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ORCIDYing Xu 0001
Person information
- affiliation: Jilin University, College of Computer Science and Technology, China
- affiliation (2004 - 2011): University of Georgia, Department of Biochemistry and Molecular Biology, Athens, GA, USA
- affiliation (1993 - 2003): Oak Ridge National Laboratory, Life Sciences Division, Computational Biosciences Section, TN, USA
- affiliation (1991 - 1993): Colorado School of Mines, Mathematics and Computer Sciences Department, Golden, CO, USA
- affiliation (1986 - 1991): University of Colorado, Computer Science Department, Boulder, CO, USA
Other persons with the same name
- Ying Xu — disambiguation page
- Ying Xu 0002 — Stanford University, USA
- Ying Xu 0003 — University of Alberta, Alberta Machine Intelligence Institute, Edmonton, AB, Canada
- Ying Xu 0004
![[0000-0001-9586-1716]](https://dblp.uni-trier.de./img/orcid-mark.12x12.png "0000-0001-9586-1716")
— Xi'an Jiaotong University, School of Electronic and Information Engineering, China
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2020 – today
- 2023
[j88]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): 1133-1148 (2023)- [j87]Renbo Tan, Yi Zhou, Zheng An, Ying Xu:
Cancer is a Survival Process under Persistent Microenvironmental and Cellular Stresses. Genom. Proteom. Bioinform. 21(6): 1260-1265 (2023) - [j86]Lai Xiang, Ying Xu, Jianhui Cui, Yang Liu, Ruozhou Wang, Guofeng Li:
GM(1,1)-Based Weighted K-Nearest Neighbor Algorithm for Indoor Localization. Remote. Sens. 15(15): 3706 (2023) - 2022
- [j85]Ying Xu, Guofeng Li, Zeyu Li, Hao Yu, Jianhui Cui, Jin Wang, Yu Chen:
Smartphone-Based Unconstrained Step Detection Fusing a Variable Sliding Window and an Adaptive Threshold. Remote. Sens. 14(12): 2926 (2022) - [j84]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): 3636 (2022) - [j83]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): 652-662 (2022) - 2020
- [j82]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): 938-948 (2020) - [j81]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): 2197 (2020) - [c50]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: 108-114
2010 – 2019
- 2019
- [j80]Huansheng Cao, Qin Ma, Xin Chen, Ying Xu:
DOOR: a prokaryotic operon database for genome analyses and functional inference. Briefings Bioinform. 20(4): 1568-1577 (2019) - [j79]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): 1590-1603 (2019) - [j78]Jin Zhao, Haodi Feng, Daming Zhu, Chi Zhang, Ying Xu:
DTA-SiST: de novo transcriptome assembly by using simplified suffix trees. BMC Bioinform. 20-S(25): 698 (2019) - [j77]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): 273-286 (2019) - [j76]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): 1484-1493 (2019) - [c49]Hongyang Jiang, Qiang Huang, Liang Chen, Zhi Li, Ying Xu, Huiyan Sun, Yi Chang:
Multi-Classification of Cancer Samples Based on Co-Expression Analyses. BIBM 2019: 197-201 - [c48]Mengfei Li, Ying Xu, Hongwei Li:
Modified Edge-Weighted Centroidal Voronoi Tessellation for Image Segmentation. ISICDM 2019: 161-165 - 2018
- [c47]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: 604-609 - [c46]Jin Zhao, Haodi Feng, Daming Zhu, Chi Zhang, Ying Xu:
DTAST: A Novel Radical Framework for de Novo Transcriptome Assembly Based on Suffix Trees. ICIC (1) 2018: 740-745 - 2017
