孙啸

职  称：教授、博士生导师

实 验 室：数字医学工程全国重点实验室

学  院：生物科学与医学工程学院

学  校：东南大学九龙湖校区

地  址：江苏省南京市

电子邮箱：xsun@seu.edu.cn

邮  编：211189





















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主要论文

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  • [1] Zhang R, Shu H, Wang Y, Tao T, Tu J, Wang C, Mergny JL, Sun X. G-Quadruplex Structures Are Key Modulators of Somatic Structural Variants in Cancers. Cancer Res. 2023 Apr 14;83(8):1234-1248. doi: 10.1158/0008-5472.CAN-22-3089. PMID: 36791413; PMCID: PMC10102852.
  • [2] Chen Y, Zhang H, Sun X. Improving the performance of single-cell RNA-seq data mining based on relative expression orderings. Brief Bioinform. 2023 Jan 19;24(1):bbac556. doi: 10.1093/bib/bbac556. PMID: 36528803; PMCID: PMC9851298.
  • [3] Ming W, Zhu Y, Li F, Bai Y, Gu W, Liu Y, Sun X, Liu X, Liu H. Identifying Associations between DCE-MRI Radiomic Features and Expression Heterogeneity of Hallmark Pathways in Breast Cancer: A Multi-Center Radiogenomic Study. Genes (Basel). 2022 Dec 22;14(1):28. doi: 10.3390/genes14010028. PMID: 36672769; PMCID: PMC9858814.
  • [4] Zhang Z, Zhang R, Xiao K, Sun X. G4Beacon: An In Vivo G4 Prediction Method Using Chromatin and Sequence Information. Biomolecules. 2023 Feb 3;13(2):292. doi: 10.3390/biom13020292. PMID: 36830661; PMCID: PMC9953394.
  • [5] Shu H, Zhang R, Xiao K, Yang J, Sun X. G-Quadruplex-Binding Proteins: Promising Targets for Drug Design. Biomolecules. 2022 Apr 29;12(5):648. doi: 10.3390/biom12050648.
  • [6] Ming W, Zhu Y, Bai Y, Gu W, Li F, Hu Z, Xia T, Dai Z, Yu X, Li H, Gu Y, Yuan S, Zhang R, Li H, Zhu W, Ding J, Sun X, Liu Y, Liu H, Liu X. Radiogenomics analysis reveals the associations of dynamic contrast-enhanced-MRI features with gene expression characteristics, PAM50 subtypes, and prognosis of breast cancer. Front Oncol. 2022 Jul 28;12:943326. doi: 10.3389/fonc.2022.943326. PMID: 35965527; PMCID: PMC9366134.
  • [7] Ming W, Li F, Zhu Y, Bai Y, Gu W, Liu Y, Sun X, Liu X, Liu H. Predicting hormone receptors and PAM50 subtypes of breast cancer from multi-scale lesion images of DCE-MRI with transfer learning technique. Comput Biol Med. 2022 Sep 28;150:106147. doi: 10.1016/j.compbiomed.2022.106147. Epub ahead of print. PMID: 36201887.
  • [8] Chen Y, Li H, Sun X. Construction and analysis of sample-specific driver modules for breast cancer. BMC Genomics. 2022 Oct 20;23(1):717. doi: 10.1186/s12864-022-08928-4. PMID: 36266635.
  • [9] Ming W, Li F, Zhu Y, Bai Y, Gu W, Liu Y, Liu X, Sun X, Liu H. Unsupervised Analysis Based on DCE-MRI Radiomics Features Revealed Three Novel Breast Cancer Subtypes with Distinct Clinical Outcomes and Biological Characteristics. Cancers (Basel). 2022 Nov 9;14(22):5507. doi: 10.3390/cancers14225507. PMID: 36428600.
  • [10] Chen Y, Gu Y, Hu Z, Sun X. Sample-specific perturbation of gene interactions identifies breast cancer subtypes. Brief Bioinform. 2021 Jul 20;22(4):bbaa268. doi: 10.1093/bib/bbaa268. PMID: 33126248; PMCID: PMC8293822.
  • [11] Li HT, Yuan SX, Wu JS, Gu Y, Sun X. Predicting Conversion from MCI to AD Combining Multi-Modality Data and Based on Molecular Subtype. Brain Sci. 2021 May 21;11(6):674. doi: 10.3390/brainsci11060674. PMID: 34064186; PMCID: PMC8224289.
