PlasmoDB: the Plasmodium genome resource. An integrated database providing tools for accessing, analyzing and mapping expression and sequence data (both finished and unfinished). - Amit Bahl; Brian P. Brunk; Ross L. Coppel; Jonathan Crabtree; Sharon J. Diskin; Martin J. Fraunholz; Gregory R. Grant; Dinesh Gupta; Robert L. Huestis; Jessica C. Kissinger; Philip Labo; Li Li; et al. (Nucleic Acids Res., 2002)

TandTRAQ: an open-source tool for integrated protein identification and quantitation. - Ted Laderas; Cory Bystrom; Debra McMillen; Guang Fan; Shannon K. McWeeney (Bioinform., 2007)

Conserved host response to highly pathogenic avian influenza virus infection in human cell culture, mouse and macaque model systems. - Jason E. McDermott; Harish Shankaran; Amie J. Eisfeld; Sarah E. Belisle; Gabriele Neumann; Chengjun Li; Shannon K. McWeeney; Carol Sabourin; Yoshihiro Kawaoka; Michael G. Katze; Katrina M. Waters (BMC Syst. Biol., 2011)

A Simulation Framework to Investigate in vitro Viral Infection Dynamics. - Armand Bankhead III; Emiliano Mancini; Amy C. Sims; Ralph S. Baric; Shannon K. McWeeney; Peter M. A. Sloot (ICCS, 2011)

Utilizing RNA-Seq data for de novo coexpression network inference. - Ovidiu D. Iancu; Sunita Kawane; Daniel Bottomly; Robert P. Searles; Robert Hitzemann; Shannon K. McWeeney (Bioinform., 2012)

The GA and the GWAS: Using Genetic Algorithms to Search for Multilocus Associations. - Michael Mooney; Beth Wilmot; Shannon K. McWeeney (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

HitWalker: variant prioritization for personalized functional cancer genomics. - Daniel Bottomly; Beth Wilmot; Jeffrey W. Tyner; Christopher A. Eide; Marc M. Loriaux; Brian J. Druker; Shannon K. McWeeney (Bioinform., 2013)

Protein co-expression network analysis (ProCoNA). - David L. Gibbs; Arie Baratt; Ralph S. Baric; Yoshihiro Kawaoka; Richard D. Smith; Eric S. Orwoll; Michael G. Katze; Shannon K. McWeeney (J. Clin. Bioinform., 2013)

Challenges in Secondary Analysis of High Throughput Screening Data. - Aurora S. Blucher; Shannon K. McWeeney (Pacific Symposium on Biocomputing, 2014)

oligoMask: A Framework for Assessing and Removing the Effect of Genetic Variants on Microarray Probes. - Daniel Bottomly; Beth Wilmot; Shannon K. McWeeney (R J., 2014)

Data Like This: Ranked Search of Genomic Data Vision Paper. - V. M. Megler; David Maier 001; Daniel Bottomly; Libbey White; Shannon K. McWeeney; Beth Wilmot (ExploreDB@SIGMOD/PODS, 2015)

plethy: management of whole body plethysmography data in R. - Daniel Bottomly; Beth Wilmot; Shannon K. McWeeney (BMC Bioinform., 2015)

HitWalker2: visual analytics for precision medicine and beyond. - Daniel Bottomly; Shannon K. McWeeney; Beth Wilmot (Bioinform., 2016)

The effect of inhibition of PP1 and TNFα signaling on pathogenesis of SARS coronavirus. - Jason E. McDermott; Hugh D. Mitchell; Lisa E. Gralinski; Amie J. Eisfeld; Laurence Josset; Armand Bankhead III; Gabriele Neumann; Susan C. Tilton; Alexandra Schäfer; Chengjun Li; Shufang Fan; Shannon K. McWeeney; et al. (BMC Syst. Biol., 2016)

Data Science in Biomedical Informatics Education: Critical Problems and Innovative Solutions. - Harry Hochheiser; Javed Mostafa; Nils Gehlenborg; Shannon K. McWeeney; Valerie Florance (AMIA, 2018)

Biology and medicine in the landscape of quantum advantages. - Benjamin A. Cordier; Nicolas P. D. Sawaya; Gian Giacomo Guerreschi; Shannon K. McWeeney (CoRR, 2021)

Biology-inspired graph neural network encodes reactome and reveals biochemical reactions of disease. - Joshua G. Burkhart; Guanming Wu; Xubo Song; Francesco Raimondi 001; Shannon K. McWeeney; Melissa H. Wong; Youping Deng (Patterns, 2023)

Data Valuation with Gradient Similarity. - Nathaniel J. Evans; Gordon B. Mills; Guanming Wu; Xubo Song; Shannon K. McWeeney (CoRR, 2024)

Recent Advances, Applications and Open Challenges in Machine Learning for Health: Reflections from Research Roundtables at ML4H 2024 Symposium. - Amin Adibi; Xu Cao; Zongliang Ji; Jivat Neet Kaur; Winston Chen; Elizabeth Healey; Brighton Nuwagira; Wenqian Ye; Geoffrey Woollard; Maxwell A. Xu; Hejie Cui; Johnny Xi; et al. (CoRR, 2025)