Tao Huang

Summary

Affiliation: Shanghai Institutes for Biological Sciences
Country: China

Publications

  1. doi Crosstissue coexpression network of aging
    Tao Huang
    Department of Ophthalmology, Yangpu District Central Hospital, Shanghai, People s Republic of China
    OMICS 15:665-71. 2011
  2. ncbi Growth and differentiation of mouse tracheal epithelial cells: selection of a proliferative population
    Yingjian You
    Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri 63110, USA
    Am J Physiol Lung Cell Mol Physiol 283:L1315-21. 2002
  3. pmc The prediction of interferon treatment effects based on time series microarray gene expression profiles
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, PR China
    J Transl Med 6:44. 2008
  4. pmc Predicting transcriptional activity of multiple site p53 mutants based on hybrid properties
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    PLoS ONE 6:e22940. 2011
  5. ncbi A sequence-based approach for predicting protein disordered regions
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
    Protein Pept Lett 20:243-8. 2013
  6. doi Deciphering the effects of gene deletion on yeast longevity using network and machine learning approaches
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    Biochimie 94:1017-25. 2012
  7. doi The role of Hepatitis C Virus in the dynamic protein interaction networks of hepatocellular cirrhosis and carcinoma
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
    Int J Comput Biol Drug Des 4:5-18. 2011
  8. pmc TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interactions and protein post-translational modifications information
    Qi Liu
    School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
    BMC Bioinformatics 11:S5. 2010
  9. ncbi Inter- and intra-chain disulfide bond prediction based on optimal feature selection
    Shen Niu
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P R China
    Protein Pept Lett 20:324-35. 2013
  10. doi Predicting protein oxidation sites with feature selection and analysis approach
    Shen Niu
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P R China
    J Biomol Struct Dyn 29:650-8. 2012