  • [12] Yuan S, Li H, Wu J, Sun X. Classification of Mild Cognitive Impairment with Multimodal Data using both Labeled and Unlabeled Samples. IEEE/ACM Trans Comput Biol Bioinform. 2021 Jan 20;PP. doi: 10.1109/TCBB.2021.3053061. Epub ahead of print. PMID: 33471765.
  • [13] Yuan SX, Li HT, Gu Y, Sun X. Brain-Specific Gene Expression and Quantitative Traits Association Analysis for Mild Cognitive Impairment. Biomedicines. 2021 Jun 8;9(6):658. doi: 10.3390/biomedicines9060658. PMID: 34201204; PMCID: PMC8229744.
  • [14] Zhang R, Liu Y, Zhang X, Xiao K, Hou Y, Liu H, Sun X. Detecting and Profiling Endogenous RNA G-Quadruplexes in the Human Transcriptome. Int J Mol Sci. 2021 Jul 27;22(15):8012. doi: 10.3390/ijms22158012. PMID: 34360778.
  • [15] Shu C, Xiao K, Sun X. Structural Basis for the High Conductivity of Microbial Pili as Potential Nanowires. J Nanosci Nanotechnol. 2020 Jan 1;20(1):64-80. doi: 10.1166/jnn.2020.16883.
  • [16] Ding D, Shu C, Sun X. Transcriptional regulatory module analysis reveals that bridge proteins reconcile multiple signals in extracellular electron transfer pathways. Proteins. 2020 Jan;88(1):196-205. doi: 10.1002/prot.25789.
  • [17] Shu C, Zhu Q, Xiao K, Hou Y, Ma H, Ma J, Sun X. Direct Extracellular Electron Transfer of the Geobacter sulfurreducens Pili Relevant to Interaromatic Distances. Biomed Res Int. 2019:6151587. doi:10.1155/2019/6151587
  • [18] Hai-tao Li, Yajun Liu, Hongde Liu, Xiao Sun. Effect for Human Genomic Variation During the BMP4-Induced Conversion From Pluripotent Stem Cells to Trophoblast. Front Genet. 2020; 11: 230. Published online 2020 Apr 7. doi: 10.3389/fgene.2020.00230
  • [19] Li H, Sharma A, Luo K, Qin ZS, Sun X, Liu H. DeconPeaker, a Deconvolution Model to Identify Cell Types Based on Chromatin Accessibility in ATAC-Seq Data of Mixture Samples. Front Genet. 2020 May 8;11:392. doi: 10.3389/fgene.2020.00392. eCollection 2020.
  • [20] Liu H, Li H, Luo K, Sharma A, Sun X. Prognostic gene expression signature revealed the involvement of mutational pathways in cancer genome. J Cancer. 2020 May 18;11(15):4510-4520. doi: 10.7150/jca.40237. eCollection 2020.
  • [21] Huamei Li, Amit Sharma, Wenglong Ming, Xiao Sun, Hongde Liu, A deconvolution method and its application in analyzing the cellular fractions in acute myeloid leukemia samples. BMC Genomics, 2020, 21(1):652. doi: 10.1186/s12864-020-06888-1.
  • [22] Rongxin Zhang, Ke Xiao, Yu Gu, Hongde Liu, Xiao Sun. Whole genome identification of potential G-quadruplexes and analysis of the G-quadruplex binding domain for SARS-CoV-2. Front Genet. 2020; 11: 587829. Published online 2020 Nov 27. doi: 10.3389/fgene.2020.587829.
  • [23] Yumin Nie, Chuanjun Shu, Xiao Sun. Cooperative binding of transcription factors in the human genome. Genomics, 2020, S0888-7543(19)30258-7. doi: 10.1016/j.ygeno.2020.06.029.
  • [24] Li HT, Yuan SX, Wu JS, Zhang XZ, Liu Y, Sun X. Molecular Subtyping of Mild Cognitive Impairment based on Genetic Polymorphism and Gene Expression. The Journal of Prevention of Alzheimer's Disease, 2020: 1-10.
