Ying Xu, Ph.D.
Department of Biochemistry and Molecular Biology
A110, Life Science Building
120 Green Street
University of Georgia
Athens, GA 30602-7229
Phone: 706-542-9779 (CSBL)
Phone: 706-542-7783 (IOB)
Email: xyn bmb.uga.edu
Our group's research and development center around the following areas:
- Cancer Computational and Systems Biology: We are interested in
developing integrated computational and omic techniques for (a) identification
of biomarkers for a number of human cancers, detetable through analyses of
serum/urine samples, and (b) understanding the relationships between
molecular signatures and cancer formation & development. Our work involves
microarray gene expression data generation and analyses, comparative genome
analyses and analyses of other experimental data.
- Study of Microbial Genome Structure and Application to Pathway &
We are interested in understanding both the micro- and macro-structures
of microbial genomes through computational studies and experimental
validation, and in understanding why microbial genomes are organized the
way they are. We are also interested applying the knowledge and information
gained through such studies to prediction of pathways and networks in
Our research work has been sponsored by NSF, DOE, NIH, Georgia Research
Alliance, Georgia Cancer Coalition and the University of Georgia.
In addition, our work had been generously supported by Oak
Ridge National Lab and Pacific Northwest National Lab.
SELECTED PUBLICATIONS IN THE PAST FIVE YEARS
- Xin Chen, Wen-Chi Chou, Xizeng Mao, Qin Ma, Ying Xu, SeqTU: A Web Server for RNA-Seq based Transcription Unit Identification in Bacteria, submitted to Bioinformatics, 2015.
- Xin Chen, Qin Ma, Xiaolan Rao, Yuhong Tang, Yan Wang, Gaoyang Li, Chi Zhang, Xizeng Mao, Richard A. Dixon and Ying Xu, Genome-Scale Identification of Cell-Wall Related Genes in Switchgrass through Comparative Genomics and Computational Analyses of Transcriptomic Data, Bioenergy Research, Volume 9, Issue 1, pp 172-1802015, 2016.
- S. Cao, C. Zhang and Ying Xu, Somatic Mutations Are Facilitators Rather Than Drivers of Cancer Formation, International Journal of Cancer, 06/2015; 137(11), DOI: 10.1002/ijc.29639, 2015.
- Fang Yao, Chi Zhang, Wei Du, Ying Xu, Identification of Gene-Expression Signatures for Breast Cancer Grading and Staging, Plos One, DOI:10.1371/journal.pone.0138213, 2015.
- Sha Chao, Chi Zhang, Chao Liu, Fei Ji, Tony Szempruch, Ye Zhang, Yuan Yuan, Quincy Teng, Can Wang, Jing Jiang, Jingkai Gu, Ying Xu, Oxidized Cholesterol Plays a Key Role in Driving the Rapid Growth of Metastatic Cancer, Journal of Molecular and Cellular Biology, 2015 (to appear).
- Xizeng Mao, Qin Ma, Bingqiang Liu, Xin Chen, Hunyuan Zhang, Ying Xu. Revisiting Operons: An Analysis of the Landscape of Transcriptional Units in E. coli, BMC Bioinformatics, 2015 (on-line publication).
- Chi Zhang, Chao Liu, Sha Cao and Ying Xu, Elucidation of Divers of High-Level Production of Lactates throughout a Cancer Development, Journal of Molecular and Cellular Biology, 2015 (to appear).
- Wen-Chi Chou, Qin Ma, Shihui Yang, Xizeng Mao, Xin Chen, Sha Cao, Steven D. Brown, Ying Xu, Analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum, Nucleic Acid Research, gkv177, 2015.
- Chi Zhang, Sha Cao, Ying Xu, Cancer may be a pathway to cell survival under persistent hypoxia and elevated ROS: a model for solid-cancer initiation and early development, International Journal of Cancer, DOI: 10.1002/ijc.28975, 2014.
