Genomes and Genes
Experts and Doctors on dna sequence analysis in California, United States
Locale: California, United States
Topic: dna sequence analysis
Publications108 found, 100 shown here
- Chaisson M, Pevzner P. Short read fragment assembly of bacterial genomes. Genome Res. 2008;18:324-30 pubmed
- Snyder M, Du J, Gerstein M. Personal genome sequencing: current approaches and challenges. Genes Dev. 2010;24:423-31 pubmed publisher..Finally, we consider the possible individual and societal benefits of personal genome sequences. ..
- Chan E, Di Donato F, Hamel J, Tseng C, Buyon J. 52-kD SS-A/Ro: genomic structure and identification of an alternatively spliced transcript encoding a novel leucine zipper-minus autoantigen expressed in fetal and adult heart. J Exp Med. 1995;182:983-92 pubmed..26 (87%) of 30 sera tested from mothers whose children were known to have neonatal lupus immunoprecipitated the 52 beta form.(ABSTRACT TRUNCATED AT 400 WORDS) ..
- Li R, Faraco J, Lin L, Lin X, Hinton L, Rogers W, et al. Physical and radiation hybrid mapping of canine chromosome 12, in a region corresponding to human chromosome 6p12-q12. Genomics. 2001;73:299-315 pubmed..These data further establish the dog as a system for studying disease genes of interest to human populations and highlight feasible approaches for positional cloning of disease genes in organisms where genomic resources are limited. ..
- Agron P, Walker R, Kinde H, Sawyer S, Hayes D, Wollard J, et al. Identification by subtractive hybridization of sequences specific for Salmonella enterica serovar enteritidis. Appl Environ Microbiol. 2001;67:4984-91 pubmed publisher..These results provide a basis for developing a rapid, sensitive, and highly specific detection system for Salmonella serovar Enteritidis and provide sequence information that may be relevant to the unique characteristics of this serovar...
- Alekseyev M. Multi-break rearrangements and breakpoint re-uses: from circular to linear genomes. J Comput Biol. 2008;15:1117-31 pubmed publisher..We further use these results to analyze comparative genomic architecture of mammalian genomes. ..
- Apfel R, Benbrook D, Lernhardt E, Ortiz M, Salbert G, Pfahl M. A novel orphan receptor specific for a subset of thyroid hormone-responsive elements and its interaction with the retinoid/thyroid hormone receptor subfamily. Mol Cell Biol. 1994;14:7025-35 pubmed..Our data suggest a highly specific role for this novel receptor within the network of gene regulation by the thyroid/retinoid receptor subfamily. ..
- Toyoshima H, Hunter T. p27, a novel inhibitor of G1 cyclin-Cdk protein kinase activity, is related to p21. Cell. 1994;78:67-74 pubmed..p27 is identical to p27Kip1, a cyclin-Cdk inhibitor present in TGF beta-treated cells. p27 has the hallmarks of a negative regulator of G1 progression and may mediate TGF beta-induced G1 arrest. ..
- McNeill H, Yang C, Brodsky M, Ungos J, Simon M. mirror encodes a novel PBX-class homeoprotein that functions in the definition of the dorsal-ventral border in the Drosophila eye. Genes Dev. 1997;11:1073-82 pubmed..Mirror is a member of the class of homeoproteins defined by the human proto-oncogene PBX1. mrr is similar to the Iroquois genes ara and caup and is located adjacent to them in this recently described homeotic cluster. ..
- Han S, Chen R, Paronetto M, Conti M. Wee1B is an oocyte-specific kinase involved in the control of meiotic arrest in the mouse. Curr Biol. 2005;15:1670-6 pubmed..Thus, mWee1B is a key MPF inhibitory kinase in mouse oocytes, functions downstream of PKA, and is required for maintaining meiotic arrest. ..
- Brunner A, Johnson D, Kim S, Valouev A, Reddy T, Neff N, et al. Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res. 2009;19:1044-56 pubmed publisher..Taken together, our results indicate that hESC differentiation has a unique DNA methylation signature that may not be indicative of in vivo differentiation. ..
