Ying Xu

ORCID

Publication Activity (10 Years)

Years Active: 1989-2023
Publications (10 Years): 15

Top Venues

IEEE ACM Trans. Comput. Biol. Bioinform.

Briefings Bioinform.

Genom. Proteom. Bioinform.

Nucleic Acids Res.

Publications

Yi Zhou, Wennan Chang, Xiaoyu Lu, Jin Wang, Chi Zhang, Ying Xu
Acid-Base Homeostasis and Implications to the Phenotypic Behaviors of Cancer. Genom. Proteom. Bioinform. 21 (6) (2023)
Renbo Tan, Yi Zhou, Zheng An, Ying Xu
Cancer is a Survival Process under Persistent Microenvironmental and Cellular Stresses. Genom. Proteom. Bioinform. 21 (6) (2023)
Sifeng He, Hui Tang, Zhongyuan Zhu, Peiyuan Zhang, Ying Xu, Xin Chen
A Novel Flexure Piezomotor With Minimized Backward and Nonlinear Motion Effect. IEEE Trans. Ind. Electron. 69 (1) (2022)
Ying Xu, Xin Chen, Min Liu, Jin Wang, Fangzhao Zhang, Jianhui Cui, Hongzhan Zhou
Spatial-Temporal Relationship Study between NWP PWV and Precipitation: A Case Study of 'July 20' Heavy Rainstorm in Zhengzhou. Remote. Sens. 14 (15) (2022)
Jin Zhao, Haodi Feng, Daming Zhu, Chi Zhang, Ying Xu
Corrections to "IsoTree: A New Framework for de novo Transcriptome Assembly from RNA-seq Reads". IEEE ACM Trans. Comput. Biol. Bioinform. 17 (6) (2020)
Hongyang Jiang, Zhihang Wang, Chaoyi Yin, Peishuo Sun, Ying Xu, Huiyan Sun
Identification of Cancer Development Related Pathways Based on Co-Expression Analyses. BIBM (2020)
Jin Zhao, Haodi Feng, Daming Zhu, Chi Zhang, Ying Xu
IsoTree: A New Framework for de novo Transcriptome Assembly from RNA-seq Reads. IEEE ACM Trans. Comput. Biol. Bioinform. 17 (3) (2020)
Mengfei Li, Ying Xu, Hongwei Li
Modified Edge-Weighted Centroidal Voronoi Tessellation for Image Segmentation. ISICDM (2019)
Huansheng Cao, Qin Ma, Xin Chen, Ying Xu
DOOR: a prokaryotic operon database for genome analyses and functional inference. Briefings Bioinform. 20 (4) (2019)
Gaoyang Li, Huansheng Cao, Ying Xu
Structural and functional analyses of microbial metabolic networks reveal novel insights into genome-scale metabolic fluxes. Briefings Bioinform. 20 (4) (2019)
Jiedong Li, Hui Tang, Zelong Wu, Hongcheng Li, Guixin Zhang, Xin Chen, Jian Gao, Ying Xu, Yunbo He
A Stable Autoregressive Moving Average Hysteresis Model in Flexure Fast Tool Servo Control. IEEE Trans Autom. Sci. Eng. 16 (3) (2019)
Huiyan Sun, Liang Chen, Sha Cao, Yanchun Liang, Ying Xu
Warburg Effects in Cancer and Normal Proliferating Cells: Two Tales of the Same Name. Genom. Proteom. Bioinform. 17 (3) (2019)
Zelong Wu, Hui Tang, Xin Chen, Jian Gao, Yunbo He, Ying Xu, Xun Chen, Suet To, Yangmin Li, Chengqiang Cui
High Dynamic Control of a Flexure Fast Tool Servo Using On-line Sequential Extreme Learning Machine. AIM (2018)
Sha Cao, Yi Zhou, Yue Wu, Tianci Song, Burair Alsaihati, Ying Xu
Transcription regulation by DNA methylation under stressful conditions in human cancer. Quant. Biol. 5 (4) (2017)
Yan Wang, Wei Du, Yanchun Liang, Xin Chen, Chi Zhang, Wei Pang, Ying Xu
PUEPro: A Computational Pipeline for Prediction of Urine Excretory Proteins. ADMA (2016)
Ying Xu
Editorial from the Editor-in-Chief. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (1) (2015)
Xizeng Mao, Qin Ma, Bingqiang Liu, Xin Chen, Hanyuan Zhang, Ying Xu
Revisiting operons: an analysis of the landscape of transcriptional units in E. coli. BMC Bioinform. 16 (2015)