- [j75]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): 328-337 (2017) - [c45]Jin Zhao, Haodi Feng, Daming Zhu, Chi Zhang, Ying Xu:
IsoTree: De Novo Transcriptome Assembly from RNA-Seq Reads - (Extended Abstract). ISBRA 2017: 71-83 - 2016
- [j74]Yinglei Song, Junfeng Qu, Ying Xu, Liming Cai:
A New Graph Theoretic Approach for Protein Threading. Fundam. Informaticae 145(2): 151-170 (2016) - [c44]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: 714-725 - 2015
- [j73]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: 356:1-356:9 (2015) - [j72]Ying Xu:
Carrying out Phylogenetic Analyses through Computational Model Checking. Computer 48(1): 12 (2015) - [j71]Ying Xu:
Editorial from the Editor-in-Chief. IEEE ACM Trans. Comput. Biol. Bioinform. 12(1): 1 (2015) - 2014
- [b1]Ying Xu, Juan Cui, David Puett:
Cancer Bioinformatics. Springer 2014, ISBN 978-1-4939-1380-0, pp. 1-362 - [j70]Qi Liu, Han Zhou, Ruixin Zhu, Ying Xu, Zhiwei Cao:
Reconsideration of in silico siRNA design from a perspective of heterogeneous data integration: problems and solutions. Briefings Bioinform. 15(2): 292-305 (2014) - [j69]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) - [j68]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): 654-659 (2014) - [j67]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): 12-19 (2014) - [j66]Chi Zhang, Sha Cao, Ying Xu:
Population dynamics inside cancer biomass driven by repeated hypoxia-reoxygenation cycles. Quant. Biol. 2(3): 85-99 (2014) - [j65]Ying Xu:
Editorial from the Editor-in-Chief. IEEE ACM Trans. Comput. Biol. Bioinform. 11(1): 1-4 (2014) - [j64]Ying Xu:
Reviewer Appreciation Editorial. IEEE ACM Trans. Comput. Biol. Bioinform. 11(4): 613 (2014) - 2013
- [j63]Qin Ma, Bingqiang Liu, Chuan Zhou, Yanbin Yin, Guojun Li, Ying Xu:
An integrated toolkit for accurate prediction and analysis of cis-regulatory motifs at a genome scale. Bioinform. 29(18): 2261-2268 (2013) - [j62]Qin Ma, Ying Xu:
Global Genomic Arrangement of Bacterial Genes Is Closely Tied with the Total Transcriptional Efficiency. Genom. Proteom. Bioinform. 11(1): 66-71 (2013) - [j61]Ying Xu:
Editorial from the New Editor-in-Chief. IEEE ACM Trans. Comput. Biol. Bioinform. 10(1): 1 (2013) - [c43]Ying Xu:
Elucidation of drivers for cancer initiation and metastasis: A data-mining approach. BIBM 2013: 3 - 2012
- [j60]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: 123 (2012) - [j59]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): 445-451 (2012) - 2011
- [j58]Yong Chen, Fenglou Mao, Guojun Li, Ying Xu:
Genome-wide discovery of missing genes in biological pathways of prokaryotes. BMC Bioinform. 12(S-1): S1 (2011) - 2010
- [j57]Fengfeng Zhou, Ying Xu:
cBar: a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data. Bioinform. 26(16): 2051-2052 (2010) - [j56]Qi Liu, Juan Cui, Qiang Yang, Ying Xu:
In-silico prediction of blood-secretory human proteins using a ranking algorithm. BMC Bioinform. 11: 250 (2010) - [j55]Ying Xu, Peter W. Markstein:
Foreword: Advances in Computational Systems Bioinformatics. J. Bioinform. Comput. Biol. 8(2) (2010) - [j54]Xingqin Qi, Guojun Li, Shuguang Li, Ying Xu:
Sorting Genomes by Reciprocal Translocations, Insertions, and Deletions. IEEE ACM Trans. Comput. Biol. Bioinform. 7(2): 365-374 (2010)
