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2020 – today
- 2021
[j37]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, Yehia M. Ibrahim, Samuel H. Payne, Christer Jansson, Richard D. Smith, Thomas O. Metz:
AutoCCS: automated collision cross-section calculation software for ion mobility spectrometry-mass spectrometry. Bioinform. 37(22): 4193-4201 (2021)- [j36]Richard D. Smith, Heather A. Carlson:
Identification of Cryptic Binding Sites Using MixMD with Standard and Accelerated Molecular Dynamics. J. Chem. Inf. Model. 61(3): 1287-1299 (2021)
2010 – 2019
- 2019
- [j35]Jordan J. Clark, Mark L. Benson, Richard D. Smith, Heather A. Carlson:
Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures. PLoS Comput. Biol. 15(1) (2019) - 2018
- [j34]Sarah E. Graham, Richard D. Smith, Heather A. Carlson:
Predicting Displaceable Water Sites Using Mixed-Solvent Molecular Dynamics. J. Chem. Inf. Model. 58(2): 305-314 (2018) - 2017
- [j33]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:
LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data. Bioinform. 33(11): 1744-1746 (2017) - [j32]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, Thomas O. Metz:
PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association. Bioinform. 33(17): 2715-2722 (2017) - [j31]Richard D. Smith, Jing Lu, Heather A. Carlson:
Are there physicochemical differences between allosteric and competitive ligands? PLoS Comput. Biol. 13(11) (2017) - 2016
- [j30]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, David Baker, Heather A. Carlson:
CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge. J. Chem. Inf. Model. 56(6): 1022-1031 (2016) - [j29]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, James B. Dunbar Jr.:
CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma. J. Chem. Inf. Model. 56(6): 1063-1077 (2016) - 2015
- [j28]Aqeel Ahmed, Richard D. Smith, Jordan J. Clark, James B. Dunbar Jr., Heather A. Carlson:
Recent improvements to Binding MOAD: a resource for protein-ligand binding affinities and structures. Nucleic Acids Res. 43(Database-Issue): 465-469 (2015) - 2014
- [j27]So Young Ryu, Wei-Jun Qian, David G. Camp II, Richard D. Smith, Ronald G. Tompkins, Ronald W. Davis, Wenzhong Xiao:
Detecting differential protein expression in large-scale population proteomics. Bioinform. 30(19): 2741-2746 (2014) - 2013
- [j26]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:
LC-IMS-MS Feature Finder: detecting multidimensional liquid chromatography, ion mobility and mass spectrometry features in complex datasets. Bioinform. 29(21): 2804-2805 (2013) - [j25]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, Richard D. Smith:
MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis. BMC Bioinform. 14: 49 (2013) - [j24]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, Thomas O. Metz, Richard D. Smith, Katrina M. Waters, Ralph S. Baric, Yoshihiro Kawaoka, Michael G. Katze:
Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice. BMC Syst. Biol. 7: 69 (2013) - [j23]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:
CSAR Data Set Release 2012: Ligands, Affinities, Complexes, and Docking Decoys. J. Chem. Inf. Model. 53(8): 1842-1852 (2013) - [j22]Kelly L. Damm-Ganamet, Richard D. Smith, James B. Dunbar Jr., Jeanne A. Stuckey, Heather A. Carlson:
CSAR Benchmark Exercise 2011-2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series. J. Chem. Inf. Model. 53(8): 1853-1870 (2013) - [j21]David L. Gibbs, Arie Baratt, Ralph S. Baric, Yoshihiro Kawaoka, Richard D. Smith, Eric S. Orwoll, Michael G. Katze, Shannon K. McWeeney:
Protein co-expression network analysis (ProCoNA). J. Clin. Bioinform. 3: 11 (2013) - 2012
- [j20]Xuan Wang, Gordon A. Anderson, Richard D. Smith, Alan R. Dabney:
A hybrid approach to protein differential expression in mass spectrometry-based proteomics. Bioinform. 28(12): 1586-1591 (2012) - [j19]Thomas Taverner, Yuliya V. Karpievitch, Ashoka D. Polpitiya, Joseph N. Brown, Alan R. Dabney, Gordon A. Anderson, Richard D. Smith:
DanteR: an extensible R-based tool for quantitative analysis of -omics data. Bioinform. 28(18): 2404-2406 (2012) - [j18]Yuliya V. Karpievitch, Alan R. Dabney, Richard D. Smith:
Normalization and missing value imputation for label-free LC-MS analysis. BMC Bioinform. 13(S-16): S5 (2012) - [j17]Richard D. Smith, Alaina L. Engdahl, James B. Dunbar Jr., Heather A. Carlson:
Biophysical Limits of Protein-Ligand Binding. J. Chem. Inf. Model. 52(8): 2098-2106 (2012) - 2011
- [j16]Hyunjin Yoon, Charles Ansong, Jason E. McDermott, Marina A. Gritsenko, Richard D. Smith, Fred Heffron, Joshua N. Adkins:
Systems analysis of multiple regulator perturbations allows discovery of virulence factors in Salmonella. BMC Syst. Biol. 5: 100 (2011) - [j15]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:
Dynamic proteomic profiling of a unicellular cyanobacterium Cyanothece ATCC51142 across light-dark diurnal cycles. BMC Syst. Biol. 5: 194 (2011) - [j14]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:
CSAR Benchmark Exercise of 2010: Selection of the Protein-Ligand Complexes. J. Chem. Inf. Model. 51(9): 2036-2046 (2011) - [j13]Richard D. Smith, James B. Dunbar Jr., Peter Man-Un Ung, Emilio Xavier Esposito, Chao-Yie Yang, Shaomeng Wang, Heather A. Carlson:
CSAR Benchmark Exercise of 2010: Combined Evaluation Across All Submitted Scoring Functions. J. Chem. Inf. Model. 51(9): 2115-2131 (2011) - [j12]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:
Correction to CSAR Benchmark Exercise of 2010: Selection of the Protein-Ligand Complexes. J. Chem. Inf. Model. 51(9): 2146 (2011) - 2010
- [j11]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:
Machine learning based prediction for peptide drift times in ion mobility spectrometry. Bioinform. 26(13): 1601-1607 (2010)
2000 – 2009
- 2009
- [j10]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:
A statistical framework for protein quantitation in bottom-up MS-based proteomics. Bioinform. 25(16): 2028-2034 (2009) - [j9]Yuliya V. Karpievitch, Thomas Taverner, Joshua N. Adkins, Stephen J. Callister, Gordon A. Anderson, Richard D. Smith, Alan R. Dabney:
Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition. Bioinform. 25(19): 2573-2580 (2009) - [j8]Navdeep Jaitly, Anoop M. Mayampurath, Kyle Littlefield, Joshua N. Adkins, Gordon A. Anderson, Richard D. Smith:
Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data. BMC Bioinform. 10 (2009) - [c1]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:
An Architecture for Real Time Data Acquisition and Online Signal Processing for High Throughput Tandem Mass Spectrometry. eScience 2009: 88-93 - 2008
- [j7]Anoop M. Mayampurath, Navdeep Jaitly, Samuel O. Purvine, Matthew E. Monroe, Kenneth J. Auberry, Joshua N. Adkins, Richard D. Smith:
DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra. Bioinform. 24(7): 1021-1023 (2008) - [j6]Ashoka D. Polpitiya, Wei-Jun Qian, Navdeep Jaitly, Vladislav A. Petyuk, Joshua N. Adkins, David G. Camp II, Gordon A. Anderson, Richard D. Smith:
DAnTE: a statistical tool for quantitative analysis of -omics data. Bioinform. 24(13): 1556-1558 (2008) - [j5]Matthew E. Monroe, Jason L. Shaw, Don Simone Daly, Joshua N. Adkins, Richard D. Smith:
MASIC: A software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC-MS(/MS) features. Comput. Biol. Chem. 32(3): 215-217 (2008) - [j4]Mark L. Benson, Richard D. Smith, Nickolay A. Khazanov, Brandon Dimcheff, John E. Beaver, Peter Dresslar, Jason Nerothin, Heather A. Carlson:
Binding MOAD, a high-quality protein-ligand database. Nucleic Acids Res. 36(Database-Issue): 674-678 (2008) - 2007
- [j3]Matthew E. Monroe, Nikola Tolic, Navdeep Jaitly, Jason L. Shaw, Joshua N. Adkins, Richard D. Smith:
VIPER: an advanced software package to support high-throughput LC-MS peptide identification. Bioinform. 23(15): 2021-2023 (2007)
1960 – 1969
- 1969
- [j2]Richard D. Smith, Richard A. Dudek:
Errata. Oper. Res. 17(4): 756 (1969) - 1967
- [j1]Richard D. Smith, Richard A. Dudek:
A General Algorithm for Solution of the n-Job, M-Machine Sequencing Problem of the Flow Shop. Oper. Res. 15(1): 71-82 (1967)
Coauthor Index
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