Research Topics
| BING contact ZHANGSummaryAffiliation: Vanderbilt University Country: USA Publications
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Publications
Co-expression module analysis reveals biological processes, genomic gain, and regulatory mechanisms associated with breast cancer progressionZhiao Shi
Advanced Computing Center for Research and Education, Vanderbilt University, Nashville, TN 37240, USA
BMC Syst Biol 4:74. 2010..Gene expression signatures are typically identified by correlating gene expression patterns to a disease phenotype of interest. However, individual gene-based signatures usually suffer from low reproducibility and interpretability...- Proteomics reveals a core molecular response of Pseudomonas putida F1 to acute chromate challengeDorothea K Thompson
Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
BMC Genomics 11:311. 2010..putida strain F1 was characterized within the context of two disparate nutritional environments: rich (LB) media and minimal (M9L) media containing lactate as the sole carbon source... - Fast network centrality analysis using GPUsZhiao Shi
Advanced Computing Center for Research and Education, Vanderbilt University, Nashville, TN 37203, USA
BMC Bioinformatics 12:149. 2011..Designing algorithms that maximize data parallelism is the key in leveraging the power of GPUs... - Relating protein adduction to gene expression changes: a systems approachBing Zhang
Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
Mol Biosyst 7:2118-27. 2011..Although developed for analyzing protein adduction data, the framework can be easily adapted for phosphoproteomics and other types of protein modification data... - Detecting differential and correlated protein expression in label-free shotgun proteomicsBing Zhang
Computer Science and Mathematics Division, Computational Biology Institute, Chemical Science Division, and Life Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
J Proteome Res 5:2909-18. 2006.... - A unified mixed effects model for gene set analysis of time course microarray experimentsLily Wang
Vanderbilt University, USA
Stat Appl Genet Mol Biol 8:Article 47. 2009.... - An integrated approach for the analysis of biological pathways using mixed modelsLily Wang
Department of Biostatistics, Vanderbilt University, Nashville, Tennessee, United States of America
PLoS Genet 4:e1000115. 2008..We compare the properties of this mixed models approach with nonparametric method GSEA and parametric method PAGE using a simulation study, and illustrate its application with a diabetes data set and a dose-response data set... - Characterization of anaerobic catabolism of p-coumarate in Rhodopseudomonas palustris by integrating transcriptomics and quantitative proteomicsChongle Pan
Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
Mol Cell Proteomics 7:938-48. 2008..The integrated gene expression data provided strong support for the non-beta-oxidation route in R. palustris. A putative gene was proposed for every step in the non-beta-oxidation route... - Association analysis for large-scale gene set dataStefan A Kirov
Oak Ridge National Laboratory, University of Tennessee, USA
Methods Mol Biol 408:19-33. 2007..In this chapter, using WebGestalt as an example, it will be explained in detail how to associate gene sets with functional annotations, pathways, publication records, and protein domains... - WebGestalt: an integrated system for exploring gene sets in various biological contextsBing Zhang
Graduate School in Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
Nucleic Acids Res 33:W741-8. 2005..Exploration of all the 48 gene sets using WebGestalt is available for the public at http://genereg.ornl.gov/webgestalt/wg_enrich.php... - GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchiesBing Zhang
Graduate School in Genome Science and Technology, University of Tennessee Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
BMC Bioinformatics 5:16. 2004..Microarray and other high-throughput technologies are producing large sets of interesting genes that are difficult to analyze directly. Bioinformatics tools are needed to interpret the functional information in the gene sets... - From pull-down data to protein interaction networks and complexes with biological relevanceBing Zhang
Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
Bioinformatics 24:979-86. 2008..Protein identification bias in pull-down technology, such as the hydrophilic bias could result in false negatives... - Comparative temporal proteomics of a response regulator (SO2426)-deficient strain and wild-type Shewanella oneidensis MR-1 during chromate transformationKaruna Chourey
Environmental Sciences Division, Oak Ridge National Laboratory, Tennessee 37831, USA
J Proteome Res 8:59-71. 2009..In addition, the proteome data sets were mined for amino acids with potential post-translational modifications (PTMs) indicative of a level of gene expression regulation extending beyond the transcriptional control imposed by SO2426... - Proteomic parsimony through bipartite graph analysis improves accuracy and transparencyBing Zhang
