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Transcription factors (TFs) regulate gene expression through complex and co-operative mechanisms. While many TFs act together, the logic underlying TFs binding and their interactions is not fully understood yet. Most current approaches for…
The berry size is one of the most important fruit traits in grapevine breeding. Non-invasive, image-based phenotyping promises a fast and precise method for the monitoring of the grapevine berry size. In the present study an automated image…
Motivation: Assigning RNA-seq reads to their transcript of origin is a fundamental task in transcript expression estimation. Where ambiguities in assignments exist due to transcripts sharing sequence, e.g. alternative isoforms or alleles,…
We introduce the vine copula autoencoder (VCAE), a flexible generative model for high-dimensional distributions built in a straightforward three-step procedure. First, an autoencoder (AE) compresses the data into a lower dimensional…
MotifbreakR is a software tool that scans genetic variants against position weight matrices of transcription factors (TF) to determine the potential for the disruption of TF binding at the site of the variant. It leverages the Bioconductor…
Transcriptome-wide association studies (TWAS) link genetic variation to complex traits by leveraging expression quantitative trait loci (eQTL) data. However, most implementations are typically limited to local (cis-acting) effects and fail…
With the increasing amount of experimental data on gene expression and regulation, there is a growing need for quantitative models to describe the data and relate them to the different contexts. The thermodynamic models reviewed in the…
Bovine Respiratory Disease Complex (BRDC) is a complex respiratory disease in cattle with multiple etiologies, including bacterial and viral. It is estimated that mortality, morbidity, therapy, and quarantine resulting from BRDC account for…
Motivation: Histone modifications are among the most important factors that control gene regulation. Computational methods that predict gene expression from histone modification signals are highly desirable for understanding their…
Accumulated clinical studies show that microbes living in humans interact closely with human hosts, and get involved in modulating drug efficacy and drug toxicity. Microbes have become novel targets for the development of antibacterial…
Constructing cell developmental trajectories is a critical task in single-cell RNA sequencing (scRNA-seq) analysis, enabling the inference of potential cellular progression paths. However, current automated methods are limited to…
Cellular response to a perturbation is the result of a dynamic system of biological variables linked in a complex network. A major challenge in drug and disease studies is identifying the key factors of a biological network that are…
Genomic Selection (GS) uses whole-genome information to predict crop phenotypes and accelerate breeding. Traditional GS methods, however, struggle with prediction accuracy for complex traits and large datasets. We propose DPCformer, a deep…
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer, and comparative-genomics…
Designing protein sequences with specific biological functions and structural stability is crucial in biology and chemistry. Generative models already demonstrated their capabilities for reliable protein design. However, previous models are…
This study creates a physiologically realistic virtual patient database (VPD), representing the human arterial system, for the primary purpose of studying the affects of arterial disease on haemodynamics. A low dimensional representation of…
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…
Gene expression datasets offer insights into gene regulation mechanisms, biochemical pathways, and cellular functions. Additionally, comparing gene expression profiles between disease and control patients can deepen the understanding of…
This thesis is focused in the study of the evolution of the metabolic repertoire of Streptomyces, which are renowned as proficient producers of bioactive Natural Products (NPs). The main goal of my work was to contribute into the…
In this paper, we introduce TigerVector, a system that integrates vector search and graph query within TigerGraph, a Massively Parallel Processing (MPP) native graph database. We extend the vertex attribute type with the embedding type. To…