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Journal Articles
- 2019
[j13]Geremy Clair
, Sarah Reehl, Kelly G. Stratton, Matthew E. Monroe, Malak M. Tfaily, Charles Ansong, Jennifer E. Kyle:
Lipid Mini-On: mining and ontology tool for enrichment analysis of lipidomic data. Bioinform. 35(21): 4507-4508 (2019)- 2017
- [j12]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) - 2015
- [j11]Bryson C. Gibbons, Matthew Chambers, Matthew E. Monroe, David L. Tabb, Samuel H. Payne:
Correcting systematic bias and instrument measurement drift with mzRefinery. Bioinform. 31(23): 3838-3840 (2015) - 2013
- [j10]Eugene Kolker, Vural Özdemir, Lennart Martens, William Hancock, Gordon A. Anderson, Nathaniel Anderson, Sukru Aynacioglu, Ancha V. Baranova, Shawn R. Campagna, Rui Chen, John Choiniere, Stephen P. Dearth, Wu-Chun Feng, Lynnette Ferguson, Geoffrey C. Fox, Dmitrij Frishman, Robert Grossman, Allison P. Heath, Roger Higdon, Mara H. Hutz, Imre Janko, Lihua Jiang, Sanjay Joshi, Alexander E. Kel, Joseph W. Kemnitz, Isaac S. Kohane, Natali Kolker, Doron Lancet, Elaine Lee, Weizhong Li, Andrey Lisitsa, Adrian Llerena, Courtney MacNealy-Koch, Jean-Claude Marshall, Paola Masuzzo, Amanda May, George Mias, Matthew E. Monroe, Elizabeth Montague, Sean D. Mooney, Alexey I. Nesvizhskii, Santosh Noronha, Gilbert S. Omenn, Harsha Rajasimha, Preveen Ramamoorthy, Jerry Sheehan, Larry Smarr, Charles V. Smith, Todd Smith, Michael Snyder, Srikanth Rapole, Sanjeeva Srivastava, Larissa Stanberry, Elizabeth Stewart, Stefano Toppo, Peter Uetz, Kenneth Verheggen, Brynn H. Voy, Louise Warnich, Steven W. Wilhelm, Gregory Yandl:
Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications. Big Data 1(4): 196-201 (2013) - [j9]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) - [j8]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) - [j7]Dong Wang, Surendra Dasari, Matthew Chambers, Jerry D. Holman, Kan Chen, Daniel C. Liebler, Daniel J. Orton, Samuel O. Purvine, Matthew E. Monroe, Chang Y. Chung, Kristie L. Rose, David L. Tabb:
Basophile: Accurate Fragment Charge State Prediction Improves Peptide Identification Rates. Genom. Proteom. Bioinform. 11(2): 86-95 (2013) - 2011
- [j6]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) - 2010
- [j5]Anuj R. Shah, Joshua N. Adkins, Douglas J. Baxter, William R. Cannon, Daniel G. Chavarría-Miranda, Sutanay Choudhury, Ian Gorton, Deborah K. Gracio, Todd D. Halter, Navdeep Jaitly, John R. Johnson, Richard T. Kouzes, Matthew C. Macduff, Andrès Márquez, Matthew E. Monroe, Christopher S. Oehmen, William A. Pike, Chad Scherrer, Oreste Villa, Bobbie-Jo M. Webb-Robertson, Paul D. Whitney, Nino Zuljevic:
Applications in Data-Intensive Computing. Adv. Comput. 79: 1-70 (2010) - [j4]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) - 2008
- [j3]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) - [j2]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) - 2007
- [j1]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)
Conference and Workshop Papers
- 2009
- [c2]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 - 2004
- [c1]Kevin K. Anderson, Matthew E. Monroe, Don Simone Daly:
Estimating Probabilities of Peptide Assignments to LC-FTICR-MS Observations. METMBS 2004: 151-156
Coauthor Index
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