Department of Biomedical Informatics, Mass Spectrometry Research Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232 8575, USA
J Proteome Res 6:3549-57. 2007..We have implemented the tool in the IDPicker package. The source code and binaries for this protein assembly pipeline are available under Mozilla Public License at the following URL: http://www.mc.vanderbilt.edu/msrc/bioinformatics/... - Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removalPaul Wilmes
Department of Earth and Planetary Sciences, University of California at Berkeley, Berkeley, CA 94720, USA
ISME J 2:853-64. 2008.... - Complete genome of Phenylobacterium zucineum--a novel facultative intracellular bacterium isolated from human erythroleukemia cell line K562Yingfeng Luo
Cancer Institute, Key Laboratory for Cancer Intervention and Prevention, Key Laboratory of Molecular Biology in Medical Sciences, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, PR China
BMC Genomics 9:386. 2008..Unlike the known intracellular pathogens, P. zucineum maintains a stable association with its host cell without affecting the growth and morphology of the latter... - Environmental adaptation: genomic analysis of the piezotolerant and psychrotolerant deep-sea iron reducing bacterium Shewanella piezotolerans WP3Fengping Wang
Key Laboratory of Marine Biogenetic Resources, State Oceanic Administration, Xiamen, People s Republic of China
PLoS ONE 3:e1937. 2008..The two sets of flagellum systems were found to be differentially regulated under low temperature and high pressure; the lateral flagellum system was found essential for its motility and living at low temperature... - Supervised principal component analysis for gene set enrichment of microarray data with continuous or survival outcomesXi Chen
Department of Quantitative Health Sciences, The Cleveland Clinic, 9500 Euclid Ave Cleveland, OH 44195, USA
Bioinformatics 24:2474-81. 2008..SOFTWARE: The R code for the analysis used in this article are available upon request, we are currently working on implementing the proposed method in an R package... - Adenovirus-mediated expression of both antisense ornithine decarboxylase and s-adenosylmethionine decarboxylase induces G1 arrest in HT-29 cellsLei Gong
Institute of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan 250012, China
J Biochem Mol Biol 39:730-6. 2006..As a new anticancer reagent, the recombinant adenovirus Ad-ODC-AdoMetDCas holds promising hope for the therapy of colorectal cancers... - Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structureSuvobrata Chakravarty
Department of Structural and Chemical Biology, Mount Sinai School of Medicine, 1425 Madison Avenue, New York, NY 10029, USA
BMC Struct Biol 8:31. 2008.... - Elucidation of the hrp clusters of Xanthomonas oryzae pv. oryzicola that control the hypersensitive response in nonhost tobacco and pathogenicity in susceptible host riceLi-Fang Zou
Key Laboratory of Monitoring and Management for Plant Diseases and Insects, Ministry of Agriculture, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
Appl Environ Microbiol 72:6212-24. 2006..oryzae pv. oryzicola compared with those of X. oryzae pv. oryzae... - The subunit composition of the human NADH dehydrogenase obtained by rapid one-step immunopurificationJames Murray
Department of Molecular Biology, University of Oregon, Eugene 97403, USA
J Biol Chem 278:13619-22. 2003..The concordance of data from human and bovine complex I isolated by different procedures adds to the certainty that these novel proteins of seemingly diverse function are a part of complex I... - Distinct role and functional mode of TR3 and RARalpha in mediating ATRA-induced signalling pathway in breast and gastric cancer cellsXiao feng Ye
Key Laboratory of the Ministry of Education for Cell Biology and Tumor Cell Engineering, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian Province, China
Int J Biochem Cell Biol 36:98-113. 2004..In conclusion, these results reveal the novel mechanism that cellular expression and location of protein is associated with diverse signalling transduction pathways and the resultant physiological process... - Roles of PLC-gamma2 and PKCalpha in TPA-induced apoptosis of gastric cancer cellsBing Zhang
Key Laboratory of the Ministry of Education for Cell Biology and Tumor Cell Engineering, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian Province, China
World J Gastroenterol 9:2413-8. 2003..To investigate the roles of PLCgamma2 and PKCalpha in TPA-induced apoptosis of gastric cancer cells... - Gene expression profiling in human preadipocytes and adipocytes by microarray analysisSumithra Urs
Department of Nutrition, The University of Tennessee, Knoxville, TN 37996-1920, USA
J Nutr 134:762-70. 2004..In conclusion, these studies offer an overview of the gene expression profiles in PA and AD and identify new genes with potentially important functions in adipose tissue development and obesity that merit further investigation... - Ubiquitinated or sumoylated retinoic acid receptor alpha determines its characteristic and interacting model with retinoid X receptor alpha in gastric and breast cancer cellsQiao Wu
