-
1
-
-
84940502214
-
Predicting effective microRNA target sites in mammalian mRNAs
-
Agarwal V., Bell G.W., Nam J.W., et al. Predicting effective microRNA target sites in mammalian mRNAs. eLife 2015, 4:e05005.
-
(2015)
eLife
, vol.4
-
-
Agarwal, V.1
Bell, G.W.2
Nam, J.W.3
-
3
-
-
77949430343
-
The DIANA-mirExTra web server: from gene expression data to MicroRNA function
-
Alexiou P., Maragkakis M., Papadopoulos G.L., et al. The DIANA-mirExTra web server: from gene expression data to MicroRNA function. PLoS ONE. 2010, 5:e9171.
-
(2010)
PLoS ONE.
, vol.5
-
-
Alexiou, P.1
Maragkakis, M.2
Papadopoulos, G.L.3
-
4
-
-
0034069495
-
Gene ontology: tool for the unification of biology. The gene ontology consortium
-
Ashburner M., Ball C.A., Blake J.A., et al. Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat. Genet. 2000, 25:25-29.
-
(2000)
Nat. Genet.
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
-
5
-
-
34547602163
-
GeneTrail-advanced gene set enrichment analysis
-
Backes C., Keller A., Kuentzer J., et al. GeneTrail-advanced gene set enrichment analysis. Nucleic Acids Res. 2007, 35:W186-W192.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. W186-W192
-
-
Backes, C.1
Keller, A.2
Kuentzer, J.3
-
6
-
-
84979227262
-
MiEAA: microRNA enrichment analysis and annotation
-
Backes C., Khaleeq Q.T., Meese E., et al. miEAA: microRNA enrichment analysis and annotation. Nucleic Acids Res. 2016, 44:W110-W116.
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. W110-W116
-
-
Backes, C.1
Khaleeq, Q.T.2
Meese, E.3
-
7
-
-
70350000602
-
TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples
-
Bandyopadhyay S., Mitra R. TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples. Bioinformatics 2009, 25:2625-2631.
-
(2009)
Bioinformatics
, vol.25
, pp. 2625-2631
-
-
Bandyopadhyay, S.1
Mitra, R.2
-
8
-
-
84922932221
-
MBSTAR: multiple instance learning for predicting specific functional binding sites in microRNA targets
-
Bandyopadhyay S., Ghosh D., Mitra R., et al. MBSTAR: multiple instance learning for predicting specific functional binding sites in microRNA targets. Sci. Rep. 2015, 5:8004.
-
(2015)
Sci. Rep.
, vol.5
, pp. 8004
-
-
Bandyopadhyay, S.1
Ghosh, D.2
Mitra, R.3
-
9
-
-
70349643725
-
Chromatin poises miRNA- and protein-coding genes for expression
-
Barski A., Jothi R., Cuddapah S., et al. Chromatin poises miRNA- and protein-coding genes for expression. Genome Res. 2009, 19:1742-1751.
-
(2009)
Genome Res.
, vol.19
, pp. 1742-1751
-
-
Barski, A.1
Jothi, R.2
Cuddapah, S.3
-
10
-
-
58249088751
-
MicroRNAs: target recognition and regulatory functions
-
Bartel D.P. MicroRNAs: target recognition and regulatory functions. Cell 2009, 136:215-233.
-
(2009)
Cell
, vol.136
, pp. 215-233
-
-
Bartel, D.P.1
-
11
-
-
77955963884
-
Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites
-
Betel D., Koppal A., Agius P., et al. Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome. Biol. 2010, 11:R90.
-
(2010)
Genome. Biol.
, vol.11
, pp. R90
-
-
Betel, D.1
Koppal, A.2
Agius, P.3
-
12
-
-
84885912472
-
IncRNome: a comprehensive knowledgebase of human long noncoding RNAs
-
Database (Oxford)bat034
-
Bhartiya D., Pal K., Ghosh S., et al. IncRNome: a comprehensive knowledgebase of human long noncoding RNAs. Database (Oxford) 2013, bat034.
