Nucleic acid secondary structure (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Nucleic acid secondary structure" in English language version.

Last modified: 10:45:55, 9 February 2026 (UTC)

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3632nih.gov

5^th place

2220doi.org

2^nd place

76adsabs.harvard.edu

14^th place

9^th place

55worldcat.org

4^th place

22semanticscholar.org

15^th place

8^th place

22rochester.edu

2,816^th place

1,888^th place

11web.archive.org

1^st place

11owczarzy.net

low place

11wiley.com

150^th place

174^th place

11arxiv.org

49^th place

31^st place

11psu.edu

299^th place

159^th place

11umontreal.ca

5,721^st place

6,116^th place

adsabs.harvard.edu (Global: 14^th place; English: 9^th place)

ui.adsabs.harvard.edu

Breslauer KJ, Frank R, Blöcker H, Marky LA (1986). "Predicting DNA duplex stability from the base sequence". PNAS. 83 (11): 3746–3750. Bibcode:1986PNAS...83.3746B. doi:10.1073/pnas.83.11.3746. PMC 323600. PMID 3459152.
Chen JL, Greider CW (2005). "Functional analysis of the pseudoknot structure in human telomerase RNA". Proc Natl Acad Sci USA. 102 (23): 8080–5. Bibcode:2005PNAS..102.8080C. doi:10.1073/pnas.0502259102. PMC 1149427. PMID 15849264.
Doudna, Jennifer A.; Ferré-D'Amaré, Adrian R.; Zhou, Kaihong (October 1998). "Crystal structure of a hepatitis delta virus ribozyme". Nature. 395 (6702): 567–574. Bibcode:1998Natur.395..567F. doi:10.1038/26912. PMID 9783582. S2CID 4359811.
Liu, Tianshuo; Xu, Ling; Chung, Kevin; Sisto, Luke J.; Hwang, Jimin; Zhang, Chengxin; Van Zandt, Michael C.; Pyle, Anna Marie (2025-05-13). "Molecular insights into de novo small-molecule recognition by an intron RNA structure". Proceedings of the National Academy of Sciences. 122 (19) e2502425122. Bibcode:2025PNAS..12202425L. doi:10.1073/pnas.2502425122. ISSN 0027-8424. PMC 12088405. PMID 40339124.
Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH (May 2004). "Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure". PNAS. 101 (19): 7287–92. Bibcode:2004PNAS..101.7287M. doi:10.1073/pnas.0401799101. PMC 409911. PMID 15123812.
Zuker, M. (1989-04-07). "On finding all suboptimal foldings of an RNA molecule". Science. 244 (4900): 48–52. Bibcode:1989Sci...244...48Z. doi:10.1126/science.2468181. ISSN 0036-8075. PMID 2468181.

arxiv.org (Global: 49^th place; English: 31^st place)

Rivas E, Eddy SR (1999). "A dynamic programming algorithm for RNA structure prediction including pseudoknots". J Mol Biol. 285 (5): 2053–2068. arXiv:physics/9807048. doi:10.1006/jmbi.1998.2436. PMID 9925784. S2CID 2228845.

doi.org (Global: 2^nd place; English: 2^nd place)

