Publications

2021

  • Zhou, Z. et al. Functional analysis of brain derived neurotrophic factor (BDNF) in Huntington's disease. Aging (Albany NY) 13, 6103-6114, doi:10.18632/aging.202603 (2021).
  • Zhou, Z. et al. Serum Uric Acid and the Risk of Dementia: A Systematic Review and Meta-Analysis. Front Aging Neurosci 13, 625690, doi:10.3389/fnagi.2021.625690 (2021).
  • Zhou, Z. et al. Integrative Functional Genomic Analysis of Molecular Signatures and Mechanistic Pathways in the Cell Cycle Underlying Alzheimer's Disease. Oxidative medicine and cellular longevity 2021, 5552623, doi:10.1155/2021/5552623 (2021).
  • Zhou, Z. et al. Downregulation of ATP6V1A Involved in Alzheimer's Disease via Synaptic Vesicle Cycle, Phagosome, and Oxidative Phosphorylation. Oxidative medicine and cellular longevity 2021, 5555634, doi:10.1155/2021/5555634 (2021).
  • Zhang, L. et al. Transcriptomic analysis identifies organ-specific metastasis genes and pathways across different primary sites. Journal of translational medicine 19, 31, doi:10.1186/s12967-020-02696-z (2021).
  • Qiu, S. et al. Understanding the unimodal distributions of cancer occurrence rates: it takes two factors for a cancer to occur. Brief Bioinform 22, doi:10.1093/bib/bbaa349 (2021).
  • Li, H. et al. An Interpretable Computer-Aided Diagnosis Method for Periodontitis From Panoramic Radiographs. Front Physiol 12, 655556, doi:10.3389/fphys.2021.655556 (2021).
  • Baramidze, G., Baramidze, V. & Xu, Y. Mathematical model and computational scheme for multi-phase modeling of cellular population and microenvironmental dynamics in soft tissue. PLoS One 16, e0260108, doi:10.1371/journal.pone.0260108 (2021).

2020

  • Zhou, Z. et al. Molecular identification of protein kinase C beta in Alzheimer's disease. Aging (Albany NY) 12, 21798-21808, doi:10.18632/aging.103994 (2020).
  • Yu, X., Cao, S., Zhou, Y., Yu, Z. & Xu, Y. Co-expression based cancer staging and application. Scientific reports 10, 10624, doi:10.1038/s41598-020-67476-7 (2020).
  • Wang, Y. et al. Clear Cell Meningioma in the Central Nervous System: Analysis of Surveillance, Epidemiology, and End Results Database. Front Oncol 10, 592800, doi:10.3389/fonc.2020.592800 (2020).
  • Tan, R. et al. Neural Functions Play Different Roles in Triple Negative Breast Cancer (TNBC) and non-TNBC. Scientific reports 10, 3065, doi:10.1038/s41598-020-60030-5 (2020).
  • Sun, H. et al. Metabolic Reprogramming in Cancer Is Induced to Increase Proton Production. Cancer Res 80, 1143-1155, doi:10.1158/0008-5472.Can-19-3392 (2020).
  • Sun, H., Zhou, Y., Jiang, H. & Xu, Y. Elucidation of Functional Roles of Sialic Acids in Cancer Migration. Front Oncol 10, 401, doi:10.3389/fonc.2020.00401 (2020).
  • Liu, L., Cui, H. & Xu, Y. Quantitative Estimation of Oxidative Stress in Cancer Tissue Cells Through Gene Expression Data Analyses. Front Genet 11, 494, doi:10.3389/fgene.2020.00494 (2020).
  • Liu, G., Liu, G., Cui, X. & Xu, Y. Transcriptomic Data Analyses Reveal a Reprogramed Lipid Metabolism in HCV-Derived Hepatocellular Cancer. Front Cell Dev Biol 8, 581863, doi:10.3389/fcell.2020.581863 (2020).
  • Li, H. et al. CaMeRe: A Novel Tool for Inference of Cancer Metabolic Reprogramming. Front Oncol 10, 207, doi:10.3389/fonc.2020.00207 (2020).
  • Li, H. et al. Modern deep learning in bioinformatics. Journal of molecular cell biology 12, 823-827, doi:10.1093/jmcb/mjaa030 (2020).

