Publications

@article{galvanetto2022unfolding,

title = {Unfolding and identification of membrane proteins in situ},

author = {Nicola Galvanetto and Zhongjie Ye and Arin Marchesi and Simone Mortal and Sourav Maity and Alessandro Laio and Vincent Torre},

year  = {2022},

date = {2022-01-01},

journal = {Elife},

volume = {11},

pages = {e77427},

publisher = {eLife Sciences Publications Limited},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{glielmo2022ranking,

title = {Ranking the information content of distance measures},

author = {Aldo Glielmo and Claudio Zeni and Bingqing Cheng and Gábor Csányi and Alessandro Laio},

year  = {2022},

date = {2022-01-01},

journal = {PNAS nexus},

volume = {1},

number = {2},

pages = {pgac039},

publisher = {Oxford University Press},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{doimo2022redundant,

title = {Redundant representations help generalization in wide neural networks},

author = {Diego Doimo and Aldo Glielmo and Sebastian Goldt and Alessandro Laio},

year  = {2022},

date = {2022-01-01},

journal = {Advances in Neural Information Processing Systems},

volume = {35},

pages = {19659–19672},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{laio2022kinetics,

title = {When kinetics plays strange tricks},

author = {Alessandro Laio},

year  = {2022},

date = {2022-01-01},

journal = {Proceedings of the National Academy of Sciences},

volume = {119},

number = {4},

pages = {e2122078119},

publisher = {National Academy of Sciences},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ochoa2022multiple,

title = {Multiple-allele MHC class II epitope engineering by a molecular dynamics-based evolution protocol},

author = {Rodrigo Ochoa and Victoria Alves Santos Lunardelli and Daniela Santoro Rosa and Alessandro Laio and Pilar Cossio},

year  = {2022},

date = {2022-01-01},

journal = {Frontiers in immunology},

volume = {13},

pages = {862851},

publisher = {Frontiers Media SA},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{glielmo2022dadapy,

title = {DADApy: Distance-based analysis of data-manifolds in Python},

author = {Aldo Glielmo and Iuri Macocco and Diego Doimo and Matteo Carli and Claudio Zeni and Romina Wild and Maria d’Errico and Alex Rodriguez and Alessandro Laio},

year  = {2022},

date = {2022-01-01},

journal = {Patterns},

volume = {3},

number = {10},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{muratore2022prune,

title = {Prune and distill: similar reformatting of image information along rat visual cortex and deep neural networks},

author = {Paolo Muratore and Sina Tafazoli and Eugenio Piasini and Alessandro Laio and Davide Zoccolan},

year  = {2022},

date = {2022-01-01},

journal = {Advances in Neural Information Processing Systems},

volume = {35},

pages = {30206–30218},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{laio2022monte,

title = {Monte Carlo approach to the conformal bootstrap},

author = {Alessandro Laio and Uriel Luviano Valenzuela and Marco Serone},

year  = {2022},

date = {2022-01-01},

journal = {Physical Review D},

volume = {106},

number = {2},

pages = {025019},

publisher = {American Physical Society},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{russo2022dpcfam,

title = {Dpcfam: unsupervised protein family classification by density peak clustering of large sequence datasets},

author = {Elena Tea Russo and Federico Barone and Alex Bateman and Stefano Cozzini and Marco Punta and Alessandro Laio},

year  = {2022},

date = {2022-01-01},

journal = {PLOS Computational Biology},

volume = {18},

number = {10},

pages = {e1010610},

publisher = {Public Library of Science San Francisco, CA USA},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{denti2022generalized,

title = {The generalized ratios intrinsic dimension estimator},

author = {Francesco Denti and Diego Doimo and Alessandro Laio and Antonietta Mira},

year  = {2022},

date = {2022-01-01},

journal = {Scientific Reports},

volume = {12},

number = {1},

pages = {20005},

publisher = {Nature Publishing Group UK London},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{danquah2022machine,

