L Li

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. doi request reprint T-KDE: a method for genome-wide identification of constitutive protein binding sites from multiple ChIP-seq data sets
    Yuanyuan Li
    Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, Morrisville, NC 27709, USA
    BMC Genomics 15:27. 2014
  2. pmc Characterization of constitutive CTCF/cohesin loci: a possible role in establishing topological domains in mammalian genomes
    Yuanyuan Li
    Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC 27709, USA
    BMC Genomics 14:553. 2013
  3. pmc Gene set enrichment analysis for non-monotone association and multiple experimental categories
    Rongheng Lin
    Biostatistics Branch, National Institute of Environmental Health Science, Research Triangle Park, NC 27713, USA
    BMC Bioinformatics 9:481. 2008
  4. pmc Optimized mixed Markov models for motif identification
    Weichun Huang
    Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27606, USA
    BMC Bioinformatics 7:279. 2006
  5. pmc Phase analysis of circadian-related genes in two tissues
    Delong Liu
    Biostatistics Branch, National Institute of Environmental Health Sciences, MD A3 03, 111 TW Alexander Dr, Research Triangle Park, NC 27709, USA
    BMC Bioinformatics 7:87. 2006
  6. ncbi request reprint GAPWM: a genetic algorithm method for optimizing a position weight matrix
    Leping Li
    Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
    Bioinformatics 23:1188-94. 2007
  7. pmc GADEM: a genetic algorithm guided formation of spaced dyads coupled with an EM algorithm for motif discovery
    Leping Li
    Biostatistics Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
    J Comput Biol 16:317-29. 2009
  8. ncbi request reprint Gene selection for sample classification based on gene expression data: study of sensitivity to choice of parameters of the GA/KNN method
    L Li
    Biostatistics Branch Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
    Bioinformatics 17:1131-42. 2001
  9. pmc fdrMotif: identifying cis-elements by an EM algorithm coupled with false discovery rate control
    Leping Li
    Biostatistics Branch, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA
    Bioinformatics 24:629-36. 2008
  10. ncbi request reprint Application of the GA/KNN method to SELDI proteomics data
    Leping Li
    Biostatistics Branch, National Institute of Environmental Health Sciences, National Institute of Health, Research Triangle Park, NC 27709, USA
    Bioinformatics 20:1638-40. 2004

Collaborators

Detail Information

Publications36

  1. doi request reprint T-KDE: a method for genome-wide identification of constitutive protein binding sites from multiple ChIP-seq data sets
    Yuanyuan Li
    Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, Morrisville, NC 27709, USA
    BMC Genomics 15:27. 2014
    ..Genome-wide discovery of constitutive binding sites requires robust and efficient computational methods to integrate results from numerous binding experiments. Such methods are lacking, however...
  2. pmc Characterization of constitutive CTCF/cohesin loci: a possible role in establishing topological domains in mammalian genomes
    Yuanyuan Li
    Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC 27709, USA
    BMC Genomics 14:553. 2013
    ..It remains unclear whether a subset of CTCF binding sites plays a functional role in establishing/maintaining chromatin topological domains...
  3. pmc Gene set enrichment analysis for non-monotone association and multiple experimental categories
    Rongheng Lin
    Biostatistics Branch, National Institute of Environmental Health Science, Research Triangle Park, NC 27713, USA
    BMC Bioinformatics 9:481. 2008
    ..Methods applicable to continuous non-monotone relationships are needed. Furthermore, for multiple experimental categories, methods that combine multiple GSEA/SAFE analyses are needed...
  4. pmc Optimized mixed Markov models for motif identification
    Weichun Huang
    Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27606, USA
    BMC Bioinformatics 7:279. 2006
    ..Identifying functional elements, such as transcriptional factor binding sites, is a fundamental step in reconstructing gene regulatory networks and remains a challenging issue, largely due to limited availability of training samples...