2019

  • Zhu, X., Luo, H. & Xu, Y. Transcriptome analysis reveals an important candidate gene involved in both nodal metastasis and prognosis in lung adenocarcinoma. Cell & bioscience 9, 92, doi:10.1186/s13578-019-0356-1 (2019).
  • Zhao, J., Feng, H., Zhu, D., Zhang, C. & Xu, Y. DTA-SiST: de novo transcriptome assembly by using simplified suffix trees. BMC bioinformatics 20, 698, doi:10.1186/s12859-019-3272-9 (2019).
  • Sun, H., Chen, L., Cao, S., Liang, Y. & Xu, Y. Warburg Effects in Cancer and Normal Proliferating Cells: Two Tales of the Same Name. Genomics Proteomics Bioinformatics 17, 273-286, doi:10.1016/j.gpb.2018.12.006 (2019).
  • Liang, S. et al. A novel matched-pairs feature selection method considering with tumor purity for differential gene expression analyses. Math Biosci 311, 39-48, doi:10.1016/j.mbs.2019.02.007 (2019).
  • Li, G., Cao, H. & Xu, Y. Structural and functional analyses of microbial metabolic networks reveal novel insights into genome-scale metabolic fluxes. Brief Bioinform 20, 1590-1603, doi:10.1093/bib/bby022 (2019).

2018

  • Zuo, C. et al. Elucidation and analyses of the regulatory networks of upland and lowland ecotypes of switchgrass in response to drought and salt stresses. PLoS One 13, e0204426, doi:10.1371/journal.pone.0204426 (2018).
  • Zuo, C. et al. Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing. Biotechnol Biofuels 11, 170, doi:10.1186/s13068-018-1167-z (2018).
  • Zhang, H. et al. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 46, W95-w101, doi:10.1093/nar/gky418 (2018).
  • Sun, H. et al. Fenton reactions drive nucleotide and ATP syntheses in cancer. Journal of molecular cell biology 10, 448-459, doi:10.1093/jmcb/mjy039 (2018).
  • Ren, Y. et al. Proteomic biomarkers for lung cancer progression. Biomark Med 12, 205-215, doi:10.2217/bmm-2018-0015 (2018).
  • Ren, Y. et al. Gender specificity improves the early-stage detection of clear cell renal cell carcinoma based on methylomic biomarkers. Biomark Med 12, 607-618, doi:10.2217/bmm-2018-0084 (2018).
  • Liu, G., Ma, Q. & Xu, Y. Physical properties of DNA may direct the binding of nucleoid-associated proteins along the E. coli genome. Math Biosci 301, 50-58, doi:10.1016/j.mbs.2018.03.026 (2018).

2017

  • Tian, Y. et al. Systematic analyses of glutamine and glutamate metabolisms across different cancer types. Chin J Cancer 36, 88, doi:10.1186/s40880-017-0255-y (2017).
  • Chen, X., Chou, W. C., Ma, Q. & Xu, Y. SeqTU: A Web Server for Identification of Bacterial Transcription Units. Scientific reports 7, 43925, doi:10.1038/srep43925 (2017).
  • Cao, S. et al. Competition between DNA Methylation, Nucleotide Synthesis, and Antioxidation in Cancer versus Normal Tissues. Cancer Res 77, 4185-4195, doi:10.1158/0008-5472.Can-17-0262 (2017).
  • Cao, H. et al. Systems-level understanding of ethanol-induced stresses and adaptation in E. coli. Scientific reports 7, 44150, doi:10.1038/srep44150 (2017).

2016

  • Yang, J. et al. Nitrogen remobilization and conservation, and underlying senescence-associated gene expression in the perennial switchgrass Panicum virgatum. New Phytol 211, 75-89, doi:10.1111/nph.13898 (2016).

