open reading frames

Summary

Summary: A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).

Top Publications

  1. ncbi Ribonucleoprotein particle formation is necessary but not sufficient for LINE-1 retrotransposition
    Deanna A Kulpa
    Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109 0618, USA
    Hum Mol Genet 14:3237-48. 2005
  2. pmc The RAST Server: rapid annotations using subsystems technology
    Ramy K Aziz
    Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA
    BMC Genomics 9:75. 2008
  3. pmc The transcriptional landscape of the yeast genome defined by RNA sequencing
    Ugrappa Nagalakshmi
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Science 320:1344-9. 2008
  4. pmc Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes
    Nicholas T Ingolia
    Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
    Cell 147:789-802. 2011
  5. ncbi Functional profiling of the Saccharomyces cerevisiae genome
    Guri Giaever
    Stanford Genome Technology Center, Stanford University, Palo Alto, California 94304, USA
    Nature 418:387-91. 2002
  6. ncbi Global analysis of protein expression in yeast
    Sina Ghaemmaghami
    Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California 94143 2240, USA
    Nature 425:737-41. 2003
  7. ncbi MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation
    Yvonne Tay
    Stem Cell and Developmental Biology, Genome Institute of Singapore, Agency for Science Technology and Research, 08 01, Genome, 60 Biopolis Street, Singapore 138672, Singapore
    Nature 455:1124-8. 2008
  8. pmc GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions
    J Besemer
    School of Biology and School of Mathematics, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA
    Nucleic Acids Res 29:2607-18. 2001
  9. ncbi A novel influenza A virus mitochondrial protein that induces cell death
    W Chen
    Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
    Nat Med 7:1306-12. 2001
  10. pmc Exome sequencing identifies the cause of a mendelian disorder
    Sarah B Ng
    Department of Genome Sciences, University of Washington, Seattle, Washington, USA
    Nat Genet 42:30-5. 2010

Detail Information

Publications328 found, 100 shown here

  1. ncbi Ribonucleoprotein particle formation is necessary but not sufficient for LINE-1 retrotransposition
    Deanna A Kulpa
    Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109 0618, USA
    Hum Mol Genet 14:3237-48. 2005
    ..Thus, these data indicate that RNP formation is important but not sufficient for L1 retrotransposition and suggest that ORF1p also may function at downstream steps in the L1 retrotransposition pathway...
  2. pmc The RAST Server: rapid annotations using subsystems technology
    Ramy K Aziz
    Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA
    BMC Genomics 9:75. 2008
    ..The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them...
  3. pmc The transcriptional landscape of the yeast genome defined by RNA sequencing
    Ugrappa Nagalakshmi
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Science 320:1344-9. 2008
    ..Alternative initiation codons and upstream open reading frames also were identified for many yeast genes...
  4. pmc Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes
    Nicholas T Ingolia
    Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
    Cell 147:789-802. 2011
    ..These include amino-terminal extensions and truncations and upstream open reading frames with regulatory potential, initiated at both AUG and non-AUG codons, whose translation changes after ..
  5. ncbi Functional profiling of the Saccharomyces cerevisiae genome
    Guri Giaever
    Stanford Genome Technology Center, Stanford University, Palo Alto, California 94304, USA
    Nature 418:387-91. 2002
    ..We systematically constructed a nearly complete collection of gene-deletion mutants (96% of annotated open reading frames, or ORFs) of the yeast Saccharomyces cerevisiae...
  6. ncbi Global analysis of protein expression in yeast
    Sina Ghaemmaghami
    Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California 94143 2240, USA
    Nature 425:737-41. 2003
    ..Many of these molecules, including essential proteins and most transcription factors, are present at levels that are not readily detectable by other proteomic techniques nor predictable by mRNA levels or codon bias measurements...
  7. ncbi MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation
    Yvonne Tay
    Stem Cell and Developmental Biology, Genome Institute of Singapore, Agency for Science Technology and Research, 08 01, Genome, 60 Biopolis Street, Singapore 138672, Singapore
    Nature 455:1124-8. 2008
    ....
  8. pmc GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions
    J Besemer
    School of Biology and School of Mathematics, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA
    Nucleic Acids Res 29:2607-18. 2001
    ..We have also observed that GeneMarkS detects prokaryotic genes, in terms of identifying open reading frames containing real genes, with an accuracy matching the level of the best currently used gene detection ..
  9. ncbi A novel influenza A virus mitochondrial protein that induces cell death
    W Chen
    Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
    Nat Med 7:1306-12. 2001
    ..We propose that PB1-F2 functions to kill host immune cells responding to influenza virus infection...
  10. pmc Exome sequencing identifies the cause of a mendelian disorder
    Sarah B Ng
    Department of Genome Sciences, University of Washington, Seattle, Washington, USA
    Nat Genet 42:30-5. 2010
    ..Exome sequencing of a small number of unrelated affected individuals is a powerful, efficient strategy for identifying the genes underlying rare mendelian disorders and will likely transform the genetic analysis of monogenic traits...
  11. pmc Proto-genes and de novo gene birth
    Anne Ruxandra Carvunis
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
    Nature 487:370-4. 2012
    ..the genome scale in Saccharomyces cerevisiae, we detect translation of hundreds of short species-specific open reading frames (ORFs) located in non-genic sequences...
  12. pmc Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans
    Sarah E Calvo
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 106:7507-12. 2009
    ..Together, our results suggest that uORFs influence the protein expression of thousands of mammalian genes and that variation in these elements can influence human phenotype and disease...
  13. pmc Reinitiation involving upstream ORFs regulates ATF4 mRNA translation in mammalian cells
    Krishna M Vattem
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Proc Natl Acad Sci U S A 101:11269-74. 2004
    ..These results suggest that the mechanism of translation reinitiation involving uORFs is conserved from yeast to mammals...
  14. pmc Human L1 retrotransposition: cis preference versus trans complementation
    W Wei
    Department of Human Genetics, The University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
    Mol Cell Biol 21:1429-39. 2001
    ..This mechanism could enable L1 to remain retrotransposition competent in the presence of the overwhelming number of nonfunctional L1s present in human DNA...
  15. pmc The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes
    Kim D Pruitt
    National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20894, USA
    Genome Res 19:1316-23. 2009
    ..The CCDS database thus centralizes the function of identifying well-supported, identically-annotated, protein-coding regions...
  16. ncbi Identification of herpesvirus-like DNA sequences in AIDS-associated Kaposi's sarcoma
    Y Chang
    Department of Pathology, College of Physicians and Surgeons, Columbia University, New York, NY 10032
    Science 266:1865-9. 1994
    ..These KS-associated herpesvirus-like (KSHV) sequences appear to define a new human herpesvirus...
