Related papers: SERpredict: Detection of tissue- or tumor-specific…
Despite recent technological advances in genomic sciences, our understanding of cancer progression and its driving genetic alterations remains incomplete. Here, we introduce TiMEx, a generative probabilistic model for detecting patterns of…
Predicting spatial gene expression from H&E histology offers a scalable and clinically accessible alternative to sequencing, but realizing clinical impact requires models that generalize across cancer types and capture biologically coherent…
A-to-I RNA editing by ADARs is a post-transcriptional mechanism for expanding the proteomic repertoire. Genetic recoding by editing was so far observed for only a few mammalian RNAs that are predominantly expressed in nervous tissues.…
Cellular heterogeneity is important to biological processes, including cancer and development. However, proteome heterogeneity is largely unexplored because of the limitations of existing methods for quantifying protein levels in single…
The task of Named Entity Recognition (NER) is an important component of many natural language processing systems, such as relation extraction and knowledge graph construction. In this work, we present a simple and effective approach for…
Phobias are common and impairing, and exposure therapy, which involves confronting patients with fear-provoking visual stimuli, is the most effective treatment. Scalable computerized exposure therapy requires automated prediction of fear…
A major challenge in biology is explaining how novel characters originate, however, the molecular mechanisms that underlie the emergence of evolutionary innovations are unclear. Here we show that while gene expression in the uterus evolves…
The nucleotide composition of human genes with a special emphasis on transcription-related strand asymmetries is analyzed. Such asymmetries may be associated with different mutational rates in two principal factors. The first one is…
Shear stress, hormones like parathyroid and mineral elements like calcium mediate the amplitude of stimulus signal which affects the rate of bone remodeling. The current study investigates the theoretical effects of different metabolic…
We introduce Extrema-Segmented Entropy (ExSEnt), a feature-decomposed framework for quantifying time-series complexity that separates temporal from amplitude contributions. The method partitions a signal into monotonic segments by detecting…
Dysregulation in signal transduction pathways can lead to a variety of complex disorders, including cancer. Computational approaches such as network analysis are important tools to understand system dynamics as well as to identify critical…
In oncology the efficacy of novel therapeutics often differs across patient subgroups, and these variations are difficult to predict during the initial phases of the drug development process. The relation between the power of randomized…
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.…
Much research in recent years has focused on using empirical machine learning approaches to extract useful insights on the structure-property relationships of superconductor material. Notably, these approaches are bringing extreme benefits…
Large, pre-trained neural networks consisting of self-attention layers (transformers) have recently achieved state-of-the-art results on several speech emotion recognition (SER) datasets. These models are typically pre-trained in…
In personalised decision making, evidence is required to determine whether an action (treatment) is suitable for an individual. Such evidence can be obtained by modelling treatment effect heterogeneity in subgroups. The existing…
Acute ischaemic stroke, caused by an interruption in blood flow to brain tissue, is a leading cause of disability and mortality worldwide. The selection of patients for the most optimal ischaemic stroke treatment is a crucial step for a…
The somatic mutations in the pathways that drive cancer development tend to be mutually exclusive across tumors, providing a signal for distinguishing driver mutations from a larger number of random passenger mutations. This mutual…
Cancer, a leading cause of death globally, occurs due to genomic changes and manifests heterogeneously across patients. To advance research on personalized treatment strategies, the effectiveness of various drugs on cells derived from…
Melanoma is a sort of skin cancer that starts in the cells known as melanocytes. It is more dangerous than other types of skin cancer because it can spread to other organs. Melanoma can be fatal if it spreads to other parts of the body.…