Somatic Mutation Signatures of Cancer. - Stephen R. Piccolo; Lewis J. Frey (AMIA, 2008)

ML-Flex: A Flexible Toolbox for Performing Classification Analyses In Parallel. - Stephen R. Piccolo; Lewis J. Frey (J. Mach. Learn. Res., 2012)

Clinical and molecular models of Glioblastoma multiforme survival. - Stephen R. Piccolo; Lewis J. Frey (Int. J. Data Min. Bioinform., 2013)

Alternative preprocessing of RNA-Sequencing data in The Cancer Genome Atlas leads to improved analysis results. - Mumtahena Rahman; Laurie K. Jackson; W. Evan Johnson; Dean Y. Li; Andrea H. Bild; Stephen R. Piccolo (Bioinform., 2015)

ASSIGN: context-specific genomic profiling of multiple heterogeneous biological pathways. - Ying Shen; Mumtahena Rahman; Stephen R. Piccolo; Daniel Gusenleitner; Nader N. El-Chaar; Luis Cheng; Stefano Monti; Andrea H. Bild; W. Evan Johnson (Bioinform., 2015)

DeuteRater: a tool for quantifying peptide isotope precision and kinetic proteomics. - Bradley C. Naylor; Michael T. Porter; Elise Wilson; Adam Herring; Spencer Lofthouse; Austin Hannemann; Stephen R. Piccolo; Alan L. Rockwood; John C. Price (Bioinform., 2017)

CompoundHetVIP: Compound Heterozygous Variant Identification Pipeline. - Dustin B. Miller; Stephen R. Piccolo (F1000Research, 2020)

trioPhaser: using Mendelian inheritance logic to improve genomic phasing of trios. - Dustin B. Miller; Stephen R. Piccolo (BMC Bioinform., 2021)

The ability to classify patients based on gene-expression data varies by algorithm and performance metric. - Stephen R. Piccolo; Avery Mecham; Nathan P. Golightly; Jérémie L. Johnson; Dustin B. Miller (PLoS Comput. Biol., 2022)

Many bioinformatics programming tasks can be automated with ChatGPT. - Stephen R. Piccolo; Paul Denny 001; Andrew Luxton-Reilly; Samuel H. Payne; Perry G. Ridge (CoRR, 2023)

Evaluating a large language model's ability to solve programming exercises from an introductory bioinformatics course. - Stephen R. Piccolo; Paul Denny 001; Andrew Luxton-Reilly; Samuel H. Payne; Perry G. Ridge (PLoS Comput. Biol., 2023)

Automatic Extraction of Medication Mentions from Tweets - Overview of the BioCreative VII Shared Task 3 Competition. - Davy Weissenbacher; Karen O'Connor; Siddharth Rawal; Yu Zhang 202; Richard Tzong-Han Tsai; Timothy Miller 002; Dongfang Xu; Carol Anderson; Bo Liu; Qing Han; Jinfeng Zhang; Igor Kulev; et al. (Database J. Biol. Databases Curation, 2023)

TidyGEO: preparing analysis-ready datasets from Gene Expression Omnibus. - Avery Mecham; Ashlie Stephenson; Badi I. Quinteros; Grace S. Brown; Stephen R. Piccolo (J. Integr. Bioinform., 2024)