Key Laboratory of the Ministry of Education for Cell Biology and Tumor Cell Engineering, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian Province, China
J Mol Endocrinol 32:595-613. 2004..In conclusion, our results reveal a novel mechanism for the regulation of RARalpha-dependent signal transduction through the ubiquitin/proteasome pathway in breast cancer cells and the sumoylation pathway in gastric cancer cells... - Expanded coverage of the human heart mitochondrial proteome using multidimensional liquid chromatography coupled with tandem mass spectrometrySara P Gaucher
Buck Institute for Age Research, Novato, California 94945, USA
J Proteome Res 3:495-505. 2004..Nat. Biotechnol. 2003, 21, 281-286). We now report two subsequent studies where multidimensional liquid chromatography MS/MS was investigated as an alternative means for characterizing the same sample... - [Analysis of gene expression profiles in heart tissues from two breeds of pigs]Yan-Wu Zeng
College of Life Sciences, Zhejiang University, Hangzhou 310029, China
Yi Chuan Xue Bao 31:565-71. 2004..The results indicate that the physiological activities of Landrace heart are more active and effective than Erhualian heart... - [Growth inhibition of human hepatocellular carcinoma xenograft in nude mice by combined treatment with human cytokine-induced killer cells and chemotherapy]Ming Shi
Division of Biological Engineering, Beijing Institute of Infectious Disease, The 302 Hospital of PLA, Beijing 100039, China
Zhonghua Zhong Liu Za Zhi 26:465-8. 2004..CONCLUSION: The growth inhibitory effect on human HCC transplanted in nude mice of combined CIK cells and MMC treatment is more potent than that of CIK cells or MMC alone... - Drosophila spastin regulates synaptic microtubule networks and is required for normal motor functionNina Tang Sherwood
Broad Center, Division of Biology, California Institute of Technology Pasadena, California, USA
PLoS Biol 2:e429. 2004.... - EST-based analysis of gene expression in the porcine brainBing Zhang
James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou Genomics Institute, Hangzhou 310008, China
Genomics Proteomics Bioinformatics 2:237-44. 2004..3% matched known porcine ESTs; and 21.5% had no matches to any known sequences in GenBank. We used the categories defined by the Gene Ontology to survey gene expression in the porcine brain... - Insulin-like growth factor-I receptor/human epidermal growth factor receptor 2 heterodimerization contributes to trastuzumab resistance of breast cancer cellsRita Nahta
Department of Breast Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030-4009, USA
Cancer Res 65:11118-28. 2005.... - Gene expression profiling in porcine mammary gland during lactation and identification of breed- and developmental-stage-specific genesZhixi Su
James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China
Sci China C Life Sci 49:26-36. 2006..The unknown EST sequences and expression profiles at different developmental stages and breeds are very important resources for further research... - [Cytotoxicity of cytotoxic T lymphocytes induced by the dendritic cells phagocytosing PLA-AFP218-226 micospheres Against hepatocellular carcinoma cell lines]Bing Zhang
Department of Immunology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu 610041, China
Sichuan Da Xue Xue Bao Yi Xue Ban 37:378-80, 448. 2006.... - Transcriptome analysis of Deinagkistrodon acutus venomous gland focusing on cellular structure and functional aspects using expressed sequence tagsBing Zhang
James D Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, China
BMC Genomics 7:152. 2006..As far as the molecular mechanism of toxin secretion and metabolism is concerned, we still knew a little. Therefore, a fundamental question being arisen is what genes are expressed in the snake venom glands besides many toxin components?.. - Combination of cytosine deaminase with uracil phosphoribosyl transferase leads to local and distant bystander effects against RM1 prostate cancer in miceAparajita Khatri
Oncology Research Centre, Prince of Wales Hospital Clinical School of Medicine, The University of New South Wales, Randwick, NSW 2031, Australia
J Gene Med 8:1086-96. 2006..The product of the fusion gene, CDUPRT, converts the prodrug, 5-fluorocytosine (5FC), into 5-fluorouracil (5FU) and other cytotoxic metabolites that kill both CDUPRT-expressing and surrounding cells, via a 'bystander effect'... - Characterization of the human heart mitochondrial proteomeSteven W Taylor
MitoKor, 11494 Sorrento Valley Road, San Diego, California 92121, USA
Nat Biotechnol 21:281-6. 2003..The biochemical roles of 19% of the identified proteins have not been defined. This database of proteins provides a comprehensive resource for the discovery of novel mitochondrial functions and pathways...
Research Grants
- Systems Approach to the Biological Basis of Colon Cancer MetastasesBING contact ZHANG; Fiscal Year: 2010..The proposed studies will provide important information on the network mechanisms of CRC metastasis and use this information to improve patient prognosis and discover novel therapeutic targets. ..