Experts and Doctors on dna sequence analysis in Los Angeles, California, United States

Summary

Locale: Los Angeles, California, United States
Topic: dna sequence analysis

Top Publications

  1. Danciger M, Hendrickson J, Lyon J, Toomes C, McHale J, Fishman G, et al. CORD9 a new locus for arCRD: mapping to 8p11, estimation of frequency, evaluation of a candidate gene. Invest Ophthalmol Vis Sci. 2001;42:2458-65 pubmed
    ..However, only 2 loci for arCRD have been documented. This is the report of a third. ..
  2. Meyer E, Manahan D. Nutrient uptake by marine invertebrates: cloning and functional analysis of amino acid transporter genes in developing sea urchins (Strongylocentrotus purpuratus). Biol Bull. 2009;217:6-24 pubmed
    ..The functional characterization of these genes establishes a molecular biological basis for amino acid transport by developmental stages of marine invertebrates. ..
  3. Chodavarapu R, Feng S, Bernatavichute Y, Chen P, Stroud H, Yu Y, et al. Relationship between nucleosome positioning and DNA methylation. Nature. 2010;466:388-92 pubmed publisher
    ..DNA methylation is also enriched on exons, consistent with the targeting of DNA methylation to nucleosomes, and suggesting a role for DNA methylation in exon definition. ..
  4. Haiman C, Garcia R, Hsu C, Xia L, Ha H, Sheng X, et al. Screening and association testing of common coding variation in steroid hormone receptor co-activator and co-repressor genes in relation to breast cancer risk: the Multiethnic Cohort. BMC Cancer. 2009;9:43 pubmed publisher
  5. Pushkin A, Abuladze N, Lee I, Newman D, Hwang J, Kurtz I. Cloning, tissue distribution, genomic organization, and functional characterization of NBC3, a new member of the sodium bicarbonate cotransporter family. J Biol Chem. 1999;274:16569-75 pubmed
    ..Expression of mNBC3 cRNA in Xenopus laevis oocytes demonstrated that the protein encodes a novel stilbene-insensitive 5-(N-ethyl-N-isopropyl)-amiloride-inhibitable sodium bicarbonate cotransporter. ..
  6. Roy M, Kim N, Xing Y, Lee C. The effect of intron length on exon creation ratios during the evolution of mammalian genomes. RNA. 2008;14:2261-73 pubmed publisher
    ..This suggests that the observed correlation of longer intron lengths with alternatively spliced exons may be at least partly due to biases in the probability of exon creation, which is higher in long introns. ..
  7. Haake S, Yoder S, Attarian G, Podkaminer K. Native plasmids of Fusobacterium nucleatum: characterization and use in development of genetic systems. J Bacteriol. 2000;182:1176-80 pubmed
    ..pHS17 was stably maintained in the F. nucleatum transformants, and differences in the transformation efficiencies suggested the presence of a restriction-modification system in F. nucleatum...
  8. Wetzel G, Ding S, Chen F. Molecular cloning of junctin from human and developing rabbit heart. Mol Genet Metab. 2000;69:252-8 pubmed publisher
    ..Furthermore, the previously described increase in SR Ca(2+) release with development is associated with the increased expression of junctin...
  9. Wei B, Dalwadi H, Gordon L, Landers C, Bruckner D, Targan S, et al. Molecular cloning of a Bacteroides caccae TonB-linked outer membrane protein identified by an inflammatory bowel disease marker antibody. Infect Immun. 2001;69:6044-54 pubmed publisher
    ..These findings suggest that OmpW may be a target of the IBD-associated immune response and reveal its structural relationship to a bacterial virulence factor of P. gingivalis and periodontal disease...
  10. Wallace S, Lachman R, Mekikian P, Bui K, Wilcox W. Marked phenotypic variability in progressive diaphyseal dysplasia (Camurati-Engelmann disease): report of a four-generation pedigree, identification of a mutation in TGFB1, and review. Am J Med Genet A. 2004;129A:235-47 pubmed
    ..Cranial involvement, which occurs in 61% of patients, can be severe, entrapping cranial nerves or causing increased intracranial pressure. Therapy with corticosteroids should be attempted in all symptomatic patients...

