Xia Li

Summary

Affiliation: Harbin Medical University
Country: China

Publications

  1. ncbi request reprint Identification of a lncRNA involved functional module for esophageal cancer subtypes
    Shang Li
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
    Mol Biosyst 12:3312-3323. 2016
  2. doi request reprint Identifying the crosstalk of dysfunctional pathways mediated by lncRNAs in breast cancer subtypes
    Li Wang
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
    Mol Biosyst 12:711-20. 2016
  3. doi request reprint Identification of module biomarkers from the dysregulated ceRNA-ceRNA interaction network in lung adenocarcinoma
    Tingting Shao
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
    Mol Biosyst 11:3048-58. 2015
  4. doi request reprint Functional dissection of virus-human crosstalk mediated by miRNAs based on the VmiReg database
    Tingting Shao
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
    Mol Biosyst 11:1319-28. 2015
  5. doi request reprint A global view of network of lncRNAs and their binding proteins
    Desi Shang
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
    Mol Biosyst 11:656-63. 2015
  6. doi request reprint Integrating analysis reveals microRNA-mediated pathway crosstalk among Crohn's disease, ulcerative colitis and colorectal cancer
    Jing Bai
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
    Mol Biosyst 10:2317-28. 2014
  7. pmc LincSNP: a database of linking disease-associated SNPs to human large intergenic non-coding RNAs
    Shangwei Ning
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
    BMC Bioinformatics 15:152. 2014
  8. pmc MiRNA-miRNA synergistic network: construction via co-regulating functional modules and disease miRNA topological features
    Juan Xu
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
    Nucleic Acids Res 39:825-36. 2011
  9. pmc Subpathway-GM: identification of metabolic subpathways via joint power of interesting genes and metabolites and their topologies within pathways
    Chunquan Li
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China
    Nucleic Acids Res 41:e101. 2013
  10. doi request reprint A network-based, integrative approach to identify genes with aberrant co-methylation in colorectal cancer
    Yongsheng Li
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
    Mol Biosyst 10:180-90. 2014

Collaborators

  • Yun Xiao
  • Wei Jiang
  • Juan Xu
  • Junwei Han
  • Li Wang
  • Jing Li
  • Feng Li
  • Yan Zhang
  • Jing Bai
  • Hong Chen
  • Fei Su
  • Chunquan Li
  • Chunlong Zhang
  • Desi Shang
  • Yanjun Xu
  • Yongsheng Li
  • Qianghu Wang
  • Meng Zhou
  • Peng Wang
  • Shangwei Ning
  • Yan Li
  • Binsheng Gong
  • Qianlan Yao
  • Haixiu Yang
  • Fan Zhang
  • Lina Chen
  • Zheng Guo
  • Tingting Shao
  • Xinrui Shi
  • Hongying Zhao
  • Jie Sun
  • Ruijie Zhang
  • Shuyuan Wang
  • Shaoqi Rao
  • Mingzhu Yin
  • Sali Lv
  • Li Feng
  • Wan Li
  • Liangde Xu
  • Zeguo Sun
  • YongShuai Jiang
  • Zheng Zhao
  • Xuexin Yu
  • Jingrun Ye
  • Ronghong Li
  • Xiuhua Guo
  • Wei Wang
  • Teng Huang
  • Baofeng Lian
  • Yanqiu Wang
  • Bin Sheng Gong
  • Xin Chen
  • Xi Chen
  • Yan Xu
  • Liangcai Zhang
  • Yingying Wang
  • Xuehong Zhang
  • Shihua Zhang
  • Lin Pang
  • Chunjie Jiang
  • Chuanxing Li
  • Xinyi Liu
  • Zuxianglan Zhao
  • Yanxia Luo
  • Da Huo
  • Shaojun Zhang
  • Wei Li
  • Yingli Lv
  • Hongbo Shi
  • Weiming He
  • Xiaowen Chen
  • Qiang Hu Wang
  • Peng Sun
  • Hong Wang
  • Jing Hu
  • Chao Wu
  • Shang Li
  • Yujia Lan
  • Ling Liu
  • Guanxiong Zhang
  • Fulong Yu
  • Huihui Fan
  • Wei Zhang
  • Chunsheng Kang
  • Aiwei Wu
  • Tao Jiang
  • Huan Ren
  • Chaohan Xu
  • Enyu Dai
  • Fanlin Meng

Detail Information

Publications131 found, 100 shown here

  1. ncbi request reprint Identification of a lncRNA involved functional module for esophageal cancer subtypes
    Shang Li
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
    Mol Biosyst 12:3312-3323. 2016
    ..Novel candidate lncRNAs were identified, in addition to lncRNAs known to be functionally connected to EC, and could be responsible for the subtype disparities in the GO biological process and at pathway levels...
  2. doi request reprint Identifying the crosstalk of dysfunctional pathways mediated by lncRNAs in breast cancer subtypes
    Li Wang
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
    Mol Biosyst 12:711-20. 2016
    ....
