Research Topics
| Hua XuSummaryAffiliation: The Ohio State University Country: USA Publications
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Detail Information
Publications
A mass accuracy sensitive probability based scoring algorithm for database searching of tandem mass spectrometry dataHua Xu
Department of Chemistry, The Ohio State University, Columbus 43210, OH, USA
BMC Bioinformatics 8:133. 2007..Various algorithms have since been developed to automate the process for modern high-throughput LC-MS/MS experiments...- A robust linear regression based algorithm for automated evaluation of peptide identifications from shotgun proteomics by use of reversed-phase liquid chromatography retention timeHua Xu
Department of Molecular Virology Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University Medical Center, Columbus, OH 43210, USA
BMC Bioinformatics 9:347. 2008..This report describes the implementation of an automated approach to reduce false positives and validate peptide matches... - Mass spectrometry profiles superoxide-induced intramolecular disulfide in the FMN-binding subunit of mitochondrial Complex ILiwen Zhang
Campus Chemical Instrument Center, Proteomics and Mass Spectrometry Facility, The Ohio State University, Columbus, Ohio 43210, USA
J Am Soc Mass Spectrom 19:1875-86. 2008.... - Assaying pharmacodynamic endpoints with targeted therapy: flavopiridol and 17AAG induced dephosphorylation of histone H1.5 in acute myeloid leukemiaLiwen Wang
Department of Chemistry, The Ohio State University, Columbus OH, USA
Proteomics 10:4281-92. 2010..As such, this approach may be a highly informative marker for response to targeted therapies influencing histone phosphorylation... - A hierarchical MS2/MS3 database search algorithm for automated analysis of phosphopeptide tandem mass spectraHua Xu
Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, OH, USA
Proteomics 9:1763-70. 2009..The additional MS(3) spectral data also improved the overall reliability and the number of true positives (TPs) due to the fact that the TPs of the MS(2)/MS(3) search results had higher scores than those of the MS(2)... - MassMatrix: a database search program for rapid characterization of proteins and peptides from tandem mass spectrometry dataHua Xu
Department of Chemistry, The Ohio State University, Columbus, OH 43210, USA
Proteomics 9:1548-55. 2009..The algorithm is available for public searches at (http://www.massmatrix.net)... - Monte carlo simulation-based algorithms for analysis of shotgun proteomic dataHua Xu
Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, Ohio 43210, USA
J Proteome Res 7:2605-15. 2008..Receiver operating characteristic analysis of the data sets confirmed that MCS-based models improved the overall performance of the MassMatrix search software, especially for low-mass accuracy data sets... - Identification and characterization of disulfide bonds in proteins and peptides from tandem MS data by use of the MassMatrix MS/MS search engineHua Xu
Department of Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
J Proteome Res 7:138-44. 2008..0) during digestion, only one nonnative disulfide bond was observed. The MassMatrix algorithm offers an additional approach for the discovery of disulfide bond from tandem mass spectrometry data... - Validation of an LC-MS based approach for profiling histones in chronic lymphocytic leukemiaXiaodan Su
Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA
Proteomics 9:1197-206. 2009..Protein identities were determined using high mass accuracy MS and shotgun proteomics... - Controlled photochemical release of nitric oxide from O2-substituted diazeniumdiolatesChristopher M Pavlos
Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
Free Radic Biol Med 37:745-52. 2004..In addition, the photochemistry of diazeniumdiolate salts themselves is covered... - Automated acquisition of disease drug knowledge from biomedical and clinical documents: an initial studyElizabeth S Chen
Clinical Informatics Research and Development, Partners HealthCare System, 93 Worcester Street, PO Box 81902, Wellesley, MA 02481, USA
J Am Med Inform Assoc 15:87-98. 2008..Explore the automated acquisition of knowledge in biomedical and clinical documents using text mining and statistical techniques to identify disease-drug associations... - Gene symbol disambiguation using knowledge-based profilesHua Xu
Department of Biomedical Informatics, Columbia University, New York City, New York, USA
Bioinformatics 23:1015-22. 2007..Existing knowledge sources, such as Entrez Gene and the MEDLINE database, contain information concerning the characteristics of a particular gene that could be used to disambiguate gene symbols... - Natural language processing and visualization in the molecular imaging domainP Karina Tulipano
Department of Biomedical Informatics, Columbia University, 622 West 168th Street, Vanderbilt Clinic Floor 5, NY 10032, USA
J Biomed Inform 40:270-81. 2007..74 (95% CI: [.70-.76]) and 0.70 (95% CI [.63-.76]), respectively. We adapt a JAVA viewer known as PGviewer for the simultaneous visualization of images with NLP extracted information... - Machine learning and word sense disambiguation in the biomedical domain: design and evaluation issuesHua Xu
Department of Biomedical Informatics, Columbia University, 622 168th St, New York City, New York, USA
BMC Bioinformatics 7:334. 2006..Thus, there is a need to explicitly address the factors and to systematically quantify their effects on performance...