Log on / register
Feedback | Support | My details
Computational identification of Drosophila microRNA genes.
Lai EC, Tomancak P, Williams RW, Rubin GM
Genome Biol 2003, 4:R42
[Full text] [PubMed] [Related articles] [Cited on BioMed Central]


printer friendly 
to  [Help]

PubMed Central articles that cite the above article:

1.
Identification of Drosophila MicroRNA targets.
Stark A, Brennecke J, Russell RB, Cohen SM
PLoS Biol 2003 Dec, 1:E60
[PubMed Central] [PubMed] [Related articles]

2.
The microRNA Registry.
Griffiths-Jones S
Nucleic Acids Res 2004 Jan 1, 32:D109-11
[PubMed Central] [PubMed] [Related articles]

3.
Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes.
Bonnet E, Wuyts J, Rouzé P, Van de Peer Y
Proc Natl Acad Sci U S A 2004 Aug 3, 101:11511-6
[PubMed Central] [PubMed] [Related articles]

4.
Effects of length and location on the cellular response to double-stranded RNA.
Wang Q, Carmichael GG
Microbiol Mol Biol Rev 2004 Sep, 68:432-52
[PubMed Central] [PubMed] [Related articles]

5.
Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis.
Sunkar R, Zhu JK
Plant Cell 2004 Aug, 16:2001-19
[PubMed Central] [PubMed] [Related articles]

6.
Human MicroRNA targets.
John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS
PLoS Biol 2004 Nov, 2:e363
[PubMed Central] [PubMed] [Related articles]

7.
Substrate requirements for let-7 function in the developing zebrafish embryo.
Kloosterman WP, Wienholds E, Ketting RF, Plasterk RH
Nucleic Acids Res 2004, 32:6284-91
[PubMed Central] [PubMed] [Related articles]

8.
Computational prediction of miRNAs in Arabidopsis thaliana.
Adai A, Johnson C, Mlotshwa S, Archer-Evans S, Manocha V, Vance V, Sundaresan V
Genome Res 2005 Jan, 15:78-91
[PubMed Central] [PubMed] [Related articles]

9.
Development of a micro-array to detect human and mouse microRNAs and characterization of expression in human organs.
Sun Y, Koo S, White N, Peralta E, Esau C, Dean NM, Perera RJ
Nucleic Acids Res 2004, 32:e188
[PubMed Central] [PubMed] [Related articles]

10.
Principles of microRNA-target recognition.
Brennecke J, Stark A, Russell RB, Cohen SM
PLoS Biol 2005 Mar, 3:e85
[PubMed Central] [PubMed] [Related articles]

11.
*** Unable to retrieve article 15723116 ***

[PubMed Central] [PubMed] [Related articles]

12.
A computational study of off-target effects of RNA interference.
Qiu S, Adema CM, Lane T
Nucleic Acids Res 2005, 33:1834-47
[PubMed Central] [PubMed] [Related articles]

13.
Pervasive regulation of Drosophila Notch target genes by GY-box-, Brd-box-, and K-box-class microRNAs.
Lai EC, Tam B, Rubin GM
Genes Dev 2005 May 1, 19:1067-80
[PubMed Central] [PubMed] [Related articles]

14.
Clustering and conservation patterns of human microRNAs.
Altuvia Y, Landgraf P, Lithwick G, Elefant N, Pfeffer S, Aravin A, Brownstein MJ, Tuschl T, Margalit H
Nucleic Acids Res 2005, 33:2697-706
[PubMed Central] [PubMed] [Related articles]

15.
Processing of pre-microRNAs by the Dicer-1-Loquacious complex in Drosophila cells.
Saito K, Ishizuka A, Siomi H, Siomi MC
PLoS Biol 2005 Jul, 3:e235
[PubMed Central] [PubMed] [Related articles]

16.
Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing.
Glazov EA, Pheasant M, McGraw EA, Bejerano G, Mattick JS
Genome Res 2005 Jun, 15:800-8
[PubMed Central] [PubMed] [Related articles]

