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Stem-loop structure preference for site-specific RNA editing by APOBEC3A and APOBEC3G

STEM and diversify

Baysal BE.
GSID: 8WZHK0FLSjYJ
S Sharma, BE Baysal - PeerJ, 2017 - peerj.com

… that have a predicted stem-loop with the reactive C at the 3′-end of the loop. The size of the loop, the nucleotides immediately 5′ to the target cytosine and stability of the stem have a …

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Sharma, S., & Baysal, B. E. (2017). Stem-loop structure preference for site-specific RNA editing by APOBEC3A and APOBEC3G. PeerJ, 5, e4136.
Sharma, Shraddha, and Bora E. Baysal. "Stem-loop structure preference for site-specific RNA editing by APOBEC3A and APOBEC3G." PeerJ 5 (2017): e4136.
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Mutations in the promoter region of the androgen receptor gene are not common in males with idiopathic infertility

STEM and males

Yong EL.
GSID: FyNsctrunaMJ
FJ Ghadessy, SL Liow, EL Yong - Molecular human …, 1999 - academic.oup.com

… We have therefore screened for the first time the androgen receptor gene 5′ untranslated region (nucleotides –153 to +237 ) in 240 males with idiopathic infertility for lesions which …

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Ghadessy, F. J., Liow, S. L., & Yong, E. L. (1999). Mutations in the promoter region of the androgen receptor gene are not common in males with idiopathic infertility. Molecular human reproduction, 5(3), 287-290.
Ghadessy, F. J., S. L. Liow, and E. L. Yong. "Mutations in the promoter region of the androgen receptor gene are not common in males with idiopathic infertility." Molecular human reproduction 5.3 (1999): 287-290.
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Nucleotide sequence of Escherichia coli K-12 replication origin

k-12

Oka A.
GSID: MSPgaKSxB38J
K Sugimoto, A Oka, H Sugisaki… - Proceedings of the …, 1979 - National Acad Sciences

… coli K-12. The strains used were C600 (F- thr leu thi lac tonA supE), LC248 (HfrKL16 recA), W3623polA (F- trp galstr polAI 1) (8), MM383 (F… coli K-12. Nucleotides are numbered from BamHI site 4 (junction between BamHI...

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Sugimoto, K., Oka, A., Sugisaki, H., Takanami, M., Nishimura, A., Yasuda, Y., & Hirota, Y. (1979). Nucleotide sequence of Escherichia coli K-12 replication origin. Proceedings of the National Academy of Sciences, 76(2), 575-579.
Sugimoto, K., et al. "Nucleotide sequence of Escherichia coli K-12 replication origin." Proceedings of the National Academy of Sciences 76.2 (1979): 575-579.
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SROOGLE: webserver for integrative, user-friendly visualization of splicing signals

pipeline programs

Ast G, Schwartz S.
GSID: 5QUb9RSviYQJ
S Schwartz, E Hall, G Ast - Nucleic Acids Research, 2009 - academic.oup.com

Exons are typically only 140 nt in length and are surrounded by intronic oceans that are thousands of nucleotides long. Four core splicing signals, aided by splicing-regulatory …

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Schwartz, S., Hall, E., & Ast, G. (2009). SROOGLE: webserver for integrative, user-friendly visualization of splicing signals. Nucleic Acids Research, 37(suppl_2), W189-W192.
Schwartz, Schraga, Eitan Hall, and Gil Ast. "SROOGLE: webserver for integrative, user-friendly visualization of splicing signals." Nucleic Acids Research 37.suppl_2 (2009): W189-W192.
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Splice site prediction with quadratic discriminant analysis using diversity measure

diversity

[No authors listed]
GSID: h-FPVbTi464J
L Zhang, L Luo - Nucleic acids research, 2003 - academic.oup.com

Based on the conservation of nucleotides at splicing sites and the features of base composition and base correlation around these sites we use the method of increment of …