-
(2013)
-
-
Bhartiya, D.1
Pal, K.2
Ghosh, S.3
-
13
-
-
84864443057
-
MAGIA2: from miRNA and genes expression data integrative analysis to microRNA-transcription factor mixed regulatory circuits (2012 update)
-
Bisognin A., Sales G., Coppe A., et al. MAGIA2: from miRNA and genes expression data integrative analysis to microRNA-transcription factor mixed regulatory circuits (2012 update). Nucleic Acids Res. 2012, 40:W13-W21.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. W13-W21
-
-
Bisognin, A.1
Sales, G.2
Coppe, A.3
-
15
-
-
80054715378
-
A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA
-
Cesana M., Cacchiarelli D., Legnini I., et al. A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell 2011, 147:358-369.
-
(2011)
Cell
, vol.147
, pp. 358-369
-
-
Cesana, M.1
Cacchiarelli, D.2
Legnini, I.3
-
16
-
-
67749132423
-
Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps
-
Chi S.W., Zang J.B., Mele A., et al. Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature. 2009, 460:479-486.
-
(2009)
Nature.
, vol.460
, pp. 479-486
-
-
Chi, S.W.1
Zang, J.B.2
Mele, A.3
-
17
-
-
82255185653
-
Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data
-
Chien C.H., Sun Y.M., Chang W.C., et al. Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data. Nucleic Acids Res. 2011, 39:9345-9356.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 9345-9356
-
-
Chien, C.H.1
Sun, Y.M.2
Chang, W.C.3
-
18
-
-
84976904131
-
MiRTarBase 2016: updates to the experimentally validated miRNA-target interactions database
-
Chou C.H., Chang N.W., Shrestha S., et al. miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database. Nucleic Acids Res. 2016, 44:D239-D247.
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. D239-D247
-
-
Chou, C.H.1
Chang, N.W.2
Shrestha, S.3
-
19
-
-
65449183132
-
Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data
-
Corcoran D.L., Pandit K.V., Gordon B., et al. Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data. PLoS ONE. 2009, 4:e5279.
-
(2009)
PLoS ONE.
, vol.4
-
-
Corcoran, D.L.1
Pandit, K.V.2
Gordon, B.3
-
20
-
-
84891753483
-
The reactome pathway knowledgebase
-
Croft D., Mundo A.F., Haw R., et al. The reactome pathway knowledgebase. Nucleic Acids Res. 2014, 42:D472-D477.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D472-D477
-
-
Croft, D.1
Mundo, A.F.2
Haw, R.3
-
21
-
-
0036123111
-
Computational detection and location of transcription start sites in mammalian genomic DNA
-
Down T.A., Hubbard T.J. Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res. 2002, 12:458-461.
-
(2002)
Genome Res.
, vol.12
, pp. 458-461
-
-
Down, T.A.1
Hubbard, T.J.2
-
22
-
-
79959805164
-
MiRWalk-database: prediction of possible miRNA binding sites by "walking" the genes of three genomes
-
Dweep H., Sticht C., Pandey P., et al. miRWalk-database: prediction of possible miRNA binding sites by "walking" the genes of three genomes. J. Biomed. Inform. 2011, 44:839-847.
-
(2011)
J. Biomed. Inform.
, vol.44
, pp. 839-847
-
-
Dweep, H.1
Sticht, C.2
Pandey, P.3
-
24
-
-
84907500627
-
RNA-Seq gene profiling-a systematic empirical comparison
-
Fonseca N.A., Marioni J., Brazma A. RNA-Seq gene profiling-a systematic empirical comparison. PLoS ONE. 2014, 9:e107026.
-
(2014)
PLoS ONE.
, vol.9
-
-
Fonseca, N.A.1
Marioni, J.2
Brazma, A.3
-
25
-
-
77956520986
-
CircuitsDB: a database of mixed microRNA/transcription factor feed-forward regulatory circuits in human and mouse
-
Friard O., Re A., Taverna D., et al. CircuitsDB: a database of mixed microRNA/transcription factor feed-forward regulatory circuits in human and mouse. BMC Bioinform. 2010, 11:435.
-
(2010)
BMC Bioinform.
, vol.11
, pp. 435
-
-
Friard, O.1
Re, A.2
Taverna, D.3
-
26
-
-
80455154984
-
Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs
-
Garcia D.M., Baek D., Shin C., et al. Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nat. Struct. Mol. Biol. 2011, 18:1139-1146.
-
(2011)
Nat. Struct. Mol. Biol.