2015

  • Zhang, C., Liu, C., Cao, S. & Xu, Y. Elucidation of drivers of high-level production of lactates throughout a cancer development. Journal of molecular cell biology 7, 267-279, doi:10.1093/jmcb/mjv031 (2015).
  • Zhang, C., Cao, S., Toole, B. P. & Xu, Y. Cancer may be a pathway to cell survival under persistent hypoxia and elevated ROS: a model for solid-cancer initiation and early development. Int J Cancer 136, 2001-2011, doi:10.1002/ijc.28975 (2015).
  • Yao, F., Zhang, C., Du, W., Liu, C. & Xu, Y. Identification of Gene-Expression Signatures and Protein Markers for Breast Cancer Grading and Staging. PLoS One 10, e0138213, doi:10.1371/journal.pone.0138213 (2015).
  • Mao, X. et al. Revisiting operons: an analysis of the landscape of transcriptional units in E. coli. BMC bioinformatics 16, 356, doi:10.1186/s12859-015-0805-8 (2015).
  • Cui, J. et al. Comprehensive characterization of the genomic alterations in human gastric cancer. Int J Cancer 137, 86-95, doi:10.1002/ijc.29352 (2015).
  • Chou, W. C. et al. Analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum. Nucleic Acids Res 43, e67, doi:10.1093/nar/gkv177 (2015).
  • Cao, S., Zhang, C. & Xu, Y. Somatic mutations may not be the primary drivers of cancer formation. Int J Cancer 137, 2762-2765, doi:10.1002/ijc.29639 (2015).

2014

  • Zhou, C. et al. AST: an automated sequence-sampling method for improving the taxonomic diversity of gene phylogenetic trees. PLoS One 9, e98844, doi:10.1371/journal.pone.0098844 (2014).
  • Wollaston-Hayden, E. E. et al. Global O-GlcNAc Levels Modulate Transcription of the Adipocyte Secretome during Chronic Insulin Resistance. Front Endocrinol (Lausanne) 5, 223, doi:10.3389/fendo.2014.00223 (2014).
  • Wang, Y. et al. Identification of essential proteins based on ranking edge-weights in protein-protein interaction networks. PLoS One 9, e108716, doi:10.1371/journal.pone.0108716 (2014).
  • Mao, X. et al. DOOR 2.0: presenting operons and their functions through dynamic and integrated views. Nucleic Acids Res 42, D654-659, doi:10.1093/nar/gkt1048 (2014).
  • Ma, Q. et al. DMINDA: an integrated web server for DNA motif identification and analyses. Nucleic Acids Res 42, W12-19, doi:10.1093/nar/gku315 (2014).
  • Ma, Q. et al. A phylogenetic model for understanding the effect of gene duplication on cancer progression. Nucleic Acids Res 42, 2870-2878, doi:10.1093/nar/gkt1320 (2014).
  • Ma, Q. et al. Understanding the commonalities and differences in genomic organizations across closely related bacteria from an energy perspective. Sci China Life Sci 57, 1121-1130, doi:10.1007/s11427-014-4734-y (2014).
  • Liu, Q., Zhou, H., Zhu, R., Xu, Y. & Cao, Z. Reconsideration of in silico siRNA design from a perspective of heterogeneous data integration: problems and solutions. Brief Bioinform 15, 292-305, doi:10.1093/bib/bbs073 (2014).
  • Hammond, D. A., Olman, V. & Xu, Y. Functional understanding of the diverse exon-intron structures of human GPCR genes. J Bioinform Comput Biol 12, 1350019, doi:10.1142/s0219720013500194 (2014).

2013

  • Xu, K. et al. Elucidation of how cancer cells avoid acidosis through comparative transcriptomic data analysis. PLoS One 8, e71177, doi:10.1371/journal.pone.0071177 (2013).
  • Wilson, C. M. et al. Clostridium thermocellum transcriptomic profiles after exposure to furfural or heat stress. Biotechnol Biofuels 6, 131, doi:10.1186/1754-6834-6-131 (2013).
  • Mao, F., Olman, V., Wang, Y. & Xu, Y. Barcode server: a visualization-based genome analysis system. PLoS One 8, e56726, doi:10.1371/journal.pone.0056726 (2013).
  • Ma, Q. et al. Computational analyses of transcriptomic data reveal the dynamic organization of the Escherichia coli chromosome under different conditions. Nucleic Acids Res 41, 5594-5603, doi:10.1093/nar/gkt261 (2013).
  • Ma, Q. & Xu, Y. Global genomic arrangement of bacterial genes is closely tied with the total transcriptional efficiency. Genomics Proteomics Bioinformatics 11, 66-71, doi:10.1016/j.gpb.2013.01.004 (2013).
  • Ma, Q. et al. An integrated toolkit for accurate prediction and analysis of cis-regulatory motifs at a genome scale. Bioinformatics 29, 2261-2268, doi:10.1093/bioinformatics/btt397 (2013).
  • Cui, J., Xu, Y. & Puett, D. Microarray-based transcriptome profiling of ovarian cancer cells. Methods in molecular biology (Clifton, N.J.) 1049, 119-137, doi:10.1007/978-1-62703-547-7_11 (2013).