  • [25] Hou Y, Li F, Zhang R, Li S, Liu H, Qin Z, Sun X. Integrative characterization of G-Quadruplexes in the three-dimensional chromatin structure. EPIGENETICS. 2019, 14(9):894-911. doi: 10.1080/15592294.2019.1621140.
  • [26] Hou Y, Zhang R, Sun X. Enhancer LncRNAs Influence Chromatin Interactions in Different Ways. Front Genet. 2019 Oct 16;10:936. doi: 10.3389/fgene.2019.00936. eCollection 2019.
  • [27] Zhao X, Wu S, Fang N, Sun X, Fan J. Evaluation of single-cell classifiers for single-cell RNA sequencing data sets. Brief Bioinform. 2019 Oct 23. pii: bbz096. doi: 10.1093/bib/bbz096.
  • [28] Yuan S, Li H, Xie J, Sun X. Quantitative Trait Module-based Genetic Analysis of Alzheimer's Disease. Int J Mol Sci. 2019 Nov 25;20(23). pii: E5912. doi: 10.3390/ijms20235912.
  • [29] Ming W, Xie H, Hu Z, Chen Y, Zhu Y, Bai Y, Liu H, Sun X, Liu Y and Gu W. Two Distinct Subtypes Revealed in Blood Transcriptome of Breast Cancer Patients with an Unsupervised Analysis. Front Oncol. 2019 Oct 1; 9:985. doi:10.3389/fonc.2019.00985.
  • [30] Shu C, Xiao K, Sun X. Structural Basis for the Influence of A1, 5A, and W51W57 Mutations on the Conductivity of the Geobacter sulfurreducens Pili. Crystals. 2018, 8(1), 10; doi:10.3390/cryst8010010
  • [31] Ding D, Sun X. Network-Based Methods for Identifying Key Active Proteins in the Extracellular Electron Transfer Process in Shewanella oneidensis MR-1. Genes (Basel). 2018 Jan 16;9(1). pii: E41. doi: 10.3390/genes9010041.
  • [32] Ding D, Sun X. A Comparative Study of Network Motifs in the Integrated Transcriptional Regulation and Protein Interaction Networks of Shewanella. IEEE/ACM Trans Comput Biol Bioinform. 2018. doi: 10.1109/TCBB.2018.2804393.
  • [33] Cheng X, Hou Y, Nie Y, Zhang Y, Huang H, Liu H, Sun X. Nucleosome Positioning of Intronless Genes in the Human Genome. IEEE/ACM Trans Comput Biol Bioinform. 2018 Jul-Aug;15(4):1111-1121. doi: 10.1109/TCBB.2015.2476811.
  • [34] Hou Y, Huang H, Hu W, Liu H, Sun X. Histone Modifications Influence Skipped Exons Inclusion. J Bioinform Comput Biol. 2017 Feb; 15(1): 1750003. doi: 10.1142/S0219720017500032.
  • [35] Shu C, Xiao K, Yan Q, Sun X. Comparative Analysis of Type IV Pilin in Desulfuromonadales. Front Microbiol. 2016 Dec 21;7:2080. doi: 10.3389/fmicb.2016.02080.
  • [36] Liu Y, Ding D, Liu H, Sun X. The accessible chromatin landscape during conversion of human embryonic stem cells to trophoblast by BMP4. Biol Reprod. 2017, 96(6):1267-1278. doi: 10.1093/biolre/iox028.
  • [37] Cao C, Pan R, Tan J, Sun X, Xiao P. Efficient identification of SNPs in pooled DNA samples using a dual mononucleotide addition-based sequencing method. Mol Genet Genomics. 2017 Jun 13. doi: 10.1007/s00438-017-1332-2.
  • [38] Shu C, Xiao K, Cao C, Ding D, Sun X. Predicting and Interpreting the Structure of Type IV Pilus of Electricigens by Molecular Dynamics Simulations. Molecules. 2017, 22(8). pii: E1342. doi: 10.3390/molecules22081342.
  • [39] Fu Y, Li L, Hao S, Guan R, Fan G, Shi C, Wan H, Chen W, Zhang H, Liu G, Wang J, Ma L, You J, Ni X, Yue Z, Xu X, Sun X, Liu X, Lee SM. Draft genome sequence of the Tibetan medicinal herb, Rhodiola crenulata. Gigascience. 2017, 6(6):1-5. doi: 10.1093/gigascience/gix033.
