Publications and Submissions
Members of the Du-Lab Team are underlined.
Conference oral or workshop presentations are indicated by [ORAL].
Conference poster presentations are indicated by [POSTER].
Book or Book chapters are indicated by [BOOK] or [BOOK CHAPTER].
Jounral publications are indicated by [JOURNAL].
2023
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[POSTER] 71st American Society for Mass Spectrometry Annual Conference on Mass Spectrometry and Allied
Topics,
June 4-8, 2023, Houston, Texas.
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ADAP informatics for untargeted mass spectrometry-based metabolomics and exposomics
big data.
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Using internal standards to harmonize untargeted metabolomics data: lessons from an
inter-laboratory ring trial.
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[ORAL] ADAP: An Integrated Informatics Framework for Mass Spectrometry-Based Metabolomics and Exposomics
National Institute of Environmental Health Sciences (NIEHS) Keystone Science Lecture, January 30, 2023.
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[ORAL] ADAP Informatics for Untargeted Mass Spectrometry-Based Exposomics, Human Health Exposure
Analysis Resource (HHEAR) webinar, January 13, 2023
2022
- [JOURNAL] Smirnov A, Liao Y, Du X*: Memory-Efficient Searching of Gas-Chromatography
Mass Spectra Accelerated by Prescreening. Metabolites 2022, 12(6). [Pubmed] [Journal Website]
- [ORAL] Xiuxia Du: Advances in the development of open-source software, compound libraries, and web
resources for untargeted mass spectrometry-based exposomics. December 13, 2022, Human Health Exposure
Analysis Resource (HHEAR) Grantee Meeting.
- [ORAL] Aleksandr Smirnov and Xiuxia Du: Hands-on analysis of mass spectrometry-based exposomics data
using ADAP-BIG and ADAP-KDB
[virtual], September 25-29, 2022, Lisbon, Portugal, International Society of Exposome Science annual conference.
- [ORAL] Xiuxia Du: Generating Benchmarking Dataset for Developing and Evaluating Untargeted Mass
Spectrometry- Based
Metabolomics Data Processing Software. 4th Annual Metabolomics Association of North America (MANA),
September 16-18, 2022, Edmonton, Canada.
- [ORAL] NIH Common Fund Metabolomics Consortium Final Meeting, May 31, 2022
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Xiuxia Du: ADAP-BIG: A Cross-platform and Graphical Software Tool for Preprocessing Metabolomics
Data
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Xiuxia Du: ADAP-KDB: Tracking Known and Unknown Mass Spectral Features in NMDR
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Aleksandr Smirnov: Approaches to optimize speed and memory management in ADAP-BIG
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Ciara Conway: Towards prediction of unknown lipids
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[POSTER] Aleksandr Smirnov, Joel Hall, Yunfei Liao, Daisy Brumit, Yuanyuan Li,
Blake Rushing, Susan McRitchie, Susan Sumner, Radha Krishna Balaji Ponnuru, Komal
Madamwar, Varun Suresh, Xiuxia Du: ADAP: An Integrated Informatics Pipeline
for Untargeted MassSpectrometry-Based Metabolomics
Big Data, 4th Annual Metabolomics Association of North America (MANA), September 16-18, 2022,
Edmonton, Canada.
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[POSTER] 70th American Society for Mass Spectrometry Conference (ASMS), June 5-9, 2022, Minneapolis
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Joel Hall, Aleksandr Smirnov, Yuanyuan Li, Blake Rushing, Yunfei Liao, Susan
McRitchie, Susan Sumner, Xiuxia Du: ADAP-BIG: A platform-independent and
graphical softwaretool for preprocessing large-scale mass-spectrometry based metabolomics and
exposomics data
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Aleksandr Smirnov, Yunfei Liao, Eoin Fahy, Shankar Subramaniam, and Xiuxia Du:
ADAP-KDB: an online platform for searching against private and public harmonized untargeted mass
spectrometry metabolomics data
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Ciara Conway, Aleksandr Smirnov, Yuanyuan Li, Blake Rushing, Susan McRitchie,
Timothy Fennell, Susan Sumner, and Xiuxia Du: Developing a Web Resource for Exposome
Research
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Yunfei Liao, Aleksandr Smirnov, Xiuxia Du: Extraction of Metabolic
Signatures from Untargeted Metabolomics Data in Metabolomics Workbench
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Colin Kay, Aleksandr Smirnov, Ciara Conway, Zhaocong Yang, Jing Yang, Yuanyuan
Li, Blake Rushing, Susan Sumner, Xiuxia Du: MetaboFood: A cloud knowledgebase for
massspectrometry-based precision nutrition
2021
- [JOURNAL] Smirnov A, Liao Y, Fahy E, Subramaniam S, Du X*: ADAP-KDB: A Spectral
Knowledgebase for Tracking and Prioritizing Unknown GC-MS Spectra in the NIH's Metabolomics Data Repository.