2000 – 2009
- 2009
- [j53]Thao T. Tran, Fengfeng Zhou, Sarah Marshburn, Mark Stead, Sidney R. Kushner, Ying Xu:
De novo computational prediction of non-coding RNA genes in prokaryotic genomes. Bioinform. 25(22): 2897-2905 (2009) - [j52]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) - [j51]Fengfeng Zhou, Victor Olman, Ying Xu:
Large-Scale Analyses of Glycosylation in Cellulases. Genom. Proteom. Bioinform. 7(4): 194-199 (2009) - [j50]Guojun Li, Dongsheng Che, Ying Xu:
A Universal operon Predictor for prokaryotic genomes. J. Bioinform. Comput. Biol. 7(1): 19-38 (2009) - [j49]Ying Xu, Ming Li, Tao Jiang:
Preface. J. Comput. Sci. Technol. 25(1): 1-2 (2009) - [j48]Ying Xu:
Computational Challenges in Deciphering Genomic Structures of Bacteria. J. Comput. Sci. Technol. 25(1): 53-70 (2009) - [j47]Fenglou Mao, PhuongAn Dam, Jacky Chou, Victor Olman, Ying Xu:
DOOR: a database for prokaryotic operons. Nucleic Acids Res. 37(Database-Issue): 459-463 (2009) - [j46]Guojun Li, Xiaotie Deng, Ying Xu:
A polynomial-time approximation scheme for embedding hypergraph in a cycle. ACM Trans. Algorithms 5(2): 20:1-20:12 (2009) - [j45]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): 344-352 (2009) - [c42]Mi-Chia Ma, Hsiao-Fang Lin, Ying Xu:
Detect the Different Isoforms Using GeneChip Human Exon 1.0 ST Arrays. BMEI 2009: 1-5 - 2008
- [j44]Guojun Li, Zhijie Liu, Jun-tao Guo, Ying Xu:
An Algorithm for Simultaneous Backbone Threading and Side-Chain Packing. Algorithmica 51(4): 435-450 (2008) - [j43]Juan Cui, Qi Liu, David Puett, Ying Xu:
Computational prediction of human proteins that can be secreted into the bloodstream. Bioinform. 24(20): 2370-2375 (2008) - [j42]Fengfeng Zhou, Victor Olman, Ying Xu:
Barcodes for genomes and applications. BMC Bioinform. 9 (2008) - [j41]Hongwei Wu, Fenglou Mao, Victor Olman, Ying Xu:
On application of directons to functional classification of genes in prokaryotes. Comput. Biol. Chem. 32(3): 176-184 (2008) - [j40]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): 585-602 (2008) - [j39]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): 1517-1526 (2008) - [c41]Dongsheng Che, Guojun Li, Shane T. Jensen, Jun S. Liu, Ying Xu:
PFP: A Computational Framework for Phylogenetic Footprinting in Prokaryotic Genomes. ISBRA 2008: 110-121 - 2007
- [j38]Guojun Li, Zhijie Liu, Jun-tao Guo, Ying Xu:
An Algorithm for Simultaneous Backbone Threading and Side-Chain Packing. Algorithmica 48(4): 329-342 (2007) - [j37]Guojun Li, Jizhu Lu, Victor Olman, Ying Xu:
Prediction of cis-Regulatory Elements: from High-Information Content Analysis to Motif Identification. J. Bioinform. Comput. Biol. 5(4): 817-838 (2007) - [c40]Dongsheng Che, Jizhen Zhao, Liming Cai, Ying Xu:
Operon Prediction in Microbial Genomes Using Decision Tree Approach. CIBCB 2007: 135-142 - [c39]Hongwei Wu, Fenglou Mao, Victor Olman, Ying Xu:
An Algorithm for Hierarchical Classification of Genes of Prokaryotic Genomes. ISBRA 2007: 551-563 - 2006
- [j36]Fengfeng Zhou, Yu Xue, Xuebiao Yao, Ying Xu:
CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy (CSS). Bioinform. 22(7): 894-896 (2006) - [j35]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): 999-1014 (2006) - [j34]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): 254-257 (2006) - [j33]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): 129-134 (2006) - [j32]Yinglei Song, Chunmei Liu, Xiuzhen Huang, Russell L. Malmberg, Ying Xu, Liming Cai:
Efficient Parameterized Algorithms for Biopolymer Structure-Sequence Alignment. IEEE ACM Trans. Comput. Biol. Bioinform. 3(4): 423-432 (2006) - [c38]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: 23-24 - [c37]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: 855-862 - [c36]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: 307-313 - [c35]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: 255-266 - [c34]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: 327-338 - 2005
- [j31]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): 563-574 (2005) - [j30]Guojun Li, Ying Xu, Chuanping Chen, Zhenhong Liu:
On Connected [g, f +1]-Factors in Graphs. Comb. 25(4): 393-405 (2005) - [j29]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): 455-476 (2005) - [j28]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): 129-146 (2005) - [j27]Ying Xu, Liming Cai, Zhiping Weng:
Preface. J. Comput. Sci. Technol. 20(4): 433 (2005) - [j26]Bo Yan, Youxing Qu, Fenglou Mao, Victor Olman, Ying Xu:
PRIME: A Mass Spectrum Data Mining Tool for De Nova Sequencing and PTMs Identification. J. Comput. Sci. Technol. 20(4): 483-490 (2005) - [c33]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: 35-36 - [c32]PhuongAn Dam, Victor Olman, Ying Xu:
Improving Operon Prediction in E. coli. CSB Workshops 2005: 69-70 - [c31]Hongwei Wu, Fenglou Mao, Victor Olman, Ying Xu:
Accurate Prediction of Orthologous Gene Groups in Microbes. CSB 2005: 73-79 - [c30]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: 217- - [c29]Yinglei Song, Chunmei Liu, Xiuzhen Huang, Russell L. Malmberg, Ying Xu, Liming Cai:
Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment. WABI 2005: 376-388 - [p1]PhuongAn Dam, Zhengchang Su, Victor Olman, Ying Xu:
Computational Reconstruction of the carbon fixation pathway in Synechococcus SP. Wh 8102. Advances in Bioinformatics and Its Applications 2005 - 2004
- [j25]Jinbo Xu, Ming Li, Ying Xu:
Protein Threading by Linear Programming: Theoretical Analysis and Computational Results. J. Comb. Optim. 8(4): 403-418 (2004) - [j24]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): 522-525 (2004) - [c28]Zhengchang Su, PhuongAn Dam, Victor Olman, Ying Xu:
Computational Inference of Transcription Regulation and Response Networks in Synechococcus sp. WH8102. BIBE 2004: 5-8 - [c27]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: 236-244 - [c26]Victor Olman, Hanchuan Peng, Zhengchang Su, Ying Xu:
Mapping of Microbial Pathways through Constrained Mapping of Orthologous Genes. CSB 2004: 363-370 - [c25]Peng Wang, Zhengchang Su, PhuongAn Dam, Ying Xu:
A Knowledge Base for Computational Pathway Reconstruction. CSB 2004: 612-613 - [c24]PhuongAn Dam, Zhengchang Su, Victor Olman, Ying Xu:
In Silico Construction of the Carbon Fixation Pathway in Synechococcus sp. WH8102. CSB 2004: 614-615 - [c23]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: 640-641 - [c22]Fenglou Mao, Zhengchang Su, Victor Olman, David Chuang, Ying Xu:
Pathway Mapping with Operon Information: An Integer-Programming Method. CSB 2004: 642-643 - [c21]Victor Olman, Jizhu Lu, PhuongAn Dam, Zhengchang Su, Ying Xu:
