Oxford Index Search Results

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RIDOM: Ribosomal Differentiation of Medical Micro-organisms Database

Dag Harmsen, Jörg Rothgänger, Matthias Frosch and Jürgen Albert.

in Nucleic Acids Research

January 2002; p ublished online January 2002 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 833 words.

The ribosomal differentiation of medical micro-organisms (RIDOM) web server, first described by Harmsen et al. [Harmsden,D., Rothganger,J., Singer,C., Albert,J. and Frosch,M. (1999) Lancet, null...

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Conserved codon composition of ribosomal protein coding genes in Escherichia coli, Mycobacterium tuberculosis and Saccharomyces cerevisiae: lessons from supervised machine learning in functional genomics

Kui Lin, Yuyu Kuang, Jeremiah S. Joseph and Prasanna R. Kolatkar.

in Nucleic Acids Research

June 2002; p ublished online June 2002 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 6575 words.

Genomics projects have resulted in a flood of sequence data. Functional annotation currently relies almost exclusively on inter-species sequence comparison and is restricted in cases of...

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A Promoter Directing α-Amanitin-Sensitive Transcription of GARP, the Major Surface Antigen of Insect Stage Trypanosoma Congolense

Sheila V. Graham, David Jefferies and J. David Barry.

in Nucleic Acids Research

January 1996; p ublished online January 1996 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 7552 words.

The major surface antigen of procyclic and epimastigote forms of Trypanosoma congolense in the tsetse fly is GARP (glutamic acid/alanine-rich protein), which is thought to be the analogue...

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The PRP31 Gene Encodes a Novel Protein Required for Pre-mRNA Splicing in Saccharomyces Cerevisiae

Elaine M. Weidenhammer, Manbir Singh, Monica Ruiz-Noriega and John L. Woolford.

in Nucleic Acids Research

March 1996; p ublished online March 1996 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 4372 words.

The pre-mRNA splicing factor Prp31p was identified in a screen of temperature-sensitive yeast strains for those exhibiting a splicing defect upon shift to the non-permissive temperature....

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A conserved structural element in horse and mouse IGF2 genes binds a methylation sensitive factor

Kerstin Otte, Devapriya Choudhury, Marika Charalambous, Wilhelm Engström and Björn Rozell.

in Nucleic Acids Research

April 1998; p ublished online April 1998 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 4923 words.

The equine IGF2 gene has been cloned and characterised. It spans a 9 kb region, which is substantially less than the corresponding human gene. Three coding exons and three untranslated...

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SUMO modification of Rad22, the Schizosaccharomyces pombe homologue of the recombination protein Rad52

Jenny C. Y. Ho, Nicholas J. Warr, Harumi Shimizu and Felicity Z. Watts.

in Nucleic Acids Research

October 2001; p ublished online October 2001 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 5872 words.

The Schizosaccharomyces pombe rad31 and hus5 genes are required for the DNA damage response, as mutants defective in these genes are sensitive to DNA damaging agents, such as UV and ionising...

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U1 snRNA is cleaved by RNase III and processed through an Sm site-dependent pathway

Rebecca L. Seipelt, Binhai Zheng, Agatha Asuru and Brian C. Rymond.

in Nucleic Acids Research

January 1999; p ublished online January 1999 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 7562 words.

Core snRNP proteins bind snRNA through the conserved Sm site, PuA(U)n≥3GPu. While yeast U1 snRNA has three matches to the Sm consensus, the U1 3′-terminal Sm site was found to be both...

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CEGA—a catalog of conserved elements from genomic alignments

Aline Dousse, Thomas Junier and Evgeny M. Zdobnov.

in Nucleic Acids Research

January 2016; p ublished online November 2015 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 3191 words.

By identifying genomic sequence regions conserved among several species, comparative genomics offers opportunities to discover putatively functional elements without any prior knowledge of...

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SR1—a small RNA with two remarkably conserved functions

Matthias Gimpel, Heike Preis, Emanuel Barth, Lydia Gramzow and Sabine Brantl.

in Nucleic Acids Research

December 2012; p ublished online October 2012 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 10079 words.

SR1 is a dual-function sRNA that acts as a base-pairing regulatory RNA on the ahrC mRNA and as a peptide-encoding mRNA on the gapA operon. The SR1-encoded peptide SR1P binds GapA thereby...

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SL-quant: a fast and flexible pipeline to quantify spliced leader trans-splicing events from RNA-seq data

Carlo Yague-Sanz and Damien Hermand.

in GigaScience

P ublished online July 2018 .

Journal Article. Subjects: Biological Sciences; Bioinformatics and Computational Biology; Evolutionary Biology; Genetics and Genomics; Research Methods in Life Sciences. 3843 words.

Abstract

Background

The spliceosomal transfer of a short spliced leader (SL) RNA to an independent pre-mRNA...

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Removal of 8-oxo-GTP by MutT hydrolase is not a major contributor to transcriptional fidelity

Alasdair J.E. Gordon, Dominik Satory, Mengyu Wang, Jennifer A. Halliday, Ido Golding and Christophe Herman.

in Nucleic Acids Research

October 2014; p ublished online October 2014 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 8816 words.

