Mary Qu Yang

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc Promoting synergistic research and education in genomics and bioinformatics
    Jack Y Yang
    Harvard University, PO Box 400888, Cambridge, Massachusetts 02140 0888, USA
    BMC Genomics 9:I1. 2008
  2. pmc Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare research
    Jack Y Yang
    Harvard Medical School, Harvard University, Cambridge, Massachusetts 02115, USA
    BMC Genomics 9:I1. 2008
  3. pmc 3D protein structure prediction with genetic tabu search algorithm
    Xiaolong Zhang
    School of Computer Science and Technology, Wuhan University of Science and Technology, Wuhan, Hubei, PR China
    BMC Syst Biol 4:S6. 2010
  4. pmc BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features
    Liangjiang Wang
    Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
    BMC Syst Biol 4:S3. 2010
  5. pmc Analyzing adjuvant radiotherapy suggests a non monotonic radio-sensitivity over tumor volumes
    Jack Y Yang
    Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
    BMC Genomics 9:S9. 2008
  6. pmc Selecting subsets of newly extracted features from PCA and PLS in microarray data analysis
    Guo Zheng Li
    Department of Control Science and Engineering, Tongji University, Shanghai 201804, PR China
    BMC Genomics 9:S24. 2008
  7. pmc Word-based characterization of promoters involved in human DNA repair pathways
    Jens Lichtenberg
    Bioinformatics Laboratory, School of Electrical Engineering and Computer Science, Ohio University, Athens, Ohio, USA
    BMC Genomics 10:S18. 2009
  8. pmc Investigation of transmembrane proteins using a computational approach
    Jack Y Yang
    Department of Radiology, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    BMC Genomics 9:S7. 2008
  9. pmc Comparison of feature selection and classification for MALDI-MS data
    Qingzhong Liu
    Department of Computer Science, New Mexico Tech, Socorro, NM 87801 USA
    BMC Genomics 10:S3. 2009
  10. pmc A comparative study of different machine learning methods on microarray gene expression data
    Mehdi Pirooznia
    Department of Biological Sciences, University of Southern Mississippi, Hattiesburg 39406, USA
    BMC Genomics 9:S13. 2008