  3. doi request reprint Identification of module biomarkers from the dysregulated ceRNA-ceRNA interaction network in lung adenocarcinoma
    Tingting Shao
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
    Mol Biosyst 11:3048-58. 2015
    ..95. Our study about LDCCNet opens up the possibility of a new biological mechanism in cancer that could serve as a biomarker for diagnosis. ..
  4. doi request reprint Functional dissection of virus-human crosstalk mediated by miRNAs based on the VmiReg database
    Tingting Shao
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
    Mol Biosyst 11:1319-28. 2015
    ....
  5. doi request reprint A global view of network of lncRNAs and their binding proteins
    Desi Shang
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
    Mol Biosyst 11:656-63. 2015
    ....
  6. doi request reprint Integrating analysis reveals microRNA-mediated pathway crosstalk among Crohn's disease, ulcerative colitis and colorectal cancer
    Jing Bai
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
    Mol Biosyst 10:2317-28. 2014
    ..Our results make sense for the prevention and treatment of intestinal-related chronic inflammation or cancer. ..
  7. pmc LincSNP: a database of linking disease-associated SNPs to human large intergenic non-coding RNAs
    Shangwei Ning
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
    BMC Bioinformatics 15:152. 2014
    ..There is, therefore, a need to specifically record these SNPs and annotate them as potential candidates for disease...
  8. pmc MiRNA-miRNA synergistic network: construction via co-regulating functional modules and disease miRNA topological features
    Juan Xu
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
    Nucleic Acids Res 39:825-36. 2011
    ..In addition, miRNAs associated with the same disease are close to each other. The structure of the MFSN and the features of disease miRNAs are validated to be robust using different miRNA target data sets...
  9. pmc Subpathway-GM: identification of metabolic subpathways via joint power of interesting genes and metabolites and their topologies within pathways
    Chunquan Li
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China
    Nucleic Acids Res 41:e101. 2013
    ..Further analysis indicated that the power of a joint genes/metabolites and subpathway strategy based on their topologies may play a key role in reliably recalling disease-relevant subpathways and finding novel subpathways...
  10. doi request reprint A network-based, integrative approach to identify genes with aberrant co-methylation in colorectal cancer
    Yongsheng Li
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
    Mol Biosyst 10:180-90. 2014
    ..These results show that the network-centric method could identify novel disease biomarkers and model how oncogenic lesions mediate epigenetic changes, providing important insights into tumorigenesis. ..
  11. doi request reprint Dissection of human MiRNA regulatory influence to subpathway
    Xia Li
    College of Bioinformatics Science and Technology and Bio pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, P R China
    Brief Bioinform 13:175-86. 2012
    ..A web server to query, visualize and download for all the data can be freely accessed at http://bioinfo.hrbmu.edu.cn/miR2Subpath...
  12. pmc A robust approach based on Weibull distribution for clustering gene expression data
    Huakun Wang
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, PR China
    Algorithms Mol Biol 6:14. 2011
    ..As a result, evaluating the performance of clustering methods in terms of the functional consistency of the resulting clusters is of great interest...
  13. pmc The implications of relationships between human diseases and metabolic subpathways
    Xia Li
    Bio pharmaceutical Key Laboratory of Heilongjiang Province, and College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
    PLoS ONE 6:e21131. 2011
    ....
  14. pmc Prioritizing human cancer microRNAs based on genes' functional consistency between microRNA and cancer
    Xia Li
    College of Bioinformatics Science and Technology, Cancer Hospital Affiliated to Harbin Medical University, Harbin, 150081, China
    Nucleic Acids Res 39:e153. 2011
    ..hrbmu.edu.cn/CMP. This time- and cost-effective computational framework can be a valuable complement to experimental studies and can assist with future studies of miRNA involvement in the pathogenesis of cancers...
  15. doi request reprint 'Traffic light rules': Chromatin states direct miRNA-mediated network motifs running by integrating epigenome and regulatome
    Hongying Zhao
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
    Biochim Biophys Acta 1860:1475-88. 2016
    ..However, it remains elusive as to how epigenetic marks cooperate in the operations of regulatory network...
  16. pmc Characterizing genes with distinct methylation patterns in the context of protein-protein interaction network: application to human brain tissues
    Yongsheng Li
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
    PLoS ONE 8:e65871. 2013
    ..DNA methylation is an essential epigenetic mechanism involved in transcriptional control. However, how genes with different methylation patterns are assembled in the protein-protein interaction network (PPIN) remains a mystery...
  17. pmc A global map for dissecting phenotypic variants in human lincRNAs
    Shangwei Ning
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
    Eur J Hum Genet 21:1128-33. 2013
    ..All the data in this study can be accessed and retrieved freely via a web server at http://bioinfo.hrbmu.edu.cn/lincPoly. ..
  18. pmc Allele-specific behavior of molecular networks: understanding small-molecule drug response in yeast
    Fan Zhang
    College of Bioinformatics Science and Technology and The Second Affiliated Hospital, Harbin Medical University, Harbin, PR China
    PLoS ONE 8:e53581. 2013
    ..Literature mining results provided strong independent evidence for the effectiveness of these genetic perturbing networks in the elucidation of small-molecule responses in yeast...
