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Showing 2005 to 2016 of 2016 entries
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Targeting genomic SARS-CoV-2 RNA with siRNAs allows efficient inhibition of viral replication and spread.

Nucleic acids research

Ambike S, Cheng CC, Feuerherd M, Velkov S, Baldassi D, Afridi SQ, Porras-Gonzalez D, Wei X, Hagen P, Kneidinger N, Stoleriu MG, Grass V, Burgstaller G, Pichlmair A, Merkel OM, Ko C, Michler T.
PMID: 34928377
Nucleic Acids Res. 2022 Jan 11;50(1):333-349. doi: 10.1093/nar/gkab1248.

A promising approach to tackle the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) could be small interfering (si)RNAs. So far it is unclear, which viral replication steps can be efficiently inhibited with siRNAs. Here, we report that siRNAs can target...

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Ambike S, Cheng CC, Feuerherd M, et al. Targeting genomic SARS-CoV-2 RNA with siRNAs allows efficient inhibition of viral replication and spread. Nucleic Acids Res. 2022;50(1):333-349doi: 10.1093/nar/gkab1248.
Ambike, S., Cheng, C. C., Feuerherd, M., Velkov, S., Baldassi, D., Afridi, S. Q., Porras-Gonzalez, D., Wei, X., Hagen, P., Kneidinger, N., Stoleriu, M. G., Grass, V., Burgstaller, G., Pichlmair, A., Merkel, O. M., Ko, C., & Michler, T. (2022). Targeting genomic SARS-CoV-2 RNA with siRNAs allows efficient inhibition of viral replication and spread. Nucleic acids research, 50(1), 333-349. https://doi.org/10.1093/nar/gkab1248
Ambike, Shubhankar, et al. "Targeting genomic SARS-CoV-2 RNA with siRNAs allows efficient inhibition of viral replication and spread." Nucleic acids research vol. 50,1 (2022): 333-349. doi: https://doi.org/10.1093/nar/gkab1248
Ambike S, Cheng CC, Feuerherd M, Velkov S, Baldassi D, Afridi SQ, Porras-Gonzalez D, Wei X, Hagen P, Kneidinger N, Stoleriu MG, Grass V, Burgstaller G, Pichlmair A, Merkel OM, Ko C, Michler T. Targeting genomic SARS-CoV-2 RNA with siRNAs allows efficient inhibition of viral replication and spread. Nucleic Acids Res. 2022 Jan 11;50(1):333-349. doi: 10.1093/nar/gkab1248. PMID: 34928377; PMCID: PMC8754636.
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Constraints on error rate revealed by computational study of G•U tautomerization in translation.

Nucleic acids research

Kazantsev A, Ignatova Z.
PMID: 34669948
Nucleic Acids Res. 2021 Nov 18;49(20):11823-11833. doi: 10.1093/nar/gkab947.

In translation, G•U mismatch in codon-anticodon decoding is an error hotspot likely due to transition of G•U from wobble (wb) to Watson-Crick (WC) geometry, which is governed by keto/enol tautomerization (wb-WC reaction). Yet, effects of the ribosome on the...

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Kazantsev A, Ignatova Z. Constraints on error rate revealed by computational study of G•U tautomerization in translation. Nucleic Acids Res. 2021;49(20):11823-11833doi: 10.1093/nar/gkab947.
Kazantsev, A., & Ignatova, Z. (2021). Constraints on error rate revealed by computational study of G•U tautomerization in translation. Nucleic acids research, 49(20), 11823-11833. https://doi.org/10.1093/nar/gkab947
Kazantsev, Andriy, and Ignatova, Zoya. "Constraints on error rate revealed by computational study of G•U tautomerization in translation." Nucleic acids research vol. 49,20 (2021): 11823-11833. doi: https://doi.org/10.1093/nar/gkab947
Kazantsev A, Ignatova Z. Constraints on error rate revealed by computational study of G•U tautomerization in translation. Nucleic Acids Res. 2021 Nov 18;49(20):11823-11833. doi: 10.1093/nar/gkab947. PMID: 34669948; PMCID: PMC8599798.
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Suppression of liquid-liquid phase separation by 1,6-hexanediol partially compromises the 3D genome organization in living cells.

