List of works - Ugo Bastolla

A Numerical Study of the Critical Line of Kauffman Networks ⬇️

scientific article published on July 7, 1997

A framework for protein structure prediction on the grid

A protein evolution model with independent sites that reproduces site-specific amino acid distributions from the Protein Data Bank

scientific article

An efficient conformational sampling method for homology modeling.

scientific article

Attraction basins in discretized maps

Bacteria dialog with Santa Rosalia: Are aggregations of cosmopolitan bacteria mainly explained by habitat filtering or by ecological interactions?

scientific article

Biodiversity in model ecosystems, I: coexistence conditions for competing species

scientific article

Biodiversity in model ecosystems, II: species assembly and food web structure.

scientific article

Bioinformatics

scientific article (2011)

Can Conformational Changes of Proteins Be Represented in Torsion Angle Space? A Study with Rescaled Ridge Regression

scientific article published on 29 October 2019

Characterizing conformation changes in proteins through the torsional elastic response.

scientific article published on 19 February 2013

Comparison of translation loads for standard and alternative genetic codes

scientific article

Computational proteomics on the grid

Computing protein dynamics from protein structure with elastic network models

article

Connectivity of Neutral Networks, Overdispersion, and Structural Conservation in Protein Evolution

article published in 2003

Cross-biome microbial networks reveal functional redundancy and suggest genome reduction through functional complementarity

scientific article published on 11 September 2022

Cross-over between discrete and continuous protein structure space: insights into automatic classification and networks of protein structures.

scientific article

Detecting selection for negative design in proteins through an improved model of the misfolded state

scientific article published on 10 April 2013

Detecting selection on protein stability through statistical mechanical models of folding and evolution

scientific article published on 07 March 2014

Differences in firing efficiency, chromatin and transcription underlie the developmental plasticity of Arabidopsis originome

scholarly article published 1 February 2018

Differences in firing efficiency, chromatin, and transcription underlie the developmental plasticity of the Arabidopsis DNA replication origins

scientific article published on 07 March 2019

Diversity patterns from ecological models at dynamical equilibrium

scientific article published in September 2001

Dynamics and topology of species networks

article

Editorial overview: Proteins: bridging theory and experiment

scientific article published on 10 January 2017

Effective competition determines the global stability of model ecosystems

scientific article published in 2016

Effective connectivity profile: a structural representation that evidences the relationship between protein structures and sequences.

scientific article

Emergence of structure through protein-protein interactions and pH changes in dually predicted coiled-coil and disordered regions of centrosomal proteins.

scientific article published in August 2014

Exactness of the annealed and the replica symmetric approximations for random heteropolymers

scientific article published on 14 February 2001

Genomic determinants of protein folding thermodynamics in prokaryotic organisms

scientific article published in November 2004

High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABER-TOOTH.

scientific article

High-resolution analysis of DNA synthesis start sites and nucleosome architecture at efficient mammalian replication origins.

scientific article published on 30 August 2013

How lethal is the novel coronavirus, and how many undetected cases there are? The importance of being tested.

scientific article published on 01 April 2020

How to guarantee optimal stability for most representative structures in the Protein Data Bank.

scientific article published in August 2001

In memoriam. Angel Ramírez Ortiz (1966-2008).

scientific article published in January 2010

Influence of mutation bias and hydrophobicity on the substitution rates and sequence entropies of protein evolution

scientific article published on 05 October 2018

Influence of mutation bias and hydrophobicity on the substitution rates and sequence entropies of protein evolution

Lack of self-averaging in neutral evolution of proteins

scientific article published in Physical Review Letters

Learning protein folding and evolution with a snake puzzle

Local interactions in protein folding determined through an inverse folding model

scientific article published in April 2008

Local interactions in protein folding determined through an inverse folding model

scholarly article by Ugo Bastolla published in July 2008

Looking at structure, stability, and evolution of proteins through the principal eigenvector of contact matrices and hydrophobicity profiles.

scientific article

Maximum-Likelihood Phylogenetic Inference with Selection on Protein Folding Stability

scientific article published on 2 April 2015

Modeling Structural and Genomic Constraints in the Evolution of Proteins

Molecular and Functional Bases of Selection against a Mutation Bias in an RNA Virus.

scientific article

Mutation bias favors protein folding stability in the evolution of small populations

scientific article

Mutualism supports biodiversity when the direct competition is weak

scientific article

Neutral evolution of model proteins: diffusion in sequence space and overdispersion

article

New Monte Carlo Algorithm for Protein Folding

scientific article published in Physical Review Letters

Phase Transitions of Single Semistiff Polymer Chains

article by Ugo Bastolla & Peter Grassberger published December 1997 in Journal of Statistical Physics