  • [40] Liu L, Xie J, Sun X, Luo K, Qin ZS, Liu H. An approach of identifying differential nucleosome regions in multiple samples. BMC Genomics. 2017, 18(1):135.
  • [41] Li C, Cao CC, Tu J, Sun X. An accurate clone-based haplotyping method by overlapping pool sequencing. Nucleic Acids Res. 2016:gkw284.
  • [42] Xiao K, Malvankar NS, Shu CJ, Martz E, Lovley DR, Sun X. Low Energy Atomic Models Suggesting a Pilus Structure that could Account for Electrical Conductivity of Geobacter sulfurreducens Pili. Sci Rep. 2016, 6:23385.
  • [43] Cao CC, Sun X. Combinatorial pooled sequencing: experiment design and decoding. Quantitative Biology. 2016, 4(1): 36-46.
  • [44] Cao CC, Sun X. Ehapp2: Estimate haplotype frequencies from pooled sequencing data with prior database information. J Bioinform Comput Biol. 2016, 14(4):1650017.
  • [45] Ding D, Li L, Shu C, Sun X. K-shell Analysis Reveals Distinct Functional Parts in an Electron Transfer Network and Its Implications for Extracellular Electron Transfer. Front Microbiol. 2016 Apr 20;7:530. doi: 10.3389/fmicb.2016.00530.
  • [46] Ding X, Cao CC, Liu XY, Cheng FD, Luo X, Sun X. HSS-Bin: An Unsupervised Metagenomic Binning Method Based on Hybrid Sequence Feature Recognition and Spectral Clustering. Current Bioinformatics, 2016, 11(3): 330-339.
  • [47] Ma X, Guo J, Xiao K, Sun X. PRBP: Prediction of RNA-binding proteins using a random forest algorithm combined with an RNA-binding residue predictor, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2015, 12(6):1385-1393.
  • [48] Cao CC, Sun X. Accurate estimation of haplotype frequency from pooled sequencing data and cost-effective identification of rare haplotype carriers by overlapping pool sequencing. Bioinformatics. 2015, 31(4):515-522.
  • [49] Xiao K, Shu CJ, Yan Q, Sun X. Predicting Homogeneous Pilus Structure from Monomeric Data and Sparse Constraints. Biomed Res Int. 2015:817134.
  • [50] Ding X, Cheng F, Cao CC, Sun X. DectICO: an alignment-free supervised metagenomic classification method based on feature extraction and dynamic selection. BMC Bioinformatics. 2015, 16(1):323.
  • [51] Cheng XF, Hou Y, Nie YM, Zhang YR, Huang H, Liu HD, Sun X. Nucleosome Positioning of Intronless Genes in the Human Genome. IEEE/ACM Trans Comput Biol Bioinform. 2015.
  • [52] Zhang YR, Cao CC, Liu HD, Sun X. A dynamic programming algorithm for nucleosome positions alignment. International Conference on Systems Biology. 2014.
  • [53] Yu JF, Guo J, Liu QB, Hou Y, Xiao K, Chen QL, Wang JH, Sun X. A hybrid strategy for comprehensive annotation of the protein coding genes in prokaryotic genome. Gene & Genomics. 2015,37:347-355.
  • [54] Yu JF, Chen QL, Ren J, Yang YL, Wang JH, Sun X. Analysis of the multi-copied genes and the impact of the redundant protein coding sequences on gene annotation in prokaryotic genomes. J Theor Biol. 2015, 376:8-14.
  • [55] Yu JF, Dou XH, Wang HB, Sun X, Zhao HY, Wang JH. A Novel Cylindrical Representation for Characterizing Intrinsic Properties of Protein Sequences. J Chem Inf Model. 2015, 55(6):1261-70.
  • [56] Ma X, Guo J, Sun X. Sequence-Based Prediction of RNA-Binding Proteins Using Random Forest with Minimum Redundancy Maximum Relevance Feature Selection. Biomed Res Int. 2015: 425810.
  • [57] Ma X, Sun X. Sequence-based predictor of ATP-binding residues using random forest and mRMR-IFS feature selection. J Theor Biol. 2014, 360:59-66.
  • [58] Ding DW, Xu J, Li L, Xie JM, Sun X. Identifying the potential extracellular electron transfer pathways from c-type cytochrome network. Mol Biosyst. 2014,10(12):3138-3146.
