Xiao Sun

Summary

Affiliation: Southeast University
Country: China

Publications

  1. ncbi request reprint Quantitative group testing-based overlapping pool sequencing to identify rare variant carriers
    Chang Chang Cao
    State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
    BMC Bioinformatics 15:195. 2014
  2. pmc Nucleosome organization in the vicinity of transcription factor binding sites in the human genome
    Yumin Nie
    State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, 210096 Nanjing, China
    BMC Genomics 15:493. 2014
  3. pmc MicroRNA genes derived from repetitive elements and expanded by segmental duplication events in mammalian genomes
    Zhidong Yuan
    State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
    PLoS ONE 6:e17666. 2011
  4. pmc The patterns of histone modifications in the vicinity of transcription factor binding sites in human lymphoblastoid cell lines
    Yumin Nie
    State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
    PLoS ONE 8:e60002. 2013
  5. pmc Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature
    Jiansheng Wu
    State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, P R China
    Bioinformatics 25:30-5. 2009
  6. pmc Identification of novel microRNAs in primates by using the synteny information and small RNA deep sequencing data
    Zhidong Yuan
    School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
    Int J Mol Sci 14:20820-32. 2013
  7. pmc The nucleosome regulates the usage of polyadenylation sites in the human genome
    Huan Huang
    State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
    BMC Genomics 14:912. 2013
  8. pmc Mechanism-anchored profiling derived from epigenetic networks predicts outcome in acute lymphoblastic leukemia
    Xinan Yang
    Center for Biomedical Informatics and Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
    BMC Bioinformatics 10:S6. 2009
  9. pmc RF-DYMHC: detecting the yeast meiotic recombination hotspots and coldspots by random forest model using gapped dinucleotide composition features
    Peng Jiang
    State Key Laboratory of Bioelectronics, Department of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, PR China
    Nucleic Acids Res 35:W47-51. 2007
  10. ncbi request reprint RFRCDB-siRNA: improved design of siRNAs by random forest regression model coupled with database searching
    Peng Jiang
    State Key Laboratory of Bioelectronics, Department of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, PR China
    Comput Methods Programs Biomed 87:230-8. 2007