title = {Do Machine-Learning Atomic Descriptors and Order Parameters Tell the Same Story? The Case of Liquid Water},

author = {Edward Danquah Donkor and Alessandro Laio and Ali Hassanali},

year  = {2022},

date = {2022-01-01},

journal = {arXiv e-prints},

pages = {arXiv–2211},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{wild2022high,

title = {High dimensional feature selection using informative distance measures: Application to COVID-19 severity prediction},

author = {Romina Wild and Emanuela Sozio and Riccardo Giuseppe Margiotta and Fabiana Dellai and Angela Acquasanta and Fabio Del Ben and Carlo Tascini and Francesco Curcio and Alessandro Laio},

year  = {2022},

date = {2022-01-01},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{mlynsky2022toward,

title = {Toward convergence in folding simulations of RNA tetraloops: Comparison of enhanced sampling techniques and effects of force field modifications},

author = {Vojtech Mlynsky and Michal Janec ek and Petra Kuhrova and Thorben Frohlking and Michal Otyepka and Giovanni Bussi and Pavel Banas and Jiri Sponer},

year  = {2022},

date = {2022-01-01},

journal = {Journal of Chemical Theory and Computation},

volume = {18},

number = {4},

pages = {2642–2656},

publisher = {American Chemical Society},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{frohlking2022automatic,

title = {Automatic learning of hydrogen-bond fixes in an AMBER RNA force field},

author = {Thorben Fröhlking and Vojtěch Ml`ynsk`y and Michal Janeček and Petra Kührová and Miroslav Krepl and Pavel Banáš and Jiří Šponer and Giovanni Bussi},

year  = {2022},

date = {2022-01-01},

journal = {Journal of Chemical Theory and Computation},

volume = {18},

number = {7},

pages = {4490–4502},

keywords = {Student Paper},

pubstate = {published},

tppubtype = {article}

}

@article{del2022molecular,

title = {Molecular Dynamics of Solids at Constant Pressure and Stress Using Anisotropic Stochastic Cell Rescaling},

author = {Vittorio Del Tatto and Paolo Raiteri and Mattia Bernetti and Giovanni Bussi},

year  = {2022},

date = {2022-01-01},

journal = {Applied Sciences},

volume = {12},

number = {3},

pages = {1139},

publisher = {Multidisciplinary Digital Publishing Institute},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{piomponi2022molecular,

title = {Molecular simulations matching denaturation experiments for N6-Methyladenosine},

author = {Valerio Piomponi and Thorben Fro hlking and Mattia Bernetti and Giovanni Bussi},

year  = {2022},

date = {2022-01-01},

journal = {ACS central science},

volume = {8},

number = {8},

pages = {1218–1228},

publisher = {American Chemical Society},

keywords = {Student Paper},

pubstate = {published},

tppubtype = {article}

}

@article{hsu2022adding,

title = {Adding alchemical variables to metadynamics to enhance sampling in free energy calculations},

author = {Wei-Tse Hsu and Valerio Piomponi and Pascal T Merz and Giovanni Bussi and Michael R Shirts},

year  = {2022},

date = {2022-01-01},

journal = {arXiv preprint arXiv:2206.01329},

keywords = {Student Paper},

pubstate = {published},

tppubtype = {article}

}

@article{grothaus2022exploration,

title = {Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans},

author = {Isabell Louise Grothaus and Giovanni Bussi and Lucio Colombi Ciacchi},

year  = {2022},

date = {2022-01-01},

journal = {Journal of Chemical Information and Modeling},

volume = {62},

number = {20},

pages = {4992–5008},

publisher = {American Chemical Society},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{dutta2022molecular,

title = {Molecular states and spin crossover of hemin studied by DNA origami enabled single-molecule surface-enhanced Raman scattering},

author = {Anushree Dutta and Kosti Tapio and Antonio Suma and Amr Mostafa and Yuya Kanehira and Vincenzo Carnevale and Giovanni Bussi and Ilko Bald},