  5. pmc Phase analysis of circadian-related genes in two tissues
    Delong Liu
    Biostatistics Branch, National Institute of Environmental Health Sciences, MD A3 03, 111 TW Alexander Dr, Research Triangle Park, NC 27709, USA
    BMC Bioinformatics 7:87. 2006
    ..These interesting biological observations prompt a statistical question regarding how to distinguish the synchronized genes from genes that are systematically lagged in phase/peak expression time across two tissues...
  6. ncbi request reprint GAPWM: a genetic algorithm method for optimizing a position weight matrix
    Leping Li
    Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
    Bioinformatics 23:1188-94. 2007
    ..We propose a novel but simple method to improve a poorly estimated PWM using ChIP data...
  7. pmc GADEM: a genetic algorithm guided formation of spaced dyads coupled with an EM algorithm for motif discovery
    Leping Li
    Biostatistics Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
    J Comput Biol 16:317-29. 2009
    ..The GADEM software is available at (www.niehs.nih.gov/research/resources/software/GADEM/)...
  8. ncbi request reprint Gene selection for sample classification based on gene expression data: study of sensitivity to choice of parameters of the GA/KNN method
    L Li
    Biostatistics Branch Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
    Bioinformatics 17:1131-42. 2001
    ..As an extension to our earlier work, we systematically examine the sensitivity, reproducibility and stability of gene selection/sample classification to the choice of parameters of the algorithm...
  9. pmc fdrMotif: identifying cis-elements by an EM algorithm coupled with false discovery rate control
    Leping Li
    Biostatistics Branch, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA
    Bioinformatics 24:629-36. 2008
    ..We propose a new normalization procedure in the E-step for updating the model. This process is repeated until either the model converges or the number of iterations exceeds a maximum...
  10. ncbi request reprint Application of the GA/KNN method to SELDI proteomics data
    Leping Li
    Biostatistics Branch, National Institute of Environmental Health Sciences, National Institute of Health, Research Triangle Park, NC 27709, USA
    Bioinformatics 20:1638-40. 2004
    ....
  11. ncbi request reprint Accurate anchoring alignment of divergent sequences
    Weichun Huang
    Biostatistics Branch, The National Institute of Environmental Health Sciences NIH, Research Triangle Park, NC 27709, USA
    Bioinformatics 22:29-34. 2006
    ..Obtaining high quality alignments of divergent homologous sequences for cross-species sequence comparison remains a challenge...
  12. ncbi request reprint Triptolide induces apoptotic death of T lymphocyte
    Y Yang
    Division of Basic Sciences, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Immunopharmacology 40:139-49. 1998
    ..These results indicate that triptolide induces T cell apoptosis through activating caspases, and suggest the growth arrest and apoptotic effect of triptolide may contribute to the immunosuppressive activity of TWHf extract...
  13. ncbi request reprint Prediction of compound signature using high density gene expression profiling
    Hisham K Hamadeh
    National Institute of Environmental Health Sciences, P O Box 12233, MD2 04, Research Triangle Park, NC 27709, USA
    Toxicol Sci 67:232-40. 2002
    ..This validates our initial hypothesis and lends credibility to the concept that the further development of a gene expression database for chemical effects will greatly enhance the hazard identification processes...
  14. ncbi request reprint Gene selection and clustering for time-course and dose-response microarray experiments using order-restricted inference
    Shyamal D Peddada
    Biostatistics Branch, Laboratory of Molecular Carcinogenesis, Research Triangle Park, NC 27709, USA
    Bioinformatics 19:834-41. 2003
    ..In this example, our method was able to identify several biologically interesting genes that previous analyses failed to reveal...
  15. ncbi request reprint ATM-dependent and -independent gene expression changes in response to oxidative stress, gamma irradiation, and UV irradiation
    Alexandra N Heinloth
    Growth Control and Cancer Group, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
    Radiat Res 160:273-90. 2003
    ..ATM-dependent and ATM-independent components were detected within these patterns, as were novel indications of involvement of ATM in regulation of transcription factors such as SP1, AP1 and MTF1...
