H J Edenberg

Summary

Affiliation: Indiana University
Country: USA

Publications

  1. pmc Prioritizing single-nucleotide variations that potentially regulate alternative splicing
    Mingxiang Teng
    School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
    BMC Proc 5:S40. 2011
  2. pmc Alt Event Finder: a tool for extracting alternative splicing events from RNA-seq data
    Ao Zhou
    Bioinformatics Program, School of Informatics, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA
    BMC Genomics 13:S10. 2012
  3. pmc Multi-species data integration and gene ranking enrich significant results in an alcoholism genome-wide association study
    Zhongming Zhao
    Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
    BMC Genomics 13:S16. 2012
  4. pmc Cyclic changes in gene expression induced by Peg-interferon alfa-2b plus ribavirin in peripheral blood monocytes (PBMC) of hepatitis C patients during the first 10 weeks of treatment
    Milton W Taylor
    Department of Biology, Indiana University, Bloomington, IN 47401, USA
    J Transl Med 6:66. 2008
  5. pmc Candidate genes for alcohol preference identified by expression profiling in alcohol-preferring and -nonpreferring reciprocal congenic rats
    Tiebing Liang
    Indiana University School of Medicine, Department of Medicine, IB424G, 975 West Walnut Street, Indianapolis, IN 46202, USA
    Genome Biol 11:R11. 2010
  6. pmc Mapping of trans-acting regulatory factors from microarray data
    Jeanette N McClintick
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, MS4063, Indianapolis, Indiana 46202, USA
    BMC Proc 1:S155. 2007
  7. pmc Alteration of gene expression by alcohol exposure at early neurulation
    Feng C Zhou
    Department of Anatomy and Cell Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA
    BMC Genomics 12:124. 2011
  8. pmc Using RNase sequence specificity to refine the identification of RNA-protein binding regions
    Xin Wang
    Division of Biostatistics Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    BMC Genomics 9:S17. 2008
  9. pmc Reproducibility of oligonucleotide arrays using small samples
    Jeanette N McClintick
    Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, Indiana, USA
    BMC Genomics 4:4. 2003
  10. pmc Epigenetics of gene expression in human hepatoma cells: expression profiling the response to inhibition of DNA methylation and histone deacetylation
    Luke O Dannenberg
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, MS4063, Indianapolis, IN, USA
    BMC Genomics 7:181. 2006

Research Grants

  1. STRUCTURE & EXPRESSION OF MAMMAL ALC DEHYDROGENASE GENES
    Howard Edenberg; Fiscal Year: 2007
  2. Indiana Gene Array Core
    Howard Edenberg; Fiscal Year: 2007

Collaborators

Detail Information

Publications126 found, 100 shown here

  1. pmc Prioritizing single-nucleotide variations that potentially regulate alternative splicing
    Mingxiang Teng
    School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
    BMC Proc 5:S40. 2011
    ..Based on the affecting SNVs on the quantitative traits simulated in GAW17, we further identified two and four functional SNVs that are predicted to be involved in alternative splicing regulation in traits Q1 and Q2, respectively...
  2. pmc Alt Event Finder: a tool for extracting alternative splicing events from RNA-seq data
    Ao Zhou
    Bioinformatics Program, School of Informatics, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA
    BMC Genomics 13:S10. 2012
    ..Identifying alternative splicing events from RNA-seq experiments is important for understanding the diversity of transcripts and for investigating the regulation of splicing...
  3. pmc Multi-species data integration and gene ranking enrich significant results in an alcoholism genome-wide association study
    Zhongming Zhao
    Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
    BMC Genomics 13:S16. 2012
    ..Integration of these heterogeneous data can be used to produce a ranked target gene list for additional investigation...
  4. pmc Cyclic changes in gene expression induced by Peg-interferon alfa-2b plus ribavirin in peripheral blood monocytes (PBMC) of hepatitis C patients during the first 10 weeks of treatment
    Milton W Taylor
    Department of Biology, Indiana University, Bloomington, IN 47401, USA
    J Transl Med 6:66. 2008
    ....
  5. pmc Candidate genes for alcohol preference identified by expression profiling in alcohol-preferring and -nonpreferring reciprocal congenic rats
    Tiebing Liang
    Indiana University School of Medicine, Department of Medicine, IB424G, 975 West Walnut Street, Indianapolis, IN 46202, USA
    Genome Biol 11:R11. 2010
    ..NP congenic rats: amygdala, nucleus accumbens, hippocampus, caudate putamen, and frontal cortex...
  6. pmc Mapping of trans-acting regulatory factors from microarray data
    Jeanette N McClintick
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, MS4063, Indianapolis, Indiana 46202, USA
    BMC Proc 1:S155. 2007
    ..This work demonstrates that composite measures for genes with correlated expression can be used to identify loci that affect multiple co-expressed genes...
  7. pmc Alteration of gene expression by alcohol exposure at early neurulation
    Feng C Zhou
    Department of Anatomy and Cell Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA
    BMC Genomics 12:124. 2011
    ..To explore the global gene expression changes which may underline these developmental defects, microarray analyses were performed in a whole embryo mouse culture model that allows control over alcohol and embryonic variables...
