Riboswitch (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Riboswitch" in English language version.

refsWebsite

Global rank English rank

84nih.gov

4^th place

53doi.org

2^nd place

11harvard.edu

18^th place

17^th place

5worldcat.org

5^th place

3semanticscholar.org

11^th place

8^th place

1psu.edu

207^th place

136^th place

1igem.org

low place

1sciencedirect.com

149^th place

178^th place

1handle.net

102^nd place

76^th place

1biorxiv.org

5,061^st place

5,698^th place

biorxiv.org

Fernandez-de-Cossio-Diaz, Jorge; Hardouin, Pierre; Moutier, Francois-Xavier Lyonnet du; Gioacchino, Andrea Di; Marchand, Bertrand; Ponty, Yann; Sargueil, Bruno; Monasson, Rémi; Cocco, Simona (2024-04-20), Designing Molecular RNA Switches with Restricted Boltzmann Machines, doi:10.1101/2023.05.10.540155, retrieved 2024-11-10

doi.org

Nudler E, Mironov AS (January 2004). "The riboswitch control of bacterial metabolism". Trends in Biochemical Sciences. 29 (1): 11–17. doi:10.1016/j.tibs.2003.11.004. PMID 14729327.
Tucker BJ, Breaker RR (June 2005). "Riboswitches as versatile gene control elements". Current Opinion in Structural Biology. 15 (3): 342–348. doi:10.1016/j.sbi.2005.05.003. PMID 15919195.
Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS (January 2004). "Riboswitches: the oldest mechanism for the regulation of gene expression?". Trends in Genetics. 20 (1): 44–50. CiteSeerX 10.1.1.312.9100. doi:10.1016/j.tig.2003.11.008. PMID 14698618.
Batey RT (June 2006). "Structures of regulatory elements in mRNAs". Current Opinion in Structural Biology. 16 (3): 299–306. doi:10.1016/j.sbi.2006.05.001. PMID 16707260.
Nahvi A, Sudarsan N, Ebert MS, Zou X, Brown KL, Breaker RR (September 2002). "Genetic control by a metabolite binding mRNA". Chemistry & Biology. 9 (9): 1043–1049. doi:10.1016/S1074-5521(02)00224-7. PMID 12323379.
Sudarsan N, Barrick JE, Breaker RR (June 2003). "Metabolite-binding RNA domains are present in the genes of eukaryotes". RNA. 9 (6): 644–647. doi:10.1261/rna.5090103. PMC 1370431. PMID 12756322.
Nou X, Kadner RJ (June 2000). "Adenosylcobalamin inhibits ribosome binding to btuB RNA". Proceedings of the National Academy of Sciences of the United States of America. 97 (13): 7190–7195. Bibcode:2000PNAS...97.7190N. doi:10.1073/pnas.130013897. PMC 16521. PMID 10852957.
Gelfand MS, Mironov AA, Jomantas J, Kozlov YI, Perumov DA (November 1999). "A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes". Trends in Genetics. 15 (11): 439–442. doi:10.1016/S0168-9525(99)01856-9. PMID 10529804.
Miranda-Ríos J, Navarro M, Soberón M (August 2001). "A conserved RNA structure (thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria". Proceedings of the National Academy of Sciences of the United States of America. 98 (17): 9736–9741. doi:10.1073/pnas.161168098. PMC 55522. PMID 11470904.
Stormo GD, Ji Y (August 2001). "Do mRNAs act as direct sensors of small molecules to control their expression?". Proceedings of the National Academy of Sciences of the United States of America. 98 (17): 9465–9467. Bibcode:2001PNAS...98.9465S. doi:10.1073/pnas.181334498. PMC 55472. PMID 11504932.
Gold L, Brown D, He Y, Shtatland T, Singer BS, Wu Y (January 1997). "From oligonucleotide shapes to genomic SELEX: novel biological regulatory loops". Proceedings of the National Academy of Sciences of the United States of America. 94 (1): 59–64. Bibcode:1997PNAS...94...59G. doi:10.1073/pnas.94.1.59. PMC 19236. PMID 8990161.