- Juan Cui, Yanbin Yin, Qin Ma, Guoqing Wang, Victor Olman, Yu Zhang, Wen-Chi Chou, Celine S. Hong, Chi Zhang, Sha Cao, Xizheng Mao, Ying Li, Steve Qin, Shaying Zhao, Jing Jiang, Phil Hastings, Fan Li, Ying Xu, Towards Understanding the Genomic Alterations in Human Gastric Cancer, International Journal of Cancer, DOI: 10.1002/ijc.29352, 2014.
- Chan Zhou, Fenglou Mao, Yanbin Yin, Jinling Huang, Johann Peter Gogarten, Ying Xu, An Automated Sequence-Sampling Method for Improving the Taxonomic Diversity of Gene Phylogenetic Trees, PLoS ONE, 3:9(6):e98844, 2014.
- Chi Zhang, Sha Cao, Ying Xu, Population Dynamics inside Cancer Biomass Driven by Repeated Hypoxia-Reoxygenation Cycles, Quantitative Biology, 2, 3 ,
pp 85-99, 2014.
- Dorothy A. Hammond and Ying Xu, functional understanding of the diverse exon-intron structures of Hman CPGR genes, Journal of Bioinformatics and Computational Biology, 12(1), 1350019, 2014.
- Qin MA, Xin CHEN, Chao LIU, Xizeng MAO, Hanyuan ZHANG, Fei JI, Chunguo WU, Ying Xu Understanding the commonalities and differences in genomic organization across multiple closely related organisms from an energy perspective,Science China, 57 (11), 1121-1130, 2014.
- Qin Ma, Chuan Zhou, Xizeng Mao, Yanbin Yin, Ying Xu, Insights into Biofuel Production through Comparative Genomic Analysis of Clostridium Genomes, BioEnergy Research, 1-12, 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 analysis. Nucleic Acids Research, doi: 10.1093/nar/gku315, 2014.
- Luis L. Escamilla-Treviño, Hui Shen, Tim Hernandez, Yanbin Yin, Ying Xu, and Richard A. Dixon, Early lignin pathway enzymes and routes to chlorogenic acid in switchgrass (Panicum virgatum L.), Plant Molecular Biology, 84(4-5):565-76, 2014.
- Yan Wang, Huiyan Sun, Wei Du, Enrico Blanzieri, Gabriella Viero, Ying Xu and Yanchun Liang, Identification of Essential Proteins Based on Ranking Edge-Weights in
Protein-Protein Interaction Networks, PLoS ONE, 9(9): e108716. doi:10.1371/journal.pone.0108716, 2014.
- 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, Nucl. Acids Res. doi: 10.1093/nar/gkt1048. 2013.
- Charlotte M Wilson, Shihui Yang, Qin Ma, Courtney M Johnson,Miguel Rodriguez Jr, Lezlee Dice, Ying Xu and Steven D Brown Clostridium thermocellum Transcriptomic Profiles after Exposure to Furfural or Heat Stress, Biotechnology for BioFuels, 6:131, doi: 10.1186/1754-6834-6-131, 2013.
- Q. Ma*, B. Liu*, C. Zhou, Y. Yin, G. Li, Ying Xu, BoBro2.0: An integrated toolkit for accurate prediction and analysis of cis regulatory elements at a genome scale, Bioinformatics, doi: 10.1093/bioinformatics/btt397. 2013.
- Qin Ma, Ying Xu, Global Genomic Arrangement of Bacterial Genes Is Closely Tied with the Total Transcriptional Efficiency, Genomics, Proteomics and Bioinformatics, http://dx.doi.org/10.1016/j.gpb.2013.01.004, 2013.
- F. Mao, V. Olman and Ying Xu, Barcode server: a visualization-based genome analysis system, PLOS ONE, e56726. doi:10.1371/journal.pone.0056726, 2013.
- Qin Ma*, Yanbin Yin*, Mark A. Shell, Han Zhang, Guojun Li, Ying Xu, Computational Analyses of Transcriptomic Data Reveal the Dynamic Organization of the E. coli Chromosome under Different Conditions. Nucleic Acids Research, doi:10.1093/nar/gkt261. 2013.
