Cross-linking immunoprecipitation (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Cross-linking immunoprecipitation" in English language version.

refsWebsite

Global rank English rank

86nih.gov

4^th place

46doi.org

2^nd place

19worldcat.org

5^th place

5harvard.edu

18^th place

17^th place

3semanticscholar.org

11^th place

8^th place

doi.org

Ule, Jernej; Jensen, Kirk B.; Ruggiu, Matteo; Mele, Aldo; Ule, Aljaz; Darnell, Robert B. (2003-11-14). "CLIP identifies Nova-regulated RNA networks in the brain". Science. 302 (5648): 1212–1215. Bibcode:2003Sci...302.1212U. doi:10.1126/science.1090095. ISSN 1095-9203. PMID 14615540. S2CID 23420615.
Hafner, Markus; Katsantoni, Maria; Köster, Tino; Marks, James; Mukherjee, Joyita; Staiger, Dorothee; Ule, Jernej; Zavolan, Mihaela (2021-03-04). "CLIP and complementary methods". Nature Reviews Methods Primers. 1 (1): 1–23. doi:10.1038/s43586-021-00018-1. ISSN 2662-8449. S2CID 233834798.
Ule, Jernej; Hwang, Hun-Way; Darnell, Robert B. (2018-08-01). "The Future of Cross-Linking and Immunoprecipitation (CLIP)". Cold Spring Harbor Perspectives in Biology. 10 (8): a032243. doi:10.1101/cshperspect.a032243. ISSN 1943-0264. PMC 6071486. PMID 30068528.
Lee, Flora C. Y.; Ule, Jernej (2018-02-01). "Advances in CLIP Technologies for Studies of Protein-RNA Interactions". Molecular Cell. 69 (3): 354–369. doi:10.1016/j.molcel.2018.01.005. ISSN 1097-4164. PMID 29395060.
Darnell 2010. Darnell, RB (2010). "HITS-CLIP: panoramic views of protein-RNA regulation in living cells". Wiley Interdiscip Rev RNA. 1 (2): 266–286. doi:10.1002/wrna.31. PMC 3222227. PMID 21935890.
König, Julian; Zarnack, Kathi; Rot, Gregor; Curk, Tomaz; Kayikci, Melis; Zupan, Blaz; Turner, Daniel J.; Luscombe, Nicholas M.; Ule, Jernej (July 2010). "iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution". Nature Structural & Molecular Biology. 17 (7): 909–915. doi:10.1038/nsmb.1838. ISSN 1545-9985. PMC 3000544. PMID 20601959.
Licatalosi et al. 2008. Licatalosi, DD; Mele, A; Fak, JJ; Ule, J; Kayikci, M; Chi, SW; Clark, TA; Schweitzer, AC; Blume, JE; Wang, X; Darnell, JC; Darnell, RB (2008). "HITS-CLIP yields genome-wide insights into brain alternative RNA processing". Nature. 456 (7221): 464–469. Bibcode:2008Natur.456..464L. doi:10.1038/nature07488. PMC 2597294. PMID 18978773.
Xue et al. 2009. Xue, Y; Zhou, Y; Wu, T; Zhu, T; Ju, X; Kwon, YS; Zhang, C; Yeo, G; Black, DL; Sun, H; Fu, XD; Zhang, Y (2009). "Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping". Molecular Cell. 36 (6): 996–1006. doi:10.1016/j.molcel.2009.12.003. PMC 2807993. PMID 20064465.
Yeo et al. 2009. Yeo, GW; Coufal, NG; Liang, TY; Peng, GE; Fu, XD; Gage, FH (2009). "An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells". Nat Struct Mol Biol. 16 (2): 130–137. doi:10.1038/nsmb.1545. PMC 2735254. PMID 19136955.
Sanford et al. 2009. Sanford, JR; Wang, X; Mort, M; Fanduyn, N; Cooper, DN; Mooney, SD; Edenberg, HJ; Liu, Y (2009). "Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts". Genome Research. 19 (3): 381–394. doi:10.1101/gr.082503.108. PMC 2661799. PMID 19116412.
Chi et al. 2009. Chi, SW; Zang, JB; Mele, A; Darnell, RB (2009). "Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps". Nature. 460 (7254): 479–486. Bibcode:2009Natur.460..479C. doi:10.1038/nature08170. PMC 2733940. PMID 19536157.
Moore et al. 2014. Moore, JJ; Zhang, C; Gantman, EC; Mele, A; Darnell, JC; Darnell, RB (2014). "Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis". Nature Protocols. 9 (2): 263–293. doi:10.1038/nprot.2014.012. PMC 4156013. PMID 24407355.
Chi, Sung Wook; Hannon, Gregory J.; Darnell, Robert B. (2012-02-12). "An alternative mode of microRNA target recognition". Nature Structural & Molecular Biology. 19 (3): 321–327. doi:10.1038/nsmb.2230. ISSN 1545-9985. PMC 3541676. PMID 22343717.
Darnell et al. 2011. Darnell, JC; Van Driesche, SJ; Zhang, C; Hung, KY; Mele, A; Fraser, CE; Stone, EF; Chen, C; Fak, JJ; Chi, SW; Licatalosi, DD; Richter, JD; Darnell, RB (2011). "FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism". Cell. 146 (2): 247–261. doi:10.1016/j.cell.2011.06.013. PMC 3232425. PMID 21784246.
Hale, Caryn R.; Sawicka, Kirsty; Mora, Kevin; Fak, John J.; Kang, Jin Joo; Cutrim, Paula; Cialowicz, Katarzyna; Carroll, Thomas S.; Darnell, Robert B. (2021-12-23). "FMRP regulates mRNAs encoding distinct functions in the cell body and dendrites of CA1 pyramidal neurons". eLife. 10: e71892. doi:10.7554/eLife.71892. ISSN 2050-084X. PMC 8820740. PMID 34939924.
Licatalosi et al. 2012. Licatalosi, DD; Yano, M; Fak, JJ; Mele, A; Grabinski, SE; Zhang, C; Darnell, RB (2012). "Ptbp2 represses adult-specific splicing to regulate the generation of neuronal precursors in the embryonic brain". Genes Dev. 26 (14): 1626–1642. doi:10.1101/gad.191338.112. PMC 3404389. PMID 22802532.
Charizanis et al. 2012. Charizanis, K; Lee, KY; Batra, R; Goodwin, M; Zhang, C; Yuan, Y; Shiue, L; Cline, M; Scotti, MM; Xia, G; Kumar, A; Ashizawa, T; Clark, HB; Kimura, T; Takahashi, MP; Fujimura, H; Jinnai, K; Yoshikawa, H; Gomes–Pereira, M; Gourdon, G; Sakai, N; Nishino, S; Foster, TC; Ares, M; Darnell, RB; Swanson, MS (2012). "Muscleblind-like 2-mediated alternative splicing in the developing brain and dysregulation in myotonic dystrophy". Neuron. 75 (3): 437–450. doi:10.1016/j.neuron.2012.05.029. PMC 3418517. PMID 22884328.
Ince-Dunn et al. 2012. Ince-Dunn, G; Okano, HJ; Jensen, KB; Park, WY; Zhong, R; Ule, J; Mele, A; Fak, JJ; Yang, CW; Zhang, C; Yoo, J; Herre, M; Okano, H; Noebels, JL; Darnell, RB (2012). "Neuronal Elav-like (Hu) proteins regulate RNA splicing and abundance to control glutamate levels and neuronal excitability". Neuron. 75 (6): 1067–1080. doi:10.1016/j.neuron.2012.07.009. PMC 3517991. PMID 22998874.
Holmqvist et al. 2016. Holmqvist, E; Wright, PR; Li, L; Bischler, T; Barquist, L; Reinhardt, R; Backofen, R; Vogel, J (2016). "Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo". EMBO J. 35 (9): 991–1011. doi:10.15252/embj.201593360. PMC 5207318. PMID 27044921.
Thomson, Bracken & Goodall 2011. Thomson, DW; Bracken, CP; Goodall, GJ (2011). "Experimental strategies for microRNA target identification". Nucleic Acids Research. 39 (16): 6845–6853. doi:10.1093/nar/gkr330. PMC 3167600. PMID 21652644.
Yang et al. 2011. Yang, JH; Li, JH; Shao, P; Zhou, H; Chen, YQ; Qu, LH (2011). "starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data". Nucleic Acids Res. 39 (Database issue): D202–D209. doi:10.1093/nar/gkq1056. PMC 3013664. PMID 21037263.
Wolf, Joshua J.; Dowell, Robin D.; Mahony, Shaun; Rabani, Michal; Gifford, David K.; Fink, Gerald R. (June 2010). "Feed-forward regulation of a cell fate determinant by an RNA-binding protein generates asymmetry in yeast". Genetics. 185 (2): 513–522. doi:10.1534/genetics.110.113944. ISSN 1943-2631. PMC 2881133. PMID 20382833.
Zisoulis et al. 2010. Zisoulis, DG; Lovci, MT; Wilbert, ML; Hutt, KR; Liang, TY; Pasquinelli, AE; Yeo, GW (2010). "Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans". Nat Struct Mol Biol. 17 (2): 173–179. doi:10.1038/nsmb.1745. PMC 2834287. PMID 20062054.
Leung et al. 2011. Leung, AK; Young, AG; Bhutkar, A; Zheng, GX; Bosson, AD; Nielsen, CB; Sharp, PA (2011). "Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs". Nat Struct Mol Biol. 19 (9): 1084. doi:10.1038/nsmb0911-1084a. PMC 3078052.
