[HTML][HTML] Discovery of pathway-independent protein signatures associated with clinical outcome in human cancer cohorts

MM Konaté, MC Li, LM McShane, Y Zhao - Scientific Reports, 2022 - nature.com
Proteomic data provide a direct readout of protein function, thus constituting an information-
rich resource for prognostic and predictive modeling. However, protein array data may not …

[HTML][HTML] Personalized integrated network modeling of the cancer proteome atlas

MJ Ha, S Banerjee, R Akbani, H Liang, GB Mills… - Scientific reports, 2018 - nature.com
Personalized (patient-specific) approaches have recently emerged with a precision
medicine paradigm that acknowledges the fact that molecular pathway structures and …

[HTML][HTML] Robust phenotype prediction from gene expression data using differential shrinkage of co-regulated genes

K Zarringhalam, D Degras, C Brockel, D Ziemek - Scientific reports, 2018 - nature.com
Discovery of robust diagnostic or prognostic biomarkers is a key to optimizing therapeutic
benefit for select patient cohorts-an idea commonly referred to as precision medicine. Most …

[HTML][HTML] Topological integration of RPPA proteomic data with multi-omics data for survival prediction in breast cancer via pathway activity inference

TR Kim, HH Jeong, KA Sohn - BMC Medical Genomics, 2019 - Springer
Background The analysis of integrated multi-omics data enables the identification of disease-
related biomarkers that cannot be identified from a single omics profile. Although protein …

[HTML][HTML] Revealing prognosis-related pathways at the individual level by a comprehensive analysis of different cancer transcription data

J Fang, C Pian, M Xu, L Kong, Z Li, J Ji, L Zhang… - Genes, 2020 - mdpi.com
Identifying perturbed pathways at an individual level is important to discover the causes of
cancer and develop individualized custom therapeutic strategies. Though prognostic gene …

[HTML][HTML] Unique protein expression signatures of survival time in kidney renal clear cell carcinoma through a pan-cancer screening

G Han, W Zhao, X Song, P Kwok-Shing Ng, JA Karam… - BMC genomics, 2017 - Springer
Background In 2016, it is estimated that there will be 62,700 new cases of kidney cancer in
the United States, and 14,240 patients will die from the disease. Because the incidence of …

[HTML][HTML] Biological convergence of cancer signatures

X Solé, N Bonifaci, N López-Bigas, A Berenguer… - PLoS …, 2009 - journals.plos.org
Gene expression profiling has identified cancer prognostic and predictive signatures with
superior performance to conventional histopathological or clinical parameters …

[HTML][HTML] Transforming RNA-Seq data to improve the performance of prognostic gene signatures

I Zwiener, B Frisch, H Binder - PloS one, 2014 - journals.plos.org
Gene expression measurements have successfully been used for building prognostic
signatures, ie for identifying a short list of important genes that can predict patient outcome …

Pathway-structured predictive model for cancer survival prediction: a two-stage approach

X Zhang, Y Li, T Akinyemiju, AI Ojesina, P Buckhaults… - Genetics, 2017 - academic.oup.com
Heterogeneity in terms of tumor characteristics, prognosis, and survival among cancer
patients has been a persistent problem for many decades. Currently, prognosis and …

Bayesian hierarchical varying-sparsity regression models with application to cancer proteogenomics

Y Ni, FC Stingo, MJ Ha, R Akbani… - Journal of the …, 2019 - Taylor & Francis
Identifying patient-specific prognostic biomarkers is of critical importance in developing
personalized treatment for clinically and molecularly heterogeneous diseases such as …