  19. pmc HHMD: the human histone modification database
    Yan Zhang
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
    Nucleic Acids Res 38:D149-54. 2010
    ..HisModView facilitates the acquisition and visualization of histone modifications. The database also has manually curated information of histone modification dysregulation in nine human cancers...
  20. doi request reprint Identification of active transcription factor and miRNA regulatory pathways in Alzheimer's disease
    Wei Jiang
    College of Bioinformatics Science and Technology, Department of Internal Neurology, Fourth Affiliated Hospital and Institute of Cancer Prevention and Treatment, Harbin Medical University, Harbin 150081, China
    Bioinformatics 29:2596-602. 2013
    ..However, the pathology of AD has yet to be fully elucidated...
  21. pmc Identifying and functionally characterizing tissue-specific and ubiquitously expressed human lncRNAs
    Chunjie Jiang
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
    Oncotarget 7:7120-33. 2016
    ..Our characterization of UE and TS lncRNAs may provide a foundation for lncRNA genomics and the delineation of complex disease mechanisms. ..
  22. pmc Discovering dysfunction of multiple microRNAs cooperation in disease by a conserved microRNA co-expression network
    Yun Xiao
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
    PLoS ONE 7:e32201. 2012
    ....
  23. pmc mirTarPri: improved prioritization of microRNA targets through incorporation of functional genomics data
    Peng Wang
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
    PLoS ONE 8:e53685. 2013
    ..We have also developed a web-based server for implementing mirTarPri method, which is freely accessible at http://bioinfo.hrbmu.edu.cn/mirTarPri...
  24. pmc Walking the interactome to identify human miRNA-disease associations through the functional link between miRNA targets and disease genes
    Hongbo Shi
    College of Bioinformatics Science and Technology and State Province Key Laboratories of Biomedicine Pharmaceutics of China, Harbin Medical University, Harbin, Heilongjiang 150081, PR China
    BMC Syst Biol 7:101. 2013
    ..However, miRNA-disease associations identified by previous computational methods are far from completeness and more effort is needed...
  25. pmc Comprehensive analysis of the functional microRNA-mRNA regulatory network identifies miRNA signatures associated with glioma malignant progression
    Yongsheng Li
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150080, China, Department of Neurosurgery, Tiantan Hospital, Capital Medical University, Beijing 100050, China, College of Fundamental Medical Sciences, Harbin Medical University, Harbin 150080, China and Department of Neurosurgery, Tianjin Medical University General Hospital, Laboratory of Neuro Oncology, Tianjin Neurological Institute, Laboratory of Neurotrauma, Variation and Regeneration, Ministry of Education and Tianjin Municipal Government, Tianjin 300052, China
    Nucleic Acids Res 41:e203. 2013
    ..Therefore, network-based biomarkers are expected to be more effective and provide deep insights into the molecular mechanism of glioma malignant progression. ..
  26. pmc A novel method to quantify gene set functional association based on gene ontology
    Sali Lv
    College of Bioinformatics Science and Technology and Bio pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin, People s Republic of China
    J R Soc Interface 9:1063-72. 2012
    ....
  27. doi request reprint Dissection of the potential characteristic of miRNA-miRNA functional synergistic regulations
    Juan Xu
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
    Mol Biosyst 9:217-24. 2013
    ....
  28. doi request reprint DBGSA: a novel method of distance-based gene set analysis
    Jin Li
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
    J Hum Genet 57:642-53. 2012
    ..Additionally, we have prepared a simple and publically available Perl and R package (http://bioinfo.hrbmu.edu.cn/dbgsa or http://cran.r-project.org/web/packages/DBGSA/)...
  29. pmc DOSim: an R package for similarity between diseases based on Disease Ontology
    Jiang Li
    College of Bioinformatics Science and Technology, Harbin Medical University, 194 XueFu Road, Harbin 150081, China
    BMC Bioinformatics 12:266. 2011
    ..However, bioinformatics tools that provide easy and straight forward ways to use DO to study disease and gene similarity simultaneously are required...
  30. pmc QDMR: a quantitative method for identification of differentially methylated regions by entropy
    Yan Zhang
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
    Nucleic Acids Res 39:e58. 2011
    ..This approach provides an effective tool for the high-throughput identification of potential functional regions involved in epigenetic regulation...
  31. pmc Prioritizing cancer-related key miRNA-target interactions by integrative genomics
    Yun Xiao
    College of Bioinformatics Science and Technology, Department of Neurology, The Affiliated Hospital and Harbin Medical University, Harbin, Heilongjiang 150086, China
    Nucleic Acids Res 40:7653-65. 2012
    ..The approach described here offers a new way for the discovery of novel cancer-related key miRNA-target interactions...
  32. pmc Prioritizing cancer therapeutic small molecules by integrating multiple OMICS datasets
    Sali Lv
    College of Bioinformatics Science and Technology and Bio pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin, P R China
    OMICS 16:552-9. 2012
    ....
