Hao Li

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Functional bias and spatial organization of genes in mutational hot and cold regions in the human genome
    Jeffrey H Chuang
    Department of Biochemistry and Biophysics, University of California, San Francisco, USA
    PLoS Biol 2:E29. 2004
  2. pmc c-REDUCE: incorporating sequence conservation to detect motifs that correlate with expression
    Katerina Kechris
    Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Denver, 4200 East Ninth Avenue, B 119, Denver, CO 80262, USA
    BMC Bioinformatics 9:506. 2008
  3. ncbi request reprint Dissecting the transcription networks of a cell using computational genomics
    Hao Li
    Department of Biochemistry and Biophysics, University of California at San Francisco, 600 16th Street, San Francisco, CA 94143 2240, USA
    Curr Opin Genet Dev 13:611-6. 2003
  4. pmc Evolution of transcription networks--lessons from yeasts
    Hao Li
    Department of Biochemistry and Biophysics, University of California San Francisco, CA, USA
    Curr Biol 20:R746-53. 2010
  5. pmc Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysis
    Emmitt R Jolly
    Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
    BMC Bioinformatics 6:275. 2005
  6. pmc fREDUCE: detection of degenerate regulatory elements using correlation with expression
    Randy Z Wu
    Department of Biochemistry and Biophysics, UCSF, 1700 4th Street, San Francisco, CA 94143 2542, USA
    BMC Bioinformatics 8:399. 2007
  7. pmc CompMoby: comparative MobyDick for detection of cis-regulatory motifs
    Christina Chaivorapol
    Department of Biochemistry and Biophysics, California Institute for Quantitative Biomedical Research, Graduate Program in Biological and Medical Informatics, University of California, San Francisco, CA 94143 2540, USA
    BMC Bioinformatics 9:455. 2008
  8. ncbi request reprint Comparing genomic expression patterns across species identifies shared transcriptional profile in aging
    Steven A McCarroll
    Program in Neuroscience, University of California, San Francisco, California 94143, USA
    Nat Genet 36:197-204. 2004
  9. pmc Cell- and gene-specific regulation of primary target genes by the androgen receptor
    Eric C Bolton
    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94143, USA
    Genes Dev 21:2005-17. 2007
  10. pmc Microfluidic affinity and ChIP-seq analyses converge on a conserved FOXP2-binding motif in chimp and human, which enables the detection of evolutionarily novel targets
    Christopher S Nelson
    Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94131, USA
    Nucleic Acids Res 41:5991-6004. 2013

Collaborators

Detail Information

Publications67

  1. pmc Functional bias and spatial organization of genes in mutational hot and cold regions in the human genome
    Jeffrey H Chuang
    Department of Biochemistry and Biophysics, University of California, San Francisco, USA
    PLoS Biol 2:E29. 2004
    ..Overall, our results show that genes are located nonrandomly with respect to hot and cold regions, offering the possibility that selection acts at the level of gene location in the human genome...
  2. pmc c-REDUCE: incorporating sequence conservation to detect motifs that correlate with expression
    Katerina Kechris
    Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Denver, 4200 East Ninth Avenue, B 119, Denver, CO 80262, USA
    BMC Bioinformatics 9:506. 2008
    ..Correlation-based motif finding strategies are used to identify motifs that correlate with expression data and do not rely on promoter sequences from a pre-determined set of genes...
  3. ncbi request reprint Dissecting the transcription networks of a cell using computational genomics
    Hao Li
    Department of Biochemistry and Biophysics, University of California at San Francisco, 600 16th Street, San Francisco, CA 94143 2240, USA
    Curr Opin Genet Dev 13:611-6. 2003
    ..Genomic approaches have profoundly changed the way biologists investigate transcriptional regulation, and global pictures of the transcription networks for several model organisms are beginning to emerge...