2012

  • Zhang, H., Yin, Y., Olman, V. & Xu, Y. Genomic arrangement of regulons in bacterial genomes. PLoS One 7, e29496, doi:10.1371/journal.pone.0029496 (2012).
  • Yin, Y. et al. dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 40, W445-451, doi:10.1093/nar/gks479 (2012).
  • Xu, K. et al. A comparative study of gene-expression data of basal cell carcinoma and melanoma reveals new insights about the two cancers. PLoS One 7, e30750, doi:10.1371/journal.pone.0030750 (2012).
  • Mao, X., Zhang, H., Yin, Y. & Xu, Y. The percentage of bacterial genes on leading versus lagging strands is influenced by multiple balancing forces. Nucleic Acids Res 40, 8210-8218, doi:10.1093/nar/gks605 (2012).
  • Mao, X., Chen, X., Zhang, Y., Pangle, S. & Xu, Y. CINPER: an interactive web system for pathway prediction for prokaryotes. PLoS One 7, e51252, doi:10.1371/journal.pone.0051252 (2012).
  • Mao, F. et al. Quartet decomposition server: a platform for analyzing phylogenetic trees. BMC bioinformatics 13, 123, doi:10.1186/1471-2105-13-123 (2012).
  • Cui, J., Liang, Y. C. & Xu, Y. Systems biology in the frontier of cancer research: a report of the Second International Workshop of Cancer Systems Biology. Chin J Cancer 31, 409-412, doi:10.5732/cjc.012.10205 (2012).

2011

  • Yin, Y., Huang, J., Gu, X., Bar-Peled, M. & Xu, Y. Evolution of plant nucleotide-sugar interconversion enzymes. PLoS One 6, e27995, doi:10.1371/journal.pone.0027995 (2011).
  • Mao, X., Zhang, Y. & Xu, Y. SEAS: a system for SEED-based pathway enrichment analysis. PLoS One 6, e22556, doi:10.1371/journal.pone.0022556 (2011).
  • Li, G. et al. Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes. Nucleic Acids Res 39, e150, doi:10.1093/nar/gkr766 (2011).
  • Li, G., Liu, B., Ma, Q. & Xu, Y. A new framework for identifying cis-regulatory motifs in prokaryotes. Nucleic Acids Res 39, e42, doi:10.1093/nar/gkq948 (2011).
  • Kong, Y. et al. Molecular analysis of a family of Arabidopsis genes related to galacturonosyltransferases. Plant Physiol 155, 1791-1805, doi:10.1104/pp.110.163220 (2011).
  • Hong, C. S. et al. A computational method for prediction of excretory proteins and application to identification of gastric cancer markers in urine. PLoS One 6, e16875, doi:10.1371/journal.pone.0016875 (2011).
  • Dam, P. et al. Insights into plant biomass conversion from the genome of the anaerobic thermophilic bacterium Caldicellulosiruptor bescii DSM 6725. Nucleic Acids Res 39, 3240-3254, doi:10.1093/nar/gkq1281 (2011).
  • Cui, J. et al. Regulation of gene expression in ovarian cancer cells by luteinizing hormone receptor expression and activation. BMC Cancer 11, 280, doi:10.1186/1471-2407-11-280 (2011).
  • Cui, J. et al. Gene-expression signatures can distinguish gastric cancer grades and stages. PLoS One 6, e17819, doi:10.1371/journal.pone.0017819 (2011).
  • Cui, J., Eldredge, J. B., Xu, Y. & Puett, D. MicroRNA expression and regulation in human ovarian carcinoma cells by luteinizing hormone. PLoS One 6, e21730, doi:10.1371/journal.pone.0021730 (2011).
  • Cui, J. et al. An integrated transcriptomic and computational analysis for biomarker identification in gastric cancer. Nucleic Acids Res 39, 1197-1207, doi:10.1093/nar/gkq960 (2011).
  • Chen, Y., Mao, F., Li, G. & Xu, Y. Genome-wide discovery of missing genes in biological pathways of prokaryotes. BMC bioinformatics 12 Suppl 1, S1, doi:10.1186/1471-2105-12-s1-s1 (2011).
  • Chen, H. et al. Optimal mutation sites for PRE data collection and membrane protein structure prediction. Structure 19, 484-495, doi:10.1016/j.str.2011.02.002 (2011).

