WormBase: a comprehensive data resource for Caenorhabditis biology and genomics. - Nansheng Chen; Todd W. Harris; Igor Antoshechkin; Carol Bastiani; Tamberlyn Bieri; Darin Blasiar; Keith Bradnam; Payan Canaran; Juancarlos Chan; Chao-Kung Chen; Wen J. Chen; Fiona Cunningham; et al. (Nucleic Acids Res., 2005)

RCy3: Network biology using Cytoscape from within R. - Julia A. Gustavsen; Shraddha Pai; Ruth Isserlin; Barry Demchak; Alexander R. Pico (F1000Research, 2019)

netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks. - Shraddha Pai; Philipp Weber; Ruth Isserlin; Hussam Kaka; Shirley Hui; Muhammad Ahmad Shah; Luca Giudice; Rosalba Giugno; Anne Krogh Nøhr; Jan Baumbach; Gary D. Bader (F1000Research, 2020)

Fourteen quick tips for crowdsourcing geographically linked data for public health advocacy. - Joshua Atienza; Anjalee Benedict; Lincoln D. Stein; Kashif Pirzada; Cheryl White; Shraddha Pai (PLoS Comput. Biol., 2023)