- I. Kataeva, M. Foston, S. Yang, S. Pattathil, A. K. Biswal, F. L. Poole II, T. P. Thomas, P. Azadi, V. Olman, D. L. Lewis, C. Doeppke, T. Tschaplinsky, M. Davis, D. Mohnen, Ying Xu, A. Ragauskas, R. M. Kelly, M. G. Hahn and M. W.W. Adams, Carbohydrate and Lignin are Simultaneously Solubilized from Unpretreated Switchgrass by Microbial Action at High Temperature, Energy & Environmental Science, 6, 2186-2195, 2013.
- F. Mao, V. Olman and Ying Xu, Barcode server: a visualization-based genome analysis system, PLOS ONE, e56726. doi:10.1371/journal.pone.0056726, 2013.
- Qin Ma, Jaxk Reeves, David A. Liberles, Lili Yu, Zheng Chang, Jing Zhao, Ying Xu*, Liang Liu, A phylogenetic model for understanding the effect of gene duplication on cancer progression, Nucleic Acids Research, doi: 10.1093/nar/gkt1320, 2013.
- Jiaxin Wang, Yanchun Liang, Yan Wang, Juan Cui, Ming Liu, Wei Du, Ying Xu, Computational Prediction of Human Salivary Proteins from Blood Circulation and Application to Diagnostic Biomarker Identification, PLoS ONE, DOI: 10.1371/journal.pone.0080211, 2013.
- Kun Xu, Xizeng Mao, Minesh Mehta, Juan Cui, Chi Zhang, Fenglou Mao, Ying Xu, A Systems Biology Approach to Elucidation of How Cancer Cells Avoid Acidosis, PLoS ONE, e71177, 2013.
- X. Dong, G. Wang, G. Zhang, Z. Ni, J. Suo, J. Cui, A. Cui, Q. Yang, Ying Xu* and Fan Li, The endothelial lipase protein is promising urinary biomarker for diagnosis of gastric cancer, Diagnostic pathology, 8 (1), 45, 2013.
- J. Zhang, Y. Lee, I. Torres-Jerez, M. Wang, Y. Yin, W. Chou, J. He, H. Shen, C. Pennacchio, E. Lindquist, J. Grimwood, J. Schmutz, Ying Xu, .L E. Bartley, P. Ronald, M. Saha, R. Dixon, Y. Tang and M. Udvardi, Development of an integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass (Panicum virgatum L.), Plant Physiology, 74(1):160-73, 2013.
- G. Li, T.G. Kollner, Y. Yin, Y. Jiang, Ying Xu, J. Gershenzon, E.
Pichersky and F Chen, Evolution of terpene synthase genes in
selaginella through vertical and horizontal gene transfer, Proc Natl
Acad Sci USA, doi/10.1073/pnas.1204300109, 2012.
- S. E. Blumer-Schuette, R. J. Giannon, J. V. Zurawski, I. Ozdemir, D. B.
Mistry, Q. Ma, Y. Yin, Ying Xu, F. L. Poole II, I. Kataeva, M. W. W.
Adams, S. D. Hamilton-Brehm, J. G. Elkins, F. W. Larimer, M. L. Land,
L. Hauser, R. W. Cottingham, R. L. Hettich and R. M. Kelly,
Caldicellulosiruptor core and pan genomes reveal determinants for
non-cellulosomal thermophilic deconstruction of lignocellulose,
Journal of Bacteriology, 194(15):4015-28, 2012.
- S. Wang, Y. Yin, Q. Ma, D. Hao and Ying Xu, Identification of cell-wall
related genes in Arabidopsis through biclustering analysis of
expression data, BMC Plant Biology, 12:138;
- F. Mao, M. Poptsova, D. Williams, O Zhaxybayeva, P. Gogarten and Ying
Xu*, Quartet decomposition server: a platform for analyzing
phylogenetic trees, BMC Bioinformatics, 13:123
- Q Liu, H Zhou, J Gao, R Zhu, J Cui, Z Cao and Ying Xu, Improved siRNA
design through cross-platform feature selection based on a comprehensive
siRNA meta-dataset, submitted to BMC Bioinformatics, 2012.
