Open Reading Frames

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  Subject Areas on Research

  • A CaMK cascade activates CRE-mediated transcription in neurons of Caenorhabditis elegans. 
  • A comprehensive mutation analysis of RP2 and RPGR in a North American cohort of families with X-linked retinitis pigmentosa. 
  • A conserved amino acid sequence directing intracellular type III secretion by Salmonella typhimurium. 
  • A mutation in a mitochondrial transmembrane protein is responsible for the pleiotropic hematological and skeletal phenotype of flexed-tail (f/f) mice. 
  • A novel chloroplast gene reported for flagellate plants. 
  • ATM: genome stability, neuronal development, and cancer cross paths. 
  • African strains of hepatitis E virus that are distinct from Asian strains. 
  • Analysis of non-synonymous-coding variants of Parkinson's disease-related pathogenic and susceptibility genes in East Asian populations. 
  • Aquaporins in Saccharomyces: Characterization of a second functional water channel protein. 
  • Arabidopsis cDNA sequence encoding myrosinase. 
  • Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. 
  • COT drives resistance to RAF inhibition through MAP kinase pathway reactivation. 
  • Cellular immune response to cryptic epitopes during therapeutic gene transfer. 
  • Characterization of a putative periplasmic transport system for octopine accumulation encoded by Agrobacterium tumefaciens Ti plasmid pTiA6. 
  • Characterization of cDNA encoding mouse DNA repair protein O6-methylguanine-DNA methyltransferase and high-level expression of the wild-type and mutant proteins in Escherichia coli. 
  • Characterization of the MFalpha pheromone of the human fungal pathogen cryptococcus neoformans. 
  • Characterization of the transcriptional trans activator of human foamy retrovirus. 
  • Cloning and characterization of a cAMP-specific cyclic nucleotide phosphodiesterase. 
  • Cloning and expression of a functional serotonin transporter from rat brain. 
  • Competitive translation efficiency at the picornavirus type 1 internal ribosome entry site facilitated by viral cis and trans factors. 
  • Complete genomic nucleotide sequence of the temperate bacteriophage Aa Phi 23 of Actinobacillus actinomycetemcomitans. 
  • Composition and dynamics of the Caenorhabditis elegans early embryonic transcriptome. 
  • Correction of dystrophin expression in cells from Duchenne muscular dystrophy patients through genomic excision of exon 51 by zinc finger nucleases. 
  • Cytosine deaminase MX cassettes as positive/negative selectable markers in Saccharomyces cerevisiae. 
  • Determinants of poliovirus neurovirulence. 
  • Dicistronic polioviruses as expression vectors for foreign genes. 
  • Differential expression of alternatively spliced pX mRNAs in HTLV-I-infected cell lines. 
  • Differentiation of strains in Mycobacterium tuberculosis complex by DNA sequence polymorphisms, including rapid identification of M. bovis BCG. 
  • Diverse proteins homologous to inositol monophosphatase. 
  • Endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(A) tracts. 
  • Exon 10b of the NF1 gene represents a mutational hotspot and harbors a recurrent missense mutation Y489C associated with aberrant splicing. 
  • Expression cloning of the TGF-beta type II receptor, a functional transmembrane serine/threonine kinase. 
  • Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. 
  • FHIT and FRA3B 3p14.2 allele loss are common in lung cancer and preneoplastic bronchial lesions and are associated with cancer-related FHIT cDNA splicing aberrations. 
  • Fasciola hepatica: molecular cloning, nucleotide sequence, and expression of a gene encoding a polypeptide homologous to a Schistosoma mansoni fatty acid-binding protein. 
  • Fluorescence-based isolation of bacterial genes expressed within host cells. 
  • Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. 
  • Genetic composition of the Bacillus subtilis SOS system. 
  • Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789. 
  • Genomes of Ashbya fungi isolated from insects reveal four mating-type loci, numerous translocations, lack of transposons, and distinct gene duplications. 
  • Heterogeneity in codon usages of sobemovirus genes. 