  4. pmc Evolution of transcription networks--lessons from yeasts
    Hao Li
    Department of Biochemistry and Biophysics, University of California San Francisco, CA, USA
    Curr Biol 20:R746-53. 2010
    ....
  5. pmc Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysis
    Emmitt R Jolly
    Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
    BMC Bioinformatics 6:275. 2005
    ..We present a method for target identification that combines experimental characterization of binding requirements with computational genomic analysis...
  6. pmc fREDUCE: detection of degenerate regulatory elements using correlation with expression
    Randy Z Wu
    Department of Biochemistry and Biophysics, UCSF, 1700 4th Street, San Francisco, CA 94143 2542, USA
    BMC Bioinformatics 8:399. 2007
    ..A major challenge is to decipher transcription factor binding sites from sequence and functional genomic data using computational means. While current methods can detect strong binding sites, they are less sensitive to degenerate motifs...
  7. pmc CompMoby: comparative MobyDick for detection of cis-regulatory motifs
    Christina Chaivorapol
    Department of Biochemistry and Biophysics, California Institute for Quantitative Biomedical Research, Graduate Program in Biological and Medical Informatics, University of California, San Francisco, CA 94143 2540, USA
    BMC Bioinformatics 9:455. 2008
    ..Therefore, a computational algorithm should account for both conserved and nonconserved cis-regulatory elements in metazoans...
  8. ncbi request reprint Comparing genomic expression patterns across species identifies shared transcriptional profile in aging
    Steven A McCarroll
    Program in Neuroscience, University of California, San Francisco, California 94143, USA
    Nat Genet 36:197-204. 2004
    ..Using this approach to search databases of gene expression data, we found conserved transcriptional signatures in larval development, embryogenesis, gametogenesis and mRNA degradation...
  9. pmc Cell- and gene-specific regulation of primary target genes by the androgen receptor
    Eric C Bolton
    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94143, USA
    Genes Dev 21:2005-17. 2007
    ..Our results provide new insights into cell- and gene-specific mechanisms of transcriptional regulation of androgen-responsive gene networks...
  10. pmc Microfluidic affinity and ChIP-seq analyses converge on a conserved FOXP2-binding motif in chimp and human, which enables the detection of evolutionarily novel targets
    Christopher S Nelson
    Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94131, USA
    Nucleic Acids Res 41:5991-6004. 2013
    ..Combined, these data present a comprehensive portrait of FOXP2's-binding properties and imply that although its sequence specificity has been conserved, some of its genomic binding sites are newly evolved. ..
  11. doi request reprint Evolution of eukaryotic transcription circuits
    Brian B Tuch
    Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
    Science 319:1797-9. 2008
    ....
  12. pmc Genomic selection identifies vertebrate transcription factor Fezf2 binding sites and target genes
    Lishan Chen
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94158, USA
    J Biol Chem 286:18641-9. 2011
    ....
  13. ncbi request reprint Evolution of alternative transcriptional circuits with identical logic
    Annie E Tsong
    Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California 94143 2200, USA
    Nature 443:415-20. 2006
    ..These changes indicate specific mechanisms by which fitness barriers were traversed during the transition...
  14. pmc The evolution of combinatorial gene regulation in fungi
    Brian B Tuch
    Department of Biochemistry and Biophysics, University of California, San Francisco, California, United States of America
    PLoS Biol 6:e38. 2008
    ..The large turnover of Mcm1 binding sites and the evolution of new Mcm1-cofactor interactions illuminate in sharp detail the rapid evolution of combinatorial transcription networks...
  15. ncbi request reprint Identification of transcriptional regulatory elements in chemosensory receptor genes by probabilistic segmentation
    Steven A McCarroll
    Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143 USA
    Curr Biol 15:347-52. 2005
    ..This approach may be of particular value for rapidly evolving genes in the immune system and the nervous system...