- X Mao, X Chen, Y Zhang, S Pangleand Ying Xu, CINBER: an interactive web
platform for biological pathway prediction for prokaryotes, PLoS ONE,
2012 (in press).
- X. Mao, H Zhang, Y.Yin, Ying Xu, The percentage of bacterial genes on
leading versus lagging strands is influenced by multiple balancing forces,
Nucleic Acids Researchdoi:10.1093/nar/gks605, 2012.
- Y Yin, X Mao, J Yang, X Chen and Ying Xu, dbCAN: A web-based DataBase
for automated Carbohydrate-active enzyme Annotation, Nucleic Acids
Research, 10.1093/nar/gks479, 2012.
- F. Zhou, Q. Ma, G. Li, Ying Xu, QServer: a biclustering-based server
for prediction and assessment of co-expressed genes clusters,
PLoS ONE, 7(3): e32660. doi:10.1371, 2012.
- J Cui, X, Mao, and Ying Xu, Hypoxia and Miscoupling between Reduced
Energy Efficiency and Signaling to Cell Proliferation Drive
Cancer to Grow Increasingly Faster, Journal of Molecular Cell Biology
, doi: 10.1093/jmcb/mjs017, 2012.
- Juan Cui, Ying Xu, Dave Puett, "Transcriptomic Profiling of Human Ovarian
Cancer Cells: Changes Mediated by Luteinizing Hormone Receptor Activation",
Chapter 12 in Ovarian Cancer, Samir A. Farghaly (eds.), InTech, 2012.
- K Xu, X. Mao, M Mehta, J Cui, C Zhang, D Puett, Ying Xu, A comparative
study of gene-expression data of basal cell carcinoma and melanoma
reveal new insights about the two cancer, PLoS ONE, PLoS ONE, 7(1):
- H Zhang, YB Yin, Ying Xu, Genomic Arrangement of Regulons in Bacteria,
PLoS ONE, 10.1371/journal.pone.0029496, 2011.
- Y Yin, J Huang, X Gu, M Bar-Peled and Ying Xu, Evolution of plant
nucleotide sugar interconversion enzymes, PLoS ONE,
- Y. Yin, M. G. Hahn, I Gelineo-Albersheim, Ying Xu, D. Mohnen,
Glycosyltransferases of Family (GT8), in Plant Cell Polysacharides:
Biosynthesis and Bioengineering: Annual Plant Review Series, Blackwell
Publishing, 47, 167 -212, 2011.
- G Li, Q Ma, X Mao, X Zhu, Y Yin, Ying Xu, Integration of sequence
similarity and functional association information can overcome intrinsic
problems in orthology mapping across bacterial genomes, Nucleic Acids
Research, doi: 10.1093/nar/gkr766, 2011.
- S Wang, S Yang, B An, S Wang, Y Yin, Y Lu, Ying Xu and D Hao, Molecular
Dynamics Analysis Reveals Structural Insights into Mechanism of Nicotine
N-Demethylation Catalyzed by Tobacco Cytochrome P450 Mono-oxygenase,
PLoS ONE, 6(8): e23342. 2011.
- J. Cui, J. Eldredge, Ying Xu, JD Puett, MicroRNA Expression and
Regulation in Human Ovarian Carcinoma Cells by Luteinizing Hormone,
PLoS ONE, 6(7): e21730, 2011.
- J. Cui, B. M. Miner, J. B. Eldredge, S. W. Warrenfeltz, P. Dam, Ying Xu,
D. Puett. Regulation of gene expression in ovarian cancer cells by
luteinizing hormone receptor expression and activation.
BMC Cancer, 11:280, 2011.