  33. pmc Identifying dysfunctional miRNA-mRNA regulatory modules by inverse activation, cofunction, and high interconnection of target genes: a case study of glioblastoma
    Yun Xiao
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
    Neuro Oncol 15:818-28. 2013
    ..Thus, identifying abnormal functions cooperatively regulated by multiple miRNAs is useful for understanding the pathogenesis of complex diseases...
  34. doi request reprint Up-regulation of EphA2 and down-regulation of EphrinA1 are associated with the aggressive phenotype and poor prognosis of malignant glioma
    Xia Li
    Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi an, 710032, Shaan Xi Province, People s Republic of China
    Tumour Biol 31:477-88. 2010
    ..EphA2 suppression partially reversed the aggressive phenotypes of malignant gliomas, possibly through up-regulating EphrinA1 expression, which may help explain how EphA2 modulates the malignant progression of gliomas...
  35. pmc Prioritising risk pathways of complex human diseases based on functional profiling
    Yan Li
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
    Eur J Hum Genet 21:666-72. 2013
    ..Furthermore, we predicted the risk pathways of 413 diseases by using FPPP to build a disease similarity landscape that systematically reveals the global modular organisation of disease associations...
  36. pmc Systematically characterizing and prioritizing chemosensitivity related gene based on Gene Ontology and protein interaction network
    Xin Chen
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
    BMC Med Genomics 5:43. 2012
    ..In addition, CRGs potentially share functional characteristics and network features in protein interaction networks (PPIN)...
  37. pmc Discovery of Time-Delayed Gene Regulatory Networks based on temporal gene expression profiling
    Xia Li
    Department of Bioinformatics, Harbin Medical University, Harbin 150086, PR China
    BMC Bioinformatics 7:26. 2006
    ..The vast amount of large-scale and genome-wide time-resolved data is becoming increasing available, which provides the golden opportunity to unravel the challenging reverse-engineering problem of time-delayed gene regulatory networks...
  38. doi request reprint Predicting human microRNA precursors based on an optimized feature subset generated by GA-SVM
    Yanqiu Wang
    College of Bioinformatics Science and Technology and Bio pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, PR China
    Genomics 98:73-8. 2011
    ..Compared with microPred and miPred, miR-SF achieved much higher classification performance. Accuracies were 93.97%, 86.21% and 64.66% for miR-SF, microPred and miPred, respectively. Thus, miR-SF is effective for identifying pre-miRNAs...
  39. pmc Identification of links between small molecules and miRNAs in human cancers based on transcriptional responses
    Wei Jiang
    College of Bioinformatics Science and Technology and State Province Key Laboratories of Biomedicine Pharmaceutics of China, Harbin Medical University, Harbin, Heilongjiang 150081, PR China
    Sci Rep 2:282. 2012
    ..These modules can be used to identify drug candidates and new indications for existing drugs. Therefore, our approach is valuable to drug discovery and cancer therapy...
  40. doi request reprint Identifying disease related sub-pathways for analysis of genome-wide association studies
    Chunquan Li
    Harbin Medical University, Harbin, China
    Gene 503:101-9. 2012
    ..The result showed that our method can efficiently identify statistically significant sub-pathways associated with the pathogenesis of complex diseases. The approach identified sub-pathways that may inform the interpretation of GWAS data...
  41. pmc Characterizing the network of drugs and their affected metabolic subpathways
    Chunquan Li
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, People s Republic of China
    PLoS ONE 7:e47326. 2012
    ..Taken together, the DRSN could provide great insights into understanding the global relationship between drugs and metabolic subpathways...
  42. pmc MLH1 promoter methylation frequency in colorectal cancer patients and related clinicopathological and molecular features
    Xia Li
    Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang Province, P R China
    PLoS ONE 8:e59064. 2013
    ..To describe the frequency of MLH1 promoter methylation in colorectal cancer (CRC); to explore the associations between MLH1 promoter methylation and clinicopathological and molecular factors using a systematic review and meta-analysis...
  43. doi request reprint Functional combination strategy for prioritization of human miRNA target
    Jing Li
    College of Bioinformatics Science and Technology, Harbin Medical University, 194 XueFu Road, Harbin 150081, China
    Gene 533:132-41. 2014
    ..Top genes in ranking lists generated by this strategy were either validated by experiments or share same functions with the corresponding miRNA/its validated genes in disease related biological processes. ..
  44. pmc Association between γ-glutamyl transferase and metabolic syndrome: a cross-sectional study of an adult population in Beijing
    Lixin Tao
    School of Public Health, Capital Medical University, 10 Xitoutiao, Youanmen, Beijing 100069, China
    Int J Environ Res Public Health 10:5523-40. 2013
    ..50 U/L (sensitivity 76.00% and specificity 70.00%). GGT is therefore recommended as a useful diagnostic marker for MetS, because the test is inexpensive, highly sensitive, and frequently encountered in clinical practice. ..
  45. doi request reprint Topologically inferring risk-active pathways toward precise cancer classification by directed random walk
    Wei Liu
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
    Bioinformatics 29:2169-77. 2013
    ..However, current methods consider the pathways as simple gene sets but ignore the pathway topological information, which is essential to infer a more robust pathway activity...