Ying Xu
Carrying out Phylogenetic Analyses through Computational Model Checking. Computer 48 (1) (2015)
Xizeng Mao, Qin Ma, Chuan Zhou, Xin Chen, Hanyuan Zhang, Jincai Yang, Fenglou Mao, Wei Lai, Ying Xu
DOOR 2.0: presenting operons and their functions through dynamic and integrated views. Nucleic Acids Res. 42 (Database-Issue) (2014)
Ying Xu
Editorial from the Editor-in-Chief. IEEE ACM Trans. Comput. Biol. Bioinform. 11 (1) (2014)
Ying Xu
Reviewer Appreciation Editorial. IEEE ACM Trans. Comput. Biol. Bioinform. 11 (4) (2014)
Dorothy A. Hammond, Victor Olman, Ying Xu
Functional Understanding of the Diverse exon-intron Structures of Human GPCR genes. J. Bioinform. Comput. Biol. 12 (1) (2014)
Qi Liu, Han Zhou, Ruixin Zhu, Ying Xu, Zhiwei Cao
siRNA design from a perspective of heterogeneous data integration: problems and solutions. Briefings Bioinform. 15 (2) (2014)
Chi Zhang, Sha Cao, Ying Xu
Population dynamics inside cancer biomass driven by repeated hypoxia-reoxygenation cycles. Quant. Biol. 2 (3) (2014)
Qin Ma, Hanyuan Zhang, Xizeng Mao, Chuan Zhou, Bingqiang Liu, Xin Chen, Ying Xu
DMINDA: an integrated web server for DNA motif identification and analyses. Nucleic Acids Res. 42 (Webserver-Issue) (2014)
Qin Ma, Ying Xu
Global Genomic Arrangement of Bacterial Genes Is Closely Tied with the Total Transcriptional Efficiency. Genom. Proteom. Bioinform. 11 (1) (2013)
Ying Xu
Editorial from the New Editor-in-Chief. IEEE ACM Trans. Comput. Biol. Bioinform. 10 (1) (2013)
Qin Ma, Bingqiang Liu, Chuan Zhou, Yanbin Yin, Guojun Li, Ying Xu
regulatory motifs at a genome scale. Bioinform. 29 (18) (2013)
Ying Xu
Elucidation of drivers for cancer initiation and metastasis: A data-mining approach. BIBM (2013)
Fenglou Mao, David Williams, Olga Zhaxybayeva, Maria S. Poptsova, Pascal Lapierre, J. Peter Gogarten, Ying Xu
Quartet decomposition server: a platform for analyzing phylogenetic trees. BMC Bioinform. 13 (2012)
Yanbin Yin, Xizeng Mao, Jincai Yang, Xin Chen, Fenglou Mao, Ying Xu
dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 40 (Web-Server-Issue) (2012)
Yong Chen, Fenglou Mao, Guojun Li, Ying Xu
Genome-wide discovery of missing genes in biological pathways of prokaryotes. BMC Bioinform. 12 (S-1) (2011)
Xingqin Qi, Guojun Li, Shuguang Li, Ying Xu
Sorting Genomes by Reciprocal Translocations, Insertions, and Deletions. IEEE ACM Trans. Comput. Biol. Bioinform. 7 (2) (2010)
Ying Xu, Peter W. Markstein
Foreword: Advances in Computational Systems Bioinformatics. J. Bioinform. Comput. Biol. 8 (2) (2010)
Fengfeng Zhou, Ying Xu
cBar: a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data. Bioinform. 26 (16) (2010)
Qi Liu, Juan Cui, Qiang Yang, Ying Xu
prediction of blood-secretory human proteins using a ranking algorithm. BMC Bioinform. 11 (2010)
Guojun Li, Xiaotie Deng, Ying Xu
A polynomial-time approximation scheme for embedding hypergraph in a cycle. ACM Trans. Algorithms 5 (2) (2009)
Qi Liu, Jinling Huang, Huiqing Liu, Ping Wan, Xiuzi Ye, Ying Xu
Analyses of domains and domain fusions in human proto-oncogenes. BMC Bioinform. 10 (2009)
Guojun Li, Dongsheng Che, Ying Xu
A Universal operon Predictor for prokaryotic genomes. J. Bioinform. Comput. Biol. 7 (1) (2009)
Fengfeng Zhou, Victor Olman, Ying Xu
