101 citations · 474 across the 28 of their papers we have counts for
29 papers
How genome redundancy can promote evolutionary innovation
Domenico Caudo, Mattia Miotto, Giancarlo Ruocco +1
Polyploidy is defined as the existence of more than two complete sets of homologous chromosomes. Despite it being a widespread phenomenon across the tree of life, its role as eithe…
Deciphering the chemical grammar of protein-RNA condensates
Greta Grassmann, Giancarlo Ruocco, Mattia Miotto
Biomolecular phase separation is typically attributed to the polymer physics of long, disordered chains. However, the underlying chemical grammar, i.e. the specific interactions be…
VertAX: a differentiable vertex model for learning epithelial tissue mechanics
Alessandro Pasqui, Jim Martin Catacora Ocana, Anshuman Sinha +7
Epithelial tissues dynamically reshape through local mechanical interactions among cells, a process well captured by vertex models. Yet their many tunable parameters make inference…
A mother-machine microfluidic device for non-adherent mammalian cells reveals the population growth strategies
Simone Scalise, Giovanna Peruzzi, Davide Caprini +3
We develop a mother machine-like microfluidic device specifically designed to track the proliferation of T-cells via live-cell microscopy. Although numerous microfluidic setups hav…
Insights into the role of dynamical features in protein complex formation: the case of SARS-CoV-2 spike binding with ACE2
Greta Grassmann, Mattia Miotto, Francesca Alessandrini +4
The functionality of protein-protein complexes is closely tied to the strength of their interactions, making the evaluation of binding affinity a central focus in structural biolog…
Rosette formations as symmetry-breaking events: theory and experiment
Mattia Miotto, Giorgio Gosti, Maria Rosito +6
Multicellular rosettes are observed in different situations such as morphogenesis, wound healing, and cancer progression. While some molecular insights have been gained to explain…
A new pathway to generative artificial intelligence by minimizing the maximum entropy
Mattia Miotto, Lorenzo Monacelli
Generative artificial intelligence revolutionized society. Current models are trained by minimizing the distance between the produced data and the training set. Consequently, devel…
Non-equilibrium phase transitions in hybrid Voronoi models of cell colonies
Mattia Miotto, Giancarlo Ruocco, Matteo Paoluzzi
Eukaryotic cells are characterized by a stiff nucleus whose effect in modeling the collective behavior of cell aggregates is usually underestimated. However, increasing experimenta…
Robust assessment of asymmetric division in colon cancer cells
Domenico Caudo, Chiara Giannattasio, Simone Scalise +6
Asymmetric partition of fate determinants during cell division is a hallmark of cell differentiation. Recent work suggested that such a mechanism is hijacked by cancer cells to inc…
Probing leukemia cells behavior under starvation
Simone Scalise, Giorgio Gosti, Giancarlo Ruocco +2
The ability of a cancer cell population to achieve heterogeneity in their phenotype distributions offers advantages in tumor invasiveness and drug resistance. Studying the mechanis…
Compact assessment of molecular surface complementarities enhances neural network-aided prediction of key binding residues
Greta Grassmann, Lorenzo Di Rienzo, Giancarlo Ruocco +2
Predicting interactions between biomolecules, such as protein-protein complexes, remains a challenging problem. Despite the many advancements done so far, the performances of docki…
Zepyros: A webserver to evaluate the shape complementarity of protein-protein interfaces
Mattia Miotto, Lorenzo Di Rienzo, Leonardo Bo' +2
Shape complementarity of molecular surfaces at the interfaces is a well-known characteristic of protein-protein binding regions, and it is critical in influencing the stability of…
High throughput interactome determination via sulfur anomalous scattering
Mattia Miotto, Edoardo Milanetti, Riccardo Mincigrucci +2
We propose a novel approach to detect the binding between proteins making use of the anomalous diffraction of natively present heavy elements inside the molecule 3D structure. In p…
Determining cancer cells division strategy
Mattia Miotto, Simone Scalise, Marco Leonetti +3
Heterogeneity in the size distribution of cancer cell populations has been recently linked to drug resistance and invasiveness. However, despite many progresses have been made in u…
Osmolyte-Induced Protein Stability Changes Explained by Graph Theory
Mattia Miotto, Nina Warner, Giancarlo Ruocco +3
Enhanced stabilisation of protein structures via the presence of inert excipients is a key mechanism adopted both by physiological systems and in biotechnological applications. Whi…
Electrostatic complementarity at the interface drives transient protein-protein interactions
Greta Grassmann, Lorenzo Di Rienzo, Giorgio Gosti +4
Understanding the molecular mechanisms driving the binding between bio-molecules is a crucial challenge in molecular biology. In this respect, characteristics like the preferential…
A computational approach to investigate TDP-43 C-terminal fragments aggregation in Amyotrophic Lateral Sclerosis
Greta Grassmann, Mattia Miotto, Lorenzo Di Rienzo +7
Many of the molecular mechanisms underlying the pathological aggregation of proteins observed in neurodegenerative diseases are still not fully understood. Among the diseases assoc…
Investigating the side-chain structural organization behind the stability of protein folding and binding
Fausta Desantis, Mattia Miotto, Lorenzo Di Rienzo +2
What are the molecular mechanisms that dictate protein-protein binding stability and whether those are related to the ones behind protein fold stability are still largely open ques…
New algorithm to determine a minimal representation of the molecular surface
Greta Grassmann, Mattia Miotto, Lorenzo Di Rienzo +3
Most proteins perform their biological function by interacting with one or more molecular partners. In this respect, characterizing the features of the molecular surface, especiall…
Shape Complementarity Optimization of Antibody-Antigen Interfaces: the Application to SARS-CoV-2 Spike Protein
Alfredo De Lauro, Lorenzo Di Rienzo, Mattia Miotto +3
Many factors influence biomolecules binding, and its assessment constitutes an elusive challenge in computational structural biology. In this respect, the evaluation of shape compl…
Molecular mechanisms behind anti SARS-CoV-2 action of lactoferrin
Mattia Miotto, Lorenzo Di Rienzo, Leonardo Bò +3
Despite the huge effort to contain the infection, the novel SARS-CoV-2 coronavirus has rapidly become pandemics, mainly due to its extremely high human-to-human transmission capabi…
Does blood type affect the COVID-19 infection pattern?
Mattia Miotto, Lorenzo Di Rienzo, Giorgio Gosti +2
Among the many aspects that characterize the COVID-19 pandemic, two seem particularly challenging to understand: (i) the great geographical differences in the degree of virus conta…
In-Silico evidence for two receptors based strategy of SARS-CoV-2
Edoardo Milanetti, Mattia Miotto, Lorenzo Di Rienzo +3
We propose a novel numerical method able to determine efficiently and effectively the relationship of complementarity between portions of proteins surfaces. This innovative and gen…
Genome heterogeneity drives the evolution of species
Mattia Miotto, Lorenzo Monacelli
Most of the DNA that composes a complex organism is non-coding and defined as junk. Even the coding part is composed of genes that affect the phenotype differently. Therefore, a ra…