Detail Information

Publications39

  1. Danciger M, Hendrickson J, Lyon J, Toomes C, McHale J, Fishman G, et al. CORD9 a new locus for arCRD: mapping to 8p11, estimation of frequency, evaluation of a candidate gene. Invest Ophthalmol Vis Sci. 2001;42:2458-65 pubmed
    ..However, only 2 loci for arCRD have been documented. This is the report of a third. ..
  2. Meyer E, Manahan D. Nutrient uptake by marine invertebrates: cloning and functional analysis of amino acid transporter genes in developing sea urchins (Strongylocentrotus purpuratus). Biol Bull. 2009;217:6-24 pubmed
    ..The functional characterization of these genes establishes a molecular biological basis for amino acid transport by developmental stages of marine invertebrates. ..
  3. Chodavarapu R, Feng S, Bernatavichute Y, Chen P, Stroud H, Yu Y, et al. Relationship between nucleosome positioning and DNA methylation. Nature. 2010;466:388-92 pubmed publisher
    ..DNA methylation is also enriched on exons, consistent with the targeting of DNA methylation to nucleosomes, and suggesting a role for DNA methylation in exon definition. ..
  4. Haiman C, Garcia R, Hsu C, Xia L, Ha H, Sheng X, et al. Screening and association testing of common coding variation in steroid hormone receptor co-activator and co-repressor genes in relation to breast cancer risk: the Multiethnic Cohort. BMC Cancer. 2009;9:43 pubmed publisher
  5. Pushkin A, Abuladze N, Lee I, Newman D, Hwang J, Kurtz I. Cloning, tissue distribution, genomic organization, and functional characterization of NBC3, a new member of the sodium bicarbonate cotransporter family. J Biol Chem. 1999;274:16569-75 pubmed
    ..Expression of mNBC3 cRNA in Xenopus laevis oocytes demonstrated that the protein encodes a novel stilbene-insensitive 5-(N-ethyl-N-isopropyl)-amiloride-inhibitable sodium bicarbonate cotransporter. ..
  6. Roy M, Kim N, Xing Y, Lee C. The effect of intron length on exon creation ratios during the evolution of mammalian genomes. RNA. 2008;14:2261-73 pubmed publisher
    ..This suggests that the observed correlation of longer intron lengths with alternatively spliced exons may be at least partly due to biases in the probability of exon creation, which is higher in long introns. ..
  7. Haake S, Yoder S, Attarian G, Podkaminer K. Native plasmids of Fusobacterium nucleatum: characterization and use in development of genetic systems. J Bacteriol. 2000;182:1176-80 pubmed
    ..pHS17 was stably maintained in the F. nucleatum transformants, and differences in the transformation efficiencies suggested the presence of a restriction-modification system in F. nucleatum...
  8. Wetzel G, Ding S, Chen F. Molecular cloning of junctin from human and developing rabbit heart. Mol Genet Metab. 2000;69:252-8 pubmed publisher
    ..Furthermore, the previously described increase in SR Ca(2+) release with development is associated with the increased expression of junctin...
  9. Wei B, Dalwadi H, Gordon L, Landers C, Bruckner D, Targan S, et al. Molecular cloning of a Bacteroides caccae TonB-linked outer membrane protein identified by an inflammatory bowel disease marker antibody. Infect Immun. 2001;69:6044-54 pubmed publisher
    ..These findings suggest that OmpW may be a target of the IBD-associated immune response and reveal its structural relationship to a bacterial virulence factor of P. gingivalis and periodontal disease...
  10. Wallace S, Lachman R, Mekikian P, Bui K, Wilcox W. Marked phenotypic variability in progressive diaphyseal dysplasia (Camurati-Engelmann disease): report of a four-generation pedigree, identification of a mutation in TGFB1, and review. Am J Med Genet A. 2004;129A:235-47 pubmed
    ..Cranial involvement, which occurs in 61% of patients, can be severe, entrapping cranial nerves or causing increased intracranial pressure. Therapy with corticosteroids should be attempted in all symptomatic patients...
  11. Liu M, Gingery M, Doulatov S, Liu Y, Hodes A, Baker S, et al. Genomic and genetic analysis of Bordetella bacteriophages encoding reverse transcriptase-mediated tropism-switching cassettes. J Bacteriol. 2004;186:1503-17 pubmed
    ..Bordetella bacteriophages are capable of transducing genetic markers in vitro, and by using animal models, we demonstrated that lysogenic conversion can take place in the mouse respiratory tract during infection. ..
  12. Wang Y, Adamczyk A, Shugart Y, Samuels J, Grados M, Greenberg B, et al. A screen of SLC1A1 for OCD-related alleles. Am J Med Genet B Neuropsychiatr Genet. 2010;153B:675-679 pubmed publisher