Collaborators

Detail Information

Publications45

  1. ncbi request reprint Quantitative group testing-based overlapping pool sequencing to identify rare variant carriers
    Chang Chang Cao
    State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
    BMC Bioinformatics 15:195. 2014
    ....
  2. pmc Nucleosome organization in the vicinity of transcription factor binding sites in the human genome
    Yumin Nie
    State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, 210096 Nanjing, China
    BMC Genomics 15:493. 2014
    ..Here, we investigated the nucleosome occupancy profiles around computationally inferred binding sites, based on 519 TF binding motifs, in human GM12878 and K562 cells...
  3. pmc MicroRNA genes derived from repetitive elements and expanded by segmental duplication events in mammalian genomes
    Zhidong Yuan
    State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
    PLoS ONE 6:e17666. 2011
    ..Our study is a valuable contribution to the knowledge of evolution and function of non-coding region in genome...
  4. pmc The patterns of histone modifications in the vicinity of transcription factor binding sites in human lymphoblastoid cell lines
    Yumin Nie
    State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
    PLoS ONE 8:e60002. 2013
    ..These findings have epigenetic implications for future analysis of regulatory elements...
  5. pmc Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature
    Jiansheng Wu
    State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, P R China
    Bioinformatics 25:30-5. 2009
    ..The numbers of binding and non-binding residues in proteins are highly unbalanced, so a novel scheme is proposed to deal with the problem of imbalanced datasets by downsizing the majority class...
  6. pmc Identification of novel microRNAs in primates by using the synteny information and small RNA deep sequencing data
    Zhidong Yuan
    School of Life Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
    Int J Mol Sci 14:20820-32. 2013
    ..The results show that our approach can effectively identify novel miRNAs and some miRNAs that supported by small RNA sequencing data maybe play roles in the nervous system. ..
  7. pmc The nucleosome regulates the usage of polyadenylation sites in the human genome
    Huan Huang
    State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
    BMC Genomics 14:912. 2013
    ..However, the association between nucleosome occupancy and polyadenylation site usage is still unclear...
  8. pmc Mechanism-anchored profiling derived from epigenetic networks predicts outcome in acute lymphoblastic leukemia
    Xinan Yang
    Center for Biomedical Informatics and Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
    BMC Bioinformatics 10:S6. 2009
    ....
  9. pmc RF-DYMHC: detecting the yeast meiotic recombination hotspots and coldspots by random forest model using gapped dinucleotide composition features
    Peng Jiang
    State Key Laboratory of Bioelectronics, Department of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, PR China
    Nucleic Acids Res 35:W47-51. 2007
    ..bioinf.seu.edu.cn/Recombination/rf_dymhc.htm. Given a yeast genome and prediction parameters (RI-value and non-overlapping window scan size), the program reports the predicted hot/cold spots and marks them in color...
  10. ncbi request reprint RFRCDB-siRNA: improved design of siRNAs by random forest regression model coupled with database searching
    Peng Jiang
    State Key Laboratory of Bioelectronics, Department of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, PR China
    Comput Methods Programs Biomed 87:230-8. 2007
    ..The matched sequences with the exceeding the user defined functionality value threshold are kept. (2) The mismatched sequences are then processed into the RFR prediction system for further analysis...
  11. pmc An integrative method for identifying the over-annotated protein-coding genes in microbial genomes
    Jia Feng Yu
    State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
    DNA Res 18:435-49. 2011
    ..Our analysis also indicates that the over-annotated protein-coding genes can cause the false positive of horizontal gene transfers detection. The webserver of the proposed algorithm can be freely accessible from www.cbi.seu.edu.cn/RPGM...
  12. doi request reprint Prediction of RNA-binding residues in proteins from primary sequence using an enriched random forest model with a novel hybrid feature
    Xin Ma
    State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, People s Republic of China
    Proteins 79:1230-9. 2011
    ..8675) which represents that PRBR attains excellent performance on predicting the RNA-binding residues in proteins. The PRBR web-server implementation is freely available at http://www.cbi.seu.edu.cn/PRBR/...
  13. pmc Characteristics of nucleosome core DNA and their applications in predicting nucleosome positions
    Hongde Liu
    State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
    Biophys J 94:4597-604. 2008
    ..Based on predictions, nucleosome distributions near the beginning and end of open reading frames were analyzed. Results indicated that the majority of open reading frames' start and end sites were occupied by nucleosomes...
  14. doi request reprint Meta-analysis of cancer gene-profiling data
    Xinan Yang
    Division of Bioinformatics, State Key Laboratory of Bioelectronics Chien Shiung Wu Laboratory, Southeast University, Nanjing, China
    Methods Mol Biol 576:409-26. 2010
    ..This chapter introduces the R implementation of this methodology on real data sets to identify biomarkers for adenocarcinoma lung cancer...
  15. ncbi request reprint Sequence-based prediction of DNA-binding residues in proteins with conservation and correlation information
    Xin Ma
    State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University and Nanjing Audit University, Nanjing, P R China
    IEEE/ACM Trans Comput Biol Bioinform 9:1766-75. 2012
    ..The DNABR web-server system is freely available at http://www.cbi.seu.edu.cn/DNABR/...
  16. ncbi request reprint Nucleosome distribution near the 3' ends of genes in the human genome
    Huan Huang
    State Key Laboratory of Bioelectronics, Southeast University
    Biosci Biotechnol Biochem 77:2051-5. 2013