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Zhang, L., & Luo, L. (2003). Splice site prediction with quadratic discriminant analysis using diversity measure. Nucleic acids research, 31(21), 6214-6220.
Zhang, Lirong, and Liaofu Luo. "Splice site prediction with quadratic discriminant analysis using diversity measure." Nucleic acids research 31.21 (2003): 6214-6220.
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RNA diversification by a self-reproducing ribozyme revealed by deep sequencing and kinetic modelling

STEM and diversification

Jeancolas C, Matsubara YJ, Vybornyi M.
GSID: Ply-sJ_iKTwJ
C Jeancolas, YJ Matsubara, M Vybornyi… - Chemical …, 2021 - pubs.rsc.org

… 1 RNA substrates are composed of a “stem” (blue) and a tag (red). RNA1 stem differs from RNA2 and RNA3 stems by two nucleotides (bold). RNA2 and RNA3 have a self-…

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JEANCOLAS, Cyrille, et al. RNA diversification by a self-reproducing ribozyme revealed by deep sequencing and kinetic modelling. Chemical Communications, 2021, vol. 57, no 61, p. 7517-7520.
Jeancolas, C., Matsubara, Y. J., Vybornyi, M., Lambert, C. N., Blokhuis, A., Alline, T., ... & Nghe, P. (2021). RNA diversification by a self-reproducing ribozyme revealed by deep sequencing and kinetic modelling. Chemical Communications, 57(61), 7517-7520.
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Nucleotide pyrophosphatases/phosphodiesterases on the move

diversity

Bollen M, Ceulemans H.
GSID: ztkDhuJZMOkJ
M Bollen, R Gijsbers, H Ceulemans… - Critical reviews in …, 2000 - Taylor & Francis

Nucleotide pyrophosphatases/phosphodiesterases (NPPs) release nucleoside 5′-monophosphates from nucleotides and their derivatives. They exist both as membrane …

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Bollen, M., Gijsbers, R., Ceulemans, H., Stalmans, W., & Stefan, C. (2000). Nucleotide pyrophosphatases/phosphodiesterases on the move. Critical reviews in biochemistry and molecular biology, 35(6), 393-432.
Bollen, Mathieu, et al. "Nucleotide pyrophosphatases/phosphodiesterases on the move." Critical reviews in biochemistry and molecular biology 35.6 (2000): 393-432.
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The 1-Particle-per-k-Nucleotides (1PkN) Elastic Network Model of DNA Dynamics with Sequence-Dependent Geometry.

Frontiers in physiology

Kameda T, Isami S, Togashi Y, Nishimori H, Sakamoto N, Awazu A.
PMID: 28382002
Front Physiol. 2017 Mar 14;8:103. doi: 10.3389/fphys.2017.00103. eCollection 2017.

Coarse-grained models of DNA have made important contributions to the determination of the physical properties of genomic DNA, working as a molecular machine for gene regulation. In this study, to analyze the global dynamics of long DNA sequences with...

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Kameda T, Isami S, Togashi Y, et al. The 1-Particle-per-k-Nucleotides (1PkN) Elastic Network Model of DNA Dynamics with Sequence-Dependent Geometry. Front Physiol. 2017;8:103doi: 10.3389/fphys.2017.00103.
Kameda, T., Isami, S., Togashi, Y., Nishimori, H., Sakamoto, N., & Awazu, A. (2017). The 1-Particle-per-k-Nucleotides (1PkN) Elastic Network Model of DNA Dynamics with Sequence-Dependent Geometry. Frontiers in physiology, 8103. https://doi.org/10.3389/fphys.2017.00103
Kameda, Takeru, et al. "The 1-Particle-per-k-Nucleotides (1PkN) Elastic Network Model of DNA Dynamics with Sequence-Dependent Geometry." Frontiers in physiology vol. 8 (2017): 103. doi: https://doi.org/10.3389/fphys.2017.00103
Kameda T, Isami S, Togashi Y, Nishimori H, Sakamoto N, Awazu A. The 1-Particle-per-k-Nucleotides (1PkN) Elastic Network Model of DNA Dynamics with Sequence-Dependent Geometry. Front Physiol. 2017 Mar 14;8:103. doi: 10.3389/fphys.2017.00103. eCollection 2017. PMID: 28382002; PMCID: PMC5361685.
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Electrical detection and quantification of single and mixed DNA nucleotides in suspension.

