MMBGX: a method for estimating expression at the isoform level and detecting differential splicing using whole-transcript Affymetrix arrays.

abstract：:The design and synthesis of metal complexes that can specifically target DNA secondary structure has attracted considerable attention. Chiral metallosupramolecular complexes (e.g. helicates) in particular display unique DNA-binding behavior, however until recently few examples which are both water-compatible and enant...

journal_title：Nucleic acids research

authors： Zhao A,Howson SE,Zhao C,Ren J,Scott P,Wang C,Qu X

更新日期：2017-05-19 00:00:00

abstract：:Myotonic dystrophy type 1 (DM1) is caused by the expansion of a (CTG).(CAG) repeat in the DMPK gene on chromosome 19q13.3. At least 17 neurological diseases have similar genetic mutations, the expansion of DNA repeats. In most of these disorders, the disease severity is related to the length of the repeat expansion, a...

journal_title：Nucleic acids research

authors： Hashem VI,Pytlos MJ,Klysik EA,Tsuji K,Khajavi M,Ashizawa T,Sinden RR

更新日期：2004-12-01 00:00:00

abstract：:Natural transformation is a major mechanism of horizontal gene transfer in bacteria that depends on DNA recombination. RecA is central to the homologous recombination pathway, catalyzing DNA strand invasion and homology search. DprA was shown to be a key binding partner of RecA acting as a specific mediator for its lo...

journal_title：Nucleic acids research

authors： Lisboa J,Andreani J,Sanchez D,Boudes M,Collinet B,Liger D,van Tilbeurgh H,Guérois R,Quevillon-Cheruel S

更新日期：2014-06-01 00:00:00

abstract：:A complete nucleotide sequence of human aldolase B mRNA was determined with a recombinant cDNA (pHABL120-3). The cDNA insert was composed of 1,652 bases excluding poly(A) tail and the sequence was consistent with the previous results reported by others. However, S1 nuclease mapping and subsequent genomic analysis allo...

journal_title：Nucleic acids research

authors： Sakakibara M,Mukai T,Yatsuki H,Hori K

更新日期：1985-07-25 00:00:00

abstract：:Chromatin immunoprecipitation (ChIP) has ushered in a new era of scientific discovery by allowing new insights into DNA-protein interactions. ChIP is used to quantify enriched genomic regions using qPCR, and more recently is combined with next generation sequencing (ChIP-seq) to obtain a genome wide profile of protein...

journal_title：Nucleic acids research

authors： Kurtenbach S,Reddy R,Harbour JW

更新日期：2019-01-08 00:00:00

abstract：:Immunoglobulin genes contain a conserved eight base sequence element 5' to the site of transcription initiation. This octamer can serve as a site for the binding of nuclear proteins which are presumably involved in the cell type specific expression of this family of genes. In studying the binding of nuclear proteins t...

journal_title：Nucleic acids research

authors： Landolfi NF,Yin XM,Capra JD,Tucker PW

更新日期：1988-06-24 00:00:00

abstract：:We analyzed the effects of site-directed mutations in the SUC2 promoter of Saccharomyces cerevisiae. Analyses were performed in wild-type as well as mig1 and tup1 mutant strains after the promoter mutants were reintroduced into the native SUC2 locus on the left arm of chromosome IX. Mutation of the two GC boxes reveal...

journal_title：Nucleic acids research

authors： Bu Y,Schmidt MC

更新日期：1998-02-15 00:00:00

abstract：:More than 20 different heterogeneous nuclear ribonucleoproteins (hnRNPs) are associated with pre-mRNAs in the nucleus of mammalian cells and these proteins appear to influence pre-mRNA processing and other aspects of mRNA metabolism and transport. The arrangement of hnRNP proteins on pre-mRNAs is likely to be unique f...

journal_title：Nucleic acids research

authors： Matunis MJ,Xing J,Dreyfuss G

更新日期：1994-03-25 00:00:00

abstract：:Leishmania species are protozoan parasites whose remarkably plastic genome limits the establishment of effective genetic manipulation and leishmaniasis treatment. The strategies used by Leishmania to maintain its genome while allowing variability are not fully understood. Here, we used DiCre-mediated conditional gene ...

journal_title：Nucleic acids research

authors： Damasceno JD,Obonaga R,Silva GLA,Reis-Cunha JL,Duncan SM,Bartholomeu DC,Mottram JC,McCulloch R,Tosi LRO

更新日期：2018-12-14 00:00:00

abstract：:Advancement in the field of computational research has made it possible for the in silico methods to offer significant benefits to both regulatory needs and requirements for risk assessments, and pharmaceutical industry to assess the safety profile of a chemical. Here, we present ProTox-II that incorporates molecular ...

journal_title：Nucleic acids research

authors： Banerjee P,Eckert AO,Schrey AK,Preissner R

更新日期：2018-07-02 00:00:00

abstract：:Point mutations in mitochondrial tRNA genes are responsible for individual subgroups of mitochondrial encephalomyopathies. We have recently reported that point mutations in the tRNA(Leu)(UUR) and tRNA(Lys) genes cause a defect in the normal modification at the first nucleotide of the anticodon. As part of a systematic...