, vol.18
, pp. 1139-1146
-
-
Garcia, D.M.1
Baek, D.2
Shin, C.3
-
27
-
-
84923263791
-
MicroTSS: accurate microRNA transcription start site identification reveals a significant number of divergent pri-miRNAs
-
Georgakilas G., Vlachos I.S., Paraskevopoulou M.D., et al. microTSS: accurate microRNA transcription start site identification reveals a significant number of divergent pri-miRNAs. Nat. Commun. 2014, 5:5700.
-
(2014)
Nat. Commun.
, vol.5
, pp. 5700
-
-
Georgakilas, G.1
Vlachos, I.S.2
Paraskevopoulou, M.D.3
-
28
-
-
84976872185
-
DIANA-miRGen v3.0: accurate characterization of microRNA promoters and their regulators
-
Georgakilas G., Vlachos I.S., Zagganas K., et al. DIANA-miRGen v3.0: accurate characterization of microRNA promoters and their regulators. Nucleic Acids Res. 2016, 44:D190-D195.
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. D190-D195
-
-
Georgakilas, G.1
Vlachos, I.S.2
Zagganas, K.3
-
29
-
-
34250805982
-
MicroRNA targeting specificity in mammals: determinants beyond seed pairing
-
Grimson A., Farh K.K., Johnston W.K., et al. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol. Cell. 2007, 27:91-105.
-
(2007)
Mol. Cell.
, vol.27
, pp. 91-105
-
-
Grimson, A.1
Farh, K.K.2
Johnston, W.K.3
-
30
-
-
84930275224
-
Accurate transcriptome-wide prediction of microRNA targets and small interfering RNA off-targets with MIRZA-G
-
Gumienny R., Zavolan M. Accurate transcriptome-wide prediction of microRNA targets and small interfering RNA off-targets with MIRZA-G. Nucleic Acids Res. 2015, 43:9095.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. 9095
-
-
Gumienny, R.1
Zavolan, M.2
-
31
-
-
84901952075
-
Genome-wide survey of tissue-specific microRNA and transcription factor regulatory networks in 12 tissues
-
Guo Z., Maki M., Ding R., et al. Genome-wide survey of tissue-specific microRNA and transcription factor regulatory networks in 12 tissues. Sci. Rep. 2014, 4:5150.
-
(2014)
Sci. Rep.
, vol.4
, pp. 5150
-
-
Guo, Z.1
Maki, M.2
Ding, R.3
-
32
-
-
77950920903
-
Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP
-
Hafner M., Landthaler M., Burger L., et al. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 2010, 141:129-141.
-
(2010)
Cell
, vol.141
, pp. 129-141
-
-
Hafner, M.1
Landthaler, M.2
Burger, L.3
-
33
-
-
84979851759
-
TFmiR: a web server for constructing and analyzing disease-specific transcription factor and miRNA co-regulatory networks
-
Hamed M., Spaniol C., Nazarieh M., et al. TFmiR: a web server for constructing and analyzing disease-specific transcription factor and miRNA co-regulatory networks. Nucleic Acids Res. 2015, 43:W283-W288.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. W283-W288
-
-
Hamed, M.1
Spaniol, C.2
Nazarieh, M.3
-
34
-
-
84875372911
-
Natural RNA circles function as efficient microRNA sponges
-
Hansen T.B., Jensen T.I., Clausen B.H., et al. Natural RNA circles function as efficient microRNA sponges. Nature. 2013, 495:384-388.
-
(2013)
Nature.
, vol.495
, pp. 384-388
-
-
Hansen, T.B.1
Jensen, T.I.2
Clausen, B.H.3
-
35
-
-
84865760395
-
GENCODE: the reference human genome annotation for The ENCODE Project
-
Harrow J., Frankish A., Gonzalez J.M., et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012, 22:1760-1774.
-
(2012)
Genome Res.
, vol.22
, pp. 1760-1774
-
-
Harrow, J.1
Frankish, A.2
Gonzalez, J.M.3
-
36
-
-
78651266827
-
MiRTarBase: a database curates experimentally validated microRNA-target interactions
-
Hsu S.D., Lin F.M., Wu W.Y., et al. miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res. 2011, 39:D163-D169.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. D163-D169
-
-
Hsu, S.D.1
Lin, F.M.2
Wu, W.Y.3
-
37
-
-
58549112996
-
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
-
Huang da W., Sherman B.T., Lempicki R.A. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009, 37:1-13.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 1-13
-
-
Huang da, W.1
Sherman, B.T.2
Lempicki, R.A.3
-
38
-
-
79959997653
-
MirConnX: condition-specific mRNA-microRNA network integrator
-
Huang G.T., Athanassiou C., Benos P.V. mirConnX: condition-specific mRNA-microRNA network integrator. Nucleic Acids Res. 2011, 39:W416-W423.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. W416-W423
-
-
Huang, G.T.1
Athanassiou, C.2
Benos, P.V.3
-
39
-
-
78751477191
-
Gene silencing by microRNAs: contributions of translational repression and mRNA decay
-
Huntzinger E., Izaurralde E. Gene silencing by microRNAs: contributions of translational repression and mRNA decay. Nat. Rev. Genet. 2011, 12:99-110.
