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According to the World Health Organization (WHO), cancer is the second leading cause of death globally. Scientific research on different types of cancers grows at an ever-increasing rate, publishing large volumes of research articles every…
Cancer is one of the diseases that kill the most women in the world, with breast cancer being responsible for the highest number of cancer cases and consequently deaths. However, it can be prevented by early detection and, consequently,…
Cancer subtyping is crucial for understanding the nature of tumors and providing suitable therapy. However, existing labelling methods are medically controversial, and have driven the process of subtyping away from teaching signals.…
One of the central goals in precision health is the understanding and interpretation of high-dimensional biological data to identify genes and markers associated with disease initiation, development, and outcomes. Though significant effort…
Proteins are the essential drivers of biological processes. At the molecular level, they are chains of amino acids that can be viewed through a linguistic lens where the twenty standard residues serve as an alphabet combining to form a…
Accurate identification of protein nucleic-acid-binding residues poses a significant challenge with important implications for various biological processes and drug design. Many typical computational methods for protein analysis rely on a…
Tokenization is a promising path to multi-modal models capable of jointly understanding protein sequences, structure, and function. Existing protein structure tokenizers create tokens by pooling information from local neighborhoods, an…
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…
The integration of multi-omics data has emerged as a promising approach for gaining comprehensive insights into complex diseases such as cancer. This paper proposes a novel approach to identify cancer subtypes through the integration of…
Modelling and predicting protein configurations is crucial for advancing drug discovery, enabling the design of treatments for life-threatening diseases. A critical aspect of this challenge is rotamer optimisation - the determination of…
Most human tumors result from the accumulation of multiple genetic and epigenetic alterations in a single cell. Mutations that confer a fitness advantage to the cell are known as driver mutations and are causally related to tumorigenesis.…
The recognition of essential proteins not only can help to understand the mechanism of cell operation, but also help to study the mechanism of biological evolution. At present, many scholars have been discovering essential proteins…
The fitness of somatic cells of metazoan, the ability of proliferation and survival, depends on microenvironment. In somatic evolution, a mutated cell in a tissue clonally expands abnormally because of its high fitness as normal cells in a…
Compound-protein pairs dominate FDA-approved drug-target pairs and the prediction of compound-protein affinity and contact (CPAC) could help accelerate drug discovery. In this study we consider proteins as multi-modal data including 1D…
Despite the significant increase in computational power, molecular modeling of protein structure using classical all-atom approaches remains inefficient, at least for most of the protein targets in the focus of biomedical research. Perhaps…
Background: Intra-tumour heterogeneity (ITH) is the result of ongoing evolutionary change within each cancer. The expansion of genetically distinct sub-clonal populations may explain the emergence of drug resistance and if so would have…
We present an efficient algorithm to recover the three dimensional structure of a protein from its contact map representation. First we show that when a physically realizable map is used as target, our method generates a structure whose…
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…
Precision medicine has become a central focus in breast cancer management, advancing beyond conventional methods to deliver more precise and individualized therapies. Traditionally, histopathology images have been used primarily for…
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…