2010

  • Zhou, W., Xu, Y. & Schüttler, H. B. Cellulose hydrolysis in evolving substrate morphologies III: time-scale analysis. Biotechnol Bioeng 107, 224-234, doi:10.1002/bit.22814 (2010).
  • Zhou, F. & Xu, Y. cBar: a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data. Bioinformatics 26, 2051-2052, doi:10.1093/bioinformatics/btq299 (2010).
  • Zhou, F., Chen, H. & Xu, Y. GASdb: a large-scale and comparative exploration database of glycosyl hydrolysis systems. BMC Microbiol 10, 69, doi:10.1186/1471-2180-10-69 (2010).
  • Zhou, C., Yin, Y., Dam, P. & Xu, Y. Identification of novel proteins involved in plant cell-wall synthesis based on protein-protein interaction data. J Proteome Res 9, 5025-5037, doi:10.1021/pr100249c (2010).
  • Yin, Y., Zhang, H., Olman, V. & Xu, Y. Genomic arrangement of bacterial operons is constrained by biological pathways encoded in the genome. Proc Natl Acad Sci U S A 107, 6310-6315, doi:10.1073/pnas.0911237107 (2010).
  • Yin, Y., Chen, H., Hahn, M. G., Mohnen, D. & Xu, Y. Evolution and function of the plant cell wall synthesis-related glycosyltransferase family 8. Plant Physiol 153, 1729-1746, doi:10.1104/pp.110.154229 (2010).
  • Yang, S. J. et al. Classification of 'Anaerocellum thermophilum' strain DSM 6725 as Caldicellulosiruptor bescii sp. nov. Int J Syst Evol Microbiol 60, 2011-2015, doi:10.1099/ijs.0.017731-0 (2010).
  • Xu, K. et al. A comparative analysis of gene-expression data of multiple cancer types. PLoS One 5, e13696, doi:10.1371/journal.pone.0013696 (2010).
  • Wang, G., Zhou, F., Olman, V., Li, F. & Xu, Y. Prediction of pathogenicity islands in enterohemorrhagic Escherichia coli O157:H7 using genomic barcodes. FEBS Lett 584, 194-198, doi:10.1016/j.febslet.2009.11.067 (2010).
  • Mao, X. et al. Computational prediction of the osmoregulation network in Synechococcus sp. WH8102. BMC Genomics 11, 291, doi:10.1186/1471-2164-11-291 (2010).
  • Liu, Q., Cui, J., Yang, Q. & Xu, Y. In-silico prediction of blood-secretory human proteins using a ranking algorithm. BMC bioinformatics 11, 250, doi:10.1186/1471-2105-11-250 (2010).
  • Li, G., Liu, B. & Xu, Y. Accurate recognition of cis-regulatory motifs with the correct lengths in prokaryotic genomes. Nucleic Acids Res 38, e12, doi:10.1093/nar/gkp907 (2010).
  • Diao, H. et al. Progesterone receptor-mediated up-regulation of transthyretin in preimplantation mouse uterus. Fertility and sterility 93, 2750-2753, doi:10.1016/j.fertnstert.2010.01.009 (2010).
  • Chou, W. C., Yin, Y. & Xu, Y. GolgiP: prediction of Golgi-resident proteins in plants. Bioinformatics 26, 2464-2465, doi:10.1093/bioinformatics/btq446 (2010).