- Niu B, Fu L, Sun S, Li W. Artificial and natural duplicates in pyrosequencing reads of metagenomic data. BMC Bioinformatics. 2010;11:187 pubmed publisher..We provide a tool to estimate the number of natural duplicates according to user-defined sample types, so users can decide whether to retain or remove duplicates in their projects. ..
- Tang Y, Reed S. The Cdk-associated protein Cks1 functions both in G1 and G2 in Saccharomyces cerevisiae. Genes Dev. 1993;7:822-32 pubmed..It is likely, therefore, that Cks1 mediates a more specialized function of the Cdc28 kinase such as its ability to form specific multimeric complexes or to localize properly in cellular compartments. ..
- Underhill P, Shen P, Lin A, Jin L, Passarino G, Yang W, et al. Y chromosome sequence variation and the history of human populations. Nat Genet. 2000;26:358-61 pubmed..A minority of contemporary East Africans and Khoisan represent the descendants of the most ancestral patrilineages of anatomically modern humans that left Africa between 35,000 and 89,000 years ago. ..
- Martinez D, Larrondo L, Putnam N, Gelpke M, Huang K, Chapman J, et al. Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nat Biotechnol. 2004;22:695-700 pubmed..This genome provides a high quality draft sequence of a basidiomycete, a major fungal phylum that includes important plant and animal pathogens...
- Mao F, Leung W, Xin X. Characterization of EvaGreen and the implication of its physicochemical properties for qPCR applications. BMC Biotechnol. 2007;7:76 pubmed..The favorable DNA-binding profile of EG, coupled with its good stability and instrument-compatibility, should make EG a promising dye for qPCR and related applications. ..
- Harrington J, Lieber M. Functional domains within FEN-1 and RAD2 define a family of structure-specific endonucleases: implications for nucleotide excision repair. Genes Dev. 1994;8:1344-55 pubmed..The polarity of these branched DNA structures allows us to predict the placement of DNA scissions by RAD2 and RAD1/RAD10 in this reaction. ..
- Imai H, Chan E, Kiyosawa K, Fu X, Tan E. Novel nuclear autoantigen with splicing factor motifs identified with antibody from hepatocellular carcinoma. J Clin Invest. 1993;92:2419-26 pubmed
- Song Y, Liu C, McTeague M, Finegold S. 16S ribosomal DNA sequence-based analysis of clinically significant gram-positive anaerobic cocci. J Clin Microbiol. 2003;41:1363-9 pubmed..This finding is in contrast to the phenotypic identification results, by which only 56% of isolates were correctly identified to species level. ..
- Stanfield G, Villeneuve A. Regulation of sperm activation by SWM-1 is required for reproductive success of C. elegans males. Curr Biol. 2006;16:252-63 pubmed
- Anderson I, Ulrich L, Lupa B, Susanti D, Porat I, Hooper S, et al. Genomic characterization of methanomicrobiales reveals three classes of methanogens. PLoS ONE. 2009;4:e5797 pubmed publisher..While these organisms appear to be more closely related to the Methanosarcinales in ribosomal-based phylogenetic analyses, they are metabolically more similar to Class I methanogens...
- Witten D, Tibshirani R, Gu S, Fire A, Lui W. Ultra-high throughput sequencing-based small RNA discovery and discrete statistical biomarker analysis in a collection of cervical tumours and matched controls. BMC Biol. 2010;8:58 pubmed publisher..001. This approach can potentially be applied to any kind of RNA sequencing data for analysing differential sequence representation between biological sample sets. ..
- Dunn B, Sherlock G. Reconstruction of the genome origins and evolution of the hybrid lager yeast Saccharomyces pastorianus. Genome Res. 2008;18:1610-23 pubmed publisher..cerevisiae ancestral parent for each of the independent S. pastorianus groups was an ale yeast, with different, but closely related ale strains contributing to each group's parentage. ..