Dirks, Robert M.; Lin, Milo; Winfree, Erik & Pierce, Niles A. (2004). "Paradigms for computational nucleic acid design". Nucleic Acids Research. 32 (4): 1392–1403. doi:10.1093/nar/gkh291. PMC 390280. PMID 14990744.
Yakovchuk, Peter; Protozanova, Ekaterina; Frank-Kamenetskii, Maxim D. (2006). "Base-stacking and base-pairing contributions into thermal stability of the DNA double helix". Nucleic Acids Research. 34 (2): 564–574. doi:10.1093/nar/gkj454. PMC 1360284. PMID 16449200.
Hopfinger, MC; Kirkpatrick, CC; Znosko, BM (18 September 2020). "Predictions and analyses of RNA nearest neighbor parameters for modified nucleotides". Nucleic Acids Research. 48 (16): 8901–8913. doi:10.1093/nar/gkaa654. PMC 7498315. PMID 32810273.
Breslauer KJ, Frank R, Blöcker H, Marky LA (1986). "Predicting DNA duplex stability from the base sequence". PNAS. 83 (11): 3746–3750. Bibcode:1986PNAS...83.3746B. doi:10.1073/pnas.83.11.3746. PMC 323600. PMID 3459152.
Antczak, M; Popenda, M; Zok, T; Zurkowski, M; Adamiak, RW; Szachniuk, M (15 April 2018). "New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation". Bioinformatics. 34 (8): 1304–1312. doi:10.1093/bioinformatics/btx783. PMC 5905660. PMID 29236971.
Mattei, E.; Ausiello, G.; Ferrè, F.; Helmer-Citterich, M. (2014). "A novel approach to represent and compare RNA secondary structures". Nucleic Acids Research. 42 (10): 6146–6157. doi:10.1093/nar/gku283. PMC 4041456. PMID 24753415.
Churkin, Alexander; Barash, Danny (2013). "RNA dot plots: An image representation for RNA secondary structure analysis and manipulations". WIREs RNA. 4 (2): 205–216. doi:10.1002/wrna.1154. PMID 23386427.
Pabo C, Sauer R (1984). "Protein-DNA recognition". Annu Rev Biochem. 53: 293–321. doi:10.1146/annurev.bi.53.070184.001453. PMID 6236744.
Chen JL, Greider CW (2005). "Functional analysis of the pseudoknot structure in human telomerase RNA". Proc Natl Acad Sci USA. 102 (23): 8080–5. Bibcode:2005PNAS..102.8080C. doi:10.1073/pnas.0502259102. PMC 1149427. PMID 15849264.
Rivas E, Eddy SR (1999). "A dynamic programming algorithm for RNA structure prediction including pseudoknots". J Mol Biol. 285 (5): 2053–2068. arXiv:physics/9807048. doi:10.1006/jmbi.1998.2436. PMID 9925784. S2CID 2228845.
Staple, David W.; Butcher, Samuel E. (2005-06-14). "Pseudoknots: RNA Structures with Diverse Functions". PLOS Biol. 3 (6) e213. doi:10.1371/journal.pbio.0030213. ISSN 1545-7885. PMC 1149493. PMID 15941360.
Doudna, Jennifer A.; Ferré-D'Amaré, Adrian R.; Zhou, Kaihong (October 1998). "Crystal structure of a hepatitis delta virus ribozyme". Nature. 395 (6702): 567–574. Bibcode:1998Natur.395..567F. doi:10.1038/26912. PMID 9783582. S2CID 4359811.
Lai, Michael M. C. (1995-06-01). "The Molecular Biology of Hepatitis Delta Virus". Annual Review of Biochemistry. 64 (1): 259–286. doi:10.1146/annurev.bi.64.070195.001355. ISSN 0066-4154. PMID 7574482.
Vicens, Quentin; Cech, Thomas R. (2005-12-13). "Atomic level architecture of group I introns revealed". Trends in Biochemical Sciences. 31 (1): 41–51. doi:10.1016/j.tibs.2005.11.008. ISSN 0968-0004. PMID 16356725.
Liu, Tianshuo; Xu, Ling; Chung, Kevin; Sisto, Luke J.; Hwang, Jimin; Zhang, Chengxin; Van Zandt, Michael C.; Pyle, Anna Marie (2025-05-13). "Molecular insights into de novo small-molecule recognition by an intron RNA structure". Proceedings of the National Academy of Sciences. 122 (19) e2502425122. Bibcode:2025PNAS..12202425L. doi:10.1073/pnas.2502425122. ISSN 0027-8424. PMC 12088405. PMID 40339124.
Xia T, SantaLucia J Jr, Burkard ME, Kierzek R, Schroeder SJ, Jiao X, Cox C, Turner DH (October 1998). "Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs". Biochemistry. 37 (42): 14719–35. CiteSeerX 10.1.1.579.6653. doi:10.1021/bi9809425. PMID 9778347. {{cite journal}}: Cite uses deprecated parameter |citeseerx= (help)
Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH (May 2004). "Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure". PNAS. 101 (19): 7287–92. Bibcode:2004PNAS..101.7287M. doi:10.1073/pnas.0401799101. PMC 409911. PMID 15123812.
Zuker, M. (1989-04-07). "On finding all suboptimal foldings of an RNA molecule". Science. 244 (4900): 48–52. Bibcode:1989Sci...244...48Z. doi:10.1126/science.2468181. ISSN 0036-8075. PMID 2468181.
Lin, Chien-Ling; Taggart, Allison J.; Lim, Kian Huat; Cygan, Kamil J.; Ferraris, Luciana; Creton, Robert; Huang, Yen-Tsung; Fairbrother, William G. (13 November 2015). "RNA structure replaces the need for U2AF2 in splicing". Genome Research. 26 (1): 12–23. doi:10.1101/gr.181008.114. PMC 4691745. PMID 26566657.
Lu, XJ; Bussemaker, HJ; Olson, WK (2 December 2015). "DSSR: an integrated software tool for dissecting the spatial structure of RNA". Nucleic Acids Research. 43 (21): e142. doi:10.1093/nar/gkv716. PMC 4666379. PMID 26184874.