Nucleic acids research

Ulianov SV, Velichko AK, Magnitov MD, Luzhin AV, Golov AK, Ovsyannikova N, Kireev II, Gavrikov AS, Mishin AS, Garaev AK, Tyakht AV, Gavrilov AA, Kantidze OL, Razin SV.
PMID: 33836078
Nucleic Acids Res. 2021 Oct 11;49(18):10524-10541. doi: 10.1093/nar/gkab249.

Liquid-liquid phase separation (LLPS) contributes to the spatial and functional segregation of molecular processes within the cell nucleus. However, the role played by LLPS in chromatin folding in living cells remains unclear. Here, using stochastic optical reconstruction microscopy (STORM)...

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Ulianov SV, Velichko AK, Magnitov MD, et al. Suppression of liquid-liquid phase separation by 1,6-hexanediol partially compromises the 3D genome organization in living cells. Nucleic Acids Res. 2021;49(18):10524-10541doi: 10.1093/nar/gkab249.
Ulianov, S. V., Velichko, A. K., Magnitov, M. D., Luzhin, A. V., Golov, A. K., Ovsyannikova, N., Kireev, I. I., Gavrikov, A. S., Mishin, A. S., Garaev, A. K., Tyakht, A. V., Gavrilov, A. A., Kantidze, O. L., & Razin, S. V. (2021). Suppression of liquid-liquid phase separation by 1,6-hexanediol partially compromises the 3D genome organization in living cells. Nucleic acids research, 49(18), 10524-10541. https://doi.org/10.1093/nar/gkab249
Ulianov, Sergey V, et al. "Suppression of liquid-liquid phase separation by 1,6-hexanediol partially compromises the 3D genome organization in living cells." Nucleic acids research vol. 49,18 (2021): 10524-10541. doi: https://doi.org/10.1093/nar/gkab249
Ulianov SV, Velichko AK, Magnitov MD, Luzhin AV, Golov AK, Ovsyannikova N, Kireev II, Gavrikov AS, Mishin AS, Garaev AK, Tyakht AV, Gavrilov AA, Kantidze OL, Razin SV. Suppression of liquid-liquid phase separation by 1,6-hexanediol partially compromises the 3D genome organization in living cells. Nucleic Acids Res. 2021 Oct 11;49(18):10524-10541. doi: 10.1093/nar/gkab249. PMID: 33836078; PMCID: PMC8501969.
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Dynamic 23S rRNA modification ho5C2501 benefits Escherichia coli under oxidative stress.

Nucleic acids research

Fasnacht M, Gallo S, Sharma P, Himmelstoß M, Limbach PA, Willi J, Polacek N.
PMID: 34904663
Nucleic Acids Res. 2021 Dec 14; doi: 10.1093/nar/gkab1224. Epub 2021 Dec 14.

Post-transcriptional modifications are added to ribosomal RNAs (rRNAs) to govern ribosome biogenesis and to fine-tune protein biosynthesis. In Escherichia coli and related bacteria, RlhA uniquely catalyzes formation of a 5-hydroxycytidine (ho5C) at position 2501 of 23S rRNA. However, the...

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Fasnacht M, Gallo S, Sharma P, et al. Dynamic 23S rRNA modification ho5C2501 benefits Escherichia coli under oxidative stress. Nucleic Acids Res. 2021;doi: 10.1093/nar/gkab1224.
Fasnacht, M., Gallo, S., Sharma, P., Himmelstoß, M., Limbach, P. A., Willi, J., & Polacek, N. (2021). Dynamic 23S rRNA modification ho5C2501 benefits Escherichia coli under oxidative stress. Nucleic acids research, . https://doi.org/10.1093/nar/gkab1224
Fasnacht, Michel, et al. "Dynamic 23S rRNA modification ho5C2501 benefits Escherichia coli under oxidative stress." Nucleic acids research vol. (2021). doi: https://doi.org/10.1093/nar/gkab1224
Fasnacht M, Gallo S, Sharma P, Himmelstoß M, Limbach PA, Willi J, Polacek N. Dynamic 23S rRNA modification ho5C2501 benefits Escherichia coli under oxidative stress. Nucleic Acids Res. 2021 Dec 14; doi: 10.1093/nar/gkab1224. Epub 2021 Dec 14. PMID: 34904663.
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Bipartite interaction sites differentially modulate RNA-binding affinity of a protein complex essential for germline stem cell self-renewal.