journal_title：Nucleic acids research

authors： Yasukawa T,Hino N,Suzuki T,Watanabe K,Ueda T,Ohta S

更新日期：2000-10-01 00:00:00

abstract：:Ionizing radiation induces clustered DNA damage, which presents a challenge to the cellular repair machinery. The repair efficiency of a single-strand break (SSB) is approximately 4x less than that for repair of an abasic (AP) site when in a bistranded cluster containing 8-oxoG. To explore whether this difference in r...

journal_title：Nucleic acids research

authors： Mourgues S,Lomax ME,O'Neill P

更新日期：2007-01-01 00:00:00

abstract：:We characterised the human hSuv3p protein belonging to the family of NTPases/helicases. In yeast mitochondria the hSUV3 orthologue is a component of the degradosome complex and participates in mtRNA turnover and processing, while in Caenorhabditis elegans the hSUV3 orthologue is necessary for viability of early embryo...

journal_title：Nucleic acids research

authors： Minczuk M,Piwowarski J,Papworth MA,Awiszus K,Schalinski S,Dziembowski A,Dmochowska A,Bartnik E,Tokatlidis K,Stepien PP,Borowski P

更新日期：2002-12-01 00:00:00

abstract：:The VISTA portal for comparative genomics is designed to give biomedical scientists a unified set of tools to lead them from the raw DNA sequences through the alignment and annotation to the visualization of the results. The VISTA portal also hosts the alignments of a number of genomes computed by our group, allowing ...

journal_title：Nucleic acids research

authors： Brudno M,Poliakov A,Minovitsky S,Ratnere I,Dubchak I

更新日期：2007-07-01 00:00:00

abstract：:In fission yeast and other eukaryotes, Rec12 (Spo11) is thought to catalyze the formation of dsDNA breaks (DSBs) that initiate homologous recombination in meiosis. Rec12 is orthologous to the catalytic subunit of topoisomerase VI (Top6A). Guided by the crystal structure of Top6A, we engineered the rec12 locus to encod...

journal_title：Nucleic acids research

authors： Kan F,Davidson MK,Wahls WP

更新日期：2011-03-01 00:00:00

abstract：:Mitochondrial DNA maintenance and segregation are dependent on the actin cytoskeleton in budding yeast. We found two cytoskeletal proteins among six proteins tightly associated with rat liver mitochondrial DNA: non-muscle myosin heavy chain IIA and β-actin. In human cells, transient gene silencing of MYH9 (encoding no...

journal_title：Nucleic acids research

authors： Reyes A,He J,Mao CC,Bailey LJ,Di Re M,Sembongi H,Kazak L,Dzionek K,Holmes JB,Cluett TJ,Harbour ME,Fearnley IM,Crouch RJ,Conti MA,Adelstein RS,Walker JE,Holt IJ

更新日期：2011-07-01 00:00:00

abstract：:MicroRNAs (miRNAs) are small RNA molecules that regulate gene expression. They are characterized by specific maturation processes defined by canonical and non-canonical biogenic pathways. Analysis of ∼0.5 billion sequences from mouse data sets derived from different tissues, developmental stages and cell types, partly...

journal_title：Nucleic acids research

authors： Castellano L,Stebbing J

更新日期：2013-03-01 00:00:00

abstract：:Partial acid cleavage, comparative HPLC tryptic peptide mapping and amino acid sequencing of the C1 and C2 proteins of HeLa heterogeneous nuclear ribonucleoprotein (hnRNP) particles demonstrate that proteins C1 and C2 differ in primary structure by the presence of a 13 amino acid insert sequence in C2. This C2 insert ...

journal_title：Nucleic acids research

authors： Merrill BM,Barnett SF,LeStourgeon WM,Williams KR

更新日期：1989-11-11 00:00:00

abstract：:Allele-specific protospacer adjacent motif (asPAM)-positioning SNPs and CRISPRs are valuable resources for gene therapy of dominant disorders. However, one technical hurdle is to identify the haplotype comprising the disease-causing allele and the distal asPAM SNPs. Here, we describe a novel CRISPR-based method (CRISP...

journal_title：Nucleic acids research

authors： Yu J,Xiang X,Huang J,Liang X,Pan X,Dong Z,Petersen TS,Qu K,Yang L,Zhao X,Li S,Zheng T,Xu Z,Liu C,Han P,Xu F,Yang H,Liu X,Zhang X,Bolund L,Luo Y,Lin L

更新日期：2020-03-18 00:00:00

abstract：:The FlyRNAi database at the Drosophila RNAi Screening Center and Transgenic RNAi Project (DRSC/TRiP) provides a suite of online resources that facilitate functional genomics studies with a special emphasis on Drosophila melanogaster. Currently, the database provides: gene-centric resources that facilitate ortholog map...