Mironov AS, Gusarov I, Rafikov R, Lopez LE, Shatalin K, Kreneva RA, Perumov DA, Nudler E (November 2002). "Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria". Cell. 111 (5): 747–756. doi:10.1016/S0092-8674(02)01134-0. PMID 12464185.
Winkler W, Nahvi A, Breaker RR (October 2002). "Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression". Nature. 419 (6910): 952–956. Bibcode:2002Natur.419..952W. doi:10.1038/nature01145. PMID 12410317. S2CID 4408592.
Winkler WC, Cohen-Chalamish S, Breaker RR (December 2002). "An mRNA structure that controls gene expression by binding FMN". Proceedings of the National Academy of Sciences of the United States of America. 99 (25): 15908–15913. Bibcode:2002PNAS...9915908W. doi:10.1073/pnas.212628899. PMC 138538. PMID 12456892.
Grundy FJ, Henkin TM (November 1998). "The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria". Molecular Microbiology. 30 (4): 737–749. doi:10.1046/j.1365-2958.1998.01105.x. PMID 10094622.
Franklund CV, Kadner RJ (June 1997). "Multiple transcribed elements control expression of the Escherichia coli btuB gene". Journal of Bacteriology. 179 (12): 4039–4042. doi:10.1128/jb.179.12.4039-4042.1997. PMC 179215. PMID 9190822.
Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J, Lee M, Roth A, Sudarsan N, Jona I, Wickiser JK, Breaker RR (April 2004). "New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control". Proceedings of the National Academy of Sciences of the United States of America. 101 (17): 6421–6426. Bibcode:2004PNAS..101.6421B. doi:10.1073/pnas.0308014101. PMC 404060. PMID 15096624.
Corbino KA, Barrick JE, Lim J, Welz R, Tucker BJ, Puskarz I, Mandal M, Rudnick ND, Breaker RR (2005). "Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria". Genome Biology. 6 (8): R70. doi:10.1186/gb-2005-6-8-r70. PMC 1273637. PMID 16086852.
Weinberg Z, Barrick JE, Yao Z, Roth A, Kim JN, Gore J, Wang JX, Lee ER, Block KF, Sudarsan N, Neph S, Tompa M, Ruzzo WL, Breaker RR (2007). "Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline". Nucleic Acids Research. 35 (14): 4809–4819. doi:10.1093/nar/gkm487. PMC 1950547. PMID 17621584.
Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR (March 2010). "Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes". Genome Biology. 11 (3): R31. doi:10.1186/gb-2010-11-3-r31. PMC 2864571. PMID 20230605.
Cheah MT, Wachter A, Sudarsan N, Breaker RR (May 2007). "Control of alternative RNA splicing and gene expression by eukaryotic riboswitches". Nature. 447 (7143): 497–500. Bibcode:2007Natur.447..497C. doi:10.1038/nature05769. PMID 17468745. S2CID 4393918.
Wachter A, Tunc-Ozdemir M, Grove BC, Green PJ, Shintani DK, Breaker RR (November 2007). "Riboswitch control of gene expression in plants by splicing and alternative 3' end processing of mRNAs". The Plant Cell. 19 (11): 3437–3450. doi:10.1105/tpc.107.053645. PMC 2174889. PMID 17993623.
Bocobza S, Adato A, Mandel T, Shapira M, Nudler E, Aharoni A (November 2007). "Riboswitch-dependent gene regulation and its evolution in the plant kingdom". Genes & Development. 21 (22): 2874–2879. doi:10.1101/gad.443907. PMC 2049190. PMID 18006684.
André G, Even S, Putzer H, Burguière P, Croux C, Danchin A, Martin-Verstraete I, Soutourina O (October 2008). "S-box and T-box riboswitches and antisense RNA control a sulfur metabolic operon of Clostridium acetobutylicum". Nucleic Acids Research. 36 (18): 5955–5969. doi:10.1093/nar/gkn601. PMC 2566862. PMID 18812398.