  • [59] Nie Y, Cheng X, Chen J and Sun X. Nucleosome organization in the vicinity of transcription factor binding sites in the human genome. BMC Genomics. 2014,15(1):493.
  • [60] Cao CC, Li C, Sun X. Quantitative group testing-based overlapping pool sequencing to identify rare variant carriers. BMC Bioinformatics. 2014,15(1):195.
  • [61] Huang H, Chen J, Liu H, Sun X. The nucleosome regulates the usage of polyadenylation sites in the human genome. BMC Genomics. 2013, 14(1):912.
  • [62] Ding X, Cao CC, Sun X. Intrinsic correlation of oligonucleotides: A novel genomic signature for metagenome analysis. J. Theor Biol. 2014, 353:9-18.
  • [63] Nie Y, Cheng X, Chen J and Sun X. Nucleosome organization in the vicinity of transcription factor binding sites in the human genome. BMC Genomics. 2014,15(1):493.
  • [64] Cao CC, Li C, Sun X. Quantitative group testing-based overlapping pool sequencing to identify rare variant carriers. BMC Bioinformatics. 2014,15(1):195.
  • [65] Huang H, Chen J, Liu H, Sun X. The nucleosome regulates the usage of polyadenylation sites in the human genome. BMC Genomics. 2013, 14(1):912.
  • [66] Ding X, Cao CC, Sun X. Intrinsic correlation of oligonucleotides: A novel genomic signature for metagenome analysis. J. Theor Biol. 2014, 353:9-18.
  • [67] Yu J, Guo Z, Sun X, Wang J. A review of the computational methods for identifying the over-annotated genes and missing genes in microbial genomes. Current Bioinformatics, 2014,9(2): 147-154.
  • [68] Huang Z, Li Q,Jin W, Liao Q, and Sun X. A Novel Method for Detecting Contaminated Sample Based on Illumina Sequencing Data. International Journal of Bioscience, Biochemistry and Bioinformatics. 2014, 4(2):116-120.
  • [69] Gong L, Yan Q, Yang R, and Sun X. Prediction and extraction of microRNAs2target interactions associated with leukemia. Genetics and Molecular Research. 2014. 13(1):2120-2129.
  • [70] Nie Y, Liu H, Sun X. The patterns of histone modifications in the vicinity of transcription factor binding sites in human lymphoblastoid cell lines. PLoS One. 2013;8(3):e60002.
  • [71] Cao CC, Li C, Huang Z, Ma X, Sun X. Identifying rare variants with optimal depth of coverage and cost-effective overlapping pool sequencing. Genet Epidemiol. 2013,37(8):820-30.
  • [72] Gong L, Yang R, Yan Q, Sun X. Prioritization of disease susceptibility genes using LSM/SVD. IEEE Trans Biomed Eng. 2013,60(12):3410-3417.
  • [73] Meng J, Xu Z, Guo J, Yue Y, Sun X. Analysis of enhanced current-generating mechanism of Geobacter sulfurreducens strain via model-driven metabolism simulation. PLoS One. 2013;8(9):e73907.
  • [74] Huang H, Liu H, Sun X. Nucleosome Distribution near the 3' Ends of Genes in the Human Genome. Biosci Biotechnol Biochem. 2013, 77(10):2051-2055.
  • [75] Liu H, Luo K, Wen H, Ma X, Xie J, Sun X. Quantitative analysis reveals increased histone modifications and a broad nucleosome-free region bound by histone acetylases in highly expressed genes in human CD4(+) T cells. Genomics. 2013,101(2):113-119.
  • [76] Liu H, Luo K, Ma X, Zhai J, Xie J, Sun X, Wan Y. Patterns of nucleosome and Chromatin Modifications and Their Effects on Chromatin States, Progress in Biochemistry and Biophysics, 2013, 40(11): 1088-1099.
  • [77] Gong L, Yan Y, Sun X. Target Identification and Target-centered Network Construction from Biomedical Literature. JOURNAL OF SOFTWARE, 2013, 8(2):316-319.
  • [78] Gong L, Yang R and Sun X. BRES: EXTRACTING MULTICLASS BIOMEDICAL RELATIONS WITH SEMANTIC NETWORK. Biomedical Engineering: Applications, Basis and Communications. 2013,25(1)
  • [79] Yuan Z, Liu H, Nie Y, Ding S, Yan M, Tan S, Jin Y and Sun X. Identification of Novel MicroRNAs in Primates by Using the Synteny Information and Small RNA Deep Sequencing Data. Int. J. Mol. Sci. 2013, 14, 20820-20832.