  8. pmc Using RNase sequence specificity to refine the identification of RNA-protein binding regions
    Xin Wang
    Division of Biostatistics Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    BMC Genomics 9:S17. 2008
    ..We present two regions to which multiple amplicons map as examples to demonstrate this approach...
  9. pmc Reproducibility of oligonucleotide arrays using small samples
    Jeanette N McClintick
    Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, Indiana, USA
    BMC Genomics 4:4. 2003
    ..We systematically explore the effects of using different starting amounts of RNA on the ability to detect differential gene expression...
  10. pmc Epigenetics of gene expression in human hepatoma cells: expression profiling the response to inhibition of DNA methylation and histone deacetylation
    Luke O Dannenberg
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, MS4063, Indianapolis, IN, USA
    BMC Genomics 7:181. 2006
    ..Treatment with 5-aza-2'-deoxycytidine (5-aza-dC) to inhibit DNA methylation with and/or Trichostatin A (TSA) to inhibit histone deacetylation should allow us to identify genes that are regulated epigenetically in hepatoma cells...
  11. pmc Effects of filtering by Present call on analysis of microarray experiments
    Jeanette N McClintick
    Department of Medical and Molecular Genetics, Indiana University, Indianapolis, Indiana, USA
    BMC Bioinformatics 7:49. 2006
    ..We explore the effects of various thresholds for removing data in experiments of different size (from 3 to 10 arrays per treatment), as well as their relative power to detect significant differences in expression...
  12. ncbi request reprint Association of NFKB1, which encodes a subunit of the transcription factor NF-kappaB, with alcohol dependence
    Howard J Edenberg
    Indiana University School of Medicine, Indianapolis, IN, USA
    Hum Mol Genet 17:963-70. 2008
    ..Thus, variations in NFKB1 appear to affect the risk for alcoholism, particularly contributing to an earlier onset of the disease...
  13. pmc Genome-wide association study of alcohol dependence implicates a region on chromosome 11
    Howard J Edenberg
    Department of Biochemistry, Indiana University School of Medicine, Indianapolis, 46202 5122, USA
    Alcohol Clin Exp Res 34:840-52. 2010
    ..Alcohol dependence is a complex disease, and although linkage and candidate gene studies have identified several genes associated with the risk for alcoholism, these explain only a portion of the risk...
  14. ncbi request reprint The genetics of alcoholism: identifying specific genes through family studies
    Howard J Edenberg
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis 46202 5122, USA
    Addict Biol 11:386-96. 2006
    ..These successes demonstrate that genes contributing to the risk for alcoholism can be reliably identified using human subjects...
  15. pmc A regulatory variation in OPRK1, the gene encoding the kappa-opioid receptor, is associated with alcohol dependence
    Howard J Edenberg
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Hum Mol Genet 17:1783-9. 2008
    ..This indel is, therefore, a functional regulatory variation likely to explain at least part of the association of OPRK1 with alcohol dependence...
  16. ncbi request reprint GATA-2 and HNF-3beta regulate the human alcohol dehydrogenase 1A (ADH1A) gene
    Luke O Dannenberg
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, 46202, USA
    DNA Cell Biol 24:543-52. 2005
    ..Positive regulation of the ADH1A gene may be influenced by GATA-2 binding, while differences in HNF-3beta binding in cells/tissues may contribute to tissue specificity...
  17. ncbi request reprint Polymorphism of the human alcohol dehydrogenase 4 (ADH4) promoter affects gene expression
    H J Edenberg
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis 46202 5122, USA
    Pharmacogenetics 9:25-30. 1999
    ..Alcohol dehydrogenase activity is rate limiting for ethanol oxidation. We hypothesize that the different ADH4 alleles lead to different amounts of pi-ADH in liver, which affects the risk for alcoholism by modulating alcohol metabolism...
  18. ncbi request reprint Association of alcohol dehydrogenase genes with alcohol dependence: a comprehensive analysis
    Howard J Edenberg
    Indiana University School of Medicine, Indianapolis, USA
    Hum Mol Genet 15:1539-49. 2006
    ..01) There was weaker evidence that variations in ADH1A and ADH1B might also play a role in modifying risk. Among African-Americans, there was evidence that the ADH1B*3 allele was protective...
  19. pmc Description of the data from the Collaborative Study on the Genetics of Alcoholism (COGA) and single-nucleotide polymorphism genotyping for Genetic Analysis Workshop 14
    Howard J Edenberg
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN, USA
    BMC Genet 6:S2. 2005
    ..CIDR, Affymetrix, and Illumina provided single-nucleotide polymorphism genotyping of a large subset of the COGA subjects. This article briefly describes the dataset that was provided...
  20. pmc Variations in GABRA2, encoding the alpha 2 subunit of the GABA(A) receptor, are associated with alcohol dependence and with brain oscillations
    Howard J Edenberg
    Indiana University School of Medicine, Indianapolis 46202, USA
    Am J Hum Genet 74:705-14. 2004
    ....
