Enter the matrix: factorization uncovers knowledge from omics
Omics data contain signals from the molecular, physical, and kinetic inter-and intracellular
interactions that control biological systems. Matrix factorization (MF) techniques can reveal …
interactions that control biological systems. Matrix factorization (MF) techniques can reveal …
Perturbation-response genes reveal signaling footprints in cancer gene expression
M Schubert, B Klinger, M Klünemann, A Sieber… - Nature …, 2018 - nature.com
Aberrant cell signaling can cause cancer and other diseases and is a focal point of drug
research. A common approach is to infer signaling activity of pathways from gene …
research. A common approach is to infer signaling activity of pathways from gene …
Aging-like spontaneous epigenetic silencing facilitates Wnt activation, stemness, and BrafV600E-induced tumorigenesis
We addressed the precursor role of aging-like spontaneous promoter DNA hypermethylation
in initiating tumorigenesis. Using mouse colon-derived organoids, we show that promoter …
in initiating tumorigenesis. Using mouse colon-derived organoids, we show that promoter …
Consistency and overfitting of multi-omics methods on experimental data
Abstract Knowledge on the relationship between different biological modalities (RNA,
chromatin, etc.) can help further our understanding of the processes through which …
chromatin, etc.) can help further our understanding of the processes through which …
Functional genomics uncover the biology behind the responsiveness of head and neck squamous cell cancer patients to cetuximab
Purpose: To identify the tumor portrait of the minority of head and neck squamous cell
carcinoma (HNSCC) patients with recurrent–metastatic (RM) disease who upon treatment …
carcinoma (HNSCC) patients with recurrent–metastatic (RM) disease who upon treatment …
PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF
GL Stein-O'Brien, JL Carey, WS Lee… - …, 2017 - academic.oup.com
Abstract Summary Non-negative Matrix Factorization (NMF) algorithms associate gene
expression with biological processes (eg time-course dynamics or disease subtypes) …
expression with biological processes (eg time-course dynamics or disease subtypes) …
Cleaved NOTCH1 expression pattern in head and neck squamous cell carcinoma is associated with NOTCH1 mutation, HPV status, and high-risk features
The Notch pathway is frequently altered in head and neck squamous cell carcinomas
(HNSCC); however, the clinical significance of NOTCH1 dysregulation is poorly understood …
(HNSCC); however, the clinical significance of NOTCH1 dysregulation is poorly understood …
Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance
Background Targeted therapies specifically act by blocking the activity of proteins that are
encoded by genes critical for tumorigenesis. However, most cancers acquire resistance and …
encoded by genes critical for tumorigenesis. However, most cancers acquire resistance and …
Variation of human neural stem cells generating organizer states in vitro before committing to cortical excitatory or inhibitory neuronal fates
Better understanding of the progression of neural stem cells (NSCs) in the developing
cerebral cortex is important for modeling neurogenesis and defining the pathogenesis of …
cerebral cortex is important for modeling neurogenesis and defining the pathogenesis of …
Learning dysregulated pathways in cancers from differential variability analysis
Analysis of gene sets can implicate activity in signaling pathways that is responsible for
cancer initiation and progression, but is not discernible from the analysis of individual genes …
cancer initiation and progression, but is not discernible from the analysis of individual genes …