  16. pmc De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis
    Polly M Fordyce
    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA
    Nat Biotechnol 28:970-5. 2010
    ..We expect that these data and future use of this technique will provide information essential for understanding transcription factor specificity, improving identification of regulatory sites and reconstructing regulatory interactions...
  17. pmc Epistatic relationships reveal the functional organization of yeast transcription factors
    Jiashun Zheng
    Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94143 2542, USA
    Mol Syst Biol 6:420. 2010
    ..Collectively, these data suggest that parallel/compensating relationships between regulators, rather than linear pathways, often characterize transcriptional circuits...
  18. pmc Alternative 3' pre-mRNA processing in Saccharomyces cerevisiae is modulated by Nab4/Hrp1 in vivo
    Karen S Kim Guisbert
    Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
    PLoS Biol 5:e6. 2007
    ..We propose that alternative 3' pre-mRNA processing is mediated by a Nab4-based mechanism and that these alternative processing events could help control gene expression as part of a physiological response in S. cerevisiae...
  19. pmc Systematic identification of cis-regulatory sequences active in mouse and human embryonic stem cells
    Marica Grskovic
    Institute for Regeneration Medicine, University of California San Francisco, San Francisco, California, United States of America
    PLoS Genet 3:e145. 2007
    ..Our results suggest that this systematic approach can be broadly applied to understanding transcriptional networks in mammalian species...
  20. ncbi request reprint Regulation of cellular plasticity in Drosophila imaginal disc cells by the Polycomb group, trithorax group and lama genes
    Ansgar Klebes
    Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
    Development 132:3753-65. 2005
    ..Our findings are likely to be relevant to the mechanisms that lead to disease when homologs of Wingless are expressed at abnormal levels and to the manifestation of pluripotency of stem cells...
  21. pmc Determinants of cell- and gene-specific transcriptional regulation by the glucocorticoid receptor
    Alex Yick Lun So
    Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America
    PLoS Genet 3:e94. 2007
    ..We conclude that GR occupancy is a primary determinant of glucocorticoid responsiveness in A549 cells and that core GR binding sequences as well as GRE architecture likely harbor gene-specific regulatory information...
  22. pmc An enhanced single base extension technique for the analysis of complex viral populations
    Dale R Webster
    Biological and Medical Informatics Program, University of California San Francisco, San Francisco, California, United States of America
    PLoS ONE 4:e7453. 2009
    ....
  23. pmc A systematic approach to identify functional motifs within vertebrate developmental enhancers
    Qiang Li
    Department of Biopharmaceutical Sciences, Programs in Biological Sciences and Human Genetics, University of California, San Francisco, CA 94143 2811, USA
    Dev Biol 337:484-95. 2010
    ..Moreover, this dataset provides a useful resource for further dissection of vertebrate brain development and function...
  24. pmc Genome-wide regulatory complexity in yeast promoters: separation of functionally conserved and neutral sequence
    Chen Shan Chin
    Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, USA
    Genome Res 15:205-13. 2005
    ..The separation of functionally conserved sequence from the neutral background allows us to estimate the complexity of cis-regulation on a genomic scale...
  25. pmc Regulatory architecture determines optimal regulation of gene expression in metabolic pathways
    Victor Chubukov
    Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
    Proc Natl Acad Sci U S A 109:5127-32. 2012
    ..Our results suggest that the parameters regulating metabolic enzyme expression are optimized by evolution, under the strong constraint of the underlying regulatory architecture...
  26. pmc Positioned and G/C-capped poly(dA:dT) tracts associate with the centers of nucleosome-free regions in yeast promoters
    Randy Wu
    Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143 2542, USA
    Genome Res 20:473-84. 2010
    ..These observations are consistent with a model in which localized and G:C-capped poly(dA:dT) tracts initiate or facilitate the formation of NFRs at their center, possibly with chromatin remodeling and transcriptional machines involved...
