The paper describes the Common Fund Data Ecosystem (CFDE), which integrates NIH Common Fund data resources to enable discovery, analysis, and collaboration across heterogeneous datasets.

bioRxiv · Apr 16, 2026 · PreprintScientific Communication & Education

KSMoFinder - Knowledge graph embedding of proteins and motifs for predicting kinases of human phosphosites

Manju Anandakrishnan, Karen E. ROSS, Chuming Chen, K. Vijay‐Shanker, Cathy H. Wu

KSMoFinder predicts kinase-phosphosite relationships by integrating protein context and motif composition using a knowledge graph embedding approach, outperforming existing methods.

Bioinformatics Advances · Dec 26, 2024Peer-reviewedBioinformatics

piNET: a versatile web platform for downstream analysis and visualization of proteomics data

Behrouz Shamsaei, Szymon Chojnacki, Marcin Pilarczyk, Mehdi Fazel Najafabadi, Wen Niu, Chuming Chen, Karen E. ROSS, Andrea D. Matlock, Jeremy L. Muhlich, Somchai Chutipongtanate, Jie Zheng, John Turner, Dušica Vidović, Jacob D. Jaffe, Michael J. MacCoss, , Jarek Meller

piNET is a web platform for analyzing and visualizing proteomics data, including PTMs, by connecting them to biological knowledge and LINCS signatures.

Nucleic Acids Research · May 27, 2020Peer-reviewedBioinformatics