Loh E, Dussurget O, Gripenland J, Vaitkevicius K, Tiensuu T, Mandin P, Repoila F, Buchrieser C, Cossart P, Johansson J (November 2009). "A trans-acting riboswitch controls expression of the virulence regulator PrfA in Listeria monocytogenes". Cell. 139 (4): 770–779. doi:10.1016/j.cell.2009.08.046. PMID 19914169.
Sherman EM, Esquiaqui J, Elsayed G, Ye JD (March 2012). "An energetically beneficial leader-linker interaction abolishes ligand-binding cooperativity in glycine riboswitches". RNA. 18 (3): 496–507. doi:10.1261/rna.031286.111. PMC 3285937. PMID 22279151.
Bocobza SE, Aharoni A (October 2008). "Switching the light on plant riboswitches". Trends Plant Sci. 13 (10): 526–33. Bibcode:2008TPS....13..526B. doi:10.1016/j.tplants.2008.07.004. PMID 18778966.
Barrick JE (2009). "Predicting Riboswitch Regulation on a Genomic Scale". Riboswitches. Methods in Molecular Biology. Vol. 540. pp. 1–13. doi:10.1007/978-1-59745-558-9_1. ISBN 978-1-934115-88-6. PMID 19381548.
Barash D, Gabdank I (January 2010). "Energy minimization applied to riboswitches: a perspective and challenges". RNA Biology. 7 (1): 90–97. doi:10.4161/rna.7.1.10657. PMID 20061789.
Nawrocki EP, Kolbe DL, Eddy SR (May 2009). "Infernal 1.0: inference of RNA alignments". Bioinformatics. 25 (10): 1335–1337. doi:10.1093/bioinformatics/btp157. PMC 2732312. PMID 19307242.
Abreu-Goodger C, Merino E (July 2005). "RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements". Nucleic Acids Research. 33 (Web Server issue): W690-2. doi:10.1093/nar/gki445. PMC 1160206. PMID 15980564.
Chang TH, Huang HD, Wu LC, Yeh CT, Liu BJ, Horng JT (July 2009). "Computational identification of riboswitches based on RNA conserved functional sequences and conformations". RNA. 15 (7): 1426–1430. doi:10.1261/rna.1623809. PMC 2704089. PMID 19460868.
Voss B, Meyer C, Giegerich R (July 2004). "Evaluating the predictability of conformational switching in RNA". Bioinformatics. 20 (10): 1573–1582. doi:10.1093/bioinformatics/bth129. PMID 14962925.
Janssen S, Giegerich R (February 2015). "The RNA shapes studio". Bioinformatics. 31 (3): 423–425. doi:10.1093/bioinformatics/btu649. PMC 4308662. PMID 25273103.
Freyhult E, Moulton V, Clote P (August 2007). "Boltzmann probability of RNA structural neighbors and riboswitch detection". Bioinformatics. 23 (16): 2054–2062. doi:10.1093/bioinformatics/btm314. PMID 17573364.
Clote P, Lou F, Lorenz WA (April 2012). "Maximum expected accuracy structural neighbors of an RNA secondary structure". BMC Bioinformatics. 13 (Suppl 5): S6. doi:10.1186/1471-2105-13-S5-S6. PMC 3358666. PMID 22537010.
Barsacchi M, Novoa EM, Kellis M, Bechini A (November 2016). "SwiSpot: modeling riboswitches by spotting out switching sequences". Bioinformatics. 32 (21): 3252–3259. doi:10.1093/bioinformatics/btw401. hdl:11568/817190. PMID 27378291.
Rekand, Illimar Hugo; Brenk, Ruth (2021-08-23). "DrugPred_RNA—A Tool for Structure-Based Druggability Predictions for RNA Binding Sites". Journal of Chemical Information and Modeling. 61 (8): 4068–4081. doi:10.1021/acs.jcim.1c00155. ISSN 1549-9596. PMC 8389535. PMID 34286972. Retrieved 2024-03-12.
Ramaswamy Krishnan, Sowmya; Roy, Arijit; Wong, Limsoon; Gromiha, M Michael (2025-04-11). "DRLiPS: a novel method for prediction of druggable RNA-small molecule binding pockets using machine learning". Nucleic Acids Research. 53 (6): 239. doi:10.1093/nar/gkaf239. ISSN 1362-4962. PMC 11963762. PMID 40173014. Retrieved 2025-06-10.
Xie, Jingru; Frank, Aaron T. (2021-06-10). "Mining for Ligandable Cavities in RNA". ACS Medicinal Chemistry Letters. 12 (6): 928–934. doi:10.1021/acsmedchemlett.1c00068. PMC 8201482. PMID 34141071. Retrieved 2025-06-10.
