Discrete dynamic network modeling of oncogenic signaling: Mechanistic insights for personalized treatment of cancer

JGT Zañudo, SN Steinway, R Albert - Current Opinion in Systems Biology, 2018 - Elsevier
Targeted drugs disrupting proteins that are dysregulated in cancer have emerged as
promising treatments because of their specificity to cancer cell aberrations and thus their …

Network biology approaches to achieve precision medicine in inflammatory bowel disease

JP Thomas, D Modos, T Korcsmaros… - Frontiers in …, 2021 - frontiersin.org
Inflammatory bowel disease (IBD) is a chronic immune-mediated condition arising due to
complex interactions between multiple genetic and environmental factors. Despite recent …

Integrating gene regulatory pathways into differential network analysis of gene expression data

T Grimes, SS Potter, S Datta - Scientific reports, 2019 - nature.com
The advent of next-generation sequencing has introduced new opportunities in analyzing
gene expression data. Research in systems biology has taken advantage of these …

A bioinformatics approach to elucidate conserved genes and pathways in C. elegans as an animal model for cardiovascular research

AK Ray, A Priya, MZ Malik, TA Thanaraj, AK Singh… - Scientific Reports, 2024 - nature.com
Cardiovascular disease (CVD) is a collective term for disorders of the heart and blood
vessels. The molecular events and biochemical pathways associated with CVD are difficult …

A systems genomics approach to uncover patient-specific pathogenic pathways and proteins in ulcerative colitis

J Brooks-Warburton, D Modos, P Sudhakar… - Nature …, 2022 - nature.com
We describe a precision medicine workflow, the integrated single nucleotide polymorphism
network platform (iSNP), designed to determine the mechanisms by which SNPs affect …

Regulatory network analysis of Paneth cell and goblet cell enriched gut organoids using transcriptomics approaches

A Treveil, P Sudhakar, ZJ Matthews, T Wrzesiński… - Molecular omics, 2020 - pubs.rsc.org
The epithelial lining of the small intestine consists of multiple cell types, including Paneth
cells and goblet cells, that work in cohort to maintain gut health. 3D in vitro cultures of human …

Centrality analysis of protein-protein interaction networks and molecular docking prioritize potential drug-targets in type 1 diabetes

A Soofi, M Taghizadeh, SM Tabatabaei… - Iranian Journal of …, 2020 - pmc.ncbi.nlm.nih.gov
Type 1 diabetes (T1D) occurs as a consequence of an autoimmune attack against
pancreatic β-cells. Due to a lack of a clear understanding of the T1D pathogenesis, the …

QSAR-derived affinity fingerprints (part 2): modeling performance for potency prediction

I Cortés-Ciriano, C Škuta, A Bender, D Svozil - Journal of Cheminformatics, 2020 - Springer
Affinity fingerprints report the activity of small molecules across a set of assays, and thus
permit to gather information about the bioactivities of structurally dissimilar compounds …

An evaluation of the effectiveness of image-based texture features extracted from static B-mode ultrasound images in distinguishing between benign and malignant …

D Al-Karawi, H Al-Assam, H Du… - Ultrasonic …, 2021 - journals.sagepub.com
Significant successes in machine learning approaches to image analysis for various
applications have energized strong interest in automated diagnostic support systems for …

[HTML][HTML] Construction and contextualization approaches for protein-protein interaction networks

A Badkas, S De Landtsheer, T Sauter - Computational and Structural …, 2022 - Elsevier
Protein-protein interaction network (PPIN) analysis is a widely used method to study the
contextual role of proteins of interest, to predict novel disease genes, disease or functional …