-
(2011)
Nat. Rev. Genet.
, vol.12
, pp. 99-110
-
-
Huntzinger, E.1
Izaurralde, E.2
-
40
-
-
84865138690
-
MiRcode: a map of putative microRNA target sites in the long non-coding transcriptome
-
Jeggari A., Marks D.S., Larsson E. miRcode: a map of putative microRNA target sites in the long non-coding transcriptome. Bioinformatics. 2012, 28:2062-2063.
-
(2012)
Bioinformatics.
, vol.28
, pp. 2062-2063
-
-
Jeggari, A.1
Marks, D.S.2
Larsson, E.3
-
41
-
-
58149179989
-
MiR2Disease: a manually curated database for microRNA deregulation in human disease
-
Jiang Q., Wang Y., Hao Y., et al. miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res. 2009, 37:D98-D104.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. D98-D104
-
-
Jiang, Q.1
Wang, Y.2
Hao, Y.3
-
43
-
-
85018192719
-
MiRTarVis: an interactive visual analysis tool for microRNA-mRNA expression profile data
-
Jung D., Kim B., Freishtat R.J., et al. miRTarVis: an interactive visual analysis tool for microRNA-mRNA expression profile data. BMC Proc. 2015, 9:S2.
-
(2015)
BMC Proc.
, vol.9
, pp. S2
-
-
Jung, D.1
Kim, B.2
Freishtat, R.J.3
-
44
-
-
84976907502
-
KEGG as a reference resource for gene and protein annotation
-
Kanehisa M., Sato Y., Kawashima M., et al. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 2016, 44:D457-D462.
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. D457-D462
-
-
Kanehisa, M.1
Sato, Y.2
Kawashima, M.3
-
45
-
-
84862203775
-
WikiPathways: building research communities on biological pathways
-
Kelder T., van Iersel M.P., Hanspers K., et al. WikiPathways: building research communities on biological pathways. Nucleic Acids Res. 2011, 40:D1301-D1307.
-
(2011)
Nucleic Acids Res.
, vol.40
, pp. D1301-D1307
-
-
Kelder, T.1
van Iersel, M.P.2
Hanspers, K.3
-
46
-
-
78651271270
-
CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins
-
Khorshid M., Rodak C., Zavolan M. CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins. Nucleic Acids Res. 2011, 39:D245-D252.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. D245-D252
-
-
Khorshid, M.1
Rodak, C.2
Zavolan, M.3
-
47
-
-
84874646362
-
A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets
-
Khorshid M., Hausser J., Zavolan M., et al. A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets. Nat. Methods. 2013, 10:253-255.
-
(2013)
Nat. Methods.
, vol.10
, pp. 253-255
-
-
Khorshid, M.1
Hausser, J.2
Zavolan, M.3
-
48
-
-
2442672918
-
A combined computational-experimental approach predicts human microRNA targets
-
Kiriakidou M., Nelson P.T., Kouranov A., et al. A combined computational-experimental approach predicts human microRNA targets. Genes Dev. 2004, 18:1165-1178.
-
(2004)
Genes Dev.
, vol.18
, pp. 1165-1178
-
-
Kiriakidou, M.1
Nelson, P.T.2
Kouranov, A.3
-
49
-
-
13444312098
-
Substrate requirements for let-7 function in the developing zebrafish embryo
-
Kloosterman W.P., Wienholds E., Ketting R.F., et al. Substrate requirements for let-7 function in the developing zebrafish embryo. Nucleic Acids Res. 2004, 32:6284-6291.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 6284-6291
-
-
Kloosterman, W.P.1
Wienholds, E.2
Ketting, R.F.3
-
50
-
-
84891818318
-
MiRBase: annotating high confidence microRNAs using deep sequencing data
-
Kozomara A., Griffiths-Jones S. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 2014, 42:D68-D73.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D68-D73
-
-
Kozomara, A.1
Griffiths-Jones, S.2
-
51
-
-
84976866487
-
ORegAnno 3.0: a community-driven resource for curated regulatory annotation
-
Lesurf R., Cotto K.C., Wang G., et al. ORegAnno 3.0: a community-driven resource for curated regulatory annotation. Nucleic Acids Res. 2016, 44:D126-D132.
