Research Topics
| Bing ZhangSummaryAffiliation: Oak Ridge National Laboratory Country: USA Publications
| Collaborators
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Detail Information
Publications
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...- 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... - 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... - 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... - 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.... - 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... - 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... - Study of the inhibition of cyclin-dependent kinases with roscovitine and indirubin-3'-oxime from molecular dynamics simulationsBing Zhang
Nanoscience and Nanotechnology Initiative, National University of Singapore, 2 Engineering Drive 3, Singapore, 117576, Singapore
J Mol Model 13:79-89. 2007..This resulted in a more conserved binding pattern than the water-excluded structure. Hence, in the design of new indirubin-like inhibitors, it is important to include the water molecule in the analysis... - 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... - 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/... - 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... - [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... - 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... - 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... - 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?..