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Items: 31

1.

A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs.

McCorkindale AL, Wahle P, Werner S, Jungreis I, Menzel P, Shukla CJ, Abreu RLP, Irizarry RA, Meyer IM, Kellis M, Zinzen RP.

Development. 2019 Mar 28;146(6). pii: dev175265. doi: 10.1242/dev.175265.

2.

Transcriptional dynamics of microRNAs and their targets during Drosophila neurogenesis.

Menzel P, McCorkindale AL, Stefanov SR, Zinzen RP, Meyer IM.

RNA Biol. 2019 Jan;16(1):69-81. doi: 10.1080/15476286.2018.1558907. Epub 2019 Jan 20.

3.

In silico methods for co-transcriptional RNA secondary structure prediction and for investigating alternative RNA structure expression.

Meyer IM.

Methods. 2017 May 1;120:3-16. doi: 10.1016/j.ymeth.2017.04.009. Epub 2017 Apr 20. Review.

PMID:
28433606
4.

A comprehensive comparison of general RNA-RNA interaction prediction methods.

Lai D, Meyer IM.

Nucleic Acids Res. 2016 Apr 20;44(7):e61. doi: 10.1093/nar/gkv1477. Epub 2015 Dec 15.

6.

Four RNA families with functional transient structures.

Zhu JY, Meyer IM.

RNA Biol. 2015;12(1):5-20. doi: 10.1080/15476286.2015.1008373.

7.

e-RNA: a collection of web servers for comparative RNA structure prediction and visualisation.

Lai D, Meyer IM.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W373-6. doi: 10.1093/nar/gku292. Epub 2014 May 7.

8.

On the importance of cotranscriptional RNA structure formation.

Lai D, Proctor JR, Meyer IM.

RNA. 2013 Nov;19(11):1461-73. doi: 10.1261/rna.037390.112. Review.

9.

Transient RNA structure features are evolutionarily conserved and can be computationally predicted.

Zhu JY, Steif A, Proctor JR, Meyer IM.

Nucleic Acids Res. 2013 Jul;41(12):6273-85. doi: 10.1093/nar/gkt319. Epub 2013 Apr 26.

10.

COFOLD: an RNA secondary structure prediction method that takes co-transcriptional folding into account.

Proctor JR, Meyer IM.

Nucleic Acids Res. 2013 May;41(9):e102. doi: 10.1093/nar/gkt174. Epub 2013 Mar 19.

11.

The hok mRNA family.

Steif A, Meyer IM.

RNA Biol. 2012 Dec;9(12):1399-404. doi: 10.4161/rna.22746. Epub 2012 Dec 1.

PMID:
23324554
12.

The clonal and mutational evolution spectrum of primary triple-negative breast cancers.

Shah SP, Roth A, Goya R, Oloumi A, Ha G, Zhao Y, Turashvili G, Ding J, Tse K, Haffari G, Bashashati A, Prentice LM, Khattra J, Burleigh A, Yap D, Bernard V, McPherson A, Shumansky K, Crisan A, Giuliany R, Heravi-Moussavi A, Rosner J, Lai D, Birol I, Varhol R, Tam A, Dhalla N, Zeng T, Ma K, Chan SK, Griffith M, Moradian A, Cheng SW, Morin GB, Watson P, Gelmon K, Chia S, Chin SF, Curtis C, Rueda OM, Pharoah PD, Damaraju S, Mackey J, Hoon K, Harkins T, Tadigotla V, Sigaroudinia M, Gascard P, Tlsty T, Costello JF, Meyer IM, Eaves CJ, Wasserman WW, Jones S, Huntsman D, Hirst M, Caldas C, Marra MA, Aparicio S.

Nature. 2012 Apr 4;486(7403):395-9. doi: 10.1038/nature10933.

13.

R-CHIE: a web server and R package for visualizing RNA secondary structures.

Lai D, Proctor JR, Zhu JY, Meyer IM.

Nucleic Acids Res. 2012 Jul;40(12):e95. doi: 10.1093/nar/gks241. Epub 2012 Mar 19.