nih.gov (Global: 5^th place; English: 5^th place)

pubmed.ncbi.nlm.nih.gov

Dirks, Robert M.; Lin, Milo; Winfree, Erik & Pierce, Niles A. (2004). "Paradigms for computational nucleic acid design". Nucleic Acids Research. 32 (4): 1392–1403. doi:10.1093/nar/gkh291. PMC 390280. PMID 14990744.
Yakovchuk, Peter; Protozanova, Ekaterina; Frank-Kamenetskii, Maxim D. (2006). "Base-stacking and base-pairing contributions into thermal stability of the DNA double helix". Nucleic Acids Research. 34 (2): 564–574. doi:10.1093/nar/gkj454. PMC 1360284. PMID 16449200.
Hopfinger, MC; Kirkpatrick, CC; Znosko, BM (18 September 2020). "Predictions and analyses of RNA nearest neighbor parameters for modified nucleotides". Nucleic Acids Research. 48 (16): 8901–8913. doi:10.1093/nar/gkaa654. PMC 7498315. PMID 32810273.
Breslauer KJ, Frank R, Blöcker H, Marky LA (1986). "Predicting DNA duplex stability from the base sequence". PNAS. 83 (11): 3746–3750. Bibcode:1986PNAS...83.3746B. doi:10.1073/pnas.83.11.3746. PMC 323600. PMID 3459152.
Antczak, M; Popenda, M; Zok, T; Zurkowski, M; Adamiak, RW; Szachniuk, M (15 April 2018). "New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation". Bioinformatics. 34 (8): 1304–1312. doi:10.1093/bioinformatics/btx783. PMC 5905660. PMID 29236971.
Mattei, E.; Ausiello, G.; Ferrè, F.; Helmer-Citterich, M. (2014). "A novel approach to represent and compare RNA secondary structures". Nucleic Acids Research. 42 (10): 6146–6157. doi:10.1093/nar/gku283. PMC 4041456. PMID 24753415.
Churkin, Alexander; Barash, Danny (2013). "RNA dot plots: An image representation for RNA secondary structure analysis and manipulations". WIREs RNA. 4 (2): 205–216. doi:10.1002/wrna.1154. PMID 23386427.
Pabo C, Sauer R (1984). "Protein-DNA recognition". Annu Rev Biochem. 53: 293–321. doi:10.1146/annurev.bi.53.070184.001453. PMID 6236744.
Chen JL, Greider CW (2005). "Functional analysis of the pseudoknot structure in human telomerase RNA". Proc Natl Acad Sci USA. 102 (23): 8080–5. Bibcode:2005PNAS..102.8080C. doi:10.1073/pnas.0502259102. PMC 1149427. PMID 15849264.
Rivas E, Eddy SR (1999). "A dynamic programming algorithm for RNA structure prediction including pseudoknots". J Mol Biol. 285 (5): 2053–2068. arXiv:physics/9807048. doi:10.1006/jmbi.1998.2436. PMID 9925784. S2CID 2228845.
Staple, David W.; Butcher, Samuel E. (2005-06-14). "Pseudoknots: RNA Structures with Diverse Functions". PLOS Biol. 3 (6) e213. doi:10.1371/journal.pbio.0030213. ISSN 1545-7885. PMC 1149493. PMID 15941360.