Hafner, Markus; Landthaler, Markus; Burger, Lukas; Khorshid, Mohsen; Hausser, Jean; Berninger, Philipp; Rothballer, Andrea; Ascano, Manuel; Jungkamp, Anna-Carina; Munschauer, Mathias; Ulrich, Alexander; Wardle, Greg S.; Dewell, Scott; Zavolan, Mihaela; Tuschl, Thomas (2010-04-02). "Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP". Cell. 141 (1): 129–141. doi:10.1016/j.cell.2010.03.009. ISSN 1097-4172. PMC 2861495. PMID 20371350.
Sugimoto et al. 2012. Sugimoto, Y; König, J; Hussain, S; Zupan, B; Curk, T; Frye, M; Ule, J (Aug 3, 2012). "Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions". Genome Biology. 13 (8): R67. doi:10.1186/gb-2012-13-8-r67. PMC 4053741. PMID 22863408.
König et al. 2012. König, J; Zarnack, K; Luscombe, NM; Ule, J (2012). "Protein-RNA interactions: new genomic technologies and perspectives". Nature Reviews Genetics. 13 (2): 77–83. doi:10.1038/nrg3141. PMC 4962561. PMID 22251872.
Zhang & Darnell 2011. Zhang, C; Darnell, RB (2011). "Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data". Nature Biotechnology. 29 (7): 607–614. doi:10.1038/nbt.1873. PMC 3400429. PMID 21633356.
Burger et al. 2013. Burger, K; Mühl, B; Kellner, M; Rohrmoser, M; Gruber-Eber, A; Windhager, L; Friedel, CC; Dölken, L; Eick, D (2013). "4-thiouridine inhibits rRNA synthesis and causes a nucleolar stress response". RNA Biol. 10 (10): 1623–1630. doi:10.4161/rna.26214. PMC 3866244. PMID 24025460.
Zhang, Chaolin; Darnell, Robert B (1 June 2011). "Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data". Nature Biotechnology. 29 (7): 607–614. doi:10.1038/nbt.1873. PMC 3400429. PMID 21633356.
Hussain, Shobbir; Sajini, Abdulrahim A.; Blanco, Sandra; Dietmann, Sabine; Lombard, Patrick; Sugimoto, Yoichiro; Paramor, Maike; Gleeson, Joseph G.; Odom, Duncan T.; Ule, Jernej; Frye, Michaela (2013-07-25). "NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs". Cell Reports. 4 (2): 255–261. doi:10.1016/j.celrep.2013.06.029. ISSN 2211-1247. PMC 3730056. PMID 23871666.
Linder, Bastian; Grozhik, Anya V.; Olarerin-George, Anthony O.; Meydan, Cem; Mason, Christopher E.; Jaffrey, Samie R. (August 2015). "Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome". Nature Methods. 12 (8): 767–772. doi:10.1038/nmeth.3453. ISSN 1548-7105. PMC 4487409. PMID 26121403.
Tollervey, James R.; Curk, Tomaž; Rogelj, Boris; Briese, Michael; Cereda, Matteo; Kayikci, Melis; König, Julian; Hortobágyi, Tibor; Nishimura, Agnes L.; Zupunski, Vera; Patani, Rickie; Chandran, Siddharthan; Rot, Gregor; Zupan, Blaž; Shaw, Christopher E. (April 2011). "Characterizing the RNA targets and position-dependent splicing regulation by TDP-43". Nature Neuroscience. 14 (4): 452–458. doi:10.1038/nn.2778. ISSN 1546-1726. PMC 3108889. PMID 21358640.
Zarnack, Kathi; König, Julian; Tajnik, Mojca; Martincorena, Iñigo; Eustermann, Sebastian; Stévant, Isabelle; Reyes, Alejandro; Anders, Simon; Luscombe, Nicholas M.; Ule, Jernej (2013-01-31). "Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements". Cell. 152 (3): 453–466. doi:10.1016/j.cell.2012.12.023. ISSN 1097-4172. PMC 3629564. PMID 23374342.
Hallegger, Martina; Chakrabarti, Anob M.; Lee, Flora C. Y.; Lee, Bo Lim; Amalietti, Aram G.; Odeh, Hana M.; Copley, Katie E.; Rubien, Jack D.; Portz, Bede; Kuret, Klara; Huppertz, Ina; Rau, Frédérique; Patani, Rickie; Fawzi, Nicolas L.; Shorter, James (2021-09-02). "TDP-43 condensation properties specify its RNA-binding and regulatory repertoire". Cell. 184 (18): 4680–4696.e22. doi:10.1016/j.cell.2021.07.018. ISSN 1097-4172. PMC 8445024. PMID 34380047.
Van Nostrand, Pratt & Shishkin 2016. Van Nostrand, E; Pratt, G; Shishkin, A (2016). "Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)". Nature Methods. 13 (6): 508–514. doi:10.1038/nmeth.3810. PMC 4887338. PMID 27018577.
Van Nostrand, Eric L.; Freese, Peter; Pratt, Gabriel A.; Wang, Xiaofeng; Wei, Xintao; Xiao, Rui; Blue, Steven M.; Chen, Jia-Yu; Cody, Neal A. L.; Dominguez, Daniel; Olson, Sara; Sundararaman, Balaji; Zhan, Lijun; Bazile, Cassandra; Bouvrette, Louis Philip Benoit (July 2020). "A large-scale binding and functional map of human RNA-binding proteins". Nature. 583 (7818): 711–719. Bibcode:2020Natur.583..711V. doi:10.1038/s41586-020-2077-3. ISSN 1476-4687. PMC 7410833. PMID 32728246.
Kargapolova et al. 2017. Kargapolova, Y; Levin, M; Lackner, K; Danckwardt, S (2017). "sCLIP—an integrated platform to study RNA–protein interactomes in biomedical research: identification of CSTF2tau in alternative processing of small nuclear RNAs". Nucleic Acids Res. 45 (10): 6074–6086. doi:10.1093/nar/gkx152. PMC 5449641. PMID 28334977.
Ke, Shengdong; Alemu, Endalkachew A.; Mertens, Claudia; Gantman, Emily Conn; Fak, John J.; Mele, Aldo; Haripal, Bhagwattie; Zucker-Scharff, Ilana; Moore, Michael J.; Park, Christopher Y.; Vågbø, Cathrine Broberg; Kusśnierczyk, Anna; Klungland, Arne; Darnell, James E.; Darnell, Robert B. (2015-10-01). "A majority of m6A residues are in the last exons, allowing the potential for 3' UTR regulation". Genes & Development. 29 (19): 2037–2053. doi:10.1101/gad.269415.115. ISSN 1549-5477. PMC 4604345. PMID 26404942.
Mili & Steitz 2004. Mili, S; Steitz, JA (2004). "Evidence for reassociation of RNA-binding proteins after cell lysis: Implications for the interpretation of immunoprecipitation analyses". RNA. 10 (11): 1692–4. doi:10.1261/rna.7151404. PMC 1370654. PMID 15388877.
Chakrabarti, Anob M.; Haberman, Nejc; Praznik, Arne; Luscombe, Nicholas M.; Ule, Jernej (2018-07-20). "Data Science Issues in Studying Protein–RNA Interactions with CLIP Technologies". Annual Review of Biomedical Data Science. 1 (1): 235–261. doi:10.1146/annurev-biodatasci-080917-013525. ISSN 2574-3414. PMC 7614488. PMID 37123514. S2CID 90760475.
Ule et al. 2005. Ule, J; Jensen, K; Mele, A; Darnell, RB (2005). "CLIP: a method for identifying protein-RNA interactions sites in living cells". Methods. 37 (4): 376–386. doi:10.1016/j.ymeth.2005.07.018. PMID 16314267.
Knörlein, Anna; Sarnowski, Chris P.; de Vries, Tebbe; Stoltz, Moritz; Götze, Michael; Aebersold, Ruedi; Allain, Frédéric H.-T.; Leitner, Alexander; Hall, Jonathan (2022-05-17). "Nucleotide-amino acid π-stacking interactions initiate photo cross-linking in RNA-protein complexes". Nature Communications. 13 (1): 2719. Bibcode:2022NatCo..13.2719K. doi:10.1038/s41467-022-30284-w. ISSN 2041-1723. PMC 9114321. PMID 35581222.
Bohnsack et al. 2009. Bohnsack, MT; Martin, R; Granneman, S; Ruprecht, M; Schleiff, E; Tollervey, D (2009). "Prp43 bound at different sites on the pre-rRNA performs distinct functions in ribosome synthesis". Molecular Cell. 36 (4): 583–592. doi:10.1016/j.molcel.2009.09.039. PMC 2806949. PMID 19941819.
Kuret, Klara; Amalietti, Aram Gustav; Jones, D. Marc; Capitanchik, Charlotte; Ule, Jernej (2022-09-09). "Positional motif analysis reveals the extent of specificity of protein-RNA interactions observed by CLIP". Genome Biology. 23 (1): 191. doi:10.1186/s13059-022-02755-2. ISSN 1474-760X. PMC 9461102. PMID 36085079.
Agarwal et al. 2015. Agarwal, V; Bell, GW; Nam, J-W; Bartel, DP (2015). "Predicting effective microRNA target sites in mammalian mRNAs". eLife. 4: e05005. doi:10.7554/eLife.05005. PMC 4532895. PMID 26267216.