Large-Scale Analyses of Glycosylation in Cellulases. Genom. Proteom. Bioinform. 7 (4) (2009)
Mi-Chia Ma, Hsiao-Fang Lin, Ying Xu
Detect the Different Isoforms Using GeneChip Human Exon 1.0 ST Arrays. BMEI (2009)
Victor Olman, Fenglou Mao, Hongwei Wu, Ying Xu
Parallel Clustering Algorithm for Large Data Sets with Applications in Bioinformatics. IEEE ACM Trans. Comput. Biol. Bioinform. 6 (2) (2009)
Ying Xu, Ming Li, Tao Jiang
Preface. J. Comput. Sci. Technol. 25 (1) (2009)
Fenglou Mao, PhuongAn Dam, Jacky Chou, Victor Olman, Ying Xu
DOOR: a database for prokaryotic operons. Nucleic Acids Res. 37 (Database-Issue) (2009)
Ying Xu
Computational Challenges in Deciphering Genomic Structures of Bacteria. J. Comput. Sci. Technol. 25 (1) (2009)
Thao T. Tran, Fengfeng Zhou, Sarah Marshburn, Mark Stead, Sidney R. Kushner, Ying Xu
computational prediction of non-coding RNA genes in prokaryotic genomes. Bioinform. 25 (22) (2009)
Fengfeng Zhou, Victor Olman, Ying Xu
Barcodes for genomes and applications. BMC Bioinform. 9 (2008)
Qi Liu, Victor Olman, Huiqing Liu, Xiuzi Ye, Shilun Qiu, Ying Xu
RNACluster: An integrated tool for RNA secondary structure comparison and clustering. J. Comput. Chem. 29 (9) (2008)
Hongwei Wu, Fenglou Mao, Victor Olman, Ying Xu
On application of directons to functional classification of genes in prokaryotes. Comput. Biol. Chem. 32 (3) (2008)
Guojun Li, Zhijie Liu, Jun-tao Guo, Ying Xu
An Algorithm for Simultaneous Backbone Threading and Side-Chain Packing. Algorithmica 51 (4) (2008)
Dongsheng Che, Guojun Li, Shane T. Jensen, Jun S. Liu, Ying Xu
PFP: A Computational Framework for Phylogenetic Footprinting in Prokaryotic Genomes. ISBRA (2008)
Kyle Ellrott, Jun-tao Guo, Victor Olman, Ying Xu
Improving the Performance of protein Threading Using Insertion/Deletion Frequency Arrays. J. Bioinform. Comput. Biol. 6 (3) (2008)
Juan Cui, Qi Liu, David Puett, Ying Xu
Computational prediction of human proteins that can be secreted into the bloodstream. Bioinform. 24 (20) (2008)
Guojun Li, Zhijie Liu, Jun-tao Guo, Ying Xu
An Algorithm for Simultaneous Backbone Threading and Side-Chain Packing. Algorithmica 48 (4) (2007)
Hongwei Wu, Fenglou Mao, Victor Olman, Ying Xu
An Algorithm for Hierarchical Classification of Genes of Prokaryotic Genomes. ISBRA (2007)
Guojun Li, Jizhu Lu, Victor Olman, Ying Xu
-Regulatory Elements: from High-Information Content Analysis to Motif Identification. J. Bioinform. Comput. Biol. 5 (4) (2007)
Chunmei Liu, Yinglei Song, Bo Yan, Ying Xu, Liming Cai
Fast De novo Peptide Sequencing and Spectral Alignment via Tree Decomposition. Pacific Symposium on Biocomputing (2006)
Robin Kramer, Victor Olman, Ying Xu, Dong Xu
DigitalTree: A Tool for Displaying Biological Data in Tree Structure. International Conference on Computational Science (2) (2006)
Chunmei Liu, Bo Yan, Yinglei Song, Ying Xu, Liming Cai
Peptide sequence tag-based blind identification of post-translational modifications with point process model. ISMB (Supplement of Bioinformatics) (2006)
Yu Xue, Fengfeng Zhou, Chuanhai Fu, Ying Xu, Xuebiao Yao
SUMOsp: a web server for sumoylation site prediction. Nucleic Acids Res. 34 (Web-Server-Issue) (2006)
Bo Yan, G. Tong Zhou, Peng Wang, Zhijie Liu, Vincent A. Emanuele II, Victor Olman, Ying Xu
A Point-Process Model for Rapid Identification of Post-Translational Modifications. Pacific Symposium on Biocomputing (2006)