  17. ncbi Community structure and metabolism through reconstruction of microbial genomes from the environment
    Gene W Tyson
    Department of Environmental Science, Policy and Management, University of California, Berkeley, California 94720, USA
    Nature 428:37-43. 2004
    ..Analysis of the gene complement for each organism revealed the pathways for carbon and nitrogen fixation and energy generation, and provided insights into survival strategies in an extreme environment...
  18. ncbi Many paths to many clones: a comparative look at high-throughput cloning methods
    Gerald Marsischky
    Institute of Proteomics, Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts 02115, USA
    Genome Res 14:2020-8. 2004
    ..Alternative approaches to creating clones involving mixing of cloning methods, including gap-repair cloning, are also explored...
  19. pmc The transcription unit architecture of the Escherichia coli genome
    Byung Kwan Cho
    Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
    Nat Biotechnol 27:1043-9. 2009
    ..by structural and functional elements, including promoters, transcription start and termination sites, open reading frames, regulatory noncoding regions, untranslated regions and transcription units...
  20. ncbi Comparison of DNA sequences with protein sequences
    W R Pearson
    Department of Biochemistry, University of Virginia, Charlottesville 22908, USA
    Genomics 46:24-36. 1997
    ..We found at least 9 new protein-coding genes in the three genomes and at least 35 genes with potentially incorrect boundaries...
  21. pmc Translation reinitiation at alternative open reading frames regulates gene expression in an integrated stress response
    Phoebe D Lu
    Department of Cell Biology, School of Medicine, New York University, New York, NY 10016, USA
    J Cell Biol 167:27-33. 2004
    ..These features are common to regulated translation of GCN4 in yeast. The metazoan ISR thus resembles the yeast general control response both in its target genes and its mechanistic details...
  22. pmc Complete genome sequence of Lactobacillus plantarum WCFS1
    Michiel Kleerebezem
    Wageningen Centre for Food Sciences, P O Box 557, 6700 AN Wageningen, The Netherlands
    Proc Natl Acad Sci U S A 100:1990-5. 2003
    ..These findings suggest that these genes, which provide an important part of the interaction of L. plantarum with its environment, form a lifestyle adaptation region in the chromosome...
  23. ncbi Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast
    Lyris M F de Godoy
    Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Nature 455:1251-4. 2008
    ..Systems-wide, precise quantification directly at the protein level opens up new perspectives in post-genomics and systems biology...
  24. ncbi Role of 5'- and 3'-untranslated regions of mRNAs in human diseases
    Sangeeta Chatterjee
    Cell and Molecular Biology Laboratory, Department of Biotechnology, University of Pune, Pune 411007, India
    Biol Cell 101:251-62. 2009
    ..The highly structured UTRs, along with features such as GC-richness, upstream open reading frames and internal ribosome entry sites, significantly influence the rate of translation of mRNAs...
  25. pmc Peptidomic discovery of short open reading frame-encoded peptides in human cells
    Sarah A Slavoff
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
    Nat Chem Biol 9:59-64. 2013
    ..In addition, coding sORFs are present in a small fraction (8 out of 1,866) of long intergenic noncoding RNAs. Together, these results provide strong evidence that the human proteome is more complex than previously appreciated...
  26. pmc Upstream open reading frames: molecular switches in (patho)physiology
    Klaus Wethmar
    Max Delbrueck Center for Molecular Medicine, Berlin, Germany
    Bioessays 32:885-93. 2010
    Conserved upstream open reading frames (uORFs) are found within many eukaryotic transcripts and are known to regulate protein translation...
  27. pmc Biological basis for restriction of microRNA targets to the 3' untranslated region in mammalian mRNAs
    Shuo Gu
    The Center for Clinical Science Research, Room 2105, 269 Campus Drive, Stanford, California 94305 5164, USA
    Nat Struct Mol Biol 16:144-50. 2009
    ....
  28. ncbi hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes
    Philippe Lamesch
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Genomics 89:307-15. 2007
    Complete sets of cloned protein-encoding open reading frames (ORFs), or ORFeomes, are essential tools for large-scale proteomics and systems biology studies. Here we describe human ORFeome version 3.1 (hORFeome v3...
  29. pmc Coding potential of laboratory and clinical strains of human cytomegalovirus
    Eain Murphy
    Department of Molecular Biology, Princeton University, Princeton, NJ 80544, USA
    Proc Natl Acad Sci U S A 100:14976-81. 2003
    ..Multiple sequence alignments revealed substantial variation in the amino acid sequences encoded by many of the conserved ORFs...
  30. ncbi ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe
    Akihisa Matsuyama
    Chemical Genetics Laboratory, RIKEN, Wako, Saitama 351 0198, Japan
    Nat Biotechnol 24:841-7. 2006
    Cloning of the entire set of an organism's protein-coding open reading frames (ORFs), or 'ORFeome', is a means of connecting the genome to downstream 'omics' applications...
  31. pmc Differentiating protein-coding and noncoding RNA: challenges and ambiguities
    Marcel E Dinger
    ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
    PLoS Comput Biol 4:e1000176. 2008
    ..Therefore, the functionality of any transcript at the RNA level should not be discounted...
  32. ncbi Gene-specific regulation by general translation factors
    Thomas E Dever
    Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
    Cell 108:545-56. 2002
    ..Recent studies have enhanced our understanding of the translation initiation process and helped elucidate how modifications of the general translational machinery regulate gene-specific protein production...
  33. pmc Whole-genome comparison reveals novel genetic elements that characterize the genome of industrial strains of Saccharomyces cerevisiae
    Anthony R Borneman
    The Australian Wine Research Institute, Adelaide, Australia
    PLoS Genet 7:e1001287. 2011
    ....
  34. pmc Conserved microRNA targeting in Drosophila is as widespread in coding regions as in 3'UTRs
    Michael Schnall-Levin
    Department of Mathematics, Massachusetts Institute of Technology, Cambridge, 02139, USA
    Proc Natl Acad Sci U S A 107:15751-6. 2010
    ..Further evidence suggests that our results extend to mammals, but that the extent of ORF and 5'UTR targeting relative to 3'UTR targeting may be greater in Drosophila...
  35. pmc Chromatin- and transcription-related factors repress transcription from within coding regions throughout the Saccharomyces cerevisiae genome
    Vanessa Cheung
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
    PLoS Biol 6:e277. 2008
    ....
  36. pmc Endogenous non-retroviral RNA virus elements in mammalian genomes
    Masayuki Horie
    Department of Virology, Research Institute for Microbial Diseases BIKEN, Osaka University, Osaka 565 0871, Japan
    Nature 463:84-7. 2010
    ....
  37. pmc Phosphorylation of eIF2 facilitates ribosomal bypass of an inhibitory upstream ORF to enhance CHOP translation
    Lakshmi Reddy Palam
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
    J Biol Chem 286:10939-49. 2011
    ..This new mechanism of translational control explains how expression of CHOP and the fate of cells are tightly linked to the levels of phosphorylated eIF2 and stress damage...