  46. doi request reprint Prioritizing candidate disease miRNAs by topological features in the miRNA target-dysregulated network: case study of prostate cancer
    Juan Xu
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
    Mol Cancer Ther 10:1857-66. 2011
    ..These results show that the network-centric method could prioritize novel disease miRNAs and model how oncogenic lesions are mediated by miRNAs, providing important insights into tumorigenesis...
  47. doi request reprint A novel network-based method for measuring the functional relationship between gene sets
    Qianghu Wang
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
    Bioinformatics 27:1521-8. 2011
    ..However, biologists are still faced by the challenge of comparing gene sets and interpreting the functional relationships between gene sets into an understanding of the underlying biological mechanisms...
  48. pmc EGFRvIII/integrin β3 interaction in hypoxic and vitronectinenriching microenvironment promote GBM progression and metastasis
    Zhaoyu Liu
    Department of Immunology, Harbin Medical University, Harbin 150081, China
    Oncotarget 7:4680-94. 2016
    ....
  49. doi request reprint Systematic analysis of regulation and functions of co-expressed microRNAs in humans
    Mingzhi Liao
    College of Bioinformatics Science and Technology and Bio pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, PR China
    Mol Biosyst 6:1863-72. 2010
    ..Thus, our study may provide an important reference for miRNA regulations and functions...
  50. pmc Uncovering packaging features of co-regulated modules based on human protein interaction and transcriptional regulatory networks
    Lina Chen
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Hei Longjiang Province, China
    BMC Bioinformatics 11:392. 2010
    ..Network co-regulated modules are believed to have the functionality of packaging multiple biological entities, and can thus be assumed to coordinate many biological functions in their network neighbouring regions...
  51. doi request reprint Comparative evaluation of support vector machines for computer aided diagnosis of lung cancer in CT based on a multi-dimensional data set
    Tao Sun
    School of Public Health, Capital Medical University, Beijing 100069, China
    Comput Methods Programs Biomed 111:519-24. 2013
    ..This scheme may be used as an auxiliary tool to differentiate between benign and malignant SPNs of CT images in future. ..
  52. doi request reprint Topological properties of the drug targets regulated by microRNA in human protein-protein interaction network
    Chenqu Wang
    Department of Biomedical Engineering, Capital Medical University, Beijing, PR China
    J Drug Target 19:354-64. 2011
    ..The same topological features are observed among non-drug targets. These findings indicate that miRNA regulation has an important role in human PPIN, and may be useful in the development of novel drugs...
  53. pmc Community of protein complexes impacts disease association
    Qianghu Wang
    College of Bioinformatics Science and Technology and Bio pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin, China
    Eur J Hum Genet 20:1162-7. 2012
    ..We provide novel disease associations that cannot be identified through previous analysis. These findings will potentially provide biologists and clinicians new insights into the etiology, classification and treatment of diseases...
  54. doi request reprint Disease-driven detection of differential inherited SNP modules from SNP network
    Chuanxing Li
    College of Bioinformatics Science and Technology, Harbin Medical University, PR China
    Gene 489:119-29. 2011
    ..The integration of network biology and genetic analysis provides putative functional bridges between genetic variants and candidate genes or pathways, thereby providing new insight into the aetiology of complex diseases...
  55. doi request reprint Systematic analysis of human microRNA divergence based on evolutionary emergence
    Qiang Hu Wang
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
    FEBS Lett 585:240-8. 2011
    ..Our finds provide more useful knowledge for further exploring origins and evolution of human miRNA genes...
  56. doi request reprint CNVD: text mining-based copy number variation in disease database
    Fujun Qiu
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
    Hum Mutat 33:E2375-81. 2012
    ..The CNVD interface is accessible at http://bioinfo.hrbmu.edu.cn/CNVD...
  57. doi request reprint Systematic identification of common functional modules related to heart failure with different etiologies
    Yun Xiao
    College of Bioinformatics Science and Technology, Harbin Medical University, Nangang Region, Harbin 150081, China
    Gene 499:332-8. 2012
    ..Our findings provide important insights into the complex mechanism of HF. Further biological experimentations should be required to validate these novel biological processes...
  58. pmc Disease gene interaction pathways: a potential framework for how disease genes associate by disease-risk modules
    Lina Chen
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Hei Longjiang Province, China
    PLoS ONE 6:e24495. 2011
    ..Molecular networks, assumed as 'a form of biological systems', consist of a set of interacting biological modules (functional modules or pathways) and this notion could provide a promising insight into deciphering this topic...
  59. doi request reprint A novel paradigm for potential drug-targets discovery: quantifying relationships of enzymes and cascade interactions of neighboring biological processes to identify drug-targets
    Lina Chen
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Hei Longjiang Province, China
    Mol Biosyst 7:1033-41. 2011
    ..Thus, our method is a promising tool to aid target identification in drug discovery...