Anal Chem 2021, 93(36):12213-12220. [Pubmed] [Journal Website]
- [JOURNAL] Aksenov, A. A., I. Laponogov, Z. Zhang, S. L. F. Doran, I. Belluomo, D. Veselkov, W. Bittremieux,
L. F. Nothias, M. Nothias-Esposito, K. N. Maloney, B. B. Misra, A. V. Melnik, A. Smirnov, X. Du, K. L.
Jones, 2nd, K. Dorrestein, M. Panitchpakdi, M. Ernst, J. J. J. van der Hooft, M. Gonzalez, C. Carazzone, A. Amezquita, C.
Callewaert, J. T. Morton, R. A. Quinn, A. Bouslimani, A. A. Orio, D. Petras, A. M. Smania, S. P. Couvillion,
M. C. Burnet, C. D. Nicora, E. Zink, T. O. Metz, V. Artaev, E. Humston-Fulmer, R. Gregor, M. M. Meijler, I.
Mizrahi, S. Eyal, B. Anderson, R. Dutton, R. Lugan, P. L. Boulch, Y. Guitton, S. Prevost, A. Poirier, G.
Dervilly, B. Le Bizec, A. Fait, N. S. Persi, C. Song, K. Gashu, R. Coras, M. Guma, J. Manasson, J. U. Scher,
D. K. Barupal, S. Alseekh, A. R. Fernie, R. Mirnezami, V. Vasiliou, R. Schmid, R. S. Borisov, L. N. Kulikova,
R. Knight, M. Wang, G. B. Hanna, P. C. Dorrestein and K. Veselkov (2021). "Auto-deconvolution and molecular
networking of gas chromatography-mass spectrometry data." Nat Biotechnol 39(2): 169-173.
[Pubmed] [Journal Website]
- [JOURNAL] Krupenko NI, Sharma J, Fogle HM, Pediaditakis P, Strickland KC, Du X, Helke KL, Sumner S,
Krupenko SA: Knockout of Putative Tumor Suppressor Aldh1l1 in Mice Reprograms Metabolism to Accelerate
Growth of Tumors in a Diethylnitrosamine (DEN) Model of Liver Carcinogenesis. Cancers (Basel)
2021, 13(13).
[Pubmed] [Journal Website]
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[JOURNAL] Chang HY, Colby SM, Du X, Gomez JD, Helf MJ, Kechris K, Kirkpatrick CR, Li S, Patti GJ,
Renslow RS et al: A Practical Guide to Metabolomics Software Development. Anal Chem 2021,
93(4):1912-1923. [Pubmed] [Journal Website]
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[ORAL] Webinar hosted by the Institute for the Advancement of Food and Nutrition Sciences (IAFNS), November 22, 2021
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Aleksandr Smirnov: MetaboFood Web Application
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Ciara Conway: Data-Mining and Collection of Chemical Information
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Xiuxia Du: A research and application-driven cloud resource for precision nutrition –
Overview of the bioinformatics efforts to develop MetaboFood-KDB and beyond.
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[ORAL] Xiuxia Du: Tracking Known and Unknown Mass Spectra in Metabolomics Workbench,
September 28, 2021, NIH Common Fund Metabolomics Consortium Fall Meeting.
