Facilitating interpretation of mass spectrometry based proteomics data. - Joel C. Hunter; Joshua N. Adkins; Joel G. Pounds; John H. Miller (METMBS, 2004)

Session Introduction. - Bobbie-Jo M. Webb-Robertson; William R. Cannon; Joshua N. Adkins; Deborah K. Gracio (Pacific Symposium on Biocomputing, 2006)

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)

VIPER: an advanced software package to support high-throughput LC-MS peptide identification. - Matthew E. Monroe; Nikola Tolic; Navdeep Jaitly; Jason L. Shaw; Joshua N. Adkins; Richard D. Smith (Bioinform., 2007)

PQuad - a visual analysis platform for proteomic data exploration of microbial organisms. - Bobbie-Jo M. Webb-Robertson; Elena S. Peterson; Mudita Singhal; Kyle R. Klicker; Christopher S. Oehmen; Joshua N. Adkins; Susan L. Havre (Bioinform., 2007)

DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra. - Anoop M. Mayampurath; Navdeep Jaitly; Samuel O. Purvine; Matthew E. Monroe; Kenneth J. Auberry; Joshua N. Adkins; Richard D. Smith (Bioinform., 2008)

DAnTE: a statistical tool for quantitative analysis of -omics data. - Ashoka D. Polpitiya; Wei-Jun Qian; Navdeep Jaitly; Vladislav A. Petyuk; Joshua N. Adkins; David G. Camp II; Gordon A. Anderson; Richard D. Smith (Bioinform., 2008)

MASIC: A software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC-MS(/MS) features. - Matthew E. Monroe; Jason L. Shaw; Don Simone Daly; Joshua N. Adkins; Richard D. Smith (Comput. Biol. Chem., 2008)

An Architecture for Real Time Data Acquisition and Online Signal Processing for High Throughput Tandem Mass Spectrometry. - Anuj R. Shah; Navdeep Jaitly; Nino Zuljevic; Matthew E. Monroe; Andrei Liyu; Ashoka D. Polpitiya; Joshua N. Adkins; Mikhail E. Belov; Gordon A. Anderson; Richard D. Smith; Ian Gorton (eScience, 2009)

A statistical framework for protein quantitation in bottom-up MS-based proteomics. - Yuliya V. Karpievitch; Jeff Stanley; Thomas Taverner; Jianhua Huang; Joshua N. Adkins; Charles Ansong; Fred Heffron; Thomas O. Metz; Wei-Jun Qian; Hyunjin Yoon; Richard D. Smith; Alan R. Dabney (Bioinform., 2009)

Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition. - Yuliya V. Karpievitch; Thomas Taverner; Joshua N. Adkins; Stephen J. Callister; Gordon A. Anderson; Richard D. Smith; Alan R. Dabney (Bioinform., 2009)

Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data. - Navdeep Jaitly; Anoop M. Mayampurath; Kyle Littlefield; Joshua N. Adkins; Gordon A. Anderson; Richard D. Smith (BMC Bioinform., 2009)

Using support vector machine for improving protein-protein interaction prediction utilizing domain interactions. - Mudita Singhal; Anuj R. Shah; Joshua N. Adkins; Roslyn Brown (BCB, 2010)

Applications in Data-Intensive Computing. - Anuj R. Shah; Joshua N. Adkins; Douglas J. Baxter; William R. Cannon; Daniel G. Chavarría-Miranda; Sutanay Choudhury; Ian Gorton; Deborah K. Gracio; Todd D. Halter; Navdeep Jaitly; John R. Johnson; Richard T. Kouzes; et al. (Adv. Comput., 2010)

An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92. - Pep Charusanti; Sadhana Chauhan; Kathleen McAteer; Joshua A. Lerman; Daniel R. Hyduke; Vladimir L. Motin; Charles Ansong; Joshua N. Adkins; Bernhard O. Palsson (BMC Syst. Biol., 2011)

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. - Ines Thiele; Daniel R. Hyduke; Benjamin Steeb; Guy Fankam; Douglas K. Allen; Susanna Bazzani; Pep Charusanti; Feng-Chi Chen; Ronan M. T. Fleming; Chao A. Hsiung; Sigrid C. J. De Keersmaecker; Yu-Chieh Liao; et al. (BMC Syst. Biol., 2011)

Systems analysis of multiple regulator perturbations allows discovery of virulence factors in Salmonella. - Hyunjin Yoon; Charles Ansong; Jason E. McDermott; Marina A. Gritsenko; Richard D. Smith; Fred Heffron; Joshua N. Adkins (BMC Syst. Biol., 2011)

GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data. - Brian J. Schmidt; Ali Ebrahim; Thomas O. Metz; Joshua N. Adkins; Bernhard Ø. Palsson; Daniel R. Hyduke (Bioinform., 2013)

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)

efam: an expanded, metaproteome-supported HMM profile database of viral protein families. - Ahmed A. Zayed; Dominik Lücking; Mohamed Mohssen; Dylan Cronin; Ben Bolduc; Ann C. Gregory; Katherine R. Hargreaves; Paul D. Piehowski; Richard Allen White III; Eric L. Huang; Joshua N. Adkins; Simon Roux; et al. (Bioinform., 2021)