Collaborators

Detail Information

Publications53

  1. doi Crosstissue coexpression network of aging
    Tao Huang
    Department of Ophthalmology, Yangpu District Central Hospital, Shanghai, People s Republic of China
    OMICS 15:665-71. 2011
    ..By bridging gene-level and tissue-level research, this study could help identify targets for attenuation of critical aging-related genes, pathways, or networks for antiaging intervention...
  2. ncbi Growth and differentiation of mouse tracheal epithelial cells: selection of a proliferative population
    Yingjian You
    Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri 63110, USA
    Am J Physiol Lung Cell Mol Physiol 283:L1315-21. 2002
    ..This approach provides a high-fidelity in vitro model for evaluation of gene regulation and expression in mouse airway epithelial cells...
  3. pmc The prediction of interferon treatment effects based on time series microarray gene expression profiles
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, PR China
    J Transl Med 6:44. 2008
    ..Here, we proposed a time-dependent diagnostic model to predict the treatment effects of interferon and ribavirin to HCV infected patients by using time series microarray gene expression profiles of a published study...
  4. pmc Predicting transcriptional activity of multiple site p53 mutants based on hybrid properties
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    PLoS ONE 6:e22940. 2011
    ..Our study has provided a new and promising approach for finding functionally important sites and the relevant features for in-depth study of p53 protein and its action mechanism...
  5. ncbi A sequence-based approach for predicting protein disordered regions
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
    Protein Pept Lett 20:243-8. 2013
    ..371 on a rigorous benchmark dataset tested by 5-fold cross-validation and 0.219 on an independent test dataset. Our results suggest that conservation and secondary structure play important roles in intrinsically disordered proteins...
  6. doi Deciphering the effects of gene deletion on yeast longevity using network and machine learning approaches
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    Biochimie 94:1017-25. 2012
    ..Moreover, it has not escaped our notice that, after some modification, the current model can also be used to study many other phenotype prediction problems from the angle of systems biology...
  7. doi The role of Hepatitis C Virus in the dynamic protein interaction networks of hepatocellular cirrhosis and carcinoma
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
    Int J Comput Biol Drug Des 4:5-18. 2011
    ..Then, the relationship between dysfunctional networks and HCV infection was analysed. Our results may help understand the mechanisms of HCV-induced malignant transformation and provide clues to cirrhosis and HCC therapy or prevention...
  8. pmc TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interactions and protein post-translational modifications information
    Qi Liu
    School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
    BMC Bioinformatics 11:S5. 2010
    ..However, the low overlap between binding targets of a TF and the affected genes of the TF knockout limits the power of those methods...
  9. ncbi Inter- and intra-chain disulfide bond prediction based on optimal feature selection
    Shen Niu
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P R China
    Protein Pept Lett 20:324-35. 2013
    ....
  10. doi Predicting protein oxidation sites with feature selection and analysis approach
    Shen Niu
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P R China
    J Biomol Struct Dyn 29:650-8. 2012
    ..Also, the 16 optimal features obtained through this study may provide useful clues and insights for in-depth understanding the action mechanism of protein oxidation...
  11. pmc Identification of colorectal cancer related genes with mRMR and shortest path in protein-protein interaction network
    Bi Qing Li
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    PLoS ONE 7:e33393. 2012
    ..It has not escaped our notice that the method can be applied to identify the genes of other diseases as well...
  12. pmc Prediction and analysis of protein hydroxyproline and hydroxylysine
    Le Le Hu
    Institute of Systems Biology, Shanghai University, Shanghai, China
    PLoS ONE 5:e15917. 2010
    ..Hydroxylation is an important post-translational modification and closely related to various diseases. Besides the biotechnology experiments, in silico prediction methods are alternative ways to identify the potential hydroxylation sites...
  13. pmc Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    PLoS ONE 5:e10972. 2010
    ..The computational method can also be used as a large-scale tool for annotating the metabolic stability for the avalanche of protein sequences generated in the post-genomic age...
  14. ncbi Selection of reprogramming factors of induced pluripotent stem cells based on the protein interaction network and functional profiles
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P R China
    Protein Pept Lett 19:113-9. 2012
    ..It can be used to select reprogramming factors from millions of possibilities. It is anticipated that the novel approach will become a very useful tool for both basic research and drug development...
  15. doi Genome-wide association studies of 14 agronomic traits in rice landraces
    Xuehui Huang
    National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    Nat Genet 42:961-7. 2010
    ....
  16. doi Prediction of protein amidation sites by feature selection and analysis
    Weiren Cui
    CAS MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    Mol Genet Genomics 288:391-400. 2013
    ..And the selected features from our study could shed some light on the in-depth understanding of the mechanisms of the amidation modification, providing guidelines for experimental validation. ..
  17. pmc Prediction of protein-protein interaction sites by random forest algorithm with mRMR and IFS
    Bi Qing Li
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    PLoS ONE 7:e43927. 2012
    ..It is anticipated that our prediction method will become a useful tool for identifying PPI sites, and that the feature analysis described in this paper will provide useful insights into the mechanisms of interaction...
  18. doi A map of rice genome variation reveals the origin of cultivated rice
    Xuehui Huang
    National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
    Nature 490:497-501. 2012