- [ORAL]
Xiuxia Du: ADAP-BIG and ADAP-KDB: A Software Tool for Preprocessing Untargeted Metabolomics Big
Data and an Online Spectral Knowledgebase for Tracking Unknown Mass Spectra, August 31, 2021, RTI
International.
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[ORAL] Xiuxia Du: Harnessing the power of the NIH’s Metabolomics Data Repository using big data
analytics. August 22, 2021, American Chemical Society.
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[ORAL] Xiuxia Du: An integrated data analysis workflow for mass spectrometry-based untargeted
metabolomics and exposomics. June 29, 2021, Human Health Exposure Analysis Resource (HHEAR) spring
meeting.
- [POSTER] American Society for Mass Spectrometry (ASMS), October 31 to November 4, 2021, Philadelphia, PA and Online
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Joel Hall, Aleksandr Smirnov, Yuanyuan Li, Blake Rushing, Yunfei Liao, Susan
McRitchie, Susan Sumner, Xiuxia Du: ADAP-BIG:A graphical desktop software tool for
preprocessing multi-batch massspectrometry-based raw untargeted metabolomics data.
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Aleksandr Smirnov, Yunfei Liao, Eoin Fahy, Shankar Subramaniam, and Xiuxia
Du: ADAP-KDB:an online spectral knowledgebase of harmonized untargeted metabolomics data
from NIH’s Metabolomics Data Repository.
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Ciara Conway, Aleksandr Smirnov, Yuanyuan Li, Blake Rushing, Susan McRitchie,
Timothy Fennell, Susan Sumner, and Xiuxia Du: Development of a library of
environmentally relevant compounds for exposomics.
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Yunfei Liao, Aleksandr Smirnov, Xiuxia Du: A prescreening approach to
speedup spectral library search.
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Jerry Chen, Aleksandr Smirnov, Eric Sun, Peter Nemes, Xiuxia Du:
Trace Cloud: An online resource for detecting low-intensity signal peaks in CE/LC/GC-MS data
using neural networks.
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[POSTER] Metabolomics Association of North America (MANA), October 18-21, 2021, Online
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Aleksandr Smirnov, Yunfei Liao, Eoin Fahy, Shankar Subramaniam, Yuanyuan Li, Blake
Rushing, Susan McRitchie, Susan Sumner, and Xiuxia Du: ADAP-KDB Spectral Knowledgebase:
an online resource for searching and prioritizing untargeted metabolomics data
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Ciara Conway, Aleksandr Smirnov, Yuanyuan Li, Blake Rushing, Susan McRitchie,
Timothy Fennell, Susan Sumner, and Xiuxia Du: Development of a Knowledgebase of
Environmentally Relevant Compounds for Exposomics
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Colin Kay, Aleksandr Smirnov, Yuanyuan Li, Blake Rushing, Ciara Conway, Zhaocong
Yang, Jing Yang, Susan Sumner, Xiuxia Du: MetaboFood-KDB: A cloud knowledgebase for
searching metabolomics data for nutritionally relevant compounds
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Yunfei Liao, Aleksandr Smirnov, Xiuxia Du: A Prescreening Algorithm to
SpeedUp Spectra Search in the ADAP-KDB Spectral Knowledgebase
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Rasmus Erlemann, Ciara Conway, Aleksandr Smirnov and Xiuxia Du:
Application of the Goodness-of-Fit Test to Prioritizing Unknown Metabolites
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Jerry Chen, Aleksandr Smirnov, Eric Sun, Peter Nemes, Xiuxia Du:
TraceCloud: An Online Resource for Detecting Low-Intensity Signal Peaks in CE/LC/GC/-MS Data Using
Neural Networks
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[POSTER] 17th Annual Conference of the Metabolomics Society, June 22-24, 2021, online
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Aleksandr Smirnov, Yuanyuan Li, Blake Rushing, Eric Liao, Joel Hall, Susan
McRitchie, Susan Sumner, Xiuxia Du: ADAP-BIG: A Platform-Independent and Scalable
Software Tool for Preprocessing Large-Scale Mass Spectrometry-based Metabolomics and
Exposomics Data
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Colin Kay, Aleksandr Smirnov, Yuanyuan Li, Blake Rusing, Zhaocong Yang, Ciara
Conway, Jing Yang, Susan Sumner, Xiuxia Du: MetaboFood-KDB: A Cloud
Knowledgebase for Searching Metabolomics and Exposomics Data for Nutritionally Relevant
Compounds
2020
- [JOURNAL] Krupenko NI, Sharma J, Pediaditakis P, Helke KL, Hall MS, Du X, Sumner S, Krupenko SA:
Aldh1l2 knockout mouse metabolomics links the loss of the mitochondrial folate enzyme to deregulation
of a lipid metabolism observed in rare human disorder. Hum Genomics 2020, 14(1):41.