  60. doi request reprint Disease embryo development network reveals the relationship between disease genes and embryo development genes
    Binsheng Gong
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
    J Theor Biol 287:100-8. 2011
    ..This network-based approach could provide evidence for the intricate correlation between disease process and embryo development, and help to uncover potential mechanisms of human complex diseases...
  61. pmc Subpathway-LNCE: Identify dysfunctional subpathways competitively regulated by lncRNAs through integrating lncRNA-mRNA expression profile and pathway topologies
    Xinrui Shi
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
    Oncotarget 7:69857-69870. 2016
    ..Subpathway-LNCE has been developed as an R package freely available at https://cran.rstudio.com/web/packages/SubpathwayLNCE/...
  62. pmc Systematically characterizing dysfunctional long intergenic non-coding RNAs in multiple brain regions of major psychosis
    Jing Hu
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
    Oncotarget 7:71087-71098. 2016
    ....
  63. doi request reprint Functional homogeneity in microRNA target heterogeneity--a new sight into human microRNomics
    Yingying Wang
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, People s Republic of China
    OMICS 15:25-35. 2011
    ..Our findings reveal the "functional homogeneity in miRNA target heterogeneity." The conclusions provide a perspective of microRNomics on functional levels, which introduce a new sight into human miRNA targets...
  64. pmc Gene Perturbation Atlas (GPA): a single-gene perturbation repository for characterizing functional mechanisms of coding and non-coding genes
    Yun Xiao
    1 College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China 2 Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education
    Sci Rep 5:10889. 2015
    ..In summary, the GPA is a valuable resource for characterizing gene functions and regulatory mechanisms after single-gene perturbations. The GPA is freely accessible at http://biocc.hrbmu.edu.cn/GPA/. ..
  65. pmc Global Prioritization of Disease Candidate Metabolites Based on a Multi-omics Composite Network
    Qianlan Yao
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
    Sci Rep 5:17201. 2015
    ..A predicted disease metabolic landscape was constructed and analyzed based on the results of MetPriCNet for 87 phenotypes to help us understand the genetic and metabolic mechanism of disease from a global view. ..
  66. pmc Systematically Prioritizing Functional Differentially Methylated Regions (fDMRs) by Integrating Multi-omics Data in Colorectal Cancer
    Huihui Fan
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
    Sci Rep 5:12789. 2015
    ....
  67. pmc MeSiC: A Model-Based Method for Estimating 5 mC Levels at Single-CpG Resolution from MeDIP-seq
    Yun Xiao
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
    Sci Rep 5:14699. 2015
    ..Comparisons with methylCRF and MEDIPS showed that MeSiC achieved comparable and even better performance. These demonstrate that MeSiC can provide accurate estimations of 5 mC levels at single-CpG resolution using MeDIP-seq data alone...
  68. pmc Genome-wide DNA methylome reveals the dysfunction of intronic microRNAs in major psychosis
    Hongying Zhao
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
    BMC Med Genomics 8:62. 2015
    ..However, most studies focus on DNA methylation alteration at promoters of protein-coding genes, despite the poor correlation between DNA methylation and gene expression...
  69. pmc Subpathway-GMir: identifying miRNA-mediated metabolic subpathways by integrating condition-specific genes, microRNAs, and pathway topologies
    Li Feng
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
    Oncotarget 6:39151-64. 2015
    ..The Subpathway-GMir method has been implemented as a freely available R package. ..
  70. pmc TMREC: A Database of Transcription Factor and MiRNA Regulatory Cascades in Human Diseases
    Shuyuan Wang
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, P R China
    PLoS ONE 10:e0125222. 2015
    ..TMREC aims to help experimental biologists to comprehensively analyse gene expression regulation, to understand the aetiology and to predict novel therapeutic targets. TMREC is freely available at http://bioinfo.hrbmu.edu.cn/TMREC/...
  71. pmc Identification of lncRNA-associated competing triplets reveals global patterns and prognostic markers for cancer
    Peng Wang
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
    Nucleic Acids Res 43:3478-89. 2015
    ..In summary, this study uncovered and systematically characterized global properties of human lncACTs that may have prognostic value for predicting clinical outcome in cancer patients. ..
  72. pmc Identification of subtype specific miRNA-mRNA functional regulatory modules in matched miRNA-mRNA expression data: multiple myeloma as a case
    Yunpeng Zhang
    College of Bioinformatics Science and Technology, Harbin Medical University, 194 XueFu Road, Harbin 150081, China
    Biomed Res Int 2015:501262. 2015
    ..These subtype specific MFRMs may aid in the further elucidation of the pathogenesis of each subtype and may serve to guide MM subtype diagnosis and treatment. ..
  73. pmc SubpathwayMiner: a software package for flexible identification of pathways
    Chunquan Li
    College of Bioinformatics Science and Technology and Bio pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, People s Republic of China
    Nucleic Acids Res 37:e131. 2009
    ..in the KEGG GENE database; (iii) the system is quite efficient in cooperating with other R-based tools in biology. SubpathwayMiner is freely available at http://cran.r-project.org/web/packages/SubpathwayMiner/...