14.

Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma.

Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJ, Connors JM, Hirst M, Gascoyne RD, Marra MA.

Nature. 2011 Jul 27;476(7360):298-303. doi: 10.1038/nature10351.

15.
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17.

HMMCONVERTER 1.0: a toolbox for hidden Markov models.

Lam TY, Meyer IM.

Nucleic Acids Res. 2009 Nov;37(21):e139. doi: 10.1093/nar/gkp662.

18.

Reciprocal regulation of glycine-rich RNA-binding proteins via an interlocked feedback loop coupling alternative splicing to nonsense-mediated decay in Arabidopsis.

Schöning JC, Streitner C, Meyer IM, Gao Y, Staiger D.

Nucleic Acids Res. 2008 Dec;36(22):6977-87. doi: 10.1093/nar/gkn847. Epub 2008 Nov 4.

19.

The genome of the simian and human malaria parasite Plasmodium knowlesi.

Pain A, Böhme U, Berry AE, Mungall K, Finn RD, Jackson AP, Mourier T, Mistry J, Pasini EM, Aslett MA, Balasubrammaniam S, Borgwardt K, Brooks K, Carret C, Carver TJ, Cherevach I, Chillingworth T, Clark TG, Galinski MR, Hall N, Harper D, Harris D, Hauser H, Ivens A, Janssen CS, Keane T, Larke N, Lapp S, Marti M, Moule S, Meyer IM, Ormond D, Peters N, Sanders M, Sanders S, Sargeant TJ, Simmonds M, Smith F, Squares R, Thurston S, Tivey AR, Walker D, White B, Zuiderwijk E, Churcher C, Quail MA, Cowman AF, Turner CM, Rajandream MA, Kocken CH, Thomas AW, Newbold CI, Barrell BG, Berriman M.

Nature. 2008 Oct 9;455(7214):799-803. doi: 10.1038/nature07306.

20.

Predicting novel RNA-RNA interactions.

Meyer IM.

Curr Opin Struct Biol. 2008 Jun;18(3):387-93. doi: 10.1016/j.sbi.2008.03.006. Epub 2008 May 14. Review.

PMID:
18485695
21.

A cross-species comparison of X-chromosome inactivation in Eutheria.

Yen ZC, Meyer IM, Karalic S, Brown CJ.

Genomics. 2007 Oct;90(4):453-63. Epub 2007 Aug 28.

23.

A practical guide to the art of RNA gene prediction.

Meyer IM.

Brief Bioinform. 2007 Nov;8(6):396-414. Epub 2007 May 4. Review.

PMID:
17483123
24.
25.

A linear memory algorithm for Baum-Welch training.

Miklós I, Meyer IM.

BMC Bioinformatics. 2005 Sep 19;6:231.

26.

Moments of the Boltzmann distribution for RNA secondary structures.

Miklós I, Meyer IM, Nagy B.

Bull Math Biol. 2005 Sep;67(5):1031-47.

PMID:
15998494
27.

A comparative method for finding and folding RNA secondary structures within protein-coding regions.

Pedersen JS, Meyer IM, Forsberg R, Simmonds P, Hein J.

Nucleic Acids Res. 2004 Sep 24;32(16):4925-36. Print 2004.

28.

Co-transcriptional folding is encoded within RNA genes.

Meyer IM, Miklós I.

BMC Mol Biol. 2004 Aug 6;5:10.

29.

An evolutionary model for protein-coding regions with conserved RNA structure.

Pedersen JS, Forsberg R, Meyer IM, Hein J.

Mol Biol Evol. 2004 Oct;21(10):1913-22. Epub 2004 Jun 30.

PMID:
15229291
30.

Gene structure conservation aids similarity based gene prediction.

Meyer IM, Durbin R.

Nucleic Acids Res. 2004 Feb 4;32(2):776-83. Print 2004.

31.

Comparative ab initio prediction of gene structures using pair HMMs.

Meyer IM, Durbin R.

Bioinformatics. 2002 Oct;18(10):1309-18.

PMID:
12376375

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