Xiaowen Liu
Department of BioHealth Informatics
Indiana University-Purdue University Indianapolis
Xiaowen Liu is an associate professor of bioinformatics in the Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis (IUPUI). He received his bachelor’s and master’s degrees in computer science from Shandong University, China and obtained his PhD degree in computer science from the City University of Hong Kong. Before joining IUPUI, he worked as a postdoctoral fellow at the University of Western Ontario, the University of Waterloo, and the University of California, San Diego, from 2008 to 2012. His research focuses on computational proteomics, especially top-down proteomics, which is capable of identifying various proteoforms in biological samples. His lab has developed powerful software tools for top-down mass spectrometry-based proteoform identification, characterization, and quantitation, which have been widely used in the proteomics community.
Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typhimurium in response to infection-like conditions.
Proceedings of the National Academy of Sciences of the United States of America Jun, 2013 | Pubmed ID: 23720318
Identification of ultramodified proteins using top-down tandem mass spectra.
Journal of proteome research Dec, 2013 | Pubmed ID: 24188097
Spectral probabilities of top-down tandem mass spectra.
BMC genomics , 2014 | Pubmed ID: 24564718
De novo protein sequencing by combining top-down and bottom-up tandem mass spectra.
Journal of proteome research Jul, 2014 | Pubmed ID: 24874765
Top-down proteomics reveals concerted reductions in myofilament and Z-disc protein phosphorylation after acute myocardial infarction.
Molecular & cellular proteomics : MCP Oct, 2014 | Pubmed ID: 24969035
An efficient algorithm for the blocked pattern matching problem.
Bioinformatics (Oxford, England) Feb, 2015 | Pubmed ID: 25322837
A new scoring function for top-down spectral deconvolution.
BMC genomics Dec, 2014 | Pubmed ID: 25523396
De Novo Sequencing of Peptides from Top-Down Tandem Mass Spectra.
Journal of proteome research Nov, 2015 | Pubmed ID: 26412692
Identification of Glycopeptides with Multiple Hydroxylysine O-Glycosylation Sites by Tandem Mass Spectrometry.
Journal of proteome research Dec, 2015 | Pubmed ID: 26565680
MASH Suite Pro: A Comprehensive Software Tool for Top-Down Proteomics.
Molecular & cellular proteomics : MCP Feb, 2016 | Pubmed ID: 26598644
Top-down analysis of protein samples by de novo sequencing techniques.
Bioinformatics (Oxford, England) 09, 2016 | Pubmed ID: 27187201
Characterization of Proteoforms with Unknown Post-translational Modifications Using the MIScore.
Journal of proteome research 08, 2016 | Pubmed ID: 27291504
TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization.
Bioinformatics (Oxford, England) 11, 2016 | Pubmed ID: 27423895
Filling a Protein Scaffold With a Reference.
IEEE transactions on nanobioscience 03, 2017 | Pubmed ID: 28207401
Top-down analysis of immunoglobulin G isotypes 1 and 2 with electron transfer dissociation on a high-field Orbitrap mass spectrometer.
Journal of proteomics 04, 2017 | Pubmed ID: 28242452
A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra.
Bioinformatics (Oxford, England) 05, 2017 | Pubmed ID: 28453668
Single-Shot Top-Down Proteomics with Capillary Zone Electrophoresis-Electrospray Ionization-Tandem Mass Spectrometry for Identification of Nearly 600 Escherichia coli Proteoforms.
Analytical chemistry Nov, 2017 | Pubmed ID: 29064224
De Novo Sequencing of Peptides from High-Resolution Bottom-Up Tandem Mass Spectra using Top-Down Intended Methods.
Proteomics Dec, 2017 | Pubmed ID: 29110399
Systematic Evaluation of Protein Sequence Filtering Algorithms for Proteoform Identification Using Top-Down Mass Spectrometry.
Proteomics Feb, 2018 | Pubmed ID: 29327814
A Spectrum Graph-Based Protein Sequence Filtering Algorithm for Proteoform Identification by Top-Down Mass Spectrometry.
Proceedings. IEEE International Conference on Bioinformatics and Biomedicine Nov, 2017 | Pubmed ID: 29503761
Deep Top-Down Proteomics Using Capillary Zone Electrophoresis-Tandem Mass Spectrometry: Identification of 5700 Proteoforms from the Escherichia coli Proteome.
Analytical chemistry May, 2018 | Pubmed ID: 29620868
Native Proteomics in Discovery Mode Using Size-Exclusion Chromatography-Capillary Zone Electrophoresis-Tandem Mass Spectrometry.
Analytical chemistry Sep, 2018 | Pubmed ID: 30085653
A graph-based approach for proteoform identification and quantification using top-down homogeneous multiplexed tandem mass spectra.
BMC bioinformatics Aug, 2018 | Pubmed ID: 30367573
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