Data analysis methods for defining biomarkers from omics data

C Li, Z Gao, B Su, G Xu, X Lin - Analytical and Bioanalytical Chemistry, 2022 - Springer
Omics mainly includes genomics, epigenomics, transcriptomics, proteomics and
metabolomics. The rapid development of omics technology has opened up new ways to …

Applications of graph theory in studying protein structure, dynamics, and interactions

Z Zhou, G Hu - Journal of Mathematical Chemistry, 2023 - Springer
Being a core tool, graph theory, as a mathematical formalism in mathematical chemistry, has
become an essential approach for studying the complex behavior and interactions in protein …

Recent trends in cancer genomics and bioinformatics tools development

AA Anashkina, EY Leberfarb, YL Orlov - International Journal of …, 2021 - mdpi.com
We overview recent research trends in cancer genomics, bioinformatics tools development
and medical genetics, based on results discussed in papers collections “Medical Genetics …

[HTML][HTML] Identification of spatial proteomic signatures of colon tumor metastasis: a digital spatial profiling approach

JJ Levy, JP Zavras, EM Veziroglu, M Nasir-Moin… - The American Journal of …, 2023 - Elsevier
Over 150,000 Americans are diagnosed with colorectal cancer (CRC) every year, and
annually> 50,000 individuals are estimated to die of CRC, necessitating improvements in …

Co-expression networks unveiled long non-coding RNAs as molecular targets of drugs used to treat bipolar disorder

TTT Truong, CC Bortolasci, B Spolding… - Frontiers in …, 2022 - frontiersin.org
Long non-coding RNAs (lncRNAs) may play a role in psychiatric diseases including bipolar
disorder (BD). We investigated mRNA-lncRNA co-expression patterns in neuronal-like cells …

Network medicine approaches for identification of novel prognostic systems biomarkers and drug candidates for papillary thyroid carcinoma

M Kori, K Temiz, E Gov - Journal of Cellular and Molecular …, 2023 - Wiley Online Library
Papillary thyroid carcinoma (PTC) is one of the most common endocrine carcinomas
worldwide and the aetiology of this cancer is still not well understood. Therefore, it remains …

[HTML][HTML] Network analysis of TCGA and GTEx gene expression datasets for identification of trait-associated biomarkers in human cancer

HM Chen, JA MacDonald - STAR protocols, 2022 - Elsevier
Advances in high-throughput sequencing technologies now yield unprecedented volumes of
OMICs data with opportunities to conduct systematic data analyses and derive novel …

Genome-Wide Identification and Expression Analysis of Potential Antiviral Tripartite Motif Proteins (TRIMs) in Grass Carp (Ctenopharyngodon idella)

B Qin, T Xiao, C Ding, Y Deng, Z Lv, J Su - Biology, 2021 - mdpi.com
Simple Summary Grass carp, Ctenopharyngodon idellus, is an important freshwater cultured
teleost in China, and its annual production has reached 5,533,083 tons. However, its …

Contrast subgraphs allow comparing homogeneous and heterogeneous networks derived from omics data

T Lanciano, A Savino, F Porcu, D Cittaro, F Bonchi… - …, 2023 - academic.oup.com
Background Biological networks are often used to describe the relationships between
relevant entities, particularly genes and proteins, and are a powerful tool for functional …

miRNA–mRNA–protein dysregulated network in COPD in women

CX Li, J Gao, CM Sköld, ÅM Wheelock - Frontiers in Genetics, 2022 - frontiersin.org
Rationale: Chronic obstructive pulmonary disease (COPD) is a complex disease caused by
a multitude of underlying mechanisms, and molecular mechanistic modeling of COPD …