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1. Full Text Use of Sequence Analysis of the NS5B Region for Routine Genotyping of Hepatitis C Virus with Reference to C/E1 and 5′ Untranslated Region Sequences
by Donald G. Murphy and Bernard Willems and Marc Deschênes and Nir Hilzenrat and Roger Mousseau and Sidney Sabbah
Journal of Clinical Microbiology, ISSN 0095-1137, 04/2007, Volume 45, Issue 4, pp. 1102 - 1112
Article Usage Stats Services JCM Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley... 
INTRAVENOUS-DRUG-USERS | PHYLOGENETIC ANALYSIS | TRANSCRIPTASE PCR ASSAY | MOLECULAR EPIDEMIOLOGY | BLOOD-DONORS | MICROBIOLOGY | INFECTION | 5'-NONCODING REGION | IDENTIFICATION | FRANCE | DETERMINING SUBTYPE DISTRIBUTION | Hepacivirus - isolation & purification | Viral Envelope Proteins - genetics | Quebec - epidemiology | Humans | Middle Aged | Hepacivirus - genetics | Molecular Sequence Data | Viral Nonstructural Proteins - genetics | Genotype | Male | 5' Untranslated Regions - genetics | Phylogeny | Molecular Epidemiology - methods | Sequence Analysis, DNA | Sequence Homology | RNA, Viral - genetics | Base Sequence | Hepatitis C - epidemiology | Sensitivity and Specificity | Hepatitis C - virology | Adult | Female | Aged | Hepacivirus - classification | Virology
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2. Full Text Short intronic repeat sequences facilitate circular RNA production
by Liang, Dongming and Wilusz, Jeremy E
Genes and Development, ISSN 0890-9369, 10/2014, Volume 28, Issue 20, pp. 2233 - 2247
Recent deep sequencing studies have revealed thousands of circular noncoding RNAs generated from protein-coding genes. These RNAs are produced when the... 
Noncoding RNA | circRNA | Splicing | Alu | EPHB4 | HIPK3 | ZKSCAN1 | MOUSE TESTIS | CELLS | YIELDS | noncoding RNA | LONG NONCODING RNAS | TRIPLE-HELIX | DEVELOPMENTAL BIOLOGY | CELL BIOLOGY | EXON | GENE | GENETICS & HEREDITY | TRANSCRIPT | splicing | EXPRESSION | WORLD | RNA Splice Sites - genetics | Humans | Protein-Serine-Threonine Kinases - genetics | Molecular Sequence Data | Transcription Factors - genetics | Microsatellite Repeats - genetics | RNA - genetics | RNA - biosynthesis | Base Pairing | Base Sequence | Plasmids - genetics | Mutation | Inteins - genetics | Intracellular Signaling Peptides and Proteins - genetics | Thermodynamics | Usage | RNA | Analysis | Gene expression | Spliceosomes | Health aspects | Index Medicus | Research Paper
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3. Full Text Distribution and intensity of constraint in mammalian genomic sequence
by Cooper, Gregory M and Stone, Eric A and Asimenos, George and Green, Eric D and Batzoglou, Serafim and Sidow, Arend and NISC Comparative Sequencing Progra and NISC Comparative Sequencing Program
Genome Research, ISSN 1088-9051, 07/2005, Volume 15, Issue 7, pp. 901 - 913
Comparisons of orthologous genomic DNA sequences call be used to characterize regions that have been subject to purifying selection and are enriched for... 
