Research Topics
Genomes and Genes | Tao HuangSummaryAffiliation: Shanghai Institutes for Biological Sciences Country: China Publications
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Detail Information
Publications
Growth and differentiation of mouse tracheal epithelial cells: selection of a proliferative populationYingjian 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...
The prediction of interferon treatment effects based on time series microarray gene expression profilesTao 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...
Crosstissue coexpression network of agingTao 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...- A Sequence-based Approach for Predicting Protein Disordered RegionsTao 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... - Deciphering the effects of gene deletion on yeast longevity using network and machine learning approachesTao 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... - The role of Hepatitis C Virus in the dynamic protein interaction networks of hepatocellular cirrhosis and carcinomaTao 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... - TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interactions and protein post-translational modifications informationQi 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... - Predicting protein oxidation sites with feature selection and analysis approachShen 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... - Identification of colorectal cancer related genes with mRMR and shortest path in protein-protein interaction networkBi 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... - Predicting transcriptional activity of multiple site p53 mutants based on hybrid propertiesTao 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... - Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networksTao 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... - Selection of reprogramming factors of induced pluripotent stem cells based on the protein interaction network and functional profilesTao 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... - Genome-wide association studies of 14 agronomic traits in rice landracesXuehui 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.... - Prediction of protein-protein interaction sites by random forest algorithm with mRMR and IFSBi 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... - A map of rice genome variation reveals the origin of cultivated riceXuehui 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... - Prediction of lysine ubiquitination with mRMR feature selection and analysisYudong 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... - Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasmXuehui 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... - Prediction and analysis of protein hydroxyproline and hydroxylysineLe 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... - Hepatitis C virus network based classification of hepatocellular cirrhosis and carcinomaTao 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... - Analysis of metabolic pathway using hybrid propertiesLei 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... - Predicting functions of proteins in mouse based on weighted protein-protein interaction network and protein hybrid propertiesLele 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... - Prediction of deleterious non-synonymous SNPs based on protein interaction network and hybrid propertiesTao 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... - Inter- and intra-chain disulfide bond prediction based on optimal feature selectionShen Niu
CAS MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P R China
Protein Pept Lett 20:324-35. 2013.... - Identification of retinoblastoma related genes with shortest path in a protein-protein interaction networkBi 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... - SySAP: a system-level predictor of deleterious single amino acid polymorphismsTao 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/... - Computational analysis of HIV-1 resistance based on gene expression profiles and the virus-host interaction networkTao 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... - Prediction of body fluids where proteins are secreted into based on protein interaction networkLe 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... - Dysfunctions associated with methylation, microRNA expression and gene expression in lung cancerTao 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... - Functional association between influenza A (H1N1) virus and humanTao 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... - Prediction of tyrosine sulfation with mRMR feature selection and analysisShen 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... - Predicting protein phenotypes based on protein-protein interaction networkLele 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... - Classification and analysis of regulatory pathways using graph property, biochemical and physicochemical property, and functional propertyTao 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... - Transitional Zone Index and Intravesical Prostatic Protrusion in Benign Prostatic Hyperplasia Patients: Correlations according to Treatment Received and Other Clinical DataTao Huang
Department of Urology, Xin Hua Hospital Shanghai Jiao Tong University School of Medicine, Shanghai, China
Korean J Urol 53:253-7. 2012.... - Prediction of pharmacological and xenobiotic responses to drugs based on time course gene expression profilesTao 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... - Predicting biological functions of compounds based on chemical-chemical interactionsLe Le Hu
Institute of Systems Biology, Shanghai University, Shanghai, China
PLoS ONE 6:e29491. 2011.... - Using GeneReg to construct time delay gene regulatory networksTao 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.... - Analysis and prediction of translation rate based on sequence and functional features of the mRNATao 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... - RICD: a rice indica cDNA database resource for rice functional genomicsTingting 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... - A unified 35-gene signature for both subtype classification and survival prediction in diffuse large B-cell lymphomasYu 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... - Using WPNNA Classifier in Ubiquitination Site Prediction Based on Hybrid FeaturesKai Yan Feng
College of Animal Science and Technology, Shihezi University, Beisi Road, Shihezi City 832003, Xinjiang, China
Protein Pept Lett 20:318-23. 2013.... - Anti-tumor effects of brucine immuno-nanoparticles on hepatocellular carcinomaJian 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... - 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 obstructionTao 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... - Prediction of human genes' regulatory functions based on proteinprotein interaction networkPeng Gao
Department of Ophthalmology, Huashan Hospital Affiliated to Fudan University, Shanghai 200040, People s Republic of China
Protein Pept Lett 19:910-6. 2012.... - High-throughput genotyping by whole-genome resequencingXuehui 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.... - Suppression of adipocyte differentiation by Cordyceps militaris through activation of the aryl hydrocarbon receptorTsuyoshi 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... - Construction of eukaryotic expression vector with brain-derived neurotrophic factor receptor trkB geneTao Huang
Department of Neurosurgery, Zhujiang Hospital, Nanfang Medical University, Guangzhou 510282, China
Chin J Traumatol 8:142-6. 2005..Enzyme digestion and PCR analysis showed that the gene of trkB had been successfully cloned into vector pMD18-T and pEGFP-C2. CONCLUSIONS: The trkB gene of rat has been amplified and cloned into the eukaryotic expression vector pEGFP-C2... - Identification of a differentially expressed gene PPP1CB between porcine Longissimus dorsi of Meishan and Large WhitexMeishan hybridsTao 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...