Cochrane JC, Strobel SA (June 2008). "Riboswitch effectors as protein enzyme cofactors". RNA. 14 (6): 993–1002. doi:10.1261/rna.908408. PMC 2390802. PMID 18430893.
Yu, Ai-Ming; Choi, Young Hee; Tu, Mei-Juan (2020). "RNA Drugs and RNA Targets for Small Molecules: Principles, Progress, and Challenges". Pharmacological Reviews. 72 (4): 862–898. doi:10.1124/pr.120.019554. ISSN 1521-0081. PMC 7495341. PMID 32929000.
Panchal, Vipul; Brenk, Ruth (January 2021). "Riboswitches as Drug Targets for Antibiotics". Antibiotics. 10 (1): 45. doi:10.3390/antibiotics10010045. PMC 7824784. PMID 33466288.
Hewitt, William M.; Calabrese, David R.; Schneekloth, John S. (2019-06-01). "Evidence for ligandable sites in structured RNA throughout the Protein Data Bank". Bioorganic & Medicinal Chemistry. 27 (11): 2253–2260. doi:10.1016/j.bmc.2019.04.010. ISSN 0968-0896. PMC 8283815. PMID 30982658.
Rekand, Illimar Hugo; Brenk, Ruth (2021-08-23). "DrugPred_RNA—A Tool for Structure-Based Druggability Predictions for RNA Binding Sites". Journal of Chemical Information and Modeling. 61 (8): 4068–4081. doi:10.1021/acs.jcim.1c00155. ISSN 1549-9596. PMC 8389535. PMID 34286972. Retrieved 2024-03-12.
Rekand, Illimar; Brenk, Ruth (2017). "Design of riboswitch ligands, an emerging target class for novel antibiotics". Future Med Chem. 9 (14): 1649–1662. doi:10.4155/fmc-2017-0063. PMID 28925284.
Blount KF, Breaker RR (December 2006). "Riboswitches as antibacterial drug targets". Nature Biotechnology. 24 (12): 1558–1564. doi:10.1038/nbt1268. PMID 17160062. S2CID 34398395.
Bauer G, Suess B (June 2006). "Engineered riboswitches as novel tools in molecular biology". Journal of Biotechnology. 124 (1): 4–11. doi:10.1016/j.jbiotec.2005.12.006. PMID 16442180.
Dixon N, Duncan JN, Geerlings T, Dunstan MS, McCarthy JE, Leys D, Micklefield J (February 2010). "Reengineering orthogonally selective riboswitches". Proceedings of the National Academy of Sciences of the United States of America. 107 (7): 2830–2835. Bibcode:2010PNAS..107.2830D. doi:10.1073/pnas.0911209107. PMC 2840279. PMID 20133756.
Verhounig A, Karcher D, Bock R (April 2010). "Inducible gene expression from the plastid genome by a synthetic riboswitch". Proceedings of the National Academy of Sciences of the United States of America. 107 (14): 6204–6209. Bibcode:2010PNAS..107.6204V. doi:10.1073/pnas.0914423107. PMC 2852001. PMID 20308585.
Fernandez-de-Cossio-Diaz, Jorge; Hardouin, Pierre; Moutier, Francois-Xavier Lyonnet du; Gioacchino, Andrea Di; Marchand, Bertrand; Ponty, Yann; Sargueil, Bruno; Monasson, Rémi; Cocco, Simona (2024-04-20), Designing Molecular RNA Switches with Restricted Boltzmann Machines, doi:10.1101/2023.05.10.540155, retrieved 2024-11-10
Ketzer P, Kaufmann JK, Engelhardt S, Bossow S, von Kalle C, Hartig JS, Ungerechts G, Nettelbeck DM (February 2014). "Artificial riboswitches for gene expression and replication control of DNA and RNA viruses". Proceedings of the National Academy of Sciences of the United States of America. 111 (5): E554–562. Bibcode:2014PNAS..111E.554K. doi:10.1073/pnas.1318563111. PMC 3918795. PMID 24449891.
Strobel B, Klauser B, Hartig JS, Lamla T, Gantner F, Kreuz S (October 2015). "Riboswitch-mediated Attenuation of Transgene Cytotoxicity Increases Adeno-associated Virus Vector Yields in HEK-293 Cells". Molecular Therapy. 23 (10): 1582–1591. doi:10.1038/mt.2015.123. PMC 4817922. PMID 26137851.