17.
The developmental miRNA profiles of zebrafish as determined by small RNA cloning.
Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T
Genes Dev 2005 Jun 1, 19:1288-93
[PubMed Central] [PubMed] [Related articles]

18.
Human microRNA prediction through a probabilistic co-learning model of sequence and structure.
Nam JW, Shin KR, Han J, Lee Y, Kim VN, Zhang BT
Nucleic Acids Res 2005, 33:3570-81
[PubMed Central] [PubMed] [Related articles]

19.
MicroInspector: a web tool for detection of miRNA binding sites in an RNA sequence.
Rusinov V, Baev V, Minkov IN, Tabler M
Nucleic Acids Res 2005 Jul 1, 33:W696-700
[PubMed Central] [PubMed] [Related articles]

20.
*** Unable to retrieve article 15918769 ***

[PubMed Central] [PubMed] [Related articles]

21.
Drosophila microRNAs exhibit diverse spatial expression patterns during embryonic development.
Aboobaker AA, Tomancak P, Patel N, Rubin GM, Lai EC
Proc Natl Acad Sci U S A 2005 Dec 13, 102:18017-22
[PubMed Central] [PubMed] [Related articles]

22.
Complementary miRNA pairs suggest a regulatory role for miRNA:miRNA duplexes.
Lai EC, Wiel C, Rubin GM
RNA 2004 Feb, 10:171-5
[PubMed Central] [PubMed] [Related articles]

23.
Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification.
Ohler U, Yekta S, Lim LP, Bartel DP, Burge CB
RNA 2004 Sep, 10:1309-22
[PubMed Central] [PubMed] [Related articles]

24.
Trans-splicing and polyadenylation of let-7 microRNA primary transcripts.
Bracht J, Hunter S, Eachus R, Weeks P, Pasquinelli AE
RNA 2004 Oct, 10:1586-94
[PubMed Central] [PubMed] [Related articles]

25.
Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes.
Baskerville S, Bartel DP
RNA 2005 Mar, 11:241-7
[PubMed Central] [PubMed] [Related articles]

26.
Weighted sequence motifs as an improved seeding step in microRNA target prediction algorithms.
Saetrom O, Snøve O, Saetrom P
RNA 2005 Jul, 11:995-1003
[PubMed Central] [PubMed] [Related articles]

27.
Genome-wide analyses of two families of snoRNA genes from Drosophila melanogaster, demonstrating the extensive utilization of introns for coding of snoRNAs.
Huang ZP, Zhou H, He HL, Chen CL, Liang D, Qu LH
RNA 2005 Aug, 11:1303-16
[PubMed Central] [PubMed] [Related articles]

28.
Sequence-specific inhibition of microRNA- and siRNA-induced RNA silencing.
Meister G, Landthaler M, Dorsett Y, Tuschl T
RNA 2004 Mar, 10:544-50
[PubMed Central] [PubMed] [Related articles]

29.
A combined computational and microarray-based approach identifies novel microRNAs encoded by human gamma-herpesviruses.
Grundhoff A, Sullivan CS, Ganem D
RNA 2006 May, 12:733-50
[PubMed Central] [PubMed] [Related articles]

30.
Genome-wide analysis of mRNAs regulated by Drosha and Argonaute proteins in Drosophila melanogaster.
Rehwinkel J, Natalin P, Stark A, Brennecke J, Cohen SM, Izaurralde E
Mol Cell Biol 2006 Apr, 26:2965-75
[PubMed Central] [PubMed] [Related articles]

31.
Drosophila crinkled, mutations of which disrupt morphogenesis and cause lethality, encodes fly myosin VIIA.
Kiehart DP, Franke JD, Chee MK, Montague RA, Chen TL, Roote J, Ashburner M
Genetics 2004 Nov, 168:1337-52
[PubMed Central] [PubMed] [Related articles]

32.
Evolution of Arabidopsis microRNA families through duplication events.
Maher C, Stein L, Ware D
Genome Res 2006 Apr, 16:510-9
[PubMed Central] [PubMed] [Related articles]