- J. Cui, Ying Xu, Gene-Expression Signatures of Gastric Cancer Can
Distinguish Histological Subtypes and Stages, PLoS ONE
, 6(3): e17819, 2011.
- S Hong, J Cui, Zi Ni, Y Su, D Puett, F Li, Ying Xu, Identification
of cancer markers in urine and application to gastric cancer,
PLoS ONE, 6(2):e16875, 2011.
- H. Chen, F. Ji. V. Olman, C. K. Mobley, Y. Liu, J. H. Bushweller, J.
H. Prestegard, Ying Xu, Prediction of optimal mutation sites for
limited PRE data collection to constrain membrane protein structure
prediction, Structure, 484 - 495, 2011.
- York, W; Kulkarni, A; Pena; Mazumder, K; Avci, u; Urbanowicz, B; Yin,
Y; O'Neill, M; Roberts, A; Hahn, M; Xu, Ying; Darvill, A, The
occurrence of glucuronoxylan in plant cell walls predates the
appearance of vascular plants, Glycobiology
2011 (in press).
- X. Mao, Y Zhang, and Ying Xu, SEAS: a system for SEED-based pathway
enrichment analysis, PLoS ONE, 6(7): e22556, 2011.
- Y. Chen, F. Mao, G. Li, and Ying Xu, Genome-wide discovery of missing
genes in biological pathways in prokaryotes, BMC Bioinformatics,
(Suppl 1):S1; doi:10.1186, 2011.
- X. Mao, H Zhang, Y.Yin, Ying Xu, The percentage of bacterial genes on
leading versus lagging strands is influenced by multiple balancing
forces, submitted, 2010.
- J Cui, Y Chen, J Chou, L Sun, L Chen, J Suo, Zi Ni, M Zhang, X Kong,
E Hauffman, J Kang, X Lv, Yg Su, Y Gao, H Zhang, V Olman, G Li, J
Amster,R Orlando, J D Puett, F Li, Ying Xu, An Integrated
Transcriptomic and Proteomic Analysis for Biomarker Identification
for Gastric Cancer, Nucleic Acids Research,
- K. Xu, J. Cui, V Olman, Ying Xu, Identification of general cancer
markers through comparative analyses of gene-expression data of
multiple cancer types, PLoS ONE, Vol 5(10), e13696, 2010.
- Q. Liu, J. Cui, Q. Yang and Ying Xu, In-silico prediction of
blood-secretory human proteins using a ranking algorithm, BMC
Bioinformatics, Vol 11, 250 - , 2010.
- P Dam, I Kataeva, S Yang, F Zhou, Y Yin, W Chou, F L., Poole II, J
Westpheling, R Hettich, R Giannone, DL. Lewis, R Kelly, H J. Gilbert,
B Henrissat, Ying Xu and M. W.W. Adams, Insights into Plant Biomass
to Biofuel Conversion from the Genome Sequence of the Extremely
Thermophilic Bacterium Caldicellulosiruptor bescii DSM 6725,
to Nucleic Acids Research, doi:10.1093/nar/gkq618, 2010.
- WC Chou, Y Yin, Ying Xu, GolgiP: prediction of Golgi resident proteins
in plants, Bioinformatics, Vol 26 (19), 2464 -, 2010.
- Q Zhao, H Wang, Y Yin, Ying Xu, F Chen and R A. Dixon, Syringyl lignin
biosynthesis is directly regulated by a secondary cell wall master
switch, Proc Natl Acad Sci USA, 106, 14496-14507, 2010.
- G Li, B Liu, Q Ma, Ying Xu, A New Framework for Identifying Cis
Regulatory Motifs in Prokaryotes, Nucleic Acids Research
, doi:10.1093/nar/gkq948, 2010.
- X Zhang, J Cui, X. Song, H Wang, Ying Xu, T. Ochsenreiter, Prediction
of mitochondrial proteins in Trypanosome proteome, Nucleic Acids
Research, 38(21), 7378 - 7387, 2010.