handle.net

hdl.handle.net

Barsacchi M, Novoa EM, Kellis M, Bechini A (November 2016). "SwiSpot: modeling riboswitches by spotting out switching sequences". Bioinformatics. 32 (21): 3252–3259. doi:10.1093/bioinformatics/btw401. hdl:11568/817190. PMID 27378291.

harvard.edu

ui.adsabs.harvard.edu

Nou X, Kadner RJ (June 2000). "Adenosylcobalamin inhibits ribosome binding to btuB RNA". Proceedings of the National Academy of Sciences of the United States of America. 97 (13): 7190–7195. Bibcode:2000PNAS...97.7190N. doi:10.1073/pnas.130013897. PMC 16521. PMID 10852957.
Stormo GD, Ji Y (August 2001). "Do mRNAs act as direct sensors of small molecules to control their expression?". Proceedings of the National Academy of Sciences of the United States of America. 98 (17): 9465–9467. Bibcode:2001PNAS...98.9465S. doi:10.1073/pnas.181334498. PMC 55472. PMID 11504932.
Gold L, Brown D, He Y, Shtatland T, Singer BS, Wu Y (January 1997). "From oligonucleotide shapes to genomic SELEX: novel biological regulatory loops". Proceedings of the National Academy of Sciences of the United States of America. 94 (1): 59–64. Bibcode:1997PNAS...94...59G. doi:10.1073/pnas.94.1.59. PMC 19236. PMID 8990161.
Winkler W, Nahvi A, Breaker RR (October 2002). "Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression". Nature. 419 (6910): 952–956. Bibcode:2002Natur.419..952W. doi:10.1038/nature01145. PMID 12410317. S2CID 4408592.
Winkler WC, Cohen-Chalamish S, Breaker RR (December 2002). "An mRNA structure that controls gene expression by binding FMN". Proceedings of the National Academy of Sciences of the United States of America. 99 (25): 15908–15913. Bibcode:2002PNAS...9915908W. doi:10.1073/pnas.212628899. PMC 138538. PMID 12456892.
Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J, Lee M, Roth A, Sudarsan N, Jona I, Wickiser JK, Breaker RR (April 2004). "New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control". Proceedings of the National Academy of Sciences of the United States of America. 101 (17): 6421–6426. Bibcode:2004PNAS..101.6421B. doi:10.1073/pnas.0308014101. PMC 404060. PMID 15096624.
Cheah MT, Wachter A, Sudarsan N, Breaker RR (May 2007). "Control of alternative RNA splicing and gene expression by eukaryotic riboswitches". Nature. 447 (7143): 497–500. Bibcode:2007Natur.447..497C. doi:10.1038/nature05769. PMID 17468745. S2CID 4393918.
Bocobza SE, Aharoni A (October 2008). "Switching the light on plant riboswitches". Trends Plant Sci. 13 (10): 526–33. Bibcode:2008TPS....13..526B. doi:10.1016/j.tplants.2008.07.004. PMID 18778966.
Dixon N, Duncan JN, Geerlings T, Dunstan MS, McCarthy JE, Leys D, Micklefield J (February 2010). "Reengineering orthogonally selective riboswitches". Proceedings of the National Academy of Sciences of the United States of America. 107 (7): 2830–2835. Bibcode:2010PNAS..107.2830D. doi:10.1073/pnas.0911209107. PMC 2840279. PMID 20133756.
Verhounig A, Karcher D, Bock R (April 2010). "Inducible gene expression from the plastid genome by a synthetic riboswitch". Proceedings of the National Academy of Sciences of the United States of America. 107 (14): 6204–6209. Bibcode:2010PNAS..107.6204V. doi:10.1073/pnas.0914423107. PMC 2852001. PMID 20308585.
Ketzer P, Kaufmann JK, Engelhardt S, Bossow S, von Kalle C, Hartig JS, Ungerechts G, Nettelbeck DM (February 2014). "Artificial riboswitches for gene expression and replication control of DNA and RNA viruses". Proceedings of the National Academy of Sciences of the United States of America. 111 (5): E554–562. Bibcode:2014PNAS..111E.554K. doi:10.1073/pnas.1318563111. PMC 3918795. PMID 24449891.

