-
1
-
-
74049088856
-
Lost in translation: An assessment and perspective for computational microRNA target identification
-
Alexiou P, Maragkakis M, Papadopoulos GL, Reczko M, Hatzigeorgiou AG. 2009. Lost in translation: An assessment and perspective for computational microRNA target identification. Bioinformatics 25: 3049-3055.
-
(2009)
Bioinformatics
, vol.25
, pp. 3049-3055
-
-
Alexiou, P.1
Maragkakis, M.2
Papadopoulos, G.L.3
Reczko, M.4
Hatzigeorgiou, A.G.5
-
2
-
-
58249088751
-
MicroRNAs: Target recognition and regulatory functions
-
Bartel DP. 2009. MicroRNAs: Target recognition and regulatory functions. Cell 136: 215-233.
-
(2009)
Cell
, vol.136
, pp. 215-233
-
-
Bartel, D.P.1
-
3
-
-
0842321501
-
MicroRNA targets in Drosophila
-
Enright A, John B, Gaul U, Tuschl T, Sander C, Marks D. 2003. MicroRNA targets in Drosophila. Genome Biol 5: R1.
-
(2003)
Genome Biol
, vol.5
-
-
Enright, A.1
John, B.2
Gaul, U.3
Tuschl, T.4
Sander, C.5
Marks, D.6
-
4
-
-
79952907985
-
The impact of miRNA target sites in coding sequences and in 3′UTRs
-
Fang Z, Rajewsky N. 2011. The impact of miRNA target sites in coding sequences and in 3′UTRs. PLoS ONE 6: e18067.
-
(2011)
PLoS ONE
, vol.6
-
-
Fang, Z.1
Rajewsky, N.2
-
5
-
-
77953563697
-
The code within the code: MicroRNAs target coding regions
-
Forman JJ, Coller HA. 2010. The code within the code: microRNAs target coding regions. Cell Cycle 9: 1533-1541.
-
(2010)
Cell Cycle
, vol.9
, pp. 1533-1541
-
-
Forman, J.J.1
Coller, H.A.2
-
6
-
-
54449097149
-
A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence
-
Forman JJ, Legesse-Miller A, Coller HA. 2008. A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence. Proc Natl Acad Sci 105: 14879-14884.
-
(2008)
Proc Natl Acad Sci
, vol.105
, pp. 14879-14884
-
-
Forman, J.J.1
Legesse-Miller, A.2
Coller, H.A.3
-
7
-
-
1642356603
-
The relationship between palindrome avoidance and intragenic codon usage variations: A Monte Carlo study
-
Fuglsang A. 2004. The relationship between palindrome avoidance and intragenic codon usage variations: A Monte Carlo study. Biochem Biophys Res Commun 316: 755-762.
-
(2004)
Biochem Biophys Res Commun
, vol.316
, pp. 755-762
-
-
Fuglsang, A.1
-
8
-
-
80455154984
-
Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs
-
Garcia DM, Baek D, Shin C, Bell GW, Grimson A, Bartel DP. 2011. Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nat Struct Mol Biol 18: 1139-1146.
-
(2011)
Nat Struct Mol Biol
, vol.18
, pp. 1139-1146
-
-
Garcia, D.M.1
Baek, D.2
Shin, C.3
Bell, G.W.4
Grimson, A.5
Bartel, D.P.6
-
9
-
-
33644750115
-
MiRBase: MicroRNA sequences, targets and gene nomenclature
-
Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. 2006. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 34: D140-D144.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Griffiths-Jones, S.1
Grocock, R.J.2
Van Dongen, S.3
Bateman, A.4
Enright, A.J.5
-
10
-
-
34250805982
-
MicroRNA targeting specificity in mammals: Determinants beyond seed pairing
-
Grimson A, Farh KK-H, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP. 2007. MicroRNA targeting specificity in mammals: Determinants beyond seed pairing. Mol Cell 27: 91-105.
-
(2007)
Mol Cell
, vol.27
, pp. 91-105
-
-
Grimson, A.1
Farh, K.K.-H.2
Johnston, W.K.3
Garrett-Engele, P.4
Lim, L.P.5
Bartel, D.P.6
-
11
-
-
59649125888
-
Biological basis for restriction of microRNA targets to the 3′ untranslated region in mammalian mRNAs
-
Gu S, Jin L, Zhang F, Sarnow P, Kay MA. 2009. Biological basis for restriction of microRNA targets to the 3′ untranslated region in mammalian mRNAs. Nat Struct Mol Biol 16: 144-150.