Scientific reports

Ahmad MA, Panicker NG, Rizvi TA, Mustafa F.
PMID: 27677329
Sci Rep. 2016 Sep 28;6:34016. doi: 10.1038/srep34016.

High speed sequential identification of the building blocks of DNA, (deoxyribonucleotides or nucleotides for short) without labeling or processing in long reads of DNA is the need of the hour. This can be accomplished through exploiting their unique electrical...

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Ahmad MA, Panicker NG, Rizvi TA, et al. Electrical detection and quantification of single and mixed DNA nucleotides in suspension. Sci Rep. 2016;6:34016doi: 10.1038/srep34016.
Ahmad, M. A., Panicker, N. G., Rizvi, T. A., & Mustafa, F. (2016). Electrical detection and quantification of single and mixed DNA nucleotides in suspension. Scientific reports, 634016. https://doi.org/10.1038/srep34016
Ahmad, Mahmoud Al, et al. "Electrical detection and quantification of single and mixed DNA nucleotides in suspension." Scientific reports vol. 6 (2016): 34016. doi: https://doi.org/10.1038/srep34016
Ahmad MA, Panicker NG, Rizvi TA, Mustafa F. Electrical detection and quantification of single and mixed DNA nucleotides in suspension. Sci Rep. 2016 Sep 28;6:34016. doi: 10.1038/srep34016. PMID: 27677329; PMCID: PMC5039720.
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Phellinus noxius: molecular diversity among isolates from Taiwan and its phylogenetic relationship with other species of Phellinus based on sequences of the ITS region.

Botanical studies

Tsai JN, Ann PJ, Liou RF, Hsieh WH, Ko WH.
PMID: 28510192
Bot Stud. 2017 Dec;58(1):9. doi: 10.1186/s40529-017-0162-1. Epub 2017 Jan 16.

BACKGROUND: Analysis of phylogenetic relationship of 91 isolates of Phellinus noxius obtained from 46 plant species in Taiwan did not show distinct grouping based on ITS sequences.RESULTS: However, the ITS nucleotides showed 20 different kinds of variations including single...

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Tsai JN, Ann PJ, Liou RF, et al. Phellinus noxius: molecular diversity among isolates from Taiwan and its phylogenetic relationship with other species of Phellinus based on sequences of the ITS region. Bot Stud. 2017;58(1):9doi: 10.1186/s40529-017-0162-1.
Tsai, J. N., Ann, P. J., Liou, R. F., Hsieh, W. H., & Ko, W. H. (2017). Phellinus noxius: molecular diversity among isolates from Taiwan and its phylogenetic relationship with other species of Phellinus based on sequences of the ITS region. Botanical studies, 58(1), 9. https://doi.org/10.1186/s40529-017-0162-1
Tsai, Jyh-Nong, et al. "Phellinus noxius: molecular diversity among isolates from Taiwan and its phylogenetic relationship with other species of Phellinus based on sequences of the ITS region." Botanical studies vol. 58,1 (2017): 9. doi: https://doi.org/10.1186/s40529-017-0162-1
Tsai JN, Ann PJ, Liou RF, Hsieh WH, Ko WH. Phellinus noxius: molecular diversity among isolates from Taiwan and its phylogenetic relationship with other species of Phellinus based on sequences of the ITS region. Bot Stud. 2017 Dec;58(1):9. doi: 10.1186/s40529-017-0162-1. Epub 2017 Jan 16. PMID: 28510192; PMCID: PMC5430557.
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HIGH-THROUGHPUT SCREENING TECHNOLOGY FOR MONITORING PHYTOHORMONE PRODUCTION IN MICROALGAE(1).

Journal of phycology

Jirásková D, Poulíčková A, Novák O, Sedláková K, Hradecká V, Strnad M.
PMID: 27033650
J Phycol. 2009 Feb;45(1):108-18. doi: 10.1111/j.1529-8817.2008.00615.x. Epub 2009 Jan 13.