  • Heterologous URA3MX cassettes for gene replacement in Saccharomyces cerevisiae. 
  • Homozygous diploid deletion strains of Saccharomyces cerevisiae that determine lag phase and dehydration tolerance. 
  • Human papillomavirus 16 E6 expression disrupts the p53-mediated cellular response to DNA damage. 
  • Human retroviral gag- and gag-pol-like proteins interact with the transforming growth factor-beta receptor activin receptor-like kinase 1. 
  • Hybrid male sterility in Mimulus (Phrymaceae) is associated with a geographically restricted mitochondrial rearrangement. 
  • Identification and characterization of upstream open reading frames (uORF) in the 5' untranslated regions (UTR) of genes in Saccharomyces cerevisiae. 
  • Identification of a homogentisate-1,2-dioxygenase gene in the fungus Exophiala lecanii-corni: analysis and implications. 
  • Identification of a region of genetic variability among Bacillus anthracis strains and related species. 
  • Identification of the activation domain of equine infectious anemia virus rev. 
  • Identification of the breast cancer susceptibility gene BRCA2. 
  • Identification of the yeast cytidine deaminase CDD1 as an orphan C-->U RNA editase. 
  • Improved transcript isoform discovery using ORF graphs. 
  • Infectious pathogen detection arrays: viral detection in cell lines and postmortem brain tissue. 
  • Inositol diphosphate signaling regulates telomere length. 
  • Instability of simple sequence repeats in a mammalian cell line. 
  • Integration of DNA fragments by illegitimate recombination in Saccharomyces cerevisiae. 
  • Isolation of suppressor mutants of phosphatidylinositol 3-phosphate 5-kinase deficient cells in Schizosaccharomyces pombe. 
  • Large introns in relation to alternative splicing and gene evolution: a case study of Drosophila bruno-3. 
  • Loss of a histone deacetylase dramatically alters the genomic distribution of Spo11p-catalyzed DNA breaks in Saccharomyces cerevisiae. 
  • Low prevalence of myocilin mutations in an African American population with primary open-angle glaucoma. 
  • Lupus autoantibodies recognize the product of an alternative open reading frame of SmB/B'. 
  • Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE. 
  • Mitochondrial genetic background in Ghanaian patients with primary open-angle glaucoma. 
  • Molecular cloning and characterization of a distinct human phosphodiesterase gene family: PDE11A. 
  • Molecular cloning of rat glucose-dependent insulinotropic peptide (GIP). 
  • Molecular identification, cloning and characterization of transmitted/founder HIV-1 subtype A, D and A/D infectious molecular clones. 
  • Multifactorial determinants of protein expression in prokaryotic open reading frames. 
  • Murine noroviruses comprising a single genogroup exhibit biological diversity despite limited sequence divergence. 
  • Ninety-six haploid yeast strains with individual disruptions of open reading frames between YOR097C and YOR192C, constructed for the Saccharomyces genome deletion project, have an additional mutation in the mismatch repair gene MSH3. 
  • Novel FOXF1 mutations in sporadic and familial cases of alveolar capillary dysplasia with misaligned pulmonary veins imply a role for its DNA binding domain. 
  • Novel imprinted DLK1/GTL2 domain on human chromosome 14 contains motifs that mimic those implicated in IGF2/H19 regulation. 
  • Nucleotide sequence of mouse SCIP cDNA, a POU-domain transcription factor. 
  • Nucleotide sequence of the LYS2 gene of Saccharomyces cerevisiae: homology to Bacillus brevis tyrocidine synthetase 1. 
  • Observation of dually decoded regions of the human genome using ribosome profiling data. 
  • Optineurin coding variants in Ghanaian patients with primary open-angle glaucoma. 
  • Orion: Detecting regions of the human non-coding genome that are intolerant to variation using population genetics. 
  • PRKACA mediates resistance to HER2-targeted therapy in breast cancer cells and restores anti-apoptotic signaling. 
  • Phylogenetic and Phylogenomic Definition of Rhizopus Species. 
