Huai Li

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. ncbi request reprint Inferring regulatory networks
    Huai Li
    Bioinformatics Unit, Branch of Research Resources, National Institute on Aging, NIH, Baltimore, MD, USA
    Front Biosci 13:263-75. 2008
  2. pmc Unraveling transcriptional regulatory programs by integrative analysis of microarray and transcription factor binding data
    Huai Li
    Bioinformatics Unit, Branch of Research Resources, National Institute on Aging, NIH, Baltimore, MD 21224, USA
    Bioinformatics 24:1874-80. 2008
  3. pmc Motif-guided sparse decomposition of gene expression data for regulatory module identification
    Ting Gong
    Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA 22203, USA
    BMC Bioinformatics 12:82. 2011
  4. pmc Knowledge-guided gene ranking by coordinative component analysis
    Chen Wang
    Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA, USA
    BMC Bioinformatics 11:162. 2010
  5. pmc Transcriptome coexpression map of human embryonic stem cells
    Huai Li
    Bioinformatics Unit, Branch of Research Resources, National Institute on Aging, NIH, Baltimore, MD 21224, USA
    BMC Genomics 7:103. 2006
  6. pmc Evolutionarily conserved transcriptional co-expression guiding embryonic stem cell differentiation
    Yu Sun
    Bioinformatics Unit, Research Resources Branch, National Institute on Aging, NIH, Baltimore, MD, USA
    PLoS ONE 3:e3406. 2008
  7. pmc Cross-species transcriptional profiles establish a functional portrait of embryonic stem cells
    Yu Sun
    Bioinformatics Unit, Research Resources Branch, National Institute on Aging, National Institutes of Health, 333 Cassall Drive, Baltimore, MD 21224, USA
    Genomics 89:22-35. 2007
  8. ncbi request reprint Systematic intervention of transcription for identifying network response to disease and cellular phenotypes
    Huai Li
    Bioinformatics Unit, Branch of Research Resources, National Institute on Aging NIH, Baltimore, MD 21224, USA
    Bioinformatics 22:96-102. 2006
  9. ncbi request reprint The discovery of transcriptional modules by a two-stage matrix decomposition approach
    Huai Li
    Bioinformatics Unit, Branch of Research Resources, National Institute on Aging, NIH, Baltimore, MD 21224, USA
    Bioinformatics 23:473-9. 2007
  10. pmc Genome wide profiling of human embryonic stem cells (hESCs), their derivatives and embryonal carcinoma cells to develop base profiles of U.S. Federal government approved hESC lines
    Ying Liu
    Laboratory of Neurosciences, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
    BMC Dev Biol 6:20. 2006