[Pubmed] [Journal Website]
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[BOOK CHAPTER] Tomas Pluskal, Ansgar Korf, Aleksandr Smirnov, Robin Schmid, Timothy R Fallon,
Xiuxia Du, and Jing-Ke Weng: Metabolomics Data Analysis Using MZmine. Processing
Metabolomics and Proteomics Data with Open Software. 2020, 232-254. [Pubmed] [Journal Website]
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[BOOK CHAPTER] Xiuxia Du, Aleksandr Smirnov, Tomas Pluskal, Wei Jia, and Susan Sumner:
Metabolomics Data Preprocessing Using ADAP and MZmine 2. Computational Methods and Data
Analysis for Metabolomics, 2020, 25-48. [Journal Website]
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[POSTER and LIGHTNING TALK] Aleksandr Smirnov, Yunfei Liao, Eoin Fahy, Shankar Subramaniam,
and Xiuxia Du: ADAP-KDB: A Spectral Knowledgebase for tracking and prioritizing unknown mass
spectra across studies in NIH's Metabolomics Data Repository. Metabolomics Association of North
America annual meeting, September 2020.
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[ORAL] Hands-on Analysis of Mass Spectrometry-Based Exposomics Data using ADAP/MZmine, September 20, 2020,
International Society of Exposure Sciences (ISES) annual conference.
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[POSTER] Aleksandr Smirnov, Eoin Fahy, Shankar Subramaniam, and Xiuxia Du: Tracking
Unknown Mass Spectra in Metabolomics Workbench using ADAP Spectral Knowledgebase. Human Health
Exposure Analysis Resource (HHEAR) meeting, March 2020.
2019
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[JOURNAL] Aleksandr Smirnov, Yunping Qiu, Wei Jia, Douglas I. Walker, Dean P. Jones, and Xiuxia
Du: ADAP-GC 4.0: Application of Clustering-Assisted Multivariate Curve Resolution to Spectral
Deconvolution of Gas Chromatography Mass Spectrometry Metabolomics Data. Analytical Chemistry
2019, 91, 9069-9077.
[Pubmed]
[Journal Website] [Related information]
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[JOURNAL] Krupenko NI, Sharma J, Pediaditakis P, Fekry B, Helke KL, Du X, Sumner S, Krupenko SA:
Cytosolic 10-formyltetrahydrofolate dehydrogenase regulates glycine metabolism in mouse liver. Sci
Rep 2019, 9(1):14937.
[Pubmed]
[Journal Website]
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[JOURNAL] Balasubramaniam M, Ayyadevara S, Ganne A, Kakraba S, Penthala NR, Du X, Crooks PA, Griffin
ST, Shmookler Reis RJ: Aggregate Interactome Based on Protein Cross-linking Interfaces Predicts Drug
Targets to Limit Aggregation in Neurodegenerative Diseases. iScience
2019, 20:248-264.
[Pubmed]
[Journal Website]
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[POSTER] Aleksandr Smirnov, Eoin Fahy, Shankar Subramaniam, and Xiuxia Du:
Prioritization of unknown compounds in Metabolomics Workbench. Metabolomics Association of
North America annual meeting, November 2019.