- Boore J, Staton J. The mitochondrial genome of the Sipunculid Phascolopsis gouldii supports its association with Annelida rather than Mollusca. Mol Biol Evol. 2002;19:127-37 pubmed..This requires reinterpretation of the homology of several embryological features and of patterns of animal body plan evolution...
- Gupta N, Benhamida J, Bhargava V, Goodman D, Kain E, Kerman I, et al. Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes. Genome Res. 2008;18:1133-42 pubmed publisher..We therefore argue that complementing DNA sequencing projects by comparative proteogenomics projects can be a viable approach to improve both genomic and proteomic annotations. ..
- Garrett Engele P, Moilanen B, Cyert M. Calcineurin, the Ca2+/calmodulin-dependent protein phosphatase, is essential in yeast mutants with cell integrity defects and in mutants that lack a functional vacuolar H(+)-ATPase. Mol Cell Biol. 1995;15:4103-14 pubmed..We discuss possible roles for calcineurin in regulating intracellular ion homeostasis and in maintaining cell integrity. ..
- Rahman A, Friedman D, Goldstein L. Two kinesin light chain genes in mice. Identification and characterization of the encoded proteins. J Biol Chem. 1998;273:15395-403 pubmed..These results indicate that the mammalian nervous system contains multiple kinesin light chain gene products with potentially distinct functions. ..
- Lee P, Gelbart T, West C, Halloran C, Felitti V, Beutler E. A study of genes that may modulate the expression of hereditary hemochromatosis: transferrin receptor-1, ferroportin, ceruloplasmin, ferritin light and heavy chains, iron regulatory proteins (IRP)-1 and -2, and hepcidin. Blood Cells Mol Dis. 2001;27:783-802 pubmed..These were further examined for association with differences in iron accumulation as measured by plasma transferrin saturation and ferritin levels, but no such association could be documented. ..
- Hosfield D, Frank G, Weng Y, Tainer J, Shen B. Newly discovered archaebacterial flap endonucleases show a structure-specific mechanism for DNA substrate binding and catalysis resembling human flap endonuclease-1. J Biol Chem. 1998;273:27154-61 pubmed..Thus, these archaeal enzymes may provide a means to dissect the specific binding and catalytic mechanisms of the entire FEN-1 family of structure-specific nucleases...
- Liu K, Li L, Cohen S. Antisense RNA-mediated deficiency of the calpain protease, nCL-4, in NIH3T3 cells is associated with neoplastic transformation and tumorigenesis. J Biol Chem. 2000;275:31093-8 pubmed..Our results implicate deficiency of the nCL-4 calpain protease in neoplastic transformation. ..
- Yamamoto M, Lin X, Kominato Y, Hata Y, Noda R, Saitou N, et al. Murine equivalent of the human histo-blood group ABO gene is a cis-AB gene and encodes a glycosyltransferase with both A and B transferase activity. J Biol Chem. 2001;276:13701-8 pubmed..Cloning of the murine AB gene may be helpful in establishing a mouse model system to assess the functionality of the ABO genes in the future. ..
- Chen A, Perrin M, Brar B, Li C, Jamieson P, Digruccio M, et al. Mouse corticotropin-releasing factor receptor type 2alpha gene: isolation, distribution, pharmacological characterization and regulation by stress and glucocorticoids. Mol Endocrinol. 2005;19:441-58 pubmed
- Mendonca H, Arkush K. Development of PCR-based methods for detection of Sphaerothecum destruens in fish tissues. Dis Aquat Organ. 2004;61:187-97 pubmed..This report introduces the first DNA-based detection method for S. destruens, to be used alone as a diagnostic tool or in conjunction with histologic tests for confirmatory identification of the parasite. ..
- Morin P, Archer F, Foote A, Vilstrup J, Allen E, Wade P, et al. Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species. Genome Res. 2010;20:908-16 pubmed publisher..We predict that phylogeographic mitogenomics will become an important tool for improved statistical phylogeography and more precise estimates of divergence times. ..
