Related papers: KEGGexpressionMapper allows for analysis of pathwa…
Transcriptional regulatory network inference methods have been studied for years. Most of them relie on complex mathematical and algorithmic concepts, making them hard to adapt, re-implement or integrate with other methods. To address this…
Effectively modeling multimodal spatial omics data is critical for understanding tissue complexity and underlying biological mechanisms. While spatial transcriptomics, proteomics, and epigenomics capture molecular features, they lack…
Integrating multiple observational studies for meta-analysis has sparked much interest. The presented R package WMAP (Weighted Meta-Analysis with Pseudo-Population) addresses a critical gap in the implementation of integrative weighting…
Knowledge Graph (KG) alignment aims at finding equivalent entities and relations (i.e., mappings) between two KGs. The existing approaches utilize either reasoning-based or semantic embedding-based techniques, but few studies explore their…
The R package panelPomp supports analysis of panel data via a general class of partially observed Markov process models (PanelPOMP). This package tutorial describes how the mathematical concept of a PanelPOMP is represented in the software…
Gene set analysis, a popular approach for analyzing high-throughput gene expression data, aims to identify sets of related genes that show significantly enriched or depleted expression patterns between different conditions. In the last…
By integrating heterogeneous functional genomic datasets, we have developed a new framework for detecting combinatorial control of gene expression, which includes estimating transcription factor activities using a singular value…
Background: The inception of next generations sequencing technologies have exponentially increased the volume of biological sequence data. Protein sequences, being quoted as the `language of life', has been analyzed for a multitude of…
Concerning NMR-based metabolomics, 1D spectra processing often requires an expert eye for disentangling the intertwined peaks, and so far the best way is to proceed interactively with a spectra viewer. NMRProcFlow is a graphical and…
Metabonomics time-course experiments provide the opportunity to understand the changes to an organism by observing the evolution of metabolic profiles in response to internal or external stimuli. Along with other omic longitudinal profiling…
Rapidly growing public gene expression databases contain a wealth of data for building an unprecedentedly detailed picture of human biology and disease. This data comes from many diverse measurement platforms that make integrating it all…
Expressive Range Analysis (ERA), an approach for visualising the output of Procedural Content Generation (PCG) systems, is widely used within PCG research to evaluate and compare generators, often to make comparative statements about their…
Understanding how small molecules perturb gene expression is essential for uncovering drug mechanisms, predicting off-target effects, and identifying repurposing opportunities. While prior deep learning frameworks have integrated multimodal…
Background and objective: Cell migration is essential for many biological phenomena with direct impact on human health and disease. One conventional approach to study cell migration involves the quantitative analysis of individual cell…
RNAnet provides a bridge between two widely used Human gene databases. Ensembl describes DNA sequences and transcripts but not experimental gene expression. Whilst NCBI's GEO contains actual expression levels from Human samples. RNAnet…
This work presents the use of graph learning for the prediction of multi-step experimental outcomes for applications across experimental research, including material science, chemistry, and biology. The viability of geometric learning for…
As gene expression measurement technology is shifting from microarrays to sequencing, the statistical tools available for their analysis must be adapted since RNA-seq data are measured as counts. Recently, it has been proposed to tackle the…
Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication…
In recent years, there have been valuable efforts and contributions to make the process of RDF knowledge graph creation traceable and transparent; extending and applying declarative mapping languages is an example. One challenging step is…
Research done using model organisms has been fundamental to the biological understanding of human genes, diseases and phenotypes. Model organisms provide tractable systems for experiments to enhance understanding of biological mechanisms…