year  = {2022},

date = {2022-01-01},

journal = {Nanoscale},

volume = {14},

number = {44},

pages = {16467–16478},

publisher = {Royal Society of Chemistry},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{rolband2022biomotors,

title = {Biomotors, viral assembly, and RNA nanobiotechnology: Current achievements and future directions},

author = {Lewis Rolband and Damian Beasock and Yang Wang and Yao-Gen Shu and Jonathan D Dinman and Tamar Schlick and Yaoqi Zhou and Jeffrey S Kieft and Shi-Jie Chen and Giovanni Bussi and others},

year  = {2022},

date = {2022-01-01},

journal = {Computational and Structural Biotechnology Journal},

volume = {20},

pages = {6120–6137},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{becchi2021rna,

title = {RNA Pore Translocation with Static and Periodic Forces: Effect of Secondary and Tertiary Elements on Process Activation and Duration},

author = {Matteo Becchi and Pietro Chiarantoni and Antonio Suma and Cristian Micheletti},

year  = {2021},

date = {2021-01-01},

journal = {The Journal of Physical Chemistry B},

volume = {125},

number = {4},

pages = {1098–1106},

publisher = {American Chemical Society},

keywords = {Student Paper},

pubstate = {published},

tppubtype = {article}

}

@article{franzini2021esshi,

title = {essHi-C: essential component analysis of Hi-C matrices},

author = {Stefano Franzini and Marco Di Stefano and Cristian Micheletti},

year  = {2021},

date = {2021-01-01},

journal = {Bioinformatics},

volume = {37},

number = {15},

pages = {2088–2094},

publisher = {Oxford University Press},

keywords = {Student Paper},

pubstate = {published},

tppubtype = {article}

}

@article{micheletti2021polymer,

title = {Polymer physics by quantum computing},

author = {Cristian Micheletti and Philipp Hauke and Pietro Faccioli},

year  = {2021},

date = {2021-01-01},

journal = {Physical Review Letters},

volume = {127},

number = {8},

pages = {080501},

publisher = {American Physical Society},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fonseka2021unfolding,

title = {Unfolding and translocation of knotted proteins by Clp biological nanomachines: synergistic contribution of primary sequence and topology revealed by molecular dynamics simulations},

author = {Hewafonsekage Yasan Y Fonseka and Alex Javidi and Luiz FL Oliveira and Cristian Micheletti and George Stan},

year  = {2021},

date = {2021-01-01},

journal = {The Journal of Physical Chemistry B},

volume = {125},

number = {27},

pages = {7335–7350},

publisher = {American Chemical Society},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{orlandini2021topological,

title = {Topological and physical links in soft matter systems},

author = {Enzo Orlandini and Cristian Micheletti},

year  = {2021},

date = {2021-01-01},

journal = {Journal of Physics: Condensed Matter},

volume = {34},

number = {1},

pages = {013002},

publisher = {IOP Publishing},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{tagliabue2021tunable,

title = {Tunable Knot Segregation in Copolyelectrolyte Rings Carrying a Neutral Segment},

author = {Andrea Tagliabue and Cristian Micheletti and Massimo Mella},

year  = {2021},

date = {2021-01-01},

journal = {ACS Macro Letters},

volume = {10},

number = {11},

pages = {1365–1370},

publisher = {American Chemical Society},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{amici2021topological,

title = {Topological friction and relaxation dynamics of spatially confined catenated polymers},

author = {Giulia Amici and Michele Caraglio and Enzo Orlandini and Cristian Micheletti},

year  = {2021},

date = {2021-01-01},

journal = {ACS macro letters},

volume = {11},

number = {1},

pages = {1–6},

publisher = {American Chemical Society},

keywords = {Student Paper},

pubstate = {published},

tppubtype = {article}

}

@article{d2021automatic,

title = {Automatic topography of high-dimensional data sets by non-parametric density peak clustering},