harvard.edu

ui.adsabs.harvard.edu

Ule, Jernej; Jensen, Kirk B.; Ruggiu, Matteo; Mele, Aldo; Ule, Aljaz; Darnell, Robert B. (2003-11-14). "CLIP identifies Nova-regulated RNA networks in the brain". Science. 302 (5648): 1212–1215. Bibcode:2003Sci...302.1212U. doi:10.1126/science.1090095. ISSN 1095-9203. PMID 14615540. S2CID 23420615.
Licatalosi et al. 2008. Licatalosi, DD; Mele, A; Fak, JJ; Ule, J; Kayikci, M; Chi, SW; Clark, TA; Schweitzer, AC; Blume, JE; Wang, X; Darnell, JC; Darnell, RB (2008). "HITS-CLIP yields genome-wide insights into brain alternative RNA processing". Nature. 456 (7221): 464–469. Bibcode:2008Natur.456..464L. doi:10.1038/nature07488. PMC 2597294. PMID 18978773.
Chi et al. 2009. Chi, SW; Zang, JB; Mele, A; Darnell, RB (2009). "Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps". Nature. 460 (7254): 479–486. Bibcode:2009Natur.460..479C. doi:10.1038/nature08170. PMC 2733940. PMID 19536157.
Van Nostrand, Eric L.; Freese, Peter; Pratt, Gabriel A.; Wang, Xiaofeng; Wei, Xintao; Xiao, Rui; Blue, Steven M.; Chen, Jia-Yu; Cody, Neal A. L.; Dominguez, Daniel; Olson, Sara; Sundararaman, Balaji; Zhan, Lijun; Bazile, Cassandra; Bouvrette, Louis Philip Benoit (July 2020). "A large-scale binding and functional map of human RNA-binding proteins". Nature. 583 (7818): 711–719. Bibcode:2020Natur.583..711V. doi:10.1038/s41586-020-2077-3. ISSN 1476-4687. PMC 7410833. PMID 32728246.
Knörlein, Anna; Sarnowski, Chris P.; de Vries, Tebbe; Stoltz, Moritz; Götze, Michael; Aebersold, Ruedi; Allain, Frédéric H.-T.; Leitner, Alexander; Hall, Jonathan (2022-05-17). "Nucleotide-amino acid π-stacking interactions initiate photo cross-linking in RNA-protein complexes". Nature Communications. 13 (1): 2719. Bibcode:2022NatCo..13.2719K. doi:10.1038/s41467-022-30284-w. ISSN 2041-1723. PMC 9114321. PMID 35581222.