  16. ncbi request reprint Identification of distinct and common gene expression changes after oxidative stress and gamma and ultraviolet radiation
    Alexandra N Heinloth
    Growth Control and Cancer Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
    Mol Carcinog 37:65-82. 2003
    ..In addition, cell cultures from different individuals displayed significant differences in their gene expression responses to DNA damage...
  17. pmc Estrogen-mediated regulation of Igf1 transcription and uterine growth involves direct binding of estrogen receptor alpha to estrogen-responsive elements
    Sylvia C Hewitt
    Receptor Biology Section, Laboratory of Reproductive and Developmental Toxicology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
    J Biol Chem 285:2676-85. 2010
    ..Additionally, full ER alpha function is needed to mediate other cellular signals of the growth factor for uterine growth...
  18. ncbi request reprint Regulation of DNA replication fork genes by 17beta-estradiol
    Edward K Lobenhofer
    Gene Regulation Group, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
    Mol Endocrinol 16:1215-29. 2002
    ..The coexpression of DNA replication fork genes by estrogen without the support of serum growth factors indicates an important estrogen regulatory component of the molecular mechanism driving estrogen-induced mitogenesis...
  19. ncbi request reprint Capsaicin inhibits activation of voltage-gated sodium currents in capsaicin-sensitive trigeminal ganglion neurons
    L Liu
    Department of Anesthesiology and Neurobiology, Duke University Medical Center, Durham, North Carolina 27710, USA
    J Neurophysiol 85:745-58. 2001
    ..These mechanisms are likely to be important in understanding the analgesic effects of capsaicin...
  20. pmc NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly
    Daniel A Gilchrist
    Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
    Genes Dev 22:1921-33. 2008
    ..These findings identify a novel, positive role for stalled Pol II in regulating gene expression and suggest that there is a dynamic interplay between stalled Pol II and chromatin structure...
  21. pmc DNA methylation prevents CTCF-mediated silencing of the oncogene BCL6 in B cell lymphomas
    Anne Y Lai
    Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
    J Exp Med 207:1939-50. 2010
    ..These data indicate that BCL6 expression is maintained during lymphomagenesis in part through DNA methylation that prevents CTCF-mediated silencing...
  22. ncbi request reprint Refinement of the NMR solution structure of the gamma-carboxyglutamic acid domain of coagulation factor IX using molecular dynamics simulation with initial Ca2+ positions determined by a genetic algorithm
    L Li
    National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
    Biochemistry 36:2132-8. 1997
    ..It is likely that the placement of calcium ions in the protein is critical for refinement. The calcium ions apparently induce structural changes during the course of the simulation that result in a more compact structure...
  23. ncbi request reprint Heparan sulphate N-sulphotransferase activity: reaction mechanism and substrate recognition
    Y Kakuta
    Pharmacogenetics Section, Laboratory of Reproductive and Developmental Toxicology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, U S A
    Biochem Soc Trans 31:331-4. 2003
    ..Glu-642 may play the critical role of catalytic base in the sulphuryl group transfer reaction, as indicated by its hydrogen-bonding distance to the NH(3) (+) group of the glucosamine moiety in the model and by mutational data...
  24. ncbi request reprint Cloning of CYP2J2 gene and identification of functional polymorphisms
    Lorraine M King
    Division of Intramural Research, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
    Mol Pharmacol 61:840-52. 2002
    ..Insofar as CYP2J2 products have effects in the cardiovascular system, we speculate that these variants may be functionally relevant...
  25. ncbi request reprint Negatively charged 2- and 10-microm particles activate vanilloid receptors, increase cAMP, and induce cytokine release
    N Agopyan
    Department of Anesthesiology, Duke University Medical Center, Durham, NC 27710, USA
    Toxicol Appl Pharmacol 186:63-76. 2003
    ..These data suggest that pharmacological manipulation of such receptors could prevent the physiological actions of PMs...
  26. ncbi request reprint Novel consensus DNA-binding sequence for BRCA1 protein complexes
    P LouAnn Cable
    Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
    Mol Carcinog 38:85-96. 2003
    ....
