text miningvisualizationgene pathwayPubMedMEDLINEinformationextractionlinguistic analysisco-occurrenceAutomatically extracting gene-pathway relations from medical research texts gives researchers access to the latest findings in a structured format. Such relations must be precise to be useful. We present two ...
Text mining has become a useful tool for biologists trying to understand the genetics of diseases. In particular, it can help identify the most interesting candidate genes for a disease for further experimental analysis. Many text mining approaches have
We extract the words around the spotted gene occurrences and used them to represent the gene for GO domain code annotation. We regard the task as a text categorization problem and adopt a variant of NN with supervised term weighting schemes, making our method among the top-performing systems ...
Pigeonpea (Cajanus cajan (L.) Millsp) is one of the major grain legume crops of the tropics and subtropics, but biotic stresses [Fusarium wilt (FW), sterility mosaic disease (SMD), etc.] are serious challenges for sustainable crop production. Modern geno
Various computational approaches have been developed to annotate epigenomes on a per-position basis by modeling combinatorial and spatial patterns within epigenomic data. However, such annotations are less suitable for gene-based analyses. We present Chr
Inference and analysis of gene regulatory networks (GRNs) require software that integrates multi-omic data from various sources. The Network Zoo (netZoo; netzoo.github.io) is a collection of open-source methods to infer GRNs, conduct differential network analyses, estimate community structure, and...
Transcriptome data revealed sexually dimorphic gene expression in control placentas per se, whereas in intervention placentas sex-specific expression changed, and more n-3 LCPUFA-regulated genes were found in female than male placentas. Sexually dimorphic gene expression and n-3 LCPUFA-responsive ...
The Gene Ontology is a controlled vocabulary for representing knowledge related to genes and proteins in a computable form. The current effort of manually annotating proteins with the Gene Ontology is outpaced by the rate of accumulation of biomedical kn
The single sample gene set enrichment analysis (ssGSEA) algorithm was used to quantify the relative abundance of each cell infiltration in the TME of BC patients [22]. We obtained the signature gene sets indicating a wide range of human immune cell subtypes from Charoentong’s research, includi...
Conserved gene clusters are groups of genes that are located close to one another in the genomes of several species. They tend to code for proteins that have a functional interaction. The identification of conserved gene clusters is an important step tow