  74. pmc Composite functional module inference: detecting cooperation between transcriptional regulation and protein interaction by mantel test
    Chao Wu
    Department of Bioinformatics and Bio pharmaceutical Key Laboratory of Heilongjiang Province and State, Harbin Medical University, Harbin, Heilongjiang 150086, China
    BMC Syst Biol 4:82. 2010
    ....
  75. doi request reprint Association between the IL7R T244I polymorphism and multiple sclerosis: a meta-analysis
    Ruijie Zhang
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
    Mol Biol Rep 38:5079-84. 2011
    ..0004 for the C/C + C/T genotype), no heterogeneity was observed (allele C: P = 0.07; genotype C/C: P = 0.10). In conclusion, the meta-analysis demonstrated that the IL7R T244I polymorphism was associated with susceptibility to MS...
  76. doi request reprint The pan-cancer analysis of gene expression patterns in the context of inflammation
    Xuexin Yu
    College of Bioinformatics Science and Technology, Harbin Medical University, China
    Mol Biosyst 10:2270-6. 2014
    ..Therefore, the pan-cancer analysis of gene expression patterns in the context of inflammation provides a novel insight into cancers and an unprecedented opportunity to develop new therapies. ..
  77. pmc Prioritizing candidate disease metabolites based on global functional relationships between metabolites in the context of metabolic pathways
    Desi Shang
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, P R China
    PLoS ONE 9:e104934. 2014
    ..We also developed a freely accessible web-based and R-based tool at http://bioinfo.hrbmu.edu.cn/PROFANCY. ..
  78. doi request reprint The detection of risk pathways, regulated by miRNAs, via the integration of sample-matched miRNA-mRNA profiles and pathway structure
    Jing Li
    College of Bioinformatics Science and Technology and Bio pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, PR China Department of Bioinformatics, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350004, PR China
    J Biomed Inform 49:187-97. 2014
    ..Further analysis showed that the structure of a pathway plays a crucial role in the recognition of the pathway as a factor in disease risk. ..
  79. pmc Unravelling the hidden heterogeneities of diffuse large B-cell lymphoma based on coupled two-way clustering
    Wei Zhang
    The First Clinical College, Department of Bioinformatics, and the Bio pharmaceutical Key Laboratory of Heilongjiang Province and State, Harbin Medical University, Harbin 150086, China
    BMC Genomics 8:332. 2007
    ....
  80. doi request reprint Predict potential drug targets from the ion channel proteins based on SVM
    Chen Huang
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
    J Theor Biol 262:750-6. 2010
    ..and four of which were relative to some nerve diseases. It suggests that these five proteins are potential targets for drug discovery and our prediction strategies are effective...
  81. pmc Factors associated with myopia in school children in China: the Beijing childhood eye study
    Qi Sheng You
    Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
    PLoS ONE 7:e52668. 2012
    ..To assess factors associated with myopia in school children in rural and urban parts of Greater Beijing...
  82. pmc Combination of radiological and gray level co-occurrence matrix textural features used to distinguish solitary pulmonary nodules by computed tomography
    Haifeng Wu
    School of Public Health and Family Medicine, Capital Medical University, Beijing 100069, China
    J Digit Imaging 26:797-802. 2013
    ..91. The evaluation results showed that the method of selecting radiological and textural features appears to yield more effective in the distinction of malignant from benign solitary pulmonary nodules by computed tomography. ..
  83. pmc Evaluation of two single-factor models of metabolic syndrome: a confirmatory factor analysis for an adult population in Beijing
    Da Huo
    School of Public Health, Capital Medical University, No 10 Xitoutiao, You anmen Wai, Beijing, Fengtai District, China
    Lipids Health Dis 12:61. 2013
    ..This study was to evaluate and compare two single-factor models of the underlying factor structure of metabolic syndrome in a Chinese population using confirmatory factor analysis...
  84. pmc Risk factors of CVD mortality among the elderly in Beijing, 1992 - 2009: an 18-year cohort study
    Tao Zhou
    School of Public Health, Capital Medical University, 10 Xitoutiao, Youanmen, Beijing 100069, China
    Int J Environ Res Public Health 11:2193-208. 2014
    ..559, 95% CI: 1.079-2.254) and physical inactivity (p = 0.046) were associated with higher CVD mortality. The study provides an instructional foundation for the control and prevention of CVD in Beijing, China...
  85. doi request reprint Genetic control of primary microRNA insight into cis- and trans-regulatory variations by RNA-seq
    Shaojun Zhang
    Center for Biomedical Informatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, 150001, China
    Gene 517:224-9. 2013
    ..These findings revealed that the expression of pri-miRNA detected by RNA-seq can be used to identify pri-miQTLs, as an alternative method to dissect the genetic control mechanisms governing pri-miRNA expression...
  86. doi request reprint The application of gene co-expression network reconstruction based on CNVs and gene expression microarray data in breast cancer
    Yan Xu
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
    Mol Biol Rep 39:1627-37. 2012
    ....