Phase diagram of random heteropolymers: Replica approach and application of a new Monte Carlo algorithm

article published in 2000

Predicted dynamical couplings of protein residues characterize catalysis, transport and allostery

scientific article published on 01 December 2019

Prediction of site-specific amino acid distributions and limits of divergent evolutionary changes in protein sequences

scientific article published in 2005

Principal eigenvector of contact matrices and hydrophobicity profiles in proteins

ProtASR: An Evolutionary Framework for Ancestral Protein Reconstruction with Selection on Folding Stability

scientific article

Protein disorder in the centrosome correlates with complexity in cell types number

scientific article

Protein evolution along phylogenetic histories under structurally constrained substitution models.

scientific article

Protein evolution in viral quasispecies under selective pressure: A thermodynamic and phylogenetic analysis

article

Quantifying the evolutionary divergence of protein structures: the role of function change and function conservation.

scientific article published in January 2010

Reconstruction of protein structures from a vectorial representation

scientific article published in Physical Review Letters

Reductive genome evolution in Buchnera aphidicola

scientific article

Relaxation, closing probabilities and transition from oscillatory to chaotic attractors in asymmetric neural networks

SABERTOOTH: protein structural alignment based on a vectorial structure representation.

scientific article

Sequence determinants of protein folding rates: positive correlation between contact energy and contact range indicates selection for fast folding

scientific article

Shape of ecological networks

scientific article published in May 2001

Stability constraints and protein evolution: the role of chain length, composition and disulfide bonds

article

Statistical properties of neutral evolution

scientific article published in January 2003

Structural basis for allosteric transitions of a multidomain pentameric ligand-gated ion channel

scientific article published on 01 June 2020

Structure and non-structure of centrosomal proteins.

scientific article

Substitution rates predicted by stability-constrained models of protein evolution are not consistent with empirical data

scientific article published on 26 December 2017

Testing a new Monte Carlo algorithm for protein folding

scientific article published in July 1998

Testing a new Monte Carlo algorithm for protein folding

scholarly article by Ugo Bastolla published in July 1998

Testing similarity measures with continuous and discrete protein models

article

The Functional Topography of the Arabidopsis Genome Is Organized in a Reduced Number of Linear Motifs of Chromatin States

scientific article

The Influence of Protein Stability on Sequence Evolution: Applications to Phylogenetic Inference

scientific article published on 01 January 2019

The Molecular Clock in the Evolution of Protein Structures

scientific article published on 01 November 2019

The Structurally Constrained Neutral Model of Protein Evolution

article

The architecture of mutualistic networks minimizes competition and increases biodiversity

scientific article (publication date: 23 April 2009)

The emerging dynamic view of proteins: protein plasticity in allostery, evolution and self-assembly

scientific article published in May 2013

The interface of protein structure, protein biophysics, and molecular evolution

scientific article

The maximum penalty criterion for ridge regression: application to the calibration of the force constant in elastic network models.

scientific article published on 30 May 2017

Torsional Network Model: Normal Modes in Torsion Angle Space Better Correlate with Conformation Changes in Proteins

scientific article published in Physical Review Letters

What evolution tells us about protein physics, and protein physics tells us about evolution

scientific article published on 16 November 2016

List of works by Ugo Bastolla

A Numerical Study of the Critical Line of Kauffman Networks ⬇️

A framework for protein structure prediction on the grid

A protein evolution model with independent sites that reproduces site-specific amino acid distributions from the Protein Data Bank

An efficient conformational sampling method for homology modeling.

Attraction basins in discretized maps

Bacteria dialog with Santa Rosalia: Are aggregations of cosmopolitan bacteria mainly explained by habitat filtering or by ecological interactions?

Biodiversity in model ecosystems, I: coexistence conditions for competing species

Biodiversity in model ecosystems, II: species assembly and food web structure.

Bioinformatics

Can Conformational Changes of Proteins Be Represented in Torsion Angle Space? A Study with Rescaled Ridge Regression

Characterizing conformation changes in proteins through the torsional elastic response.

Comparison of translation loads for standard and alternative genetic codes

Computational proteomics on the grid

Computing protein dynamics from protein structure with elastic network models

Connectivity of Neutral Networks, Overdispersion, and Structural Conservation in Protein Evolution

Cross-biome microbial networks reveal functional redundancy and suggest genome reduction through functional complementarity

Cross-over between discrete and continuous protein structure space: insights into automatic classification and networks of protein structures.