Zhengchang Su, Fenglou Mao, Hongwei Wu, PhuongAn Dam, Xin Chen, Tao Jiang, Victor Olman, Brian Palenik, Ying Xu
Understanding microbial genomic structures and applications to biological pathway inference. GrC (2006)
Fengfeng Zhou, Yu Xue, Xuebiao Yao, Ying Xu
CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy (CSS). Bioinform. 22 (7) (2006)
Victor Olman, Chindo Hicks, Peng Wang, Ying Xu
Gene Expression Data Analysis in Subtypes of Ovarian Cancer Using Covariance Analysis. J. Bioinform. Comput. Biol. 4 (5) (2006)
Fenglou Mao, Zhengchang Su, Victor Olman, PhuongAn Dam, Zhijie Liu, Ying Xu
Mapping of orthologous genes in the context of biological pathways: An application of integer programming. Proc. Natl. Acad. Sci. USA 103 (1) (2006)
Guojun Li, Ying Xu, Chuanping Chen, Zhenhong Liu
+1]-Factors in Graphs. Comb. 25 (4) (2005)
Zhi-Zhong Chen, Guohui Lin, Romeo Rizzi, Jianjun Wen, Dong Xu, Ying Xu, Tao Jiang
More Reliable Protein NMR Peak Assignment via Improved 2-Interval Scheduling. J. Comput. Biol. 12 (2) (2005)
Guojun Li, Jizhu Lu, Victor Olman, Ying Xu
PROMOCO: a New Program for Prediction of cis Regulatory Elements: From High-Information Content Analysis to Clique Identification. CSB Workshops (2005)
Hongwei Wu, Fenglou Mao, Victor Olman, Ying Xu
Accurate Prediction of Orthologous Gene Groups in Microbes. CSB (2005)
Bo Yan, Chongle Pan, Victor Olman, Robert L. Hettich, Ying Xu
A graph-theoretic approach for the separation of b and y ions in tandem mass spectra. Bioinform. 21 (5) (2005)
Tema Fridman, Jane Razumovskaya, Nathan Verberkmoes, Gregory B. Hurst, Vladimir Protopopescu, Ying Xu
The Probability Distribution for a Random Match between an Experimental-theoretical Spectral Pair in Tandem Mass Spectrometry. J. Bioinform. Comput. Biol. 3 (2) (2005)
PhuongAn Dam, Victor Olman, Ying Xu
Improving Operon Prediction in E. coli. CSB Workshops (2005)
Peng Wang, Bo Yan, Jun-tao Guo, Chindo Hicks, Ying Xu
Structural genomics analysis of alternative splicing and its application in modeling structures of alternatively spliced variants. CSB Workshops (2005)
Bo Yan, Youxing Qu, Fenglou Mao, Victor Olman, Ying Xu
Sequencing and PTMs Identification. J. Comput. Sci. Technol. 20 (4) (2005)
Jun-tao Guo, Ying Xu
Molecular Modeling of Full-Length OxyR from Shewanella oneidensis MR-1 and Molecular Dynamics Studies of the Activation Domain. CSB (2004)
Fenglou Mao, Zhengchang Su, Victor Olman, David Chuang, Ying Xu
Pathway Mapping with Operon Information: An Integer-Programming Method. CSB (2004)
Victor Olman, Jizhu Lu, PhuongAn Dam, Zhengchang Su, Ying Xu
CUBIC: Search for Binding Sites. CSB (2004)
Peng Wang, Zhengchang Su, Jun-tao Guo, Ying Xu
Structural Analysis of FGFR1 Kinase Activation through Molecular Dynamics Simulation. CSB (2004)
Zhengchang Su, PhuongAn Dam, X. Chen, Victor Olman, Tao Jiang, Ying Xu
Computational Construction of Nitrogen Assimilation Pathway in Cyanobacteria Synechococcus sp. WH8102. CSB (2004)
Jun-tao Guo, Kyle Ellrott, Won Jae Chung, Dong Xu, Sergei Passovets, Ying Xu
PROSPECT-PSPP: an automatic computational pipeline for protein structure prediction. Nucleic Acids Res. 32 (Web-Server-Issue) (2004)
Zhengchang Su, PhuongAn Dam, Victor Olman, Ying Xu