  21. ncbi request reprint The contribution of genetics to addiction therapy approaches
    Howard J Edenberg
    Indiana University School of Medicine, 635 Barnhill Drive, MS4063, Indianapolis, IN 46202 5122, USA
    Pharmacol Ther 108:86-93. 2005
    ..Adding a genetic component to treatment trials could greatly help to understand the biological basis of variations in the efficacy of therapies and, in the future, could lead to individualized choices of therapy...
  22. ncbi request reprint Initial genomic scan of the NIMH genetics initiative bipolar pedigrees: chromosomes 3, 5, 15, 16, 17, and 22
    H J Edenberg
    Indiana University School of Medicine, Indianapolis 46202 5122, USA
    Am J Med Genet 74:238-46. 1997
    ..Thus, several regions showed modest evidence for linkage to bipolar disorder in this initial genomic scan of these chromosomes, including broad regions near previous reports of possible linkage...
  23. doi request reprint Phenomic, convergent functional genomic, and biomarker studies in a stress-reactive genetic animal model of bipolar disorder and co-morbid alcoholism
    H Le-Niculescu
    Laboratory of Neurophenomics, Indiana University School of Medicine, Indianapolis, Indiana
    Am J Med Genet B Neuropsychiatr Genet 147:134-66. 2008
    ..CFG analysis of the gene expression changes identified a series of novel candidate genes and blood biomarkers for bipolar disorder, alcoholism, and stress reactivity...
  24. pmc Differentially expressed genes strongly correlated with femur strength in rats
    Imranul Alam
    Department of Biomedical Engineering, Indiana University Purdue University Indianapolis IUPUI, Indianapolis, IN 46202 5251, USA
    Genomics 94:257-62. 2009
    ....
  25. ncbi request reprint A novel negative element in the promoter of the mouse alcohol dehydrogenase gene Adh-1
    Z Lin
    Department of Medicine, Indiana University School of Medicine, Indianapolis 46202
    J Biol Chem 268:10260-7. 1993
    ..Thus, we have identified a negative regulatory element within the Adh-1 promoter. No homology was found between this negative element and other regulatory elements, suggesting that this is a novel negative element...
  26. ncbi request reprint Candidate genes, pathways and mechanisms for alcoholism: an expanded convergent functional genomics approach
    Z A Rodd
    Department of Psychiatry, Institute of Psychiatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Pharmacogenomics J 7:222-56. 2007
    ..In conjunction with a higher reactivity to its rewarding effects, they may able to ingest enough of this nonspecific drug for a strong hedonic and addictive effect to occur...
  27. ncbi request reprint Association of the kappa-opioid system with alcohol dependence
    X Xuei
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Mol Psychiatry 11:1016-24. 2006
    ....
  28. ncbi request reprint Tissue-specific regulatory elements in the human alcohol dehydrogenase 6 gene
    X Zhi
    Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis 46202 5122, USA
    DNA Cell Biol 19:487-97. 2000
    ..Site 2 was a positive regulatory element in hepatoma cells but had no effect in fibroblasts. This combination of positive and negative regulatory elements can play a significant role in the tissue-specific expression of ADH6...
  29. ncbi request reprint Alternative splicing and promoter use in the human GABRA2 gene
    Huijun Tian
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Room 4063E, Indianapolis, IN 46202 5122, USA
    Brain Res Mol Brain Res 137:174-83. 2005
    ..The promoter activities of naturally occurring haplotypes differed, indicating genetic differences in gene expression...
  30. ncbi request reprint Alcohol dehydrogenase gene expression and cloning of the mouse chi-like ADH
    H J Edenberg
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis 46202 5122
    Adv Exp Med Biol 284:253-62. 1991
  31. ncbi request reprint Nucleotide sequence of the ADH2(3) gene encoding the human alcohol dehydrogenase beta 3 subunit
    L G Carr
    Department of Biochemistry, Indiana University School of Medicine, Indianapolis 46223
    Alcohol Clin Exp Res 13:594-6. 1989
    ..There are also two silent polymorphisms, and two changes in noncoding regions...
  32. ncbi request reprint Genotyping of human alcohol dehydrogenases at the ADH2 and ADH3 loci following DNA sequence amplification
    Y L Xu
    Department of Biochemistry, Indiana University School of Medicine, Indianapolis 46223
    Genomics 2:209-14. 1988
    ..In addition, ADH2(2) can be distinguished from ADH2(1) and ADH2(3) by detecting a new MaeIII site created in the third exon by the single base pair alteration in ADH2(2)...
  33. ncbi request reprint Expression and kinetic characterization of recombinant human stomach alcohol dehydrogenase. Active-site amino acid sequence explains substrate specificity compared with liver isozymes
    N Y Kedishvili
    Dept of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis 46202 5122
    J Biol Chem 270:3625-30. 1995
    ..The deletion of Gly-117 in human sigma-ADH and a substitution of Leu for the bulky Tyr-110 appear to facilitate retinol access to the active-site zinc...
  34. ncbi request reprint Suggestive evidence of a locus on chromosome 10p using the NIMH genetics initiative bipolar affective disorder pedigrees
    T Foroud
    Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
    Am J Med Genet 96:18-23. 2000
    ..Other chromosomal regions with lod scores over 1.50 for at least one Model Included chromosomes 8 (Model III), 16 (Model III), and 20 (Model I). Am. J. Med. Genet. (Neuropsychiatr. Genet.) 96:18-23, 2000..
