To address one of the most challenging issues at the cellular level, this paper surveys the fuzzy methods used in gene regulatory networks (GRNs) inference. GRNs represent causal relationships between genes that have a direct influence, trough protei...
Database : the journal of biological databases and curation
Mar 16, 2015
The Encyclopedia of DNA elements (ENCODE) project is an ongoing collaborative effort to create a catalog of genomic annotations. To date, the project has generated over 4000 experiments across more than 350 cell lines and tissues using a wide array o...
International journal of medical microbiology : IJMM
Feb 14, 2015
Staphylococcus aureus (S. aureus) is a prominent human and livestock pathogen investigated widely using omic technologies. Critically, due to availability, low visibility or scattered resources, robust network and statistical contextualisation of the...
BACKGROUND: Gene Ontology (GO) has been used widely to study functional relationships between genes. The current semantic similarity measures rely only on GO annotations and GO structure. This limits the power of GO-based similarity because of the li...
Database : the journal of biological databases and curation
Feb 2, 2015
During the past several decades, Escherichia coli has been a treasure chest for molecular biology. The molecular mechanisms of many fundamental cellular processes have been discovered through research on this bacterium. Although much basic research n...
Annual review of pharmacology and toxicology
Dec 12, 2014
This article reviews several techniques from machine learning that can be used to study the problem of identifying a small number of features, from among tens of thousands of measured features, that can accurately predict a drug response. Prediction ...
Liver cancer (LC) is the second leading cause of cancer-related deaths globally, yet the molecular mechanisms linking its progression with associated risk factors (RFs) remain poorly understood. To address this, we developed an integrative multi-stag...
Gene expression patterns are determined to a large extent by transcription factor (TF) binding to noncoding regulatory regions in the genome. However, gene expression cannot yet be systematically predicted from genome sequences, in part because nonfu...
This study aimed to comprehensively investigate the regulatory mechanism and clinical value of secreted phosphoprotein 1 (SPP1) in the three-stage progression of "smoking-chronic obstructive pulmonary disease (COPD)-carcinogenesis" in lung squamous ...
Artificial cells, nanomedicine, and biotechnology
Dec 1, 2025
Gestational diabetes mellitus (GDM) is a common metabolic disorder during pregnancy, involving multiple immune and inflammatory factors. Macrophages play a crucial role in its development. This study integrated scRNA-seq and RNA-seq data to explore m...
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