  • Phylogenetic comparison of protein-coding versus ribosomal RNA-coding sequence data: a case study of the Lecanoromycetes (Ascomycota). 
  • Positional cloning of zebrafish ferroportin1 identifies a conserved vertebrate iron exporter. 
  • Positive and negative selection LYS5MX gene replacement cassettes for use in Saccharomyces cerevisiae. 
  • Properties of overlapping genes are conserved across microbial genomes. 
  • Protein fabrication automation. 
  • Protein isoforms encoded by the pX region of human T-cell leukemia/lymphotropic virus type I. 
  • Proteins of purified Epstein-Barr virus. 
  • Proteome analyses using accurate mass and elution time peptide tags with capillary LC time-of-flight mass spectrometry. 
  • Pseudomonas syringae pv. tomato DC3000 HopPtoM (CEL ORF3) is important for lesion formation but not growth in tomato and is secreted and translocated by the Hrp type III secretion system in a chaperone-dependent manner. 
  • RSK3/4 mediate resistance to PI3K pathway inhibitors in breast cancer. 
  • Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii. 
  • Resolving arthropod phylogeny: exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence. 
  • Retinal phenotypes in patients homozygous for the G1961E mutation in the ABCA4 gene. 
  • Rev-independent simian immunodeficiency virus strains are nonpathogenic in neonatal macaques. 
  • SCALEs: multiscale analysis of library enrichment. 
  • Sakacin P non-producing Lactobacillus sakei strains contain homologues of the sakacin P gene cluster. 
  • Sequence of a Brassica campestris myrosinase gene. 
  • Small but Mighty: Functional Peptides Encoded by Small ORFs in Plants. 
  • Structural determinants of insert retention of poliovirus expression vectors with recombinant IRES elements. 
  • Structure of the hypothetical protein PF0899 from Pyrococcus furiosus at 1.85 A resolution. 
  • The 5' non-coding region of the BCR/ABL oncogene augments its ability to stimulate the growth of immature lymphoid cells. 
  • The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. 
  • The DNA sequence and biological annotation of human chromosome 1. 
  • The HSF-like transcription factor TBF1 is a major molecular switch for plant growth-to-defense transition. 
  • The characterization of twenty sequenced human genomes. 
  • The complete genome sequence, organization and affinities of carrot red leaf virus. 
  • The intolerance to functional genetic variation of protein domains predicts the localization of pathogenic mutations within genes. 
  • The near-naked hairless (Hr(N)) mutation disrupts hair formation but is not due to a mutation in the Hairless coding region. 
  • The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI. 
  • The obligate intracellular pathogen Chlamydia trachomatis targets host lipid droplets. 
  • The reference genome sequence of Saccharomyces cerevisiae: then and now. 
  • The roles of the bacteriophage T4 r genes in lysis inhibition and fine-structure genetics: a new perspective. 
  • The unfolded protein response triggers selective mRNA release from the endoplasmic reticulum. 
  • Transcriptional origin of Kaposi's sarcoma-associated herpesvirus microRNAs. 
  • Vaccinia and cowpox viruses encode a novel secreted interleukin-1-binding protein. 
  • Visna virus encodes a post-transcriptional regulator of viral structural gene expression. 
  • Whole genome genetic-typing in yeast using high-density oligonucleotide arrays. 
  • Yeast microarrays for genome wide parallel genetic and gene expression analysis. 
  • Zebrafish Transcription Factor ORFeome for Gene Discovery and Regulatory Network Elucidation. 
  • mig-14 is a horizontally acquired, host-induced gene required for salmonella enterica lethal infection in the murine model of typhoid fever. 
  • uORF-mediated translation allows engineered plant disease resistance without fitness costs. 
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  Keywords of People

  • Liu, Yutao, Adjunct Assistant Professor in the Department of Medicine, Medicine, Medical Genetics
  • Soderling, Scott Haydn, George Barth Geller Distinguished Professor of Molecular Biology, Cell Biology