Research Topics
| L LiSummaryAffiliation: National Institutes of Health Country: USA Publications
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Detail Information
Publications
Gene set enrichment analysis for non-monotone association and multiple experimental categoriesRongheng 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...
Optimized mixed Markov models for motif identificationWeichun 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...- Phase analysis of circadian-related genes in two tissuesDelong 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... - fdrMotif: identifying cis-elements by an EM algorithm coupled with false discovery rate controlLeping 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... 
GAPWM: a genetic algorithm method for optimizing a position weight matrixLeping 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...- GADEM: a genetic algorithm guided formation of spaced dyads coupled with an EM algorithm for motif discoveryLeping 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/)... - Application of the GA/KNN method to SELDI proteomics dataLeping Li
Biostatistics Branch, National Institute of Environmental Health Sciences, National Institute of Health, Research Triangle Park, NC 27709, USA
Bioinformatics 20:1638-40. 2004..AVAILABILITY: The source code of the program and documentation on how to use it are freely available to non-commercial users at http://dir.niehs.nih.gov/dirbb/lifiles/softlic.htm.. - Gene selection for sample classification based on gene expression data: study of sensitivity to choice of parameters of the GA/KNN methodL 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... - Accurate anchoring alignment of divergent sequencesWeichun Huang
Biostatistics Branch, The National Institute of Environmental Health Sciences/NIH, Research Triangle Park, NC 27709, USA
Bioinformatics 22:29-34. 2006..AVAILABILITY: ACANA software and test sequence data are publicly available at http://BioMedEmpire.org/.. - Triptolide induces apoptotic death of T lymphocyteY 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... - Regulation of DNA replication fork genes by 17beta-estradiolEdward 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... - Estrogen-mediated regulation of Igf1 transcription and uterine growth involves direct binding of estrogen receptor alpha to estrogen-responsive elementsSylvia 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... - Prediction of compound signature using high density gene expression profilingHisham 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... - ATM-dependent and -independent gene expression changes in response to oxidative stress, gamma irradiation, and UV irradiationAlexandra 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... - Identification of distinct and common gene expression changes after oxidative stress and gamma and ultraviolet radiationAlexandra 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... - Gene selection and clustering for time-course and dose-response microarray experiments using order-restricted inferenceShyamal 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... - NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assemblyDaniel 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... - DNA methylation prevents CTCF-mediated silencing of the oncogene BCL6 in B cell lymphomasAnne 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... - Heparan sulphate N-sulphotransferase activity: reaction mechanism and substrate recognitionY 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... - 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 algorithmL 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... - Cloning of CYP2J2 gene and identification of functional polymorphismsLorraine 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... - Oct4/Sox2-regulated miR-302 targets cyclin D1 in human embryonic stem cellsDeborah 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... - Identification of potential target genes for RFX4_v3, a transcription factor critical for brain developmentDonghui 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... - Novel consensus DNA-binding sequence for BRCA1 protein complexesP LouAnn Cable
Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
Mol Carcinog 38:85-96. 2003.... - Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulationDaniel 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.... - A random-periods model for expression of cell-cycle genesDelong 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... - Gene expression profiling of rat livers reveals indicators of potential adverse effectsAlexandra 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... - Tamoxifen functions as a molecular agonist inducing cell cycle-associated genes in breast cancer cellsLeslie 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... - Optimal lens epithelial cell proliferation is dependent on the connexin isoform providing gap junctional couplingThomas 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... - Significance analysis and multiple pharmacophore models for differentiating P-glycoprotein substratesWu 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... - Connexin50 is essential for normal postnatal lens cell proliferationCaterina 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... - Deuterium and its role in the machinery of evolutionLee G Pedersen
Department of Chemistry, The University of North Carolina, Chapel Hill, 27599, USA
J Theor Biol 238:914-8. 2006....