Differential network enrichment analysis reveals novel lipid pathways in chronic kidney disease
J Ma, A Karnovsky, F Afshinnia, J Wigginton… - …, 2019 - academic.oup.com
Motivation Functional enrichment testing methods can reduce data comprising hundreds of
altered biomolecules to smaller sets of altered biological 'concepts' that help generate …
altered biomolecules to smaller sets of altered biological 'concepts' that help generate …
Hypergraph-based connectivity measures for signaling pathway topologies
Characterizing cellular responses to different extrinsic signals is an active area of research,
and curated pathway databases describe these complex signaling reactions. Here, we …
and curated pathway databases describe these complex signaling reactions. Here, we …
Protein-Protein interactions uncover candidate 'core genes' within omnigenic disease networks
Genome wide association studies (GWAS) of human diseases have generally identified
many loci associated with risk with relatively small effect sizes. The omnigenic model …
many loci associated with risk with relatively small effect sizes. The omnigenic model …
Transferrin receptor-involved HIF-1 signaling pathway in cervical cancer
X Xu, T Liu, J Wu, Y Wang, Y Hong, H Zhou - Cancer Gene Therapy, 2019 - nature.com
Cervical cancer is one of the most prevalent gynecologic malignancies and has remained
an intractable cancer over the past decades. We analyzed the aberrant expression patterns …
an intractable cancer over the past decades. We analyzed the aberrant expression patterns …
Mapping the Multiscale Proteomic Organization of Cellular and Disease Phenotypes
While the primary sequences of human proteins have been cataloged for over a decade,
determining how these are organized into a dynamic collection of multiprotein assemblies …
determining how these are organized into a dynamic collection of multiprotein assemblies …
Dual network analysis of transcriptome data for discovery of new therapeutic targets in non-small cell lung cancer
Y Bai, L Zhou, C Zhang, M Guo, L Xia, Z Tang, Y Liu… - Oncogene, 2023 - nature.com
The drug therapy for non-small cell lung cancer (NSCLC) have always been issues of
poisonous side effect, acquired drug resistance and narrow applicable population. In this …
poisonous side effect, acquired drug resistance and narrow applicable population. In this …
Predicting anticancer hyperfoods with graph convolutional networks
Background Recent efforts in the field of nutritional science have allowed the discovery of
disease-beating molecules within foods based on the commonality of bioactive food …
disease-beating molecules within foods based on the commonality of bioactive food …
Shared and distinct lipid-lipid interactions in plasma and affected tissues in a diabetic mouse model
Lipids are ubiquitous metabolites with diverse functions; abnormalities in lipid metabolism
appear to be related to complications from multiple diseases, including type 2 diabetes …
appear to be related to complications from multiple diseases, including type 2 diabetes …
The path to routine use of genomic biomarkers in the cancer clinic
PC Boutros - Genome research, 2015 - genome.cshlp.org
It has been almost 15 years since the first microarray-based studies creating multigene
biomarkers to subtype and predict survival of cancer patients. This Perspective looks at why …
biomarkers to subtype and predict survival of cancer patients. This Perspective looks at why …
Investigating cellular network heterogeneity and modularity in cancer: a network entropy and unbalanced motif approach
Background Cancer is increasingly recognized as a cellular system phenomenon that is
attributed to the accumulation of genetic or epigenetic alterations leading to the perturbation …
attributed to the accumulation of genetic or epigenetic alterations leading to the perturbation …