Ying Xu
Affiliations:- Jilin University, College of Computer Science and Technology, China
- University of Georgia, Department of Biochemistry and Molecular Biology, Athens, GA, USA (2004 - 2011)
- Oak Ridge National Laboratory, Life Sciences Division, Computational Biosciences Section, TN, USA (1993 - 2003)
- Colorado School of Mines, Mathematics and Computer Sciences Department, Golden, CO, USA (1991 - 1993)
- University of Colorado, Computer Science Department, Boulder, CO, USA (1986 - 1991)
According to our database1,
Ying Xu
authored at least 121 papers
between 1989 and 2022.
Collaborative distances:
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Bibliography
2022
IEEE Trans. Ind. Electron., 2022
Spatial-Temporal Relationship Study between NWP PWV and Precipitation: A Case Study of 'July 20' Heavy Rainstorm in Zhengzhou.
Remote. Sens., 2022
2020
Corrections to "IsoTree: A New Framework for de novo Transcriptome Assembly from RNA-seq Reads".
IEEE ACM Trans. Comput. Biol. Bioinform., 2020
IEEE ACM Trans. Comput. Biol. Bioinform., 2020
Identification of Cancer Development Related Pathways Based on Co-Expression Analyses.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2020
2019
A Stable Autoregressive Moving Average Hysteresis Model in Flexure Fast Tool Servo Control.
IEEE Trans Autom. Sci. Eng., 2019
Warburg Effects in Cancer and Normal Proliferating Cells: Two Tales of the Same Name.
Genom. Proteom. Bioinform., 2019
Structural and functional analyses of microbial metabolic networks reveal novel insights into genome-scale metabolic fluxes.
Briefings Bioinform., 2019
Briefings Bioinform., 2019
Proceedings of the Third International Symposium on Image Computing and Digital Medicine, 2019
Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019
2018
High Dynamic Control of a Flexure Fast Tool Servo Using On-line Sequential Extreme Learning Machine.
Proceedings of the 2018 IEEE/ASME International Conference on Advanced Intelligent Mechatronics, 2018
2017
Transcription regulation by DNA methylation under stressful conditions in human cancer.
Quant. Biol., 2017
2016
Proceedings of the Advanced Data Mining and Applications - 12th International Conference, 2016
2015
Computer, 2015
Revisiting operons: an analysis of the landscape of transcriptional units in E. coli.
BMC Bioinform., 2015
2014
Population dynamics inside cancer biomass driven by repeated hypoxia-reoxygenation cycles.
Quant. Biol., 2014
DOOR 2.0: presenting operons and their functions through dynamic and integrated views.
Nucleic Acids Res., 2014
Nucleic Acids Res., 2014
J. Bioinform. Comput. Biol., 2014
Reconsideration of <i>in silico</i> siRNA design from a perspective of heterogeneous data integration: problems and solutions.
Briefings Bioinform., 2014
2013
IEEE ACM Trans. Comput. Biol. Bioinform., 2013
Global Genomic Arrangement of Bacterial Genes Is Closely Tied with the Total Transcriptional Efficiency.
Genom. Proteom. Bioinform., 2013
An integrated toolkit for accurate prediction and analysis of <i>cis-</i>regulatory motifs at a genome scale.
Bioinform., 2013
Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013
2012
Nucleic Acids Res., 2012
BMC Bioinform., 2012
2011
BMC Bioinform., 2011
2010
IEEE ACM Trans. Comput. Biol. Bioinform., 2010
J. Bioinform. Comput. Biol., 2010
<i>In-silico </i>prediction of blood-secretory human proteins using a ranking algorithm.
BMC Bioinform., 2010
cBar: a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data.
Bioinform., 2010
2009
Parallel Clustering Algorithm for Large Data Sets with Applications in Bioinformatics.
IEEE ACM Trans. Comput. Biol. Bioinform., 2009
ACM Trans. Algorithms, 2009
J. Comput. Sci. Technol., 2009
J. Bioinform. Comput. Biol., 2009
Genom. Proteom. Bioinform., 2009
BMC Bioinform., 2009
<i>De novo</i> computational prediction of non-coding RNA genes in prokaryotic genomes.
Bioinform., 2009
Proceedings of the 2nd International Conference on BioMedical Engineering and Informatics, 2009
2008
RNACluster: An integrated tool for RNA secondary structure comparison and clustering.
J. Comput. Chem., 2008
Improving the Performance of protein Threading Using Insertion/Deletion Frequency Arrays.
J. Bioinform. Comput. Biol., 2008
Comput. Biol. Chem., 2008
Computational prediction of human proteins that can be secreted into the bloodstream.
Bioinform., 2008
Proceedings of the Bioinformatics Research and Applications, 2008
2007
Prediction of <i>cis</i>-Regulatory Elements: from High-Information Content Analysis to Motif Identification.
J. Bioinform. Comput. Biol., 2007
Algorithmica, 2007
Proceedings of the Bioinformatics Research and Applications, Third International Symposium, 2007
2006
Mapping of orthologous genes in the context of biological pathways: An application of integer programming.
Proc. Natl. Acad. Sci. USA, 2006
Gene Expression Data Analysis in Subtypes of Ovarian Cancer Using Covariance Analysis.
