Related papers: GWAPP: A Web Application for Genome-wide Associati…
Motivation: Genome-wide association studies (GWASs), which assay more than a million single nucleotide polymorphisms (SNPs) in thousands of individuals, have been widely used to identify genetic risk variants for complex diseases. However,…
Understanding genetic variation, e.g., through mutations, in organisms is crucial to unravel their effects on the environment and human health. A fundamental characterization can be obtained by solving the haplotype assembly problem, which…
Darwinian evolution can be illustrated as an uphill walk in a landscape, where the surface consists of genotypes, the height coordinates represent fitness, and each step corresponds to a point mutation. Epistasis, roughly defined as the…
Protein-protein interactions are of great importance in biochemical processes. Accurate prediction of protein-protein interaction sites (PPIs) is crucial for our understanding of biological mechanism. Although numerous approaches have been…
Arabidopsis root hair patterning is controlled by a complex transcription factor network containing positive and negative feedback loops, epidermal cell-cell signalling, and positional signalling from underlying tissue. Recently, several…
Background and Aims: Prediction of phenotypic traits from new genotypes under untested environmental conditions is crucial to build simulations of breeding strategies to improve target traits. Although the plant response to environmental…
The protein-protein interaction (PPI) network provides an overview of the complex biological reactions vital to an organism's metabolism and survival. Even though in the past PPI network were compared across organisms in detail, there has…
Quantitative Systems Pharmacology (QSP) modeling is essential for drug development but it requires significant time investment that limits the throughput of domain experts. We present \textbf{GRASP} -- a multi-agent, graph-reasoning…
Biodiversity, the variation within and between species and ecosystems, is essential for human well-being and the equilibrium of the planet. It is critical for the sustainable development of human society and is an important global…
High-throughput "pathomic" analysis of Whole Slide Images (WSIs) offers new opportunities to study tissue characteristics and for biomarker discovery. However, the clinical relevance of the tissue characteristics at the micro- and…
In recent times, wireless access technology is becoming increasingly commonplace due to the ease of operation and installation of untethered wireless media. The design of wireless networking is challenging due to the highly dynamic…
One of the most important challenges in the analysis of high-throughput genetic data is the development of efficient computational methods to identify statistically significant Single Nucleotide Polymorphisms (SNPs). Genome-wide association…
This paper presents a methodology and workflow that overcome the limitations of the conventional Generative Adversarial Networks (GANs) for geological facies modeling. It attempts to improve the training stability and guarantee the…
Automatic workflow composition (AWC) is a relevant problem in automated machine learning (AutoML) that allows finding suitable sequences of preprocessing and prediction models together with their optimal hyperparameters. This problem can be…
Despite the common misconception of nearly static organisms, plants do interact continuously with the environment and with each other. It is fair to assume that during their evolution they developed particular features to overcome problems…
Genotype-phenotype (GP) maps specify how the random mutations that change genotypes generate variation by altering phenotypes, which, in turn, can trigger selection. Many GP maps share the following general properties: 1) The number of…
Global Average Pooling (GAP) [4] has been used previously to generate class activation for image classification tasks. The motivation behind SIMILARnet comes from the fact that the convolutional filters possess position information of the…
This paper proposes Genetic Algorithm with Border Trades (GAB), a novel modification of the standard genetic algorithm that enhances exploration by incorporating new chromosome patterns in the breeding process. This approach significantly…
We present the Star-Based Automated Single-locus and Epistasis analysis tool - Genetic Programming (StarBASE-GP), an automated framework for discovering meaningful genetic variants associated with phenotypic variation in large-scale genomic…
Mendelian randomization (MR) is an epidemiological method that can be used to strengthen causal inference regarding the relationship between a modifiable environmental exposure and a medically relevant trait and to estimate the magnitude of…