-
(2009)
Nat Struct Mol Biol
, vol.16
, pp. 144-150
-
-
Gu, S.1
Jin, L.2
Zhang, F.3
Sarnow, P.4
Kay, M.A.5
-
12
-
-
77950920903
-
Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP
-
Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M Jr, Jungkamp A-C, Munschauer M, et al. 2010. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141: 129-141.
-
(2010)
Cell
, vol.141
, pp. 129-141
-
-
Hafner, M.1
Landthaler, M.2
Burger, L.3
Khorshid, M.4
Hausser, J.5
Berninger, P.6
Rothballer, A.7
Ascano Jr., M.8
Jungkamp, A.-C.9
Munschauer, M.10
-
13
-
-
77955101812
-
Computational methods to identify miRNA targets
-
Hammell M. 2010. Computational methods to identify miRNA targets. Semin Cell Dev Biol 21: 738-744.
-
(2010)
Semin Cell Dev Biol
, vol.21
, pp. 738-744
-
-
Hammell, M.1
-
14
-
-
2942672580
-
Computational identification of plant microRNAs and their targets, including a stress-induced miRNA
-
Jones-Rhoades MW, Bartel DP. 2004. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 14: 787-799.
-
(2004)
Mol Cell
, vol.14
, pp. 787-799
-
-
Jones-Rhoades, M.W.1
Bartel, D.P.2
-
15
-
-
0347755531
-
The UCSC Table Browser data retrieval tool
-
Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ. 2004. The UCSC Table Browser data retrieval tool. Nucleic Acids Res 32: D493-D496.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Karolchik, D.1
Hinrichs, A.S.2
Furey, T.S.3
Roskin, K.M.4
Sugnet, C.W.5
Haussler, D.6
Kent, W.J.7
-
17
-
-
0027751663
-
The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
-
Lee R, Feinbaum R, Ambros V. 1993. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843-854.
-
(1993)
Cell
, vol.75
, pp. 843-854
-
-
Lee, R.1
Feinbaum, R.2
Ambros, V.3
-
18
-
-
11844278458
-
Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
-
Lewis BP, Burge CB, Bartel DP. 2005. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120: 15-20.
-
(2005)
Cell
, vol.120
, pp. 15-20
-
-
Lewis, B.P.1
Burge, C.B.2
Bartel, D.P.3
-
19
-
-
13944282215
-
Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs
-
Lim LP. 2005. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433: 769-773.
-
(2005)
Nature
, vol.433
, pp. 769-773
-
-
Lim, L.P.1
-
20
-
-
78651329275
-
Efficient use of accessibility in microRNA target prediction
-
Marin RM, Vanicek J. 2011. Efficient use of accessibility in microRNA target prediction. Nucleic Acids Res 39: 19-29.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. 19-29
-
-
Marin, R.M.1
Vanicek, J.2
-
21
-
-
84857570339
-
Optimal use of conservation and accessibility filters in microRNA target prediction
-
Marin RM, Vanicek J. 2012. Optimal use of conservation and accessibility filters in microRNA target prediction. PLoS ONE 7: e32208.
-
(2012)
PLoS ONE
, vol.7
-
-
Marin, R.M.1
Vanicek, J.2
-
22
-
-
38849149795
-
28-Way vertebrate alignment and conservation track in the UCSC Genome Browser
-
Miller W, Rosenbloom K, Hardison RC, Hou M, Taylor J, Raney B, Burhans R, King DC, Baertsch R, Blankenberg D, et al. 2007. 28-Way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Res 17: 1797-1808.
-
(2007)
Genome Res
, vol.17
, pp. 1797-1808
-
-
Miller, W.1
Rosenbloom, K.2
Hardison, R.C.3
Hou, M.4
Taylor, J.5
Raney, B.6
Burhans, R.7
King, D.C.8
Baertsch, R.9
Blankenberg, D.10
-
23
-
-
44449105456
-
Suppression of immediate-early viral gene expression by herpesvirus-coded microRNAs: Implications for latency
-
Murphy E, Vaníček J, Robins H, Shenk T, Levine AJ. 2008. Suppression of immediate-early viral gene expression by herpesvirus-coded microRNAs: Implications for latency. Proc Natl Acad Sci 105: 5453-5458.
-
(2008)
Proc Natl Acad Sci
, vol.105
, pp. 5453-5458
-
-
Murphy, E.1
Vaníček, J.2
Robins, H.3
Shenk, T.4
Levine, A.J.5
-
24
-
-
84859174156
-
A role for tRNA modifications in genome structure and codon usage
-
Novoa EM, Pavon-Eternod M, Pan T, Ribas de Pouplana L. 2012. A role for tRNA modifications in genome structure and codon usage. Cell 149: 202-213.