  35. pmc Association studies of ALOX5 and bone mineral density in healthy adults
    T Foroud
    Indiana University School of Medicine, Health Information and Translational Sciences Building, Indianapolis, IN 46202 3002, USA
    Osteoporos Int 19:637-43. 2008
    ..We tested this hypothesis in a sample of healthy men and women and did not find consistent evidence for an association between variation in this gene and either lumbar spine or femoral neck BMD...
  36. ncbi request reprint Alcoholism susceptibility loci: confirmation studies in a replicate sample and further mapping
    T Foroud
    Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis 46202, USA
    Alcohol Clin Exp Res 24:933-45. 2000
    ..A previous study reported linkage to chromosomes 1, 2, and 7 in a large data set that consisted of 105 families, each with at least three alcoholic members...
  37. doi request reprint Identifying blood biomarkers for mood disorders using convergent functional genomics
    H Le-Niculescu
    Laboratory of Neurophenomics, Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN 46202 4887, USA
    Mol Psychiatry 14:156-74. 2009
    ..Our studies suggest that blood biomarkers may offer an unexpectedly informative window into brain functioning and disease state...
  38. pmc A human Raf-responsive zinc-finger protein that binds to divergent sequences
    L Zhang
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202 5122, USA
    Nucleic Acids Res 27:2947-56. 1999
    ..The ability of transcription factors such as RREB1/LZ321 to bind diverse sequences gives them the potential to regulate previously unsuspected genes...
  39. ncbi request reprint Function of cis-acting elements in human alcohol dehydrogenase 4 (ADH4) promoter and role of C/EBP proteins in gene expression
    M Li
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis 46202 5122, USA
    DNA Cell Biol 17:387-97. 1998
    ..This mutation had a stronger effect in the context of a longer promoter, suggesting interaction among cis-acting elements...
  40. ncbi request reprint Structure and function of a long alternating purine-pyrimidine sequence in the mouse alcohol dehydrogenase Adh-1 gene
    M Yu
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis 46202 5122
    Arch Biochem Biophys 316:407-12. 1995
    ..Nuclear run-on experiments showed that the differential expression of Adh-1 from high- and low-activity strains is, however, controlled at the post-transcription level...
  41. ncbi request reprint Towards understanding the schizophrenia code: an expanded convergent functional genomics approach
    H Le-Niculescu
    Laboratory of Neurophenomics, Indiana University School of Medicine, Indianapolis, Indiana, USA
    Am J Med Genet B Neuropsychiatr Genet 144:129-58. 2007
    ..Other pathways are new potential targets for drug development. Lastly, a comparison with our earlier work on bipolar disorder illuminates the significant molecular overlap between schizophrenia and bipolar disorder...
  42. pmc Familial multiple-system tauopathy with presenile dementia is localized to chromosome 17
    J R Murrell
    Department of Pathology, Indiana University Medical Center, Indianapolis, IN 47202, USA
    Am J Hum Genet 61:1131-8. 1997
    ..The gene for tau also was analyzed, through samples from the family...
  43. ncbi request reprint The genetics of alcohol metabolism: role of alcohol dehydrogenase and aldehyde dehydrogenase variants
    Howard J Edenberg
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
    Alcohol Res Health 30:5-13. 2007
    ..It is becoming clear that noncoding variants in both ADH and ALDH genes also may influence alcohol metabolism and, consequently, alcoholism risk; the specific nature and effects of these variants still need further study...
  44. pmc Convergent functional genomic studies of omega-3 fatty acids in stress reactivity, bipolar disorder and alcoholism
    H Le-Niculescu
    Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Transl Psychiatry 1:e4. 2011
    ..In conclusion, our work supports the potential utility of omega-3 fatty acids, specifically DHA, for a spectrum of psychiatric disorders such as stress disorders, bipolar disorder, alcoholism and beyond...
  45. ncbi request reprint A negative regulatory element upstream from the mouse Adh-1 gene can down-regulate a heterologous promoter
    M Yu
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianopolis 46202 5122
    Gene 141:249-54. 1994
    ..Adh-1 NRE2 can function in both orientations and either upstream or downstream from the promoter, and thus has attributes characteristic of a 'silencer'. A protein that binds to the Adh-1 NRE is widespread in mouse tissues...
  46. ncbi request reprint Gene expression in the hippocampus of inbred alcohol-preferring and -nonpreferring rats
    H J Edenberg
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202 4887, USA
    Genes Brain Behav 4:20-30. 2005
    ....
  47. ncbi request reprint No association of the GABAA receptor genes on chromosome 5 with alcoholism in the collaborative study on the genetics of alcoholism sample
    Danielle M Dick
    Department of Medical and Molecular Genetics, Indiana University School of Medicine, 975 West Walnut St, Indianapolis, IN 46202 525, USA
    Am J Med Genet B Neuropsychiatr Genet 132:24-8. 2005
    ..Future studies are planned to test whether these genes are more important in influencing behavioral endophenotypes related to the risk of alcohol dependence...