Doudna, Jennifer A.; Ferré-D'Amaré, Adrian R.; Zhou, Kaihong (October 1998). "Crystal structure of a hepatitis delta virus ribozyme". Nature. 395 (6702): 567–574. Bibcode:1998Natur.395..567F. doi:10.1038/26912. PMID 9783582. S2CID 4359811.
Lai, Michael M. C. (1995-06-01). "The Molecular Biology of Hepatitis Delta Virus". Annual Review of Biochemistry. 64 (1): 259–286. doi:10.1146/annurev.bi.64.070195.001355. ISSN 0066-4154. PMID 7574482.
Vicens, Quentin; Cech, Thomas R. (2005-12-13). "Atomic level architecture of group I introns revealed". Trends in Biochemical Sciences. 31 (1): 41–51. doi:10.1016/j.tibs.2005.11.008. ISSN 0968-0004. PMID 16356725.
Liu, Tianshuo; Xu, Ling; Chung, Kevin; Sisto, Luke J.; Hwang, Jimin; Zhang, Chengxin; Van Zandt, Michael C.; Pyle, Anna Marie (2025-05-13). "Molecular insights into de novo small-molecule recognition by an intron RNA structure". Proceedings of the National Academy of Sciences. 122 (19) e2502425122. Bibcode:2025PNAS..12202425L. doi:10.1073/pnas.2502425122. ISSN 0027-8424. PMC 12088405. PMID 40339124.
Xia T, SantaLucia J Jr, Burkard ME, Kierzek R, Schroeder SJ, Jiao X, Cox C, Turner DH (October 1998). "Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs". Biochemistry. 37 (42): 14719–35. CiteSeerX 10.1.1.579.6653. doi:10.1021/bi9809425. PMID 9778347. {{cite journal}}: Cite uses deprecated parameter |citeseerx= (help)
Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH (May 2004). "Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure". PNAS. 101 (19): 7287–92. Bibcode:2004PNAS..101.7287M. doi:10.1073/pnas.0401799101. PMC 409911. PMID 15123812.
Zuker, M. (1989-04-07). "On finding all suboptimal foldings of an RNA molecule". Science. 244 (4900): 48–52. Bibcode:1989Sci...244...48Z. doi:10.1126/science.2468181. ISSN 0036-8075. PMID 2468181.
Lin, Chien-Ling; Taggart, Allison J.; Lim, Kian Huat; Cygan, Kamil J.; Ferraris, Luciana; Creton, Robert; Huang, Yen-Tsung; Fairbrother, William G. (13 November 2015). "RNA structure replaces the need for U2AF2 in splicing". Genome Research. 26 (1): 12–23. doi:10.1101/gr.181008.114. PMC 4691745. PMID 26566657.
Lu, XJ; Bussemaker, HJ; Olson, WK (2 December 2015). "DSSR: an integrated software tool for dissecting the spatial structure of RNA". Nucleic Acids Research. 43 (21): e142. doi:10.1093/nar/gkv716. PMC 4666379. PMID 26184874.