  38. ncbi Cis-preferential LINE-1 reverse transcriptase activity in ribonucleoprotein particles
    Deanna A Kulpa
    Department of Human Genetics 1241 E Catherine St, University of Michigan Medical School, Ann Arbor, Michigan 48109 0618, USA
    Nat Struct Mol Biol 13:655-60. 2006
    ..We further demonstrate that ORF2p preferentially uses its encoding RNA as a template for reverse transcription. Thus, our data provide the first biochemical evidence supporting the cis-preferential action of the L1 reverse transcriptase...
  39. pmc Cytoplasmic male sterility of rice with boro II cytoplasm is caused by a cytotoxic peptide and is restored by two related PPR motif genes via distinct modes of mRNA silencing
    Zhonghua Wang
    Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Province, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
    Plant Cell 18:676-87. 2006
    ..In the presence of both restorers, RF1A was epistatic over RF1B in the mRNA processing. We have also shown that RF1A plays an additional role in promoting the editing of atp6 mRNAs, independent of its cleavage function...
  40. ncbi The Listeria transcriptional landscape from saprophytism to virulence
    Alejandro Toledo-Arana
    Institut Pasteur, Unité des Interactions Bactéries Cellules, F 75015 Paris, France
    Nature 459:950-6. 2009
    ..Together, our data unravel successive and coordinated global transcriptional changes during infection and point to previously unknown regulatory mechanisms in bacteria...
  41. pmc The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum
    Zbynek Bozdech
    Department of Biochemistry and Biophysics, University of California, San Francisco, USA
    PLoS Biol 1:E5. 2003
    ..falciparum and provide a resource for the identification of new chemotherapeutic and vaccine candidates...
  42. ncbi The 1.2-megabase genome sequence of Mimivirus
    Didier Raoult
    Unite des Rickettsies, Faculte de Medecine, CNRS UMR6020, Universite de la Mediterranee, 13385 Marseille Cedex 05, France
    Science 306:1344-50. 2004
    ..We now present its 1,181,404-base pair genome sequence, consisting of 1262 putative open reading frames, 10% of which exhibit a similarity to proteins of known functions...
  43. pmc De novo origin of human protein-coding genes
    Dong Dong Wu
    State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
    PLoS Genet 7:e1002379. 2011
    ..Our results are inconsistent with the traditional view that the de novo origin of new genes is very rare, thus there should be greater appreciation of the importance of the de novo origination of genes...
  44. pmc Experimental annotation of the human pathogen Candida albicans coding and noncoding transcribed regions using high-resolution tiling arrays
    Adnane Sellam
    Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount, Montreal, Quebec, H4P 2R2, Canada
    Genome Biol 11:R71. 2010
    ..Compared to other model organisms and despite the clinical relevance of the pathogenic yeast Candida albicans, no comprehensive analysis has been done to provide experimental support of its in silico-based genome annotation...
  45. ncbi Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics
    David N Cooper
    Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, United Kingdom
    Hum Mutat 31:631-55. 2010
    ....
  46. ncbi Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription
    Michael J Carrozza
    Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
    Cell 123:581-92. 2005
    ..Mutants of RCO1 and EAF3 exhibited increased acetylation in the FLO8 and STE11 open reading frames (ORFs) and the appearance of aberrant transcripts initiating within the body of these ORFs...
  47. ncbi A highly active synthetic mammalian retrotransposon
    Jeffrey S Han
    Department of Molecular Biology and Genetics and High Throughput Biology Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Nature 429:314-8. 2004
    ..Transcription through L1 open reading frames is inefficient owing to an elongation defect, inhibiting the robust expression of L1 RNA and proteins, the ..
  48. ncbi Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes
    Jeffrey S Han
    Department of Molecular Biology and Genetics and High Throughput Biology Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Nature 429:268-74. 2004
    ..Bioinformatic data are consistent with the hypothesis that L1 can serve as an evolutionary fine-tuner of the human transcriptome...
  49. pmc Cytoplasmic ribonucleoprotein complexes containing human LINE-1 protein and RNA
    H Hohjoh
    Laboratory of Biochemistry, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    EMBO J 15:630-9. 1996
    ....
  50. pmc Widespread selection for local RNA secondary structure in coding regions of bacterial genes
    Luba Katz
    Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Genome Res 13:2042-51. 2003
    ..These results are interpreted in terms of possible roles of RNA structures in RNA processing, regulation of mRNA stability, and translational control...
  51. pmc Identification of small RNAs in Mycobacterium tuberculosis
    Kristine B Arnvig
    Division of Mycobacterial Research, MRC National Institute for Medical Research, London NW7 1AA, UK
    Mol Microbiol 73:397-408. 2009
    ..we have identified nine putative sRNA molecules, including cis-encoded antisense transcripts from within open reading frames and trans-encoded transcripts from intergenic regions...
  52. ncbi North American and European porcine reproductive and respiratory syndrome viruses differ in non-structural protein coding regions
    R Allende
    Department of Veterinary and Biomedical Sciences, University of Nebraska Lincoln, 68583 0905, USA
    J Gen Virol 80:307-15. 1999
    ..The 3' NCR (150 nucleotides) was 76% identical between isolates. These genomic differences confirm the presence of distinct North American and European PRRSV genotypes...
  53. pmc Discovery and annotation of small proteins using genomics, proteomics, and computational approaches
    Xiaohan Yang
    Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Genome Res 21:634-41. 2011
    Small proteins (10-200 amino acids [aa] in length) encoded by short open reading frames (sORF) play important regulatory roles in various biological processes, including tumor progression, stress response, flowering, and hormone ..
  54. ncbi Conserved regulation of cardiac calcium uptake by peptides encoded in small open reading frames
    Emile G Magny
    School of Life Sciences, University of Sussex, Falmer, Brighton, East Sussex BN1 9QG, UK
    Science 341:1116-20. 2013
    Small open reading frames (smORFs) are short DNA sequences that are able to encode small peptides of less than 100 amino acids. Study of these elements has been neglected despite thousands existing in our genomes...
  55. ncbi A perspective on mammalian upstream open reading frame function
    Joanna Somers
    Medical Research Council Toxicology Unit, Leicester, United Kingdom
    Int J Biochem Cell Biol 45:1690-700. 2013
    ..regulatory RNA elements in mammalian transcripts (present in approximately 40% of all mRNAs) are upstream open reading frames (uORFs). However, despite the prevalence of these RNA elements how they function is not well understood...
  56. pmc Discovery of the first insect nidovirus, a missing evolutionary link in the emergence of the largest RNA virus genomes
    Phan Thi Nga
    Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
    PLoS Pathog 7:e1002215. 2011
    ..is 20,192 nt and has a nidovirus-like polycistronic organization including two large, partially overlapping open reading frames (ORF) 1a and 1b followed by several smaller 3'-proximal ORFs...