  27. pmc Identification of the binding sites of regulatory proteins in bacterial genomes
    Hao Li
    Department of Biochemistry, University of California, 513 Parnassus Avenue, San Francisco, CA 94143, USA
    Proc Natl Acad Sci U S A 99:11772-7. 2002
    ..The algorithm is efficient for analyzing newly sequenced bacterial genomes for which little is known about transcriptional regulation...
  28. pmc Dynamics and design principles of a basic regulatory architecture controlling metabolic pathways
    Chen Shan Chin
    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, United States of America
    PLoS Biol 6:e146. 2008
    ..It is likely that principles emerging from this work can reveal how gene regulation has evolved to optimize performance in other metabolic pathways with similar architecture...
  29. pmc Functional specificity of shuttling hnRNPs revealed by genome-wide analysis of their RNA binding profiles
    Karen Kim Guisbert
    Department of Biochemistry and Biophysics, 600 16th Street, Genentech Hall, University of California at San Francisco, San Francisco, CA 94143, USA
    RNA 11:383-93. 2005
    ..These specialized associations of the hnRNP proteins of Saccharomyces cerevisiae suggest the opportunity to regulate the processing of particular transcripts between transcription and translation...
  30. pmc Sherlock: Detecting Gene-Disease Associations by Matching Patterns of Expression QTL and GWAS
    Xin He
    Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94143, USA Lane Center of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
    Am J Hum Genet 92:667-80. 2013
    ..It is readily generalizable to molecular traits other than gene expression, such as metabolites, noncoding RNAs, and epigenetic modifications...
  31. pmc Mitochondrial network size scaling in budding yeast
    Susanne M Rafelski
    Department of Biochemistry and Biophysics, University of California San Francisco UCSF, San Francisco, CA, USA
    Science 338:822-4. 2012
    ..Thus, yeast populations achieve a stable scaling relation between mitochondrial content and cell size despite asymmetry in inheritance...
  32. pmc A human sterile alpha motif domain polymerizome
    Mary Jane Knight
    Department of Chemistry and Biochemistry, UCLA DOE Institute of Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, USA
    Protein Sci 20:1697-706. 2011
    ....
  33. pmc Genome-wide diversity and selective pressure in the human rhinovirus
    Amy L Kistler
    Department of Microbiology and Immunology, University of California, San Francisco, California, USA
    Virol J 4:40. 2007
    ..Previous comparative genome sequence analyses indicate that recombination drives diversification in multiple genera of the picornavirus family, yet it remains unclear if this holds for HRV...
  34. ncbi request reprint Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans
    Coleen T Murphy
    Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143 2200, USA
    Nature 424:277-83. 2003
    ....
  35. ncbi request reprint Computational approaches to identifying transcription factor binding sites in yeast genome
    Hao Li
    Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, USA
    Methods Enzymol 350:484-95. 2002
  36. pmc Highly designable phenotypes and mutational buffers emerge from a systematic mapping between network topology and dynamic output
    Yigal D Nochomovitz
    Graduate Group in Biophysics, Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
    Proc Natl Acad Sci U S A 103:4180-5. 2006
    ....
  37. pmc Single cell analysis of yeast replicative aging using a new generation of microfluidic device
    Yi Zhang
    The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Center for Quantitative Biology, and School of Physics, Peking University, China
    PLoS ONE 7:e48275. 2012
    ..Utilizing the capability of the new device to trap mother-daughter pairs, we analyzed mother-daughter inheritance and found age dependent asymmetric partitioning of a general stress response reporter between mother and daughter cells...
  38. pmc The unfolded protein response in fission yeast modulates stability of select mRNAs to maintain protein homeostasis
    Philipp Kimmig
    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
    elife 1:e00048. 2012
    ..Thus, S. pombe uses a universally conserved stress-sensing machinery in novel ways to maintain homeostasis in the ER.DOI:http://dx.doi.org/10.7554/eLife.00048.001...