ncbi.nlm.nih.gov

Dirks, Robert M.; Lin, Milo; Winfree, Erik & Pierce, Niles A. (2004). "Paradigms for computational nucleic acid design". Nucleic Acids Research. 32 (4): 1392–1403. doi:10.1093/nar/gkh291. PMC 390280. PMID 14990744.
Yakovchuk, Peter; Protozanova, Ekaterina; Frank-Kamenetskii, Maxim D. (2006). "Base-stacking and base-pairing contributions into thermal stability of the DNA double helix". Nucleic Acids Research. 34 (2): 564–574. doi:10.1093/nar/gkj454. PMC 1360284. PMID 16449200.
Hopfinger, MC; Kirkpatrick, CC; Znosko, BM (18 September 2020). "Predictions and analyses of RNA nearest neighbor parameters for modified nucleotides". Nucleic Acids Research. 48 (16): 8901–8913. doi:10.1093/nar/gkaa654. PMC 7498315. PMID 32810273.
Breslauer KJ, Frank R, Blöcker H, Marky LA (1986). "Predicting DNA duplex stability from the base sequence". PNAS. 83 (11): 3746–3750. Bibcode:1986PNAS...83.3746B. doi:10.1073/pnas.83.11.3746. PMC 323600. PMID 3459152.
Antczak, M; Popenda, M; Zok, T; Zurkowski, M; Adamiak, RW; Szachniuk, M (15 April 2018). "New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation". Bioinformatics. 34 (8): 1304–1312. doi:10.1093/bioinformatics/btx783. PMC 5905660. PMID 29236971.
Mattei, E.; Ausiello, G.; Ferrè, F.; Helmer-Citterich, M. (2014). "A novel approach to represent and compare RNA secondary structures". Nucleic Acids Research. 42 (10): 6146–6157. doi:10.1093/nar/gku283. PMC 4041456. PMID 24753415.
Chen JL, Greider CW (2005). "Functional analysis of the pseudoknot structure in human telomerase RNA". Proc Natl Acad Sci USA. 102 (23): 8080–5. Bibcode:2005PNAS..102.8080C. doi:10.1073/pnas.0502259102. PMC 1149427. PMID 15849264.
Staple, David W.; Butcher, Samuel E. (2005-06-14). "Pseudoknots: RNA Structures with Diverse Functions". PLOS Biol. 3 (6) e213. doi:10.1371/journal.pbio.0030213. ISSN 1545-7885. PMC 1149493. PMID 15941360.
Liu, Tianshuo; Xu, Ling; Chung, Kevin; Sisto, Luke J.; Hwang, Jimin; Zhang, Chengxin; Van Zandt, Michael C.; Pyle, Anna Marie (2025-05-13). "Molecular insights into de novo small-molecule recognition by an intron RNA structure". Proceedings of the National Academy of Sciences. 122 (19) e2502425122. Bibcode:2025PNAS..12202425L. doi:10.1073/pnas.2502425122. ISSN 0027-8424. PMC 12088405. PMID 40339124.
Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH (May 2004). "Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure". PNAS. 101 (19): 7287–92. Bibcode:2004PNAS..101.7287M. doi:10.1073/pnas.0401799101. PMC 409911. PMID 15123812.
Lin, Chien-Ling; Taggart, Allison J.; Lim, Kian Huat; Cygan, Kamil J.; Ferraris, Luciana; Creton, Robert; Huang, Yen-Tsung; Fairbrother, William G. (13 November 2015). "RNA structure replaces the need for U2AF2 in splicing". Genome Research. 26 (1): 12–23. doi:10.1101/gr.181008.114. PMC 4691745. PMID 26566657.
Lu, XJ; Bussemaker, HJ; Olson, WK (2 December 2015). "DSSR: an integrated software tool for dissecting the spatial structure of RNA". Nucleic Acids Research. 43 (21): e142. doi:10.1093/nar/gkv716. PMC 4666379. PMID 26184874.

owczarzy.net (Global: low place; English: low place)

Richard Owczarzy (2008-08-28). "DNA melting temperature - How to calculate it?". High-throughput DNA biophysics. owczarzy.net. Archived from the original on 2015-04-30. Retrieved 2008-10-02.

psu.edu (Global: 299^th place; English: 159^th place)

citeseerx.ist.psu.edu

Xia T, SantaLucia J Jr, Burkard ME, Kierzek R, Schroeder SJ, Jiao X, Cox C, Turner DH (October 1998). "Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs". Biochemistry. 37 (42): 14719–35. CiteSeerX 10.1.1.579.6653. doi:10.1021/bi9809425. PMID 9778347. {{cite journal}}: Cite uses deprecated parameter |citeseerx= (help)

rochester.edu (Global: 2,816^th place; English: 1,888^th place)

chem.rochester.edu

"Douglas H. Turner". Turner's rules. Department of Chemistry, University of Rochester.