nih.gov

pubmed.ncbi.nlm.nih.gov

Ule, Jernej; Jensen, Kirk B.; Ruggiu, Matteo; Mele, Aldo; Ule, Aljaz; Darnell, Robert B. (2003-11-14). "CLIP identifies Nova-regulated RNA networks in the brain". Science. 302 (5648): 1212–1215. Bibcode:2003Sci...302.1212U. doi:10.1126/science.1090095. ISSN 1095-9203. PMID 14615540. S2CID 23420615.
Ule, Jernej; Hwang, Hun-Way; Darnell, Robert B. (2018-08-01). "The Future of Cross-Linking and Immunoprecipitation (CLIP)". Cold Spring Harbor Perspectives in Biology. 10 (8): a032243. doi:10.1101/cshperspect.a032243. ISSN 1943-0264. PMC 6071486. PMID 30068528.
Lee, Flora C. Y.; Ule, Jernej (2018-02-01). "Advances in CLIP Technologies for Studies of Protein-RNA Interactions". Molecular Cell. 69 (3): 354–369. doi:10.1016/j.molcel.2018.01.005. ISSN 1097-4164. PMID 29395060.
Darnell 2010. Darnell, RB (2010). "HITS-CLIP: panoramic views of protein-RNA regulation in living cells". Wiley Interdiscip Rev RNA. 1 (2): 266–286. doi:10.1002/wrna.31. PMC 3222227. PMID 21935890.
König, Julian; Zarnack, Kathi; Rot, Gregor; Curk, Tomaz; Kayikci, Melis; Zupan, Blaz; Turner, Daniel J.; Luscombe, Nicholas M.; Ule, Jernej (July 2010). "iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution". Nature Structural & Molecular Biology. 17 (7): 909–915. doi:10.1038/nsmb.1838. ISSN 1545-9985. PMC 3000544. PMID 20601959.
Licatalosi et al. 2008. Licatalosi, DD; Mele, A; Fak, JJ; Ule, J; Kayikci, M; Chi, SW; Clark, TA; Schweitzer, AC; Blume, JE; Wang, X; Darnell, JC; Darnell, RB (2008). "HITS-CLIP yields genome-wide insights into brain alternative RNA processing". Nature. 456 (7221): 464–469. Bibcode:2008Natur.456..464L. doi:10.1038/nature07488. PMC 2597294. PMID 18978773.
Xue et al. 2009. Xue, Y; Zhou, Y; Wu, T; Zhu, T; Ju, X; Kwon, YS; Zhang, C; Yeo, G; Black, DL; Sun, H; Fu, XD; Zhang, Y (2009). "Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping". Molecular Cell. 36 (6): 996–1006. doi:10.1016/j.molcel.2009.12.003. PMC 2807993. PMID 20064465.
Yeo et al. 2009. Yeo, GW; Coufal, NG; Liang, TY; Peng, GE; Fu, XD; Gage, FH (2009). "An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells". Nat Struct Mol Biol. 16 (2): 130–137. doi:10.1038/nsmb.1545. PMC 2735254. PMID 19136955.
Sanford et al. 2009. Sanford, JR; Wang, X; Mort, M; Fanduyn, N; Cooper, DN; Mooney, SD; Edenberg, HJ; Liu, Y (2009). "Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts". Genome Research. 19 (3): 381–394. doi:10.1101/gr.082503.108. PMC 2661799. PMID 19116412.
Chi et al. 2009. Chi, SW; Zang, JB; Mele, A; Darnell, RB (2009). "Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps". Nature. 460 (7254): 479–486. Bibcode:2009Natur.460..479C. doi:10.1038/nature08170. PMC 2733940. PMID 19536157.
Moore et al. 2014. Moore, JJ; Zhang, C; Gantman, EC; Mele, A; Darnell, JC; Darnell, RB (2014). "Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis". Nature Protocols. 9 (2): 263–293. doi:10.1038/nprot.2014.012. PMC 4156013. PMID 24407355.
Chi, Sung Wook; Hannon, Gregory J.; Darnell, Robert B. (2012-02-12). "An alternative mode of microRNA target recognition". Nature Structural & Molecular Biology. 19 (3): 321–327. doi:10.1038/nsmb.2230. ISSN 1545-9985. PMC 3541676. PMID 22343717.
Darnell et al. 2011. Darnell, JC; Van Driesche, SJ; Zhang, C; Hung, KY; Mele, A; Fraser, CE; Stone, EF; Chen, C; Fak, JJ; Chi, SW; Licatalosi, DD; Richter, JD; Darnell, RB (2011). "FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism". Cell. 146 (2): 247–261. doi:10.1016/j.cell.2011.06.013. PMC 3232425. PMID 21784246.
Hale, Caryn R.; Sawicka, Kirsty; Mora, Kevin; Fak, John J.; Kang, Jin Joo; Cutrim, Paula; Cialowicz, Katarzyna; Carroll, Thomas S.; Darnell, Robert B. (2021-12-23). "FMRP regulates mRNAs encoding distinct functions in the cell body and dendrites of CA1 pyramidal neurons". eLife. 10: e71892. doi:10.7554/eLife.71892. ISSN 2050-084X. PMC 8820740. PMID 34939924.
Licatalosi et al. 2012. Licatalosi, DD; Yano, M; Fak, JJ; Mele, A; Grabinski, SE; Zhang, C; Darnell, RB (2012). "Ptbp2 represses adult-specific splicing to regulate the generation of neuronal precursors in the embryonic brain". Genes Dev. 26 (14): 1626–1642. doi:10.1101/gad.191338.112. PMC 3404389. PMID 22802532.
Charizanis et al. 2012. Charizanis, K; Lee, KY; Batra, R; Goodwin, M; Zhang, C; Yuan, Y; Shiue, L; Cline, M; Scotti, MM; Xia, G; Kumar, A; Ashizawa, T; Clark, HB; Kimura, T; Takahashi, MP; Fujimura, H; Jinnai, K; Yoshikawa, H; Gomes–Pereira, M; Gourdon, G; Sakai, N; Nishino, S; Foster, TC; Ares, M; Darnell, RB; Swanson, MS (2012). "Muscleblind-like 2-mediated alternative splicing in the developing brain and dysregulation in myotonic dystrophy". Neuron. 75 (3): 437–450. doi:10.1016/j.neuron.2012.05.029. PMC 3418517. PMID 22884328.
Ince-Dunn et al. 2012. Ince-Dunn, G; Okano, HJ; Jensen, KB; Park, WY; Zhong, R; Ule, J; Mele, A; Fak, JJ; Yang, CW; Zhang, C; Yoo, J; Herre, M; Okano, H; Noebels, JL; Darnell, RB (2012). "Neuronal Elav-like (Hu) proteins regulate RNA splicing and abundance to control glutamate levels and neuronal excitability". Neuron. 75 (6): 1067–1080. doi:10.1016/j.neuron.2012.07.009. PMC 3517991. PMID 22998874.
Holmqvist et al. 2016. Holmqvist, E; Wright, PR; Li, L; Bischler, T; Barquist, L; Reinhardt, R; Backofen, R; Vogel, J (2016). "Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo". EMBO J. 35 (9): 991–1011. doi:10.15252/embj.201593360. PMC 5207318. PMID 27044921.
Thomson, Bracken & Goodall 2011. Thomson, DW; Bracken, CP; Goodall, GJ (2011). "Experimental strategies for microRNA target identification". Nucleic Acids Research. 39 (16): 6845–6853. doi:10.1093/nar/gkr330. PMC 3167600. PMID 21652644.
Yang et al. 2011. Yang, JH; Li, JH; Shao, P; Zhou, H; Chen, YQ; Qu, LH (2011). "starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data". Nucleic Acids Res. 39 (Database issue): D202–D209. doi:10.1093/nar/gkq1056. PMC 3013664. PMID 21037263.
Wolf, Joshua J.; Dowell, Robin D.; Mahony, Shaun; Rabani, Michal; Gifford, David K.; Fink, Gerald R. (June 2010). "Feed-forward regulation of a cell fate determinant by an RNA-binding protein generates asymmetry in yeast". Genetics. 185 (2): 513–522. doi:10.1534/genetics.110.113944. ISSN 1943-2631. PMC 2881133. PMID 20382833.
Zisoulis et al. 2010. Zisoulis, DG; Lovci, MT; Wilbert, ML; Hutt, KR; Liang, TY; Pasquinelli, AE; Yeo, GW (2010). "Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans". Nat Struct Mol Biol. 17 (2): 173–179. doi:10.1038/nsmb.1745. PMC 2834287. PMID 20062054.
Hafner, Markus; Landthaler, Markus; Burger, Lukas; Khorshid, Mohsen; Hausser, Jean; Berninger, Philipp; Rothballer, Andrea; Ascano, Manuel; Jungkamp, Anna-Carina; Munschauer, Mathias; Ulrich, Alexander; Wardle, Greg S.; Dewell, Scott; Zavolan, Mihaela; Tuschl, Thomas (2010-04-02). "Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP". Cell. 141 (1): 129–141. doi:10.1016/j.cell.2010.03.009. ISSN 1097-4172. PMC 2861495. PMID 20371350.