– 2009

  • Zhou, W., Schüttler, H. B., Hao, Z. & Xu, Y. Cellulose hydrolysis in evolving substrate morphologies I: A general modeling formalism. Biotechnol Bioeng 104, 261-274, doi:10.1002/bit.22389 (2009).
  • Zhou, W., Hao, Z., Xu, Y. & Schüttler, H. B. Cellulose hydrolysis in evolving substrate morphologies II: Numerical results and analysis. Biotechnol Bioeng 104, 275-289, doi:10.1002/bit.22388 (2009).
  • Zhou, F. & Xu, Y. RepPop: a database for repetitive elements in Populus trichocarpa. BMC Genomics 10, 14, doi:10.1186/1471-2164-10-14 (2009).
  • Zhou, F., Olman, V. & Xu, Y. Large-scale analyses of glycosylation in cellulases. Genomics Proteomics Bioinformatics 7, 194-199, doi:10.1016/s1672-0229(08)60049-2 (2009).
  • Yin, Y., Huang, J. & Xu, Y. The cellulose synthase superfamily in fully sequenced plants and algae. BMC Plant Biol 9, 99, doi:10.1186/1471-2229-9-99 (2009).
  • Olman, V., Mao, F., Wu, H. & Xu, Y. Parallel clustering algorithm for large data sets with applications in bioinformatics. IEEE/ACM Trans Comput Biol Bioinform 6, 344-352, doi:10.1109/tcbb.2007.70272 (2009).
  • Mao, F., Dam, P., Chou, J., Olman, V. & Xu, Y. DOOR: a database for prokaryotic operons. Nucleic Acids Res 37, D459-463, doi:10.1093/nar/gkn757 (2009).
  • Liu, Q. et al. Analyses of domains and domain fusions in human proto-oncogenes. BMC bioinformatics 10, 88, doi:10.1186/1471-2105-10-88 (2009).
  • Li, G., Ma, Q., Tang, H., Paterson, A. H. & Xu, Y. QUBIC: a qualitative biclustering algorithm for analyses of gene expression data. Nucleic Acids Res 37, e101, doi:10.1093/nar/gkp491 (2009).
  • Li, G., Che, D. & Xu, Y. A universal operon predictor for prokaryotic genomes. J Bioinform Comput Biol 7, 19-38, doi:10.1142/s0219720009003984 (2009).
  • Kong, Y. et al. Two poplar glycosyltransferase genes, PdGATL1.1 and PdGATL1.2, are functional orthologs to PARVUS/AtGATL1 in Arabidopsis. Mol Plant 2, 1040-1050, doi:10.1093/mp/ssp068 (2009).
  • Kataeva, I. A. et al. Genome sequence of the anaerobic, thermophilic, and cellulolytic bacterium "Anaerocellum thermophilum" DSM 6725. J Bacteriol 191, 3760-3761, doi:10.1128/jb.00256-09 (2009).
  • Gervais, C., Wüst, T., Landau, D. P. & Xu, Y. Application of the Wang-Landau algorithm to the dimerization of glycophorin A. J Chem Phys 130, 215106, doi:10.1063/1.3148186 (2009).
  • Chen, Y., Zhou, F., Li, G. & Xu, Y. MUST: a system for identification of miniature inverted-repeat transposable elements and applications to Anabaena variabilis and Haloquadratum walsbyi. Gene 436, 1-7, doi:10.1016/j.gene.2009.01.019 (2009).
  • Zhou, F., Tran, T. & Xu, Y. Nezha, a novel active miniature inverted-repeat transposable element in cyanobacteria. Biochem Biophys Res Commun 365, 790-794, doi:10.1016/j.bbrc.2007.11.038 (2008).
  • Zhou, F., Olman, V. & Xu, Y. Insertion Sequences show diverse recent activities in Cyanobacteria and Archaea. BMC Genomics 9, 36, doi:10.1186/1471-2164-9-36 (2008).
  • Zhou, F., Olman, V. & Xu, Y. Barcodes for genomes and applications. BMC bioinformatics 9, 546, doi:10.1186/1471-2105-9-546 (2008).
  • Liu, Z., Guo, J. T., Li, T. & Xu, Y. Structure-based prediction of transcription factor binding sites using a protein-DNA docking approach. Proteins 72, 1114-1124, doi:10.1002/prot.22002 (2008).
  • Guo, J. T., Ellrott, K. & Xu, Y. A historical perspective of template-based protein structure prediction. Methods in molecular biology (Clifton, N.J.) 413, 3-42, doi:10.1007/978-1-59745-574-9_1 (2008).
  • Ellrott, K., Guo, J. T., Olman, V. & Xu, Y. Improving the performance of protein threading using insertion/deletion frequency arrays. J Bioinform Comput Biol 6, 585-602, doi:10.1142/s0219720008003552 (2008).