rna.urmc.rochester.edu

"Nearest Neighbor Database - Turner 2004 parameters, Coaxial Stacking". rna.urmc.rochester.edu.

semanticscholar.org (Global: 15^th place; English: 8^th place)

api.semanticscholar.org

Rivas E, Eddy SR (1999). "A dynamic programming algorithm for RNA structure prediction including pseudoknots". J Mol Biol. 285 (5): 2053–2068. arXiv:physics/9807048. doi:10.1006/jmbi.1998.2436. PMID 9925784. S2CID 2228845.
Doudna, Jennifer A.; Ferré-D'Amaré, Adrian R.; Zhou, Kaihong (October 1998). "Crystal structure of a hepatitis delta virus ribozyme". Nature. 395 (6702): 567–574. Bibcode:1998Natur.395..567F. doi:10.1038/26912. PMID 9783582. S2CID 4359811.

umontreal.ca (Global: 5,721^st place; English: 6,116^th place)

www-lbit.iro.umontreal.ca

"MC-Annotate". www-lbit.iro.umontreal.ca.

web.archive.org (Global: 1^st place; English: 1^st place)

Richard Owczarzy (2008-08-28). "DNA melting temperature - How to calculate it?". High-throughput DNA biophysics. owczarzy.net. Archived from the original on 2015-04-30. Retrieved 2008-10-02.

wiley.com (Global: 150^th place; English: 174^th place)

wires.onlinelibrary.wiley.com

Churkin, Alexander; Barash, Danny (2013). "RNA dot plots: An image representation for RNA secondary structure analysis and manipulations". WIREs RNA. 4 (2): 205–216. doi:10.1002/wrna.1154. PMID 23386427.

worldcat.org (Global: 4^th place; English: 4^th place)

search.worldcat.org

Staple, David W.; Butcher, Samuel E. (2005-06-14). "Pseudoknots: RNA Structures with Diverse Functions". PLOS Biol. 3 (6) e213. doi:10.1371/journal.pbio.0030213. ISSN 1545-7885. PMC 1149493. PMID 15941360.
Lai, Michael M. C. (1995-06-01). "The Molecular Biology of Hepatitis Delta Virus". Annual Review of Biochemistry. 64 (1): 259–286. doi:10.1146/annurev.bi.64.070195.001355. ISSN 0066-4154. PMID 7574482.
Vicens, Quentin; Cech, Thomas R. (2005-12-13). "Atomic level architecture of group I introns revealed". Trends in Biochemical Sciences. 31 (1): 41–51. doi:10.1016/j.tibs.2005.11.008. ISSN 0968-0004. PMID 16356725.
Liu, Tianshuo; Xu, Ling; Chung, Kevin; Sisto, Luke J.; Hwang, Jimin; Zhang, Chengxin; Van Zandt, Michael C.; Pyle, Anna Marie (2025-05-13). "Molecular insights into de novo small-molecule recognition by an intron RNA structure". Proceedings of the National Academy of Sciences. 122 (19) e2502425122. Bibcode:2025PNAS..12202425L. doi:10.1073/pnas.2502425122. ISSN 0027-8424. PMC 12088405. PMID 40339124.
Zuker, M. (1989-04-07). "On finding all suboptimal foldings of an RNA molecule". Science. 244 (4900): 48–52. Bibcode:1989Sci...244...48Z. doi:10.1126/science.2468181. ISSN 0036-8075. PMID 2468181.

Nucleic acid secondary structure (English Wikipedia)

adsabs.harvard.edu (Global: 14th place; English: 9th place)

ui.adsabs.harvard.edu

arxiv.org (Global: 49th place; English: 31st place)

doi.org (Global: 2nd place; English: 2nd place)

nih.gov (Global: 5th place; English: 5th place)