相关论文: Biases in the Experimental Annotations of Protein …
Using data retrieved from the INSPEC database we have quantitatively discussed a few syndromes of the publish-or-perish phenomenon, including continuous growth of rate of scientific productivity, and continuously decreasing percentage of…
The burst approximation is a widely used technique to simplify stochastic gene expression models. However, the dynamics and analytical properties of the protein number distribution in gene expression models under the burst approximation are…
The interactions of a protein, its phase behavior, and ultimately, its ability to function, are all influenced by the interactions between the protein and its hydration waters. Here we study proteins with a variety of sizes, shapes,…
Thanks to the increasing growth of computational power and data availability, the research in machine learning has advanced with tremendous rapidity. Nowadays, the majority of automatic decision making systems are based on data. However, it…
Attempting to imitate the brain functionalities, researchers have bridged between neuroscience and artificial intelligence for decades; however, experimental neuroscience has not directly advanced the field of machine learning. Here, using…
Despite the recent successes of deep learning, such models are still far from some human abilities like learning from few examples, reasoning and explaining decisions. In this paper, we focus on organ annotation in medical images and we…
Functional protein-protein interactions are crucial in most cellular processes. They enable multi-protein complexes to assemble and to remain stable, and they allow signal transduction in various pathways. Functional interactions between…
Background: Biological networks have a growing importance for the interpretation of high-throughput omics data. Integrative network analysis makes use of statistical and combinatorial methods to extract smaller subnetwork modules, and…
Deep neural networks have achieved state of the art accuracy at classifying molecules with respect to whether they bind to specific protein targets. A key breakthrough would occur if these models could reveal the fragment pharmacophores…
Determining the interaction strength between proteins and small molecules is key to analyzing their biological function. Quantum-mechanical calculations such as \emph{Density Functional Theory} (DFT) give accurate and theoretically…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. Proteins are peptide chains decorated by amino…
In the present work, we review the fundamental methods which have been developed in the last few years for classifying into families and clans the distribution of amino acids in protein databases. This is done through functions of random…
The knowledge regarding the function of proteins is necessary as it gives a clear picture of biological processes. Nevertheless, there are many protein sequences found and added to the databases but lacks functional annotation. The…
The study of biological processes can greatly benefit from tools that automatically predict gene functions or directly cluster genes based on shared functionality. Existing data mining methods predict protein functionality by exploiting…
Analyzing a large data set of publications drawn from the most competitive journals in the natural and social sciences we show that research careers exhibit the broad distributions of individual achievement characteristic of systems in…
Protein interaction networks are a promising type of data for studying complex biological systems. However, despite the rich information embedded in these networks, they face important data quality challenges of noise and incompleteness…
An original cross sectional dataset referring to a medium sized Italian university is implemented in order to analyze the determinants of scientific research production at individual level. The dataset includes 942 permanent researchers of…
The function of proteins arises from cooperative interactions and rearrangements of their amino acids, which exhibit large-scale dynamical modes. Long-range correlations have also been revealed in protein sequences, and this has motivated…
Annotating datasets for question answering (QA) tasks is very costly, as it requires intensive manual labor and often domain-specific knowledge. Yet strategies for annotating QA datasets in a cost-effective manner are scarce. To provide a…
Proteins, essential to biological systems, perform functions intricately linked to their three-dimensional structures. Understanding the relationship between protein structures and their amino acid sequences remains a core challenge in…