Related papers: Capturing coevolutionary signals in repeat protein…
Inferring protein-protein interactions from sequences is an important task in computational biology. Recent methods based on Direct Coupling Analysis (DCA) or Mutual Information (MI) allow to find interaction partners among paralogs of two…
The sequence of amino acids in a protein is believed to determine its native state structure, which in turn is related to the functionality of the protein. In addition, information pertaining to evolutionary relationships is contained in…
The inverse Potts problem for estimating evolutionary single-site fields and pairwise couplings in homologous protein sequences from their single-site and pairwise amino acid frequencies observed in their multiple sequence alignment would…
We introduce a graph generating model aimed at representing the evolution of protein interaction networks. The model is based on the hypotesis of evolution by duplications and divergence of the genes which produce proteins. The obtained…
Conformational transitions are ubiquitous in biomolecular systems, have significant functional roles and are subject to evolutionary pressures. Here we provide a first theoretical framework for topological transition, i.e. conformational…
To construct models of large, multivariate complex systems, such as those in biology, one needs to constrain which variables are allowed to interact. This can be viewed as detecting "local" structures among the variables. In the context of…
Recently, persistent homology has had tremendous success in biomolecular data analysis. It works by examining the topological relationship or connectivity of a group of atoms in a molecule at a variety of scales, then rendering a family of…
Reticulate evolutionary processes result in phylogenetic histories that cannot be modeled using a tree topology. Here, we apply methods from topological data analysis to molecular sequence data with reticulations. Using a simple example, we…
Measuring gene expression simultaneously in both hosts and symbionts offers a powerful approach to explore the biology underlying species interactions. Such dual or simultaneous RNAseq approaches have primarily been used to gain insight…
Protein function does not solely depend on structure but often relies on dynamical transitions between distinct conformations. Despite this fact, our ability to characterize or predict protein dynamics is substantially less developed…
Proteins created by combinatorial methods in vitro are an important source of information for understanding sequence-structure-function relationships. Alignments of folded proteins from combinatorial libraries can be analyzed using methods…
Function of proteins or a network of interacting proteins often involves communication between residues that are well separated in sequence. The classic example is the participation of distant residues in allosteric regulation.…
All known terrestrial proteins are coded as continuous strings of ~20 amino acids. The patterns formed by the repetitions of elements in groups of finite sequences describes the natural architectures of protein families. We present a method…
Background: Coevolution within a protein family is often predicted using statistics that measure the degree of covariation between positions in the protein sequence. Mutual Information is a measure of dependence between two random variables…
Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended timescales. Our methodology involves simulating proteins with molecular…
Learning Ising or Potts models from data has become an important topic in statistical physics and computational biology, with applications to predictions of structural contacts in proteins and other areas of biological data analysis. The…
Systems of interacting random replicators are studied using generating functional techniques. While replica analyses of such models are limited to systems with symmetric couplings, dynamical approaches as presented here allow specifically…
Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology, and disease. Comparison and alignment of biological networks will likely have a similar impact. Existing network alignments use…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
Most amino acids are encoded by multiple synonymous codons. For an amino acid, some of its synonymous codons are used much more rarely than others. Analyses of positions of such rare codons in protein sequences revealed that rare codons can…