igem.org

2011.igem.org

"Team:BYU Provo/Results - 2011.igem.org". 2011.igem.org.

nih.gov

pubmed.ncbi.nlm.nih.gov

Nudler E, Mironov AS (January 2004). "The riboswitch control of bacterial metabolism". Trends in Biochemical Sciences. 29 (1): 11–17. doi:10.1016/j.tibs.2003.11.004. PMID 14729327.
Tucker BJ, Breaker RR (June 2005). "Riboswitches as versatile gene control elements". Current Opinion in Structural Biology. 15 (3): 342–348. doi:10.1016/j.sbi.2005.05.003. PMID 15919195.
Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS (January 2004). "Riboswitches: the oldest mechanism for the regulation of gene expression?". Trends in Genetics. 20 (1): 44–50. CiteSeerX 10.1.1.312.9100. doi:10.1016/j.tig.2003.11.008. PMID 14698618.
Batey RT (June 2006). "Structures of regulatory elements in mRNAs". Current Opinion in Structural Biology. 16 (3): 299–306. doi:10.1016/j.sbi.2006.05.001. PMID 16707260.
Nahvi A, Sudarsan N, Ebert MS, Zou X, Brown KL, Breaker RR (September 2002). "Genetic control by a metabolite binding mRNA". Chemistry & Biology. 9 (9): 1043–1049. doi:10.1016/S1074-5521(02)00224-7. PMID 12323379.
Sudarsan N, Barrick JE, Breaker RR (June 2003). "Metabolite-binding RNA domains are present in the genes of eukaryotes". RNA. 9 (6): 644–647. doi:10.1261/rna.5090103. PMC 1370431. PMID 12756322.
Nou X, Kadner RJ (June 2000). "Adenosylcobalamin inhibits ribosome binding to btuB RNA". Proceedings of the National Academy of Sciences of the United States of America. 97 (13): 7190–7195. Bibcode:2000PNAS...97.7190N. doi:10.1073/pnas.130013897. PMC 16521. PMID 10852957.
Gelfand MS, Mironov AA, Jomantas J, Kozlov YI, Perumov DA (November 1999). "A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes". Trends in Genetics. 15 (11): 439–442. doi:10.1016/S0168-9525(99)01856-9. PMID 10529804.
Miranda-Ríos J, Navarro M, Soberón M (August 2001). "A conserved RNA structure (thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria". Proceedings of the National Academy of Sciences of the United States of America. 98 (17): 9736–9741. doi:10.1073/pnas.161168098. PMC 55522. PMID 11470904.
Stormo GD, Ji Y (August 2001). "Do mRNAs act as direct sensors of small molecules to control their expression?". Proceedings of the National Academy of Sciences of the United States of America. 98 (17): 9465–9467. Bibcode:2001PNAS...98.9465S. doi:10.1073/pnas.181334498. PMC 55472. PMID 11504932.
Gold L, Brown D, He Y, Shtatland T, Singer BS, Wu Y (January 1997). "From oligonucleotide shapes to genomic SELEX: novel biological regulatory loops". Proceedings of the National Academy of Sciences of the United States of America. 94 (1): 59–64. Bibcode:1997PNAS...94...59G. doi:10.1073/pnas.94.1.59. PMC 19236. PMID 8990161.
Mironov AS, Gusarov I, Rafikov R, Lopez LE, Shatalin K, Kreneva RA, Perumov DA, Nudler E (November 2002). "Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria". Cell. 111 (5): 747–756. doi:10.1016/S0092-8674(02)01134-0. PMID 12464185.
Winkler W, Nahvi A, Breaker RR (October 2002). "Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression". Nature. 419 (6910): 952–956. Bibcode:2002Natur.419..952W. doi:10.1038/nature01145. PMID 12410317. S2CID 4408592.