author = {Maria d’Errico and Elena Facco and Alessandro Laio and Alex Rodriguez},

year  = {2021},

date = {2021-01-01},

journal = {Information Sciences},

volume = {560},

pages = {476–492},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{everaers2021single,

title = {Single-molecule stretching experiments of flexible (wormlike) chain molecules in different ensembles: Theory and a potential application of finite chain length effects to nick-counting in DNA},

author = {Ralf Everaers and Nils B. Becker and Angelo Rosa},

year  = {2021},

date = {2021-01-01},

journal = {The Journal of Chemical Physics},

volume = {154},

number = {2},

pages = {024903},

publisher = {American Institute of Physics},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{papale2021nanorheology,

title = {Nanorheology of active–passive polymer mixtures differentiates between linear and ring polymer topology},

author = {Andrea Papale and Jan Smrek and Angelo Rosa},

year  = {2021},

date = {2021-01-01},

journal = {Soft Matter},

volume = {17},

number = {30},

pages = {7111–7117},

publisher = {Royal Society of Chemistry},

keywords = {Student Paper},

pubstate = {published},

tppubtype = {article}

}

@article{ubertini2021computer,

title = {Computer simulations of melts of ring polymers with nonconserved topology: A dynamic Monte Carlo lattice model},

author = {Mattia Alberto Ubertini and Angelo Rosa},

year  = {2021},

date = {2021-01-01},

journal = {Physical Review E},

volume = {104},

number = {5},

pages = {054503},

publisher = {American Physical Society},

keywords = {Student Paper},

pubstate = {published},

tppubtype = {article}

}

@article{ochoa2021parce,

title = {PARCE: protocol for amino acid refinement through computational evolution},

author = {Rodrigo Ochoa and Miguel A Soler and Alessandro Laio and Pilar Cossio},

year  = {2021},

date = {2021-01-01},

journal = {Computer Physics Communications},

volume = {260},

pages = {107716},

publisher = {North-Holland},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{margazoglou2021dynamical,

title = {Dynamical landscape and multistability of a climate model},

author = {Georgios Margazoglou and Tobias Grafke and Alessandro Laio and Valerio Lucarini},

year  = {2021},

date = {2021-01-01},

journal = {Proceedings of the Royal Society A},

volume = {477},

number = {2250},

pages = {20210019},

publisher = {The Royal Society Publishing},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{lasave2021proton,

title = {Proton strings and rings in atypical nucleation of ferroelectricity in ice},

author = {Jorge Lasave and Sergio Koval and Alessandro Laio and Erio Tosatti},

year  = {2021},

date = {2021-01-01},

journal = {Proceedings of the National Academy of Sciences},

volume = {118},

number = {1},

pages = {e2018837118},

publisher = {National Academy of Sciences},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{carli2021statistically,

title = {Statistically unbiased free energy estimates from biased simulations},

author = {Matteo Carli and Alessandro Laio},

year  = {2021},

date = {2021-01-01},

journal = {Molecular Physics},

volume = {119},

number = {19-20},

pages = {e1899323},

publisher = {Taylor & Francis},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{sormani2021rosetta,

title = {A Rosetta-based protein design protocol converging to natural sequences},

author = {Giulia Sormani and Zander Harteveld and Stéphane Rosset and Bruno Correia and Alessandro Laio},

year  = {2021},

date = {2021-01-01},

journal = {The Journal of Chemical Physics},

volume = {154},

number = {7},

publisher = {AIP Publishing},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{russo2021density,

title = {Density Peak clustering of protein sequences associated to a Pfam clan reveals clear similarities and interesting differences with respect to manual family annotation},

author = {Elena Tea Russo and Alessandro Laio and Marco Punta},

year  = {2021},

date = {2021-01-01},

journal = {BMC bioinformatics},

volume = {22},

pages = {1–28},

publisher = {BioMed Central},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{denti2021distributional,