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. D126-D132
-
-
Lesurf, R.1
Cotto, K.C.2
Wang, G.3
-
52
-
-
0346094457
-
Prediction of mammalian microRNA targets
-
Lewis B.P., Shih I.H., Jones-Rhoades M.W., et al. Prediction of mammalian microRNA targets. Cell 2003, 115:787-798.
-
(2003)
Cell
, vol.115
, pp. 787-798
-
-
Lewis, B.P.1
Shih, I.H.2
Jones-Rhoades, M.W.3
-
53
-
-
84891818924
-
StarBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data
-
Li J.-H., Liu S., Zhou H., et al. starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res. 2014, 42:D92-D97.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D92-D97
-
-
Li, J.-H.1
Liu, S.2
Zhou, H.3
-
54
-
-
84891781832
-
HMDD v2.0: a database for experimentally supported human microRNA and disease associations
-
Li Y., Qiu C., Tu J., et al. HMDD v2.0: a database for experimentally supported human microRNA and disease associations. Nucleic Acids Res. 2014, 42:D1070-D1074.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D1070-D1074
-
-
Li, Y.1
Qiu, C.2
Tu, J.3
-
55
-
-
84938828494
-
MiRNA expression profile and miRNA-mRNA integrated analysis (MMIA) during podocyte differentiation
-
Li Z., Wang L., Xu J., et al. MiRNA expression profile and miRNA-mRNA integrated analysis (MMIA) during podocyte differentiation. Mol. Genet. Genomics. 2015, 290:863-875.
-
(2015)
Mol. Genet. Genomics.
, vol.290
, pp. 863-875
-
-
Li, Z.1
Wang, L.2
Xu, J.3
-
56
-
-
84864777932
-
MiRSystem: an integrated system for characterizing enriched functions and pathways of microRNA targets
-
Lu T.-P., Lee C.-Y., Tsai M.-H., et al. miRSystem: an integrated system for characterizing enriched functions and pathways of microRNA targets. PLoS ONE. 2012, 7:e42390.
-
(2012)
PLoS ONE.
, vol.7
-
-
Lu, T.-P.1
Lee, C.-Y.2
Tsai, M.-H.3
-
57
-
-
34547441263
-
Target mRNAs are repressed as efficiently by microRNA-binding sites in the 5' UTR as in the 3' UTR
-
Lytle J.R., Yario T.A., Steitz J.A. Target mRNAs are repressed as efficiently by microRNA-binding sites in the 5' UTR as in the 3' UTR. Proc. Natl. Acad. Sci. USA 2007, 104:9667-9672.
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 9667-9672
-
-
Lytle, J.R.1
Yario, T.A.2
Steitz, J.A.3
-
58
-
-
84918542774
-
PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs
-
Marsico A., Huska M.R., Lasserre J., et al. PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs. Genome Biol. 2013, 14:R84.
-
(2013)
Genome Biol.
, vol.14
, pp. R84
-
-
Marsico, A.1
Huska, M.R.2
Lasserre, J.3
-
59
-
-
48449084118
-
Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells
-
Marson A., Levine S.S., Cole M.F., et al. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 2008, 134:521-533.
-
(2008)
Cell
, vol.134
, pp. 521-533
-
-
Marson, A.1
Levine, S.S.2
Cole, M.F.3
-
60
-
-
84891808382
-
JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles
-
Mathelier A., Zhao X., Zhang A.W., et al. JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res. 2014, 42:D142-D147.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D142-D147
-
-
Mathelier, A.1
Zhao, X.2
Zhang, A.W.3
-
61
-
-
63849237976
-
A transcription factor affinity-based code for mammalian transcription initiation
-
Megraw M., Pereira F., Jensen S.T., et al. A transcription factor affinity-based code for mammalian transcription initiation. Genome Res. 2009, 19:644-656.
-
(2009)
Genome Res.