    ..The domestication-associated traits are analysed through high-resolution genetic mapping. This study provides an important resource for rice breeding and an effective genomics approach for crop domestication research...
  19. doi Prediction of lysine ubiquitination with mRMR feature selection and analysis
    Yudong Cai
    Institute of Systems Biology, Shanghai University, Shanghai, 200444, People s Republic of China
    Amino Acids 42:1387-95. 2012
    ..These findings might provide useful insights for studying the mechanisms of ubiquitination and modulating the ubiquitination pathway, potentially leading to potential therapeutic strategies in the future...
  20. doi Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm
    Xuehui Huang
    National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    Nat Genet 44:32-9. 2012
    ..This study shows that the integrated approach of sequence-based GWAS and functional genome annotation has the potential to match complex traits to their causal polymorphisms in rice...
  21. ncbi Using WPNNA classifier in ubiquitination site prediction based on hybrid features
    Kai Yan Feng
    Shanghai Center for Bioinformation Technology, Shanghai, China
    Protein Pept Lett 20:318-23. 2013
    ....
  22. pmc Identification of lung-cancer-related genes with the shortest path approach in a protein-protein interaction network
    Bi Qing Li
    The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
    Biomed Res Int 2013:267375. 2013
    ..Furthermore, these genes possessed more functional similarity with the known cancer genes than those identified from the gene expression profiles. This study proved the efficiency of the proposed method and showed promising results...
  23. pmc Hepatitis C virus network based classification of hepatocellular cirrhosis and carcinoma
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    PLoS ONE 7:e34460. 2012
    ..It may also provide useful insights for in-depth study of the biological mechanisms of HCV-induced cirrhosis and hepatocellular carcinoma...
  24. ncbi Analysis of metabolic pathway using hybrid properties
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, Shanghai, People s Republic of China
    Protein Pept Lett 19:99-107. 2012
    ..26%. It is anticipated that this novel approach and encouraging result may give meaningful illumination to investigate this important topic...
  25. pmc Predicting functions of proteins in mouse based on weighted protein-protein interaction network and protein hybrid properties
    Lele Hu
    Institute of Systems Biology, Shanghai University, Shanghai, China
    PLoS ONE 6:e14556. 2011
    ..The information thus obtained would be very useful for both basic research and drug development in a timely manner...
  26. pmc Prediction of deleterious non-synonymous SNPs based on protein interaction network and hybrid properties
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    PLoS ONE 5:e11900. 2010
    ..Our results suggest that the protein interaction context could provide important clues to help better illustrate SAP's functional association. This research will facilitate the post genome-wide association studies...
  27. doi Prediction of tyrosine sulfation with mRMR feature selection and analysis
    Shen Niu
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, PR China
    J Proteome Res 9:6490-7. 2010
    ..The detailed feature analysis in this paper might help understand more of the sulfation mechanism and guide the related experimental validation...
  28. doi Identification of retinoblastoma related genes with shortest path in a protein-protein interaction network
    Bi Qing Li
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, People s Republic of China
    Biochimie 94:1910-7. 2012
    ..This study shows promising results and proves the efficiency of the proposed methods...
  29. doi SySAP: a system-level predictor of deleterious single amino acid polymorphisms
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    Protein Cell 3:38-43. 2012
    ..SySAP is freely available at http://www.biosino.org/ SySAP/ and http://lifecenter.sgst.cn/SySAP/...
  30. pmc Computational analysis of HIV-1 resistance based on gene expression profiles and the virus-host interaction network
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    PLoS ONE 6:e17291. 2011
    ..These proteins may be useful targets for AIDS prevention or therapy, as intervention in these pathways could disrupt communication with virus-targeted proteins and HIV-1 infection...
  31. pmc Prediction of body fluids where proteins are secreted into based on protein interaction network
    Le Le Hu
    Institute of Systems Biology, Shanghai University, Shanghai, China
    PLoS ONE 6:e22989. 2011
    ..These encouraging results indicate that the network-based prediction method is quite promising. It is anticipated that the method will benefit the relevant areas for both basic research and drug development...
  32. pmc Identifying chemicals with potential therapy of HIV based on protein-protein and protein-chemical interaction network
    Bi Qing Li
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, PR China
    PLoS ONE 8:e65207. 2013
    ..All these indicate that our method as presented in this paper is quite promising. The method may become a useful tool, or at least plays a complementary role to the existing method, for identifying novel anti-HIV drugs...
  33. pmc Dysfunctions associated with methylation, microRNA expression and gene expression in lung cancer
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    PLoS ONE 7:e43441. 2012
    ..Our results provide a systematic view of the functional alterations during tumorigenesis that may help to elucidate the mechanisms of lung cancer and lead to improved treatments for patients...
  34. doi Functional association between influenza A (H1N1) virus and human
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, PR China
    Biochem Biophys Res Commun 390:1111-3. 2009
    ..One hundred and one core proteins were identified. The results provide some knowledge of the possible biological processes and molecular interactions caused by the viral infection, including the host responses...
  35. pmc Predicting protein phenotypes based on protein-protein interaction network
    Lele Hu
    Institute of Systems Biology, Shanghai University, Shanghai, China
    PLoS ONE 6:e17668. 2011
    ..Besides the high-through phenotype assays, the computational methods are alternative ways to identify the phenotypes of proteins...
  36. pmc Classification and analysis of regulatory pathways using graph property, biochemical and physicochemical property, and functional property
    Tao Huang
