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 …

Hypergraph-based connectivity measures for signaling pathway topologies

N Franzese, A Groce, TM Murali… - PLoS computational …, 2019 - journals.plos.org
Characterizing cellular responses to different extrinsic signals is an active area of research,
and curated pathway databases describe these complex signaling reactions. Here, we …

Protein-Protein interactions uncover candidate 'core genes' within omnigenic disease networks

A Ratnakumar, N Weinhold, JC Mar, N Riaz - PLoS genetics, 2020 - journals.plos.org
Genome wide association studies (GWAS) of human diseases have generally identified
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 …

Mapping the Multiscale Proteomic Organization of Cellular and Disease Phenotypes

A Cesnik, LV Schaffer, I Gaur, M Jain… - Annual Review of …, 2024 - annualreviews.org
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 …

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 …

Predicting anticancer hyperfoods with graph convolutional networks

G Gonzalez, S Gong, I Laponogov, M Bronstein… - Human Genomics, 2021 - Springer
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 …

Shared and distinct lipid-lipid interactions in plasma and affected tissues in a diabetic mouse model

KM Sas, J Lin, TM Rajendiran, T Soni, V Nair… - Journal of lipid …, 2018 - ASBMB
Lipids are ubiquitous metabolites with diverse functions; abnormalities in lipid metabolism
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 …

Investigating cellular network heterogeneity and modularity in cancer: a network entropy and unbalanced motif approach

F Cheng, C Liu, B Shen, Z Zhao - BMC systems biology, 2016 - Springer
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 …