    ..Our results reveal influences on nucleosome occupancy near polyadenylation sites and constitute evidence indicating that nucleosome distribution regulates 3' end processing of protein-coding genes. ..
  17. pmc MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features
    Peng Jiang
    State Key Laboratory of Bioelectronics, Department of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, PR China
    Nucleic Acids Res 35:W339-44. 2007
    ..bioinf.seu.edu.cn/miRNA/. Given a sequence, MiPred decides whether it is a pre-miRNA-like hairpin sequence or not. If the sequence is a pre-miRNA-like hairpin, the RF classifier will predict whether it is a real pre-miRNA or a pseudo one...
  18. pmc Origin and evolution of a placental-specific microRNA family in the human genome
    Zhidong Yuan
    State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
    BMC Evol Biol 10:346. 2010
    ..With the rapid development of technology, more and more miRNAs are being discovered. However, the origin and evolution of most miRNAs remain obscure. Here we report the origin and evolution dynamics of a human miRNA family...
  19. ncbi request reprint A novel feature-based method for whole genome phylogenetic analysis without alignment: application to HEV genotyping and subtyping
    Zhihua Liu
    State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, PR China
    Biochem Biophys Res Commun 368:223-30. 2008
    ..BBC algorithm can serve as an alternative to rapidly construct phylogenetic trees and infer evolutionary relationships...
  20. ncbi request reprint Reannotation of protein-coding genes based on an improved graphical representation of DNA sequence
    Jia Feng Yu
    State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, People s Republic of China
    J Comput Chem 31:2126-35. 2010
    ..The present method could also be extended to other genomes with or without adaptation of training sets with high accuracy...
  21. doi request reprint Nucleosome organization in sequences of alternative events in human genome
    Huan Huang
    State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
    Biosystems 109:214-9. 2012
    ..These results provided a new approach for better appreciation of the connection between chromatin structure and gene expression regulation...
  22. ncbi request reprint TN curve: a novel 3D graphical representation of DNA sequence based on trinucleotides and its applications
    Jia Feng Yu
    State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, PR China
    J Theor Biol 261:459-68. 2009
    ....
  23. ncbi request reprint Global analysis of in vivo EGR1-binding sites in erythroleukemia cell using chromatin immunoprecipitation and massively parallel sequencing
    Chao Tang
    School of Basic Medical Sciences, Southeast University, Nanjing, P R China
    Electrophoresis 31:2936-43. 2010
    ..This whole genome study on the EGR1 targets may provide a better understanding of the EGR1 regulated genes and the downstream pathway in megakaryocyte differentiation...
  24. pmc Analysis of nucleosome positioning determined by DNA helix curvature in the human genome
    Hongde Liu
    State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
    BMC Genomics 12:72. 2011
    ..What role does sequence-dependent positioning play? In this paper, using a curvature profile model, nucleosomes are predicted in the human genome and patterns of nucleosomes near some key sites are investigated...
  25. ncbi request reprint Identifying rare variants with optimal depth of coverage and cost-effective overlapping pool sequencing
    Chang Chang Cao
    State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
    Genet Epidemiol 37:820-30. 2013
    ..93% accuracy. Utilizing overlapping pool sequencing, the cost for screening variant carriers with frequency equaled 1% in 200 diploid individuals dropped to at least 66% at which target sequencing region was set to 30 Mb. ..
  26. pmc Support vector machine for classification of meiotic recombination hotspots and coldspots in Saccharomyces cerevisiae based on codon composition
    Tong Zhou
    State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
    BMC Bioinformatics 7:223. 2006
    ..Hotspots and coldspots are receiving increasing attention in research into the mechanism of meiotic recombination. However, predicting hotspots and coldspots from DNA sequence information is still a challenging task...
  27. ncbi request reprint Analysis of synonymous codon usage in Aeropyrum pernix K1 and other Crenarchaeota microorganisms
    Peng Jiang
    State Key Laboratory of Bioelectronics, Department of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
    J Genet Genomics 34:275-84. 2007
    ..The extent of codon bias in A. pernix K1 and S. acidocaldarius DSM 639 were highly correlated with the gene expression level, but no such association was detected in P. aerophilum str. IM2 genomes...
  28. ncbi request reprint Prediction of autism susceptibility genes based on association rules
    Lejun Gong
    State Key Laboratory of Bioelectronics, Department of Biological Science and Medical Engineering, Southeast University, Nanjing, People s Republic of China
    J Neurosci Res 90:1119-25. 2012
    ..The web portal for the predicted results, which is freely available at http://biolab.hyit.edu.cn/ar, can be a valuable resource in studies of diseases related to genes...
  29. ncbi request reprint Cluster analysis of the codon use frequency of MHC genes from different species
    Jianmin Ma
    Chien Shiung WU Laboratory, Southeast University, 210096 Jiangsu Province, Nanjing, People s Republic of China
    Biosystems 65:199-207. 2002
    ..The conclusion may be useful in gene classification and gene function prediction...
  30. ncbi request reprint Classifying genomic sequences by sequence feature analysis
    Zhi Hua Liu
    State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
    Genomics Proteomics Bioinformatics 3:201-5. 2005
    ..The results show that we could classify the functional regions of genome based on sequence feature and discriminant analysis...
  31. pmc Meta-analysis of several gene lists for distinct types of cancer: a simple way to reveal common prognostic markers
    Xinan Yang
    State Key Laboratory of Bioelectronics, Southeast University, Nanjing, PR China
    BMC Bioinformatics 8:118. 2007