Nucleic acids research

Qiu C, Wine RN, Campbell ZT, Hall TMT.
PMID: 34908132
Nucleic Acids Res. 2022 Jan 11;50(1):536-548. doi: 10.1093/nar/gkab1220.

In C. elegans, PUF proteins promote germline stem cell self-renewal. Their functions hinge on partnerships with two proteins that are redundantly required for stem cell maintenance. Here we focus on understanding how the essential partner protein, LST-1, modulates mRNA...

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Qiu C, Wine RN, Campbell ZT, et al. Bipartite interaction sites differentially modulate RNA-binding affinity of a protein complex essential for germline stem cell self-renewal. Nucleic Acids Res. 2022;50(1):536-548doi: 10.1093/nar/gkab1220.
Qiu, C., Wine, R. N., Campbell, Z. T., & Hall, T. M. T. (2022). Bipartite interaction sites differentially modulate RNA-binding affinity of a protein complex essential for germline stem cell self-renewal. Nucleic acids research, 50(1), 536-548. https://doi.org/10.1093/nar/gkab1220
Qiu, Chen, et al. "Bipartite interaction sites differentially modulate RNA-binding affinity of a protein complex essential for germline stem cell self-renewal." Nucleic acids research vol. 50,1 (2022): 536-548. doi: https://doi.org/10.1093/nar/gkab1220
Qiu C, Wine RN, Campbell ZT, Hall TMT. Bipartite interaction sites differentially modulate RNA-binding affinity of a protein complex essential for germline stem cell self-renewal. Nucleic Acids Res. 2022 Jan 11;50(1):536-548. doi: 10.1093/nar/gkab1220. PMID: 34908132; PMCID: PMC8754657.
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Functional correction of CFTR mutations in human airway epithelial cells using adenine base editors.

Nucleic acids research

Krishnamurthy S, Traore S, Cooney AL, Brommel CM, Kulhankova K, Sinn PL, Newby GA, Liu DR, McCray PB.
PMID: 34520545
Nucleic Acids Res. 2021 Oct 11;49(18):10558-10572. doi: 10.1093/nar/gkab788.

Mutations in the CFTR gene that lead to premature stop codons or splicing defects cause cystic fibrosis (CF) and are not amenable to treatment by small-molecule modulators. Here, we investigate the use of adenine base editor (ABE) ribonucleoproteins (RNPs)...

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Krishnamurthy S, Traore S, Cooney AL, et al. Functional correction of CFTR mutations in human airway epithelial cells using adenine base editors. Nucleic Acids Res. 2021;49(18):10558-10572doi: 10.1093/nar/gkab788.
Krishnamurthy, S., Traore, S., Cooney, A. L., Brommel, C. M., Kulhankova, K., Sinn, P. L., Newby, G. A., Liu, D. R., & McCray, P. B. (2021). Functional correction of CFTR mutations in human airway epithelial cells using adenine base editors. Nucleic acids research, 49(18), 10558-10572. https://doi.org/10.1093/nar/gkab788
Krishnamurthy, Sateesh, et al. "Functional correction of CFTR mutations in human airway epithelial cells using adenine base editors." Nucleic acids research vol. 49,18 (2021): 10558-10572. doi: https://doi.org/10.1093/nar/gkab788
Krishnamurthy S, Traore S, Cooney AL, Brommel CM, Kulhankova K, Sinn PL, Newby GA, Liu DR, McCray PB. Functional correction of CFTR mutations in human airway epithelial cells using adenine base editors. Nucleic Acids Res. 2021 Oct 11;49(18):10558-10572. doi: 10.1093/nar/gkab788. PMID: 34520545; PMCID: PMC8501978.
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Coordinated glucocorticoid receptor and MAFB action induces tolerogenesis and epigenome remodeling in dendritic cells.

