Youping Deng

Summary

Affiliation: Rush University Medical Center
Country: USA

Publications

  1. pmc In vitro gene regulatory networks predict in vivo function of liver
    Youping Deng
    Rush University Medical Center, Chicago, IL 60612, USA
    BMC Syst Biol 4:153. 2010
  2. ncbi request reprint Identification of biomarkers that distinguish chemical contaminants based on gene expression profiles
    Xiaomou Wei
    Department of Internal Medicine, Rush University Cancer Center, Rush University Medical Center, Kidston House, 630 S, Hermitage Ave, Room 408, Chicago, IL 60612, USA
    BMC Genomics 15:248. 2014
  3. pmc State Space Model with hidden variables for reconstruction of gene regulatory networks
    Xi Wu
    School of Computing, University of Southern Mississippi, Hattiesburg, MS 39406, USA
    BMC Syst Biol 5:S3. 2011
  4. pmc A transcriptional dynamic network during Arabidopsis thaliana pollen development
    Jigang Wang
    College of Life Sciences, Northeast Forestry University, Heilongjiang, Harbin 150040, China
    BMC Syst Biol 5:S8. 2011
  5. pmc Mass segmentation using a combined method for cancer detection
    Jun Liu
    College of Computer Science and Technology, Wuhan University of Science and Technology, Wuhan, Hubei, China
    BMC Syst Biol 5:S6. 2011
  6. pmc Statistical methods on detecting differentially expressed genes for RNA-seq data
    Zhongxue 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 Syst Biol 5:S1. 2011
  7. pmc From genes to networks: in systematic points of view
    Ke Zhang
    Department of Pathology, Bioinformatics Core, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58201, USA
    BMC Syst Biol 5:I1. 2011
  8. pmc Exploring the pathogenetic association between schizophrenia and type 2 diabetes mellitus diseases based on pathway analysis
    Yanli Liu
    Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
    BMC Med Genomics 6:S17. 2013
  9. pmc Short and long term gene expression variation and networking in human proximal tubule cells when exposed to cadmium
    Scott H Garrett
    Department of Pathology, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
    BMC Med Genomics 6:S2. 2013
  10. pmc Detecting differentially methylated loci for Illumina Array methylation data based on human ovarian cancer data
    Zhongxue Chen
    Department of Epidemiology and Biostatistics, School of Public Health, Indiana University Bloomington, 1025 E, 7th Street, Bloomington, IN 47405, USA
    BMC Med Genomics 6:S9. 2013

Collaborators

  • Edward J Perkins
  • David R Johnson
  • Natalia Garcia-Reyero
  • Chaoyang Zhang
  • Sharon A Meyer
  • Renee Drabier
  • Fan Zhang
  • Zhongxue Chen
  • Ke Zhang
  • Tieliu Shi
  • Xudong Huang
  • Qingzhong Liu
  • Chen Zhao
  • Ke K Zhang
  • Yanli Liu
  • Hamid R Arabnia
  • Jianzhong Liu
  • Junmei Ai
  • Xiaoming Liu
  • Jun Liu
  • Jack Y Yang
  • Xiaomou Wei
  • Benqiong Hu
  • Scott H Garrett
  • Zhenghui Yi
  • Meiwei Jia
  • Meixia Zhang
  • Hon Keung Tony Ng
  • Xin Guan
  • Saralees Nadarajah
  • Lajos Pusztai
  • Jinghe Mao
  • Jinshan Tang
  • Weida Tong
  • Jigang Wang
  • W Fraser Symmans
  • Lei Chun
  • Chang Chang
  • Xi Wu
  • Sudhir Chowbina
  • Jianxin Wang
  • Choo Y Ang
  • Charles R Vanderburg
  • Zezhi Li
  • Kaitlin Clarke
  • Chaoyang Pang
  • Chengping Wen
  • Seema Somji
  • Hanwen Huang
  • Jack T Rogers
  • Yunliang Wang
  • Shipeng Wang
  • Gang Jiang
  • Donald A Sens
  • Zhongchao Shen
  • Hans Peter Piepho
  • Monnie McGee
  • Ping Gong
  • Junwei Wang
  • Xin Xu
  • Yunlong Liu
  • Peng Li
  • Xiaonan Wang
  • Linglin Xie
  • Solomon W Harrar
  • Jennifer Fostel
  • Weizhong Li
  • John D Shaughnessy
  • Megan Kong
  • Andrzej Niemierko
  • Arif Ghafoor
  • Howard L Kaufman
  • Manuel Ong
  • Jasmine T Washington
  • Sens Donald
  • Pierre R Bushel
  • Xiaojie Qiu
  • Viswanath Devanarayan
  • Ming Shenwu
  • Mehdi Pirooznia
  • Marketta Blue
  • Arne C Bathke
  • Andrew H Sung
  • Xinchun Zhou
  • Jianxun Chen
  • Nan Wang
  • Lei Chen
  • Leming Shi
  • Andre Oberthuer
  • Yi Yang

