Youping DengSummaryAffiliation: Rush University Medical Center Country: USA Publications
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Publications
In vitro gene regulatory networks predict in vivo function of liverYouping Deng
Rush University Medical Center, Chicago, IL 60612, USA
BMC Syst Biol 4:153. 2010..However, the degree to which we can extend in vitro results to in vivo activity and possible mechanisms of action remains to be fully addressed...- Recursive SVM biomarker selection for early detection of breast cancer in peripheral bloodFan Zhang
Department of Academic and Institutional Resources and Technology, University of North Texas Health Science Center, Fort Worth, TX, USA
BMC Med Genomics 6:S4. 2013.... - A robust detail preserving anisotropic diffusion for speckle reduction in ultrasound imagesXiaoming Liu
College of Computer Science and Technology, Wuhan University of Science and Technology, Wuhan, Hubei, China
BMC Genomics 12:S14. 2011..Thus a detail preserved anisotropic diffusion speckle reduction with less sensitive to the number of iterations is needed. This paper aims to develop this kind of technologies... - A hidden Markov model-based algorithm for identifying tumour subtype using array CGH dataKe Zhang
Department of Pathology, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58201, USA
BMC Genomics 12:S10. 2011..A mixture hidden Markov model based algorithm was developed to address these two challenges... - Gene selection and classification for cancer microarray data based on machine learning and similarity measuresQingzhong Liu
Department of Computer Science, Sam Houston State University, Huntsville, TX 77341, USA
BMC Genomics 12:S1. 2011..Associations among genetic markers mean one can exploit information redundancy to potentially reduce classification cost in terms of time and money... - Maximum predictive power of the microarray-based models for clinical outcomes is limited by correlation between endpoint and gene expression profileChen Zhao
The Center for Bioinformatics and The institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
BMC Genomics 12:S3. 2011..Fine-tuning of model parameters and optimizing each step of the modeling process often results in over-fitting problems without improving performance... - A gene selection method for GeneChip array data with small sample sizesZhongxue Chen
Biostatistics Epidemiology Research Design Core, Center for Clinical and Translational Sciences, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
BMC Genomics 12:S7. 2011..Furthermore, estimated permutation-based p-values for true nulls are highly correlated and not uniformly distributed between zero and one, making it difficult to use current false discovery rate (FDR)-controlling methods... - Maximizing biomarker discovery by minimizing gene signaturesChang Chang
The Center for Bioinformatics and Institute of Biomedical Sciences, School of Life Science, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
BMC Genomics 12:S6. 2011.... - Genomic signatures and gene networking: challenges and promisesKe Zhang
Department of Pathology, Bioinformatics Core, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58201, USA
BMC Genomics 12:I1. 2011..We hope this supplement presents the current computational and statistical challenges faced in genomics studies, and shows the enormous promises and opportunities in the genomic future... - Transcriptomic profiles of peripheral white blood cells in type II diabetes and racial differences in expression profilesJinghe Mao
Department of Biology, Tougaloo College, Tougaloo, MS 39174, USA
BMC Genomics 12:S12. 2011.... - A new approach to construct pathway connected networks and its application in dose responsive gene expression profiles of rat liver regulated by 2,4DNTSudhir Chowbina
Indiana University School of Informatics, Indianapolis, IN 46202, USA
BMC Genomics 11:S4. 2010..Although a series of methods for gene network construction have been developed, few instances of applying such technology to generate pathway connected networks have been reported... - Recent advances in clustering methods for protein interaction networksJianxin Wang
School of Information Science and Engineering, Central South University, Changsha 410083, China
BMC Genomics 11:S10. 2010..The predictions of protein functions and interactions based on modules will be covered. Finally, the performance of different clustering methods will be compared and the directions for future research will be discussed... - Gene set analysis for longitudinal gene expression dataKe Zhang
School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
BMC Bioinformatics 12:273. 2011..In these longitudinal studies, gene expression is repeatedly measured over time such that a GSA needs to take into account the within-gene correlations in addition to possible between-gene correlations... - Analysis of common and specific mechanisms of liver function affected by nitrotoluene compoundsYouping Deng
Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, United States of America
PLoS ONE 6:e14662. 2011....