- F. Mao, V. Olman, Ying Xu, Barcode server: a visualization-based
genome analysis system, submitted to Nucleic Acids Research,
- F. Zhou and Ying Xu, cBar: an algorithm for accurate identification
of chromosomal sequence fragments from metagenome data,
Bioinformatics, 26(16), 2051 - 2052, 2010.
- W. Zhou, Ying Xu, HB Schuttler, Cellulose Hydrolysis in Evolving
Substrate Morphologies III: Time Scale Analysis,
Biotechnology and Bioengineering, 107(2), 224-234, 2010.
- Y Yin, J Huang, X Gu, M Bar-Peled and Ying Xu, On the evolution of
plant nucleotide sugar interconversion enzymes: common and ancient
origin from bacteria, Molecular Biology and Evolution, 2010
- Ying Xu, "Computational Challenges in Deciphering Genomic Structures
of Bacteria", Journal of Computer Science and Technology,
25(1), pp 53 - 70, 2010 (invited review) (freely downloadable
from the journal site).
- G. Wang, F Zhou, V Olman, Y Su, F. Li, and Ying Xu, Prediction of
pathogenicity islands in Escherichia coli O157:H7 using genomic barcode,
FEBS Letter, 584, 194 - 198, 2010.
- F. Zhou, H. Chen, and Ying Xu, GASdb: a large-scale and comparative
exploration database of glycosyl hydrolysis systems, BMC
Microbiology, 10, 69 - , 2010.
- F Zhou, G Wang, F Li, Ying Xu, Analyses of the landscape of insertion
sequences in three sequenced genomes of E. coli O157:H7 strains, 2010
- X. Mao and Ying Xu, "In silico reconstruction of osmoregulation network
in Synechococcus sp. WH8102", BMC Genomics, 11, 291 - , 2010.
- YB Yin, H Chen, M. Hahn, D. Mohnen, Ying Xu, "Plant
galacturonosyltransferase (GAUT) related genes have a different
origin than the other glycosyltransferase family 8 genes and may
be anciently acquired from Cyanobacteria", Plant Physiology
153, 1729 - 1746, , 2010.
- YB Yin, H Zhang and Ying Xu, "Genomic arrangement of bacterial operons
is constrained by biological pathways encoded in the genome",
Proc Natl Acad Sci USA, 107 (14), 6310 - 6315, 2010.
- H Zhang, P Wang, N Papangelopoulos, Ying Xu, A Sette, PE. Bourne,
O Lund, J Ponomarenko, M Nielsen, B PetersLimitations of ab initio
predictions of peptide binding to MHC class II molecules, PLoS ONE
, 5(2), e9272, 2010.
- X Gu, J Glushka, Y Yin, Ying Xu, T Denny, J Smith, Y Jiang and M
Bar-Peled, "Identification of UDP-4-keto-pentose/UDP-xylose synthase:
a member of the 4,6-dehydratase & decarboxylase family in the
devastating plant pathogenic bacterium Ralstonia solanacearum str.
GMI1000", Journal of Biological Chemistry, 285(12), 9030 -
- C. Zhou, YB Yin, P. Dam, Ying Xu, "Identification of novel genes
involved in plant cell wall biosynthesis by protein-protein interaction
data", Journal of Proteome Research, 9(10):5025-37, 2010.
- F. Mao, Y. Yin, FF. Zhou, WC Chou, C. Zhou, H Chen and Ying Xu,
"pDAWG: an integrated database for plant cell-wall genes",
Bioenergy Research, 2(4), 209 - 216, 2009.
- FF Zhou, V Olman, Ying Xu, Large-Scale Analyses of Glycosylation in
Cellulases, Genomics, Proteomics and Bioinformatics, 7(4),
- H Shen, YB Yin, F. Chen, Ying Xu and RA Dixon, "The bioinformatics
baseline analysis of the NAC genes for plant cell wall development
in bioenergy production", Bioenergy Research, 2(4), 217-232,
- X Ren, Y Li, Q Pan, J Yu, R Xu, Ying Xu, An Open-Framework Germanate
with 30-Ring Channels Built from Ge7 and Ge9 Clusters, Journal of
American Society of Chemistry,pp 14128 - 14129, 2009.