  87. pmc Constructing disease-specific gene networks using pair-wise relevance metric: application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements
    Wei Jiang
    College of Bioinformatics Science and Technology and Bio pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, PR China
    BMC Syst Biol 2:72. 2008
    ..The aim of this study was thus to develop such a novel networking approach based on the relevance concept, which is ideal to reveal integrative effects of multiple genes in the underlying genetic circuit for complex diseases...
  88. ncbi request reprint [Association analysis of gene expression and gene function]
    Na Xu
    Department of Bioinformatics, Harbin Medical University, Harbin 150086, China
    Sheng Wu Yi Xue Gong Cheng Xue Za Zhi 24:385-8. 2007
    ..2) The mRNA expression level is consistent with the intensity of functional relationships between genes. So it can be concluded that the function of genes involved in any pathway is correlated with the mRNA expression level of genes...
  89. pmc The expanded human disease network combining protein-protein interaction information
    Xuehong Zhang
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
    Eur J Hum Genet 19:783-8. 2011
    ..In the eHDN, we found some new associations among diseases resulting from the shared genes interacting with disease genes. The new eHDN will provide a valuable reference for clinicians and medical researchers...
  90. pmc Identifying highly conserved and highly differentiated gene ontology categories in human populations
    YongShuai Jiang
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
    PLoS ONE 6:e27871. 2011
    ..These results may provide a new insight into the understanding of human evolutionary history at the system-level...
  91. pmc Systematic identification of core transcription factors mediating dysregulated links bridging inflammatory bowel diseases and colorectal cancer
    Yun Xiao
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
    PLoS ONE 8:e83495. 2013
    ....
  92. pmc Identification of miRNA-mediated core gene module for glioma patient prediction by integrating high-throughput miRNA, mRNA expression and pathway structure
    Chunlong Zhang
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
    PLoS ONE 9:e96908. 2014
    ..Our findings suggested that the expression signatures, which were identified by integration of miRNA and gene level, were closely associated with overall survival among the glioma patients with various grades. ..
  93. doi request reprint Computational identification of human long intergenic non-coding RNAs using a GA-SVM algorithm
    Yanqiu Wang
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China
    Gene 533:94-9. 2014
    ..Because the recognition rates for the two lincRNA sets were 100% and 99.8%, the linc-SF was found to be effective for the prediction of human lincRNAs...
  94. doi request reprint Cancer-related marketing centrality motifs acting as pivot units in the human signaling network and mediating cross-talk between biological pathways
    Wan Li
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Hei Longjiang Province, China
    Mol Biosyst 9:3026-35. 2013
    ..Finally, we analyzed the pivotal roles of cancer genes in these marketing centrality motifs in the pathogenesis of cancers, and found that non-cancer genes were potential cancer-related genes. ..
  95. doi request reprint Differential expression pattern-based prioritization of candidate genes through integrating disease-specific expression data
    Yun Xiao
    College of Bioinformatics Science and Technology, Harbin Medical University, Heilongjiang, China
    Genomics 98:64-71. 2011
    ..Additionally, our approach showed higher performance in comparison with other expression-based approaches and better capability of identification of less well-studied disease genes in comparison with other integration-based approaches...
  96. doi request reprint The toxicity and long-term efficacy of nedaplatin and paclitaxel treatment as neoadjuvant chemotherapy for locally advanced cervical cancer
    Mingzhu Yin
    Department of Gynecology Oncology, The Tumor Hospital of Harbin Medical University, Harbin, P R China
    J Surg Oncol 105:206-11. 2012
    ..Comparisons between NP and paclitaxel and cisplatin (PC) in terms of toxicity and long-term efficacy are also presented...
  97. doi request reprint MicroRNA regulation constrains the organization of target genes on mammalian chromosomes
    Zhen Zhen Wang
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, PR China
    FEBS Lett 585:1897-904. 2011
    ..The clustering pattern of TGs provides an insight into the complexity of miRNA regulation...
  98. doi request reprint Comparative genomic analysis reveals evolutionary characteristics and patterns of microRNA clusters in vertebrates
    Jie Sun
    College of Bioinformatics Science and Technology and The Second Affiliated Hospital, Harbin Medical University, Harbin 150081, PR China
    Gene 512:383-91. 2013
    ..Our study provides novel insights for further exploring the origins and evolution of miRNA clusters in vertebrates at a genome scale...
  99. doi request reprint From phenotype to gene: detecting disease-specific gene functional modules via a text-based human disease phenotype network construction
    Shihua Zhang
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
    FEBS Lett 584:3635-43. 2010
    ..We believe the investigation may facilitate the ultimate understanding of the common pathophysiologic basis of associated diseases...
  100. doi request reprint Genome-wide analysis of clustering patterns and flanking characteristics for plant microRNA genes
    Meng Zhou
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
    FEBS J 278:929-40. 2011
    ..The results presented provide a new insight into the transcriptional regulation and processing of plant miRNAs...
  101. pmc Network analysis reveals functional cross-links between disease and inflammation genes
    Yunpeng Zhang
    1 College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, Chin 2
    Sci Rep 3:3426. 2013
    ..Collectively, The network-based analysis provides us a rather promising insight into the intricate relationship between inflammation and disease genes. ..