33.
Differential repression of alternative transcripts: a screen for miRNA targets.
Legendre M, Ritchie W, Lopez F, Gautheret D
PLoS Comput Biol 2006 May, 2:e43
[PubMed Central] [PubMed] [Related articles]

34.
Target prediction for small, noncoding RNAs in bacteria.
Tjaden B, Goodwin SS, Opdyke JA, Guillier M, Fu DX, Gottesman S, Storz G
Nucleic Acids Res 2006, 34:2791-802
[PubMed Central] [PubMed] [Related articles]

35.
*** Unable to retrieve article 16699595 ***

[PubMed Central] [PubMed] [Related articles]

36.
Prediction and identification of herpes simplex virus 1-encoded microRNAs.
Cui C, Griffiths A, Li G, Silva LM, Kramer MF, Gaasterland T, Wang XJ, Coen DM
J Virol 2006 Jun, 80:5499-508
[PubMed Central] [PubMed] [Related articles]

37.
ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs.
Nam JW, Kim J, Kim SK, Zhang BT
Nucleic Acids Res 2006 Jul 1, 34:W455-8
[PubMed Central] [PubMed] [Related articles]

38.
Computational Prediction of MicroRNAs Encoded in Viral and Other Genomes.
Thomassen GO, Røsok O, Rognes T
J Biomed Biotechnol 2006, 2006:95270
[PubMed Central] [PubMed] [Related articles]

39.
RNA editing in Drosophila melanogaster: New targets and functional consequences.
Stapleton M, Carlson JW, Celniker SE
RNA 2006 Nov, 12:1922-32
[PubMed Central] [PubMed] [Related articles]

40.
snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome.
Yang JH, Zhang XC, Huang ZP, Zhou H, Huang MB, Zhang S, Chen YQ, Qu LH
Nucleic Acids Res 2006, 34:5112-23
[PubMed Central] [PubMed] [Related articles]

41.
Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array.
Biemar F, Nix DA, Piel J, Peterson B, Ronshaugen M, Sementchenko V, Bell I, Manak JR, Levine MS
Proc Natl Acad Sci U S A 2006 Aug 22, 103:12763-8
[PubMed Central] [PubMed] [Related articles]

42.
Unique folding of precursor microRNAs: quantitative evidence and implications for de novo identification.
Ng Kwang Loong S, Mishra SK
RNA 2007 Feb, 13:170-87
[PubMed Central] [PubMed] [Related articles]

43.
RNA stem-loops: to be or not to be cleaved by RNAse III.
Ritchie W, Legendre M, Gautheret D
RNA 2007 Apr, 13:457-62
[PubMed Central] [PubMed] [Related articles]

44.
Query-dependent banding (QDB) for faster RNA similarity searches.
Nawrocki EP, Eddy SR
PLoS Comput Biol 2007 Mar 30, 3:e56
[PubMed Central] [PubMed] [Related articles]

45.
MicroRNAs: regulators of gene expression and cell differentiation.
Shivdasani RA
Blood 2006 Dec 1, 108:3646-53
[PubMed Central] [PubMed] [Related articles]

46.
MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features.
Jiang P, Wu H, Wang W, Ma W, Sun X, Lu Z
Nucleic Acids Res 2007 Jul, 35:W339-44
[PubMed Central] [PubMed] [Related articles]

47.
The Drosophila nerfin-1 mRNA requires multiple microRNAs to regulate its spatial and temporal translation dynamics in the developing nervous system.
Kuzin A, Kundu M, Brody T, Odenwald WF
Dev Biol 2007 Oct 1, 310:35-43
[PubMed Central] [PubMed] [Related articles]

48.
miRRim: a novel system to find conserved miRNAs with high sensitivity and specificity.
Terai G, Komori T, Asai K, Kin T
RNA 2007 Dec, 13:2081-90
[PubMed Central] [PubMed] [Related articles]

49.
Identification of novel Drosophila melanogaster microRNAs.
Sandmann T, Cohen SM
PLoS ONE 2007, 2:e1265
[PubMed Central] [PubMed] [Related articles]