Detecting selection for negative design in proteins through an improved model of the misfolded state

Detecting selection on protein stability through statistical mechanical models of folding and evolution

Differences in firing efficiency, chromatin and transcription underlie the developmental plasticity of Arabidopsis originome

Differences in firing efficiency, chromatin, and transcription underlie the developmental plasticity of the Arabidopsis DNA replication origins

Diversity patterns from ecological models at dynamical equilibrium

Dynamics and topology of species networks

Editorial overview: Proteins: bridging theory and experiment

Effective competition determines the global stability of model ecosystems

Effective connectivity profile: a structural representation that evidences the relationship between protein structures and sequences.

Emergence of structure through protein-protein interactions and pH changes in dually predicted coiled-coil and disordered regions of centrosomal proteins.

Exactness of the annealed and the replica symmetric approximations for random heteropolymers

Genomic determinants of protein folding thermodynamics in prokaryotic organisms

High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABER-TOOTH.

High-resolution analysis of DNA synthesis start sites and nucleosome architecture at efficient mammalian replication origins.

How lethal is the novel coronavirus, and how many undetected cases there are? The importance of being tested.

How to guarantee optimal stability for most representative structures in the Protein Data Bank.

In memoriam. Angel Ramírez Ortiz (1966-2008).

Influence of mutation bias and hydrophobicity on the substitution rates and sequence entropies of protein evolution

Influence of mutation bias and hydrophobicity on the substitution rates and sequence entropies of protein evolution

Influence of mutation bias and hydrophobicity on the substitution rates and sequence entropies of protein evolution

Lack of self-averaging in neutral evolution of proteins

Learning protein folding and evolution with a snake puzzle

Learning protein folding and evolution with a snake puzzle

Local interactions in protein folding determined through an inverse folding model

Local interactions in protein folding determined through an inverse folding model

Looking at structure, stability, and evolution of proteins through the principal eigenvector of contact matrices and hydrophobicity profiles.

Maximum-Likelihood Phylogenetic Inference with Selection on Protein Folding Stability

Modeling Structural and Genomic Constraints in the Evolution of Proteins

Molecular and Functional Bases of Selection against a Mutation Bias in an RNA Virus.

Mutation bias favors protein folding stability in the evolution of small populations

Mutualism supports biodiversity when the direct competition is weak

Neutral evolution of model proteins: diffusion in sequence space and overdispersion

New Monte Carlo Algorithm for Protein Folding

Phase Transitions of Single Semistiff Polymer Chains

Phase diagram of random heteropolymers: Replica approach and application of a new Monte Carlo algorithm

Predicted dynamical couplings of protein residues characterize catalysis, transport and allostery

Prediction of site-specific amino acid distributions and limits of divergent evolutionary changes in protein sequences

Principal eigenvector of contact matrices and hydrophobicity profiles in proteins

ProtASR: An Evolutionary Framework for Ancestral Protein Reconstruction with Selection on Folding Stability

Protein disorder in the centrosome correlates with complexity in cell types number

Protein evolution along phylogenetic histories under structurally constrained substitution models.

Protein evolution in viral quasispecies under selective pressure: A thermodynamic and phylogenetic analysis

Quantifying the evolutionary divergence of protein structures: the role of function change and function conservation.

Reconstruction of protein structures from a vectorial representation

Reductive genome evolution in Buchnera aphidicola

Relaxation, closing probabilities and transition from oscillatory to chaotic attractors in asymmetric neural networks

SABERTOOTH: protein structural alignment based on a vectorial structure representation.

Sequence determinants of protein folding rates: positive correlation between contact energy and contact range indicates selection for fast folding

Shape of ecological networks

Stability constraints and protein evolution: the role of chain length, composition and disulfide bonds

Statistical properties of neutral evolution

Structural basis for allosteric transitions of a multidomain pentameric ligand-gated ion channel

Structure and non-structure of centrosomal proteins.

Substitution rates predicted by stability-constrained models of protein evolution are not consistent with empirical data

Testing a new Monte Carlo algorithm for protein folding

Testing a new Monte Carlo algorithm for protein folding

Testing similarity measures with continuous and discrete protein models

The Functional Topography of the Arabidopsis Genome Is Organized in a Reduced Number of Linear Motifs of Chromatin States

The Influence of Protein Stability on Sequence Evolution: Applications to Phylogenetic Inference

The Molecular Clock in the Evolution of Protein Structures

The Structurally Constrained Neutral Model of Protein Evolution

The architecture of mutualistic networks minimizes competition and increases biodiversity