, vol.19
, pp. 644-656
-
-
Megraw, M.1
Pereira, F.2
Jensen, S.T.3
-
62
-
-
85003365400
-
MirMark: a site-level and UTR-level classifier for miRNA target prediction
-
Menor M., Ching T., Zhu X., et al. mirMark: a site-level and UTR-level classifier for miRNA target prediction. Genome Biol. 2014, 15:500.
-
(2014)
Genome Biol.
, vol.15
, pp. 500
-
-
Menor, M.1
Ching, T.2
Zhu, X.3
-
63
-
-
84948672434
-
MiRNA-target chimeras reveal miRNA 3'-end pairing as a major determinant of Argonaute target specificity
-
Moore M.J., Scheel T.K., Luna J.M., et al. miRNA-target chimeras reveal miRNA 3'-end pairing as a major determinant of Argonaute target specificity. Nat. Commun. 2015, 6:8864.
-
(2015)
Nat. Commun.
, vol.6
, pp. 8864
-
-
Moore, M.J.1
Scheel, T.K.2
Luna, J.M.3
-
64
-
-
77952833904
-
BioCarta. Biotech. Softw. Internet Rep.
-
Nishimura D. BioCarta. Biotech. Softw. Internet Rep. 2001, 2:117-120.
-
(2001)
, vol.2
, pp. 117-120
-
-
Nishimura, D.1
-
65
-
-
56549129538
-
Chromatin structure analyses identify miRNA promoters
-
Ozsolak F., Poling L.L., Wang Z., et al. Chromatin structure analyses identify miRNA promoters. Genes Dev. 2008, 22:3172-3183.
-
(2008)
Genes Dev.
, vol.22
, pp. 3172-3183
-
-
Ozsolak, F.1
Poling, L.L.2
Wang, Z.3
-
66
-
-
67650754354
-
DIANA-mirPath: integrating human and mouse microRNAs in pathways
-
Papadopoulos G.L., Alexiou P., Maragkakis M., et al. DIANA-mirPath: integrating human and mouse microRNAs in pathways. Bioinformatics. 2009, 25:1991-1993.
-
(2009)
Bioinformatics.
, vol.25
, pp. 1991-1993
-
-
Papadopoulos, G.L.1
Alexiou, P.2
Maragkakis, M.3
-
67
-
-
58149203235
-
The database of experimentally supported targets: a functional update of TarBase
-
Papadopoulos G.L., Reczko M., Simossis V.A., et al. The database of experimentally supported targets: a functional update of TarBase. Nucleic Acids Res. 2009, 37:D155-D158.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. D155-D158
-
-
Papadopoulos, G.L.1
Reczko, M.2
Simossis, V.A.3
-
68
-
-
84876523096
-
DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs
-
Paraskevopoulou M.D., Georgakilas G., Kostoulas N., et al. DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs. Nucleic Acids Res. 2013, 41:D239-D245.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D239-D245
-
-
Paraskevopoulou, M.D.1
Georgakilas, G.2
Kostoulas, N.3
-
69
-
-
84883579190
-
DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows
-
Paraskevopoulou M.D., Georgakilas G., Kostoulas N., et al. DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows. Nucleic Acids Res. 2013, 41:W169-W173.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. W169-W173
-
-
Paraskevopoulou, M.D.1
Georgakilas, G.2
Kostoulas, N.3
-
71
-
-
84976875164
-
DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts
-
Paraskevopoulou M.D., Vlachos I.S., Karagkouni D., et al. DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts. Nucleic Acids Res. 2016, 44:D231-238.
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. D231-238
-
-
Paraskevopoulou, M.D.1
Vlachos, I.S.2
Karagkouni, D.3
-
72
-
-
84962124791
-
MiTALOS v2: analyzing tissue specific microRNA function
-
Preusse M., Theis F.J., Mueller N.S. miTALOS v2: analyzing tissue specific microRNA function. PLoS ONE. 2016, 11:e0151771.
-
(2016)
PLoS ONE.
, vol.11
-
-
Preusse, M.1
Theis, F.J.2
Mueller, N.S.3
-
73
-
-
84859067415
-
Functional microRNA targets in protein coding sequences
-
Reczko M., Maragkakis M., Alexiou P., et al. Functional microRNA targets in protein coding sequences. Bioinformatics. 2012, 28:771-776.
-
(2012)
Bioinformatics.
