Marco Riani, Mia Hubert, Robust, Monitoring of Time Series with Application to Fraud Detection, Econometrics and Statistics (2018), doi: 10.1016/j.ecosta.2018.05.001
  * Wild adaptive trimming for robust estimation and cluster analysis, Andrea Cerioli, Alessio Farcomeni, Marco Riani, Scandinavian Journal of Statistics, DOI: 10.1111/sjos.12349 (2018)
  * Optimization of Finite-Differencing Kernels for Numerical Relativity Applications, Alfieri R, Bernuzzi S., Perego A, Radice D,  J. Low Power Electron. Appl. 2018, 8, 15; doi:10.3390/jlpea8020015   [[http://www.mdpi.com/2079-9268/8/2/15/pdf | pdf]]
  * L718Q mutant EGFR escapes covalent inhibition by stabilizing a non-reactive conformation of the lung cancer drug osimertinib. Callegari D, Ranaghan KE, Woods CJ, Minari R, Tiseo M, Mor M, Mulholland AJ, Lodola A. Chem Sci. 2018; 9(10):2740-2749.
  * Tetrahydroquinoline Ring as a Versatile Bioisostere of Tetralin for Melatonin Receptor Ligands. Rivara S, Scalvini L, Lodola A, Mor M, Caignard DH, Delagrange P, Collina S, Lucini V, Scaglione F, Furiassi L, Mari M, Lucarini S, Bedini A, Spadoni G. J Med Chem. 2018; 61(8):3726-3737.
  * Phylogenetic classification of six novel species belonging to the genus Bifidobacterium comprising Bifidobacterium anseris sp. nov., Bifidobacterium criceti sp. nov., Bifidobacterium imperatoris sp. nov., Bifidobacterium italicum sp. nov., Bifidobacterium margollesii sp. nov. and Bifidobacterium parmae sp. nov.,  Lugli GA, Mangifesta M, Duranti S, Anzalone R, Milani C, Mancabelli L, Alessandri G, Turroni F, Ossiprandi MC, van Sinderen D, Ventura M. , Syst Appl Microbiol. 2018 Jan 26. pii: S0723-2020(18)30017-1. doi: 10.1016/j.syapm.2018.01.002. [Epub ahead of print] [[https://www.ncbi.nlm.nih.gov/pubmed/29395537 | 29395537]]
  * Tracking the Taxonomy of the Genus Bifidobacterium Based on a Phylogenomic Approach. Lugli GA, Milani C, Duranti S, Mancabelli L, Mangifesta M, Turroni F, Viappiani A, van Sinderen D, Ventura M.,  Appl Environ Microbiol. 2018 Jan 31;84(4). pii: e02249-17. doi: 10.1128/AEM.02249-17. Print 2018 Feb 15. PMID: [[https://www.ncbi.nlm.nih.gov/pubmed/29222102 | 29222102 ]]

===2017===
  * Identification of universal gut microbial biomarkers of common human intestinal diseases by meta-analysis. Mancabelli L, Milani C, Lugli GA, Turroni F, Cocconi D, van Sinderen D, Ventura M., FEMS Microbiol Ecol. 2017 Dec 1;93(12). doi: 10.1093/femsec/fix153.  PMID: [[https://www.ncbi.nlm.nih.gov/pubmed/29126267 | 29126267 ]]
  * The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota.  Milani C, Duranti S, Bottacini F, Casey E, Turroni F, Mahony J, Belzer C, Delgado Palacio S, Arboleya Montes S, Mancabelli L, Lugli GA, Rodriguez JM, Bode L, de Vos W, Gueimonde M, Margolles A, van Sinderen D, Ventura M., Microbiol Mol Biol Rev. 2017 Nov 8;81(4). pii: e00036-17. doi: 10.1128/MMBR.00036-17. Print 2017 Dec. Review. PMID: [[https://www.ncbi.nlm.nih.gov/pubmed/29118049 | 29118049 ]]
  * Glycan Utilization and Cross-Feeding Activities by Bifidobacteria. Turroni F, Milani C, Duranti S, Mahony J, van Sinderen D, Ventura M. Trends Microbiol. 2017 Oct 28. pii: S0966-842X(17)30228-7. doi: 10.1016/j.tim.2017.10.001. [Epub ahead of print] Review. [[https://www.ncbi.nlm.nih.gov/pubmed/29089173 | 29089173 ]]
  * Untangling the cecal microbiota of feral chickens by culturomic and metagenomic analyses,  Ferrario C, Alessandri G, Mancabelli L, Gering E, Mangifesta M, Milani C, Lugli GA, Viappiani A, Duranti S, Turroni F, Ossiprandi MC, Hiyashi R, Mackie R, van Sinderen D, Ventura M. , Environ Microbiol. 2017 Oct 2. doi: 10.1111/1462-2920.13943. [Epub ahead of print],  PMID: 28967204, https://www.ncbi.nlm.nih.gov/pubmed/28967204
