Proteogenomic data and resources for pan-cancer analysis
Summary The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium
(CPTAC) investigates tumors from a proteogenomic perspective, creating rich multi-omics …
(CPTAC) investigates tumors from a proteogenomic perspective, creating rich multi-omics …
MicroRNAs as biomarkers for prostate cancer prognosis: a systematic review and a systematic reanalysis of public data
Background Reliable prognostic biomarkers to distinguish indolent from aggressive prostate
cancer (PCa) are lacking. Many studies investigated microRNAs (miRs) as PCa prognostic …
cancer (PCa) are lacking. Many studies investigated microRNAs (miRs) as PCa prognostic …
cGAS–STING drives the IL-6-dependent survival of chromosomally instable cancers
Chromosomal instability (CIN) drives cancer cell evolution, metastasis and therapy
resistance, and is associated with poor prognosis. CIN leads to micronuclei that release …
resistance, and is associated with poor prognosis. CIN leads to micronuclei that release …
oncoPredict: an R package for predicting in vivo or cancer patient drug response and biomarkers from cell line screening data
D Maeser, RF Gruener, RS Huang - Briefings in bioinformatics, 2021 - academic.oup.com
Cell line drug screening datasets can be utilized for a range of different drug discovery
applications from drug biomarker discovery to building translational models of drug …
applications from drug biomarker discovery to building translational models of drug …
Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer
WR Becker, SA Nevins, DC Chen, R Chiu… - Nature …, 2022 - nature.com
To chart cell composition and cell state changes that occur during the transformation of
healthy colon to precancerous adenomas to colorectal cancer (CRC), we generated single …
healthy colon to precancerous adenomas to colorectal cancer (CRC), we generated single …
[HTML][HTML] Spatially confined sub-tumor microenvironments in pancreatic cancer
Intratumoral heterogeneity is a critical frontier in understanding how the tumor
microenvironment (TME) propels malignant progression. Here, we deconvolute the human …
microenvironment (TME) propels malignant progression. Here, we deconvolute the human …
Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness
Clear cell renal cell carcinomas (ccRCCs) represent∼ 75% of RCC cases and account for
most RCC-associated deaths. Inter-and intratumoral heterogeneity (ITH) results in varying …
most RCC-associated deaths. Inter-and intratumoral heterogeneity (ITH) results in varying …
IL-1β+ macrophages fuel pathogenic inflammation in pancreatic cancer
N Caronni, F La Terza, FM Vittoria, G Barbiera… - Nature, 2023 - nature.com
Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with high resistance to
therapies. Inflammatory and immunomodulatory signals co-exist in the pancreatic tumour …
therapies. Inflammatory and immunomodulatory signals co-exist in the pancreatic tumour …
Persistent mutation burden drives sustained anti-tumor immune responses
Tumor mutation burden is an imperfect proxy of tumor foreignness and has therefore failed
to consistently demonstrate clinical utility in predicting responses in the context of …
to consistently demonstrate clinical utility in predicting responses in the context of …
MOGONET integrates multi-omics data using graph convolutional networks allowing patient classification and biomarker identification
To fully utilize the advances in omics technologies and achieve a more comprehensive
understanding of human diseases, novel computational methods are required for integrative …
understanding of human diseases, novel computational methods are required for integrative …