Nucleic acids research

Morante-Palacios O, Ciudad L, Micheroli R, de la Calle-Fabregat C, Li T, Barbisan G, Houtman M, Edalat SG, Frank-Bertoncelj M, Ospelt C, Ballestar E.
PMID: 34893889
Nucleic Acids Res. 2022 Jan 11;50(1):108-126. doi: 10.1093/nar/gkab1182.

Glucocorticoids (GCs) exert potent anti-inflammatory effects in immune cells through the glucocorticoid receptor (GR). Dendritic cells (DCs), central actors for coordinating immune responses, acquire tolerogenic properties in response to GCs. Tolerogenic DCs (tolDCs) have emerged as a potential treatment...

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Morante-Palacios O, Ciudad L, Micheroli R, et al. Coordinated glucocorticoid receptor and MAFB action induces tolerogenesis and epigenome remodeling in dendritic cells. Nucleic Acids Res. 2022;50(1):108-126doi: 10.1093/nar/gkab1182.
Morante-Palacios, O., Ciudad, L., Micheroli, R., de la Calle-Fabregat, C., Li, T., Barbisan, G., Houtman, M., Edalat, S. G., Frank-Bertoncelj, M., Ospelt, C., & Ballestar, E. (2022). Coordinated glucocorticoid receptor and MAFB action induces tolerogenesis and epigenome remodeling in dendritic cells. Nucleic acids research, 50(1), 108-126. https://doi.org/10.1093/nar/gkab1182
Morante-Palacios, Octavio, et al. "Coordinated glucocorticoid receptor and MAFB action induces tolerogenesis and epigenome remodeling in dendritic cells." Nucleic acids research vol. 50,1 (2022): 108-126. doi: https://doi.org/10.1093/nar/gkab1182
Morante-Palacios O, Ciudad L, Micheroli R, de la Calle-Fabregat C, Li T, Barbisan G, Houtman M, Edalat SG, Frank-Bertoncelj M, Ospelt C, Ballestar E. Coordinated glucocorticoid receptor and MAFB action induces tolerogenesis and epigenome remodeling in dendritic cells. Nucleic Acids Res. 2022 Jan 11;50(1):108-126. doi: 10.1093/nar/gkab1182. PMID: 34893889.
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Oxidation alters the architecture of the phenylalanyl-tRNA synthetase editing domain to confer hyperaccuracy.

Nucleic acids research

Srinivas P, Steiner RE, Pavelich IJ, Guerrero-Ferreira R, Juneja P, Ibba M, Dunham CM.
PMID: 34581811
Nucleic Acids Res. 2021 Nov 18;49(20):11800-11809. doi: 10.1093/nar/gkab856.

High fidelity during protein synthesis is accomplished by aminoacyl-tRNA synthetases (aaRSs). These enzymes ligate an amino acid to a cognate tRNA and have proofreading and editing capabilities that ensure high fidelity. Phenylalanyl-tRNA synthetase (PheRS) preferentially ligates a phenylalanine to...

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Srinivas P, Steiner RE, Pavelich IJ, et al. Oxidation alters the architecture of the phenylalanyl-tRNA synthetase editing domain to confer hyperaccuracy. Nucleic Acids Res. 2021;49(20):11800-11809doi: 10.1093/nar/gkab856.
Srinivas, P., Steiner, R. E., Pavelich, I. J., Guerrero-Ferreira, R., Juneja, P., Ibba, M., & Dunham, C. M. (2021). Oxidation alters the architecture of the phenylalanyl-tRNA synthetase editing domain to confer hyperaccuracy. Nucleic acids research, 49(20), 11800-11809. https://doi.org/10.1093/nar/gkab856
Srinivas, Pooja, et al. "Oxidation alters the architecture of the phenylalanyl-tRNA synthetase editing domain to confer hyperaccuracy." Nucleic acids research vol. 49,20 (2021): 11800-11809. doi: https://doi.org/10.1093/nar/gkab856
Srinivas P, Steiner RE, Pavelich IJ, Guerrero-Ferreira R, Juneja P, Ibba M, Dunham CM. Oxidation alters the architecture of the phenylalanyl-tRNA synthetase editing domain to confer hyperaccuracy. Nucleic Acids Res. 2021 Nov 18;49(20):11800-11809. doi: 10.1093/nar/gkab856. PMID: 34581811; PMCID: PMC8599791.
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SCoV2-MD: a database for the dynamics of the SARS-CoV-2 proteome and variant impact predictions.