  * How to Feed the Mammalian Gut Microbiota: Bacterial and Metabolic Modulation by Dietary Fibers,  Ferrario C, Statello R, Carnevali L, Mancabelli L, Milani C, Mangifesta M, Duranti S, Lugli GA, Jimenez B, Lodge S, Viappiani A, Alessandri G, Dall'Asta M, Del Rio D, Sgoifo A, van Sinderen D, Ventura M, Turroni F.,  Front Microbiol. 2017 Sep 12;8:1749. doi: 10.3389/fmicb.2017.01749. eCollection 2017,  PMID: 28955319 Free PMC Article  https://www.ncbi.nlm.nih.gov/pubmed/28955319
  * Bifidobacterium vansinderenii sp. nov., isolated from faeces of emperor tamarin (Saguinus imperator),  Duranti S, Mangifesta M, Lugli GA, Turroni F, Anzalone R, Milani C, Mancabelli L, Ossiprandi MC, Ventura M.,  Int J Syst Evol Microbiol. 2017 Oct;67(10):3987-3995. doi: 10.1099/ijsem.0.002243. Epub 2017 Sep 12.,  PMID: 28893355  https://www.ncbi.nlm.nih.gov/pubmed/28893355
  * Unveiling the gut microbiota composition and functionality associated with constipation through metagenomic analyses., Mancabelli L, Milani C, Lugli GA, Turroni F, Mangifesta M, Viappiani A, Ticinesi A, Nouvenne A, Meschi T, van Sinderen D, Ventura M., Sci Rep. 2017 Aug 29;7(1):9879. doi: 10.1038/s41598-017-10663-w.,  PMID: 28852182 Free PMC Article, https://www.ncbi.nlm.nih.gov/pubmed/28852182
  * ISME J. (Nature’s Publishing Group) 2017 Aug 22. doi: 10.1038/ismej.2017.138. [Epub ahead of print]. Unveiling bifidobacterial biogeography across the mammalian branch of the tree of life.  Milani C1, Mangifesta M1,2, Mancabelli L1, Lugli GA1, James K3, Duranti S1, Turroni F1, Ferrario C1, Ossiprandi MC4, van Sinderen D3, Ventura M1.  [[  https://www.ncbi.nlm.nih.gov/pubmed/28837128 | PubMed link ]],  [[http://parma.repubblica.it/cronaca/2017/09/07/news/medicina_studio_dell_universita_di_parma_scopre_nuovi_batteri_intestinali-174835880/ | see also ]]
  * Sci Rep. 2017 Aug 29;7(1):9879. doi: 10.1038/s41598-017-10663-w.  Unveiling the gut microbiota composition and functionality associated with constipation through metagenomic analyses. Mancabelli L1, Milani C1, Lugli GA1, Turroni F1, Mangifesta M1,2, Viappiani A2, Ticinesi A3, Nouvenne A3, Meschi T3, van Sinderen D4, Ventura M5. [[ https://www.ncbi.nlm.nih.gov/pubmed/28852182 | PubMed link ]]
  *   BMC Genomics. 2017 Aug 1;18(1):568. doi: 10.1186/s12864-017-3955-4.  Comparative genomic and phylogenomic analyses of the Bifidobacteriaceae family.  Lugli GA1, Milani C1, Turroni F1, Duranti S1, Mancabelli L1, Mangifesta M2, Ferrario C1, Modesto M3, Mattarelli P3, Jiří K4,5, van Sinderen D6, Ventura M7.  [[ https://www.ncbi.nlm.nih.gov/pubmed/28764658 |  PubMed link]]
  *  Appl Environ Microbiol. 2017 Jul 28. pii: AEM.01295-17. doi: 10.1128/AEM.01295-17. [Epub ahead of print]  The sortase-dependent fimbriome of the genus Bifidobacterium: extracellular structures with potential to modulate microbe-host dialogue. Milani C1, Mangifesta M2, Mancabelli L1, Lugli GA1, Mancino W1, Viappiani A2, Faccini A3, van Sinderen D4, Ventura M1, Turroni F5.   [[ https://www.ncbi.nlm.nih.gov/pubmed/28754709 PubMed link ]]
   * [[https://www.ncbi.nlm.nih.gov/pubmed/28651630 | “Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission.” ]] Microbiome. 2017 Jun 26;5(1):66. doi: 10.1186/s40168-017-0282-6.
  * [[ https://www.ncbi.nlm.nih.gov/pubmed/28578266 | “Next generation sequencing-based multigene panel for high throughput detection of food-borne pathogens” ]] , International Journal of Food Microbiology 256 (2017) 20–29