- Stevens T, Iacovoni J, Edelman D, Meech R. Identification of novel binding elements and gene targets for the homeodomain protein BARX2. J Biol Chem. 2004;279:14520-30 pubmed..The data suggest that BARX2 can coordinate the expression of a network of genes that influence the growth of MCF7 cells. ..
- McDowall K, Hernandez R, Lin Chao S, Cohen S. The ams-1 and rne-3071 temperature-sensitive mutations in the ams gene are in close proximity to each other and cause substitutions within a domain that resembles a product of the Escherichia coli mre locus. J Bacteriol. 1993;175:4245-9 pubmed..coli, which has been implicated previously in determining bacterial cell shape. ..
- Derry J, Ochs H, Francke U. Isolation of a novel gene mutated in Wiskott-Aldrich syndrome. Cell. 1994;78:635-44 pubmed..WASP encodes a 501 amino acid proline-rich protein that is likely to be a key regulator of lymphocyte and platelet function. ..
- Nievergelt C, Mutschler T, Feistner A, Woodruff D. Social system of the Alaotran gentle lemur (Hapalemur griseus alaotrensis): genetic characterization of group composition and mating system. Am J Primatol. 2002;57:157-76 pubmed..At least 8% of paternities involved extragroup males. Additional data on life history and reproduction are presented, and the social system of the Alaotran gentle lemur is discussed in the light of the new genetic findings...
- Hoebe K, Du X, Georgel P, Janssen E, Tabeta K, Kim S, et al. Identification of Lps2 as a key transducer of MyD88-independent TIR signalling. Nature. 2003;424:743-8 pubmed..This reveals that an alternative MyD88-dependent 'adaptor X' pathway is present in some, but not all, macrophages, and implies afferent immune specialization. ..
- Labhart P, Morgan G. Identification of novel genes encoding transcription elongation factor TFIIS (TCEA) in vertebrates: conservation of three distinct TFIIS isoforms in frog, mouse, and human. Genomics. 1998;52:278-88 pubmed..Phylogenetic analysis of TFIIS sequences demonstrates the ancient origins of the three vertebrate isoforms, although they appeared functionally equivalent in in vitro RNA cleavage assays. ..
- Guo B, Godzik A, Reed J. Bcl-G, a novel pro-apoptotic member of the Bcl-2 family. J Biol Chem. 2001;276:2780-5 pubmed..A mutant of Bcl-G(L) in which the BH2 domain was deleted displayed increased apoptotic activity and coimmunoprecipitated with Bcl-X(L), suggesting that the BH2 domain autorepresses Bcl-G(L). ..
- Arkush K, McBride A, Mendonca H, Okihiro M, Andree K, Marshall S, et al. Genetic characterization and experimental pathogenesis of Piscirickettsia salmonis isolated from white seabass Atractoscion nobilis. Dis Aquat Organ. 2005;63:139-49 pubmed..The results from this study clearly indicate that infections with P. salmonis are not restricted to salmonid fishes and that the bacterium can cause a disease similar to piscirickettsiosis in nonsalmonid hosts...
- Margolin W, Bramhill D, Long S. The dnaA gene of Rhizobium meliloti lies within an unusual gene arrangement. J Bacteriol. 1995;177:2892-900 pubmed..Downstream of dnaA, there are two open reading frames that are probably expressed but are not highly similar to any genes in the databases. These results show that R. meliloti dnaA is located within a novel gene arrangement. ..
- de Lecea L, Ruiz Lozano P, Danielson P, Peelle Kirley J, Foye P, Frankel W, et al. Cloning, mRNA expression, and chromosomal mapping of mouse and human preprocortistatin. Genomics. 1997;42:499-506 pubmed..The human putative cortistatin peptide has an arginine for lysine substitution, compared to the rat and mouse products, and is N-terminally extended by 3 amino acids. ..
- McAdara Berkowitz J, Catz S, Johnson J, Ruedi J, Thon V, Babior B. JFC1, a novel tandem C2 domain-containing protein associated with the leukocyte NADPH oxidase. J Biol Chem. 2001;276:18855-62 pubmed..From the data presented here, it is proposed that JFC1 is acting as an adaptor protein between phosphatidylinositol 3-kinase products and the oxidase cytosolic complex. ..