  • [80] Xu Z, Sun X, Sun J. Construction and Analysis of the Model of Energy Metabolism in E. coli. PLoS One. 2013;8(1):e55137. doi: 10.1371/journal.pone.0055137.
  • [81] Gong L, Yan Y, Xie J, Liu H, Sun X. Prediction of autism susceptibility genes based on association rules. Journal of Neuroscience Research. 2012, 90(6):1119-1125.
  • [82] Yu J, Jiang D, Xiao K, Jin Y, Wang J, Sun X. Discriminate the Falsely Predicted Protein Coding Genes in Aeropyrum Pernix K1 Genome Based on Graphical Representation. MATCH Commun. Math. Comput. Chem. 2012, 67: 845-866.
  • [83] Huang H, Yu S, Liu H, Sun X. Nucleosome organization in sequences of alternative events in human genome. Biosystems. 2012, 109:214-219.
  • [84] Ma X, Guo J, Liu H, Xie J, Sun X. Sequence-based Prediction of DNA-binding Residues in Proteins with Conservation and Correlation Information. IEEE/ACM Trans Comput Biol Bioinform. 2012,9(6):1766-1775.
  • [85] Yu J, Xiao K, Jiang D, Guo J, Wang J, Sun X. An Integrative Method for Identifying the Over-Annotated Protein-Coding Genes in Microbial Genomes. DNA Res. 2011,18(6):435-49.
  • [86] Liu H, Lin S, Cai Z, Sun X. Role of 10-11 bp periodicities of eukaryotic DNA sequence in nucleosome positioning. BioSystems. 2011, 105:295-299.
  • [87] Wu J, Hu D, Xu X, Ding Y, Yan S and Sun X. A Novel Method for Quantitatively Predicting Non-Covalent Interactions from Protein and NucleicAcid Sequence. J Mol Graph Model. 2011,31:28-34.
  • [88] Ma X, Guo J, Wu J, Liu H, Yu J, Xie J, Sun X. Prediction of RNA-binding residues in proteins from primary sequence using an enriched random forest model with a novel hybrid feature. Proteins. 2011, 79(4):1230-9.
  • [89] Liu H, Duan X, Yu S, Sun X. Analysis of nucleosome positioning determined by DNA helix curvature in the human genome. BMC Genomics. 2011 Jan 27;12(1):72.
  • [90] Yuan ZD, Sun X, Liu HD, Xie JM. MicroRNA Genes Derived from Repetitive Elements and Expanded by Segmental Duplication Events in Mammalian Genomes. PLoS ONE, 2011, 6(3):e17666.
  • [91] Liu H, Sun X, Analysis of nucleosome positioning in the vicinity of sites of nucleotide polymorphism in human genome, Prog. Biochem. Biophys., 2011, 38(5): 427-432.
  • [92] Gong L, Sun X, Jiang D, Gong S. AutMiner: a system for extracting ASD-related genes using text mining. Journal of biological systems. 2011. 19(1): 113-125.
  • [93] Gong L, Sun X. Extraction of biomedical events related to disease based on deep parsing. Advanced science letters. 2011,4: 3470-3474.
  • [94] Yu J, Sun X, Wang J. A Novel 2D Graphical Representation of Protein Sequence Based on Individual Amino Acid. International Journal of Quantum Chemistry, 2011, Vol 111, 2835-2843.
  • [95] Yuan Z, Sun X, Jiang D, Ding Y, Lu Z, Gong L, Liu H, Xie J. Origin and evolution of a placental-specific microRNA family in the human genome. BMC Evol Biol. 2010 Nov 10;10(1):346.
  • [96] Yang X, Sun X. "Meta-analysis of Cancer Gene Profiling Data", Methods in Molecular Medicine: Cancer gene profiling. Edited by Robert Grützmann & Christian Pilarsky, The Humana Press Inc., 2010, 409-426. (DOI: 10.1007/978-1-59745-545-9_21)
  • [97] Liu H, Zhang D, Xie J, Yuan Z, Ma X, Lu Z, Gong L & Sun X. Analysis of nucleosome positioning in promoters of miRNA genes and protein-coding genes. Chinese Science Bulletin. 2010,55(22):2347-2352.