  • Cui, J., Liu, Q., Puett, D. & Xu, Y. Computational prediction of human proteins that can be secreted into the bloodstream. Bioinformatics 24, 2370-2375, doi:10.1093/bioinformatics/btn418 (2008).
  • Chen, Y., Zhou, F., Li, G. & Xu, Y. A recently active miniature inverted-repeat transposable element, Chunjie, inserted into an operon without disturbing the operon structure in Geobacter uraniireducens Rf4. Genetics 179, 2291-2297, doi:10.1534/genetics.108.089995 (2008).
  • Wu, H., Mao, F., Olman, V. & Xu, Y. Hierarchical classification of functionally equivalent genes in prokaryotes. Nucleic Acids Res 35, 2125-2140, doi:10.1093/nar/gkl1114 (2007).
  • McLean, A. B. et al. Activin a efficiently specifies definitive endoderm from human embryonic stem cells only when phosphatidylinositol 3-kinase signaling is suppressed. Stem Cells 25, 29-38, doi:10.1634/stemcells.2006-0219 (2007).
  • Liu, H., Dalton, S. & Xu, Y. Transcriptional profiling of definitive endoderm derived from human embryonic stem cells. Comput Syst Bioinformatics Conf 6, 79-82 (2007).
  • Guo, J. T., Jaromczyk, J. W. & Xu, Y. Analysis of chameleon sequences and their implications in biological processes. Proteins 67, 548-558, doi:10.1002/prot.21285 (2007).
  • Ellrott, K., Guo, J. T., Olman, V. & Xu, Y. Improvement in protein sequence-structure alignment using insertion/deletion frequency arrays. Comput Syst Bioinformatics Conf 6, 335-342 (2007).
  • Dam, P., Olman, V., Harris, K., Su, Z. & Xu, Y. Operon prediction using both genome-specific and general genomic information. Nucleic Acids Res 35, 288-298, doi:10.1093/nar/gkl1018 (2007).
  • Zhou, F., Xue, Y., Yao, X. & Xu, Y. CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy (CSS). Bioinformatics 22, 894-896, doi:10.1093/bioinformatics/btl013 (2006).
  • Zhou, F., Xue, Y., Yao, X. & Xu, Y. A general user interface for prediction servers of proteins' post-translational modification sites. Nat Protoc 1, 1318-1321, doi:10.1038/nprot.2006.209 (2006).
  • Yan, B. et al. A point-process model for rapid identification of post-translational modifications. Pac Symp Biocomput, 327-338 (2006).
  • Su, Z. et al. Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102. Nucleic Acids Res 34, 1050-1065, doi:10.1093/nar/gkj496 (2006).
  • Song, Y. et al. Efficient parameterized algorithms for biopolymer structure-sequence alignment. IEEE/ACM Trans Comput Biol Bioinform 3, 423-432, doi:10.1109/tcbb.2006.52 (2006).
  • Olman, V., Hicks, C., Wang, P. & Xu, Y. Gene expression data analysis in subtypes of ovarian cancer using covariance analysis. J Bioinform Comput Biol 4, 999-1014, doi:10.1142/s0219720006002296 (2006).
  • Mao, F. et al. Mapping of orthologous genes in the context of biological pathways: An application of integer programming. Proc Natl Acad Sci U S A 103, 129-134, doi:10.1073/pnas.0509737102 (2006).
  • Liu, C., Yan, B., Song, Y., Xu, Y. & Cai, L. Peptide sequence tag-based blind identification of post-translational modifications with point process model. Bioinformatics 22, e307-313, doi:10.1093/bioinformatics/btl226 (2006).
  • Liu, C., Song, Y., Yan, B., Xu, Y. & Cai, L. Fast de novo peptide sequencing and spectral alignment via tree decomposition. Pac Symp Biocomput, 255-266 (2006).
  • Guo, J. T. & Xu, Y. Amyloid fibril structure modeling using protein threading and molecular dynamics simulations. Methods Enzymol 412, 300-314, doi:10.1016/s0076-6879(06)12018-2 (2006).
  • Ellrott, K., Guo, J. T., Olman, V. & Xu, Y. A generalized threading model using integer programming that allows for secondary structure element deletion. Genome Inform 17, 248-258 (2006).
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