-
(2012)
Cell
, vol.149
, pp. 202-213
-
-
Novoa, E.M.1
Pavon-Eternod, M.2
Pan, T.3
Ribas De Pouplana, L.4
-
25
-
-
20844463414
-
Identification of microRNAs of the herpesvirus family
-
Pfeffer S, Sewer A, Lagos-Quintana M, Sheridan R, Sander C, Grasser FA, van Dyk LF, Ho CK, Shuman S, Chien MC, et al. 2005. Identification of microRNAs of the herpesvirus family. Nat Methods 2: 269-276.
-
(2005)
Nat Methods
, vol.2
, pp. 269-276
-
-
Pfeffer, S.1
Sewer, A.2
Lagos-Quintana, M.3
Sheridan, R.4
Sander, C.5
Grasser, F.A.6
Van Dyk, L.F.7
Ho, C.K.8
Shuman, S.9
Chien, M.C.10
-
26
-
-
84859067415
-
Functional microRNA targets in protein coding sequences
-
Reczko M, Maragkakis M, Alexiou P, Grosse I, Hatzigeorgiou AG. 2012. Functional microRNA targets in protein coding sequences. Bioinformatics 28: 771-776.
-
(2012)
Bioinformatics
, vol.28
, pp. 771-776
-
-
Reczko, M.1
Maragkakis, M.2
Alexiou, P.3
Grosse, I.4
Hatzigeorgiou, A.G.5
-
27
-
-
27344448283
-
Human microRNAs target a functionally distinct population of genes with AT-rich 3′UTRs
-
Robins H, Press WH. 2005. Human microRNAs target a functionally distinct population of genes with AT-rich 3′UTRs. Proc Natl Acad Sci 102: 15557-15562.
-
(2005)
Proc Natl Acad Sci
, vol.102
, pp. 15557-15562
-
-
Robins, H.1
Press, W.H.2
-
28
-
-
28844468371
-
A relative-entropy algorithm for genomic fingerprinting captures host-phage similarities
-
Robins H, Krasnitz M, Barak H, Levine AJ. 2005. A relative-entropy algorithm for genomic fingerprinting captures host-phage similarities. J Bacteriol 187: 8370-8374.
-
(2005)
J Bacteriol
, vol.187
, pp. 8370-8374
-
-
Robins, H.1
Krasnitz, M.2
Barak, H.3
Levine, A.J.4
-
29
-
-
46449089502
-
The computational detection of functional nucleotide sequence motifs in the coding regions of organisms
-
Robins H, Krasnitz M, Levine AJ. 2008. The computational detection of functional nucleotide sequence motifs in the coding regions of organisms. Exp Biol Med 233: 665-673.
-
(2008)
Exp Biol Med
, vol.233
, pp. 665-673
-
-
Robins, H.1
Krasnitz, M.2
Levine, A.J.3
-
30
-
-
77957662209
-
Conserved microRNA targeting in Drosophila is as widespread in coding regions as in 3′UTRs
-
Schnall-Levin M, Zhao Y, Perrimon N, Berger B. 2010. Conserved microRNA targeting in Drosophila is as widespread in coding regions as in 3′UTRs. Proc Natl Acad Sci 107: 15751-15756.
-
(2010)
Proc Natl Acad Sci
, vol.107
, pp. 15751-15756
-
-
Schnall-Levin, M.1
Zhao, Y.2
Perrimon, N.3
Berger, B.4
-
31
-
-
79960489634
-
Unusually effective microRNA targeting within repeat-rich coding regions of mammalian mRNAs
-
Schnall-Levin M, Rissland OS, Johnston WK, Perrimon N, Bartel DP, Berger B. 2011. Unusually effective microRNA targeting within repeat-rich coding regions of mammalian mRNAs. Genome Res 21: 1395-1403.
-
(2011)
Genome Res
, vol.21
, pp. 1395-1403
-
-
Schnall-Levin, M.1
Rissland, O.S.2
Johnston, W.K.3
Perrimon, N.4
Bartel, D.P.5
Berger, B.6
-
32
-
-
49949117302
-
Widespread changes in protein synthesis induced by microRNAs
-
Selbach M, Schwanhausser B, Thierfelder N, Fang Z, Khanin R, Rajewsky N. 2008. Widespread changes in protein synthesis induced by microRNAs. Nature 455: 58-63.
-
(2008)
Nature
, vol.455
, pp. 58-63
-
-
Selbach, M.1
Schwanhausser, B.2
Thierfelder, N.3
Fang, Z.4
Khanin, R.5
Rajewsky, N.6
|