  • [98] Yang X, Lee Y, Fan H, Sun X & Lussier Y. Identification of common microRNA-mRNA regulatory biomodules in human epithelial cancer. Chinese Science Bulletin. 2010,55 (31): 3576-3589.
  • [99] Yu J, Wang J, Sun X. Analysis of Similarities/Dissimilarities of DNA Sequences based on a Novel Graphical Representation. MATCH Commun Math Comput Chem. 63 (2010) 493-512.
  • [100] Yu J, Sun X. Reannotation of Protein-Coding Genes Based on an Improved Graphical Representation of DNA Sequence. Journal of Computational Chemistry. 31(2010) ,2126-2135.
  • [101] Liu H, Zhang D, Xie J, Yuan Z, Ma X, Lu Z, Gong L & Sun X. Analysis of nucleosome positioning in promoters of miRNA genes and protein-coding genes. Chinese Science Bulletin. 2010,55(22):2347-2352.
  • [102] Gong L, Sun X. Extracting relationship both gene2disease and gene2gene from biomedical literatures. iCBBE 2010. Chengdu, China.
  • [103] Yu J, Sun X. Gene sequences analysis using a new graphical representation of DNA sequence. iCBBE 2010. Chengdu, China.
  • [104] Yuan Z, Sun X. Genome-wide identification of orthologs of miR-1302 genes in placental mammals. iCBBE 2010. Chengdu, China.
  • [105] Duan X, Liu H, Sun X. Causal relationship of histone modifications and gene expression indicated by variable bayeasian network methods. iCBBE 2010. Chengdu, China.
  • [106] Lu Z, Xie J, Sun X. Umap: use unique sequence for alignment of short sequence reads and SNP detection. iCBBE 2010. Chengdu, China.
  • [107] Sun X, Xie J, Yang X, Xue W, He N. DNA Microarray Design and Data Analysis. BIOCHIPS NANOTECHNOLOGY, Edited by Nongyue He and Hari Singh Nalwa, American Scientific Publishers, USA, 2009, 173-209.
  • [108] Wu J, Liu H, Duan X, Ding Y, Wu H, Bai Y, Sun X. Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature. Bioinformatics. 2009, 25(1):30-35.
  • [109] Xu Z, Sun X, Yu S. Genome-Scale Analysis to the Impact of Gene deletion on the Metabolism of E. coli: Constraint-Based Simulation Approach. BMC Bioinformatics. 2009, 10(Suppl 1):S62.
  • [110] Yang X, Huang Y, Chen JL, Xie JM, Sun X, Lussier YA. Mechanism-anchored profiling derived from epigenetic networks predicts outcome in acute lymphoblastic leukemia. BMC Bioinformatics, 2009, 10(Suppl 9):S6.
  • [111] Yu JF, Sun X, Wang JH. TN curve: A novel 3D graphical representation of DNA sequence based on trinucleotides and its applications. J Theor Biol. 2009, 261(3):459-468.
  • [112] Yang X, Xie JM, Sun X, Lussier Y. PGnet: A Novel Method for Predicting Epigenetic Regulatory Networks in Gene Expression Arrays of Acute Lymphoblastic Leukemia. 2009 Summit on Translational Bioinformatics, San Francisco, March 15-17, 2009.
  • [113] Gong L, Yuan Y, Wei Y, Sun X. A Hybrid Approach for Biomedical Entity Name Recognition. BMEI'2009（International Conference on BioMedical Engineering and Informatics）. Oct. 17-19 2009. Tianjin, China.
  • [114] Ma X, Wu J, Liu H, Yang X, Xie J and Sun X. A SVM-based Approach for Predicting DNA-binding Residues in Proteins from Amino Acid Sequences. International Joint Conferences on Bioinformatics, Systems Biology and Intelligent computing, 2009, 225-229.
  • [115] Liu Z, Meng J, Sun X. A novel feature-based method for whole genome phylogenetic analysis without alignment: application to HEV genotyping and subtyping. Biochem Biophys Res Commun. 2008 Apr 4;368(2):223-30. Epub 2008 Jan 28.
  • [116] Liu H, Wu J, Xie J,Yang X, Lu Z, Sun X. Characteristics of nucleosome core DNA and their applications in predicting nucleosome positions, Biophys. J. 2008 (doi:10.1529/biophysj.107.117028).