Collaborators

Detail Information

Publications21

  1. ncbi request reprint Inferring regulatory networks
    Huai Li
    Bioinformatics Unit, Branch of Research Resources, National Institute on Aging, NIH, Baltimore, MD, USA
    Front Biosci 13:263-75. 2008
    ..Popular solutions to each of these problems and their relative merits are discussed...
  2. pmc Unraveling transcriptional regulatory programs by integrative analysis of microarray and transcription factor binding data
    Huai Li
    Bioinformatics Unit, Branch of Research Resources, National Institute on Aging, NIH, Baltimore, MD 21224, USA
    Bioinformatics 24:1874-80. 2008
    ..Unraveling the transcriptional regulatory program mediated by transcription factors (TFs) is a fundamental objective of computational biology, yet still remains a challenge...
  3. pmc Motif-guided sparse decomposition of gene expression data for regulatory module identification
    Ting Gong
    Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA 22203, USA
    BMC Bioinformatics 12:82. 2011
    ..However, traditional gene clustering often yields unsatisfactory results for regulatory module identification because the resulting gene clusters are co-expressed but not necessarily co-regulated...
  4. pmc Knowledge-guided gene ranking by coordinative component analysis
    Chen Wang
    Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA, USA
    BMC Bioinformatics 11:162. 2010
    ..However, current integration strategies are often heuristic and fail to incorporate fully the true interplay between biological knowledge and gene expression data...
  5. pmc Transcriptome coexpression map of human embryonic stem cells
    Huai Li
    Bioinformatics Unit, Branch of Research Resources, National Institute on Aging, NIH, Baltimore, MD 21224, USA
    BMC Genomics 7:103. 2006
    ..However, no systematic analysis has yet addressed whether gene expression in human ES cells may be regulated in chromosomal domains, and no chromosomal domains of coexpression have been identified...
  6. pmc Evolutionarily conserved transcriptional co-expression guiding embryonic stem cell differentiation
    Yu Sun
    Bioinformatics Unit, Research Resources Branch, National Institute on Aging, NIH, Baltimore, MD, USA
    PLoS ONE 3:e3406. 2008
    ..Cross-species examination of transcriptional co-expression allows elucidation of fundamental and species-specific mechanisms regulating ESC self-renewal or differentiation...
  7. pmc Cross-species transcriptional profiles establish a functional portrait of embryonic stem cells
    Yu Sun
    Bioinformatics Unit, Research Resources Branch, National Institute on Aging, National Institutes of Health, 333 Cassall Drive, Baltimore, MD 21224, USA
    Genomics 89:22-35. 2007
    ..The data and analyses resulting from this study provide a framework for new hypotheses and research directions and a public resource for functional genomics of ESCs...
  8. ncbi request reprint Systematic intervention of transcription for identifying network response to disease and cellular phenotypes
    Huai Li
    Bioinformatics Unit, Branch of Research Resources, National Institute on Aging NIH, Baltimore, MD 21224, USA
    Bioinformatics 22:96-102. 2006
    ..Here, we addressed this issue by developing an algorithm to mimic the behavior of regulatory networks in silico and to identify the dynamic response to disease and changing cellular conditions...
  9. ncbi request reprint The discovery of transcriptional modules by a two-stage matrix decomposition approach
    Huai Li
    Bioinformatics Unit, Branch of Research Resources, National Institute on Aging, NIH, Baltimore, MD 21224, USA
    Bioinformatics 23:473-9. 2007
    ..Unraveling such transcriptional modules is important for understanding biological network, deciphering regulatory mechanisms and identifying biomarkers...
  10. pmc Genome wide profiling of human embryonic stem cells (hESCs), their derivatives and embryonal carcinoma cells to develop base profiles of U.S. Federal government approved hESC lines
    Ying Liu
    Laboratory of Neurosciences, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
    BMC Dev Biol 6:20. 2006
    ....
  11. ncbi request reprint Mechanisms controlling embryonic stem cell self-renewal and differentiation
    Yu Sun
    Bioinformatics Unit, Research Resources Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA
    Crit Rev Eukaryot Gene Expr 16:211-31. 2006
    ..Here, we review recent findings on mechanisms controlling ES cell development. By integrating data from different sources, we present a global picture of how ES cells reach the decision of self-renewal or differentiation...
  12. pmc Exploring pathways from gene co-expression to network dynamics
    Huai Li
    Bioinformatics Unit, Branch of Research Resources, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
    Methods Mol Biol 541:249-67. 2009
    ..The analysis using these newly developed algorithms show the great usefulness of computational systems biology approaches for biological and medical research...
  13. pmc Temporal and spatial transcriptional profiles of aging in Drosophila melanogaster
    Ming Zhan
    Bioinformatics Unit, Branch of Research Resources, National Institute on Aging, NIH, Baltimore, MD 21224, USA
    Genome Res 17:1236-43. 2007
    ..The spatial and temporal transcriptome data presented in this study provide a basis and a valuable resource for further genetic and genomic investigation of tissue-specific regulation of aging...
  14. pmc Gene expression atlas of the mouse central nervous system: impact and interactions of age, energy intake and gender
    Xiangru Xu
    Laboratory of Neurosciences, National Institute on Aging Intramural Research Program, 5600 Nathan Shock Drive, Baltimore, MD 21224, USA
    Genome Biol 8:R234. 2007
    ..The structural and functional complexity of the mammalian central nervous system (CNS) is organized and modified by complicated molecular signaling processes that are poorly understood...
  15. ncbi request reprint Latent variable and nICA modeling of pathway gene module composite
    Ting Gong
    Dept of ECE, Virginia Polytech Inst and State Univ, Arlington, VA, USA
    Conf Proc IEEE Eng Med Biol Soc 1:5872-5. 2006
    ..The experimental results show that significant enrichment of gene annotations within clusters can be obtained...
  16. ncbi request reprint VISDA: an open-source caBIG analytical tool for data clustering and beyond
    Jiajing Wang
    Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
    Bioinformatics 23:2024-7. 2007
    ..The distinctive features of VISDA are particularly useful for users across the cancer research and broader research communities to analyze complex biological data. AVAILABILITY: http://gforge.nci.nih.gov/projects/visda/..
  17. pmc Elucidation of a C-rich signature motif in target mRNAs of RNA-binding protein TIAR
    Henry S Kim
    Department of Biochemistry and Molecular Biology, Monash University, Victoria, Australia
    Mol Cell Biol 27:6806-17. 2007
    ..In sum, we report the identification of a C-rich signature motif present in TIAR target mRNAs whose association with TIAR decreases following exposure to a stress-causing agent...
  18. ncbi request reprint Optimization of wavelet decomposition for image compression and feature preservation
    Shih Chung B Lo
    Center of Imaging Science and Information Systems, Radiology Department, Georgetown University Medical Center, 2115 Wisconsin Avenue N W, Suite 603, Washington, D C 20007, USA
    IEEE Trans Med Imaging 22:1141-51. 2003
    ..This newly developed optimization approach can be generalized to other image analysis applications where a wavelet decomposition is employed...
  19. ncbi request reprint Identification of signature genes by microarray for acute myeloid leukemia without maturation and acute promyelocytic leukemia with t(15;17)(q22;q12)(PML/RARalpha)
    Jun Morikawa
    The Second Department of Internal Medicine, Mie University School of Medicine, 2 174 Edobashi, Tsu 514 8507, Japan
    Int J Oncol 23:617-25. 2003
    ....
  20. ncbi request reprint A multiple circular path convolution neural network system for detection of mammographic masses
    Shih Chung B Lo
    Center for Imaging Science and Information System, Radiology Department, Georgetown University Medical Center, Washington, DC 20007, USA
    IEEE Trans Med Imaging 21:150-8. 2002
    ..84 to 0.89 using the MCPCNN. This paper does not intend to claim the best mass detection system. Instead it reports a potentially better neural network structure for analyzing a set of the mass features defined by an investigator...