title = {Distributional results for model-based intrinsic dimension estimators},

author = {Francesco Denti and Diego Doimo and Alessandro Laio and Antonietta Mira},

year  = {2021},

date = {2021-01-01},

journal = {arXiv preprint arXiv:2104.13832},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{glielmo2021unsupervised,

title = {Unsupervised learning methods for molecular simulation data},

author = {Aldo Glielmo and Brooke E Husic and Alex Rodriguez and Cecilia Clementi and Frank Noé and Alessandro Laio},

year  = {2021},

date = {2021-01-01},

journal = {Chemical Reviews},

volume = {121},

number = {16},

pages = {9722–9758},

publisher = {American Chemical Society},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{furlanis2021improving,

title = {Improving acute stroke assessment in non-enhanced CT: Automated tool for early ischemic lesion volume detection},

author = {Giovanni Furlanis and Mara Bernardi and Alex Rodriguez and Paola Caruso and Marcello Naccarato and Alessandro Laio and Daniele Amati and Paolo Manganotti},

year  = {2021},

date = {2021-01-01},

journal = {Journal of the Neurological Sciences},

volume = {429},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{azizi2021model,

title = {Model folded hydrophobic polymers reside in highly branched voids},

author = {Khatereh Azizi and Alessandro Laio and Ali Hassanali},

year  = {2021},

date = {2021-01-01},

journal = {The Journal of Physical Chemistry Letters},

volume = {13},

number = {1},

pages = {183–189},

publisher = {American Chemical Society},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bottaro2021conformational,

title = {Conformational Ensembles of Noncoding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations},

author = {Sandro Bottaro and Giovanni Bussi and Kresten Lindorff-Larsen},

year  = {2021},

date = {2021-01-01},

journal = {Journal of the American Chemical Society},

volume = {143},

number = {22},

pages = {8333–8343},

publisher = {American Chemical Society},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{paloni2021arginine,

title = {Arginine multivalency stabilizes protein/RNA condensates},

author = {Matteo Paloni and Giovanni Bussi and Alessandro Barducci},

year  = {2021},

date = {2021-01-01},

journal = {Protein Science},

volume = {30},

number = {7},

pages = {1418–1426},

publisher = {John Wiley & Sons, Inc. Hoboken, USA},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bernetti2021comparing,

title = {Comparing state-of-the-art approaches to back-calculate SAXS spectra from atomistic molecular dynamics simulations},

author = {Mattia Bernetti and Giovanni Bussi},

year  = {2021},

date = {2021-01-01},

journal = {The European Physical Journal B},

volume = {94},

pages = {1–8},

publisher = {Springer Berlin Heidelberg},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bernetti2021reweighting,

title = {Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles},

author = {Mattia Bernetti and Kathleen B Hall and Giovanni Bussi},

year  = {2021},

date = {2021-01-01},

journal = {Nucleic Acids Research},

volume = {49},

number = {14},

pages = {e84},

publisher = {Oxford University Press},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{agostinelli2020micromotility,

title = {MicroMotility: State of the art, recent accomplishments and perspectives on the mathematical modeling of bio-motility at microscopic scales},

author = {Daniele Agostinelli and Roberto Cerbino and Juan C Del Alamo and Antonio De Simone and Stephanie Höhn and Cristian Micheletti and Giovanni Noselli and Eran Sharon and Julia Yeomans and others},

year  = {2020},

date = {2020-01-01},

journal = {Mathematics in Engineering},

volume = {2},

number = {2},

pages = {230–252},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{suma2020directional,

title = {Directional translocation resistance of Zika xrRNA},

author = {Antonio Suma and Lucia Coronel and Giovanni Bussi and Cristian Micheletti},

year  = {2020},

date = {2020-01-01},

journal = {Nature communications},

volume = {11},

number = {1},

pages = {3749},

publisher = {Nature Publishing Group UK London},

keywords = {Student Paper},

pubstate = {published},

tppubtype = {article}

}