  57. pmc Putatively noncoding transcripts show extensive association with ribosomes
    Benjamin A Wilson
    Department of Ecology and Evolutionary Biology, University of Arizona, USA
    Genome Biol Evol 3:1245-52. 2011
    ..Our analysis is also proof of principle of the utility of ribosomal profiling data for the purpose of gene annotation...
  58. ncbi PEDV ORF3 encodes an ion channel protein and regulates virus production
    Kai Wang
    Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    FEBS Lett 586:384-91. 2012
    ..Interestingly, the ORF3 gene from an attenuated PEDV encodes a truncated protein with 49 nucleotide deletions, which lacks the ion channel activity...
  59. pmc A public genome-scale lentiviral expression library of human ORFs
    Xiaoping Yang
    RNA interference RNAi Platform, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    Nat Methods 8:659-61. 2011
    ..Using this ORFeome resource, we created a genome-scale expression collection in a lentiviral vector, thereby enabling both targeted experiments and high-throughput screens in diverse cell types...
  60. pmc Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library
    Jean François Rual
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 14:2162-8. 2004
    ..The versatility inherent to the Gateway system suggests that additional HT-RNAi libraries can now be readily generated to perform gene knockdowns under various conditions, increasing the possibilities for phenome mapping in C. elegans...
  61. pmc Hundreds of putatively functional small open reading frames in Drosophila
    Emmanuel Ladoukakis
    School of Life Sciences, University of Sussex, Falmer, Brighton, UK
    Genome Biol 12:R118. 2011
    ..Functional small open reading frames (smORFs) are known to exist in several organisms...
  62. pmc Genomic and proteomic characterization of the broad-host-range Salmonella phage PVP-SE1: creation of a new phage genus
    Silvio B Santos
    Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4700 057 Braga, Portugal
    J Virol 85:11265-73. 2011
    ..Its G+C content, 45.6 mol%, is lower than that of its hosts (50 to 54 mol%). We found a total of 244 open reading frames (ORFs), representing 91.6% of the coding capacity of the genome...
  63. pmc Microbial gene identification using interpolated Markov models
    S L Salzberg
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 26:544-8. 1998
    ..As a result, GLIMMER is more flexible and more powerful than fixed-order Markov methods, which have previously been the primary content-based technique for finding genes in microbial DNA...
  64. ncbi Angiosperm mitochondrial genomes and mutations
    Tomohiko Kubo
    Laboratory of Genetic Engineering, Research Faculty of Agriculture, Hokkaido University, N 9, W 9, Kita ku, Sapporo 060 8589, Japan
    Mitochondrion 8:5-14. 2008
    ..The involvement of nuclear genes in mitochondrial genome stability and organization is currently being revealed through the analysis of mutants...
  65. pmc PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions
    Michael F Lin
    Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street 32 D510, Cambridge, MA 02139, USA
    Bioinformatics 27:i275-82. 2011
    ....
  66. pmc Comparative genomics of protoploid Saccharomycetaceae
    Jean Luc Souciet
    Universite de Strasbourg, CNRS UMR, France
    Genome Res 19:1696-709. 2009
    ..Ancient, conserved paralogs as well as novel, lineage-specific paralogs were identified...
  67. pmc Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates
    Hameed Khan
    Department of Biology, Queens College, The City University of New York, Flushing, New York 11367, USA
    Genome Res 16:78-87. 2006
    ..The correlation between the high activity of L1 families and adaptive evolution could result from the coevolution of L1 and a host-encoded repressor of L1 activity...
  68. pmc Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence
    Ozan Gundogdu
    Pathogen Molecular Department, London School of Hygiene and Tropical Medicine, UK
    BMC Genomics 8:162. 2007
    ..We now describe the complete re-annotation and re-analysis of the C. jejuni NCTC11168 genome using current database information, novel tools and annotation techniques not used during the original annotation...
  69. pmc CRD-BP protects the coding region of betaTrCP1 mRNA from miR-183-mediated degradation
    Irina Elcheva
    Department of Dermatology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
    Mol Cell 35:240-6. 2009
    ..Here we demonstrate that CRD-BP prevents degradation of betaTrCP1 mRNA by attenuating its miR-183-dependent interaction with Ago2...
  70. ncbi LINE-1 retrotransposition requires the nucleic acid chaperone activity of the ORF1 protein
    Sandra L Martin
    Department of Cell and Developmental Biology, University of Colorado School of Medicine, 12801 E 17th Ave, Aurora, CO 80045, USA
    J Mol Biol 348:549-61. 2005
    ..L1 encodes two essential polypeptides for retrotransposition, the products of its two open reading frames, ORF1 and ORF2...
  71. pmc USER fusion: a rapid and efficient method for simultaneous fusion and cloning of multiple PCR products
    Fernando Geu-Flores
    Plant Biochemistry Laboratory, Institute of Plant Biology, Faculty of Life Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Denmark
    Nucleic Acids Res 35:e55. 2007
    ..We expect this method to replace overlapping PCR and the use of type IIS restriction enzymes in many of their applications...
  72. pmc LINE-1 ORF1 protein localizes in stress granules with other RNA-binding proteins, including components of RNA interference RNA-induced silencing complex
    John L Goodier
    Dept of Genetics, University of Pennsylvania School of Medicine, Rm 515 CRB, 415 Curie Blvd, Philadelphia, PA 19104, USA
    Mol Cell Biol 27:6469-83. 2007
    ..We suggest that targeting ORF1p, and possibly the L1 RNP, to stress granules is a mechanism for controlling retrotransposition and its associated genetic and cellular damage...
  73. pmc Transcription profiling of Candida albicans cells undergoing the yeast-to-hyphal transition
    Andre Nantel
    Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, Canada H4P 2R2
    Mol Biol Cell 13:3452-65. 2002
    ..Thus Efg1p and Cph1p are needed for the activation of the transcriptional program that is induced by the presence of serum...
  74. ncbi The complete sequence of the mitochondrial genome of Saccharomyces cerevisiae
    F Foury
    Unite de Biochimie Physiologique, Louvain la Neuve, Belgium
    FEBS Lett 440:325-31. 1998
    ..We give a list of seven small hypothetical open reading frames (ORFs)...
  75. pmc Broadly targeted human cytomegalovirus-specific CD4+ and CD8+ T cells dominate the memory compartments of exposed subjects
    Andrew W Sylwester
    Vaccine and Gene Therapy Institute, Department of Pathology, Oregon Health and Science University, Beaverton, 97006, USA
    J Exp Med 202:673-85. 2005
    ..Here, using cytokine flow cytometry and 13,687 overlapping 15mer peptides comprising 213 HCMV open reading frames (ORFs), we found that 151 HCMV ORFs were immunogenic for CD4(+) and/or CD8(+) T cells, and that ORF ..
  76. pmc Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes
    Michael F Lin
    Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Genome Res 21:1916-28. 2011
    ..Our results show that overlapping functional elements are common in mammalian genes, despite the vast genomic landscape...