- Rhee S, Kantor R, Katzenstein D, Camacho R, Morris L, Sirivichayakul S, et al. HIV-1 pol mutation frequency by subtype and treatment experience: extension of the HIVseq program to seven non-B subtypes. AIDS. 2006;20:643-51 pubmed
- Zhang S, Lawton M, Hunter T, Lamb C. atpk1, a novel ribosomal protein kinase gene from Arabidopsis. I. Isolation, characterization, and expression. J Biol Chem. 1994;269:17586-92 pubmed..The first intron of atpk1 functions as an enhancer in atpk1 expression. ..
- Soans C, Holash J, Pavlova Y, Pasquale E. Developmental expression and distinctive tyrosine phosphorylation of the Eph-related receptor tyrosine kinase Cek9. J Cell Biol. 1996;135:781-95 pubmed..Since autophosphorylation of receptor protein-tyrosine kinases typically correlates with increased enzymatic activity, this suggests that Cek9 plays an active role in embryonic signal transduction pathways. ..
- Amler L, Bauer A, Corvi R, Dihlmann S, Praml C, Cavenee W, et al. Identification and characterization of novel genes located at the t(1;15)(p36.2;q24) translocation breakpoint in the neuroblastoma cell line NGP. Genomics. 2000;64:195-202 pubmed..A preliminary assessment of transcription and sequence of both genes in several neuroblastoma cell lines does not, thus far, support a causal role in neuroblastoma. However, further analyses are required to confirm these results. ..
- Ye C, Galbraith S, Liao J, Eskin E. Using network component analysis to dissect regulatory networks mediated by transcription factors in yeast. PLoS Comput Biol. 2009;5:e1000311 pubmed publisher..The software package implementing the algorithms discussed in this work is available as a MATLAB package upon request. ..
- Margolin W, Long S. Rhizobium meliloti contains a novel second homolog of the cell division gene ftsZ. J Bacteriol. 1994;176:2033-43 pubmed..The two ftsZ genes were genetically mapped to the R. meliloti main chromosome, approximately 100 kb apart...
- Tobe T, Schoolnik G, Sohel I, Bustamante V, Puente J. Cloning and characterization of bfpTVW, genes required for the transcriptional activation of bfpA in enteropathogenic Escherichia coli. Mol Microbiol. 1996;21:963-75 pubmed..From these results we conclude that bfpTV W causes transcriptional activation of bfpA, and possibly eaeA, by a trans-acting mechanism that may co-ordinately regulate the expression of EPEC virulence determinants...
- Lee P, Gelbart T, West C, Adams M, Blackstone R, Beutler E. Three genes encoding zinc finger proteins on human chromosome 6p21.3: members of a new subclass of the Kruppel gene family containing the conserved SCAN box domain. Genomics. 1997;43:191-201 pubmed..One of the three polymorphisms, Pro163Leu, is the second proline in a proline cluster (PEPP) in a region separating the SCAN box from the zinc finger motifs. ..
- Khambata Ford S, Liu Y, Gleason C, Dickson M, Altman R, Batzoglou S, et al. Identification of promoter regions in the human genome by using a retroviral plasmid library-based functional reporter gene assay. Genome Res. 2003;13:1765-74 pubmed..This method promises to be a useful genome-wide function-based approach that can complement existing methods to look for promoters. ..
- Ma Z, Yoshimura M, Michailides T. Identification and characterization of benzimidazole resistance in Monilinia fructicola from stone fruit orchards in California. Appl Environ Microbiol. 2003;69:7145-52 pubmed..Based on these point mutations in the beta-tubulin gene, allele-specific PCR assays were developed for rapid detection of benzimidazole-resistant isolates of M. fructicola from stone fruit...