  39. pmc A systematic approach to reconstructing transcription networks in Saccharomycescerevisiae
    Wei Wang
    Department of Genetics, Stanford University, Stanford, CA 94305 5120, USA
    Proc Natl Acad Sci U S A 99:16893-8. 2002
    ..Correlating the activation of a module to a specific perturbation predicts links in the cell's regulatory networks, and examining coactivated modules suggests specific instances of crosstalk between regulatory pathways...
  40. pmc Gcn4p and novel upstream activating sequences regulate targets of the unfolded protein response
    Christopher K Patil
    Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
    PLoS Biol 2:E246. 2004
    ..The discovery of a role for Gcn4p in the yeast UPR reveals an additional level of complexity and demonstrates a surprising conservation of the signaling circuit between yeast and metazoan cells...
  41. pmc Analysis of oligonucleotide array experiments with repeated measures using mixed models
    Hao Li
    Department of Statistics, 815 Patterson Office Tower, University of Kentucky, Lexington, Kentucky 40506 0027, USA
    BMC Bioinformatics 5:209. 2004
    ..In addition, multiple testing problems are more complicated in experiments with multi-level treatments or treatment combinations...
  42. pmc Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation
    Wei Wang
    Department of Genetics, Stanford University, Stanford, CA 94305 5120, USA
    Proc Natl Acad Sci U S A 102:1998-2003. 2005
    ..We show that this model accounts for the temporal control of the "middle" sporulation genes and suggest a similar regulatory arrangement can be found in developmental programs in higher organisms...
  43. doi request reprint Characterization of human rabies virus vaccine strain in China
    Jialiang Du
    Department of Viral Encephalitis, Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention and State Key Laboratory for Infectious Disease Prevention and Control, Xuan Wu District, Beijing, China
    Virus Res 135:260-6. 2008
    ..In addition, some mutations and new functional regions were discovered that are presumed crucial to the function of leader region and L protein. There is an equal role for all five genes in the phylogenetics of rabies virus...
  44. pmc Identification of gene expression patterns using planned linear contrasts
    Hao Li
    Department of Statistics, University of Kentucky, Lexington, KY 40536 0027, USA
    BMC Bioinformatics 7:245. 2006
    ..In addition, multiple testing problems are complicated in experiments with multi-level treatments when thousands of genes are involved...
  45. ncbi request reprint Preparation, characterization and transfection efficiency of cationic PEGylated PLA nanoparticles as gene delivery systems
    Jiji Chen
    National Key Laboratory of Nanobiological Technology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
    J Biotechnol 130:107-13. 2007
    ..These results suggested that MePEG-PLA-CS NPs have favorable properties for non-viral gene delivery...
  46. ncbi request reprint Protein kinase C-dependent activation of P44/42 mitogen-activated protein kinase and heat shock protein 70 in signal transduction during hepatocyte ischemic preconditioning
    Yi Gao
    Department of Hepatobiliary Surgery, Zhujiang Hospital, 253 Gongye Road, Guangzhou 510282, Guangdong Province, China
    World J Gastroenterol 10:1019-27. 2004
    ..To investigate the significance of protein kinase C(PKC), P44/42 mitogen-activated protein kinase (MAPKs) and heat shock protein (HSP)70 signal transduction during hepatocyte ischemic preconditioning...
  47. ncbi request reprint Similarity of synonymous substitution rates across mammalian genomes
    Jeffrey H Chuang
    Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
    J Mol Evol 65:236-48. 2007
    ..Genes with above-average substitution rates also exhibit significant, though somewhat weaker, rate correlations, suggesting that some neutral processes may have persisted in the phylogeny as well...
  48. ncbi request reprint intersex, a gene required for female sexual development in Drosophila, is expressed in both sexes and functions together with doublesex to regulate terminal differentiation
    Carrie M Garrett-Engele
    Department of Biological Sciences, Stanford University, Stanford, CA 94305 5020, USA
    Development 129:4661-75. 2002
    ..Taken together, the above findings strongly suggest that IX and DSX(F) function in a complex, in which IX acts as a transcriptional co-factor for the DNA-binding DSX(F)...