  77. pmc An upstream open reading frame regulates translation of GADD34 during cellular stresses that induce eIF2alpha phosphorylation
    Yun Young Lee
    Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
    J Biol Chem 284:6661-73. 2009
    ..The human GADD34 5'UTR contains two non-overlapping upstream open reading frames (uORFs), whereas the mouse version contains two overlapping and out of frame uORFs...
  78. pmc Linking cell cycle to histone modifications: SBF and H2B monoubiquitination machinery and cell-cycle regulation of H3K79 dimethylation
    Julia M Schulze
    Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, BC, Canada
    Mol Cell 35:626-41. 2009
    ....
  79. ncbi Exploring the metabolic and genetic control of gene expression on a genomic scale
    J L DeRisi
    Department of Biochemistry, Stanford University School of Medicine, Howard Hughes Medical Institute, Stanford, CA 94305 5428, USA
    Science 278:680-6. 1997
    ..These results demonstrate the feasibility and utility of this approach to genomewide exploration of gene expression patterns...
  80. pmc Identification of proteins in human cytomegalovirus (HCMV) particles: the HCMV proteome
    Susan M Varnum
    Department of Molecular Microbiology and Immunology, Oregon Health Sciences University, Portland, OR 97201, USA
    J Virol 78:10960-6. 2004
    ..In this study, we identified 71 HCMV-encoded proteins that included 12 proteins encoded by known viral open reading frames (ORFs) previously not associated with virions and 12 proteins from novel viral ORFs...
  81. ncbi Bacterial contingency loci: the role of simple sequence DNA repeats in bacterial adaptation
    Richard Moxon
    Oxford University Department of Paediatrics, Molecular Infectious Diseases Group, Weatherall Institute of Molecular Medicine Oxford, United Kingdom
    Annu Rev Genet 40:307-33. 2006
    ..These SSRs are located within the reading frame or in the promoter of a subset of genes, often termed contingency loci, whose functions are usually involved in direct interactions with host structures...
  82. pmc Nucleic acid chaperone activity of the ORF1 protein from the mouse LINE-1 retrotransposon
    S L Martin
    Department of Cellular and Structural Biology, University of Colorado School of Medicine, Denver, Colorado 80262, USA
    Mol Cell Biol 21:467-75. 2001
    ..These findings suggest a role for L1 ORF1p in mediating nucleic acid strand transfer steps during L1 reverse transcription...
  83. ncbi A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes
    Kevin C Miranda
    Bioinformatics and Pattern Discovery Group, IBM Thomas J Watson Research Center, Yorktown Heights, P O Box 218, NY 10598, USA
    Cell 126:1203-17. 2006
    ..We also extended the method's key idea to a low-error microRNA-precursor-discovery scheme; our studies suggest that the number of microRNA precursors in mammalian genomes likely ranges in the tens of thousands...
  84. pmc Metagenomic analysis of the human distal gut microbiome
    Steven R Gill
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 312:1355-9. 2006
    ..Thus, humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes...
  85. pmc Molecular correlates of host specialization in Staphylococcus aureus
    Lisa Herron-Olson
    Department of Microbiology, Veterinary Pathobiology and Biomedical Genomics Center, University of Minnesota, Saint Paul, Minnesota, United States of America
    PLoS ONE 2:e1120. 2007
    ..aureus clonal groups associated with human and ruminant infection. However, the molecular basis of host specialization in S. aureus is not understood...
  86. pmc The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages
    Tony Kwan
    Targanta Therapeutics, 7170 Frederick Banting, Second Floor, Ville Saint Laurent, QC, Canada H4S 2A1
    Proc Natl Acad Sci U S A 102:5174-9. 2005
    ..These phage genomes offer an exciting opportunity to discern molecular mechanisms of phage evolution and diversity...
  87. pmc MetaGene: prokaryotic gene finding from environmental genome shotgun sequences
    Hideki Noguchi
    Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277 8562, Japan
    Nucleic Acids Res 34:5623-30. 2006
    ..Applied to the Sargasso Sea dataset, MetaGene predicted almost all of the annotated genes and a notable number of novel genes. MetaGene can be applied to wide variety of metagenomic projects and expands the utility of metagenomics...
  88. pmc Mitochondrial genome sequencing helps show the evolutionary mechanism of mitochondrial genome formation in Brassica
    Shengxin Chang
    State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, PR China
    BMC Genomics 12:497. 2011
    ..We analyzed the evolutionary relationships of Brassica mitotypes by sequencing...
  89. pmc A high-throughput platform for lentiviral overexpression screening of the human ORFeome
    Dubravka Skalamera
    University of Queensland Diamantina Institute, Princess Alexandra Hospital, Brisbane, Queensland, Australia
    PLoS ONE 6:e20057. 2011
    ..Protein-coding human open reading frames (ORFs) from the Mammalian Gene Collection were transferred into lentiviral expression vector using the ..
  90. ncbi Proteome survey reveals modularity of the yeast cell machinery
    Anne Claude Gavin
    Cellzome AG, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nature 440:631-6. 2006
    ..Through systematic tagging of open reading frames (ORFs), the majority of complexes were purified several times, suggesting screen saturation...
  91. pmc Whole-genome sequencing of sake yeast Saccharomyces cerevisiae Kyokai no. 7
    Takeshi Akao
    National Research Institute of Brewing, Higashi Hiroshima, Japan
    DNA Res 18:423-34. 2011
    ..Sequence comparisons suggest that these gene conversions were caused by cDNA-mediated recombination of Ty elements. The present study advances our understanding of the functional and evolutionary genomics of the sake yeast...
  92. pmc Genetic diagnosis by whole exome capture and massively parallel DNA sequencing
    Murim Choi
    Department of Genetics, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA
    Proc Natl Acad Sci U S A 106:19096-101. 2009
    ..These results demonstrate the clinical utility of whole-exome sequencing and have implications for disease gene discovery and clinical diagnosis...
  93. pmc A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes
    Diego Cortez
    Institut Pasteur, Departement de Microbiologie, Unite de Biologie Moleculaire du Gene chez les Extremophiles, Paris, France
    Genome Biol 10:R65. 2009
    ..Moreover, it is not known whether IEs play an important role in the origin of ORFans (open reading frames without matches in current sequence databases), whose proportion remains stable despite the growing number ..
  94. ncbi De novo origin of new genes with introns in Plasmodium vivax
    Zefeng Yang
    Department of Biology, East Carolina University, Greenville, NC 27858, USA
    FEBS Lett 585:641-4. 2011
    ..We discuss the potential mechanisms for intron formation in these genes and propose that intronization be considered in the formation of de novo originated genes...