  27. pmc Oct4/Sox2-regulated miR-302 targets cyclin D1 in human embryonic stem cells
    Deborah A Greer Card
    Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
    Mol Cell Biol 28:6426-38. 2008
    ..The transcriptional activation of miR-302 and the translational repression of its targets, such as cyclin D1, may provide a link between Oct4/Sox2 and cell cycle regulation in pluripotent cells...
  28. ncbi request reprint Identification of potential target genes for RFX4_v3, a transcription factor critical for brain development
    Donghui Zhang
    Laboratory of Neurobiology, National Institute of Environmental Health Sciences, National Institutes of Health Research Triangle Park, North Carolina 27709, USA
    J Neurochem 98:860-75. 2006
    ..These data suggest that RFX4_v3 may act upstream of critical signaling pathways in the process of brain development...
  29. ncbi request reprint Gene expression profiling of rat livers reveals indicators of potential adverse effects
    Alexandra N Heinloth
    National Center for Toxicogenomics, National Institute of Environmental Health Sciences, P O Box 12233, Research Triangle Park, North Carolina 27709, USA
    Toxicol Sci 80:193-202. 2004
    ..In conclusion, this study provides evidence that supports the hypothesis that gene expression profiling may be a sensitive means of identifying indicators of potential adverse effects in the absence of the occurrence of overt toxicity...
  30. pmc A random-periods model for expression of cell-cycle genes
    Delong Liu
    Biostatistics Branch, National Institute of Environmental Health Sciences, National Institutes of Health, P O Box 12233, Research Triangle Park, NC 27709, USA
    Proc Natl Acad Sci U S A 101:7240-5. 2004
    ..The model permits estimation of and hypothesis testing about biologically meaningful parameters that characterize cycling genes...
  31. pmc Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation
    Daniel A Gilchrist
    Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
    Cell 143:540-51. 2010
    ....
  32. ncbi request reprint Tamoxifen functions as a molecular agonist inducing cell cycle-associated genes in breast cancer cells
    Leslie C Hodges
    Department of Carcinogenesis, UT M D Anderson Cancer Center, Smithville, TX 78957, USA
    Mol Cancer Res 1:300-11. 2003
    ..However, cyclin D1 was a key estrogen-induced gene not expressed in response to tamoxifen or raloxifene but constitutively expressed in tamoxifen-resistant cells...
  33. ncbi request reprint Optimal lens epithelial cell proliferation is dependent on the connexin isoform providing gap junctional coupling
    Thomas W White
    Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York, USA
    Invest Ophthalmol Vis Sci 48:5630-7. 2007
    ..To determine which connexins functionally contribute to epithelial cell coupling and proliferation, junctional coupling from epithelial cells of wild-type and knockin mice was examined...
  34. ncbi request reprint Significance analysis and multiple pharmacophore models for differentiating P-glycoprotein substrates
    Wu Xiong Li
    Amgen Inc, 1120 Veterans Boulevard, South San Francisco, CA 94080, USA
    J Chem Inf Model 47:2429-38. 2007
    ..An overall accuracy of 87.7% was achieved for the training set and 87.6% for the external independent test set. Furthermore, each of nine pharmacophores can be independently utilized as an accurate marker for potential Pgp substrates...
  35. ncbi request reprint Connexin50 is essential for normal postnatal lens cell proliferation
    Caterina Sellitto
    Department of Physiology and Biophysics, State University of New York, Stony Brook, New York, 11794 8661, USA
    Invest Ophthalmol Vis Sci 45:3196-202. 2004
    ..Deletion of Cx50 or replacement with Cx46 by knockin resulted in smaller lenses containing fewer cells. To determine why Cx50-deficient lenses fail to grow normally, cell proliferation was assayed during the period of growth failure...
  36. ncbi request reprint Deuterium and its role in the machinery of evolution
    Lee G Pedersen
    Department of Chemistry, The University of North Carolina, Chapel Hill, 27599, USA
    J Theor Biol 238:914-8. 2006
    ....