Related papers: Bioinformatic analysis for structure and function …
Deep neural networks such as AlphaFold and RoseTTAFold predict remarkably accurate structures of proteins compared to other algorithmic approaches. It is known that biologically small perturbations in the protein sequence do not lead to…
Gliomas are brain tumors composed of different highly heterogeneous histological subregions. Image analysis techniques to identify relevant tumor substructures have high potential for improving patient diagnosis, treatment and prognosis.…
Accurately simulating soft tissue deformation is crucial for surgical training, pre-operative planning, and real-time haptic feedback systems. While physics-based models such as the finite element method (FEM) provide high-fidelity results,…
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…
Using an improved "analytic K-matrix model", we reconsider the extraction of the sigma/f_0(600) and f_0(980) gamma-gamma widths from gamma-gamma to pi-pi scatterings data of Crystal Ball and Belle. Our main results are summarized in Tables…
We present a statistical approach to protein structure by introducing a representation of protein folds based on simple observables defined as frequencies of oriented cycles in contact graphs. Motivated by the idea that these cycles may…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Proteomics is the large-scale analysis of the proteins. The common method for identifying proteins and characterising their amino acid sequences is to digest the proteins into peptides, analyse the peptides using mass spectrometry and…
The aim of the systematic review was to assess recently published studies on diagnostic test accuracy of glioblastoma treatment response monitoring biomarkers in adults, developed through machine learning (ML). Articles were searched for…
Male infertility is a disease which affects approximately 7% of men. Sperm morphology analysis (SMA) is one of the main diagnosis methods for this problem. Manual SMA is an inexact, subjective, non-reproducible, and hard to teach process.…
Overall survival (OS) time is one of the most important evaluation indices for gliomas situations. Multimodal Magnetic Resonance Imaging (MRI) scans play an important role in the study of glioma prognosis OS time. Several deep…
We introduce a generative model for protein backbone design utilizing geometric products and higher order message passing. In particular, we propose Clifford Frame Attention (CFA), an extension of the invariant point attention (IPA)…
A highly fluorinated anatase lattice has been recently reported, providing a new class of materials whose general chemical formula is $\rm Ti_{1- \mathit x}\square_{\mathit x}X_{4\mathit x}O_{2- 4\mathit x}$ (X$^-$ = F$^-$ or OH$^-$). To…
Intermittent density fluctuations of nucleotide molecules (adenine, guanine, cytosine and thymine) along DNA sequences are studied in the framework of a hierarchical structure (HS) model originally proposed for the study of fully developed…
Coarse-graining is a powerful tool for extending the reach of dynamic models of proteins and other biological macromolecules. Topological coarse-graining, in which biomolecules or sets thereof are represented via graph structures, is a…
Information on the $^{38}$S level scheme was expanded through experimental work utilizing a fusion-evaporation reaction and in-beam $\gamma$-ray spectroscopy. Prompt $\gamma$-ray transitions were detected by the Gamma-Ray Energy Tracking…
Pseudoprogression (PsP) occurs in 20-30% of patients with glioblastoma multiforme (GBM) after receiving the standard treatment. In the course of post-treatment magnetic resonance imaging (MRI), PsP exhibits similarities in shape and…
Motivation: Networks underlie the generation and interpretation of many biological datasets: gene networks shed light on the regulatory structure of the genome, and cell networks can capture structure of the tumor micro-environment.…
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…
Past few years have witnessed the artificial intelligence inspired evolution in various medical fields. The diagnosis and treatment of gliomas -- one of the most commonly seen brain tumors with low survival rate -- rely heavily on the…