  48. pmc Genomic expression analysis of rat chromosome 4 for skeletal traits at femoral neck
    Imranul Alam
    Department of Biomedical Engineering, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, USA
    Physiol Genomics 35:191-6. 2008
    ..This study provides a shortened list of genetic determinants of skeletal traits at the hip and may lead to novel approaches for prevention and treatment of hip fracture...
  49. ncbi request reprint Expression and kinetic characterization of variants of human beta 1 beta 1 alcohol dehydrogenase containing substitutions at amino acid 47
    T D Hurley
    Department of Biochemistry, Indiana University School of Medicine, Indianapolis 46202 5122
    J Biol Chem 265:16366-72. 1990
    ..The kinetic properties of the Gly-47 enzyme are substantially different from human liver alpha alpha which also has Gly at position 47...
  50. ncbi request reprint Structure of the mouse Adh-1 gene and identification of a deletion in a long alternating purine-pyrimidine sequence in the first intron of strains expressing low alcohol dehydrogenase activity
    K Zhang
    Department of Biochemistry, Indiana University School of Medicine, Indianapolis 46223
    Gene 57:27-36. 1987
    ....
  51. pmc Identification of a FOXA-dependent enhancer of human alcohol dehydrogenase 4 (ADH4)
    Sirisha Pochareddy
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, MS4063, Indianapolis, IN 46202 5122, USA
    Gene 460:1-7. 2010
    ..6-fold, while one had small but significant effect. The differences in the functional activity in different haplotypes suggest that this region could play an important role in the risk for alcoholism...
  52. pmc Neuropeptide Y receptor genes are associated with alcohol dependence, alcohol withdrawal phenotypes, and cocaine dependence
    Leah Wetherill
    Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
    Alcohol Clin Exp Res 32:2031-40. 2008
    ..Additional studies suggest that cocaine may affect NPY expression...
  53. ncbi request reprint cis-acting sequences involved in protein binding and in vitro transcription of the human alcohol dehydrogenase gene ADH2
    L G Carr
    Department of Biochemistry, Indiana University School of Medicine, Indianapolis 46202 5122
    J Biol Chem 265:1658-64. 1990
    ....
  54. pmc Identification of transcription factor and microRNA binding sites in responsible to fetal alcohol syndrome
    Guohua Wang
    Division of Biostatistics Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    BMC Genomics 9:S19. 2008
    ..This suggests that disturbance of miRNA functions may contribute to the alcohol-induced developmental deficiencies...
  55. ncbi request reprint The opioid system in alcohol and drug dependence: family-based association study
    Xiaoling Xuei
    Indiana University School of Medicine, 1345 W 16th Street, Indianapolis, IN 46202, USA
    Am J Med Genet B Neuropsychiatr Genet 144:877-84. 2007
    ....
  56. ncbi request reprint Identification of candidate genes for alcohol preference by expression profiling of congenic rat strains
    Lucinda G Carr
    Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Alcohol Clin Exp Res 31:1089-98. 2007
    ..This study was undertaken to identify genes in the chromosome 4 QTL interval that might contribute to the differences in alcohol consumption between the alcohol-naïve congenic and background strains...
  57. ncbi request reprint Effects of glucose metabolism on the regulation of genes of fatty acid synthesis and triglyceride secretion in the liver
    Nuria Morral
    Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
    J Lipid Res 48:1499-510. 2007
    ..Overall, our data suggest that the gene expression pattern induced by glucose metabolism favors fatty acid storage in the liver rather than secretion into the circulation...
  58. ncbi request reprint Association of alcohol craving with alpha-synuclein (SNCA)
    Tatiana Foroud
    Indiana University School of Medicine, Indianapolis, Indiana 46202 5251, USA
    Alcohol Clin Exp Res 31:537-45. 2007
    ..Studies in humans have provided support for an association between SNCA and craving for alcohol...
  59. pmc Genome-wide association study of bone mineral density in premenopausal European-American women and replication in African-American women
    Daniel L Koller
    Departments of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
    J Clin Endocrinol Metab 95:1802-9. 2010
    ..Several genome-wide association studies (GWAS) have been performed to identify genes contributing to bone mineral density (BMD), typically in samples of elderly women and men...
  60. pmc Identification of genes influencing skeletal phenotypes in congenic P/NP rats
    Imranul Alam
    Department of Biomedical Engineering, Indiana University Purdue University Indianapolis IUPUI, Indianapolis, IN 46202, USA
    J Bone Miner Res 25:1314-25. 2010
    ..We identified several candidate genes, including some novel genes on chromosome 4 segregating for skeletal phenotypes in reciprocal congenic P and NP rats...
  61. pmc Changes in gene expression in regions of the extended amygdala of alcohol-preferring rats after binge-like alcohol drinking
    William J McBride
    Department of Psychiatry, Institute of Psychiatric Research, Indiana University Purdue University at Indianapolis, Indianapolis, 46202 4887, USA
    Alcohol 44:171-83. 2010
    ....
  62. ncbi request reprint Lack of association of alcohol dependence and habitual smoking with catechol-O-methyltransferase
    Tatiana Foroud
    Indiana University School of Medicine, Indianapolis, Indiana 46202 3002, USA
    Alcohol Clin Exp Res 31:1773-9. 2007
    ....