Sugimoto et al. 2012. Sugimoto, Y; König, J; Hussain, S; Zupan, B; Curk, T; Frye, M; Ule, J (Aug 3, 2012). "Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions". Genome Biology. 13 (8): R67. doi:10.1186/gb-2012-13-8-r67. PMC 4053741. PMID 22863408.
König et al. 2012. König, J; Zarnack, K; Luscombe, NM; Ule, J (2012). "Protein-RNA interactions: new genomic technologies and perspectives". Nature Reviews Genetics. 13 (2): 77–83. doi:10.1038/nrg3141. PMC 4962561. PMID 22251872.
Zhang & Darnell 2011. Zhang, C; Darnell, RB (2011). "Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data". Nature Biotechnology. 29 (7): 607–614. doi:10.1038/nbt.1873. PMC 3400429. PMID 21633356.
Burger et al. 2013. Burger, K; Mühl, B; Kellner, M; Rohrmoser, M; Gruber-Eber, A; Windhager, L; Friedel, CC; Dölken, L; Eick, D (2013). "4-thiouridine inhibits rRNA synthesis and causes a nucleolar stress response". RNA Biol. 10 (10): 1623–1630. doi:10.4161/rna.26214. PMC 3866244. PMID 24025460.
Zhang, Chaolin; Darnell, Robert B (1 June 2011). "Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data". Nature Biotechnology. 29 (7): 607–614. doi:10.1038/nbt.1873. PMC 3400429. PMID 21633356.
Hussain, Shobbir; Sajini, Abdulrahim A.; Blanco, Sandra; Dietmann, Sabine; Lombard, Patrick; Sugimoto, Yoichiro; Paramor, Maike; Gleeson, Joseph G.; Odom, Duncan T.; Ule, Jernej; Frye, Michaela (2013-07-25). "NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs". Cell Reports. 4 (2): 255–261. doi:10.1016/j.celrep.2013.06.029. ISSN 2211-1247. PMC 3730056. PMID 23871666.
Linder, Bastian; Grozhik, Anya V.; Olarerin-George, Anthony O.; Meydan, Cem; Mason, Christopher E.; Jaffrey, Samie R. (August 2015). "Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome". Nature Methods. 12 (8): 767–772. doi:10.1038/nmeth.3453. ISSN 1548-7105. PMC 4487409. PMID 26121403.
Tollervey, James R.; Curk, Tomaž; Rogelj, Boris; Briese, Michael; Cereda, Matteo; Kayikci, Melis; König, Julian; Hortobágyi, Tibor; Nishimura, Agnes L.; Zupunski, Vera; Patani, Rickie; Chandran, Siddharthan; Rot, Gregor; Zupan, Blaž; Shaw, Christopher E. (April 2011). "Characterizing the RNA targets and position-dependent splicing regulation by TDP-43". Nature Neuroscience. 14 (4): 452–458. doi:10.1038/nn.2778. ISSN 1546-1726. PMC 3108889. PMID 21358640.
Zarnack, Kathi; König, Julian; Tajnik, Mojca; Martincorena, Iñigo; Eustermann, Sebastian; Stévant, Isabelle; Reyes, Alejandro; Anders, Simon; Luscombe, Nicholas M.; Ule, Jernej (2013-01-31). "Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements". Cell. 152 (3): 453–466. doi:10.1016/j.cell.2012.12.023. ISSN 1097-4172. PMC 3629564. PMID 23374342.
Hallegger, Martina; Chakrabarti, Anob M.; Lee, Flora C. Y.; Lee, Bo Lim; Amalietti, Aram G.; Odeh, Hana M.; Copley, Katie E.; Rubien, Jack D.; Portz, Bede; Kuret, Klara; Huppertz, Ina; Rau, Frédérique; Patani, Rickie; Fawzi, Nicolas L.; Shorter, James (2021-09-02). "TDP-43 condensation properties specify its RNA-binding and regulatory repertoire". Cell. 184 (18): 4680–4696.e22. doi:10.1016/j.cell.2021.07.018. ISSN 1097-4172. PMC 8445024. PMID 34380047.
Van Nostrand, Pratt & Shishkin 2016. Van Nostrand, E; Pratt, G; Shishkin, A (2016). "Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)". Nature Methods. 13 (6): 508–514. doi:10.1038/nmeth.3810. PMC 4887338. PMID 27018577.
Van Nostrand, Eric L.; Freese, Peter; Pratt, Gabriel A.; Wang, Xiaofeng; Wei, Xintao; Xiao, Rui; Blue, Steven M.; Chen, Jia-Yu; Cody, Neal A. L.; Dominguez, Daniel; Olson, Sara; Sundararaman, Balaji; Zhan, Lijun; Bazile, Cassandra; Bouvrette, Louis Philip Benoit (July 2020). "A large-scale binding and functional map of human RNA-binding proteins". Nature. 583 (7818): 711–719. Bibcode:2020Natur.583..711V. doi:10.1038/s41586-020-2077-3. ISSN 1476-4687. PMC 7410833. PMID 32728246.
Kargapolova et al. 2017. Kargapolova, Y; Levin, M; Lackner, K; Danckwardt, S (2017). "sCLIP—an integrated platform to study RNA–protein interactomes in biomedical research: identification of CSTF2tau in alternative processing of small nuclear RNAs". Nucleic Acids Res. 45 (10): 6074–6086. doi:10.1093/nar/gkx152. PMC 5449641. PMID 28334977.
Ke, Shengdong; Alemu, Endalkachew A.; Mertens, Claudia; Gantman, Emily Conn; Fak, John J.; Mele, Aldo; Haripal, Bhagwattie; Zucker-Scharff, Ilana; Moore, Michael J.; Park, Christopher Y.; Vågbø, Cathrine Broberg; Kusśnierczyk, Anna; Klungland, Arne; Darnell, James E.; Darnell, Robert B. (2015-10-01). "A majority of m6A residues are in the last exons, allowing the potential for 3' UTR regulation". Genes & Development. 29 (19): 2037–2053. doi:10.1101/gad.269415.115. ISSN 1549-5477. PMC 4604345. PMID 26404942.
Mili & Steitz 2004. Mili, S; Steitz, JA (2004). "Evidence for reassociation of RNA-binding proteins after cell lysis: Implications for the interpretation of immunoprecipitation analyses". RNA. 10 (11): 1692–4. doi:10.1261/rna.7151404. PMC 1370654. PMID 15388877.
Chakrabarti, Anob M.; Haberman, Nejc; Praznik, Arne; Luscombe, Nicholas M.; Ule, Jernej (2018-07-20). "Data Science Issues in Studying Protein–RNA Interactions with CLIP Technologies". Annual Review of Biomedical Data Science. 1 (1): 235–261. doi:10.1146/annurev-biodatasci-080917-013525. ISSN 2574-3414. PMC 7614488. PMID 37123514. S2CID 90760475.
Ule et al. 2005. Ule, J; Jensen, K; Mele, A; Darnell, RB (2005). "CLIP: a method for identifying protein-RNA interactions sites in living cells". Methods. 37 (4): 376–386. doi:10.1016/j.ymeth.2005.07.018. PMID 16314267.
Knörlein, Anna; Sarnowski, Chris P.; de Vries, Tebbe; Stoltz, Moritz; Götze, Michael; Aebersold, Ruedi; Allain, Frédéric H.-T.; Leitner, Alexander; Hall, Jonathan (2022-05-17). "Nucleotide-amino acid π-stacking interactions initiate photo cross-linking in RNA-protein complexes". Nature Communications. 13 (1): 2719. Bibcode:2022NatCo..13.2719K. doi:10.1038/s41467-022-30284-w. ISSN 2041-1723. PMC 9114321. PMID 35581222.
Bohnsack et al. 2009. Bohnsack, MT; Martin, R; Granneman, S; Ruprecht, M; Schleiff, E; Tollervey, D (2009). "Prp43 bound at different sites on the pre-rRNA performs distinct functions in ribosome synthesis". Molecular Cell. 36 (4): 583–592. doi:10.1016/j.molcel.2009.09.039. PMC 2806949. PMID 19941819.
Kuret, Klara; Amalietti, Aram Gustav; Jones, D. Marc; Capitanchik, Charlotte; Ule, Jernej (2022-09-09). "Positional motif analysis reveals the extent of specificity of protein-RNA interactions observed by CLIP". Genome Biology. 23 (1): 191. doi:10.1186/s13059-022-02755-2. ISSN 1474-760X. PMC 9461102. PMID 36085079.
Agarwal et al. 2015. Agarwal, V; Bell, GW; Nam, J-W; Bartel, DP (2015). "Predicting effective microRNA target sites in mammalian mRNAs". eLife. 4: e05005. doi:10.7554/eLife.05005. PMC 4532895. PMID 26267216.