2018
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[JOURNAL] Xiuxia Du, Aleksandr Smirnov, and Wei Jia: A preparatory study of how to
construct consensus mass spectra of recurrent unknown metabolites from untargeted GC-MS metabolomics
data. International Journal of Mass Spectrometry 2018, 427:73-78. [Journal
Website] [Related information]
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[JOURNAL] Aleksandr Smirnov, Wei Jia, Douglas I. Walker, Dean P. Jones, and Xiuxia Du:
ADAP-GC 3.2: Graphical Software Tool for Efficient Spectral Deconvolution of Gas Chromatography-High
Resolution Mass Spectrometry Metabolomics Data. Journal of Proteome Research 2018, 17
(1):470-478. [Pubmed] [Journal Website] [Related information]
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[ORAL] Aleksandr Smirnov, Wei Jia, Douglas I. Walker, Dean P. Jones, and Xiuxia Du:
ADAP-GC 4.0: Application of non-negative matrix factorization to spectral deconvolution of gas
chromatography-mass spectrometry metabolomics data. Abstract accepted for presentation at the
American Society for Mass Spectrometry annual conference, San Diego, California, USA, June 3-7, 2018.
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[POSTER] Aleksandr Smirnov, Yuanyuan Li, Wimal Pathmasiri, Susan J. Sumner, and Xiuxia Du:
A workflow for detecting unknown compounds from untargeted GC/MS and LC/MS metabolomics data and an
online library of unknowns detected in plasma and urine. Abstract submitted to the 14th Annual
Conference of the Metabolomics Society, Seattle, Washington, USA, June 24-28, 2018.
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[POSTER] Xiuxia Du, Owen D. Myers, Aleksandr Smirnov, Dharak Shah, Susan J.
Sumner, Stephen Barnes, and Keqi Tang: ADAP-3D: An algorithm for reducing false positive and missing
peaks detected from raw mass spectrometry metabolomics data. Abstract accepted for presentation at
the American Society for Mass Spectrometry annual conference, San Diego, California, USA, June 3-7, 2018.
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[POSTER] Xiuxia Du, Aleksandr Smirnov, and Susan Sumner: ADAP: A suite of computational
algorithms and software tool for preprocessing mass spectrometry-based metabolomics data. Defining
Precision Nutrition Symposium, Kannapolis, North Carolina, USA, May 1-2, 2018. [Poster]
2017
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[JOURNAL] Owen Myers, Susan Sumner, Shuzhao Li, Stephen Barnes, and Xiuxia Du: One step
forward for reducing false positive and false negative compound identifications from mass spectrometry
metabolomics data: new algorithms for constructing extracted ion chromatograms and detecting
chromatographic peaks. Analytical Chemistry 2017, 89(17):8696-9703. [Pubmed] [Journal Website] [Related information]
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[JOURNAL] Owen Myers, Susan Sumner, Shuzhao Li, Stephen Barnes, and Xiuxia Du: A
detailed investigation and comparison of the XCMS and MZmine 2 chromatogram construction and
chromatographic peak detection methods for preprocessing mass spectrometry metabolomics data.
Analytical Chemistry 2017, 89(17):8689-8695. [Pubmed] [Journal Website] [Related information]
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[JOURNAL] Zahra Ashkavand, Ciara O'Flanagan, Mirko Hennig, Xiuxia Du, Stephen D. Hursting, and
Sergey A. Krupenko: Metabolic reprogramming by folate restriction leads to a less aggressive
phenotype. Molecular Cancer Research. DOI: 10.1158/1541-7786. [Pubmed] [Journal Website]
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American Society for Mass Spectrometry annual conference, Indianapolis, Indiana, USA, June 4-8, 2017.
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[POSTER] Aleksandr Smirnov, Owen Myers, Wei Jia, Douglas I. Walker, Shuzhao Li, Dean P.
