Related papers: Minimal Immunogenic Epitopes Have Nine Amino Acids
In recent years, disease mapping studies have become a routine application within geographical epidemiology and are typically analysed within a Bayesian hierarchical model formulation. A variety of model formulations for the latent level…
Identification of biomarkers is an emerging area in Oncology. In this article, we develop an efficient statistical procedure for classification of protein markers according to their effect on cancer progression. A high-dimensional…
Folding properties of a two-dimensional toy protein model containing only two amino-acid types, hydrophobic and hydrophilic, respectively, are analyzed. An efficient Monte Carlo procedure is employed to ensure that the ground states are…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
International challenges have become the standard for validation of biomedical image analysis methods. Given their scientific impact, it is surprising that a critical analysis of common practices related to the organization of challenges…
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…
Epitope vaccines are a promising direction to enable precision treatment for cancer, autoimmune diseases, and allergies. Effectively designing such vaccines requires accurate prediction of proteasomal cleavage in order to ensure that the…
Antimicrobial peptides have emerged as promising molecules to combat antimicrobial resistance. However, fragmented datasets, inconsistent annotations, and the lack of standardized benchmarks hinder computational approaches and slow down the…
Growing experimental evidence shows that proteins follow one or a few distinct paths when folding. We propose in this paper a procedure to parametrize these observed pathways, and from this parametrization construct effective Hamiltonians…
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…
Pure and homogeneous biological macromolecules (i.e. proteins, nucleic acids, protein-protein or protein-nucleic acid complexes, and functional assemblies such as ribosomes and viruses) are the key for consistent and reliable biochemical…
Building blocks of life such as amino acids, nucleobases, and fatty acids are central to prebiotic chemistry and represent key targets in the search for planetary biosignatures. In planetary materials, biomolecules typically occur at trace…
Proteomics will celebrate its 20th year in 2014. In this relatively short period of time, it has invaded most areas of biology and its use will probably continue to spread in the future. These two decades have seen a considerable increase…
Medical image segmentation is particularly critical as a prerequisite for relevant quantitative analysis in the treatment of clinical diseases. For example, in clinical cervical cancer radiotherapy, after acquiring subabdominal MRI images,…
Motivation: Biomarker discovery from high-dimensional data is a crucial problem with enormous applications in biology and medicine. It is also extremely challenging from a statistical viewpoint, but surprisingly few studies have…
In computational biology and other sciences, researchers are frequently faced with a choice between several computational methods for performing data analyses. Benchmarking studies aim to rigorously compare the performance of different…
A Profile Mixture Model is a model of protein evolution, describing sequence data in which sites are assumed to follow many related substitution processes on a single evolutionary tree. The processes depend in part on different amino acid…
An efficient computational approach for imaging binary-type physical properties suitable for various models in biomedical applications is developed and validated. The proposed methodology includes gradient-based multiscale optimization with…
As protein therapeutics play an important role in almost all medical fields, numerous studies have been conducted on proteins using artificial intelligence. Artificial intelligence has enabled data driven predictions without the need for…
Epitopes are short antigenic peptide sequences which are recognized by antibodies or immune cell receptors. These are central to the development of immunotherapies, vaccines, and diagnostics. However, the rational design of synthetic…