- Cummings C, Brinig M, Lepp P, van de Pas S, Relman D. Bordetella species are distinguished by patterns of substantial gene loss and host adaptation. J Bacteriol. 2004;186:1484-92 pubmed
- Budman J, Kim S, Chu G. Processing of DNA for nonhomologous end-joining is controlled by kinase activity and XRCC4/ligase IV. J Biol Chem. 2007;282:11950-9 pubmed..Surprisingly, all polymerase and most nuclease activity required XRCC4/Ligase IV. This suggests a mechanism for how NHEJ suppresses processing to optimize the preservation of DNA sequence. ..
- Chen J, Xie G, Han S, Chertkov O, Sims D, Civerolo E. Whole genome sequences of two Xylella fastidiosa strains (M12 and M23) causing almond leaf scorch disease in California. J Bacteriol. 2010;192:4534 pubmed publisher..Genome information greatly facilitates research on this nutritionally fastidious organism. Here we report the complete genome sequences of two ALSD strains of this bacterium, M12 and M23...
- Feng L, Sun W, Xia Y, Tang W, Chanmugam P, Soyoola E, et al. Cloning two isoforms of rat cyclooxygenase: differential regulation of their expression. Arch Biochem Biophys. 1993;307:361-8 pubmed..Thus, the two COX isoforms were differentially expressed, and COX-2 was selectively induced in response to inflammatory stimuli in rats. ..
- Diaz E, Schimmöller F, Pfeffer S. A novel Rab9 effector required for endosome-to-TGN transport. J Cell Biol. 1997;138:283-90 pubmed..These data are consistent with a model in which p40 and Rab9 act together to drive the process of transport vesicle docking. ..
- Stuart R, Pavlova A, Beier D, Li Z, Krijanovski Y, Nigam S. EEG1, a putative transporter expressed during epithelial organogenesis: comparison with embryonic transporter expression during nephrogenesis. Am J Physiol Renal Physiol. 2001;281:F1148-56 pubmed..The data raise the possibility that EEG1 and POV1 may define a new family of transport proteins involved in the transport of nutrients or metabolites in rapidly growing and/or developing tissues...
- Johnson S, Tan F, McCullough H, Riordan D, Fire A. Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin. Genome Res. 2006;16:1505-16 pubmed..elegans, this analysis provides a reference from which to begin an investigation of relationships between the nucleosomal pattern, chromosomal architecture, and lineage-based gene activity on a genome-wide scale. ..
- Wooley J, Godzik A, Friedberg I. A primer on metagenomics. PLoS Comput Biol. 2010;6:e1000667 pubmed publisher..Finally, the last section of this article provides a few representative studies illustrating different facets of recent scientific discoveries made using metagenomics. ..
- Cooper G, Stone E, Asimenos G, Green E, Batzoglou S, Sidow A. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res. 2005;15:901-13 pubmed..We anticipate that GERP and the types of analyses it facilitates will provide further insights and improved annotation for the human genome as mammalian genome sequence data become richer. ..
- Dingwall A, Beek S, McCallum C, Tamkun J, Kalpana G, Goff S, et al. The Drosophila snr1 and brm proteins are related to yeast SWI/SNF proteins and are components of a large protein complex. Mol Biol Cell. 1995;6:777-91 pubmed
- Mahajan R, Delphin C, Guan T, Gerace L, Melchior F. A small ubiquitin-related polypeptide involved in targeting RanGAP1 to nuclear pore complex protein RanBP2. Cell. 1997;88:97-107 pubmed..Inhibition of nuclear protein import resulting from antibodies directed at NPC-associated RanGAP1 cannot be overcome by soluble cytosolic RanGAP1, indicating that GTP hydrolysis by Ran at RanBP2 is required for nuclear protein import. ..
- Yildiz F, Schoolnik G. Role of rpoS in stress survival and virulence of Vibrio cholerae. J Bacteriol. 1998;180:773-84 pubmed..In addition, the rpoS mutation led to reduced production or secretion of hemagglutinin/protease. However, rpoS is not critical for in vivo survival, as determined by an infant mouse intestinal competition assay. ..
