相关论文: Using profiles based on hydropathy properties to d…
Protein splicing is a post-translational autocatalystic excision of internal protein sequence (intein) with the subsequent ligation of the flanking polypeptides (exteins). The high specificity of excision ensured by intein makes it possible…
The Dissertation is focused on the studies of associations between functional elements in human genome and their nucleotide structure. The asymmetry in nucleotide content (skew, bias) was chosen as the main feature for nucleotide structure.…
We present a fully automated, anatomically guided deep learning pipeline for prostate cancer (PCa) risk stratification using routine MRI. The pipeline integrates three key components: an nnU-Net module for segmenting the prostate gland and…
Characterization of entropy functions is of fundamental importance in information theory. By imposing constraints on their Shannon outer bound, i.e., the polymatroidal region, one obtains the faces of the region and entropy functions on…
Histopathologists establish cancer grade by assessing histological structures, such as glands in prostate cancer. Yet, digital pathology pipelines often rely on grid-based tiling that ignores tissue architecture. This introduces irrelevant…
Clinical adoption of human genome sequencing requires methods with known accuracy of genotype calls at millions or billions of positions across a genome. Previous work showing discordance amongst sequencing methods and algorithms has made…
Background: Data driven stratification of patients into biologically informed subtypes holds promise for precision neuropsychiatry, yet neuroimaging-based clustering methods often fail to generalize across cohorts. While algorithmic…
The genes of eukaryotes are characterized by protein coding fragments, the exons, interrupted by introns, i.e. stretches of DNA which do not carry any useful information for the protein synthesis. We have analyzed the melting behavior of…
Characterization of entropy functions is of fundamental importance in information theory. By imposing constraints on their Shannon outer bound, i.e., the polymatroidal region, one obtains the faces of the region and entropy functions on…
By use of complex network dynamics and graph-based machine learning, we identified critical determinants of lineage-specific plasticity across the single-cell transcriptomics of pediatric high-grade glioma (pHGGs) subtypes: IDHWT…
Motivation: Alternative splicing is an important mechanism in which the regions of pre-mRNAs are differentially joined in order to form different transcript isoforms. Alternative splicing is involved in the regulation of normal…
Driver event discovery is a crucial demand for breast cancer diagnosis and therapy. Especially, discovering subtype-specificity of drivers can prompt the personalized biomarker discovery and precision treatment of cancer patients. still,…
We report simulation studies of 33 single intrinsically disordered proteins (IDPs) using coarse-grained (CG) bead-spring models where interactions among different amino acids are introduced through a hydropathy matrix and additional…
Isoforms are mRNAs produced from the same gene site in the phenomenon called Alternative Splicing. Studies have shown that more than 95% of human multi-exon genes have undergone alternative splicing. Although there are few changes in mRNA…
Spatial transcriptomics (ST) is a promising technique that characterizes the spatial gene profiling patterns within the tissue context. Comprehensive ST analysis depends on consecutive slices for 3D spatial insights, whereas the missing…
Motivation: DNA methylation is an intensely studied epigenetic mark, yet its functional role is incompletely understood. Attempts to quantitatively associate average DNA methylation to gene expression yield poor correlations outside of the…
Parts of DNA sequences known as exons and introns play very different role in coding and storage of genetic information. Here we show that their conducting properties are also very different. Taking into account long-range correlations…
The accurate prediction and characterization of DNA melting domains by computational tools could facilitate a broad range of biological applications. However, no algorithm for melting domain prediction has been available until now. The main…
Trans-splicing of leader sequences onto the 59ends of mRNAs is a widespread phenomenon in protozoa, nematodes and some chordates. Using parallel sequencing we have developed a method to simultaneously map 59splice sites and analyze the…
Splicing sites provide unique statistics in human genome due to their large number and reasonably complete annotation. Analyses of the cumulative SNPs distribution in splicing sites reveal a few interesting observations. While a degree of…