50.
Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs.
Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC
Genome Res 2007 Dec, 17:1850-64
[PubMed Central] [PubMed] [Related articles]

51.
Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes.
Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M
Genome Res 2007 Dec, 17:1865-79
[PubMed Central] [PubMed] [Related articles]

52.
Xenopus microRNA genes are predominantly located within introns and are differentially expressed in adult frog tissues via post-transcriptional regulation.
Tang GQ, Maxwell ES
Genome Res 2008 Jan, 18:104-12
[PubMed Central] [PubMed] [Related articles]

53.
Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA loci.
Tyler DM, Okamura K, Chung WJ, Hagen JW, Berezikov E, Hannon GJ, Lai EC
Genes Dev 2008 Jan 1, 22:26-36
[PubMed Central] [PubMed] [Related articles]

54.
Anopheles gambiae miRNAs as actors of defence reaction against Plasmodium invasion.
Winter F, Edaye S, Hüttenhofer A, Brunel C
Nucleic Acids Res 2007, 35:6953-62
[PubMed Central] [PubMed] [Related articles]

55.
Vir-Mir db: prediction of viral microRNA candidate hairpins.
Li SC, Shiau CK, Lin WC
Nucleic Acids Res 2008 Jan, 36:D184-9
[PubMed Central] [PubMed] [Related articles]

56.
Control of antagonistic components of the hedgehog signaling pathway by microRNAs in Drosophila.
Friggi-Grelin F, Lavenant-Staccini L, Therond P
Genetics 2008 May, 179:429-39
[PubMed Central] [PubMed] [Related articles]

57.
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.
Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J, Harvard FlyBase curators , Berkeley Drosophila Genome Project , Hodges E, Hinrichs AS, Caspi A, Paten B, Park SW, Han MV, Maeder ML, Polansky BJ, Robson BE, Aerts S, van Helden J, Hassan B, Gilbert DG, Eastman DA, Rice M, Weir M, Hahn MW, Park Y, Dewey CN, Pachter L, Kent WJ, Haussler D, Lai EC, Bartel DP, Hannon GJ, Kaufman TC, Eisen MB, Clark AG, Smith D, Celniker SE, Gelbart WM, Kellis M
Nature 2007 Nov 8, 450:219-32
[PubMed Central] [PubMed] [Related articles]

58.
Novel microRNA candidates and miRNA-mRNA pairs in embryonic stem (ES) cells.
Gu P, Reid JG, Gao X, Shaw CA, Creighton C, Tran PL, Zhou X, Drabek RB, Steffen DL, Hoang DM, Weiss MK, Naghavi AO, El-daye J, Khan MF, Legge GB, Wheeler DA, Gibbs RA, Miller JN, Cooney AJ, Gunaratne PH
PLoS ONE 2008, 3:e2548
[PubMed Central] [PubMed] [Related articles]

59.
Sequence relationships among C. elegans, D. melanogaster and human microRNAs highlight the extensive conservation of microRNAs in biology.
Ibáñez-Ventoso C, Vora M, Driscoll M
PLoS ONE 2008, 3:e2818
[PubMed Central] [PubMed] [Related articles]

60.
The silkworm (Bombyx mori) microRNAs and their expressions in multiple developmental stages.
Yu X, Zhou Q, Li SC, Luo Q, Cai Y, Lin WC, Chen H, Yang Y, Hu S, Yu J
PLoS ONE 2008, 3:e2997
[PubMed Central] [PubMed] [Related articles]

61.
Post-embryonic expression of C. elegans microRNAs belonging to the lin-4 and let-7 families in the hypodermis and the reproductive system.
Esquela-Kerscher A, Johnson SM, Bai L, Saito K, Partridge J, Reinert KL, Slack FJ
Dev Dyn 2005 Dec, 234:868-77
[PubMed Central] [PubMed] [Related articles]


This article is also cited by 21 articles in BioMed Central


You can also check ISI Web of Science for additional citations (subscription required)
  
printer friendly 
to  [Help]

© 1999-2008 BioMed Central Ltd unless otherwise stated. Part of Springer Science+Business Media.