, vol.28
, pp. 771-776
-
-
Reczko, M.1
Maragkakis, M.2
Alexiou, P.3
-
77
-
-
0242490780
-
Cytoscape: a software environment for integrated models of biomolecular interaction networks
-
Shannon P., Markiel A., Ozier O., et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003, 13:2498-2504.
-
(2003)
Genome Res.
, vol.13
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
-
78
-
-
85010257572
-
MicroRNAs databases: developmental methodologies, structural and functional annotations
-
Singh N.K. microRNAs databases: developmental methodologies, structural and functional annotations. Interdiscip. Sci. 2016, 2016:1-21.
-
(2016)
Interdiscip. Sci.
, vol.2016
, pp. 1-21
-
-
Singh, N.K.1
-
79
-
-
0036081146
-
DBTSS: DataBase of human transcriptional start sites and full-length cDNAs
-
Suzuki Y., Yamashita R., Nakai K., et al. DBTSS: DataBase of human transcriptional start sites and full-length cDNAs. Nucleic Acids Res. 2002, 30:328-331.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 328-331
-
-
Suzuki, Y.1
Yamashita, R.2
Nakai, K.3
-
80
-
-
80052451056
-
Experimental strategies for microRNA target identification
-
Thomson D.W., Bracken C.P., Goodall G.J. Experimental strategies for microRNA target identification. Nucleic Acids Res. 2011, 39:6845-6853.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 6845-6853
-
-
Thomson, D.W.1
Bracken, C.P.2
Goodall, G.J.3
-
81
-
-
57049175013
-
Detecting microRNA binding and siRNA off-target effects from expression data
-
van Dongen S., Abreu-Goodger C., Enright A.J. Detecting microRNA binding and siRNA off-target effects from expression data. Nat. Methods. 2008, 5:1023-1025.
-
(2008)
Nat. Methods.
, vol.5
, pp. 1023-1025
-
-
van Dongen, S.1
Abreu-Goodger, C.2
Enright, A.J.3
-
82
-
-
84862176128
-
TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support
-
Vergoulis T., Vlachos I.S., Alexiou P., et al. TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support. Nucleic Acids Res. 2012, 40:D222-D229.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D222-D229
-
-
Vergoulis, T.1
Vlachos, I.S.2
Alexiou, P.3
-
84
-
-
84864464973
-
DIANA miRPath v.2.0: investigating the combinatorial effect of microRNAs in pathways
-
Vlachos I.S., Kostoulas N., Vergoulis T., et al. DIANA miRPath v.2.0: investigating the combinatorial effect of microRNAs in pathways. Nucleic Acids Res. 2012, 40:W498-W504.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. W498-W504
-
-
Vlachos, I.S.1
Kostoulas, N.2
Vergoulis, T.3
-
85
-
-
84941087952
-
DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions
-
Vlachos I.S., Paraskevopoulou M.D., Karagkouni D., et al. DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions. Nucleic Acids Res. 2015, 43:D153-D159.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D153-D159
-
-
Vlachos, I.S.1
Paraskevopoulou, M.D.2
Karagkouni, D.3
-
86
-
-
84979854255
-
DIANA-miRPath v3.0: deciphering microRNA function with experimental support
-
Vlachos I.S., Zagganas K., Paraskevopoulou M.D., et al. DIANA-miRPath v3.0: deciphering microRNA function with experimental support. Nucleic Acids Res. 2015, 43:W460-W466.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. W460-W466
-
-
Vlachos, I.S.1
Zagganas, K.2
Paraskevopoulou, M.D.3
-
87
-
-
85012935580
-
DIANA-mirExTra v2.0: uncovering microRNAs and transcription factors with crucial roles in NGS expression data
-
Vlachos I.S., Vergoulis T., Paraskevopoulou M.D., et al. DIANA-mirExTra v2.0: uncovering microRNAs and transcription factors with crucial roles in NGS expression data. Nucleic Acids Res. 2016, 44:W128-W134.