  63. doi request reprint Differential gene expression in the nucleus accumbens with ethanol self-administration in inbred alcohol-preferring rats
    Zachary A Rodd
    Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN 46202 4887, United States
    Pharmacol Biochem Behav 89:481-98. 2008
    ..g., Cav2, Nrxn3, Gabrb2, Gad1, Homer1) and homeostasis (S100b, Prkca, Ftl1) categories. Overall, the results suggest that changes in gene expression in the ACB of iP rats are associated with the reinforcing effects of EtOH...
  64. pmc The tachykinin receptor 3 is associated with alcohol and cocaine dependence
    Tatiana Foroud
    Indiana University School of Medicine, Indianapolis, Indiana 46202 3002, USA
    Alcohol Clin Exp Res 32:1023-30. 2008
    ..Pharmacological studies have provided evidence that the administration of NK3R agonists attenuates the intake of alcohol and NK3R can also mediate the acute and chronic behavioral effects of cocaine...
  65. pmc Identification of a linkage disequilibrium block in chromosome 1q associated with BMD in premenopausal white women
    Shoji Ichikawa
    Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana 46202 5121, USA
    J Bone Miner Res 23:1680-8. 2008
    ....
  66. pmc CLCN7 polymorphisms and bone mineral density in healthy premenopausal white women and in white men
    Kang Chu
    Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Bone 43:995-8. 2008
    ..However, there is no study to date that has examined whether CLCN7 polymorphisms underlie normal variation of peak BMD in healthy premenopausal white women and in white men...
  67. ncbi request reprint Association analysis of genes encoding the nociceptin receptor (OPRL1) and its endogenous ligand (PNOC) with alcohol or illicit drug dependence
    Xiaoling Xuei
    Department of Biochemistry and Molecular Biology, Indiana Unviersity School of Medicine, Indianapolis, IN 46202, USA
    Addict Biol 13:80-7. 2008
    ..04-0.05). Secondary analyses suggested that two adjacent SNPs in intron 1 of OPRL1 were marginally associated with opioid dependence (P = 0.05); none of the SNPs in PNOC were associated with opioid dependence...
  68. pmc Association of adenylate cyclase 10 (ADCY10) polymorphisms and bone mineral density in healthy adults
    Shoji Ichikawa
    Department of Medicine, Indiana University School of Medicine, 541 North Clinical Drive, Clinical Building 459, Indianapolis, IN 46202 5121, USA
    Calcif Tissue Int 84:97-102. 2009
    ..However, adjacent SNPs did not corroborate the association in either men or women. In conclusion, we found a modest association between an ADCY10 polymorphism and the spinal areal BMD in premenopausal white women...
  69. doi request reprint Altering the relative abundance of GABA A receptor subunits changes GABA- and ethanol-responses in Xenopus oocytes
    Joyce H Hurley
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Alcohol Clin Exp Res 33:1089-96. 2009
    ..Therefore, we hypothesize that the associations arise from differences in gene expression...
  70. pmc Gene expression changes in the nucleus accumbens of alcohol-preferring rats following chronic ethanol consumption
    Richard L Bell
    Department of Psychiatry, Indiana University Purdue University at Indianapolis, Indianapolis, IN 46202, USA
    Pharmacol Biochem Behav 94:131-47. 2009
    ..Conversely, chronic MSA drinking, with its associated protracted withdrawal periods, results in genomic changes that may be masked by tight regulation of these genes following repeated experiences of ethanol withdrawal...
  71. ncbi request reprint Augmentation of UVB radiation-mediated early gene expression by the epidermal platelet-activating factor receptor
    Jeffrey B Travers
    Department of Dermatology, H B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
    J Invest Dermatol 128:455-60. 2008
    ..These studies provide evidence that the epidermal PAF-R can modulate UVB-mediated early gene expression...
  72. ncbi request reprint Model-based identification of cis-acting elements from microarray data
    Yunlong Liu
    Department of Biochemistry and Molecular Biology and Center for Medical Genomics, Indiana University School of Medicine, 635 Barnhill Drive MS 4063, Indianapolis, IN 46202, USA
    Genomics 88:452-61. 2006
    ..Many predicted CAE match sites known to be involved in interferon action. MotifModeler demonstrated the potential to computationally identify CAE important in gene regulation...
  73. ncbi request reprint Alcohol effects on central nervous system gene expression in genetic animal models
    William J McBride
    Indiana University School of Medicine, Indianapolis, Indiana, USA
    Alcohol Clin Exp Res 29:167-75. 2005
    ..Hashimoto and Kristine M. Wiren...
  74. ncbi request reprint Natural haplotypes in the regulatory sequences affect human alcohol dehydrogenase 1C (ADH1C) gene expression
    Hui Ju Chen
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202 5122, USA
    Hum Mutat 25:150-5. 2005
    ..We also demonstrated tissue specificity in cis-acting elements by comparing gene expression in H4IIE-C3 and HeLa cells...
  75. ncbi request reprint Contribution of the LRP5 gene to normal variation in peak BMD in women
    Daniel L Koller
    Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
    J Bone Miner Res 20:75-80. 2005
    ..Association between SNPs in LRP5 and hip and spine BMD was measured in 1301 premenopausal women. Only a small proportion of the BMD variation was attributable to LRP5 in our sample...