Nucleic acids research

Torrens-Fontanals M, Peralta-García A, Talarico C, Guixà-González R, Giorgino T, Selent J.
PMID: 34761257
Nucleic Acids Res. 2022 Jan 07;50:D858-D866. doi: 10.1093/nar/gkab977.

SCoV2-MD (www.scov2-md.org) is a new online resource that systematically organizes atomistic simulations of the SARS-CoV-2 proteome. The database includes simulations produced by leading groups using molecular dynamics (MD) methods to investigate the structure-dynamics-function relationships of viral proteins. SCoV2-MD cross-references...

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Torrens-Fontanals M, Peralta-García A, Talarico C, et al. SCoV2-MD: a database for the dynamics of the SARS-CoV-2 proteome and variant impact predictions. Nucleic Acids Res. 2022;50:D858-D866doi: 10.1093/nar/gkab977.
Torrens-Fontanals, M., Peralta-García, A., Talarico, C., Guixà-González, R., Giorgino, T., & Selent, J. (2022). SCoV2-MD: a database for the dynamics of the SARS-CoV-2 proteome and variant impact predictions. Nucleic acids research, 50D858-D866. https://doi.org/10.1093/nar/gkab977
Torrens-Fontanals, Mariona, et al. "SCoV2-MD: a database for the dynamics of the SARS-CoV-2 proteome and variant impact predictions." Nucleic acids research vol. 50 (2022): D858-D866. doi: https://doi.org/10.1093/nar/gkab977
Torrens-Fontanals M, Peralta-García A, Talarico C, Guixà-González R, Giorgino T, Selent J. SCoV2-MD: a database for the dynamics of the SARS-CoV-2 proteome and variant impact predictions. Nucleic Acids Res. 2022 Jan 07;50:D858-D866. doi: 10.1093/nar/gkab977. PMID: 34761257; PMCID: PMC8689960.
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Translational activators and mitoribosomal isoforms cooperate to mediate mRNA-specific translation in Schizosaccharomyces pombe mitochondria.

Nucleic acids research

Herbert CJ, Labarre-Mariotte S, Cornu D, Sophie C, Panozzo C, Michel T, Dujardin G, Bonnefoy N.
PMID: 34634819
Nucleic Acids Res. 2021 Nov 08;49(19):11145-11166. doi: 10.1093/nar/gkab789.

Mitochondrial mRNAs encode key subunits of the oxidative phosphorylation complexes that produce energy for the cell. In Saccharomyces cerevisiae, mitochondrial translation is under the control of translational activators, specific to each mRNA. In Schizosaccharomyces pombe, which more closely resembles...

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Herbert CJ, Labarre-Mariotte S, Cornu D, et al. Translational activators and mitoribosomal isoforms cooperate to mediate mRNA-specific translation in Schizosaccharomyces pombe mitochondria. Nucleic Acids Res. 2021;49(19):11145-11166doi: 10.1093/nar/gkab789.
Herbert, C. J., Labarre-Mariotte, S., Cornu, D., Sophie, C., Panozzo, C., Michel, T., Dujardin, G., & Bonnefoy, N. (2021). Translational activators and mitoribosomal isoforms cooperate to mediate mRNA-specific translation in Schizosaccharomyces pombe mitochondria. Nucleic acids research, 49(19), 11145-11166. https://doi.org/10.1093/nar/gkab789
Herbert, Christopher J, et al. "Translational activators and mitoribosomal isoforms cooperate to mediate mRNA-specific translation in Schizosaccharomyces pombe mitochondria." Nucleic acids research vol. 49,19 (2021): 11145-11166. doi: https://doi.org/10.1093/nar/gkab789
Herbert CJ, Labarre-Mariotte S, Cornu D, Sophie C, Panozzo C, Michel T, Dujardin G, Bonnefoy N. Translational activators and mitoribosomal isoforms cooperate to mediate mRNA-specific translation in Schizosaccharomyces pombe mitochondria. Nucleic Acids Res. 2021 Nov 08;49(19):11145-11166. doi: 10.1093/nar/gkab789. PMID: 34634819; PMCID: PMC8565316.
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Structural basis of transcription activation by the global regulator Spx.

