Analytics challenge - High-throughput visual analytics biological sciences: turning data into knowledge. - Christopher S. Oehmen; Lee Ann McCue; Joshua N. Adkins; Katrina M. Waters; Tim Carlson; William R. Cannon; Bobbie-Jo M. Webb-Robertson; Douglas J. Baxter; Elena S. Peterson; Mudita Singhal; Anuj R. Shah; Kyle R. Klicker (SC, 2006)

Enabling high-throughput data management for systems biology: The Bioinformatics Resource Manager. - Anuj R. Shah; Mudita Singhal; Kyle R. Klicker; Eric G. Stephan; H. Steven Wiley; Katrina M. Waters (Bioinform., 2007)

An Extensible, Scalable Architecture for Managing Bioinformatics Data and Analyses. - Anuj R. Shah; Mudita Singhal; Tara D. Gibson; Chandrika Sivaramakrishnan; Katrina M. Waters; Ian Gorton (eScience, 2008)

Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models. - Simon Rogers; Mark A. Girolami; Walter Kolch; Katrina M. Waters; Tao Liu 003; Brian Thrall; H. Steven Wiley (Bioinform., 2008)

A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics. - Bobbie-Jo M. Webb-Robertson; William R. Cannon; Christopher S. Oehmen; Anuj R. Shah; Vidhya Gurumoorthi; Mary S. Lipton; Katrina M. Waters (Bioinform., 2010)

Improved quality control processing of peptide-centric LC-MS proteomics data. - Melissa M. Matzke; Katrina M. Waters; Thomas O. Metz; Jon M. Jacobs; Amy C. Sims; Ralph S. Baric; Joel G. Pounds; Bobbie-Jo M. Webb-Robertson (Bioinform., 2011)

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)

Bioinformatics resource manager v2.3: an integrated software environment for systems biology with microRNA and cross-species analysis tools. - Susan C. Tilton; Tamara L. Tal; Sheena M. Scroggins; Jill A. Franzosa; Elena S. Peterson; Robert L. Tanguay; Katrina M. Waters (BMC Bioinform., 2012)

Topological analysis of protein co-abundance networks identifies novel host targets important for HCV infection and pathogenesis. - Jason E. McDermott; Deborah L. Diamond; Courtney D. Corley; Angela L. Rasmussen; Michael G. Katze; Katrina M. Waters (BMC Syst. Biol., 2012)

Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice. - Nicolas Tchitchek; Amie J. Eisfeld; Jennifer Tisoncik-Go; Laurence Josset; Lisa E. Gralinski; Christophe Bécavin; Susan C. Tilton; Bobbie-Jo M. Webb-Robertson; Martin T. Ferris; Allison L. Totura; Chengjun Li; Gabriele Neumann; et al. (BMC Syst. Biol., 2013)

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)

Unified feature association networks through integration of transcriptomic and proteomic data. - Ryan S. McClure; Jason P. Wendler; Joshua N. Adkins; Jesica Swanstrom; Ralph S. Baric; Brooke L. Deatherage Kaiser; Kristie L. Oxford; Katrina M. Waters; Jason E. McDermott (PLoS Comput. Biol., 2019)

Bioinformatics Resource Manager: a systems biology web tool for microRNA and omics data integration. - Joseph Brown; Aaron R. Phillips; David A. Lewis; Michael-Andres Mans; Yvonne Chang; Robert L. Tanguay; Elena S. Peterson; Katrina M. Waters; Susan C. Tilton (BMC Bioinform., 2019)

Hypergraph models of biological networks to identify genes critical to pathogenic viral response. - Song Feng; Emily Heath; Brett A. Jefferson; Cliff A. Joslyn; Henry Kvinge; Hugh D. Mitchell; Brenda Praggastis; Amie J. Eisfeld; Amy C. Sims; Larissa B. Thackray; Shufang Fan; Kevin B. Walters; et al. (BMC Bioinform., 2021)

Missing data in multi-omics integration: Recent advances through artificial intelligence. - Javier E. Flores; Daniel Claborne; Zachary D. Weller; Bobbie-Jo M. Webb-Robertson; Katrina M. Waters; Lisa M. Bramer (Frontiers Artif. Intell., 2023)

3′ RNA-seq is superior to standard RNA-seq in cases of sparse data but inferior at identifying toxicity pathways in a model organism. - Ryan S. McClure; Yvonne Rericha; Katrina M. Waters; Robyn L. Tanguay (Frontiers Bioinform., 2023)