Jones, and Xiuxia Du: ADAP-GC: A software package for preprocessing gas chromatography mass
spectrometry metabolomics data. [Poster]
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[POSTER] Owen Myers, Susan Sumner, Shuzhao Li, Stephen Barnes, and Xiuxia Du: New
algorithms for reducing the rate of false positive and false negative compounds detected from mass
spectrometry metabolomics data. [Poster]
2016
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[JOURNAL] Antonio Artigues, Owen W. Nadeau, Mary Ashley Rimmer, Maria T. Villar, Xiuxia Du, Aron
W. Fenton, and Gerald M. Carlson: Protein Structural Analysis via Mass Spectrometry-Based Proteomics. Book chapter.
Modern Proteomics - Sample Preparation, Analysis, and Practical Applications, Springer
International Publishing Switzerland. [Pubmed]
[Book Website]
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[JOURNAL] Yan Ni, Mingming Su, Yunping Qiu, Wei Jia, and Xiuxia Du: ADAP-GC 3.0:
Improved Peak Detection and Deconvolution of Co-eluting Metabolites from GC/TOF-MS Data for Metabolomics
Studies, Analytical Chemistry 2016, 88 (17):8802-8811.[Pubmed] [Journal Website] [Related information]
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[JOURNAL] Stephen Barnes, H. Paul Benton, Krista Casazza, Sara J. Cooper, Xiangqin Cui, Xiuxia Du,
Jeffrey Engler, Janusz H. Kabarowski, Shuzhao Li, Wimal Pathmasiri, Jeevan K. Prasain, Matthew B.
Renfrow, and Hemant K. Tiwarie: Training in metabolomics research. I. Designing the experiment,
collecting and extracting samples and generating metabolomics data. Journal of Mass
Spectrometry 2016, 51, 461-475. [Pubmed] [Journal website]
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[JOURNAL] Stephen Barnes, H. Paul Benton, Krista Casazza, Sara J. Cooper, Xiangqin Cui, Xiuxia Du,
Jeffrey Engler, Janusz H. Kabarowski, Shuzhao Li, Wimal Pathmasiri, Jeevan K. Prasain, Matthew B.
Renfrow, and Hemant K. Tiwarie: Training in metabolomics research. II. Processing and statistical
analysis of metabolomics data, metabolite identification, pathway analysis, applications of metabolomics
and its future. Journal of Mass Spectrometry 2016, 51, 535-548. [Pubmed][Journal website]
Prior to 2016 (Only journal publications are listed below)
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Clavier, S.; Du, X.; Sagan, S.; Bolbach, G.; Sachon, E.: An integrated cross-linking-MS approach to
investigate cell penetrating peptides interacting partners. EuPA OPEN PROTEOMICS 2014; 3:229-238.
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Du, X.; Zeisel, S. H.: Spectral deconvolution for gas chromatography mass spectrometry-based
metabolomics: current status and future perspectives. Computational and structural biotechnology
journal 2013, 4, e201301013.
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Watson, A. A.; Mahajan, P.; Mertens, H. D.; Deery, M. J.; Zhang, W.; Pham, P.; Du, X.; Bartke, T.; Zhang,
W.; Edlich, C.; Berridge, G.; Chen, Y.; Burgess-Brown, N. A.; Kouzarides, T.; Wiechens, N.; Owen-Hughes,
T.; Svergun, D. I.; Gileadi, O.; Laue, E. D.: The PHD and chromo domains regulate the ATPase activity
of the human chromatin remodeler CHD4. Journal of molecular biology 2012, 422 (1), 3-17.
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Ni, Y.; Qiu, Y.; Jiang, W.; Suttlemyre, K.; Su, M.; Zhang, W.; Jia, W.; Du, X.: ADAP-GC 2.0:
deconvolution of coeluting metabolites from GC/TOF-MS data for metabolomics studies. Analytical
chemistry 2012, 84 (15), 6619-29.
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Manes, N. P.; Dong, L.; Zhou, W.; Du, X.; Reghu, N.; Kool, A. C.; Choi, D.; Bailey, C. L.; Petricoin, E.
F., 3rd; Liotta, L. A.; Popov, S. G.: Discovery of mouse spleen signaling responses to anthrax using
label-free quantitative phosphoproteomics via mass spectrometry. Molecular & cellular proteomics :
MCP 2011, 10 (3), M110 000927.
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Du, X.; Chowdhury, S. M.; Manes, N. P.; Wu, S.; Mayer, M. U.; Adkins, J. N.; Anderson, G. A.; Smith, R.
