PathwaysWeb: a gene pathways API with directional interactions, expanded gene ontology, and versioning. - James M. Melott; John N. Weinstein; Bradley M. Broom (Bioinform., 2016)

TCGASpliceSeq a compendium of alternative mRNA splicing in cancer. - Michael C. Ryan; Wing Chung Wong; Robert Brown; Rehan Akbani; Xiaoping Su; Bradley M. Broom; James M. Melott; John N. Weinstein (Nucleic Acids Res., 2016)

SoS Notebook: an interactive multi-language data analysis environment. - Bo Peng 001; Gao Wang; Jun Ma; Man Chong Leong; Chris Wakefield; James M. Melott; Yulun Chiu; Di Du; John N. Weinstein (Bioinform., 2018)

Interactive Clustered Heat Map Builder: An easy web-based tool for creating sophisticated clustered heat maps. - Michael C. Ryan; Mark Stucky; Chris Wakefield; James M. Melott; Rehan Akbani; John N. Weinstein; Bradley M. Broom (F1000Research, 2019)

RPPA SPACE: an R package for normalization and quantitation of Reverse-Phase Protein Array data. - Huma Shehwana; Shwetha V. Kumar; James M. Melott; Mary A. Rohrdanz; Chris Wakefield; Zhenlin Ju; Doris R. Siwak; Yiling Lu; Bradley M. Broom; John N. Weinstein; Gordon B. Mills; Rehan Akbani (Bioinform., 2022)