Lista de obras - Ugo Bastolla - Dominio Público Uruguay

A Numerical Study of the Critical Line of Kauffman Networks ⬇️

artículo científico publicado el 7 de julio de 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

artículo científico publicado en 2006

An efficient conformational sampling method for homology modeling.

artículo científico publicado en 2008

Attraction basins in discretized maps

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

artículo científico publicado en 2014

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

artículo científico publicado en 2005

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

artículo científico publicado en 2005

Bioinformatics

artículo científico publicado en 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.

artículo científico publicado en 2013

Comparison of translation loads for standard and alternative genetic codes

artículo científico publicado en 2010

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

artículo científico publicado en 2022

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

artículo científico publicado en 2009

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

artículo científico publicado en 2013

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

artículo científico

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

artículo científico publicado en 2019

Diversity patterns from ecological models at dynamical equilibrium

artículo científico publicado en 2001

Dynamics and topology of species networks

article

Editorial overview: Proteins: bridging theory and experiment

artículo científico publicado en 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.

artículo científico publicado en 2008

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

artículo científico publicado en 2014

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

artículo científico publicado en 2001

Genomic determinants of protein folding thermodynamics in prokaryotic organisms.

artículo científico publicado en 2004

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

artículo científico publicado en 2010

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

artículo científico publicado en 2013

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

artículo científico publicado en 2020

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

artículo científico publicado en 2001

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

artículo científico publicado en 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

artículo científico publicado en 2002

Learning protein folding and evolution with a snake puzzle

Local interactions in protein folding determined through an inverse folding model

artículo científico publicado en 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.

artículo científico publicado en 2005

Maximum-Likelihood Phylogenetic Inference with Selection on Protein Folding Stability

artículo científico publicado en 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.

artículo científico publicado en 2017

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

artículo científico publicado en 2010

Mutualism supports biodiversity when the direct competition is weak

artículo científico publicado en 2017

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

artículo científico publicado en 2005

Principal eigenvector of contact matrices and hydrophobicity profiles in proteins

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

artículo científico publicado en 2017

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

artículo científico publicado en 2011

Protein evolution along phylogenetic histories under structurally constrained substitution models.

artículo científico publicado en 2013

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.

artículo científico publicado en 2010

Reconstruction of protein structures from a vectorial representation

scientific article published in Physical Review Letters

Reductive genome evolution in Buchnera aphidicola

artículo científico publicado en 2003

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

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

artículo científico publicado en 2007

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

artículo científico publicado en 2012

Shape of ecological networks

artículo científico publicado en 2001

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

article

Statistical properties of neutral evolution

artículo científico publicado en 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.

artículo científico publicado en 2013

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

artículo científico publicado en 2017

Testing a new Monte Carlo algorithm for protein folding

artículo científico publicado en 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

artículo científico publicado en 2014

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

artículo científico publicado en 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

artículo científico publicado en 2009

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

artículo científico publicado en 2013

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

artículo científico publicado en 2012

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

artículo científico publicado en 2017

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

artículo científico publicado en 2010

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

artículo científico publicado en 2016

Lista de obras de 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