Computational Inference of Transcription Regulation and Response Networks in Synechococcus sp. WH8102. BIBE (2004)
PhuongAn Dam, Zhengchang Su, Victor Olman, Ying Xu
In Silico Construction of the Carbon Fixation Pathway in Synechococcus sp. WH8102. CSB (2004)
Victor Olman, Hanchuan Peng, Zhengchang Su, Ying Xu
Mapping of Microbial Pathways through Constrained Mapping of Orthologous Genes. CSB (2004)
Peng Wang, Zhengchang Su, PhuongAn Dam, Ying Xu
A Knowledge Base for Computational Pathway Reconstruction. CSB (2004)
Bo Yan, Chongle Pan, Victor Olman, Robert L. Hettich, Ying Xu
Separation of Ion Types in Tandem Mass Spectrometry Data Interpretation - A Graph-Theoretic Approach. CSB (2004)
Jinbo Xu, Ming Li, Ying Xu
Protein Threading by Linear Programming: Theoretical Analysis and Computational Results. J. Comb. Optim. 8 (4) (2004)
Youxing Qu, Jun-tao Guo, Victor Olman, Ying Xu
Protein Fold Recognition Through Application of Residual Dipolar Coupling Data. Pacific Symposium on Biocomputing (2004)
Jane Razumovskaya, Victor Olman, Dong Xu, Edward C. Uberbacher, Nathan Verberkmoes, Ying Xu
A Computational Method for Assessing Peptide-Identification Reliability in Tandem Mass Spectrometry Analysis with SEQUEST. CSB (2003)
Zhengchang Su, PhuongAn Dam, Xin Chen, Victor Olman, Tao Jiang, Brian Palenik, Ying Xu
Computational Inference of Regulatory Pathways in Microbes. CSB (2003)
Victor Olman, Dong Xu, Ying Xu
Identification of Regulatory Binding Sites Using Minimum Spanning Trees. Pacific Symposium on Biocomputing (2003)
Zhi-Zhong Chen, Tao Jiang, Guo-Hui Lin, Jianjun Wen, Dong Xu, Jinbo Xu, Ying Xu
Approximation algorithms for NMR spectral peak assignment. Theor. Comput. Sci. 299 (1-3) (2003)
Jinbo Xu, Ming Li, Dongsup Kim, Ying Xu
Raptor: Optimal Protein Threading by Linear Programming. J. Bioinform. Comput. Biol. 1 (1) (2003)
Zhi-Zhong Chen, Tao Jiang, Guohui Lin, Romeo Rizzi, Jianjun Wen, Dong Xu, Ying Xu
More Reliable Protein NMR Peak Assignment via Improved 2-Interval Scheduling. ESA (2003)
Manesh J. Shah, Sergei Passovets, Dongsup Kim, Kyle Ellrott, Li Wang, Inna Vokler, Philip F. LoCascio, Dong Xu, Ying Xu
A Computational Pipeline for Protein Structure Prediction and Analysis at Genome Scale. BIBE (2003)
Jinbo Xu, Ming Li, Guo-Hui Lin, Dongsup Kim, Ying Xu
Protein Threading by Linear Programming. Pacific Symposium on Biocomputing (2003)
Victor Olman, Dong Xu, Ying Xu
Cubic: Identification of Regulatory Binding Sites through Data Clustering. J. Bioinform. Comput. Biol. 1 (1) (2003)
Yu Chen, Trupti Joshi, Ying Xu, Dong Xu
Towards Automated Derivation of Biological Pathways Using High-Throughput Biological Data. BIBE (2003)
Victor Olman, Dong Xu, Ying Xu
CUBIC: Identification of Regulatory Binding Sites Through Data Clustering. CSB (2003)
Manesh J. Shah, Sergei Passovets, Dongsup Kim, Kyle Ellrott, Li Wang, Inna Vokler, Philip F. LoCascio, Dong Xu, Ying Xu
A computational pipeline for protein structure prediction and analysis at genome scale. Bioinform. 19 (15) (2003)
Guohui Lin, Dong Xu, Zhi-Zhong Chen, Tao Jiang, Jianjun Wen, Ying Xu
Computational Assignment of Protein Backbone Nmr Peaks Byefficient Bounding and Filtering. J. Bioinform. Comput. Biol. 1 (2) (2003)

Ying Xu.css-eqlu8i{font-size:small;padding-left:4px;}

Publication Activity (10 Years)

Top Topics

Top Venues

Ying Xu