- Y Wang, J Cui, W Du, C Zhang, F Mao, J Wang, Y Sun, C Zhou, Y Liang,
F Li, Ying Xu, "DMarker: A Bio-Marker Inference System for Human
Diseases based on Microarray Gene Expression Data, submitted, 2009.
- L L. Escamilla-Trevino, H Shen, R Uppalapati, T Ray, Y Tang,
T Hernandez, Y Yin, Ying Xu, and R A. Dixon, "Functional
Characterization of two Cinnamoyl CoA Reductase (CCR) Genes
for lignin modification in Switchgrass (Panicum virgatum)",
New Phytologist, 185(10), 143 - 155, 2009.
- G. Li, B. Liu, Ying Xu, "Accurate Recognition of cis Regulatory Motifs
with the Correct Lengths in Prokaryotic Genomes", Nucleic Acids
Research, Nov 2009, 1-7.
- TT. Tran, F Zhou, S Marshburn, M Stead, S Kushner, and Ying Xu, "De
novo computational prediction of small non-coding RNA genes",
Bioinformatics, 25(22), 2897 - 2905, 2009.
- C. Gervais, T Wurst, D Landau, Ying Xu, "Application of the
Wang-Landau Algorithm to the Dimerization of Glycophorin A",
Journal of Physical Chemistry, 130(21), 215106 - , 2009.
- G. Li, Q. Ma, H. Tang, Ying Xu, "A close-to-optimum
bi-clustering algorithm for microarray gene expression data",
Nucleic Acids Research (online now), 2009.
- B. Liu, F Zhou, Ying Xu and X. Zhang, Functional genomic analyses
of a novel bacteriophage GVE2 from a deep-sea thermophile,
Research in Microbiology, 160, 166 - 171, 2009.
- W. Zhou, B. Schuttler, Z. Hao, Ying Xu, "Cellulose hydrolysis in
evolving substrate morphologies I: a general modeling formalism",
Biotechnology and Bioengineering, 104(2), 261-274, 2009.
- W. Zhou, Z. Hao, Ying Xu, and B. Schuttler, "Cellulose hydrolysis in
evolving substrate morphologies II: numerical results and analysis",
Biotechnology and Bioengineering, 104(2), 275-289, 2009.
- Q Liu, H Liu, P Wan, X. Ye and Ying Xu, Analyses of Domains and
Domain Fusions in Human Oncogenes , BMC Bioinformatics
, 10, 88 - 103, 2009.
- IA. Kataeva, SJ Yang, P Dam, FL Poole II, Y Yin, F Zhou, W Chou, Ying
Xu, L Goodwin, DR. Sims, JC. Detter, LG. Hauser, J Westpheling and
MWW. Adams, Genome Sequence of the Anaerobic, Thermophilic and
Cellulolytic Bacterium Anaerocellum thermophilum DSM 6725, J of
Bacteriology, 191(11):3760-1, 2009.
- Y Kong, G Zhou, U Avci, X Gu, C Jones, Y Yin, Ying Xu, M Hahn, Two
poplar glycosyltransferase genes PdGATL1.1 and PdGATL1.2 are
functional orthologs to PARVUS/AtGATL1 in Arabidopsis, Molecular
Plant, 2(5), 1040 - 1050, 2009.
- Y Yin and Ying Xu, "The cellulose synthase superfamily in fully
sequenced plants and algae", BMC Plant Biology, 9, 99 - ,
- G. Li, X Deng and Ying Xu, A polynomial time approximation scheme
for embedding hypergraph in a cycle, ACM Transactions on Algorithms
, 5(2), pp 20 - , 2009.
- Y. Chen, F. Zhou, G. Li, and Ying Xu, MUST: a system for
identification of miniature inverted repeats transposable elements
and applications to Anabaena variabilis and Haloquadratum walsbyi,
Gene, 436: 1-7, 2009.
