Matthew E. Monroe

发表

Machine learning based prediction for peptide drift times in ion mobility spectrometry

Mudita Singhal, Khushbu Agarwal, Richard D. Smith, 2010, Bioinform..

MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis

Navdeep Jaitly, Brian L. LaMarche, Richard D. Smith, 2013, BMC Bioinformatics.

VIPER: an advanced software package to support high-throughput LC-MS peptide identification

Navdeep Jaitly, Joshua N. Adkins, Richard D. Smith, 2007, Bioinform..

Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications

Lennart Martens, Stefano Toppo, Geoffrey C. Fox, 2013, Big Data.

Correcting systematic bias and instrument measurement drift with mzRefinery

Matthew Chambers, David L. Tabb, Matthew E. Monroe, 2015, Bioinform..

Applications in Data-Intensive Computing

Navdeep Jaitly, Joshua N. Adkins, Deborah K. Gracio, 2010, Adv. Comput..

Signatures for Mass Spectrometry Data Quality

Brian L. LaMarche, Landon H. Sego, Mark F. Tardiff, 2014, Journal of proteome research.

Basophile: Accurate Fragment Charge State Prediction Improves Peptide Identification Rates

Kan Chen, Dong Wang, Matthew Chambers, 2013, Genom. Proteom. Bioinform..

DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra

Navdeep Jaitly, Joshua N. Adkins, Richard D. Smith, 2008, Bioinform..

PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association

Jian Ma, Thomas O. Metz, Ryan S. Renslow, 2017, Bioinform..

MASIC: A software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC-MS(/MS) features

Joshua N. Adkins, Richard D. Smith, Don Simone Daly, 2008, Comput. Biol. Chem..

LC-IMS-MS Feature Finder: detecting multidimensional liquid chromatography, ion mobility and mass spectrometry features in complex datasets

Brian L. LaMarche, Richard D. Smith, Gordon A. Anderson, 2013, Bioinform..

Spectral Archives: Extending Spectral Libraries to Analyze both Identified and Unidentified Spectra

Pavel A. Pevzner, Ari M. Frank, Gordon A. Anderson, 2011, Nature Methods.

High-Throughput Human Serum N-Glycan Profiling with GlycoGrid 4D Visualization and Automated Annotation Using GlyQ-IQ Multi-Core Software and PNNL Institutional Computing

Joshua N. Adkins, Rui Zhao, Clay D. Hagler, 2013 .

An Architecture for Real Time Data Acquisition and Online Signal Processing for High Throughput Tandem Mass Spectrometry

Navdeep Jaitly, Ian Gorton, Joshua N. Adkins, 2009, 2009 Fifth IEEE International Conference on e-Science.

Dynamic proteomic profiling of a unicellular cyanobacterium Cyanothece ATCC51142 across light-dark diurnal cycles

Richard D. Smith, David W. Koppenaal, Marina A. Gritsenko, 2011, BMC Systems Biology.

Estimating Probabilities of Peptide Assignments to LC-FTICR-MS Observations

Kevin K. Anderson, Don Simone Daly, Matthew E. Monroe, 2004, METMBS.

Comparative Omics-Driven Genome Annotation Refinement: Application across Yersiniae

Joshua N. Adkins, Scott N. Peterson, Charles Ansong, 2012, PloS one.

A comprehensive collection of systems biology data characterizing the host response to viral infection

Qibin Zhang, Brian D. Aevermann, Brett E. Pickett, 2014, Scientific Data.

Correction: Comparative Omics-Driven Genome Annotation Refinement: Application across Yersiniae

Joshua N. Adkins, Scott N. Peterson, Charles Ansong, 2012, PLoS ONE.

SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in biofluids

Young-Mo Kim, Thomas O. Metz, Ryan S. Renslow, 2016, Clinical mass spectrometry.

Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities

Subha Madhavan, Peter B. McGarvey, Li Ding, 2019, Cell.

The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity

Joshua N. Adkins, Christopher C. Overall, Gary R. Kiebel, 2015, Scientific Data.

High Dynamic Range Characterization of the Trauma Patient Plasma Proteome*S

Ronald G. Tompkins, Tao Liu, Marina A. Gritsenko, 2006, Molecular & Cellular Proteomics.

Proteogenomic Characterization of Endometrial Carcinoma

Peter B. McGarvey, Ying Wang, Li Ding, 2020, Cell.

Comparative Bacterial Proteomics: Analysis of the Core Genome Concept

Joshua N. Adkins, Lee Ann McCue, Kenneth J. Auberry, 2008, PloS one.

Comparing identified and statistically significant lipids and polar metabolites in 15-year old serum and dried blood spot samples for longitudinal studies.

Young-Mo Kim, Karl K. Weitz, Yehia M. Ibrahim, 2017, Rapid communications in mass spectrometry : RCM.

Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability

Li Ding, Molly Brewer, Rui Zhao, 2020, Cell reports medicine.

DtaRefinery, a Software Tool for Elimination of Systematic Errors from Parent Ion Mass Measurements in Tandem Mass Spectra Data Sets*

Gordon A. Anderson, Ashoka D. Polpitiya, Anoop M. Mayampurath, 2009, Molecular & Cellular Proteomics.

Metagenome Analysis of Contaminated Sediments at the DOE Hanford Site

Lee Ann McCue, Eugene Kolker, Yunfeng Yang, 2005 .