Related papers: Identifying the Genetic Basis of Functional Protei…
The observed correlations between pairs of homologous protein sequences are typically explained in terms of a Markovian dynamic of amino acid substitution. This model assumes that every location on the protein sequence has the same…
Genomic duplication-divergence events, which are the primary source of new protein functions, occur stochastically at a wide range of genomic scales, from single gene to whole genome duplications. Clearly, this fundamental evolutionary…
Understanding and extracting the patterns of microscopy images has been a major challenge in the biomedical field. Although trained scientists can locate the proteins of interest within a human cell, this procedure is not efficient and…
The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks…
Given the amino acid sequence of a protein, researchers often infer its structure and function by finding homologous, or evolutionarily-related, proteins of known structure and function. Since structure is typically more conserved than…
This paper presents a novel approach for predicting the relative populations of protein conformations using AlphaFold 2, an AI-powered method that has revolutionized biology by enabling the accurate prediction of protein structures. While…
Proteins are essential components of living systems, capable of performing a huge variety of tasks at the molecular level, such as recognition, signalling, copy, transport, ... The protein sequences realizing a given function may largely…
This piece serves two purposes. Firstly, it aims at elucidating the role of epistasis in shaping, at a molecular level, the evolutionary paths of proteins, as well as the extent to which these epistatic effects are the outcome of an…
Thermostability is an important prerequisite for enzymes employed for industrial applications. Several machine learning based models have thus been formulated for protein classification based on this particular trait. These models have…
Enzyme is the major workhorse to carry out the diverse cellular functions. It catalyzes the biological reactions with a high specificity, with its topology playing a crucial role. For ecologically safe production of numerous bioproducts…
Generative models emerge as promising candidates for novel sequence-data driven approaches to protein design, and for the extraction of structural and functional information about proteins deeply hidden in rapidly growing sequence…
When analyzing the genome, researchers have discovered that proteins bind to DNA based on certain patterns of the DNA sequence known as "motifs". However, it is difficult to manually construct motifs due to their complexity. Recently,…
Protein structures and functions are determined by a contiguous arrangement of amino acid sequences. Designing novel protein sequences and structures with desired geometry and functions is a complex task with large state spaces. Here we…
There is an intrinsic relationship between the molecular evolution in primordial period and the properties of genomes and proteomes of contemporary species. The genomic data may help us understand the driving force of evolution of life at…
Several technological applications require the translation of a protein into a nucleic acid that codes for it (``backtranslation''). The degeneracy of the genetic code makes this translation ambiguous; moreover, not every translation is…
It is well known amongst molecular biologists that proteins with a common ancestor and that perform the same function in similar organisms, can have rather different amino-acid sequences. Mutations have altered the amino-acid sequences…
We consider resequencing studies of associated loci and the problem of prioritizing sequence variants for functional follow-up. Working within the multivariate linear regression framework helps us to account for correlation across variants,…
The interconnected processes of protein folding, mutations, epistasis, and evolution have all been the subject of extensive analysis throughout the years due to their significance for structural and evolutionary biology. The origin…
Motivation: In the last few years a growing interest in biology has been shifting towards the problem of optimal information extraction from the huge amount of data generated via large scale and high-throughput techniques. One of the most…
Background. Non-specific Lipid Transfer Proteins (nsLTPs) are widely distributed in the plant kingdom and constitute a superfamily of related proteins. More than 800 different sequences have been characterized so far, but their biological…