Developments in toxicogenomics: understanding and predicting compound-induced toxicity from gene expression data

B Alexander-Dann, LL Pruteanu, E Oerton… - Molecular omics, 2018 - pubs.rsc.org
The toxicogenomics field aims to understand and predict toxicity by using 'omics' data in
order to study systems-level responses to compound treatments. In recent years there has …

Consolidation and translation regulation

S Gal-Ben-Ari, JW Kenney, H Ounalla-Saad… - Learning & …, 2012 - learnmem.cshlp.org
mRNA translation, or protein synthesis, is a major component of the transformation of the
genetic code into any cellular activity. This complicated, multistep process is divided into …

Lipid network and moiety analysis for revealing enzymatic dysregulation and mechanistic alterations from lipidomics data

TD Rose, N Köhler, L Falk, L Klischat… - Briefings in …, 2023 - academic.oup.com
Lipidomics is of growing importance for clinical and biomedical research due to many
associations between lipid metabolism and diseases. The discovery of these associations is …

De novo pathway-based biomarker identification

N Alcaraz, M List, R Batra, F Vandin… - Nucleic acids …, 2017 - academic.oup.com
Gene expression profiles have been extensively discussed as an aid to guide the therapy by
predicting disease outcome for the patients suffering from complex diseases, such as …

Systems level analysis and identification of pathways and networks associated with liver fibrosis

MDM AbdulHameed, GJ Tawa, K Kumar, DL Ippolito… - PloS one, 2014 - journals.plos.org
Toxic liver injury causes necrosis and fibrosis, which may lead to cirrhosis and liver failure.
Despite recent progress in understanding the mechanism of liver fibrosis, our knowledge of …

KeyPathwayMinerWeb: online multi-omics network enrichment

M List, N Alcaraz, M Dissing-Hansen… - Nucleic Acids …, 2016 - academic.oup.com
We present KeyPathwayMinerWeb, the first online platform for de novo pathway enrichment
analysis directly in the browser. Given a biological interaction network (eg protein–protein …

KeyPathwayMiner 4.0: condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape

N Alcaraz, J Pauling, R Batra, E Barbosa, A Junge… - BMC systems …, 2014 - Springer
Background Over the last decade network enrichment analysis has become popular in
computational systems biology to elucidate aberrant network modules. Traditionally, these …

Machine learning-assisted network inference approach to identify a new class of genes that coordinate the functionality of cancer networks

M Ghanat Bari, CY Ung, C Zhang, S Zhu, H Li - Scientific reports, 2017 - nature.com
Emerging evidence indicates the existence of a new class of cancer genes that act as
“signal linkers” coordinating oncogenic signals between mutated and differentially …

Network and pathway analysis of toxicogenomics data

G Barel, R Herwig - Frontiers in Genetics, 2018 - frontiersin.org
Toxicogenomics is the study of the molecular effects of chemical, biological and physical
agents in biological systems, with the aim of elucidating toxicological mechanisms, building …

Gene expression patterns associated with histopathology in toxic liver fibrosis

DL Ippolito, MDM AbdulHameed, GJ Tawa… - Toxicological …, 2016 - academic.oup.com
Toxic industrial chemicals induce liver injury, which is difficult to diagnose without invasive
procedures. Identifying indicators of end organ injury can complement exposure-based …