CUBIC: Search for Binding Sites. CSB 2004: 666-667 - [c20]Peng Wang, Zhengchang Su, Jun-tao Guo, Ying Xu:
Structural Analysis of FGFR1 Kinase Activation through Molecular Dynamics Simulation. CSB 2004: 700-701 - [c19]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: 708-709 - [c18]Youxing Qu, Jun-tao Guo, Victor Olman, Ying Xu:
Protein Fold Recognition Through Application of Residual Dipolar Coupling Data. Pacific Symposium on Biocomputing 2004: 459-470 - 2003
- [j23]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): 1985-1996 (2003) - [j22]Huandong Sun, Ming Li, Ying Xu:
MOLVIE: an interactive visualization environment for molecular structures. Comput. Methods Programs Biomed. 71(1): 85-90 (2003) - [j21]Victor Olman, Dong Xu, Ying Xu:
Cubic: Identification of Regulatory Binding Sites through Data Clustering. J. Bioinform. Comput. Biol. 1(1): 21-40 (2003) - [j20]Jinbo Xu, Ming Li, Dongsup Kim, Ying Xu:
Raptor: Optimal Protein Threading by Linear Programming. J. Bioinform. Comput. Biol. 1(1): 95-118 (2003) - [j19]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): 387-410 (2003) - [j18]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): 211-229 (2003) - [c17]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: 3-10 - [c16]Yu Chen, Trupti Joshi, Ying Xu, Dong Xu:
Towards Automated Derivation of Biological Pathways Using High-Throughput Biological Data. BIBE 2003: 18-25 - [c15]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: 421-423 - [c14]Victor Olman, Dong Xu, Ying Xu:
CUBIC: Identification of Regulatory Binding Sites Through Data Clustering. CSB 2003: 448-449 - [c13]Zhengchang Su, PhuongAn Dam, Xin Chen, Victor Olman, Tao Jiang, Brian Palenik, Ying Xu:
Computational Inference of Regulatory Pathways in Microbes. CSB 2003: 631-633 - [c12]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: 580-592 - [c11]Jinbo Xu, Ming Li, Guo-Hui Lin, Dongsup Kim, Ying Xu:
Protein Threading by Linear Programming. Pacific Symposium on Biocomputing 2003: 264-275 - [c10]Victor Olman, Dong Xu, Ying Xu:
Identification of Regulatory Binding Sites Using Minimum Spanning Trees. Pacific Symposium on Biocomputing 2003: 327-338 - 2002
- [j17]Ying Xu, Victor Olman, Dong Xu:
Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees. Bioinform. 18(4): 536-545 (2002) - [j16]Dong Xu, Guangshan Li, Liyou Wu, Jizhong Zhou, Ying Xu:
PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis. Bioinform. 18(11): 1432-1437 (2002) - [j15]Ying Xu, Dong Xu, Dongsup Kim, Victor Olman, Jane Razumovskaya, Tao Jiang:
Automated assignment of backbone NMR peaks using constrained bipartite matching. Comput. Sci. Eng. 4(1): 50-62 (2002) - [c9]Guo-Hui Lin, Dong Xu, Zhi-Zhong Chen, Tao Jiang, Jianjun Wen, Ying Xu:
An Efficient Branch-and-Bound Algorithm for the Assignment of Protein Backbone NMR Peaks. CSB 2002: 165-174 - [c8]Zhi-Zhong Chen, Tao Jiang, Guo-Hui Lin, Jianjun Wen, Dong Xu, Ying Xu:
Improved Approximation Algorithms for NMR Spectral Peak Assignment. WABI 2002: 82-96 - 2000
- [j14]Dong Xu, Michael A. Unseren, Ying Xu, Edward C. Uberbacher:
Sequence-structure specificity of a knowledge based energy function at the secondary structure level. Bioinform. 16(3): 269-285 (2000) - [j13]Ying Xu, Dong Xu, Harold N. Gabow:
Protein domain decomposition using a graph-theoretic approach. Bioinform. 16(12): 1091-1104 (2000) - [j12]Ying Xu, Dong Xu, Oakley H. Crawford, J. Ralph Einstein:
A Computational Method for NMR-Constrained Protein Threading. J. Comput. Biol. 7(3-4): 449-467 (2000) - [c7]Ying Xu, Dong Xu, Oakley H. Crawford, J. Ralph Einstein, Engin Serpersu:
Protein structure determination using protein threading and sparse NMR data (extended abstract). RECOMB 2000: 299-307
1990 – 1999
- 1998
- [j11]Ying Xu, Dong Xu, Edward C. Uberbacher:
An Efficient Computational Method for Globally Optimal Threading. J. Comput. Biol. 5(3): 597-614 (1998) - [j10]Ying Xu, Victor Olman, Edward C. Uberbacher:
A segmentation algorithm for noisy images: Design and evaluation. Pattern Recognit. Lett. 19(13): 1213-1224 (1998) - [c6]Ying Xu, Dong Xu, Edward C. Uberbacher:
A new method for modeling and solving the protein fold recognition problem (extended abstract). RECOMB 1998: 285-292 - 1997
- [j9]Ying Xu, Edward C. Uberbacher:
2D image segmentation using minimum spanning trees. Image Vis. Comput. 15(1): 47-57 (1997) - [j8]Ying Xu, Edward C. Uberbacher:
Automated Gene Identification in Large-Scale Genomic Sequences. J. Comput. Biol. 4(3): 325-338 (1997) - [c5]Ying Xu, Richard J. Mural, Edward C. Uberbacher:
Inferring Gene Structures in Genomic Sequences Using Pattern Recognition and Expressed Sequence Tags. ISMB 1997: 344-353 - [c4]Ying Xu, Edward C. Uberbacher:
Reference-based gene model prediction on DNA contigs (extended abstract). RECOMB 1997: 330-336 - 1996
- [j7]Ying Xu, Edward C. Uberbacher:
A polynomial-time algorithm for a class of protein threading problems. Comput. Appl. Biosci. 12(6): 511-517 (1996) - [j6]Sherri Matis, Ying Xu, Manesh J. Shah, Xiaojun Guan, J. Ralph Einstein, Richard J. Mural, Edward C. Uberbacher:
Detection of RNA Polymerase II Promoters and Polyadenylation Sites in Human DNA Sequence. Comput. Chem. 20(1): 135-140 (1996) - [j5]Ying Xu, Richard J. Mural, Edward C. Uberbacher:
An Iterative Algorithm for Correcting Sequencing Errors in DNA Coding Regions. J. Comput. Biol. 3(3): 333-344 (1996) - [j4]Harold N. Gabow, Ying Xu:
Efficient Theoretic and Practical Algorithms for Linear Matroid Intersection Problems. J. Comput. Syst. Sci. 53(1): 129-147 (1996) - [j3]Ying Xu, Richard J. Mural, J. Ralph Einstein, Manesh B. Shah, Edward C. Uberbacher:
GRAIL: a multi-agent neural network system for gene identification. Proc. IEEE 84(10): 1544-1552 (1996) - [c3]Ying Xu, Edward C. Uberbacher:
Gene Prediction by Pattern Recognition and Homology Search. ISMB 1996: 241-251 - 1995
- [j2]Ying Xu, Richard J. Mural, Edward C. Uberbacher:
Correcting sequencing errors in DNA coding regions using a dynamic programming approach. Comput. Appl. Biosci. 11(2): 117-124 (1995) - 1994
- [j1]Ying Xu, Richard J. Mural, Edward C. Uberbacher:
Constructing gene models from accurately predicted exons: an application of dynamic programming. Comput. Appl. Biosci. 10(6): 613-623 (1994) - [c2]Ying Xu, Harold N. Gabow:
Fast Algorithms for Transversal Matroid Intersection Problems. ISAAC 1994: 625-633
1980 – 1989
- 1989
- [c1]Harold N. Gabow, Ying Xu:
Efficient Algorithms for Independent Assignments on Graphic and Linear Matroids. FOCS 1989: 106-111
Coauthor Index
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