Collaborators

Detail Information

Publications27

  1. pmc Promoting synergistic research and education in genomics and bioinformatics
    Jack Y Yang
    Harvard University, PO Box 400888, Cambridge, Massachusetts 02140 0888, USA
    BMC Genomics 9:I1. 2008
    ....
  2. pmc Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare research
    Jack Y Yang
    Harvard Medical School, Harvard University, Cambridge, Massachusetts 02115, USA
    BMC Genomics 9:I1. 2008
    ..b>Mary Qu Yang (IEEE BIBM workshop keynote lecturer on new initiatives of detecting microscopic disease using machine learning ..
  3. pmc 3D protein structure prediction with genetic tabu search algorithm
    Xiaolong Zhang
    School of Computer Science and Technology, Wuhan University of Science and Technology, Wuhan, Hubei, PR China
    BMC Syst Biol 4:S6. 2010
    ..Thus, many algorithms have been developed to solve the global optimization problem. In this paper, a hybrid algorithm, which combines genetic algorithm (GA) and tabu search (TS) algorithm, is developed to complete this task...
  4. pmc BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features
    Liangjiang Wang
    Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
    BMC Syst Biol 4:S3. 2010
    ..However, PSSM is rather designed for PSI-BLAST searches, and it may not contain all the evolutionary information for modelling DNA or RNA-binding sites in protein sequences...
  5. pmc Analyzing adjuvant radiotherapy suggests a non monotonic radio-sensitivity over tumor volumes
    Jack Y Yang
    Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
    BMC Genomics 9:S9. 2008
    ..For many years, it has been well concluded that radio-sensitivities of tumors upon radiotherapy decrease according to the sizes of tumors and RT models based on Poisson statistics have been used extensively to validate clinical data...
  6. pmc Selecting subsets of newly extracted features from PCA and PLS in microarray data analysis
    Guo Zheng Li
    Department of Control Science and Engineering, Tongji University, Shanghai 201804, PR China
    BMC Genomics 9:S24. 2008
    ..While in this paper, we prove that not all the top features are useful, but features should be selected from all the components by feature selection methods...
  7. pmc Word-based characterization of promoters involved in human DNA repair pathways
    Jens Lichtenberg
    Bioinformatics Laboratory, School of Electrical Engineering and Computer Science, Ohio University, Athens, Ohio, USA
    BMC Genomics 10:S18. 2009
    ....
  8. pmc Investigation of transmembrane proteins using a computational approach
    Jack Y Yang
    Department of Radiology, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    BMC Genomics 9:S7. 2008
    ....
  9. pmc Comparison of feature selection and classification for MALDI-MS data
    Qingzhong Liu
    Department of Computer Science, New Mexico Tech, Socorro, NM 87801 USA
    BMC Genomics 10:S3. 2009
    ..The main objective of this paper is to compare the methods of feature selection and different learning classifiers when applied to MALDI-MS data and to provide a subsequent reference for the analysis of MS proteomics data...
  10. pmc A comparative study of different machine learning methods on microarray gene expression data
    Mehdi Pirooznia
    Department of Biological Sciences, University of Southern Mississippi, Hattiesburg 39406, USA
    BMC Genomics 9:S13. 2008
    ..However there is lack of comparison between these methods to find a better framework for classification, clustering and analysis of microarray gene expression results...
  11. pmc Cross-species mapping of bidirectional promoters enables prediction of unannotated 5' UTRs and identification of species-specific transcripts
    Helen Piontkivska
    2Department of BiologicalSciences, Kent State University, Kent, Ohio 44242, USA
    BMC Genomics 10:189. 2009
    ....
  12. pmc Supervised learning method for the prediction of subcellular localization of proteins using amino acid and amino acid pair composition
    Tanwir Habib
    Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
    BMC Genomics 9:S16. 2008
    ..Taking amino-acid composition and amino acid pair composition into consideration helps improving the prediction accuracy...
  13. pmc Supervised learning-based tagSNP selection for genome-wide disease classifications
    Qingzhong Liu
    Department of Computer Science, New Mexico Institute of Mining and Technology, Socorro, NM 87801, USA
    BMC Genomics 9:S6. 2008
    ..To find that subset while reducing study burden in terms of time and costs, one can potentially reconcile information redundancy from associations between SNP markers...
  14. pmc Prediction of DNA-binding residues from protein sequence information using random forests
    Liangjiang Wang
    Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
    BMC Genomics 10:S1. 2009
    ..With the rapid accumulation of sequence data, it becomes an important but challenging task to accurately predict DNA-binding residues directly from amino acid sequence data...
  15. pmc Improving prediction accuracy of tumor classification by reusing genes discarded during gene selection
    Jack Y Yang
    Harvard Medical School, Harvard University, Cambridge, Massachusetts 02140 0888 USA
    BMC Genomics 9:S3. 2008
    ....
  16. pmc Predicting protein disorder by analyzing amino acid sequence
    Jack Y Yang
    Harvard Medical School, Harvard University, Cambridge, MA 02115, USA
    BMC Genomics 9:S8. 2008
    ..These proteins and regions are known as Intrinsically Unstructured Proteins (IUP). IUP have been associated with a wide range of protein functions, along with roles in diseases characterized by protein misfolding and aggregation...
  17. pmc A hybrid machine learning-based method for classifying the Cushing's Syndrome with comorbid adrenocortical lesions
    Jack Y Yang
    Department of Radiology, Brigham and Women s Hospital, Harvard Medical School, Boston, MA 02115, USA
    BMC Genomics 9:S23. 2008
    ....
  18. pmc Dimension reduction with redundant gene elimination for tumor classification
    Xue Qiang Zeng
    School of Computer Engineering and Science, Shanghai University, Shanghai 200072, China
    BMC Bioinformatics 9:S8. 2008
    ..Dimension reduction is often used to handle such a high dimensional problem, but it is obscured by the existence of amounts of redundant features in the microarray data set...
  19. pmc Asymmetric bagging and feature selection for activities prediction of drug molecules
    Guo Zheng Li
    Institute of Systems Biology, Shanghai University, Shanghai 200444, China
    BMC Bioinformatics 9:S7. 2008
    ..With the fact that the number of drug molecules with positive activity is rather fewer than that of negatives, it is important to predict molecular activities considering such an unbalanced situation...
  20. doi request reprint Lecture notes: 2010 and beyond, the decade of high-performance computing for the next-generation sequence analysis
    Mary Qu Yang
    Department of Health and Human Services, Oak Ridge, DOE, United States National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20852, USA
    Int J Comput Biol Drug Des 2:204-6. 2009
    ..We focus mainly on the development of high-performance genetic algorithms based on multi-core technology as an example and open to fast-moving competing platforms to be emerged...
  21. doi request reprint Promoting inter/multidisciplinary education and research in bioinformatics, systems biology and intelligent computing
    Mary Qu Yang
    Department of Health and Human Services, United States National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20852, USA
    Int J Comput Biol Drug Des 2:207-20. 2009
    ..The synergic research on integrating bioinformatics and systems biology facilitates the advances in biology and medicine...
  22. pmc High-throughput next-generation sequencing technologies foster new cutting-edge computing techniques in bioinformatics
    Mary Qu Yang
    National Human Genome Research Institute, National Institutes of Health NIH, U S Department of Health and Human Services, Bethesda, MD 20892, USA
    BMC Genomics 10:I1. 2009
    ..The theme of the conference to promote synergistic research and education has been achieved successfully...
  23. pmc Diversity of core promoter elements comprising human bidirectional promoters
    Mary Qu Yang
    National Human Genome Research Institute, National Institutes Health, Rockville, MD 20852, USA
    BMC Genomics 9:S3. 2008
    ..To define the core promoter elements of bidirectional promoters in human, we mapped motifs for TATA, INR, BRE, DPE, INR, as well as CpG-islands...
  24. pmc Prediction-based approaches to characterize bidirectional promoters in the mammalian genome
    Mary Qu Yang
    National Human Genome Research Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD 20892, USA
    BMC Genomics 9:S2. 2008
    ..We proposed that knowledge gleaned from those methods could be further refined using a multiple class predictor to separate classes of promoter elements from enhancers or nonfunctional DNA...
  25. pmc Comparative analyses of bidirectional promoters in vertebrates
    Mary Qu Yang
    Genome Technology Branch, NHGRI, NIH, MD, USA
    BMC Bioinformatics 9:S9. 2008
    ..In this report we utilize orthology assignments for pairs of genes co-regulated by bidirectional promoters to map the ancestral history of the promoter regions...
  26. pmc ILOOP--a web application for two-channel microarray interwoven loop design
    Mehdi Pirooznia
    Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
    BMC Genomics 9:S11. 2008
    ..It is freely available from http://mcbc.usm.edu/iloop...
  27. ncbi request reprint Identification of Intrinsically Unstructured Proteins using hierarchical classifier
    Jack Y Yang
    Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Harvard University, Boston, Massachusetts 02114, USA
    Int J Data Min Bioinform 2:121-33. 2008
    ..The classifier has been benchmarked against industrial standard PONDR VLXT on out-of-sample data by external evaluators. The IUP predictor is a viable alternative software tool for identifying intrinsic unstructured regions and proteins...