  95. ncbi Virus-encoded proteinases and proteolytic processing in the Nidovirales
    J Ziebuhr
    Institute of Virology and Immunology, University of Wurzburg, Versbacher Str 7, 97078 Wurzburg, Germany
    J Gen Virol 81:853-79. 2000
  96. ncbi Plant upstream ORFs can trigger nonsense-mediated mRNA decay in a size-dependent manner
    Tünde Nyikó
    Agricultural Biotechnology Center, Szent Györgyi 4, 2100 Gödöllő, Hungary
    Plant Mol Biol 71:367-78. 2009
    ....
  97. pmc Overlapping genes produce proteins with unusual sequence properties and offer insight into de novo protein creation
    Corinne Rancurel
    Architecture et Fonction des Macromolecules Biologiques, Case 932, Campus de Luminy, 13288 Marseille Cedex 9, France
    J Virol 83:10719-36. 2009
    ....
  98. ncbi Characterization of mammalian selenoproteomes
    Gregory V Kryukov
    Department of Biochemistry, University of Nebraska, Lincoln, NE 68588 0664, USA
    Science 300:1439-43. 2003
    ..The human selenoproteome consists of 25 selenoproteins...
  99. pmc The impact of the nucleosome code on protein-coding sequence evolution in yeast
    Tobias Warnecke
    Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
    PLoS Genet 4:e1000250. 2008
    ..As the intimate association of histones and DNA is a universal characteristic of genic sequence in eukaryotes, selection on coding sequence composition imposed by nucleosome positioning should be phylogenetically widespread...
  100. pmc Phosphorylated Pol II CTD recruits multiple HDACs, including Rpd3C(S), for methylation-dependent deacetylation of ORF nucleosomes
    Chhabi K Govind
    Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
    Mol Cell 39:234-46. 2010
    ..A strong correlation between increased acetylation and lower histone occupancy in HDA mutants implies that histone acetylation is important for nucleosome eviction...
  101. pmc The genome sequence of Mycoplasma hyopneumoniae strain 232, the agent of swine mycoplasmosis
    F Chris Minion
    Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA
    J Bacteriol 186:7123-33. 2004
    ..hyopneumoniae contains few genes with tandem repeat sequences that could be involved in phase switching or antigenic variation. Thus, it is not clear how M. hyopneumoniae evades the immune response and establishes a chronic infection...

Research Grants65

  1. IN VIVO INDUCED ANTIGEN TECHNOLOGY OF AA IN LJP
    Martin Handfield; Fiscal Year: 2003
    ..the cloned DNA inserts in reactive clones will be analyzed for IPTG inducibility and sequenced to determine open reading frames likely to be responsible for expression of the in vivo-induced antigens...
  2. Defining the functions of uncharacterized genes in priority pathogens
    Sean Crosson; Fiscal Year: 2013
    ..immediate goal of this project is to define the cellular and biochemical functions of 57 uncharacterized open reading frames (ORFs), hypothetical proteins, and small non-coding RNAs in B. abortus...
  3. The Roles of Conserved outer-membrane proteins in SFG rickettsia pathogenesis
    Juan J Martinez; Fiscal Year: 2013
    ..degenerate or split, at least 4 genes, sca0 (rompA), sca1, sca2, and sca5 (rompB) are present as complete open reading frames in R. conorii and many other SFG rickettsia...
  4. Function of mRNA Editing in Trypanosomes
    Stephen L Hajduk; Fiscal Year: 2010
    ..Alternatively edited mRNAs, creating novel open reading frames, were found for each of these genes...
  5. Development of a novel vaccine for protection against gammaherpesvirus infection
    Blossom A Damania; Fiscal Year: 2010
    ..RRV was originally isolated from rhesus macaques, is very closely related to KSHV and most of the eighty open reading frames (ORFs) of RRV share high homology with the corresponding ORFs of KSHV...
  6. Varicella-Zoster Virus: T Cell/Skin Tropism &Immunity
    Ann Arvin; Fiscal Year: 2013
    ..The VZV genome has at least 71 known or predicted open reading frames (ORFs) but understanding how these gene products function in virulence is difficult because VZV is highly ..
  7. DNA-Binding Protein Discovery by the Combinatorial Method REPSA
    Michael van Dyke; Fiscal Year: 2013
    ..For example, while the bacteria Escherichia coli strain K12 has 4364 open reading frames, only about half of these genes have been well characterized by genetic, biochemical or molecular ..
  8. The Viral Life Cycle of Human Endogenous Retrovirus Type K
    Derek Dube; Fiscal Year: 2013
    ..Due to their recent integration, while most HERV genomes have been mutated and deleted to render their open reading frames non-functional, many of the more than 91 HERV-K genomes present maintain intact open reading frames for ..
  9. Pathogenic mechanisms of non-01/non-0139 V. cholerae
    Michelle Dziejman; Fiscal Year: 2012
    ..genome sequencing of a clinically isolated non-O1/non-O139 strain, AM-19226, has revealed the presence of open reading frames (ORFs) having significant similarity to genes encoding a Type Three Secretion System (TTSS)...
  10. Effect of chromatin remodelers/modifiers on HIV-1 Tat activated transcription
    Fatah Kashanchi; Fiscal Year: 2010
    ..and Tat-p/CAF complexes in chromatin marking and transcription elongation on the HIV-1 promoter and open reading frames in cell lines and PBMC infected cells? (II) What is the role of the Tat- SWI/SNF (Tat-PBAF) complex in ..
  11. Molecular bssis of mef-mediated antibiotic resistance in Streptococcus pneumoniae
    David S Stephens; Fiscal Year: 2010
    ..At least four sites of insertion of mega have been identified. In addition to mefE, four other open reading frames (ORFs) organized into two convergent clusters are found in mega...
  12. Molecular mechanism of omega-3 response
    JAMES T BRENNA; Fiscal Year: 2013
    ..a) Determine the promoters and full length open reading frames (ORFs) of FADS CS and AT with RNA-Seq using human liver...
  13. Generation and validation of a comprehensive human disease mutant ORF resource
    Luke J Whitesell; Fiscal Year: 2010
    ..b>Open Reading Frames (ORFs) encoding ~10,000 different disease causing alleles will be generated using a recombinational cloning ..
  14. The Significance of Polymorphic Endogenous Retroviruses to Human Mental Health
    JULIA HALO WILDSCHUTTE; Fiscal Year: 2010
    ..Although most are defective, HML-2 proviruses with intact open reading frames in some or all genes exist...
  15. DNA REPAIR AND ANTITOPOISOMERASE DRUG EFFECTS
    John L Nitiss; Fiscal Year: 2010
    ..Successful utilization of these tools, notably a set of strains deleting all non-essential open reading frames has required us to develop new approaches to efficiently enhance the sensitivity of yeast cells to drugs ..
  16. ERV3 Control of Human Placentation
    NEAL STEWART ROTE; Fiscal Year: 2013
    ..A small number of endogenous retrovirus (ERV) integration sites retained isolated transcriptionally active open reading frames so that a variety of gag (matrix and capsid), pol (polymerase and other enzymes), and env (envelope) ..
