A General Algorithm for Solution of the n-Job, M-Machine Sequencing Problem of the Flow Shop. - Richard D. Smith; Richard A. Dudek (Oper. Res., 1967)

Errata. - Richard D. Smith; Richard A. Dudek (Oper. Res., 1969)

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)

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)

Binding MOAD, a high-quality protein-ligand database. - Mark L. Benson; Richard D. Smith; Nickolay A. Khazanov; Brandon Dimcheff; John E. Beaver; Peter Dresslar; Jason Nerothin; Heather A. Carlson (Nucleic Acids Res., 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)

Machine learning based prediction for peptide drift times in ion mobility spectrometry. - Anuj R. Shah; Khushbu Agarwal; Erin S. Baker; Mudita Singhal; Anoop M. Mayampurath; Yehia M. Ibrahim; Lars J. Kangas; Matthew E. Monroe; Rui Zhao; Mikhail E. Belov; Gordon A. Anderson; Richard D. Smith (Bioinform., 2010)

Dynamic proteomic profiling of a unicellular cyanobacterium Cyanothece ATCC51142 across light-dark diurnal cycles. - Uma K. Aryal; Jana Stöckel; Ravi K. Krovvidi; Marina A. Gritsenko; Matthew E. Monroe; Ronald J. Moore; David W. Koppenaal; Richard D. Smith; Himadri B. Pakrasi; Jon M. Jacobs (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)

CSAR Benchmark Exercise of 2010: Selection of the Protein-Ligand Complexes. - James B. Dunbar Jr.; Richard D. Smith; Chao-Yie Yang; Peter Man-Un Ung; Katrina W. Lexa; Nickolay A. Khazanov; Jeanne A. Stuckey; Shaomeng Wang; Heather A. Carlson (J. Chem. Inf. Model., 2011)

Correction to CSAR Benchmark Exercise of 2010: Selection of the Protein-Ligand Complexes. - James B. Dunbar Jr.; Richard D. Smith; Chao-Yie Yang; Peter Man-Un Ung; Katrina W. Lexa; Nickolay A. Khazanov; Jeanne A. Stuckey; Shaomeng Wang; Heather A. Carlson (J. Chem. Inf. Model., 2011)

CSAR Benchmark Exercise of 2010: Combined Evaluation Across All Submitted Scoring Functions. - Richard D. Smith; James B. Dunbar Jr.; Peter Man-Un Ung; Emilio Xavier Esposito; Chao-Yie Yang; Shaomeng Wang; Heather A. Carlson (J. Chem. Inf. Model., 2011)

DanteR: an extensible R-based tool for quantitative analysis of -omics data. - Thomas Taverner; Yuliya V. Karpievitch; Ashoka D. Polpitiya; Joseph N. Brown; Alan R. Dabney; Gordon A. Anderson; Richard D. Smith (Bioinform., 2012)

A hybrid approach to protein differential expression in mass spectrometry-based proteomics. - Xuan Wang; Gordon A. Anderson; Richard D. Smith; Alan R. Dabney (Bioinform., 2012)

Normalization and missing value imputation for label-free LC-MS analysis. - Yuliya V. Karpievitch; Alan R. Dabney; Richard D. Smith (BMC Bioinform., 2012)

Biophysical Limits of Protein-Ligand Binding. - Richard D. Smith; Alaina L. Engdahl; James B. Dunbar Jr.; Heather A. Carlson (J. Chem. Inf. Model., 2012)

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)

MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis. - Brian L. LaMarche; Kevin L. Crowell; Navdeep Jaitly; Vladislav A. Petyuk; Anuj R. Shah; Ashoka D. Polpitiya; John D. Sandoval; Gary R. Kiebel; Matthew E. Monroe; Stephen J. Callister; Thomas O. Metz; Gordon A. Anderson; et al. (BMC Bioinform., 2013)

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)

CSAR Benchmark Exercise 2011-2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series. - Kelly L. Damm-Ganamet; Richard D. Smith; James B. Dunbar Jr.; Jeanne A. Stuckey; Heather A. Carlson (J. Chem. Inf. Model., 2013)

CSAR Data Set Release 2012: Ligands, Affinities, Complexes, and Docking Decoys. - James B. Dunbar Jr.; Richard D. Smith; Kelly L. Damm-Ganamet; Aqeel Ahmed; Emilio Xavier Esposito; James Delproposto; Krishnapriya Chinnaswamy; You-Na Kang; Ginger Kubish; Jason E. Gestwicki; Jeanne A. Stuckey; Heather A. Carlson (J. Chem. Inf. Model., 2013)

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

Detecting differential protein expression in large-scale population proteomics. - So Young Ryu; Wei-Jun Qian; David G. Camp II; Richard D. Smith; Ronald G. Tompkins; Ronald W. Davis; Wenzhong Xiao (Bioinform., 2014)

Recent improvements to Binding MOAD: a resource for protein-ligand binding affinities and structures. - Aqeel Ahmed; Richard D. Smith; Jordan J. Clark; James B. Dunbar Jr.; Heather A. Carlson (Nucleic Acids Res., 2015)

CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma. - Heather A. Carlson; Richard D. Smith; Kelly L. Damm-Ganamet; Jeanne A. Stuckey; Aqeel Ahmed; Maire A. Convery; Donald O. Somers; Michael Kranz; Patricia A. Elkins; Guanglei Cui; Catherine E. Peishoff; Millard H. Lambert; et al. (J. Chem. Inf. Model., 2016)

CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge. - Richard D. Smith; Kelly L. Damm-Ganamet; James B. Dunbar Jr.; Aqeel Ahmed; Krishnapriya Chinnaswamy; James Delproposto; Ginger Kubish; Christine E. Tinberg; Sagar D. Khare; Jiayi Dou; Lindsey Doyle; Jeanne A. Stuckey; et al. (J. Chem. Inf. Model., 2016)

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)

Are there physicochemical differences between allosteric and competitive ligands? - Richard D. Smith; Jing Lu; Heather A. Carlson (PLoS Comput. Biol., 2017)

Predicting Displaceable Water Sites Using Mixed-Solvent Molecular Dynamics. - Sarah E. Graham; Richard D. Smith; Heather A. Carlson (J. Chem. Inf. Model., 2018)

Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures. - Jordan J. Clark; Mark L. Benson; Richard D. Smith; Heather A. Carlson (PLoS Comput. Biol., 2019)

Identification of Cryptic Binding Sites Using MixMD with Standard and Accelerated Molecular Dynamics. - Richard D. Smith; Heather A. Carlson (J. Chem. Inf. Model., 2021)

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)