J. Bioinform. Comput. Biol., 2006
CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy (CSS).
Bioinform., 2006
Proceedings of the Biocomputing 2006, 2006
Proceedings of the Biocomputing 2006, 2006
Peptide sequence tag-based blind identification of post-translational modifications with point process model.
Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006
Proceedings of the Computational Science, 2006
Understanding microbial genomic structures and applications to biological pathway inference.
Proceedings of the 2006 IEEE International Conference on Granular Computing, 2006
2005
PRIME: A Mass Spectrum Data Mining Tool for <i>De Nova</i> Sequencing and PTMs Identification.
J. Comput. Sci. Technol., 2005
J. Comput. Biol., 2005
The Probability Distribution for a Random Match between an Experimental-theoretical Spectral Pair in Tandem Mass Spectrometry.
J. Bioinform. Comput. Biol., 2005
A graph-theoretic approach for the separation of b and y ions in tandem mass spectra.
Bioinform., 2005
Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference, 2005
Structural genomics analysis of alternative splicing and its application in modeling structures of alternatively spliced variants.
Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference Workshops & Poster Abstracts, 2005
PROMOCO: a New Program for Prediction of cis Regulatory Elements: From High-Information Content Analysis to Clique Identification.
Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference Workshops & Poster Abstracts, 2005
Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference Workshops & Poster Abstracts, 2005
Computational Reconstruction of the carbon fixation pathway in Synechococcus SP. Wh 8102.
Proceedings of the Advances in Bioinformatics and Its Applications, 2005
2004
Nucleic Acids Res., 2004
Protein Threading by Linear Programming: Theoretical Analysis and Computational Results.
J. Comb. Optim., 2004
Proceedings of the Biocomputing 2004, 2004
Separation of Ion Types in Tandem Mass Spectrometry Data Interpretation - A Graph-Theoretic Approach.
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004
Structural Analysis of FGFR1 Kinase Activation through Molecular Dynamics Simulation.
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004
Computational Construction of Nitrogen Assimilation Pathway in Cyanobacteria Synechococcus sp. WH8102.
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004
Molecular Modeling of Full-Length OxyR from Shewanella oneidensis MR-1 and Molecular Dynamics Studies of the Activation Domain.
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004
Computational Inference of Transcription Regulation and Response Networks in Synechococcus sp. WH8102.
Proceedings of the 4th IEEE International Symposium on BioInformatics and BioEngineering (BIBE 2004), 2004
2003
J. Bioinform. Comput. Biol., 2003
J. Bioinform. Comput. Biol., 2003
Computational Assignment of Protein Backbone Nmr Peaks Byefficient Bounding and Filtering.
J. Bioinform. Comput. Biol., 2003
A computational pipeline for protein structure prediction and analysis at genome scale.
Bioinform., 2003
Proceedings of the 8th Pacific Symposium on Biocomputing, 2003
Proceedings of the 8th Pacific Symposium on Biocomputing, 2003
Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003
A Computational Method for Assessing Peptide-Identification Reliability in Tandem Mass Spectrometry Analysis with SEQUEST.
Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003
Towards Automated Derivation of Biological Pathways Using High-Throughput Biological Data.
Proceedings of the 3rd IEEE International Symposium on BioInformatics and BioEngineering (BIBE 2003), 2003
2002
Comput. Sci. Eng., 2002
Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees.
Bioinform., 2002
PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis.
Bioinform., 2002
Proceedings of the Algorithms in Bioinformatics, Second International Workshop, 2002
An Efficient Branch-and-Bound Algorithm for the Assignment of Protein Backbone NMR Peaks.
Proceedings of the 1st IEEE Computer Society Bioinformatics Conference, 2002
2000
Sequence-structure specificity of a knowledge based energy function at the secondary structure level.
Bioinform., 2000
Protein structure determination using protein threading and sparse NMR data (extended abstract).
Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, 2000
1998
Pattern Recognit. Lett., 1998
J. Comput. Biol., 1998
A new method for modeling and solving the protein fold recognition problem (extended abstract).
Proceedings of the Second Annual International Conference on Research in Computational Molecular Biology, 1998
1997
J. Comput. Biol., 1997
Proceedings of the First Annual International Conference on Research in Computational Molecular Biology, 1997
Inferring Gene Structures in Genomic Sequences Using Pattern Recognition and Expressed Sequence Tags.
Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997
1996
Efficient Theoretic and Practical Algorithms for Linear Matroid Intersection Problems.
J. Comput. Syst. Sci., 1996
J. Comput. Biol., 1996
Detection of RNA Polymerase II Promoters and Polyadenylation Sites in Human DNA Sequence.
Comput. Chem., 1996
Comput. Appl. Biosci., 1996
Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology, 1996
1995
Correcting sequencing errors in DNA coding regions using a dynamic programming approach.
Comput. Appl. Biosci., 1995
1994
Constructing gene models from accurately predicted exons: an application of dynamic programming.
Comput. Appl. Biosci., 1994
Proceedings of the Algorithms and Computation, 5th International Symposium, 1994
1989
Proceedings of the 30th Annual Symposium on Foundations of Computer Science, Research Triangle Park, North Carolina, USA, 30 October, 1989