  17. REGULATION OF CHOLESTEROL HOMEOSTASIS BY NONCODING RNAS
    Daniel S Ory; Fiscal Year: 2013
    ..The goal of this proposal is to study how these genes modulate the distribution and level of cholesterol in cells. The proposed studies may identify new targets for drug development for lowering cholesterol in disease states. ..
  18. Ribosome Profiling in Plasmodium falciparum
    Marilyn Parsons; Fiscal Year: 2013
    ..genome annotation by determining whether proteins are translated from mRNAs corresponding to individual open reading frames, particularly those annotated as hypothetical proteins and those encoded by non-canonical protein-coding ..
  19. Rhesus HHV-8 homologue in AIDS-related malignancies
    Scott W Wong; Fiscal Year: 2013
    ..needed to identify viral determinants of pathogenesis and how these specific determinants, either viral open reading frames (ORFs) or other viral-encoded macromolecules are involved in HHV8-mediated pathogenesis...
  20. Guide RNA Binding Complex
    RUSLAN AFASIZHEV; Fiscal Year: 2013
    ..encrypted: an extensive post-transcriptional uridine insertion/deletion RNA editing is required to produce open reading frames. The cascade of editing reactions is catalyzed by enzymes embedded into the ~15-subunit RNA editing core ..
  21. The Drosophila Gene Tagging Project: Transgenes with Swappable Protein Tags
    ROGER ALLEN HOSKINS; Fiscal Year: 2013
    ..One of the most useful applications of P[acman] is to incorporate tags within open reading frames of genes to express fusion proteins...
  22. Analysis of an orchestrated cell death mediated by Vibrio parahaemolytics T3SS1
    Kim Orth; Fiscal Year: 2013
    ..The effectors on the first pathogenicity island have been identified as open reading frames with no obvious homology to any known protein. Recently, we have demonstrated that the V...
  23. Evaluating the efficiency and specificity of stop codon suppression therapy
    Michael T Howard; Fiscal Year: 2013
    ..These include cellular transcripts with regulatory short 5'UTR open reading frames or long 3'UTRs, selenoprotein mRNAs, and transcripts encoded by transposable elements or non-..
  24. Creating Platforms for the Proteomics and Membrane Proteins
    PAUL CREMER; Fiscal Year: 2012
    ..PUBLIC HEALTH RELEVANCE: It is generally believed that 15 to 30% of open reading frames in the genomes of most organisms encode membrane proteins...
  25. Universal Clone Resources for Drosophila Proteomics
    Susan E Celniker; Fiscal Year: 2013
    ..these collections are and will continue to be the primary source of high quality Drosophila melanogaster open reading frames (ORFs) that are easily transferred into a number of different expression vectors...
  26. The mechanisms of eukaryotic translation termination and ribosomal recycling
    Tatyana V Pestova; Fiscal Year: 2013
    ..This mostly occurs after translation of short open reading frames (ORFs), whereas reinitiation after long ORFs is rare and appears to be limited to several virus families...
  27. Ribosome profiling of Trypanosoma brucei
    Marilyn Parsons; Fiscal Year: 2012
    ..abstract_text> ..
  28. Comprehensive transcriptome analysis for Porphyromonas gingivalis
    Tsute Chen; Fiscal Year: 2009
    ..proven invaluable to the research communities, these microarrays were designed based on computer-predicted open reading frames (ORFs) only, and are limited to gene expression studies only in the protein-coding regions...
  29. Ribosomal scanning and initiation codon selection
    Tatyana V Pestova; Fiscal Year: 2013
    ..recycled 40S subunits back to the 5'-end of the same mRNA, and reinitiation after translation of short open reading frames. PUBLIC HEALTH RELEVANCE: Protein synthesis is of central importance in cell metabolism, and its complex ..
  30. Chlamydia trachomatis proteomics
    Guangming Zhong; Fiscal Year: 2013
    ..Zhong's lab expressed all C. trachomatis open reading frames (ORFs) as soluble fusion proteins and developed a high quality whole genome scale proteome array in the ..
  31. How Genetic Variation in Protein Kinases Affects Drug Response
    EDWARD E HARLOW; Fiscal Year: 2010
    ..Our first goal will be to generate a resource of ~3000 open reading frames capturing variants of 535 human protein kinases...
  32. Viral Modulation of Genetic Stability
    Matthew D Weitzman; Fiscal Year: 2013
    ..that result in Ad genomes being joined into concatemers during infection with viruses deleted of the E4 open reading frames. Concatemerization requires host DNA repair proteins, including the Mre11/Rad50/Nbs1 complex (MRN)...
  33. Protein and Peptide Derived Cofactors
    Judith P Klinman; Fiscal Year: 2013
    ..least well understood among the pathways that lead to enzymatic cofactors, and each of the five conserved open reading frames that encode for essential proteins in PQQ production is being studied...
  34. MHC-BOUND, SIV-DERIVED, CTL AND HTL EPITOPES
    David I Watkins; Fiscal Year: 2013
    ..Finally, we recently discovered that there are several MHC class l-restricted epitopes in SIV cryptic Open Reading Frames (cORFs)...
  35. MHC-BOUND, SIV-DERIVED, CTL AND HTL EPITOPES
    David I Watkins; Fiscal Year: 2011
    ..Finally, we recently discovered that there are several MHC class l-restricted epitopes in SIV cryptic Open Reading Frames (cORFs)...
  36. Disabling of the Anaphase Promoting Complex by Human Cytomegalovirus
    DEBORAH HYE SPECTOR; Fiscal Year: 2010
    ..The first utilizes a library of cDNA constructs corresponding to all of the HCMV open reading frames (ORFs), and the second utilizes a library of HCMV Bacterial Artificial Chromosomes (BACs) that have ..
  37. Identification of Pathways Affected by Essential Proteins of Unknown Function
    SEAN DAVID MOORE; Fiscal Year: 2012
    ..coli that have not yet been assigned a function. Of the ~4,300 E. coli open reading frames, roughly a third have not had their encoded protein functions experimentally verified...
  38. Large-Scale High-Confidence Binary Protein Interaction Network for Drosophila
    Norbert Perrimon; Fiscal Year: 2013
    ..screen for high-confidence identification of binary protein interactions among 10,000 Drosophila open reading frames (ORFs)...
  39. Generating and Managing Large Scale Proteogenomic Data for ENCODE Cell Lines
    MORGAN CORINNE contact GIDDINGS; Fiscal Year: 2010
    ..approach has been used to reveal new genes, new alternative splice variants, new start sites, and upstream open reading frames (ORFs)...
  40. COMMON AND RARE SEQUENCE VARIANTS IN BREAST CANCER RISK
    SEAN VAHRAM TAVTIGIAN; Fiscal Year: 2011
    ..In the second arm, we will mutation screen the open reading frames of strong candidate susceptibility genes in both the cases and the controls...
