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

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

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

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

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

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

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

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

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

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

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

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

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

A simulation framework to investigate in vitro viral infection dynamics. - Bankhead, Armand, III; Mancini, Emiliano; Sims, Amy C.; Baric, Ralph S.; McWeeney, Shannon K.; Sloot, Peter M. A. (J. Comput. Sci., 2013)

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

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

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

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

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

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