Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE). - Evan O. Paull; Daniel E. Carlin; Mario Niepel; Peter K. Sorger; David Haussler; Joshua M. Stuart (Bioinform., 2013)

Computational Evaluation and Derivation of biological Networks in cancer and STEM cells. - Daniel E. Carlin (2014)

Pathway-Based Genomics Prediction using Generalized Elastic Net. - Artem Sokolov; Daniel E. Carlin; Evan O. Paull; Robert Baertsch; Joshua M. Stuart (PLoS Comput. Biol., 2016)

A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression. - Daniel E. Carlin; Kassi Kosnicki; Sara Garamszegi; Trey Ideker; Helga Thorvaldsdóttir; Michael Reich; Jill P. Mesirov (F1000Research, 2017)

Network propagation in the cytoscape cyberinfrastructure. - Daniel E. Carlin; Barry Demchak; Dexter Pratt; Eric Sage; Trey Ideker (PLoS Comput. Biol., 2017)

pyNBS: a Python implementation for network-based stratification of tumor mutations. - Justin K. Huang; Tongqiu Jia; Daniel E. Carlin; Trey Ideker (Bioinform., 2018)