Winkler WC, Cohen-Chalamish S, Breaker RR (December 2002). "An mRNA structure that controls gene expression by binding FMN". Proceedings of the National Academy of Sciences of the United States of America. 99 (25): 15908–15913. Bibcode:2002PNAS...9915908W. doi:10.1073/pnas.212628899. PMC 138538. PMID 12456892.
Grundy FJ, Henkin TM (November 1998). "The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria". Molecular Microbiology. 30 (4): 737–749. doi:10.1046/j.1365-2958.1998.01105.x. PMID 10094622.
Franklund CV, Kadner RJ (June 1997). "Multiple transcribed elements control expression of the Escherichia coli btuB gene". Journal of Bacteriology. 179 (12): 4039–4042. doi:10.1128/jb.179.12.4039-4042.1997. PMC 179215. PMID 9190822.
Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J, Lee M, Roth A, Sudarsan N, Jona I, Wickiser JK, Breaker RR (April 2004). "New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control". Proceedings of the National Academy of Sciences of the United States of America. 101 (17): 6421–6426. Bibcode:2004PNAS..101.6421B. doi:10.1073/pnas.0308014101. PMC 404060. PMID 15096624.
Corbino KA, Barrick JE, Lim J, Welz R, Tucker BJ, Puskarz I, Mandal M, Rudnick ND, Breaker RR (2005). "Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria". Genome Biology. 6 (8): R70. doi:10.1186/gb-2005-6-8-r70. PMC 1273637. PMID 16086852.
Weinberg Z, Barrick JE, Yao Z, Roth A, Kim JN, Gore J, Wang JX, Lee ER, Block KF, Sudarsan N, Neph S, Tompa M, Ruzzo WL, Breaker RR (2007). "Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline". Nucleic Acids Research. 35 (14): 4809–4819. doi:10.1093/nar/gkm487. PMC 1950547. PMID 17621584.
Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR (March 2010). "Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes". Genome Biology. 11 (3): R31. doi:10.1186/gb-2010-11-3-r31. PMC 2864571. PMID 20230605.
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Rekand, Illimar Hugo; Brenk, Ruth (2021-08-23). "DrugPred_RNA—A Tool for Structure-Based Druggability Predictions for RNA Binding Sites". Journal of Chemical Information and Modeling. 61 (8): 4068–4081. doi:10.1021/acs.jcim.1c00155. ISSN 1549-9596. PMC 8389535. PMID 34286972. Retrieved 2024-03-12.
Ramaswamy Krishnan, Sowmya; Roy, Arijit; Wong, Limsoon; Gromiha, M Michael (2025-04-11). "DRLiPS: a novel method for prediction of druggable RNA-small molecule binding pockets using machine learning". Nucleic Acids Research. 53 (6): 239. doi:10.1093/nar/gkaf239. ISSN 1362-4962. PMC 11963762. PMID 40173014. Retrieved 2025-06-10.
Yu, Ai-Ming; Choi, Young Hee; Tu, Mei-Juan (2020). "RNA Drugs and RNA Targets for Small Molecules: Principles, Progress, and Challenges". Pharmacological Reviews. 72 (4): 862–898. doi:10.1124/pr.120.019554. ISSN 1521-0081. PMC 7495341. PMID 32929000.
Hewitt, William M.; Calabrese, David R.; Schneekloth, John S. (2019-06-01). "Evidence for ligandable sites in structured RNA throughout the Protein Data Bank". Bioorganic & Medicinal Chemistry. 27 (11): 2253–2260. doi:10.1016/j.bmc.2019.04.010. ISSN 0968-0896. PMC 8283815. PMID 30982658.
Rekand, Illimar Hugo; Brenk, Ruth (2021-08-23). "DrugPred_RNA—A Tool for Structure-Based Druggability Predictions for RNA Binding Sites". Journal of Chemical Information and Modeling. 61 (8): 4068–4081. doi:10.1021/acs.jcim.1c00155. ISSN 1549-9596. PMC 8389535. PMID 34286972. Retrieved 2024-03-12.