Related papers: EGC: a format for expressing prokaryotic genomes c…
Genomes in living organisms consist of the nucleotides adenine (A), guanine (G), cytosine (C) and thymine (T). All prokaryotes have genomes consisting of double-stranded DNA, where the A's and G's (purines) of one strand bind respectively…
The use of rewriting-based visual formalisms is on the rise. In the formal methods community, this is due also to the introduction of adhesive categories, where most properties of classical approaches to graph transformation, such as those…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…
"Epigenetic Tracking" is a model of systems of biological cells, able to generate arbitrary 2 or 3-dimensional cellular shapes of any kind and complexity (in terms of number of cells, number of colours, etc.) starting from a single cell. If…
The GC content of prokaryotic genomes is species-specific and takes values from 16 to 77 percent. There are currently no accepted explanations for this diversity of selection for GC content. We analyzed the known correlations between GC…
We have developed a unified format for phylogenetic placements, that is, mappings of environmental sequence data (e.g. short reads) into a phylogenetic tree. We are motivated to do so by the growing number of tools for computing and…
Question answering (QA) in the field of healthcare has received much attention due to significant advancements in natural language processing. However, existing healthcare QA datasets primarily focus on medical images, clinical notes, or…
Text-conditioned molecular generation aims to translate natural-language descriptions into chemical structures, enabling scientists to specify functional groups, scaffolds, and physicochemical constraints without handcrafted rules.…
Gene regulation is an important fundamental biological process. The regulation of gene expression is managed through a variety of methods including epigenetic processes (e.g., DNA methylation). Understanding the role of epigenetic changes…
Genetic Programming is an evolutionary algorithm that generates computer programs, or mathematical expressions, to solve complex problems. In this Guide, we demonstrate how to use Genetic Programming to develop surrogate models to mitigate…
Sequence modelling approaches for epigenetic profile prediction have recently expanded in terms of sequence length, model size, and profile diversity. However, current models cannot infer on many experimentally feasible tissue and assay…
The recent advances in sequencing technologies enables the assembly of individual genomes to the reference quality. How to integrate multiple genomes from the same species and to make the integrated representation accessible to biologists…
Conventional task-specific electrocardiogram (ECG) analysis models require large annotated datasets to train. Foundation models mitigate this burden by leveraging self-supervised pretraining; however, the scarcity of open-weight ECG…
Protein contacts contain important information for protein structure and functional study, but contact prediction from sequence remains very challenging. Both evolutionary coupling (EC) analysis and supervised machine learning methods are…
Learning image classification and image generation using the same set of network parameters is a challenging problem. Recent advanced approaches perform well in one task often exhibit poor performance in the other. This work introduces an…
ECGSYN, a dynamical model that faithfully reproduces the main features of the human electrocardiogram (ECG), including heart rate variability, RR intervals and QT intervals is presented. Details of the underlying algorithm and an…
An electrocardiogram (EKG) is a common, non-invasive test that measures the electrical activity of a patient's heart. EKGs contain useful diagnostic information about patient health that may be absent from other electronic health record…
Electrocardiogram (ECG) synthesis is the area of research focused on generating realistic synthetic ECG signals for medical use without concerns over annotation costs or clinical data privacy restrictions. Traditional ECG generation models…
Much information is stored in amino acid composition of protein and base composition of DNA. We simulated the evolution of amino acid frequencies and genomic GC content by a linguistic model. It is showed that the evolution of genetic code…
Given the stochastic nature of gene expression, genetically identical cells exposed to the same environmental inputs will produce different outputs. This heterogeneity has been hypothesized to have consequences for how cells are able to…