MAXIMUM-LIKELIHOOD | PLACENTAL MAMMALS | NONCODING SEQUENCES | BIOCHEMISTRY & MOLECULAR BIOLOGY | MOUSE | TRANSPOSABLE ELEMENTS | CONSERVED SEQUENCES | REGULATORY SEQUENCES | GENE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | REGIONS | GENETICS & HEREDITY | MULTIPLE ALIGNMENT | Mammals - genetics | Computational Biology - methods | Interspersed Repetitive Sequences | Humans | Molecular Sequence Data | Gene Expression Profiling - methods | Sequence Analysis, DNA | Sequence Homology, Nucleic Acid | Cystic Fibrosis Transmembrane Conductance Regulator | Sequence Alignment | Animals | Base Sequence | Sensitivity and Specificity | Conserved Sequence | Gene Components | Genome | Evolution, Molecular | Amino acid sequence | Genetic research | Research | Genomics
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4. Full Text Conserved non-genic sequences - an unexpected feature of mammalian genomes
by Reymond, Alexandre and Dermitzakis, Emmanouil T and Antonarakis, Stylianos E
Nature Reviews Genetics, ISSN 1471-0056, 02/2005, Volume 6, Issue 2, pp. 151 - 157
Mammalian genomes contain highly conserved sequences that are not functionally transcribed. These sequences are single copy and comprise approximately 1-2% of... 
SEX REVERSAL | MOUSE GENOME | NONCODING SEQUENCES | DNA | GENETICS & HEREDITY | KB UPSTREAM | FACTOR-BINDING SITES | BETA-THALASSEMIA | TRANSCRIPTION FACTOR | REGULATORY ELEMENTS | EXPRESSION | Genetic Variation | Base Sequence - genetics | Conserved Sequence - genetics | Phenotype | Animals | Humans | Computational Biology | Models, Genetic | DNA, Intergenic - genetics | Genome | Evolution, Molecular
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5. Full Text Formation of triple-helical structures by the 3'-end sequences of MALAT1 and MENβ noncoding RNAs
by Jessica A. Brown and Max L. Valenstein and Therese A. Yario and Kazimierz T. Tycowski and Joan A. Steitz
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 11/2012, Volume 109, Issue 47, pp. 19202 - 19207
Stability of the long noncoding-polyadenylated nuclear (PAN) RNA from Kaposi's sarcoma-associated herpesvirus is conferred by an expression and nuclear... 
RNA stability | Nuclear structure | Melting | RNA | Plasmids | Chemical bases | Nucleotides | Nucleic acids | Genetic mutation | RNA tertiary interactions | DECAY | STABILITY | MULTIDISCIPLINARY SCIENCES | PSEUDOKNOT | IDENTIFICATION | NUCLEAR SPECKLES | TELOMERASE RNA | TRANSCRIPTS | ELEMENT | MESSENGER-RNA | MICE | Nucleic Acid Denaturation | RNA, Long Noncoding - chemistry | Humans | Molecular Sequence Data | Nucleotides - genetics | RNA, Long Noncoding - genetics | RNA Stability - genetics | Sequence Alignment | DNA Mutational Analysis | Base Sequence | Nucleic Acid Conformation | Transition Temperature | Hydrogen-Ion Concentration | Biological Sciences
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6. Full Text High‐throughput identification of RNA nuclear enrichment sequences
by Shukla, Chinmay J and McCorkindale, Alexandra L and Gerhardinger, Chiara and Korthauer, Keegan D and Cabili, Moran N and Shechner, David M and Irizarry, Rafael A and Maass, Philipp G and Rinn, John L
The EMBO Journal, ISSN 0261-4189, 03/2018, Volume 37, Issue 6, p. n/a
In the post‐genomic era, thousands of putative noncoding regulatory regions have been identified, such as enhancers, promoters, long noncoding RNA s (lnc RNA... 
lnc | nuclear localization | inference of regions | RNA | high‐throughput reporter assay | de novo | de novo inference of regions | lncRNA | high-throughput reporter assay | LOCALIZATION | LONG NONCODING RNAS | LNCRNAS | BIOCHEMISTRY & MOLECULAR BIOLOGY | TRANSLATION | REGULATORY ELEMENTS | CANCER | CELL BIOLOGY | EVOLUTION | GENE-EXPRESSION | REPEATS | Enrichment | Fractionation | Transcription | Nucleotide sequence | Peptides | Fluorescence | Regulatory sequences | Assaying | Ribonucleic acid--RNA | Nuclei | Gene sequencing | Enhancers | Fluorescence in situ hybridization | Cytosine | Tiling | Gene mapping | Position (location) | Localization | Deoxyribonucleic acid--DNA | Methods & Resources | Resource | RNA Biology | Systems & Computational Biology
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7. Full Text Functional annotation of noncoding sequence variants
by Ritchie, Graham R. S and Dunham, Ian and Zeggini, Eleftheria and Flicek, Paul
Nature Methods, ISSN 1548-7091, 2014, Volume 11, Issue 3, pp. 294 - 296
Identifying functionally relevant variants against the background of ubiquitous genetic variation is a major challenge in human genetics. For variants in... 
