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ORCIDThomas O. Metz
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- affiliation: Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA, USA
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Journal Articles
- 2024
[j18]Marjolein T. Oostrom
, Sean M. Colby, Thomas O. Metz:
DEIMoS GUI: An Open-Source User Interface for a High-Dimensional Mass Spectrometry Data Processing Tool. J. Chem. Inf. Model. 64(5): 1419-1424 (2024)- 2022
- [j17]Yasemin Yesiltepe, Niranjan Govind, Thomas O. Metz, Ryan S. Renslow:
An initial investigation of accuracy required for the identification of small molecules in complex samples using quantum chemical calculated NMR chemical shifts. J. Cheminformatics 14(1): 64 (2022) - [j16]David S. Wishart, Siyang Tian, Dana Allen, Eponine Oler, Harrison Peters, Vicki W. Lui, Vasuk Gautam, Yannick Djoumbou Feunang, Russell Greiner, Thomas O. Metz:
BioTransformer 3.0 - a web server for accurately predicting metabolic transformation products. Nucleic Acids Res. 50(W1): 115-123 (2022) - [j15]Fei Wang, Dana Allen, Siyang Tian, Eponine Oler, Vasuk Gautam, Russell Greiner, Thomas O. Metz, David S. Wishart:
CFM-ID 4.0 - a web server for accurate MS-based metabolite identification. Nucleic Acids Res. 50(W1): 165-174 (2022) - 2021
- [j14]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) - [j13]Jamie R. Nuñez, Monee Y. McGrady, Yasemin Yesiltepe, Ryan S. Renslow, Thomas O. Metz:
Correction to "Chespa: Streamlining Expansive Chemical Space Evaluation of Molecular Sets". J. Chem. Inf. Model. 61(5): 2509-2510 (2021) - [j12]Madison R. Blumer, Christine H. Chang, Evangelina Brayfindley, Jamie R. Nuñez, Sean M. Colby, Ryan S. Renslow, Thomas O. Metz:
Mass Spectrometry Adduct Calculator. J. Chem. Inf. Model. 61(12): 5721-5725 (2021) - 2020
- [j11]Jamie R. Nuñez, Monee Y. McGrady, Yasemin Yesiltepe, Ryan S. Renslow, Thomas O. Metz:
Chespa: Streamlining Expansive Chemical Space Evaluation of Molecular Sets. J. Chem. Inf. Model. 60(12): 6251-6257 (2020) - 2019
- [j10]Jamie R. Nuñez, Sean M. Colby, Dennis G. Thomas, Malak M. Tfaily, Nikola Tolic, Elin M. Ulrich, Jon R. Sobus, Thomas O. Metz, Justin G. Teeguarden, Ryan S. Renslow:
Evaluation of In Silico Multifeature Libraries for Providing Evidence for the Presence of Small Molecules in Synthetic Blinded Samples. J. Chem. Inf. Model. 59(9): 4052-4060 (2019) - 2018
- [j9]Yasemin Yesiltepe, Jamie R. Nuñez, Sean M. Colby, Dennis G. Thomas, Mark I. Borkum, Patrick Reardon, Nancy M. Washton, Thomas O. Metz, Justin G. Teeguarden, Niranjan Govind, Ryan S. Renslow:
An automated framework for NMR chemical shift calculations of small organic molecules. J. Cheminformatics 10(1): 52:1-52:16 (2018) - 2017
- [j8]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) - [j7]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) - 2013
- [j6]Brian J. Schmidt, Ali Ebrahim, Thomas O. Metz, Joshua N. Adkins, Bernhard Ø. Palsson, Daniel R. Hyduke:
GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data. Bioinform. 29(22): 2900-2908 (2013) - [j5]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) - [j4]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) - 2012
- [j3]Lars J. Kangas, Thomas O. Metz, Giorgis Isaac, Brian T. Schrom, Bojana Ginovska-Pangovska, Luning Wang, Li Tan, Robert R. Lewis, John H. Miller:
In silico identification software (ISIS): a machine learning approach to tandem mass spectral identification of lipids. Bioinform. 28(13): 1705-1713 (2012) - 2011
- [j2]Melissa M. Matzke, Katrina M. Waters, Thomas O. Metz, Jon M. Jacobs, Amy C. Sims, Ralph S. Baric, Joel G. Pounds, Bobbie-Jo M. Webb-Robertson:
Improved quality control processing of peptide-centric LC-MS proteomics data. Bioinform. 27(20): 2866-2872 (2011) - 2009
- [j1]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)
Conference and Workshop Papers
- 2016
- [c2]Jean-Philippe F. Gourdine, Thomas O. Metz, David Koeller, Matthew H. Brush, Melissa A. Haendel:
Building a Molecular Glyco-phenotype Ontology to Decipher Undiagnosed Diseases. ICBO/BioCreative 2016 - 2011
- [c1]Brian T. Schrom, Lars J. Kangas, Bojana Ginovska-Pangovska, Thomas O. Metz, John H. Miller:
Charge Prediction of Lipid Fragments in Mass Spectrometry. ICMLA (2) 2011: 186-188
Informal and Other Publications
- 2021
- [i2]Felicity F. Nielson, Sean M. Colby, Ryan S. Renslow, Thomas O. Metz:
Similarity Downselection: A Python implementation of a heuristic search algorithm for finding the set of the n most dissimilar items with an application in conformer sampling. CoRR abs/2105.02991 (2021) - [i1]Yasemin Yesiltepe, Ryan S. Renslow, Thomas O. Metz:
SPECTRe: Substructure Processing, Enumeration, and Comparison Tool Resource: An efficient tool to encode all substructures of molecules represented in SMILES. CoRR abs/2111.03227 (2021)
Coauthor Index
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