  76. ncbi request reprint Association of GABRG3 with alcohol dependence
    Danielle M Dick
    Indiana University School of Medicine, Indianapolis, Indiana, USA
    Alcohol Clin Exp Res 28:4-9. 2004
    ..Both linkage and association to the region on chromosome 15q that contains a cluster of GABAA receptor genes have previously been reported, but the role of these genes in alcoholism remains inconclusive...
  77. ncbi request reprint Transcriptional changes in alveolar macrophages during Pneumocystis pneumonia
    Chao Hung Lee
    Dept of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    J Eukaryot Microbiol 50:645. 2003
  78. ncbi request reprint Association of GABA(A) receptors and alcohol dependence and the effects of genetic imprinting
    Jiuzhou Song
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana 46202 5122, USA
    Am J Med Genet B Neuropsychiatr Genet 117:39-45. 2003
    ..Maternal transmissions provided no evidence for association. These data are consistent with an association between the expressed alleles in the GABA(A)-gene cluster on chromosome 15 and alcoholism that is modulated by genetic imprinting...
  79. ncbi request reprint Influence of ADH1B polymorphism on alcohol use and its subjective effects in a Jewish population
    Lucinda G Carr
    Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
    Am J Med Genet 112:138-43. 2002
    ..The ADH1B polymorphism is associated with unpleasant reactions after alcohol consumption, and frequency of alcohol consumption in these Jewish samples...
  80. ncbi request reprint Characterization of a transgenic mouse line lacking photoreceptor development within the ventral retina
    Shao Ling Fong
    Department of Ophthalmology, Indiana University, 702 Rotary Circle, Indianapolis, IN 46202, USA
    Exp Eye Res 81:376-88. 2005
    ..This new transgenic line can lead to better understanding of photoreceptor development, and may serve as a new animal model for studying photoreceptor-related retinal diseases...
  81. pmc GABRR1 and GABRR2, encoding the GABA-A receptor subunits rho1 and rho2, are associated with alcohol dependence
    Xiaoling Xuei
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Am J Med Genet B Neuropsychiatr Genet 153:418-27. 2010
    ..04), and a haplotype in GABRR2 was significantly overtransmitted to family members who met a broader definition of alcoholism (P = 0.002) as well as DSM-IV dependence (P = 0.04)...
  82. pmc Functional gene expression differences between inbred alcohol-preferring and -non-preferring rats in five brain regions
    Mark W Kimpel
    Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN 46202 4887, USA
    Alcohol 41:95-132. 2007
    ..The many regional and overall gene expression differences between the iP and iNP rat lines may contribute to the divergent alcohol drinking phenotypes of these rats...
  83. pmc A molecular signature of normal breast epithelial and stromal cells from Li-Fraumeni syndrome mutation carriers
    Brittney Shea Herbert
    Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
    Oncotarget 1:405-22. 2010
    ....
  84. ncbi request reprint Molecular cloning of mouse alcohol dehydrogenase-B2 cDNA: nucleotide sequences of the class III ADH genes evolve slowly even for silent substitutions
    M W Hur
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis 46202 5122
    DNA Seq 3:167-75. 1992
    ..Our analysis of the nucleotide sequences demonstrates that this cannot be the entire explanation, since the rate of silent (synonymous) nucleotide substitutions is also lower in the class III ADHs than in the class I ADHs...
  85. ncbi request reprint Global effects of vitamin A deficiency on gene expression in rat liver: evidence for hypoandrogenism
    Jeanette N McClintick
    Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202 5251, USA
    J Nutr Biochem 17:345-55. 2006
    ..Retinol deficiency also produces a shift toward increased protein and fat catabolism and decreased fatty acid synthesis...
  86. pmc Integration of general amino acid control and target of rapamycin (TOR) regulatory pathways in nitrogen assimilation in yeast
    Kirk A Staschke
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
    J Biol Chem 285:16893-911. 2010
    ..This study highlights the mechanisms by which the GAAC and TOR pathways are integrated to recognize changing nitrogen availability and direct the transcriptome for optimal growth adaptation...
  87. ncbi request reprint A retroviral repetitive element confers tissue-specificity to the human alcohol dehydrogenase 1C (ADH1C) gene
    Hui Ju Chen
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202 5122, USA
    DNA Cell Biol 21:793-801. 2002
    ..The ubiquitous Nuclear factor-Y (NF-Y) and an H4IIE-C3/liver-specific factor bound to the subrepeat sequence. This result suggested that tissue specificity might result from combinatorial regulation by these two transcription factors...
  88. ncbi request reprint DNA microarray analysis of differential gene expression of 6-year-old rat neural striatal progenitor cells during early differentiation
    F C Zhou
    Departments of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Restor Neurol Neurosci 18:95-104. 2001
    ..The six-year long-term neural stem cells are an excellent model for studying developmental neurobiological processes and aging...