DATABASE | BIOCHEMICAL RESEARCH METHODS | Genetic Variation | Algorithms | Untranslated Regions - genetics | Computer Simulation | Humans | Molecular Sequence Annotation | Noncoding DNA | Physiological aspects | Genomes | Research | Genetics | Genomics
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8. Full Text Predicting effects of noncoding variants with deep learning-based sequence model
by Zhou, Jian and Troyanskaya, Olga G
Nature Methods, ISSN 1548-7091, 09/2015, Volume 12, Issue 10, pp. 931 - 934
Identifying functional effects of noncoding variants is a major challenge in human genetics. To predict the noncoding-variant effects de novo from sequence, we... 
REGULATORY VARIANTS | FRAMEWORK | BIOCHEMICAL RESEARCH METHODS | Epigenomics | Humans | RNA, Untranslated | Regulatory Sequences, Nucleic Acid | Hepatocyte Nuclear Factor 3-alpha - genetics | Support Vector Machine | Transcription Factors - genetics | Transcription Factors - metabolism | Algorithms | Models, Genetic | Polymorphism, Single Nucleotide | Mutation | Genome, Human | Quantitative Trait Loci | Chromatin - genetics | Noncoding DNA | Innovations | Nucleotide sequencing | Properties | Gene expression | Observations | DNA sequencing | Chromatin | Genetic diversity | Gene loci | Genetic algorithms
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9. Full Text LNCipedia: a database for annotated human lncRNA transcript sequences and structures
by Volders, PJ and Helsens, K and Wang, XW and Menten, B and Martens, L and Gevaert, K and Vandesompele, J and Mestdagh, P
NUCLEIC ACIDS RESEARCH, ISSN 0305-1048, 01/2013, Volume 41, Issue D1, pp. D246 - D251
Here, we present LNCipedia (http://www.lncipedia.org), a novel database for human long non-coding RNA (lncRNA) transcripts and genes. LncRNAs constitute a... 
DIFFERENTIATION | LONG NONCODING RNA | GENE | TANDEM | BIOCHEMISTRY & MOLECULAR BIOLOGY | REVEALS | Proteins - genetics | RNA, Long Noncoding - chemistry | Humans | Molecular Sequence Annotation | Transcriptome | RNA, Long Noncoding - genetics | Software | Internet | Databases, Nucleic Acid | RNA, Long Noncoding - metabolism
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10. Full Text An update on LNCipedia: A database for annotated human lncRNA sequences
by Volders, Pieter-Jan and Verheggen, Kenneth and Menschaert, Gerben and Vandepoele, Klaas and Martens, Lennart and Vandesompele, Jo and Mestdagh, Pieter
Nucleic Acids Research, ISSN 0305-1048, 01/2015, Volume 43, Issue 1, pp. D174 - D180
The human genome is pervasively transcribed, producing thousands of non-coding RNA transcripts. The majority of these transcripts are long non-coding RNAs... 
INACTIVATION | CELLS | LONG NONCODING RNA | GENE | BIOCHEMISTRY & MOLECULAR BIOLOGY | RESOLUTION | DIFFERENTIATION | IDENTIFICATION | MASS-SPECTROMETRY | REVEALS | PROTEOMICS | Proteins - genetics | Animals | Sequence Analysis, RNA | RNA, Long Noncoding - chemistry | Humans | Molecular Sequence Annotation | HEK293 Cells | Mice | RNA, Long Noncoding - genetics | Internet | Databases, Nucleic Acid | Zebrafish - genetics | Database Issue
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11. Full Text Raising the estimate of functional human sequences
by Pheasant, Michael and Mattick, John S
Genome Research, ISSN 1088-9051, 09/2007, Volume 17, Issue 9, pp. 1245 - 1253
While less than 1.5% of the mammalian genome encodes proteins, it is now evident that the vast majority is transcribed, mainly into non-protein-coding RNAs.... 