journal_title：Nucleic acids research

authors： Hu Y,Comjean A,Rodiger J,Liu Y,Gao Y,Chung V,Zirin J,Perrimon N,Mohr SE

更新日期：2021-01-08 00:00:00

abstract：:Struct2Net is a web server for predicting interactions between arbitrary protein pairs using a structure-based approach. Prediction of protein-protein interactions (PPIs) is a central area of interest and successful prediction would provide leads for experiments and drug design; however, the experimental coverage of t...

journal_title：Nucleic acids research

authors： Singh R,Park D,Xu J,Hosur R,Berger B

更新日期：2010-07-01 00:00:00

abstract：:Friedreich ataxia (FRDA) is caused by hyperexpansion of GAA*TTC repeats located in the first intron of the FXN gene, which inhibits transcription leading to the deficiency of frataxin. The FXN gene is an excellent target for therapeutic intervention since (i) 98% of patients carry the same type of mutation, (ii) the m...

journal_title：Nucleic acids research

authors： Soragni E,Herman D,Dent SY,Gottesfeld JM,Wells RD,Napierala M

更新日期：2008-11-01 00:00:00

abstract：:The Pathway Tools cellular overview diagram is a visual representation of the biochemical network of an organism. The overview is automatically created from a Pathway/Genome Database describing that organism. The cellular overview includes metabolic, transport and signaling pathways, and other membrane and periplasmic...

journal_title：Nucleic acids research

authors： Paley SM,Karp PD

更新日期：2006-08-07 00:00:00

abstract：:Reverse transcription of HIV-1 RNA is initiated from the 3' end of a tRNA3Lys molecule annealed to the primer binding site (PBS). An additional interaction between the anticodon loop of tRNA3Lys and a viral A-rich loop is required for efficient initiation of reverse transcription of the HIV-1 MAL isolate. In the HIV-1...

journal_title：Nucleic acids research

authors： Rigourd M,Goldschmidt V,Brulé F,Morrow CD,Ehresmann B,Ehresmann C,Marquet R

更新日期：2003-10-01 00:00:00

abstract：:Gene trapping is a method of generating murine embryonic stem (ES) cell lines containing insertional mutations in known and novel genes. A number of international groups have used this approach to create sizeable public cell line repositories available to the scientific community for the generation of mutant mouse str...

journal_title：Nucleic acids research

authors： Nord AS,Chang PJ,Conklin BR,Cox AV,Harper CA,Hicks GG,Huang CC,Johns SJ,Kawamoto M,Liu S,Meng EC,Morris JH,Rossant J,Ruiz P,Skarnes WC,Soriano P,Stanford WL,Stryke D,von Melchner H,Wurst W,Yamamura K,Young SG,

更新日期：2006-01-01 00:00:00

abstract：:Eight base analogs were tested as third strand residues in otherwise homopyrimidine strands opposite each of the 'direct' (A.T and G.C) and 'inverted' (T.A and C.G) Watson-Crick base pairs, using UV melting profiles to assess triplex stability. The target duplexes contained 20 A.T base pairs and a central test base pa...

journal_title：Nucleic acids research

authors： Amosova OA,Fresco JR

更新日期：1999-12-01 00:00:00

abstract：:We present a multi-laboratory effort to describe the structural and dynamical properties of duplex B-DNA under physiological conditions. By processing a large amount of atomistic molecular dynamics simulations, we determine the sequence-dependent structural properties of DNA as expressed in the equilibrium distributio...

journal_title：Nucleic acids research

authors： Dans PD,Balaceanu A,Pasi M,Patelli AS,Petkevičiūtė D,Walther J,Hospital A,Bayarri G,Lavery R,Maddocks JH,Orozco M

更新日期：2019-12-02 00:00:00

abstract：:The oligomerization state and mode of binding to DNA of the GIY-YIG endonuclease II (EndoII) from bacteriophage T4 was studied using gel filtration and electrophoretic mobility shift assays with a set of mutants previously found to have altered enzyme activity. At low enzyme/DNA ratios all mutants except one bound to ...

journal_title：Nucleic acids research

authors： Lagerbäck P,Andersson E,Malmberg C,Carlson K

更新日期：2009-10-01 00:00:00

abstract：:In Saccharomyces cerevisiae, RNA polymerase II assembly is probably initiated by the formation of the RPB3-RPB11 heterodimer. RPB3 is encoded by a single copy gene in the yeast, mouse and human genomes. The RPB11 gene is also unique in yeast and mouse, but in humans a gene family has been identified that potentially e...

journal_title：Nucleic acids research

authors： Benga WJ,Grandemange S,Shpakovski GV,Shematorova EK,Kedinger C,Vigneron M

更新日期：2005-06-24 00:00:00

abstract：:We report for the first time an analysis of the ATPase activity of human DNA topoisomerase (topo) IIbeta. We show that topo IIbeta is a DNA-dependent ATPase that appears to fit Michaelis-Menten kinetics. The ATPase activity is stimulated 44-fold by DNA. The k(cat) for ATP hydrolysis by human DNA topo IIbeta in the pre...

journal_title：Nucleic acids research

authors： West KL,Turnbull RM,Willmore E,Lakey JH,Austin CA

更新日期：2002-12-15 00:00:00