  89. ncbi request reprint Cloning and characterization of the ADH5 gene encoding human alcohol dehydrogenase 5, formaldehyde dehydrogenase
    M W Hur
    Department of Biochemistry, Indiana University School of Medicine, Indianapolis 46202 5122
    Gene 121:305-11. 1992
    ..A 1.5-kb upstream fragment from ADH5 was able to drive the transcription of a cat reporter gene at high levels in monkey kidney cells (CV-1). Several processed pseudogenes were also isolated...
  90. pmc Evidence for both a regulatory mutation and a structural mutation in a family with maple syrup urine disease
    B Zhang
    Department of Biochemistry, Indiana University School of Medicine, Indianapolis 46223
    J Clin Invest 83:1425-9. 1989
    ..Our results revealed for the first time that a case of MSUD was caused by structural and regulatory mutations involving the E1 alpha subunit...
  91. ncbi request reprint A genome-wide screen for genes influencing conduct disorder
    D M Dick
    Indiana University, 975 West Walnut St, IB 130, Indianapolis, IN 46202 5251, USA
    Mol Psychiatry 9:81-6. 2004
    ..Taken together, these findings suggest that some of the genes contributing to alcohol dependence in adulthood may also contribute to conduct disorder in childhood...
  92. ncbi request reprint Polymorphisms in the bone morphogenetic protein 2 (BMP2) gene do not affect bone mineral density in white men or women
    S Ichikawa
    Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
    Osteoporos Int 17:587-92. 2006
    ..Recently, bone morphogenetic protein 2 (BMP2) was reported as a susceptibility gene for osteoporotic fractures and low BMD in Icelandic and Danish populations...
  93. ncbi request reprint Human ALOX12, but not ALOX15, is associated with BMD in white men and women
    Shoji Ichikawa
    Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana 46202 5121, USA
    J Bone Miner Res 21:556-64. 2006
    ..Polymorphisms in human ALOX12, but not ALOX15, were significantly associated with spine BMD in white men and women, suggesting that ALOX12 may contribute to normal variation in BMD...
  94. ncbi request reprint The collaborative study on the genetics of alcoholism: an update
    Howard J Edenberg
    Department of Biochemistry and Molecular Biology, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
    Alcohol Res Health 26:214-8. 2002
  95. pmc Evidence of association between brain-derived neurotrophic factor gene and bipolar disorder
    Lixiang Liu
    Indiana University, Indianapolis, Indiana 46202 3002, USA
    Psychiatr Genet 18:267-74. 2008
    ..Growing evidence suggests that BDNF is involved in the pathophysiology of mood disorders...
  96. ncbi request reprint Murine embryonic stem cell differentiation is promoted by SOCS-3 and inhibited by the zinc finger transcription factor Klf4
    Yanjun Li
    Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Blood 105:635-7. 2005
    ..These findings verify the negative role of SOCS-3 on LIF signaling and provide a novel role for Klf4 in ES cell function...
  97. ncbi request reprint Suggestive linkage on chromosome 1 for a quantitative alcohol-related phenotype
    Danielle M Dick
    Indiana University School of Medicine, Indianapolis, Indiana 46202 525, USA
    Alcohol Clin Exp Res 26:1453-60. 2002
    ..Here, we develop quantitative phenotypes that characterize drinking patterns among both alcoholic and nonalcoholic subjects, and use these phenotypes in subsequent linkage analyses...
  98. doi request reprint Cortical-striatal gene expression in neonatal hippocampal lesion (NVHL)-amplified cocaine sensitization
    R A Chambers
    Lab for Translational Neuroscience of Dual Diagnosis and Development, Department of Psychiatry, Institute for Psychiatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Genes Brain Behav 12:564-75. 2013
    ..Polygenetic interactions impacting neuronal signaling and morphology within these networks likely contribute to addiction vulnerability in mental illness. ..
  99. ncbi request reprint High-throughput quantitation of double-stranded DNA using the ABI Prism 7700 sequence detection system
    Huijun Tian
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Anal Biochem 326:287-8. 2004
  100. ncbi request reprint Differential regulation of the alcohol dehydrogenase 1B (ADH1B) and ADH1C genes by DNA methylation and histone deacetylation
    Luke O Dannenberg
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
    Alcohol Clin Exp Res 30:928-37. 2006
    ..We hypothesized that epigenetic modifications play a role in this repression and that class I ADH gene expression would be enhanced upon global inhibition of DNA methylation and histone deacetylation...
  101. ncbi request reprint Functional variants in TAS2R38 and TAS2R16 influence alcohol consumption in high-risk families of African-American origin
    Jen C Wang
    Washington University in St Louis, MO 63110, USA
    Alcohol Clin Exp Res 31:209-15. 2007
    ..The perceived bitterness of PROP has also been associated with oral sensation and drinking behaviors...

Research Grants4

  1. STRUCTURE & EXPRESSION OF MAMMAL ALC DEHYDROGENASE GENES
    Howard Edenberg; Fiscal Year: 2007
    ..Such an examination is critical to our understanding of the effects of these genes on risk for alcoholism and alcohol-related organ damage ..
  2. Indiana Gene Array Core
    Howard Edenberg; Fiscal Year: 2007
    ..This Core will provide high quality data in an efficient and economical way. We already have strong relatioinships with the users, which will benefit the overall project. ..