Related papers: Variant effects on protein-protein interactions: m…

Applying machine learning to biological sequences - DNA, RNA and protein - has enormous potential to advance human health, environmental sustainability, and fundamental biological understanding. However, many existing machine learning…

Qualitative interactions occur when a treatment effect or measure of association varies in sign by sub-population. Of particular interest in many biomedical settings are absence/presence qualitative interactions, which occur when an effect…

A critical task in systems biology is the identification of genes that interact to control cellular processes by transcriptional activation of a set of target genes. Many methods have been developed to use statistical correlations in…

Here we review the development of protein scaling theory, starting from backgrounds in mathematics and statistical mechanics, and leading to biomedical applications. Evolution has organized each protein family in different ways, but scaling…

A bioinformatics platform is introduced aimed at identifying models of disease-specific pathways, as well as a set of network measures that can quantify changes in terms of global structure or single link disruptions.The approach integrates…

Fueled by breakthrough technology developments, the biological, biomedical, and behavioral sciences are now collecting more data than ever before. There is a critical need for time- and cost-efficient strategies to analyze and interpret…

The interaction between proteins and nucleic acids is crucial for processes that sustain cellular function, including DNA maintenance and the regulation of gene expression and translation. Amino acid mutations in protein-nucleic acid…

RNA binding proteins play a crucial role in post-transcriptional gene regulation by controlling the transport, processing, and translation of their target RNAs. Post-transcriptional gene regulation leads to the differential expression of…

In the last years many powerful techniques have emerged to measure protein interactions as well as gene expression. Many progresses have been done since the introduction of these techniques but not toward quantitative analysis of data. In…

Clinical machine learning applications are often plagued with confounders that can impact the generalizability and predictive performance of the learners. Confounding is especially problematic in remote digital health studies where the…

Despite the recognized importance of the multi-scale spatio-temporal organization of proteins, most computational tools can only access a limited spectrum of time and spatial scales, thereby ignoring the effects on protein behavior of the…

The interaction lifetimes between condensate-forming biomolecules can dictate both the specificity of the condensate-forming species as well as the fluidity and exchange dynamics of these condensates. Using a heuristic modeling approach, we…

Much of the natural variation for a complex trait can be explained by variation in DNA sequence levels. As part of sequence variation, gene-gene interaction has been ubiquitously observed in nature, where its role in shaping the development…

Understanding the relationships between protein sequence, structure and function is a long-standing biological challenge with manifold implications from drug design to our understanding of evolution. Recently, protein language models have…

Genetically identical cells under the same environmental conditions can show strong variations in protein copy numbers due to inherently stochastic events in individual cells. We here develop a theoretical framework to address how…

Protein-protein interaction extraction is the key precondition of the construction of protein knowledge network, and it is very important for the research in the biomedicine. This paper extracted directional protein-protein interaction from…

Significant volumes of knowledge have been accumulated in recent years linking subtle genetic variations to a wide variety of medical disorders from Cystic Fibrosis to mental retardation. Nevertheless, there are still great challenges in…

Brain function results from communication between neurons connected by complex synaptic networks. Synapses are themselves highly complex and diverse signaling machines, containing protein products of hundreds of different genes, some in…

All living systems can function only far away from equilibrium, and for this reason chemical kinetic methods are critically important for uncovering the mechanisms of biological processes. Here we present a new theoretical method of…

Managing patients with multimorbidity often results in polypharmacy: the prescription of multiple drugs. However, the long-term effects of specific combinations of drugs and diseases are typically unknown. In particular, drugs prescribed…