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. W128-W134
-
-
Vlachos, I.S.1
Vergoulis, T.2
Paraskevopoulou, M.D.3
-
88
-
-
84946086288
-
An update on LNCipedia: a database for annotated human lncRNA sequences
-
Volders P.J., Verheggen K., Menschaert G., et al. An update on LNCipedia: a database for annotated human lncRNA sequences. Nucleic Acids Res. 2015, 43:4363-4364.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. 4363-4364
-
-
Volders, P.J.1
Verheggen, K.2
Menschaert, G.3
-
89
-
-
75549092303
-
TransmiR: a transcription factor-microRNA regulation database
-
Wang J., Lu M., Qiu C., et al. TransmiR: a transcription factor-microRNA regulation database. Nucleic Acids Res. 2010, 38:D119-D122.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. D119-D122
-
-
Wang, J.1
Lu, M.2
Qiu, C.3
-
90
-
-
84943192833
-
MiRSponge: a manually curated database for experimentally supported miRNA sponges and ceRNAs
-
Database (Oxford).
-
Wang P., Zhi H., Zhang Y., et al. miRSponge: a manually curated database for experimentally supported miRNA sponges and ceRNAs. Database (Oxford). 2015, 2015:bav098.
-
(2015)
, vol.2015
-
-
Wang, P.1
Zhi, H.2
Zhang, Y.3
-
91
-
-
84928793282
-
TMREC: a database of transcription factor and MiRNA regulatory cascades in human diseases
-
Wang S., Li W., Lian B., et al. TMREC: a database of transcription factor and MiRNA regulatory cascades in human diseases. PLoS ONE. 2015, 10:e0125222.
-
(2015)
PLoS ONE.
, vol.10
-
-
Wang, S.1
Li, W.2
Lian, B.3
-
92
-
-
38849145861
-
Prediction of both conserved and nonconserved microRNA targets in animals
-
Wang X., El Naqa I.M. Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics. 2008, 24:325-332.
-
(2008)
Bioinformatics.
, vol.24
, pp. 325-332
-
-
Wang, X.1
El Naqa, I.M.2
-
93
-
-
84884994218
-
The cancer genome atlas pan-cancer analysis project
-
Weinstein J.N., Collisson E.A., Mills G.B., et al. The cancer genome atlas pan-cancer analysis project. Nat. Genet. 2013, 45:1113-1120.
-
(2013)
Nat. Genet.
, vol.45
, pp. 1113-1120
-
-
Weinstein, J.N.1
Collisson, E.A.2
Mills, G.B.3
-
94
-
-
58149186499
-
MiRecords: an integrated resource for microRNA-target interactions
-
Xiao F., Zuo Z., Cai G., et al. miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res. 2009, 37:D105-D110.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. D105-D110
-
-
Xiao, F.1
Zuo, Z.2
Cai, G.3
-
95
-
-
84902525655
-
CGRNB: a web server for building combinatorial gene regulatory networks through integrated engineering of seed-matching sequence information and gene expression datasets
-
Xu H., Yu H., Tu K., et al. cGRNB: a web server for building combinatorial gene regulatory networks through integrated engineering of seed-matching sequence information and gene expression datasets. BMC. Syst. Biol. 2013, 7(Suppl 2):S7.
-
(2013)
BMC. Syst. Biol.
, vol.7
, pp. S7
-
-
Xu, H.1
Yu, H.2
Tu, K.3
-
96
-
-
84876566914
-
ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data
-
Yang J.H., Li J.H., Jiang S., et al. ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data. Nucleic Acids Res. 2013, 41:D177-D187.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D177-D187
-
-
Yang, J.H.1
Li, J.H.2
Jiang, S.3
-
97
-
-
62549126083
-
Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing
-
Yassour M., Kaplan T., Fraser H.B., et al. Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc. Natl. Acad. Sci. USA 2009, 106:3264-3269.
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 3264-3269
-
-
Yassour, M.1
Kaplan, T.2
Fraser, H.B.3
-
98
-
-
34047234690
-
Characterization and identification of microRNA core promoters in four model species
-
Zhou X., Ruan J., Wang G., et al. Characterization and identification of microRNA core promoters in four model species. PLoS Comput. Biol. 2007, 3:e37.
-
(2007)
PLoS Comput. Biol.
, vol.3
-
-
Zhou, X.1
Ruan, J.2
Wang, G.3
-
99
-
-
84943165926
-
LncReg: a reference resource for lncRNA-associated regulatory networks
-
Database (Oxford). 2015
-
Zhou Z., Shen Y., Khan M.R., et al. LncReg: a reference resource for lncRNA-associated regulatory networks. Database (Oxford). 2015 2015, bav083.
-
(2015)
-
-
Zhou, Z.1
Shen, Y.2
Khan, M.R.3
|