    Institute of Systems Biology, Shanghai University, Shanghai, People s Republic of China
    PLoS ONE 6:e25297. 2011
    ..It is anticipated that our report may stimulate a series of follow-up investigations in this new and challenging area...
  37. pmc An ensemble prognostic model for colorectal cancer
    Bi Qing Li
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, PR China
    PLoS ONE 8:e63494. 2013
    ..This method could be applied to the studies of other diseases and it could significantly improve the prediction performance by ensembling heterogeneous information...
  38. pmc Transitional Zone Index and Intravesical Prostatic Protrusion in Benign Prostatic Hyperplasia Patients: Correlations according to Treatment Received and Other Clinical Data
    Tao Huang
    Department of Urology, Xin Hua Hospital Shanghai Jiao Tong University School of Medicine, Shanghai, China
    Korean J Urol 53:253-7. 2012
    ....
  39. pmc Prediction of pharmacological and xenobiotic responses to drugs based on time course gene expression profiles
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    PLoS ONE 4:e8126. 2009
    ..9%. Our method can be used for pharmacological and xenobiotic responses prediction of new compounds and accelerate drug development...
  40. pmc Predicting biological functions of compounds based on chemical-chemical interactions
    Le Le Hu
    Institute of Systems Biology, Shanghai University, Shanghai, China
    PLoS ONE 6:e29491. 2011
    ....
  41. pmc Using GeneReg to construct time delay gene regulatory networks
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, PR China
    BMC Res Notes 3:142. 2010
    ....
  42. pmc Analysis and prediction of translation rate based on sequence and functional features of the mRNA
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    PLoS ONE 6:e16036. 2011
    ..Our translation rate prediction model might become a high throughput tool for annotating the translation rate of mRNAs in large-scale...
  43. doi Plasma microRNA profile as a predictor of early virological response to interferon treatment in chronic hepatitis B patients
    Xiaonan Zhang
    Research Unit, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
    Antivir Ther 17:1243-53. 2012
    ..To find novel markers associated with prognosis of IFN therapy, we investigated whether a pretreatment plasma microRNA profile could be used to predict early virological response to IFN...
  44. pmc RICD: a rice indica cDNA database resource for rice functional genomics
    Tingting Lu
    National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, PR China
    BMC Plant Biol 8:118. 2008
    ..A database of the rice indica cDNAs was therefore built to provide a comprehensive web data source for searching and retrieving the indica cDNA clones...
  45. pmc A unified 35-gene signature for both subtype classification and survival prediction in diffuse large B-cell lymphomas
    Yu Dong Cai
    Institute of Systems Biology, Shanghai University, Shanghai, People s Republic of China
    PLoS ONE 5:e12726. 2010
    ..Our results suggest that for some diseases, especially cancer, subtype classification may be used to predict survival, and, conversely, survival prediction features may shed light on subtype features...
  46. doi SRD5A1 and SRD5A2 are associated with treatment for benign prostatic hyperplasia with the combination of 5α-reductase inhibitors and α-adrenergic receptor antagonists
    Xin Gu
    Department of Urology, Xinhua Hospital, Medical School of Shanghai Jiaotong University, Shanghai, People s Republic of China
    J Urol 190:615-9. 2013
    ..SRD5A1 and SRD5A2 are 5α-reductase inhibitor targets. We investigated the association between drug efficacy and single nucleotide polymorphisms in the SRD5A1 and SRD5A2 genes in a Chinese population...
  47. pmc Anti-tumor effects of brucine immuno-nanoparticles on hepatocellular carcinoma
    Jian Min Qin
    Department of General Surgery, PuTuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, People s Republic of China
    Int J Nanomedicine 7:369-79. 2012
    ..This study evaluated the effects of brucine immuno-nanoparticles (BIN) on hepatocellular carcinoma...
  48. ncbi Prediction of human genes' regulatory functions based on proteinprotein interaction network
    Peng Gao
    Department of Ophthalmology, Huashan Hospital Affiliated to Fudan University, Shanghai 200040, People s Republic of China
    Protein Pept Lett 19:910-6. 2012
    ....
  49. doi Predictive value of resistive index, detrusor wall thickness and ultrasound estimated bladder weight regarding the outcome after transurethral prostatectomy for patients with lower urinary tract symptoms suggestive of benign prostatic obstruction
    Tao Huang
    Department of Urology, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
    Int J Urol 19:343-50. 2012
    ..To evaluate the value of three parameters from preoperative ultrasonography in predicting the outcome of transurethral prostatectomy in patients with lower urinary tract symptoms suggestive of benign prostatic obstruction...
  50. pmc High-throughput genotyping by whole-genome resequencing
    Xuehui Huang
    National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
    Genome Res 19:1068-76. 2009
    ....
  51. doi Suppression of adipocyte differentiation by Cordyceps militaris through activation of the aryl hydrocarbon receptor
    Tsuyoshi Shimada
    Department of Molecular Signaling, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo, Yamanashi, Japan
    Am J Physiol Endocrinol Metab 295:E859-67. 2008
    ..militaris on adipocyte differentiation. These results suggest that C. militaris has the potential to interfere with adipocyte differentiation through activation of AhR...
  52. ncbi Construction of eukaryotic expression vector with brain-derived neurotrophic factor receptor trkB gene
    Tao Huang
    Department of Neurosurgery, Zhujiang Hospital, Nanfang Medical University, Guangzhou 510282, China
    Chin J Traumatol 8:142-6. 2005
    ..To construct an eukaryotic expression vector carrying rat brain-derived neurotrophic factor receptor trkB gene...
  53. ncbi Identification of a differentially expressed gene PPP1CB between porcine Longissimus dorsi of Meishan and Large WhitexMeishan hybrids
    Tao Huang
    Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agriculture University, Wuhan 430070, China
    Acta Biochim Biophys Sin (Shanghai) 38:450-6. 2006
    ..The tissue expression analysis indicated that the swine PPP1CB gene is generally expressed in most tissues. The possible role of PPP1CB and its relation to porcine heterosis are discussed...