  49. ncbi request reprint Designability of protein structures: a lattice-model study using the Miyazawa-Jernigan matrix
    Hao Li
    NEC Research Institute, Princeton, New Jersey 08540, USA
    Proteins 49:403-12. 2002
    ..In particular, highly designable structures in the HP model are also highly designable in the MJ model-and vice versa-with the associated sequences having enhanced thermodynamic stability...
  50. ncbi request reprint Effect of NF-kappaB on the induction of PDGF-B transcription by angiotensin II in the ECV304 cell line
    Hao Li
    Department of Pathology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
    Chin Med J (Engl) 115:433-8. 2002
    ..To examine the effect of angiotensin II (Ang II) on nuclear factor-kappa B (NF-kappaB) activation in human endothelial cell line ECV304 and the molecular mechanism by which Ang II activates NF-kappaB...
  51. ncbi request reprint Further characterization of human DNA polymerase delta interacting protein 38
    Bin Xie
    Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
    J Biol Chem 280:22375-84. 2005
    ....
  52. pmc Transcription factor MEF2C influences neural stem/progenitor cell differentiation and maturation in vivo
    Hao Li
    Center for Neuroscience, Aging, and Stem Cell Research, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 105:9397-402. 2008
    ..Our data support a crucial role for MEF2C in programming early neuronal differentiation and proper distribution within the layers of the neocortex...
  53. ncbi request reprint Silencing invariant chain of DCs enhances Th1 response using small interfering RNA
    Shan Ke
    Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200025, PR China
    Cell Biol Int 31:663-71. 2007
    ..Our findings indicate that silencing the Ii gene in DCs with siRNA may offer a potential approach to enhancing antitumor immunotherapy...
  54. ncbi request reprint Potential target genes of EMX2 include Odz/Ten-M and other gene families with implications for cortical patterning
    Hao Li
    Molecular Neurobiology Laboratory, The Salk Institute, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
    Mol Cell Neurosci 33:136-49. 2006
    ....
  55. ncbi request reprint [Major constituent proteins in donkey hide and their interaction]
    Hao Li
    Institute of Biotechnology, Fuzhou University, China
    Zhongguo Zhong Yao Za Zhi 31:659-63. 2006
    ....
  56. ncbi request reprint An improved algorithm for vessel centerline tracking in coronary angiograms
    Yan Xu
    Department of Biomedical Engineering, Tsinghua University, China
    Comput Methods Programs Biomed 88:131-43. 2007
    ..Results show that the proposed algorithm outperforms the conventional methods. By adopting the proposed algorithm, centerlines are successfully extracted under these complicated situations, and with satisfactory accuracy...
  57. pmc Identification of novel modulators of mitochondrial function by a genome-wide RNAi screen in Drosophila melanogaster
    Jian Chen
    Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, USA
    Genome Res 18:123-36. 2008
    ....
  58. ncbi request reprint Multiple testing in the genomics era: findings from Genetic Analysis Workshop 15, Group 15
    Lisa J Martin
    Department of Pediatrics, Cincinnati Children s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
    Genet Epidemiol 31:S124-31. 2007
    ..We show that while each approach may have certain advantages, adequate error control is largely dependent upon the question under consideration and often requires the use of multiple analytic strategies...
  59. ncbi request reprint Genetic variations and treatments that affect the lifespan of the NPC1 mouse
    Benny Liu
    Department of Internal Medicine, University of Texas Southwestern Medical School, Dallas, TX 75390 9151, USA
    J Lipid Res 49:663-9. 2008
    ..It is currently not clear which of these effects is nonspecific or which might relate directly to the molecular defect present in the NPC1 syndrome...