    ..Further investigation of this variant is necessary to determine whether and how it is related to OCD. There was no other evidence of significant accumulation of deleterious coding mutations in SLC1A1 in the OCD cases. ..
  13. Chen L, Pai V, Levinson R, Sharpe A, Freeman G, Braun J, et al. Constitutive neuronal expression of the immune regulator, programmed death 1 (PD-1), identified during experimental autoimmune uveitis. Ocul Immunol Inflamm. 2009;17:47-55 pubmed publisher
    ..Programmed death-1 (PD-1) ligation downregulates active lymphocyte responses. The authors tested whether PD-1 or its ligands are expressed in the posterior segment during active intraocular inflammation...
  14. Padhukasahasram B, Wall J, Marjoram P, Nordborg M. Estimating recombination rates from single-nucleotide polymorphisms using summary statistics. Genetics. 2006;174:1517-28 pubmed
    ..We used our method to analyze a human data set recently genotyped by Perlegen Sciences. ..
  15. Aldave A, Yellore V, Principe A, Abedi G, Merrill K, Chalukya M, et al. Candidate gene screening for posterior polymorphous dystrophy. Cornea. 2005;24:151-5 pubmed
    ..The initial 3 genes chosen, ID1, BCL2L1, and VSX1, lie within the region on chromosome 20 to which the PPCD gene has been linked, and mutations in VSX1 have previously been identified in patients with PPCD...
  16. Lee H, Wang H, Jen J, Sabatti C, Baloh R, Nelson S. A novel mutation in KCNA1 causes episodic ataxia without myokymia. Hum Mutat. 2004;24:536 pubmed
    ..This mutation leads to a distinct clinical phenotype without myokymia broadening the scope of clinical characteristics of EA1 and highlighting the heterogeneity of phenotypic effects from distinct missense mutations...
  17. London S, Boulter J, Schlinger B. Cloning of the zebra finch androgen synthetic enzyme CYP17: a study of its neural expression throughout posthatch development. J Comp Neurol. 2003;467:496-508 pubmed publisher
    ..Our results support the hypothesis that neurosteroids may act to influence brain organization and function in the zebra finch...
  18. Hong H, Yang L, Stallcup M. Hormone-independent transcriptional activation and coactivator binding by novel orphan nuclear receptor ERR3. J Biol Chem. 1999;274:22618-26 pubmed
    ..Although ERR3 is much more closely related to ERR2 than to ERR1, the expression pattern for ERR3 was similar to that of ERR1 and distinct from that for ERR2, suggesting a unique role for ERR3 in development. ..
  19. Aldave A, Yellore V, Thonar E, Udar N, Warren J, Yoon M, et al. Novel mutations in the carbohydrate sulfotransferase gene (CHST6) in American patients with macular corneal dystrophy. Am J Ophthalmol. 2004;137:465-73 pubmed
    ..To further characterize the mutations within the CHST6 gene responsible for causing macular corneal dystrophy in a cohort of affected patients from the United States...
  20. Klapper E, Zhang Y, Figueroa P, Ness P, Stubbs J, Abumuhor I, et al. Toward extended phenotype matching: a new operational paradigm for the transfusion service. Transfusion. 2010;50:536-46 pubmed publisher
    ..This study demonstrates that substantial fill fractions can be achieved by selecting existing donor units for xHEA analysis and operating an inventory management system for efficient allocation of units to recipients. ..
  21. Lee H, O Connor B, Merriman B, Funari V, Homer N, Chen Z, et al. Improving the efficiency of genomic loci capture using oligonucleotide arrays for high throughput resequencing. BMC Genomics. 2009;10:646 pubmed publisher
    ..Coupled with the new massively parallel sequencing technologies, this provides a powerful approach to identifying disease-causing genetic variants that can be localized within the genome by traditional methods. ..
  22. Johnson L, Bostick M, Zhang X, Kraft E, Henderson I, Callis J, et al. The SRA methyl-cytosine-binding domain links DNA and histone methylation. Curr Biol. 2007;17:379-84 pubmed
    ..Hence, unlike the methyl-binding domain (MBD), which binds only methylated-CpG sequences, the SRA domain is a versatile new methyl-DNA-binding motif. ..
  23. Cokus S, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild C, et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008;452:215-9 pubmed publisher
  24. Edlund C, Lee W, Li D, Van Den Berg D, Conti D. Snagger: a user-friendly program for incorporating additional information for tagSNP selection. BMC Bioinformatics. 2008;9:174 pubmed publisher
  25. Pold M, Zhou J, Chen G, Hall J, Vescio R, Berenson J. Identification of a new, unorthodox member of the MAGE gene family. Genomics. 1999;59:161-7 pubmed
    ..Chromosome mapping linked MAGED1 to marker AFM119xd6 (DXS1039) on chromosome Xp11.23. ..
