相关论文: Biases in the Experimental Annotations of Protein …
Describing the processes involved in analyzing data from electrophysiology experiments to investigate the function of neural systems is inherently challenging. On the one hand, data can be analyzed by distinct methods that serve a similar…
Recent developments in next generation sequencing technology have led to the creation of extensive, open-source protein databases consisting of hundreds of millions of sequences. To render these sequences applicable in biomedical…
Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at…
Protein structure prediction can be shown to be an NP-hard problem; the number of conformations grows exponentially with the number of residues. The native conformations of proteins occupy a very small subset of these, hence an exploratory,…
As machine learning becomes increasingly central to molecular design, it is vital to ensure the reliability of learnable protein-ligand scoring functions on novel protein targets. While many scoring functions perform well on standard…
Atomic packing is an important metric for characterizing protein structures, as it significantly influences various features including the stability, the rate of evolution and the functional roles of proteins. Packing in protein structures…
In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques,…
We introduce a pioneering methodology for boosting large language models in the domain of protein representation learning. Our primary contribution lies in the refinement process for correlating the over-reliance on co-evolution knowledge,…
The Gene Ontology (GO) provides a knowledge base to effectively describe proteins. However, measuring similarity between proteins based on GO remains a challenge. In this paper, we propose a new similarity measure, information coefficient…
Gene products (RNAs, proteins) often occur at low molecular counts inside individual cells, and hence are subject to considerable random fluctuations (noise) in copy number over time. Not surprisingly, cells encode diverse regulatory…
Purpose: Researchers frequently encounter the following problems when writing scientific articles: (1) Selecting appropriate citations to support the research idea is challenging. (2) The literature review is not conducted extensively,…
Proteins encoded by genes containing regions of variable number tandem repeats (VNTRs) are known to be polymorphic within species but the influence of their instability in molecular interactions remains unclear. VNTRs are overrepresented in…
The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I…
Intrinsically disordered regions (IDRs) account for one-third of the human proteome and play essential biological roles. However, predicting the functions of IDRs remains a major challenge due to their lack of stable structures, rapid…
Foundation models in genomics have shown mixed success compared to their counterparts in natural language processing. Yet, the reasons for their limited effectiveness remain poorly understood. In this work, we investigate the role of…
The large amount of information contained in bibliographic databases has recently boosted the use of citations, and other indicators based on citation numbers, as tools for the quantitative assessment of scientific research. Citations…
Exploring the functions of genes and gene products is crucial to a wide range of fields, including medical research, evolutionary biology, and environmental science. However, discovering new functions largely relies on expensive and…
Generalizable protein function prediction is increasingly constrained by the growing mismatch between exponentially expanding sequences of environmental proteins and the comparatively slow accumulation of experimentally verified functional…
This paper investigates the stochastic fluctuations of the number of copies of a given protein in a cell. This problem has already been addressed in the past and closed-form expressions of the mean and variance have been obtained for a…
Current supervised deep learning frameworks rely on annotated data for modeling the underlying data distribution of a given task. In particular for computer vision algorithms powered by deep learning, the quality of annotated data is the…