ncbi.nlm.nih.gov

Ule, Jernej; Hwang, Hun-Way; Darnell, Robert B. (2018-08-01). "The Future of Cross-Linking and Immunoprecipitation (CLIP)". Cold Spring Harbor Perspectives in Biology. 10 (8): a032243. doi:10.1101/cshperspect.a032243. ISSN 1943-0264. PMC 6071486. PMID 30068528.
Darnell 2010. Darnell, RB (2010). "HITS-CLIP: panoramic views of protein-RNA regulation in living cells". Wiley Interdiscip Rev RNA. 1 (2): 266–286. doi:10.1002/wrna.31. PMC 3222227. PMID 21935890.
König, Julian; Zarnack, Kathi; Rot, Gregor; Curk, Tomaz; Kayikci, Melis; Zupan, Blaz; Turner, Daniel J.; Luscombe, Nicholas M.; Ule, Jernej (July 2010). "iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution". Nature Structural & Molecular Biology. 17 (7): 909–915. doi:10.1038/nsmb.1838. ISSN 1545-9985. PMC 3000544. PMID 20601959.
Licatalosi et al. 2008. Licatalosi, DD; Mele, A; Fak, JJ; Ule, J; Kayikci, M; Chi, SW; Clark, TA; Schweitzer, AC; Blume, JE; Wang, X; Darnell, JC; Darnell, RB (2008). "HITS-CLIP yields genome-wide insights into brain alternative RNA processing". Nature. 456 (7221): 464–469. Bibcode:2008Natur.456..464L. doi:10.1038/nature07488. PMC 2597294. PMID 18978773.
Xue et al. 2009. Xue, Y; Zhou, Y; Wu, T; Zhu, T; Ju, X; Kwon, YS; Zhang, C; Yeo, G; Black, DL; Sun, H; Fu, XD; Zhang, Y (2009). "Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping". Molecular Cell. 36 (6): 996–1006. doi:10.1016/j.molcel.2009.12.003. PMC 2807993. PMID 20064465.
Yeo et al. 2009. Yeo, GW; Coufal, NG; Liang, TY; Peng, GE; Fu, XD; Gage, FH (2009). "An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells". Nat Struct Mol Biol. 16 (2): 130–137. doi:10.1038/nsmb.1545. PMC 2735254. PMID 19136955.
Sanford et al. 2009. Sanford, JR; Wang, X; Mort, M; Fanduyn, N; Cooper, DN; Mooney, SD; Edenberg, HJ; Liu, Y (2009). "Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts". Genome Research. 19 (3): 381–394. doi:10.1101/gr.082503.108. PMC 2661799. PMID 19116412.
Chi et al. 2009. Chi, SW; Zang, JB; Mele, A; Darnell, RB (2009). "Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps". Nature. 460 (7254): 479–486. Bibcode:2009Natur.460..479C. doi:10.1038/nature08170. PMC 2733940. PMID 19536157.
Moore et al. 2014. Moore, JJ; Zhang, C; Gantman, EC; Mele, A; Darnell, JC; Darnell, RB (2014). "Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis". Nature Protocols. 9 (2): 263–293. doi:10.1038/nprot.2014.012. PMC 4156013. PMID 24407355.
Chi, Sung Wook; Hannon, Gregory J.; Darnell, Robert B. (2012-02-12). "An alternative mode of microRNA target recognition". Nature Structural & Molecular Biology. 19 (3): 321–327. doi:10.1038/nsmb.2230. ISSN 1545-9985. PMC 3541676. PMID 22343717.
Darnell et al. 2011. Darnell, JC; Van Driesche, SJ; Zhang, C; Hung, KY; Mele, A; Fraser, CE; Stone, EF; Chen, C; Fak, JJ; Chi, SW; Licatalosi, DD; Richter, JD; Darnell, RB (2011). "FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism". Cell. 146 (2): 247–261. doi:10.1016/j.cell.2011.06.013. PMC 3232425. PMID 21784246.
Hale, Caryn R.; Sawicka, Kirsty; Mora, Kevin; Fak, John J.; Kang, Jin Joo; Cutrim, Paula; Cialowicz, Katarzyna; Carroll, Thomas S.; Darnell, Robert B. (2021-12-23). "FMRP regulates mRNAs encoding distinct functions in the cell body and dendrites of CA1 pyramidal neurons". eLife. 10: e71892. doi:10.7554/eLife.71892. ISSN 2050-084X. PMC 8820740. PMID 34939924.
Licatalosi et al. 2012. Licatalosi, DD; Yano, M; Fak, JJ; Mele, A; Grabinski, SE; Zhang, C; Darnell, RB (2012). "Ptbp2 represses adult-specific splicing to regulate the generation of neuronal precursors in the embryonic brain". Genes Dev. 26 (14): 1626–1642. doi:10.1101/gad.191338.112. PMC 3404389. PMID 22802532.
Charizanis et al. 2012. Charizanis, K; Lee, KY; Batra, R; Goodwin, M; Zhang, C; Yuan, Y; Shiue, L; Cline, M; Scotti, MM; Xia, G; Kumar, A; Ashizawa, T; Clark, HB; Kimura, T; Takahashi, MP; Fujimura, H; Jinnai, K; Yoshikawa, H; Gomes–Pereira, M; Gourdon, G; Sakai, N; Nishino, S; Foster, TC; Ares, M; Darnell, RB; Swanson, MS (2012). "Muscleblind-like 2-mediated alternative splicing in the developing brain and dysregulation in myotonic dystrophy". Neuron. 75 (3): 437–450. doi:10.1016/j.neuron.2012.05.029. PMC 3418517. PMID 22884328.
Ince-Dunn et al. 2012. Ince-Dunn, G; Okano, HJ; Jensen, KB; Park, WY; Zhong, R; Ule, J; Mele, A; Fak, JJ; Yang, CW; Zhang, C; Yoo, J; Herre, M; Okano, H; Noebels, JL; Darnell, RB (2012). "Neuronal Elav-like (Hu) proteins regulate RNA splicing and abundance to control glutamate levels and neuronal excitability". Neuron. 75 (6): 1067–1080. doi:10.1016/j.neuron.2012.07.009. PMC 3517991. PMID 22998874.
Holmqvist et al. 2016. Holmqvist, E; Wright, PR; Li, L; Bischler, T; Barquist, L; Reinhardt, R; Backofen, R; Vogel, J (2016). "Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo". EMBO J. 35 (9): 991–1011. doi:10.15252/embj.201593360. PMC 5207318. PMID 27044921.
Thomson, Bracken & Goodall 2011. Thomson, DW; Bracken, CP; Goodall, GJ (2011). "Experimental strategies for microRNA target identification". Nucleic Acids Research. 39 (16): 6845–6853. doi:10.1093/nar/gkr330. PMC 3167600. PMID 21652644.
Yang et al. 2011. Yang, JH; Li, JH; Shao, P; Zhou, H; Chen, YQ; Qu, LH (2011). "starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data". Nucleic Acids Res. 39 (Database issue): D202–D209. doi:10.1093/nar/gkq1056. PMC 3013664. PMID 21037263.
Wolf, Joshua J.; Dowell, Robin D.; Mahony, Shaun; Rabani, Michal; Gifford, David K.; Fink, Gerald R. (June 2010). "Feed-forward regulation of a cell fate determinant by an RNA-binding protein generates asymmetry in yeast". Genetics. 185 (2): 513–522. doi:10.1534/genetics.110.113944. ISSN 1943-2631. PMC 2881133. PMID 20382833.
Zisoulis et al. 2010. Zisoulis, DG; Lovci, MT; Wilbert, ML; Hutt, KR; Liang, TY; Pasquinelli, AE; Yeo, GW (2010). "Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans". Nat Struct Mol Biol. 17 (2): 173–179. doi:10.1038/nsmb.1745. PMC 2834287. PMID 20062054.
Leung et al. 2011. Leung, AK; Young, AG; Bhutkar, A; Zheng, GX; Bosson, AD; Nielsen, CB; Sharp, PA (2011). "Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs". Nat Struct Mol Biol. 19 (9): 1084. doi:10.1038/nsmb0911-1084a. PMC 3078052.
Hafner, Markus; Landthaler, Markus; Burger, Lukas; Khorshid, Mohsen; Hausser, Jean; Berninger, Philipp; Rothballer, Andrea; Ascano, Manuel; Jungkamp, Anna-Carina; Munschauer, Mathias; Ulrich, Alexander; Wardle, Greg S.; Dewell, Scott; Zavolan, Mihaela; Tuschl, Thomas (2010-04-02). "Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP". Cell. 141 (1): 129–141. doi:10.1016/j.cell.2010.03.009. ISSN 1097-4172. PMC 2861495. PMID 20371350.
Sugimoto et al. 2012. Sugimoto, Y; König, J; Hussain, S; Zupan, B; Curk, T; Frye, M; Ule, J (Aug 3, 2012). "Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions". Genome Biology. 13 (8): R67. doi:10.1186/gb-2012-13-8-r67. PMC 4053741. PMID 22863408.
König et al. 2012. König, J; Zarnack, K; Luscombe, NM; Ule, J (2012). "Protein-RNA interactions: new genomic technologies and perspectives". Nature Reviews Genetics. 13 (2): 77–83. doi:10.1038/nrg3141. PMC 4962561. PMID 22251872.
Zhang & Darnell 2011. Zhang, C; Darnell, RB (2011). "Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data". Nature Biotechnology. 29 (7): 607–614. doi:10.1038/nbt.1873. PMC 3400429. PMID 21633356.
Burger et al. 2013. Burger, K; Mühl, B; Kellner, M; Rohrmoser, M; Gruber-Eber, A; Windhager, L; Friedel, CC; Dölken, L; Eick, D (2013). "4-thiouridine inhibits rRNA synthesis and causes a nucleolar stress response". RNA Biol. 10 (10): 1623–1630. doi:10.4161/rna.26214. PMC 3866244. PMID 24025460.
Zhang, Chaolin; Darnell, Robert B (1 June 2011). "Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data". Nature Biotechnology. 29 (7): 607–614. doi:10.1038/nbt.1873. PMC 3400429. PMID 21633356.
Hussain, Shobbir; Sajini, Abdulrahim A.; Blanco, Sandra; Dietmann, Sabine; Lombard, Patrick; Sugimoto, Yoichiro; Paramor, Maike; Gleeson, Joseph G.; Odom, Duncan T.; Ule, Jernej; Frye, Michaela (2013-07-25). "NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs". Cell Reports. 4 (2): 255–261. doi:10.1016/j.celrep.2013.06.029. ISSN 2211-1247. PMC 3730056. PMID 23871666.
Linder, Bastian; Grozhik, Anya V.; Olarerin-George, Anthony O.; Meydan, Cem; Mason, Christopher E.; Jaffrey, Samie R. (August 2015). "Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome". Nature Methods. 12 (8): 767–772. doi:10.1038/nmeth.3453. ISSN 1548-7105. PMC 4487409. PMID 26121403.
Tollervey, James R.; Curk, Tomaž; Rogelj, Boris; Briese, Michael; Cereda, Matteo; Kayikci, Melis; König, Julian; Hortobágyi, Tibor; Nishimura, Agnes L.; Zupunski, Vera; Patani, Rickie; Chandran, Siddharthan; Rot, Gregor; Zupan, Blaž; Shaw, Christopher E. (April 2011). "Characterizing the RNA targets and position-dependent splicing regulation by TDP-43". Nature Neuroscience. 14 (4): 452–458. doi:10.1038/nn.2778. ISSN 1546-1726. PMC 3108889. PMID 21358640.
Zarnack, Kathi; König, Julian; Tajnik, Mojca; Martincorena, Iñigo; Eustermann, Sebastian; Stévant, Isabelle; Reyes, Alejandro; Anders, Simon; Luscombe, Nicholas M.; Ule, Jernej (2013-01-31). "Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements". Cell. 152 (3): 453–466. doi:10.1016/j.cell.2012.12.023. ISSN 1097-4172. PMC 3629564. PMID 23374342.
Hallegger, Martina; Chakrabarti, Anob M.; Lee, Flora C. Y.; Lee, Bo Lim; Amalietti, Aram G.; Odeh, Hana M.; Copley, Katie E.; Rubien, Jack D.; Portz, Bede; Kuret, Klara; Huppertz, Ina; Rau, Frédérique; Patani, Rickie; Fawzi, Nicolas L.; Shorter, James (2021-09-02). "TDP-43 condensation properties specify its RNA-binding and regulatory repertoire". Cell. 184 (18): 4680–4696.e22. doi:10.1016/j.cell.2021.07.018. ISSN 1097-4172. PMC 8445024. PMID 34380047.
Van Nostrand, Pratt & Shishkin 2016. Van Nostrand, E; Pratt, G; Shishkin, A (2016). "Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)". Nature Methods. 13 (6): 508–514. doi:10.1038/nmeth.3810. PMC 4887338. PMID 27018577.
Van Nostrand, Eric L.; Freese, Peter; Pratt, Gabriel A.; Wang, Xiaofeng; Wei, Xintao; Xiao, Rui; Blue, Steven M.; Chen, Jia-Yu; Cody, Neal A. L.; Dominguez, Daniel; Olson, Sara; Sundararaman, Balaji; Zhan, Lijun; Bazile, Cassandra; Bouvrette, Louis Philip Benoit (July 2020). "A large-scale binding and functional map of human RNA-binding proteins". Nature. 583 (7818): 711–719. Bibcode:2020Natur.583..711V. doi:10.1038/s41586-020-2077-3. ISSN 1476-4687. PMC 7410833. PMID 32728246.
Kargapolova et al. 2017. Kargapolova, Y; Levin, M; Lackner, K; Danckwardt, S (2017). "sCLIP—an integrated platform to study RNA–protein interactomes in biomedical research: identification of CSTF2tau in alternative processing of small nuclear RNAs". Nucleic Acids Res. 45 (10): 6074–6086. doi:10.1093/nar/gkx152. PMC 5449641. PMID 28334977.
Ke, Shengdong; Alemu, Endalkachew A.; Mertens, Claudia; Gantman, Emily Conn; Fak, John J.; Mele, Aldo; Haripal, Bhagwattie; Zucker-Scharff, Ilana; Moore, Michael J.; Park, Christopher Y.; Vågbø, Cathrine Broberg; Kusśnierczyk, Anna; Klungland, Arne; Darnell, James E.; Darnell, Robert B. (2015-10-01). "A majority of m6A residues are in the last exons, allowing the potential for 3' UTR regulation". Genes & Development. 29 (19): 2037–2053. doi:10.1101/gad.269415.115. ISSN 1549-5477. PMC 4604345. PMID 26404942.
Mili & Steitz 2004. Mili, S; Steitz, JA (2004). "Evidence for reassociation of RNA-binding proteins after cell lysis: Implications for the interpretation of immunoprecipitation analyses". RNA. 10 (11): 1692–4. doi:10.1261/rna.7151404. PMC 1370654. PMID 15388877.
Chakrabarti, Anob M.; Haberman, Nejc; Praznik, Arne; Luscombe, Nicholas M.; Ule, Jernej (2018-07-20). "Data Science Issues in Studying Protein–RNA Interactions with CLIP Technologies". Annual Review of Biomedical Data Science. 1 (1): 235–261. doi:10.1146/annurev-biodatasci-080917-013525. ISSN 2574-3414. PMC 7614488. PMID 37123514. S2CID 90760475.
Knörlein, Anna; Sarnowski, Chris P.; de Vries, Tebbe; Stoltz, Moritz; Götze, Michael; Aebersold, Ruedi; Allain, Frédéric H.-T.; Leitner, Alexander; Hall, Jonathan (2022-05-17). "Nucleotide-amino acid π-stacking interactions initiate photo cross-linking in RNA-protein complexes". Nature Communications. 13 (1): 2719. Bibcode:2022NatCo..13.2719K. doi:10.1038/s41467-022-30284-w. ISSN 2041-1723. PMC 9114321. PMID 35581222.
Bohnsack et al. 2009. Bohnsack, MT; Martin, R; Granneman, S; Ruprecht, M; Schleiff, E; Tollervey, D (2009). "Prp43 bound at different sites on the pre-rRNA performs distinct functions in ribosome synthesis". Molecular Cell. 36 (4): 583–592. doi:10.1016/j.molcel.2009.09.039. PMC 2806949. PMID 19941819.
Kuret, Klara; Amalietti, Aram Gustav; Jones, D. Marc; Capitanchik, Charlotte; Ule, Jernej (2022-09-09). "Positional motif analysis reveals the extent of specificity of protein-RNA interactions observed by CLIP". Genome Biology. 23 (1): 191. doi:10.1186/s13059-022-02755-2. ISSN 1474-760X. PMC 9461102. PMID 36085079.
Agarwal et al. 2015. Agarwal, V; Bell, GW; Nam, J-W; Bartel, DP (2015). "Predicting effective microRNA target sites in mammalian mRNAs". eLife. 4: e05005. doi:10.7554/eLife.05005. PMC 4532895. PMID 26267216.

