Xiuxia Du

发表

Detailed Investigation and Comparison of the XCMS and MZmine 2 Chromatogram Construction and Chromatographic Peak Detection Methods for Preprocessing Mass Spectrometry Metabolomics Data.

Shuzhao Li, Stephen Barnes, Xiuxia Du, 2017, Analytical chemistry.

A computational strategy to analyze label-free temporal bottom-up proteomics data.

Samuel Kaplan, Nathan P Manes, Joshua N Adkins, 2008, Journal of proteome research.

The PHD and Chromo Domains Regulate the ATPase Activity of the Human Chromatin Remodeler CHD4

D. Svergun, T. Kouzarides, T. Owen-Hughes, 2012, Journal of molecular biology.

An integrated cross-linking-MS approach to investigate cell penetrating peptides interacting partners

S. Sagan, G. Bolbach, Xiuxia Du, 2014 .

Discovery of Mouse Spleen Signaling Responses to Anthrax using Label-Free Quantitative Phosphoproteomics via Mass Spectrometry*

E. Petricoin, L. Liotta, Charles L. Bailey, 2010, Molecular & Cellular Proteomics.

Training in metabolomics research. II. Processing and statistical analysis of metabolomics data, metabolite identification, pathway analysis, applications of metabolomics and its future.

S. Cooper, H. Tiwari, Shuzhao Li, 2016, Journal of mass spectrometry : JMS.

Memory-Efficient Searching of Gas-Chromatography Mass Spectra Accelerated by Prescreening

Xiuxia Du, Y. Liao, Aleksandr Smirnov, 2022, Metabolites.

Protein Structural Analysis via Mass Spectrometry-Based Proteomics.

A. Artigues, M. Villar, Xiuxia Du, 2016, Advances in experimental medicine and biology.

Identification of cross-linked peptides after click-based enrichment using sequential collision-induced dissociation and electron transfer dissociation tandem mass spectrometry.

Ronald J. Moore, Richard D. Smith, J. Adkins, 2009, Analytical chemistry.

Cytosolic 10-formyltetrahydrofolate dehydrogenase regulates glycine metabolism in mouse liver

K. Helke, S. Krupenko, P. Pediaditakis, 2019, Scientific Reports.

Phosphoproteomics Profiling of Human Skin Fibroblast Cells Reveals Pathways and Proteins Affected by Low Doses of Ionizing Radiation

Richard D. Smith, D. Camp, M. Monroe, 2010, PloS one.

Applying a targeted label-free approach using LC-MS AMT tags to evaluate changes in protein phosphorylation following phosphatase inhibition.

Ronald J. Moore, Richard D. Smith, Navdeep Jaitly, 2007, Journal of proteome research.

Aldh1l2 knockout mouse metabolomics links the loss of the mitochondrial folate enzyme to deregulation of a lipid metabolism observed in rare human disorder

K. Helke, S. Krupenko, P. Pediaditakis, 2020, Human genomics.

Comparative proteomics of human monkeypox and vaccinia intracellular mature and extracellular enveloped virions.

Ronald J Moore, Matthew E Monroe, Nathan P Manes, 2008, Journal of proteome research.

ADAP-GC 4.0: Application of Clustering-Assisted Multivariate Curve Resolution to Spectral Deconvolution of Gas Chromatography-Mass Spectrometry Metabolomics Data.

Wei Jia, Dean P. Jones, Douglas I Walker, 2019, Analytical chemistry.

Spectral Deconvolution for Gas Chromatography Mass Spectrometry-Based Metabolomics: Current Status and Future Perspectives

Xiuxia Du, S. Zeisel, Xiuxia Du, 2013, Computational and structural biotechnology journal.

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.

Shuzhao Li, Stephen Barnes, Xiuxia Du, 2017, Analytical chemistry.

Metabolic Reprogramming by Folate Restriction Leads to a Less Aggressive Cancer Phenotype

M. Hennig, S. Krupenko, C. O’Flanagan, 2016, Molecular Cancer Research.

Quantitative phosphoproteome analysis of lysophosphatidic acid induced chemotaxis applying dual-step (18)O labeling coupled with immobilized metal-ion affinity chromatography.

Ronald J. Moore, Richard D. Smith, D. Camp, 2008, Journal of proteome research.

Linear discriminant analysis-based estimation of the false discovery rate for phosphopeptide identifications.

Matthew E Monroe, Feng Yang, Xiuxia Du, 2008, Journal of proteome research.