New miniaturized techniques for multiplying microalgae and estimating their phytohormone production were developed; in these methods, the strains to be tested are cultivated in microtitre plates, and the phytohormones in suspensions of the cultures are measured by direct ELISAs....

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Jirásková D, Poulíčková A, Novák O, et al. HIGH-THROUGHPUT SCREENING TECHNOLOGY FOR MONITORING PHYTOHORMONE PRODUCTION IN MICROALGAE(1). J Phycol. 2009;45(1):108-18doi: 10.1111/j.1529-8817.2008.00615.x.
Jirásková, D., Poulíčková, A., Novák, O., Sedláková, K., Hradecká, V., & Strnad, M. (2009). HIGH-THROUGHPUT SCREENING TECHNOLOGY FOR MONITORING PHYTOHORMONE PRODUCTION IN MICROALGAE(1). Journal of phycology, 45(1), 108-18. https://doi.org/10.1111/j.1529-8817.2008.00615.x
Jirásková, Darina, et al. "HIGH-THROUGHPUT SCREENING TECHNOLOGY FOR MONITORING PHYTOHORMONE PRODUCTION IN MICROALGAE(1)." Journal of phycology vol. 45,1 (2009): 108-18. doi: https://doi.org/10.1111/j.1529-8817.2008.00615.x
Jirásková D, Poulíčková A, Novák O, Sedláková K, Hradecká V, Strnad M. HIGH-THROUGHPUT SCREENING TECHNOLOGY FOR MONITORING PHYTOHORMONE PRODUCTION IN MICROALGAE(1). J Phycol. 2009 Feb;45(1):108-18. doi: 10.1111/j.1529-8817.2008.00615.x. Epub 2009 Jan 13. PMID: 27033650.
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Preliminary evaluation of circulating microRNAs as potential biomarkers in paracoccidioidomycosis.

Biomedical reports

De Lacorte Singulani J, De Fátima Da Silva J, Gullo FP, Costa MC, Fusco-Almeida AM, Enguita FJ, Mendes-Giannini MJS.
PMID: 28451399
Biomed Rep. 2017 Mar;6(3):353-357. doi: 10.3892/br.2017.849. Epub 2017 Jan 26.

MicroRNAs (miRNAs) are small RNAs (length, 19-24 nucleotides) that regulate gene expression by either mRNA degradation or translational inhibition of proteins. Circulating miRNAs, which are extremely stable and protected from RNAse-mediated degradation in body fluids, have appeared as candidate...

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De Lacorte Singulani J, De Fátima Da Silva J, Gullo FP, et al. Preliminary evaluation of circulating microRNAs as potential biomarkers in paracoccidioidomycosis. Biomed Rep. 2017;6(3):353-357doi: 10.3892/br.2017.849.
De Lacorte Singulani, J., De Fátima Da Silva, J., Gullo, F. P., Costa, M. C., Fusco-Almeida, A. M., Enguita, F. J., & Mendes-Giannini, M. J. S. (2017). Preliminary evaluation of circulating microRNAs as potential biomarkers in paracoccidioidomycosis. Biomedical reports, 6(3), 353-357. https://doi.org/10.3892/br.2017.849
De Lacorte Singulani, Junya, et al. "Preliminary evaluation of circulating microRNAs as potential biomarkers in paracoccidioidomycosis." Biomedical reports vol. 6,3 (2017): 353-357. doi: https://doi.org/10.3892/br.2017.849
De Lacorte Singulani J, De Fátima Da Silva J, Gullo FP, Costa MC, Fusco-Almeida AM, Enguita FJ, Mendes-Giannini MJS. Preliminary evaluation of circulating microRNAs as potential biomarkers in paracoccidioidomycosis. Biomed Rep. 2017 Mar;6(3):353-357. doi: 10.3892/br.2017.849. Epub 2017 Jan 26. PMID: 28451399; PMCID: PMC5403430.
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Showing 1 to 12 of 4809 entries