semanticscholar.org

api.semanticscholar.org

Ule, Jernej; Jensen, Kirk B.; Ruggiu, Matteo; Mele, Aldo; Ule, Aljaz; Darnell, Robert B. (2003-11-14). "CLIP identifies Nova-regulated RNA networks in the brain". Science. 302 (5648): 1212–1215. Bibcode:2003Sci...302.1212U. doi:10.1126/science.1090095. ISSN 1095-9203. PMID 14615540. S2CID 23420615.
Hafner, Markus; Katsantoni, Maria; Köster, Tino; Marks, James; Mukherjee, Joyita; Staiger, Dorothee; Ule, Jernej; Zavolan, Mihaela (2021-03-04). "CLIP and complementary methods". Nature Reviews Methods Primers. 1 (1): 1–23. doi:10.1038/s43586-021-00018-1. ISSN 2662-8449. S2CID 233834798.
Chakrabarti, Anob M.; Haberman, Nejc; Praznik, Arne; Luscombe, Nicholas M.; Ule, Jernej (2018-07-20). "Data Science Issues in Studying Protein–RNA Interactions with CLIP Technologies". Annual Review of Biomedical Data Science. 1 (1): 235–261. doi:10.1146/annurev-biodatasci-080917-013525. ISSN 2574-3414. PMC 7614488. PMID 37123514. S2CID 90760475.