Aggregate Interactome Based on Protein Cross-linking Interfaces Predicts Drug Targets to Limit Aggregation in Neurodegenerative Diseases

P. Crooks, S. Ayyadevara, Xiuxia Du, 2019, iScience.

ADAP-GC 2.0: deconvolution of coeluting metabolites from GC/TOF-MS data for metabolomics studies.

Yan Ni, Wei Jia, Wenxin Jiang, 2012, Analytical chemistry.

A Practical Guide to Metabolomics Software Development

Jamey D. Young, S. Subramaniam, J. Xia, 2021, Analytical chemistry.

CHAPTER 7. Metabolomics Data Analysis Using MZmine

Robin Schmid, Xiuxia Du, Jing-Ke Weng, 2020 .

Metabolomics Data Preprocessing Using ADAP and MZmine 2.

Wei Jia, Tomáš Pluskal, Aleksandr Smirnov, 2020, Methods in molecular biology.

Integrative analysis of multimodal mass spectrometry data in MZmine 3

Timothy R. Fallon, S. Böcker, P. Dorrestein, 2023, Nature Biotechnology.

The unknown lipids project: harmonized methods improve compound identification and data reproducibility in an inter-laboratory untargeted lipidomics study

Charles R. Evans, O. Fiehn, B. Evans, 2023, bioRxiv.

Training in metabolomics research. I. Designing the experiment, collecting and extracting samples and generating metabolomics data.

S. Cooper, H. Tiwari, Shuzhao Li, 2016, Journal of mass spectrometry : JMS.

Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data

Wout Bittremieux, Zheng Zhang, Yann Guitton, 2020, Nature Biotechnology.

Knockout of Putative Tumor Suppressor Aldh1l1 in Mice Reprograms Metabolism to Accelerate Growth of Tumors in a Diethylnitrosamine (DEN) Model of Liver Carcinogenesis

K. Helke, S. Krupenko, S. Sumner, 2021, Cancers.

A preparatory study of how to construct consensus mass spectra of recurrent unknown metabolites from untargeted GC–MS metabolomics data

W. Jia, Xiuxia Du, Aleksandr Smirnov, 2017 .

An automated data analysis pipeline for GC-TOF-MS metabonomics studies.

Yan Ni, Wei Jia, Mingming Su, 2010, Journal of proteome research.

ADAP-GC 3.0: Improved Peak Detection and Deconvolution of Co-eluting Metabolites from GC/TOF-MS Data for Metabolomics Studies.

Yan Ni, Wei Jia, Mingming Su, 2016, Analytical chemistry.

Aggregate Interactome Based on Protein Cross-linking Interfaces Predicts Drug Targets to Limit Aggregation in Neurodegenerative Diseases

P. Crooks, S. Ayyadevara, Xiuxia Du, 2019, iScience.

Training in metabolomics research. II. Processing and statistical analysis of metabolomics data, metabolite identification, pathway analysis, applications of metabolomics and its future.

S. Cooper, H. Tiwari, Shuzhao Li, 2016, Journal of Mass Spectrometry.

Metabolic reprogramming by folate restriction leads to a less aggressive cancer phenotype.

M. Hennig, S. Krupenko, C. O’Flanagan, 2016, Molecular cancer research : MCR.

Discovery of Mouse Spleen Signaling Responses to Anthrax using Label-Free Quantitative Phosphoproteomics via Mass Spectrometry*

E. Petricoin, L. Liotta, Charles L. Bailey, 2010, Molecular & Cellular Proteomics.

ADAP-GC 3.2: Graphical Software Tool for Efficient Spectral Deconvolution of Gas Chromatography-High-Resolution Mass Spectrometry Metabolomics Data.

Wei Jia, Dean P. Jones, Douglas I. Walker, 2018, Journal of proteome research.

Detailed Investigation and Comparison of the XCMS and MZmine 2 Chromatogram Construction and Chromatographic Peak Detection Methods for Preprocessing Mass Spectrometry Metabolomics Data.

Shuzhao Li, S. Barnes, S. Sumner, 2017, Analytical chemistry.

Xlink-identifier: an automated data analysis platform for confident identifications of chemically cross-linked peptides using tandem mass spectrometry.

Gordon A Anderson, Nathan P Manes, Joshua N Adkins, 2011, Journal of proteome research.

Linear discriminant analysis-based estimation of the false discovery rate for phosphopeptide identifications.

Richard D. Smith, D. States, D. Camp, 2008, Journal of proteome research.