Integrating knowledge and omics to decipher mechanisms via large‐scale models of signaling networks

M Garrido‐Rodriguez, K Zirngibl, O Ivanova… - Molecular systems …, 2022 - embopress.org
Signal transduction governs cellular behavior, and its dysregulation often leads to human
disease. To understand this process, we can use network models based on prior …

[HTML][HTML] A proteogenomic portrait of lung squamous cell carcinoma

S Satpathy, K Krug, PMJ Beltran, SR Savage, F Petralia… - Cell, 2021 - cell.com
Lung squamous cell carcinoma (LSCC) remains a leading cause of cancer death with few
therapeutic options. We characterized the proteogenomic landscape of LSCC, providing a …

Platelet proteomes, pathways, and phenotypes as informants of vascular wellness and disease

JE Aslan - Arteriosclerosis, thrombosis, and vascular biology, 2021 - Am Heart Assoc
Platelets rapidly undergo responsive transitions in form and function to repair vascular
endothelium and mediate hemostasis. In contrast, heterogeneous platelet subpopulations …

Pathway Commons 2019 Update: integration, analysis and exploration of pathway data

I Rodchenkov, O Babur, A Luna, BA Aksoy… - Nucleic acids …, 2020 - academic.oup.com
Abstract Pathway Commons (https://www. pathwaycommons. org) is an integrated resource
of publicly available information about biological pathways including biochemical reactions …

[HTML][HTML] Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation

Y Geffen, S Anand, Y Akiyama, TM Yaron, Y Song… - Cell, 2023 - cell.com
Post-translational modifications (PTMs) play key roles in regulating cell signaling and
physiology in both normal and cancer cells. Advances in mass spectrometry enable high …

[HTML][HTML] Proteogenomic and metabolomic characterization of human glioblastoma

LB Wang, A Karpova, MA Gritsenko, JE Kyle, S Cao… - Cancer cell, 2021 - cell.com
Glioblastoma (GBM) is the most aggressive nervous system cancer. Understanding its
molecular pathogenesis is crucial to improving diagnosis and treatment. Integrated analysis …

[HTML][HTML] The AML microenvironment catalyzes a stepwise evolution to gilteritinib resistance

SK Joshi, T Nechiporuk, D Bottomly, PD Piehowski… - Cancer cell, 2021 - cell.com
Our study details the stepwise evolution of gilteritinib resistance in FLT3-mutated acute
myeloid leukemia (AML). Early resistance is mediated by the bone marrow …

Automated assembly of molecular mechanisms at scale from text mining and curated databases

JA Bachman, BM Gyori, PK Sorger - Molecular Systems Biology, 2023 - embopress.org
The analysis of omic data depends on machine‐readable information about protein
interactions, modifications, and activities as found in protein interaction networks, databases …

Phosphoproteomic quantitation and causal analysis reveal pathways in GPVI/ITAM-mediated platelet activation programs

Ö Babur, AR Melrose, JM Cunliffe… - Blood, The Journal …, 2020 - ashpublications.org
Platelets engage cues of pending vascular injury through coordinated adhesion, secretion,
and aggregation responses. These rapid, progressive changes in platelet form and function …

PPM1D mutations are oncogenic drivers of de novo diffuse midline glioma formation

P Khadka, ZJ Reitman, S Lu, G Buchan… - Nature …, 2022 - nature.com
The role of PPM1D mutations in de novo gliomagenesis has not been systematically
explored. Here we analyze whole genome sequences of 170 pediatric high-grade gliomas …