Nucleic acids research

Shi J, Li F, Wen A, Yu L, Wang L, Wang F, Jin Y, Jin S, Feng Y, Lin W.
PMID: 34530448
Nucleic Acids Res. 2021 Oct 11;49(18):10756-10769. doi: 10.1093/nar/gkab790.

Spx is a global transcriptional regulator in Gram-positive bacteria and has been inferred to efficiently activate transcription upon oxidative stress by engaging RNA polymerase (RNAP) and promoter DNA. However, the precise mechanism by which it interacts with RNAP and...

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Shi J, Li F, Wen A, et al. Structural basis of transcription activation by the global regulator Spx. Nucleic Acids Res. 2021;49(18):10756-10769doi: 10.1093/nar/gkab790.
Shi, J., Li, F., Wen, A., Yu, L., Wang, L., Wang, F., Jin, Y., Jin, S., Feng, Y., & Lin, W. (2021). Structural basis of transcription activation by the global regulator Spx. Nucleic acids research, 49(18), 10756-10769. https://doi.org/10.1093/nar/gkab790
Shi, Jing, et al. "Structural basis of transcription activation by the global regulator Spx." Nucleic acids research vol. 49,18 (2021): 10756-10769. doi: https://doi.org/10.1093/nar/gkab790
Shi J, Li F, Wen A, Yu L, Wang L, Wang F, Jin Y, Jin S, Feng Y, Lin W. Structural basis of transcription activation by the global regulator Spx. Nucleic Acids Res. 2021 Oct 11;49(18):10756-10769. doi: 10.1093/nar/gkab790. PMID: 34530448; PMCID: PMC8501982.
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ZFC3H1 prevents RNA trafficking into nuclear speckles through condensation.

Nucleic acids research

Wang Y, Fan J, Wang J, Zhu Y, Xu L, Tong D, Cheng H.
PMID: 34530450
Nucleic Acids Res. 2021 Oct 11;49(18):10630-10643. doi: 10.1093/nar/gkab774.

Controlling proper RNA pool for nuclear export is important for accurate gene expression. ZFC3H1 is a key controller that not only facilitates nuclear exosomal degradation, but also retains its bound polyadenylated RNAs in the nucleus upon exosome inactivation. However,...

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Wang Y, Fan J, Wang J, et al. ZFC3H1 prevents RNA trafficking into nuclear speckles through condensation. Nucleic Acids Res. 2021;49(18):10630-10643doi: 10.1093/nar/gkab774.
Wang, Y., Fan, J., Wang, J., Zhu, Y., Xu, L., Tong, D., & Cheng, H. (2021). ZFC3H1 prevents RNA trafficking into nuclear speckles through condensation. Nucleic acids research, 49(18), 10630-10643. https://doi.org/10.1093/nar/gkab774
Wang, Yimin, et al. "ZFC3H1 prevents RNA trafficking into nuclear speckles through condensation." Nucleic acids research vol. 49,18 (2021): 10630-10643. doi: https://doi.org/10.1093/nar/gkab774
Wang Y, Fan J, Wang J, Zhu Y, Xu L, Tong D, Cheng H. ZFC3H1 prevents RNA trafficking into nuclear speckles through condensation. Nucleic Acids Res. 2021 Oct 11;49(18):10630-10643. doi: 10.1093/nar/gkab774. PMID: 34530450; PMCID: PMC8501945.
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Showing 2005 to 2016 of 2016 entries