  • [117] Liu Z, Sun X: Coronavirus phylogeny based on base-base correlation. International Journal of Bioinformatics Research and Applications 2008, 4(2):211-220.
  • [118] Xu Z, Sun X. Constrain-based analysis of gene deletion on the metabolic flux redistribution of Saccharomyces cerevisiae. Journal of Biomedical Science and Engineering. 2008, 1(2): 121-126.
  • [119] Yang X, Sun X, Xie J, Lu ZH. Comparability of gene expression in human blood, immune and carcinoma cells. Applied Mathematics and Computation. 2008 (doi:10.1016/j.amc.2008.05.023).
  • [120] Yang X, Sun X. Meta-analysis of several gene lists for distinct types of cancer: A simple way to reveal common prognostic markers. BMC Bioinformatics 2007, 8:118.
  • [121] Wu J, Xie J, Zhou T, Weng J, Sun X. Support vector machine for prediction of horizontal gene transfers in bacteria genomes. Progress in Biochemistry and Biophysics, 2007,34(7):724-731.
  • [122] Wu J, Wu H, Liu H, Zhou H, Sun X. Support Vector Machine for Prediction of DNA-binding Domains in Protein-DNA Complexes. Lecture Notes in Bioinformatics, 2007,4689: 180-187.
  • [123] Liu Z, Liu H, Li J, Jiao D, Sun X: Base-Base Correlation: A novel sequence feature and its applications. Bioinformatics and Biomedical Engineering, 2007: 370-373.
  • [124] Liu Z, Sun X: Informational structure of Agrobacterium tumefaciens C58 genome. Lecture Notes in Bioinformatics 2007, Vol. 4689: 153-161.
  • [125] Xie J, Sun X, Lu ZY, Xu W, Dong X, Lu ZH. gWord: A tool for genome-wide word search and count. Int. Conf. Bioinf. Biomed. Eng. 2007, p314-317.
  • [126] Liu H, Liu Z, Sun X, Studies of Hurst index for different regions of genes, The First International Conference on Bioinformatics and Biomedical Engineering. 2007, 238-240.
  • [127] Jiang P, Wu H, Wang W, Ma W, Sun X, Lu Z. MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features. Nucleic Acids Res. 2007 Jun 6
  • [128] Jiang P, Wu H, Wei J, Sang F, Sun X, Lu Z. RF-DYMHC: detecting the yeast meiotic recombination hotspots and coldspots by random forest model using gapped dinucleotide composition features. Nucleic Acids Res. 2007 May 3
  • [129] Wu J, Hu M, Zhou T, Weng J, Jiang P, Sun X. Support vector machine for prediction of siRNA silencing efficacy. Journal of Southeast University (English Edition), 2006, 22(4):501-504.
  • [130] Zhou T, Weng J, Sun X, Lu Z. Support vector machine for classification of meiotic recombination hotspots and coldspots in Saccharomyces cerevisiae based on codon composition. BMC Bioinformatics. 2006 Apr 26;7:223.
  • [131] Zhou T, Sun X, Lu Z. Synonymous codon usage in environmental chlamydia UWE25 reflects an evolutional divergence from pathogenic chlamydiae. Gene, 2006, 368,117-125.
  • [132] Yang X, Sun X, Lu Z. Meta-analysis gene lists about subtypes of leukemia based on gene expression data. Journal of Southeast University (English Edition), 2006, 22(2):248-255.
  • [133] Liu Z, Jiao D, Sun X. Classifying Genomic Sequences by Sequence Feature Analysis. Genomics Proteomics Bioinformatics, 2005, 3(4):201-205.
  • [134] Gu W, Ma J, Sun X, Lu Z. Analysis of synonymous codon usage in SARS coronavirus and other viruses in the nidovirales. Virus Research. 2004,101,155-161.
  • [135] Gu W, Zhou T, Ma J, Sun X, Lu Z. Folding Type Specific Secondary Structure Propensities of Synonymous Codons, IEEE Transactions on NanoBioScience, 2003, 2(3),150-157.
  • [136] Xie X, Sun X, Xie J, Lu Z. An Interpolated Markov Model Polishes Gibbs Sampling's Ability in Detecting Regulatory Elements. Proceeding of 26th Annual International Conference of the IEEE EMBS. 2004, 2801-2804.
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