D.: Xlink-identifier: an automated data analysis platform for confident identifications of chemically
cross-linked peptides using tandem mass spectrometry. Journal of proteome research 2011, 10
(3), 923-31.
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Yang, F.; Waters, K. M.; Miller, J. H.; Gritsenko, M. A.; Zhao, R.; Du, X.; Livesay, E. A.; Purvine, S.
O.; Monroe, M. E.; Wang, Y.; Camp, D. G., 2nd; Smith, R. D.; Stenoien, D. L.: Phosphoproteomics
profiling of human skin fibroblast cells reveals pathways and proteins affected by low doses of ionizing
radiation. PloS one 2010, 5 (11), e14152.
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Jiang, W.; Qiu, Y.; Ni, Y.; Su, M.; Jia, W.; Du, X.: An automated data analysis pipeline for GC-TOF-MS
metabonomics studies. Journal of proteome research 2010, 9 (11), 5974-81.
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Chowdhury, S. M.; Du, X.; Tolic, N.; Wu, S.; Moore, R. J.; Mayer, M. U.; Smith, R. D.; Adkins, J. N.:
Identification of cross-linked peptides after click-based enrichment using sequential
collision-induced dissociation and electron transfer dissociation tandem mass spectrometry.
Analytical chemistry 2009, 81 (13), 5524-32.
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Manes, N. P.; Estep, R. D.; Mottaz, H. M.; Moore, R. J.; Clauss, T. R.; Monroe, M. E.; Du, X.; Adkins, J.
N.; Wong, S. W.; Smith, R. D.: Comparative proteomics of human monkeypox and vaccinia intracellular
mature and extracellular enveloped virions. Journal of proteome research 2008, 7 (3), 960-8.
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Du, X.; Yang, F.; Manes, N. P.; Stenoien, D. L.; Monroe, M. E.; Adkins, J. N.; States, D. J.; Purvine, S.
O.; Camp, D. G., 2nd; Smith, R. D.: Linear discriminant analysis-based estimation of the false
discovery rate for phosphopeptide identifications. Journal of proteome research 2008, 7 (6),
2195-203.
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Du, X.; Callister, S. J.; Manes, N. P.; Adkins, J. N.; Alexandridis, R. A.; Zeng, X.; Roh, J. H.; Smith,
W. E.; Donohue, T. J.; Kaplan, S.; Smith, R. D.; Lipton, M. S.: A computational strategy to analyze
label-free temporal bottom-up proteomics data. Journal of proteome research 2008, 7 (7),
2595-604.
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Ding, S. J.; Wang, Y.; Jacobs, J. M.; Qian, W. J.; Yang, F.; Tolmachev, A. V.; Du, X.; Wang, W.; Moore,
R. J.; Monroe, M. E.; Purvine, S. O.; Waters, K.; Heibeck, T. H.; Adkins, J. N.; Camp, D. G., 2nd;
Klemke, R. L.; Smith, R. D.: Quantitative phosphoproteome analysis of lysophosphatidic acid induced
chemotaxis applying dual-step (18)O labeling coupled with immobilized metal-ion affinity chromatography
. Journal of proteome research 2008, 7 (10), 4215-24.
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Yang, F.; Jaitly, N.; Jayachandran, H.; Luo, Q.; Monroe, M. E.; Du, X.; Gritsenko, M. A.; Zhang, R.;
Anderson, D. J.; Purvine, S. O.; Adkins, J. N.; Moore, R. J.; Mottaz, H. M.; Ding, S. J.; Lipton, M. S.;
Camp, D. G., 2nd; Udseth, H. R.; Smith, R. D.; Rossie, S.: Applying a targeted label-free approach
using LC-MS AMT tags to evaluate changes in protein phosphorylation following phosphatase inhibition.
Journal of proteome research 2007, 6 (11), 4489-97.
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Du X, Ghosh BK, Ulinski P: Encoding of motion targets by waves in turtle visual cortex. IEEE
transactions on bio-medical engineering 2006, 53(8):1688-1695.
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Du X, Ghosh BK, Ulinski P: Encoding and decoding target locations with waves in the turtle visual
cortex. IEEE transactions on bio-medical engineering 2005, 52(4):566-577.