- F. Zhou and Ying Xu, RepPop: a database for repetitive elements in
Populus trichocarpa, BMC Genomics, 10, 14 - , 2009.
- G. Li, D. Che, Ying Xu, "A universal operon predictor for prokaryotic
genomes", Journal of Binformatics and Computational Biology,
7(1), 19 - 38, 2009.
- F. Mao, P. Dam, J. Chou, V Olman, and Ying Xu, "DOOR: a database
for praokaryotic operons", Nucleic Acids Research
vol 37(1), D459 - 463, 2009.
- V Olman, F. Mao, H Wu, Ying Xu, "A parallel clustering algorithm for
very large data sets", IEEE/ACM Transaction on Computational
Biology and Bioinformatics, 6(2), 344 - 352, 2009.
Current Topics in Computational Molecular Biology, T. Jiang, Ying Xu,
Michael Zhang (eds), the MIT Press (and co-published by Tsinghua Univ. Press
in China), 2002.
Microbial Functional Genomics, J. Zhou, D. Thompson, Ying Xu,
and J. Tiedje, John Wiley and Sons, 2004.
Computational Methods for Protein Structure Prediction and Modeling, I and II
, Ying Xu, D. Xu and J Liang, Springer, 2006.
Computational Methods for Understanding Archaeal and Bacterial Genomes,
Ying Xu and J. Peter Gogarten, Imperial College Press, 2008.
,Ying Xu, Juan Cui, David Puett, Springer, 2014.
- Qianren (type B) Chair Professor (two months/year appointment),
JCSB Lab of
College of Computer Science and Technology, Jilin University, China, 2012 -
- ChangJiang (Cheung Kong) Chair Professor (two months/year appointment),
JCSB Lab of
College of Computer Science and Technology, Jilin University, China, 2009 -
- Director, Institute of Bioinformatics, University of Georgia,
2004 - 2011
- Adjunct Professor,
Computer Science Department (2004 - ),
(2006 - ), University of Georgia,
- Regents-GRA Eminent Scholar and Professor, Biochemistry and
Molecular Biology Department, University of Georgia, 2003 --
- Distinguished visiting scientist, Computational Biology Institute, Oak
Ridge National Laboratory, 2003 -- .
- Senior Staff Scientist/Group Leader (and earlier titles: staff scientist,
research associate), Protein
Informatics Group, Divisions of Life Sciences and Computer Science &
Mathematics, Oak Ridge National Laboratory, Oak Ridge, TN, 1993 -
- Visiting Assistant Professor, Mathematics and Computer Sciences
Department, Colorado School of Mines, Golden, CO, 1991 - 1993.
- Teaching/Research Assistant, Computer Science Department, Univ.
of Colorado, Boulder, CO, 1986 - 1991.
- Ph.D., Computer Science
Dept., Univ. of Colorado at Boulder (research focus: combinatorial
optimization, graph/matroid algorithm design and analysis)
- M.S., Computer Science Dept.,
Jilin Univ., China (research focus: expert system design, linear
- B.S., Computer Science Dept.,
Jilin Univ., China (senior project: natural language
The people (research scientists, postdocs, grad/under-grad students & staff)
we have at CSBL
are really a fun group to work with! Here is a
picture we recently
(Sept 2004) took after a group lunch
2009 SPRING PICNIC
We do get out of the lab once in a while. Here are some pictures (as a proof)
we took during our Lab's annual spring picnic at Tellula Gorge, Georgia
(May 2009). Most of the Lab members (and their families) participated in
this event while the other Lab members insisted to work in the office and so
missed the picnic.
photo of my family: my wife, son Tony and myself (May 2004 on vacation
(Summer 2005) recently became quite interested in chess and swimming.
A photo we
took during vacation in Changchun, China (June 2005) with my mom, dad, wife, son and myself
A photo of Hu-Niu, our family dog (2005).