  26. Homer N, Merriman B, Nelson S. Local alignment of two-base encoded DNA sequence. BMC Bioinformatics. 2009;10:175 pubmed publisher
  27. Chumakov A, Grillier I, Chumakova E, Chih D, Slater J, Koeffler H. Cloning of the novel human myeloid-cell-specific C/EBP-epsilon transcription factor. Mol Cell Biol. 1997;17:1375-86 pubmed
    ..Transient tranfection of a promyelocyte cell line (NB4) with a C/EBP-epsilon expression plasmid increased cell growth by sevenfold, while antisense C/EBP-epsilon caused a fivefold decrease in clonal growth of these cells. ..
  28. Turner T, Bourne E, von Wettberg E, Hu T, Nuzhdin S. Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils. Nat Genet. 2010;42:260-3 pubmed publisher
    ..lyrata indicates parallel differentiation of the same polymorphism at one locus, confirming ecological adaptation, and different polymorphisms at two other loci, which may indicate convergent evolution. ..
  29. Curole J, Meyer E, Manahan D, Hedgecock D. Unequal and genotype-dependent expression of mitochondrial genes in larvae of the pacific oyster Crassostrea gigas. Biol Bull. 2010;218:122-31 pubmed
    ..Differences in mitochondrial gene expression could provide a biochemical index for the metabolic basis of genetically determined differences in larval growth. ..
  30. Iyer R, Kim H, Tsoa R, Grody W, Cederbaum S. Cloning and characterization of human agmatinase. Mol Genet Metab. 2002;75:209-18 pubmed
    ..It has 56% similarity to E. coli agmatinase and 42% similarity to human arginases I and II and shares highly conserved substrate-binding domains with these well-characterized enzymes. ..
  31. Kennedy M, Venkateswaran A, Tarr P, Xenarios I, Kudoh J, Shimizu N, et al. Characterization of the human ABCG1 gene: liver X receptor activates an internal promoter that produces a novel transcript encoding an alternative form of the protein. J Biol Chem. 2001;276:39438-47 pubmed
    ..Elucidation of the various roles of different ABCG1 isoforms will be important for our understanding of mammalian cholesterol homeostasis...
  32. Goodman S, Velten N, Gao Q, Robinson S, Segall A. In vitro selection of integration host factor binding sites. J Bacteriol. 1999;181:3246-55 pubmed
    ..Despite finding individual sequences that varied over 100-fold in affinity for IHF, we found no apparent correlation between affinity and function. ..
  33. Pei L. Molecular cloning of a novel transcriptional repressor protein of the rat type 1 vasoactive intestinal peptide receptor gene. J Biol Chem. 1998;273:19902-8 pubmed
    ..These results indicate that VIPR-RP is a novel transcriptional repressor protein that regulates VIPR expression. ..
  34. Pulst S, Nechiporuk A, Nechiporuk T, Gispert S, Chen X, Lopes Cendes I, et al. Moderate expansion of a normally biallelic trinucleotide repeat in spinocerebellar ataxia type 2. Nat Genet. 1996;14:269-76 pubmed
    ..The most common disease allele contained (CAG)37, one of the shortest expansions seen in a CAG expansion syndrome. The repeat occurs in the 5'-coding region of SCA2 which is a member of a novel gene family...
  35. Koepfli K, Wayne R. Type I STS markers are more informative than cytochrome B in phylogenetic reconstruction of the Mustelidae (Mammalia: Carnivora). Syst Biol. 2003;52:571-93 pubmed
  36. Njabo K, Cornel A, Sehgal R, Loiseau C, Buermann W, Harrigan R, et al. Coquillettidia (Culicidae, Diptera) mosquitoes are natural vectors of avian malaria in Africa. Malar J. 2009;8:193 pubmed publisher
    ..The mosquito vectors of Plasmodium spp. have largely been overlooked in studies of ecology and evolution of avian malaria and other vertebrates in wildlife...
  37. Dewing P, Ching S, Zhang Y, Huang B, Peirce R, McCabe E, et al. Midkine is expressed early in rat fetal adrenal development. Mol Genet Metab. 2000;71:616-22 pubmed
    ..We conclude that Mdk is involved early in fetal development of the rat adrenal. Therefore, MDK is a candidate gene for AHC not due to DAX1 mutations. ..
  38. Clark M, Homer N, O Connor B, Chen Z, Eskin A, Lee H, et al. U87MG decoded: the genomic sequence of a cytogenetically aberrant human cancer cell line. PLoS Genet. 2010;6:e1000832 pubmed publisher
    ..The sequence analysis of U87MG provides an unparalleled level of mutational resolution compared to any cell line to date. ..
  39. Homer N, Nelson S, Merriman B. Local alignment of generalized k-base encoded DNA sequence. BMC Bioinformatics. 2010;11:347 pubmed publisher
    ..This bioinformatic solution affords greater robustness to errors, as well as lower false SNP discovery rates, only at the cost of computational time. ..