Research Topics
Species | Xiao SunSummaryAffiliation: Southeast University Country: China Publications
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Detail Information
Publications
Analysis of nucleosome positioning determined by DNA helix curvature in the human genomeHongde 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...- Origin and evolution of a placental-specific microRNA family in the human genomeZhidong 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... - Support vector machine for classification of meiotic recombination hotspots and coldspots in Saccharomyces cerevisiae based on codon compositionTong 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... - Meta-analysis of several gene lists for distinct types of cancer: a simple way to reveal common prognostic markersXinan 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... - Mechanism-anchored profiling derived from epigenetic networks predicts outcome in acute lymphoblastic leukemiaXinan 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.... - RF-DYMHC: detecting the yeast meiotic recombination hotspots and coldspots by random forest model using gapped dinucleotide composition featuresPeng 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... - MicroRNA genes derived from repetitive elements and expanded by segmental duplication events in mammalian genomesZhidong 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... - Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid featureJiansheng 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... - Characteristics of nucleosome core DNA and their applications in predicting nucleosome positionsHongde 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... 
Reannotation of protein-coding genes based on an improved graphical representation of DNA sequenceJia 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...- Prediction of RNA-binding residues in proteins from primary sequence using an enriched random forest model with a novel hybrid featureXin 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/... - Meta-analysis of cancer gene-profiling dataXinan 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... - TN curve: a novel 3D graphical representation of DNA sequence based on trinucleotides and its applicationsJia 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.... 
RFRCDB-siRNA: improved design of siRNAs by random forest regression model coupled with database searchingPeng 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...- Cluster analysis of the codon use frequency of MHC genes from different speciesJianmin 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... - [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... - Synonymous codon usage in environmental chlamydia UWE25 reflects an evolutional divergence from pathogenic chlamydiaeTong 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... - An integrative method for identifying the over-annotated protein-coding genes in microbial genomesJia 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... - Analysis of synonymous codon usage in Aeropyrum pernix K1 and other Crenarchaeota microorganismsPeng 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... - Role of 10-11bp periodicities of eukaryotic DNA sequence in nucleosome positioningHongde 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... - Global analysis of in vivo EGR1-binding sites in erythroleukemia cell using chromatin immunoprecipitation and massively parallel sequencingChao 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... - Analysis of synonymous codon usage in H5N1 virus and other influenza A virusesTong 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... - [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... - A novel feature-based method for whole genome phylogenetic analysis without alignment: application to HEV genotyping and subtypingZhihua 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... - Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the NidoviralesWanjun 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... - Expression profiles of mouse dendritic cell sarcoma are similar to those of hematopoietic stem cells or progenitors by clustering and principal component analysesShixin 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... - Genome-scale analysis to the impact of gene deletion on the metabolism of E. coli: constraint-based simulation approachZixiang 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... - Coronavirus phylogeny based on base-base correlationZhi 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... - [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.. - MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined featuresPeng 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... - Folding type specific secondary structure propensities of synonymous codonsWanjun 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... - Classifying genomic sequences by sequence feature analysisZhi 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... - The relationship between synonymous codon usage and protein structure in Escherichia coli and Homo sapiensWanjun 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...