  60. ncbi request reprint The phytoestrogen coumestrol is a naturally occurring antagonist of the human pregnane X receptor
    Hongwei Wang
    Albert Einstein College of Medicine, Albert Einstein Cancer Center, Bronx, New York 10461, USA
    Mol Endocrinol 22:838-57. 2008
    ..These studies provide the basis for development of novel small molecule inhibitors of PXR with the ultimate goal of clinical applications toward preventing drug-drug interactions...
  61. ncbi request reprint Liver X receptor activation enhances cholesterol loss from the brain, decreases neuroinflammation, and increases survival of the NPC1 mouse
    Joyce J Repa
    Department of Internal Medicine, University of Texas Southwestern Medical School, Dallas, Texas 75390 9151, USA
    J Neurosci 27:14470-80. 2007
    ..Thus, LXR activation resulted in increased cholesterol excretion from the brain, decreased neuroinflammation, and deactivation of microglia to slow neurodegeneration and extend the lifespan of the NPC1 mouse...
  62. ncbi request reprint Functional roles of p12, the fourth subunit of human DNA polymerase delta
    Hao Li
    Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
    J Biol Chem 281:14748-55. 2006
    ..We propose a model in which pol delta interacts with PCNA via at least two of its subunits, and one in which p12 could play a role in stabilizing the overall pol delta-PCNA complex as well as pol delta itself...
  63. ncbi request reprint Direct interaction of p21 with p50, the small subunit of human DNA polymerase delta
    Hao Li
    Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York 10595, USA
    Cell Cycle 5:428-36. 2006
    ..Our results suggested that p50 might target or anchor p21 to pol delta complex upon certain DNA damage such as adriamycin treatment...
  64. doi request reprint Chiral amine-catalyzed enantioselective cascade aza-ene-type cyclization reactions
    Liansuo Zu
    Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131 0001, USA
    Chemistry 14:6333-5. 2008
  65. ncbi request reprint [Human bone marrow multipotent adult progenitor cells differentiate into hepatocyte-like cells with hepatocyte growth factor plus fibroblast growth factor-4 in vitro]
    Li jun Tang
    Department of Surgery 1, 476th Fuzhou General Hospital of PLA, Fuzhou 350002, China
    Zhonghua Gan Zang Bing Za Zhi 13:652-5. 2005
    ..To investigate the possibility of the human bone marrow multipotent adult progenitor cells (hMAPCs) to differentiate into hepatocytes with hepatocyte growth factor (HGF)/ fibroblast growth factor-4 (FGF-4) in vitro...
  66. ncbi request reprint A semi-weakly confined erbium-doped waveguide amplifier with double-layered buffer/cladding
    Hengsheng Tang
    The State Key Lab for Advanced Photonic Materials and Devices, Department of Optical Science and Engineering, School of Information Science and Engineering, Fudan University, Shanghai 200433, China
    Opt Express 16:9844-9. 2008
    ..The EDWA has a passive core and double-layered buffer/cladding. A small coupling loss of 0.4 dB/facet and an internal gain of 1.9 dB via evanescent wave amplification near 1550 nm were obtained...
  67. pmc Defective dissociation of a "slow" RecA mutant protein imparts an Escherichia coli growth defect
    Julia M Cox
    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706 1544, USA
    J Biol Chem 283:24909-21. 2008
    ..RecA protein plays a sufficiently intimate role in the bacterial cell cycle that its properties can limit the growth rate of a bacterial culture...

Research Grants6

  1. Genomic Reconstruction of Yeast Transcription Networks
    Hao Li; Fiscal Year: 2007
    ..We will develop methods integrating information from the genome sequences for several yeast species and genome-wide functional data, and we will combine bioinformatics analysis with mechanistic models of gene regulation. ..
  2. Structure function and evolution of yeast transcription networks
    Hao Li; Fiscal Year: 2010
    ..A global understanding of the structure, function and evolution of the transcription networks in yeast will likely lead to general principles applicable to humans and have a significant impact on human health. ..