- Ong E, Yeh J, Ding Y, Hindsgaul O, Fukuda M. Expression cloning of a human sulfotransferase that directs the synthesis of the HNK-1 glycan on the neural cell adhesion molecule and glycolipids. J Biol Chem. 1998;273:5190-5 pubmed..The results combined together indicate that the cloned HNK-1ST directs the synthesis of the HNK-1 carbohydrate epitope on both glycoproteins and glycolipids in the nervous tissues. ..
- Jiang W, Jimenez G, Wells N, Hope T, Wahl G, Hunter T, et al. PRC1: a human mitotic spindle-associated CDK substrate protein required for cytokinesis. Mol Cell. 1998;2:877-85 pubmed..Microinjection of anti-PRC1 antibodies into HeLa cells blocked cellular cleavage, but not nuclear division, indicating a functional role for PRC1 in the process of cytokinesis. ..
- Fredricks D, Jolley J, Lepp P, Kosek J, Relman D. Rhinosporidium seeberi: a human pathogen from a novel group of aquatic protistan parasites. Emerg Infect Dis. 2000;6:273-82 pubmed..seeberi phylogeny recently suggested by another group. R. seeberi is not a classic fungus, but rather the first known human pathogen from the DRIPs clade, a novel clade of aquatic protistan parasites (Ichthyosporea)...
- Kim J, Bergmann A, Wehri E, Lu X, Stubbs L. Imprinting and evolution of two Kruppel-type zinc-finger genes, ZIM3 and ZNF264, located in the PEG3/USP29 imprinted domain. Genomics. 2001;77:91-8 pubmed..The reciprocal imprinting of two neighboring mouse genes, Zim3 and Zfp264, is consistent with a pattern observed frequently in other imprinted domains, and suggests that the imprinting of these two genes might be coregulated. ..
- Loots G, Chain P, Mabery S, Rasley A, Garcia E, Ovcharenko I. Array2BIO: from microarray expression data to functional annotation of co-regulated genes. BMC Bioinformatics. 2006;7:307 pubmed..org comparative genomics tools and integrates a system for translating co-expression data into mechanisms of gene co-regulation. Array2BIO is publicly available at http://array2bio.dcode.org. ..
- Haussecker D, Cao D, Huang Y, Parameswaran P, Fire A, Kay M. Capped small RNAs and MOV10 in human hepatitis delta virus replication. Nat Struct Mol Biol. 2008;15:714-21 pubmed publisher..The identification of capped small RNAs and the involvement of MOV10 in HDV replication further suggest a conserved mechanism related to RNA-directed transcription in lower eukaryotes. ..
- Zhang K, Li J, Gao Y, Egli D, Xie B, Deng J, et al. Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human. Nat Methods. 2009;6:613-8 pubmed publisher..Comparison of expressed SNPs on the sense and antisense transcripts suggested that allelic ratios are primarily determined by cis-regulatory mechanisms on the sense transcripts. ..
- Gent J, Schvarzstein M, Villeneuve A, Gu S, Jantsch V, Fire A, et al. A Caenorhabditis elegans RNA-directed RNA polymerase in sperm development and endogenous RNA interference. Genetics. 2009;183:1297-314 pubmed publisher..These and other data suggest a working model in which a major role of the RRF-3/ERI pathway is to generate siRNAs that set patterns of gene expression through feedback repression of a set of critical targets during spermatogenesis. ..
- Bock J, Lin R, Scheller R. A new syntaxin family member implicated in targeting of intracellular transport vesicles. J Biol Chem. 1996;271:17961-5 pubmed..The sequence homology, topology, localization, and alpha-SNAP binding suggest that syntaxin 6 is involved in intracellular vesicle trafficking. ..
- Fukuoka Y, Ember J, Hugli T. Cloning and characterization of rat C3a receptor: differential expression of rat C3a and C5a receptors by LPS stimulation. Biochem Biophys Res Commun. 1998;242:663-8 pubmed..These results suggest that expression of C3aR and C5aR is independently regulated in rat cells and tissues. ..