    ..Three data sets for leukemia and the other six for different solid tumors are used to demonstrate our method, using established statistical techniques...
  32. ncbi request reprint Role of 10-11bp periodicities of eukaryotic DNA sequence in nucleosome positioning
    Hongde Liu
    School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
    Biosystems 105:295-9. 2011
    ..Our study reveals some details about the roles of DNA sequence in positioning nucleosomes...
  33. ncbi request reprint Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses
    Tong Zhou
    Key Laboratory of Molecular and Biomolecular Electronics of the Ministry of Education, Southeast University, Nanjing, Jiangsu 210096, China
    Biosystems 81:77-86. 2005
    ..However, translational selection and gene length have no effect on the variations of synonymous codon usage in these virus genes...
  34. pmc Genome-scale analysis to the impact of gene deletion on the metabolism of E. coli: constraint-based simulation approach
    Zixiang Xu
    State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, PR China
    BMC Bioinformatics 10:S62. 2009
    ..The impact of gene deletion on flux redistribution, the functions and characters of key genes, and the performance of different reactions in entire gene deletion still lack research...
  35. pmc Analysis of enhanced current-generating mechanism of Geobacter sulfurreducens strain via model-driven metabolism simulation
    Jing Meng
    State Key Laboratory of Bioelectronics, Southeast University, Nanjing, China
    PLoS ONE 8:e73907. 2013
    ..Our simulations will provide an insight into the enhanced current-generating mechanism and identify theoretical range of respiration rates for guiding strain improvement in MFCs. ..
  36. ncbi request reprint [The progress in complex homeobox domains]
    Shi Xin Zhou
    Key Laboratory of Molecular and Biomolecular Electronics of Ministry of Education, Southeast University, Nanjing 210096, China
    Yi Chuan 26:984-90. 2004
    ..Recent reports indicate that 'complex homeobox' genes also take part in tumorigenesis by the way of gene fusions and deregulation. The progress of 'complex homeobox' in types, structures and functions have been summarized in this review...
  37. ncbi request reprint Coronavirus phylogeny based on base-base correlation
    Zhi Hua Liu
    State Key Laboratory of Bioelectronics, Southeast University, Nanjing, PR China
    Int J Bioinform Res Appl 4:211-20. 2008
    ..BBC, to study genome information structure based on information theory, provides a novel alignment-free phylogenomic methodology in postgenome informatics...
  38. ncbi request reprint [Construction and application of learning science related phenotype ontology]
    Liang Chen
    Key Laboratory of Molecular and Biomalecular Electronics of Ministry of Education, Southeast University, Nanjing 210096, China
    Sheng Wu Yi Xue Gong Cheng Xue Za Zhi 24:145-8. 2007
    ..By using this Ontology, we can integrate isomerous data. It will increase the efficiency of information acquisition, management and search,and provide a platform for data sharing and data mining...
  39. ncbi request reprint Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the Nidovirales
    Wanjun Gu
    Key Laboratory of Molecular and Biomolecular Electronics, Southeast University, Ministry of Education, Nanjing, Jiangsu 210096, China
    Virus Res 101:155-61. 2004
    ..However, translational selection and gene length have no effect on the variations of synonymous codon usage in these virus genes...
  40. ncbi request reprint Expression profiles of mouse dendritic cell sarcoma are similar to those of hematopoietic stem cells or progenitors by clustering and principal component analyses
    Shixin Zhou
    Chien Shiung WU Laboratory, Department of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
    Biochem Biophys Res Commun 331:194-202. 2005
    ..It is suggested that the DC sarcomas are more similar to the DC progenitors and hematopoietic stem cells than the relative mature DCs in gene expressions on the large-scale...
  41. ncbi request reprint Intrinsic correlation of oligonucleotides: a novel genomic signature for metagenome analysis
    Xiao Ding
    State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China Electronic address
    J Theor Biol 353:9-18. 2014
    ..ICOs perform better than tetranucleotide composition in characterizing microbial genomes. The hybrid feature that used a combination of the two kinds of sequence features had advantages over a single sequence feature...
  42. ncbi request reprint Synonymous codon usage in environmental chlamydia UWE25 reflects an evolutional divergence from pathogenic chlamydiae
    Tong Zhou
    State Key Laboratory of Bioelectronics, Southeast University, 210096 China
    Gene 368:117-25. 2006
    ..Analyzing the codon usage pattern in the environmental chlamydia and comparing it with that of the pathogenic chlamydiae may provide clues how the chlamydiae have evolved from their common ancestor...
  43. ncbi request reprint [A gene-chip image grid localization method based on profiles of image]
    Yuanyuan Hu
    Department of Biomedical Engineering, Southeast University, Nanjing 210096, China
    Sheng Wu Yi Xue Gong Cheng Xue Za Zhi 22:668-71. 2005
    ..The experiments show that the new approach correctly locates the probes while giving protection against noise affection robustly. Grid location..
  44. ncbi request reprint Folding type specific secondary structure propensities of synonymous codons
    Wanjun Gu
    Key Laboratory of Molecular and Biomolecular Electronics, Southeast University, Ministry of Education, Nanjing 210096, China
    IEEE Trans Nanobioscience 2:150-7. 2003
    ..These codon-based amino acid secondary structure propensities are helpful to in vitro protein design and protein secondary structure prediction...
  45. ncbi request reprint The relationship between synonymous codon usage and protein structure in Escherichia coli and Homo sapiens
    Wanjun Gu
    Key Laboratory of Molecular and Biomolecular Electronics Southeast University, Ministry of Education, Nanjing 210096, China
    Biosystems 73:89-97. 2004
    ..Further analysis has shown that GC content on the second codon position can distinguish coding genes for different folded proteins in both organisms...