Anna Pamela Calinawan

CPTAC Pancancer Phosphoproteomics Kinase Enrichment Analysis with ProKAP Provides Insights into Immunogenic Signaling Pathways

The paper analyzes CPTAC phosphoproteomics data to identify kinase activity differences between tumor and normal tissues across cancers and develops a web portal for querying kinase activity scores and associated data.

Learning directed acyclic graphs for ligands and receptors based on spatially resolved transcriptomic analysis of ovarian cancer

This paper introduces LRnetST, a statistical method for inferring ligand-receptor interaction networks from spatial transcriptomic data of ovarian tumors, revealing common and distinct interactions across samples.

BayesDeBulk: A Flexible Bayesian Algorithm for the Deconvolution of Bulk Tumor Data

BayesDeBulk estimates immune and stromal cell composition from bulk proteomic and transcriptomic data, outperforming existing tools in synthetic and real data examples.

Prioritization of prostate cancer to immune checkpoint therapy by ranking tumors along IFN-γ axis and identification of immune resistance mechanisms

This study ranks prostate cancer tumors along the IFN-γ/PD-L1 axis to prioritize patients for immune checkpoint therapy and identifies immune resistance mechanisms.

DreamAI: algorithm for the imputation of proteomics data

An ensemble of six imputation methods, built through the NCI-CPTAC Proteogenomics DREAM Challenge, fills missing values in labeled LC-MS/MS proteomics data, helping most for low-abundance proteins.

ProTrack: An Interactive Multi-Omics Data Browser for Proteogenomic Studies

ProTrack provides an interactive web tool for exploring CPTAC proteogenomic data across multiple cancer types, enabling users to query and visualize multi-omics profiles without coding.