- Contos J, Chun J. Complete cDNA sequence, genomic structure, and chromosomal localization of the LPA receptor gene, lpA1/vzg-1/Gpcr26. Genomics. 1998;51:364-78 pubmed..The genomic structure indicates a distinct, divergent evolutionary lineage for the vzg-1/lpA1 subfamily of receptors compared to those of homologous orphan receptor genes. ..
- Wu X, Freeze H. GLUT14, a duplicon of GLUT3, is specifically expressed in testis as alternative splice forms. Genomics. 2002;80:553-7 pubmed..Interestingly, the ortholog of GLUT14 is not found in mice. The multiple duplications of GLUT genes suggest that the GLUT family probably emerged by gene duplications and mutations during evolution in different lineages. ..
- Woyke T, Xie G, Copeland A, Gonzalez J, Han C, Kiss H, et al. Assembling the marine metagenome, one cell at a time. PLoS ONE. 2009;4:e5299 pubmed publisher..A combination of single cell genomics and metagenomics enabled us to analyze the genome content, metabolic adaptations, and biogeography of these taxa. ..
- Pushkarev D, Neff N, Quake S. Single-molecule sequencing of an individual human genome. Nat Biotechnol. 2009;27:847-50 pubmed publisher..This milestone should allow widespread application of genome sequencing to many aspects of genetics and human health, including personal genomics. ..
- Dartois V, Djavakhishvili T, Hoch J. Identification of a membrane protein involved in activation of the KinB pathway to sporulation in Bacillus subtilis. J Bacteriol. 1996;178:1178-86 pubmed..Implications of these observations on the transcriptional regulation of kinB and the role of KbaA in KinB activation are discussed. ..
- Westendorf J, Konstantinov K, Wormsley S, Shu M, Matsumoto Taniura N, Pirollet F, et al. M phase phosphoprotein 10 is a human U3 small nucleolar ribonucleoprotein component. Mol Biol Cell. 1998;9:437-49 pubmed..This association of MPP10 with U3 snoRNA was stable to 400 mM salt and suggested that MPP10 is a component of the human U3 small nucleolar ribonucleoprotein. ..
- Ohyama C, Smith P, Angata K, Fukuda M, Lowe J, Fukuda M. Molecular cloning and expression of GDP-D-mannose-4,6-dehydratase, a key enzyme for fucose metabolism defective in Lec13 cells. J Biol Chem. 1998;273:14582-7 pubmed..The results also suggest that the genomic structure encoding GMD in Lec13 cells likely has a defect different from a point mutation in the coding region. ..
- Gorman S, Haider N, Grieshammer U, Swiderski R, Kim E, Welch J, et al. The cloning and developmental expression of unconventional myosin IXA (MYO9A) a gene in the Bardet-Biedl syndrome (BBS4) region at chromosome 15q22-q23. Genomics. 1999;59:150-60 pubmed..Intron/exon boundaries were identified, and myosin IXA DNA and RNA from BBS4 patients were evaluated for mutation. ..
- Amin N, Nguyen M, Oh S, Kolodner R. exo1-Dependent mutator mutations: model system for studying functional interactions in mismatch repair. Mol Cell Biol. 2001;21:5142-55 pubmed..These results support a model in which EXO1 plays a structural role in MMR and stabilizes multiprotein complexes containing a number of MMR proteins. A similar role is proposed for PCNA based on the data presented. ..
- Brudno M, Do C, Cooper G, Kim M, Davydov E, Green E, et al. LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 2003;13:721-31 pubmed..Multi-LAGAN is a practical method for generating multiple alignments of long genomic sequences at any evolutionary distance. Our systems are publicly available at http://lagan.stanford.edu...
- Lin Y, Shin E, Campbell M, Niederhuber J. Transcription of the blk gene in human B lymphocytes is controlled by two promoters. J Biol Chem. 1995;270:25968-75 pubmed..5-kilobase blk transcript. These data suggest that the two human blk RNAs arise from the transcription of the blk gene by two distinct promoters and that these promoters may be subject to regulation by different trans-acting factors. ..