LC-IMS-MS Feature Finder: detecting multidimensional liquid chromatography, ion mobility and mass spectrometry features in complex datasets. - Kevin L. Crowell; Gordon W. Slysz; Erin S. Baker; Brian L. LaMarche; Matthew E. Monroe; Yehia M. Ibrahim; Samuel H. Payne; Gordon A. Anderson; Richard D. Smith (Bioinform., 2013)

Beyond the proteome: Mass Spectrometry Special Interest Group (MS-SIG) at ISMB/ECCB 2013. - So Young Ryu; Samuel H. Payne; Christoph Schaab; Wenzhong Xiao (Bioinform., 2014)

PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations. - Andrey Tovchigrechko; Pratap Venepally; Samuel H. Payne (Bioinform., 2014)

Correcting systematic bias and instrument measurement drift with mzRefinery. - Bryson C. Gibbons; Matthew Chambers; Matthew E. Monroe; David L. Tabb; Samuel H. Payne (Bioinform., 2015)

LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data. - Jennifer E. Kyle; Kevin L. Crowell; Cameron P. Casey; Grant M. Fujimoto; Sangtae Kim; Sydney E. Dautel; Richard D. Smith; Samuel H. Payne; Thomas O. Metz (Bioinform., 2017)

PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association. - Jian Ma; Cameron P. Casey; Xueyun Zheng; Yehia M. Ibrahim; Christopher S. Wilkins; Ryan S. Renslow; Dennis G. Thomas; Samuel H. Payne; Matthew E. Monroe; Richard D. Smith; Justin G. Teeguarden; Erin S. Baker; et al. (Bioinform., 2017)

Familiarity Vs Trust: A Comparative Study of Domain Scientists' Trust in Visual Analytics and Conventional Analysis Methods. - Aritra Dasgupta 001; Joon-Yong Lee; Ryan Wilson; Robert A. Lafrance; Nick Cramer; Kristin A. Cook; Samuel H. Payne (IEEE Trans. Vis. Comput. Graph., 2017)

Blazing Signature Filter: a library for fast pairwise similarity comparisons. - Joon-Yong Lee; Grant M. Fujimoto; Ryan Wilson; H. Steven Wiley; Samuel H. Payne (BMC Bioinform., 2018)

AutoCCS: automated collision cross-section calculation software for ion mobility spectrometry-mass spectrometry. - Joon-Yong Lee; Aivett Bilbao; Christopher R. Conant; Kent J. Bloodsworth; Daniel J. Orton; Mowei Zhou; Jesse William Wilson; Xueyun Zheng; Ian K. Webb; Ailin Li; Kim K. Hixson; John C. Fjeldsted; et al. (Bioinform., 2021)

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)

Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence. - Yingying Sun; Jun A; Zhiwei Liu; Rui Sun; Liujia Qian; Samuel H. Payne; Wout Bittremieux; Markus Ralser; Chen Li 021; Yi Chen; Zhen Dong; Yasset Pérez-Riverol; et al. (CoRR, 2025)