Machine learning methods for cancer classification using gene expression data: A review

F Alharbi, A Vakanski - Bioengineering, 2023 - mdpi.com
Cancer is a term that denotes a group of diseases caused by the abnormal growth of cells
that can spread in different parts of the body. According to the World Health Organization …

Multi-omics integration in biomedical research–A metabolomics-centric review

MA Wörheide, J Krumsiek, G Kastenmüller… - Analytica chimica …, 2021 - Elsevier
Recent advances in high-throughput technologies have enabled the profiling of multiple
layers of a biological system, including DNA sequence data (genomics), RNA expression …

[HTML][HTML] Large-scale multi-omic analysis of COVID-19 severity

KA Overmyer, E Shishkova, IJ Miller, J Balnis… - Cell systems, 2021 - cell.com
We performed RNA-seq and high-resolution mass spectrometry on 128 blood samples from
COVID-19-positive and COVID-19-negative patients with diverse disease severities and …

Single-cell biological network inference using a heterogeneous graph transformer

A Ma, X Wang, J Li, C Wang, T Xiao, Y Liu… - Nature …, 2023 - nature.com
Single-cell multi-omics (scMulti-omics) allows the quantification of multiple modalities
simultaneously to capture the intricacy of complex molecular mechanisms and cellular …

The reactome pathway knowledgebase 2024

M Milacic, D Beavers, P Conley, C Gong… - Nucleic acids …, 2024 - academic.oup.com
Abstract The Reactome Knowledgebase (https://reactome. org), an Elixir and GCBR core
biological data resource, provides manually curated molecular details of a broad range of …

[HTML][HTML] Oncogenic signaling pathways in the cancer genome atlas

F Sanchez-Vega, M Mina, J Armenia, WK Chatila… - Cell, 2018 - cell.com
Genetic alterations in signaling pathways that control cell-cycle progression, apoptosis, and
cell growth are common hallmarks of cancer, but the extent, mechanisms, and co …

Association analysis identifies 65 new breast cancer risk loci

K Michailidou, S Lindström, J Dennis, J Beesley, S Hui… - Nature, 2017 - nature.com
Breast cancer risk is influenced by rare coding variants in susceptibility genes, such as
BRCA1, and many common, mostly non-coding variants. However, much of the genetic …

Association analyses of more than 140,000 men identify 63 new prostate cancer susceptibility loci

FR Schumacher, AA Al Olama, SI Berndt, S Benlloch… - Nature …, 2018 - nature.com
Genome-wide association studies (GWAS) and fine-mapping efforts to date have identified
more than 100 prostate cancer (PrCa)-susceptibility loci. We meta-analyzed genotype data …

Integrated proteogenomic characterization of clear cell renal cell carcinoma

DJ Clark, SM Dhanasekaran, F Petralia, J Pan, X Song… - Cell, 2019 - cell.com
To elucidate the deregulated functional modules that drive clear cell renal cell carcinoma
(ccRCC), we performed comprehensive genomic, epigenomic, transcriptomic, proteomic …

Fast gene set enrichment analysis

G Korotkevich, V Sukhov, N Budin, B Shpak… - biorxiv, 2016 - biorxiv.org
Gene set enrichment analysis (GSEA) is an ubiquitously used tool for evaluating pathway
enrichment in transcriptional data. Typical experimental design consists in comparing two …