Detail Information

Publications26

  1. pmc In vitro gene regulatory networks predict in vivo function of liver
    Youping 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...
  2. ncbi request reprint Identification of biomarkers that distinguish chemical contaminants based on gene expression profiles
    Xiaomou Wei
    Department of Internal Medicine, Rush University Cancer Center, Rush University Medical Center, Kidston House, 630 S, Hermitage Ave, Room 408, Chicago, IL 60612, USA
    BMC Genomics 15:248. 2014
    ..Here, we investigated the use of microarrays to predict chemical toxicants and their possible mechanisms of action...
  3. pmc State Space Model with hidden variables for reconstruction of gene regulatory networks
    Xi Wu
    School of Computing, University of Southern Mississippi, Hattiesburg, MS 39406, USA
    BMC Syst Biol 5:S3. 2011
    ....
  4. pmc A transcriptional dynamic network during Arabidopsis thaliana pollen development
    Jigang Wang
    College of Life Sciences, Northeast Forestry University, Heilongjiang, Harbin 150040, China
    BMC Syst Biol 5:S8. 2011
    ..Here, we adopt Networks Component Analysis (NCA) to identify TF activities over time course, and infer their regulatory relationships based on the coexpression of TFs and their target genes during pollen development...
  5. pmc Mass segmentation using a combined method for cancer detection
    Jun Liu
    College of Computer Science and Technology, Wuhan University of Science and Technology, Wuhan, Hubei, China
    BMC Syst Biol 5:S6. 2011
    ..The shape of mass can be used as one of the factors to determine whether the mass is malignant or benign. However, many of the current methods are semi-automatic. In this paper, we investigate fully automatic segmentation method...
  6. pmc Statistical methods on detecting differentially expressed genes for RNA-seq data
    Zhongxue 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 Syst Biol 5:S1. 2011
    ..In statistical literature, several methods have been proposed to compare two Poisson means (rates). In this paper, we compare these methods by using simulated and real RNA-seq data...
  7. pmc From genes to networks: in systematic points of view
    Ke Zhang
    Department of Pathology, Bioinformatics Core, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58201, USA
    BMC Syst Biol 5:I1. 2011
    ..We present a report of the BIOCOMP'10 - The 2010 International Conference on Bioinformatics & Computational Biology and other related work in the area of systems biology...
  8. pmc Exploring the pathogenetic association between schizophrenia and type 2 diabetes mellitus diseases based on pathway analysis
    Yanli Liu
    Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
    BMC Med Genomics 6:S17. 2013
    ..Here we explored the pathogenetic association between SCZ and T2D based on pathway analysis and protein-protein interaction...
  9. pmc Short and long term gene expression variation and networking in human proximal tubule cells when exposed to cadmium
    Scott H Garrett
    Department of Pathology, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
    BMC Med Genomics 6:S2. 2013
    ..The most prominent network module consisted of INHBA, KIF20A, DNAJA4, AKAP12, ZFAND2A, AKR1B10, SCL7A11, and AKR1C1...
  10. pmc Detecting differentially methylated loci for Illumina Array methylation data based on human ovarian cancer data
    Zhongxue Chen
    Department of Epidemiology and Biostatistics, School of Public Health, Indiana University Bloomington, 1025 E, 7th Street, Bloomington, IN 47405, USA
    BMC Med Genomics 6:S9. 2013
    ..However, inappropriate testing approaches can result in large false positives and/or false negatives. Appropriate and powerful statistical methods are desirable but very limited in the literature...
  11. pmc The current trend of genomics research for human diseases
    Ke K Zhang
    Department of Pathology, Bioinformatics Core, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58201, USA
    BMC Med Genomics 6:S1. 2013
    ....
  12. pmc Assessment of gene order computing methods for Alzheimer's disease
    Benqiong Hu
    College of Management Science, Chengdu University of Technology, Chengdu 610059, China
    BMC Med Genomics 6:S8. 2013
    ..We thus set forth to evaluate the performances of current gene order computing methods with different distance formulas, and to identify additional features associated with gene order computation...
  13. pmc HDAM: a resource of human disease associated mutations from next generation sequencing studies
    Meiwei Jia
    Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Science, East China Normal University, Shanghai 200241, China
    BMC Med Genomics 6:S16. 2013
    ..However, mutation descriptions are hard to be compared and integrated due to various reference sequences and annotation tools adopted in different articles as well as the nomenclature of diseases/traits...
  14. pmc Recursive SVM biomarker selection for early detection of breast cancer in peripheral blood
    Fan 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
    ....
  15. pmc Maximum predictive power of the microarray-based models for clinical outcomes is limited by correlation between endpoint and gene expression profile
    Chen 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...
  16. pmc A robust detail preserving anisotropic diffusion for speckle reduction in ultrasound images
    Xiaoming 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...
  17. pmc A hidden Markov model-based algorithm for identifying tumour subtype using array CGH data
    Ke 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...
  18. pmc Gene selection and classification for cancer microarray data based on machine learning and similarity measures
    Qingzhong 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...
  19. pmc A gene selection method for GeneChip array data with small sample sizes
    Zhongxue 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...
  20. pmc Maximizing biomarker discovery by minimizing gene signatures
    Chang 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
    ....
  21. pmc Transcriptomic profiles of peripheral white blood cells in type II diabetes and racial differences in expression profiles
    Jinghe Mao
    Department of Biology, Tougaloo College, Tougaloo, MS 39174, USA
    BMC Genomics 12:S12. 2011
    ....
  22. pmc Genomic signatures and gene networking: challenges and promises
    Ke 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...
  23. pmc A new approach to construct pathway connected networks and its application in dose responsive gene expression profiles of rat liver regulated by 2,4DNT
    Sudhir 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...
  24. pmc Recent advances in clustering methods for protein interaction networks
    Jianxin 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...
  25. pmc Gene set analysis for longitudinal gene expression data
    Ke 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...
  26. pmc Analysis of common and specific mechanisms of liver function affected by nitrotoluene compounds
    Youping Deng
    Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, United States of America
    PLoS ONE 6:e14662. 2011
    ....