worldcat.org

Ule, Jernej; Jensen, Kirk B.; Ruggiu, Matteo; Mele, Aldo; Ule, Aljaz; Darnell, Robert B. (2003-11-14). "CLIP identifies Nova-regulated RNA networks in the brain". Science. 302 (5648): 1212–1215. Bibcode:2003Sci...302.1212U. doi:10.1126/science.1090095. ISSN 1095-9203. PMID 14615540. S2CID 23420615.
Hafner, Markus; Katsantoni, Maria; Köster, Tino; Marks, James; Mukherjee, Joyita; Staiger, Dorothee; Ule, Jernej; Zavolan, Mihaela (2021-03-04). "CLIP and complementary methods". Nature Reviews Methods Primers. 1 (1): 1–23. doi:10.1038/s43586-021-00018-1. ISSN 2662-8449. S2CID 233834798.
Ule, Jernej; Hwang, Hun-Way; Darnell, Robert B. (2018-08-01). "The Future of Cross-Linking and Immunoprecipitation (CLIP)". Cold Spring Harbor Perspectives in Biology. 10 (8): a032243. doi:10.1101/cshperspect.a032243. ISSN 1943-0264. PMC 6071486. PMID 30068528.
Lee, Flora C. Y.; Ule, Jernej (2018-02-01). "Advances in CLIP Technologies for Studies of Protein-RNA Interactions". Molecular Cell. 69 (3): 354–369. doi:10.1016/j.molcel.2018.01.005. ISSN 1097-4164. PMID 29395060.
König, Julian; Zarnack, Kathi; Rot, Gregor; Curk, Tomaz; Kayikci, Melis; Zupan, Blaz; Turner, Daniel J.; Luscombe, Nicholas M.; Ule, Jernej (July 2010). "iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution". Nature Structural & Molecular Biology. 17 (7): 909–915. doi:10.1038/nsmb.1838. ISSN 1545-9985. PMC 3000544. PMID 20601959.
Chi, Sung Wook; Hannon, Gregory J.; Darnell, Robert B. (2012-02-12). "An alternative mode of microRNA target recognition". Nature Structural & Molecular Biology. 19 (3): 321–327. doi:10.1038/nsmb.2230. ISSN 1545-9985. PMC 3541676. PMID 22343717.
Hale, Caryn R.; Sawicka, Kirsty; Mora, Kevin; Fak, John J.; Kang, Jin Joo; Cutrim, Paula; Cialowicz, Katarzyna; Carroll, Thomas S.; Darnell, Robert B. (2021-12-23). "FMRP regulates mRNAs encoding distinct functions in the cell body and dendrites of CA1 pyramidal neurons". eLife. 10: e71892. doi:10.7554/eLife.71892. ISSN 2050-084X. PMC 8820740. PMID 34939924.
Wolf, Joshua J.; Dowell, Robin D.; Mahony, Shaun; Rabani, Michal; Gifford, David K.; Fink, Gerald R. (June 2010). "Feed-forward regulation of a cell fate determinant by an RNA-binding protein generates asymmetry in yeast". Genetics. 185 (2): 513–522. doi:10.1534/genetics.110.113944. ISSN 1943-2631. PMC 2881133. PMID 20382833.
Hafner, Markus; Landthaler, Markus; Burger, Lukas; Khorshid, Mohsen; Hausser, Jean; Berninger, Philipp; Rothballer, Andrea; Ascano, Manuel; Jungkamp, Anna-Carina; Munschauer, Mathias; Ulrich, Alexander; Wardle, Greg S.; Dewell, Scott; Zavolan, Mihaela; Tuschl, Thomas (2010-04-02). "Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP". Cell. 141 (1): 129–141. doi:10.1016/j.cell.2010.03.009. ISSN 1097-4172. PMC 2861495. PMID 20371350.
Hussain, Shobbir; Sajini, Abdulrahim A.; Blanco, Sandra; Dietmann, Sabine; Lombard, Patrick; Sugimoto, Yoichiro; Paramor, Maike; Gleeson, Joseph G.; Odom, Duncan T.; Ule, Jernej; Frye, Michaela (2013-07-25). "NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs". Cell Reports. 4 (2): 255–261. doi:10.1016/j.celrep.2013.06.029. ISSN 2211-1247. PMC 3730056. PMID 23871666.
Linder, Bastian; Grozhik, Anya V.; Olarerin-George, Anthony O.; Meydan, Cem; Mason, Christopher E.; Jaffrey, Samie R. (August 2015). "Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome". Nature Methods. 12 (8): 767–772. doi:10.1038/nmeth.3453. ISSN 1548-7105. PMC 4487409. PMID 26121403.
Tollervey, James R.; Curk, Tomaž; Rogelj, Boris; Briese, Michael; Cereda, Matteo; Kayikci, Melis; König, Julian; Hortobágyi, Tibor; Nishimura, Agnes L.; Zupunski, Vera; Patani, Rickie; Chandran, Siddharthan; Rot, Gregor; Zupan, Blaž; Shaw, Christopher E. (April 2011). "Characterizing the RNA targets and position-dependent splicing regulation by TDP-43". Nature Neuroscience. 14 (4): 452–458. doi:10.1038/nn.2778. ISSN 1546-1726. PMC 3108889. PMID 21358640.
Zarnack, Kathi; König, Julian; Tajnik, Mojca; Martincorena, Iñigo; Eustermann, Sebastian; Stévant, Isabelle; Reyes, Alejandro; Anders, Simon; Luscombe, Nicholas M.; Ule, Jernej (2013-01-31). "Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements". Cell. 152 (3): 453–466. doi:10.1016/j.cell.2012.12.023. ISSN 1097-4172. PMC 3629564. PMID 23374342.
Hallegger, Martina; Chakrabarti, Anob M.; Lee, Flora C. Y.; Lee, Bo Lim; Amalietti, Aram G.; Odeh, Hana M.; Copley, Katie E.; Rubien, Jack D.; Portz, Bede; Kuret, Klara; Huppertz, Ina; Rau, Frédérique; Patani, Rickie; Fawzi, Nicolas L.; Shorter, James (2021-09-02). "TDP-43 condensation properties specify its RNA-binding and regulatory repertoire". Cell. 184 (18): 4680–4696.e22. doi:10.1016/j.cell.2021.07.018. ISSN 1097-4172. PMC 8445024. PMID 34380047.
Van Nostrand, Eric L.; Freese, Peter; Pratt, Gabriel A.; Wang, Xiaofeng; Wei, Xintao; Xiao, Rui; Blue, Steven M.; Chen, Jia-Yu; Cody, Neal A. L.; Dominguez, Daniel; Olson, Sara; Sundararaman, Balaji; Zhan, Lijun; Bazile, Cassandra; Bouvrette, Louis Philip Benoit (July 2020). "A large-scale binding and functional map of human RNA-binding proteins". Nature. 583 (7818): 711–719. Bibcode:2020Natur.583..711V. doi:10.1038/s41586-020-2077-3. ISSN 1476-4687. PMC 7410833. PMID 32728246.
Ke, Shengdong; Alemu, Endalkachew A.; Mertens, Claudia; Gantman, Emily Conn; Fak, John J.; Mele, Aldo; Haripal, Bhagwattie; Zucker-Scharff, Ilana; Moore, Michael J.; Park, Christopher Y.; Vågbø, Cathrine Broberg; Kusśnierczyk, Anna; Klungland, Arne; Darnell, James E.; Darnell, Robert B. (2015-10-01). "A majority of m6A residues are in the last exons, allowing the potential for 3' UTR regulation". Genes & Development. 29 (19): 2037–2053. doi:10.1101/gad.269415.115. ISSN 1549-5477. PMC 4604345. PMID 26404942.
Chakrabarti, Anob M.; Haberman, Nejc; Praznik, Arne; Luscombe, Nicholas M.; Ule, Jernej (2018-07-20). "Data Science Issues in Studying Protein–RNA Interactions with CLIP Technologies". Annual Review of Biomedical Data Science. 1 (1): 235–261. doi:10.1146/annurev-biodatasci-080917-013525. ISSN 2574-3414. PMC 7614488. PMID 37123514. S2CID 90760475.
Knörlein, Anna; Sarnowski, Chris P.; de Vries, Tebbe; Stoltz, Moritz; Götze, Michael; Aebersold, Ruedi; Allain, Frédéric H.-T.; Leitner, Alexander; Hall, Jonathan (2022-05-17). "Nucleotide-amino acid π-stacking interactions initiate photo cross-linking in RNA-protein complexes". Nature Communications. 13 (1): 2719. Bibcode:2022NatCo..13.2719K. doi:10.1038/s41467-022-30284-w. ISSN 2041-1723. PMC 9114321. PMID 35581222.
Kuret, Klara; Amalietti, Aram Gustav; Jones, D. Marc; Capitanchik, Charlotte; Ule, Jernej (2022-09-09). "Positional motif analysis reveals the extent of specificity of protein-RNA interactions observed by CLIP". Genome Biology. 23 (1): 191. doi:10.1186/s13059-022-02755-2. ISSN 1474-760X. PMC 9461102. PMID 36085079.