  41. The Discovery of Human Peptide Encoding Genes
    Alan Saghatelian; Fiscal Year: 2013
    ..Since SEPs are produced from short open reading frames (sORFs) in the genome this discovery also represents the characterization of 32 new human genes...
  42. Vpr as a Mediator Proteasomal Degradation
    CARLOS M DE NORONHA; Fiscal Year: 2010
    ..by the observation that several of these viruses, including HIV2, have duplicated vpr to generate two open reading frames, vpr and vpx...
  43. Bridging KSHV capsids to the nuclear egress complex
    Prashant Desai; Fiscal Year: 2013
    ..will test capsid-associated proteins, for example, the capsid vertex-specific component (CVSC) encoded by open reading frames (ORF) 19 and 32 for the ability to bridge capsids with nuclear membranes...
  44. Pathogenesis of Persistent Chlamydial STDs
    Deborah Dean; Fiscal Year: 2007
    ..However, the discovery of open reading frames predicted to encode a nine-member polymorphic membrane protein (Prop) gene (pmp) family in the recently ..
  45. Creation and validation of a lux-positive Candida strain
    Yue Fu; Fiscal Year: 2007
    ..albicans. Internal ribosomal entry sequences (IRES) will allow translation of multiple open reading frames from single messenger RNA (mRNA) strands. Candidal promoters will be used in lieu of S...
  46. ANTIGENIC DETERMINANTS OF VARICELLA VIRUS
    Charles Grose; Fiscal Year: 2006
    ..The VZV genome encodes about 70 open reading frames. The predominant VZV glycoprotein complex, in contrast to other alphaherpesviruses, is gE:gI...
  47. Global Identification of transcribed elements in the C. elegans genome
    Robert H Waterston; Fiscal Year: 2011
    ..mass spectrometry to distinguish protein coding transcripts from noncoding transcripts for small potential open reading frames. The result will be a set of transcripts that will approach completion for protein coding genes and their ..
  48. TYPE III COLLAGEN GENE EXPRESSION IN CARTILAGE
    SHERRILL ADAMS; Fiscal Year: 1993
    ..They will also define any open reading frames in the RNA, thus indicating whether the RNA is likely to encode a protein (either a non- collagen protein ..
  49. Nanoliter Lab-on-a-chip for Protein Crystallization
    Vamsee Pamula; Fiscal Year: 2007
    unreadable] DESCRIPTION (provided by applicant): The human genome contains at least 30,000 unique open reading frames that may yield >100,000 polypeptide products...
  50. Francisella tularensis Pathogenesis
    Thomas H Kawula; Fiscal Year: 2013
    ..This situation is due, in part, to the fact that most open reading frames in Francisella have no known orthologs...
  51. MITOCHONDRIAL RNA EDITING IN TRYPANOSOMA BRUCEI
    DONNA KOSLOWSKY; Fiscal Year: 1999
    ..It allows the generation of translatable messages by creating the open reading frames as well as proper initiation and termination signals...
  52. Scope and mechanism of eptide translation from short open reading frames in the h
    SARAH ANN SLAVOFF; Fiscal Year: 2013
    ..provided by applicant): Peptides of fewer than 100 amino acids that are directly translated from short open reading frames (sORFs) encoded in the genomes of widely divergent species, including human, have recently been discovered ..
  53. Drug abuse: Discovering ligands for pertinent GPCRs
    Marc G Caron; Fiscal Year: 2013
    ..With NIDA support over the past three years we have established a cDNA collection containing the open reading frames for almost all human addiction associated GPCRs, and more importantly an expanding repository of off-the ..
  54. SITE SPECIFIC RECOMBINATION IN STAPHYLOCOCCUS AUREUS
    Ellen Murphy; Fiscal Year: 1990
    ..The nucleotide sequence of Tn554 contains six open reading frames; two are the antibiotic resistance markers ermA and spc; three, tnpA, tnpB and tnpC, are required for ..
  55. MOLECULAR ANALYSIS OF A POTENTIAL TRANSPORT OPERON IN AA
    Karen Novak; Fiscal Year: 2001
    ..We have identified seven open reading frames (ORFs) encoding putative proteins homologous with those predicted by the ptl and virB transport operons on ..
  56. ANIMAL MODELS OF MOLECULAR PATHOGENSIS OF HTLV-1
    Michael Lairmore; Fiscal Year: 2003
    ..Regulatory and accessory genes of HTLV-1 are encoded in four open reading frames (ORF I-IV) of the pX region of the virus...
  57. Mechanisms of Protein Structure Evolution
    John Moult; Fiscal Year: 2010
    ..number of protein folds and apparently young proteins: that these (1) are the result of generation of new open reading frames or frame shifted older ones;(2) are the outcome of extensive recombination of portions of older proteins;(3)..
  58. Immunoevasive Mucosal Vaccines Against HIV-1
    Michael A Barry; Fiscal Year: 2013
    ..Current first generation adenoviral (FG-Ad) vaccines encode 17 adenoviral open reading frames that can be targeted by anti-vector T cells...
  59. Mucosal Helper-dependent Adenovirus Vaccines Against HIV
    Michael Barry; Fiscal Year: 2009
    ..Current first generation adenoviral (FG-Ad) vaccines encode 17 adenoviral open reading frames that can be targeted by anti-vector T cells...
  60. Integrated genomic approaches to identify and validate cancer targets
    William C Hahn; Fiscal Year: 2010
    ..to develop and implement genome scale RNA interference libraries, complete collections of human open reading frames (ORFs) and comprehensive protein-protein interaction maps...
  61. PHOSPHORYLATION IN RENAL CELL INJURY
    Goutam Ghosh Choudhury; Fiscal Year: 2004
    ..b>Open reading frames of interacting proteins will be determined by nucleotide sequencing...
  62. HEPATIC DRUG ELIMINATION IN PREGNANCY
    Mary Vore; Fiscal Year: 2010
    ..export pump (BSEP) from the canalicular membrane and decreased bile flow, and 3) identification of upstream open reading frames (uORF) in the 5'leader sequences of rat,human and mouse MRP2...
  63. HEPATIC DRUG ELIMINATION IN PREGNANCY
    Mary Vore; Fiscal Year: 2007
    ..export pump (BSEP) from the canalicular membrane and decreased bile flow, and 3) identification of upstream open reading frames (uORF) in the 5' leader sequences of rat, human and mouse MRP2...
  64. Gene Expression Patterns and Lifestyles in Legionella
    Howard Shuman; Fiscal Year: 2009
    ..pneumophila genome sequence and a microarray containing all known L. pneumophila genes, open reading frames and intergenic regions will permit the evaluation of several hypotheses that may account for these ..
  65. HEPATITIS B VIRUS GENE EXPRESSION
    Alan McLachlan; Fiscal Year: 1991
    ..Characterization of the four HBV open reading frames (ORFs), the surface, core, X and polymerase genes, using an amphotropic retroviral expression system, has ..