Living in an oxygen-rich environment is dangerous for a cell. Reactive oxygen species can damage DNA, RNA, protein and lipids. The MutT protein in Escherichia coli removes...

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Sequence motifs associated with hepatotoxicity of locked nucleic acid—modified antisense oligonucleotides

Andrew D. Burdick, Simone Sciabola, Srinivasa R. Mantena, Brett D. Hollingshead, Robert Stanton, James A. Warneke, Ming Zeng, Elena Martsen, Alexander Medvedev, Sergei S. Makarov, Lori A. Reed, John W. Davis and Laurence O. Whiteley.

in Nucleic Acids Research

April 2014; p ublished online February 2014 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 5717 words.

Fully phosphorothioate antisense oligonucleotides (ASOs) with locked nucleic acids (LNAs) improve target affinity, RNase H activation and stability. LNA modified ASOs can cause...

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DNA intermediates of meiotic recombination in synchronous S. pombe at optimal temperature

Randy W. Hyppa, Kyle R. Fowler, Lubos Cipak, Juraj Gregan and Gerald R. Smith.

in Nucleic Acids Research

January 2014; p ublished online October 2013 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 6868 words.

Crossovers formed by recombination between homologous chromosomes are important for proper homolog segregation during meiosis and for generation of genetic diversity. Optimal molecular...

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Chromosome-wide histone deacetylation by sirtuins prevents hyperactivation of DNA damage-induced signaling upon replicative stress

Antoine Simoneau, Étienne Ricard, Sandra Weber, Ian Hammond-Martel, Lai Hong Wong, Adnane Sellam, Guri Giaever, Corey Nislow, Martine Raymond and Hugo Wurtele.

in Nucleic Acids Research

April 2016; p ublished online January 2016 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 12922 words.

The Saccharomyces cerevisiae genome encodes five sirtuins (Sir2 and Hst1–4), which constitute a conserved family of NAD-dependent histone deacetylases. Cells lacking any individual sirtuin...

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NPGPx modulates CPEB2-controlled HIF-1α RNA translation in response to oxidative stress

Po-Jen Chen, Jui-Yun Weng, Pang-Hung Hsu, Jin-Yuh Shew, Yi-Shuian Huang and Wen-Hwa Lee.

in Nucleic Acids Research

October 2015; p ublished online October 2015 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 7878 words.

Non-selenocysteine-containing phospholipid hydroperoxide glutathione peroxidase (NPGPx or GPx7) is an oxidative stress sensor that modulates the antioxidative activity of its target...

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The UCSC Genome Browser database: extensions and updates 2011

Timothy R. Dreszer, Donna Karolchik, Ann S. Zweig, Angie S. Hinrichs, Brian J. Raney, Robert M. Kuhn, Laurence R. Meyer, Mathew Wong, Cricket A. Sloan, Kate R. Rosenbloom, Greg Roe, Brooke Rhead, Andy Pohl, Venkat S. Malladi, Chin H. Li, Katrina Learned, Vanessa Kirkup, Fan Hsu, Rachel A. Harte, Luvina Guruvadoo, Mary Goldman, Belinda M. Giardine, Pauline A. Fujita, Mark Diekhans, Melissa S. Cline, Hiram Clawson, Galt P. Barber, David Haussler and W. James Kent.

in Nucleic Acids Research

January 2012; p ublished online November 2011 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 3337 words.

The University of California Santa Cruz Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a wide variety of...

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A fluorescence-based reporter substrate for monitoring RNA editing in trypanosomatid pathogens

Houtan Moshiri and Reza Salavati.

in Nucleic Acids Research

July 2010; p ublished online May 2010 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 6497 words.

RNA editing regulates mitochondrial gene expression in trypanosomatid pathogens by creating functional mRNAs. It is catalyzed by a multi-protein complex (the editosome), and is found to be...

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Bacillus subtilis genome editing using ssDNA with short homology regions

Yang Wang, Jun Weng, Raza Waseem, Xihou Yin, Ruifu Zhang and Qirong Shen.

in Nucleic Acids Research

July 2012; p ublished online March 2012 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 5638 words.

In this study, we developed a simple and efficient Bacillus subtilis genome editing method in which targeted gene(s) could be inactivated by single-stranded PCR product(s) flanked by short...

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Flavones inhibit the hexameric replicative helicase RepA

Hai Xu, Günter Ziegelin, Werner Schröder, Joachim Frank, Sylvia Ayora, Juan Carlos Alonso, Erich Lanka and Wolfram Saenger.

in Nucleic Acids Research

December 2001; p ublished online December 2001 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 5182 words.

Helicases couple the hydrolysis of nucleoside triphosphates (NTPs) to the unwinding of double-stranded nucleic acids and are essential in DNA metabolism. Thus far, no inhibitors are known...

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Topology and replication of a nuclear episomal plasmid in the rodent malaria Plasmodium berghei

Donald H. Williamson, Chris J. Janse, Peter W. Moore, Andrew P. Waters and Peter R. Preiser.

in Nucleic Acids Research

February 2002; p ublished online February 2002 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 4599 words.

The rodent malaria Plasmodium berghei is one of a small number of species of Plasmodium that can currently be genetically transformed through experimentally controlled uptake of...

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