PROTEIN-CODING GENES | BIOCHEMISTRY & MOLECULAR BIOLOGY | TRANSPOSABLE ELEMENTS | POLYMERASE-II TRANSCRIPTION | REGULATORY ELEMENTS | MAMMALIAN GENOMES | HOST GENES | HUMAN GENOME | NONCODING RNAS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GENETICS & HEREDITY | ALU ELEMENTS | RAPID EVOLUTION | Animals | Interspersed Repetitive Sequences | Base Sequence | Humans | MicroRNAs | RNA, Untranslated | Selection, Genetic | Conserved Sequence | Molecular Sequence Data | Transcription, Genetic | Genome, Human | Evolution, Molecular | Genetic code | Nucleotide sequence | Analysis | Protein binding
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12. Full Text Transcriptional regulation by small RNAs at sequences downstream from 3′ gene termini
by Elbashir, Sayda and Younger, Scott T and Janowski, Bethany A and Chu, Yongjun and Gagnon, Keith T and Corey, David R and Schwartz, Jacob C and Yue, Xuan
Nature Chemical Biology, ISSN 1552-4450, 08/2010, Volume 6, Issue 8, pp. 621 - 629
Transcriptome studies reveal many noncoding transcripts overlapping 3' gene termini. The function of these transcripts is unknown. Here we have characterized... 
CANCER-CELLS | MESSENGER-RNA | NONCODING RNAS | HUMAN-CELLS | ANTISENSE TRANSCRIPTS | INTERFERING RNA | BIOCHEMISTRY & MOLECULAR BIOLOGY | NATURAL ANTISENSE | GROWTH-FACTOR | EXPRESSION | REPRESSES TRANSCRIPTION | Cell Line | Chromatin - metabolism | Gene Targeting | Humans | RNA, Messenger - genetics | DNA, Complementary - genetics | 3' Untranslated Regions - genetics | Gene Expression Regulation - physiology | 5' Untranslated Regions - genetics | Gene Expression Profiling | BRCA1 Protein - biosynthesis | RNA, Small Cytoplasmic - physiology | BRCA1 Protein - genetics | RNA, Messenger - biosynthesis | DNA, Complementary - biosynthesis | Protein Conformation | 3' Untranslated Regions - physiology | Chromatin | Biochemistry | RNA polymerase | Genomics | Research methodology
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13. Full Text A molecular phylogeny of the orange subfamily(Rutaceae: Aurantioideae) using nine cpDNA sequences
by Bayer, Randall J and Mabberley, David J and Morton, Cynthia and Miller, Cathy H and Sharma, Ish K and Pfeil, Bernard E and Rich, Sarah and Hitchcock, Roberta and Sykes, Steve
American Journal of Botany, ISSN 0002-9122, 03/2009, Volume 96, Issue 3, pp. 668 - 685
The breeding of new, high-quality citrus cultivars depends on dependable information about the relationships of taxa within the tribe Citreae; therefore, it is... 
Taxa | Biological taxonomies | Systematics and Phytogeography | Introns | Phylogenetics | Plants | Phylogeny | Hybridity | Genera | We they distinction | Fruits | Aurantioideae | Citrus | Citreae | Rutaceae | Clauseneae | phylogeny | cpDNA | molecular systematics | Molecular systematics | PLASTID DNA-SEQUENCES | UNIVERSAL PRIMERS | MARKERS | CHLOROPLAST DNA | CITRUS RUTACEAE | CLADISTIC-ANALYSIS | PLANT SCIENCES | GENETIC DIVERSITY | PLANTS | NONCODING REGIONS | BIOCHEMICAL SYSTEMATICS | Genetic aspects | Research | Identification and classification | Phylogeny (Botany) | Citrus fruits | Plant reproduction | Molecular chemistry | Taxonomy | Deoxyribonucleic acid--DNA | Botany
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