-
1
-
-
0347444723
-
MicroRNAs: Genomics, biogenesis, mechanism, and function
-
10.1016/S0092-8674(04)00045-5, 14744438
-
Bartel DP. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 2004, 116(2):281-297. 10.1016/S0092-8674(04)00045-5, 14744438.
-
(2004)
Cell
, vol.116
, Issue.2
, pp. 281-297
-
-
Bartel, D.P.1
-
2
-
-
0027751663
-
The C-Elegans Heterochronic Gene Lin-4 Encodes Small RNAs with Antisense Complementarity to Lin-14
-
10.1016/0092-8674(93)90529-Y, 8252621
-
Lee RC, Feinbaum RL, Ambros V. The C-Elegans Heterochronic Gene Lin-4 Encodes Small RNAs with Antisense Complementarity to Lin-14. Cell 1993, 75(5):843-854. 10.1016/0092-8674(93)90529-Y, 8252621.
-
(1993)
Cell
, vol.75
, Issue.5
, pp. 843-854
-
-
Lee, R.C.1
Feinbaum, R.L.2
Ambros, V.3
-
3
-
-
0034708122
-
The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans
-
10.1038/35002607, 10706289
-
Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR, Ruvkun G. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 2000, 403(6772):901-906. 10.1038/35002607, 10706289.
-
(2000)
Nature
, vol.403
, Issue.6772
, pp. 901-906
-
-
Reinhart, B.J.1
Slack, F.J.2
Basson, M.3
Pasquinelli, A.E.4
Bettinger, J.C.5
Rougvie, A.E.6
Horvitz, H.R.7
Ruvkun, G.8
-
4
-
-
38549150275
-
MiRBase: tools for microRNA genomics
-
10.1093/nar/gkm952, 2238936, 17991681
-
Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res 2008, 36:D154-D158. 10.1093/nar/gkm952, 2238936, 17991681.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Griffiths-Jones, S.1
Saini, H.K.2
van Dongen, S.3
Enright, A.J.4
-
5
-
-
22344449952
-
The developmental miRNA profiles of zebrafish as determined by small RNA cloning
-
10.1101/gad.1310605, 1142552, 15937218
-
Chen PY, Manninga H, Slanchev K, Chien MC, Russo JJ, Ju JY, Sheridan R, John B, Marks DS, Gaidatzis D, et al. The developmental miRNA profiles of zebrafish as determined by small RNA cloning. Genes & Development 2005, 19(11):1288-1293. 10.1101/gad.1310605, 1142552, 15937218.
-
(2005)
Genes & Development
, vol.19
, Issue.11
, pp. 1288-1293
-
-
Chen, P.Y.1
Manninga, H.2
Slanchev, K.3
Chien, M.C.4
Russo, J.J.5
Ju, J.Y.6
Sheridan, R.7
John, B.8
Marks, D.S.9
Gaidatzis, D.10
-
7
-
-
0242418246
-
Phylogenetic shadowing of primate sequences to find functional regions of the human genome
-
10.1126/science.1081331, 12610304
-
Boffelli D, McAuliffe J, Ovcharenko D, Lewis KD, Ovcharenko I, Pachter L, Rubin EM. Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 2003, 299(5611):1391-1394. 10.1126/science.1081331, 12610304.
-
(2003)
Science
, vol.299
, Issue.5611
, pp. 1391-1394
-
-
Boffelli, D.1
McAuliffe, J.2
Ovcharenko, D.3
Lewis, K.D.4
Ovcharenko, I.5
Pachter, L.6
Rubin, E.M.7
-
8
-
-
0038054470
-
Computational and experimental identification of C-elegans microRNAs
-
10.1016/S1097-2765(03)00153-9, 12769849
-
Grad Y, Aach J, Hayes GD, Reinhart BJ, Church GM, Ruvkun G, Kim J. Computational and experimental identification of C-elegans microRNAs. Molecular Cell 2003, 11(5):1253-1263. 10.1016/S1097-2765(03)00153-9, 12769849.
-
(2003)
Molecular Cell
, vol.11
, Issue.5
, pp. 1253-1263
-
-
Grad, Y.1
Aach, J.2
Hayes, G.D.3
Reinhart, B.J.4
Church, G.M.5
Ruvkun, G.6
Kim, J.7
-
9
-
-
22844440427
-
Identification of hundreds of conserved and nonconserved human microRNAs
-
10.1038/ng1590, 15965474
-
Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A, Einat P, Einav U, Meiri E, et al. Identification of hundreds of conserved and nonconserved human microRNAs. Nature Genetics 2005, 37(7):766-770. 10.1038/ng1590, 15965474.
-
(2005)
Nature Genetics
, vol.37
, Issue.7
, pp. 766-770
-
-
Bentwich, I.1
Avniel, A.2
Karov, Y.3
Aharonov, R.4
Gilad, S.5
Barad, O.6
Barzilai, A.7
Einat, P.8
Einav, U.9
Meiri, E.10
-
10
-
-
11844262661
-
Phylogenetic shadowing and computational identification of human microRNA genes
-
10.1016/j.cell.2004.12.031, 15652478
-
Berezikov E, Guryev V, Belt J, Wienholds E, Plasterk RHA, Cuppen E. Phylogenetic shadowing and computational identification of human microRNA genes. Cell 2005, 120(1):21-24. 10.1016/j.cell.2004.12.031, 15652478.
-
(2005)
Cell
, vol.120
, Issue.1
, pp. 21-24
-
-
Berezikov, E.1
Guryev, V.2
Belt, J.3
Wienholds, E.4
Plasterk, R.H.A.5
Cuppen, E.6
-
11
-
-
27844508214
-
Identification of clustered microRNAs using an ab initio prediction method
-
10.1186/1471-2105-6-267, 1315341, 16274478
-
Sewer A, Paul N, Landgraf P, Aravin A, Pfeffer S, Brownstein MJ, Tuschl T, van Nimwegen E, Zavolan M. Identification of clustered microRNAs using an ab initio prediction method. BMC Bioinformatics 2005, 6. 10.1186/1471-2105-6-267, 1315341, 16274478.
-
(2005)
BMC Bioinformatics
, vol.6
-
-
Sewer, A.1
Paul, N.2
Landgraf, P.3
Aravin, A.4
Pfeffer, S.5
Brownstein, M.J.6
Tuschl, T.7
van Nimwegen, E.8
Zavolan, M.9
-
12
-
-
30344447264
-
Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine
-
10.1186/1471-2105-6-310, 1360673, 16381612
-
Xue CH, Li F, He T, Liu GP, Li YD, Zhang XG. Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine. BMC Bioinformatics 2005, 6. 10.1186/1471-2105-6-310, 1360673, 16381612.
-
(2005)
BMC Bioinformatics
, vol.6
-
-
Xue, C.H.1
Li, F.2
He, T.3
Liu, G.P.4
Li, Y.D.5
Zhang, X.G.6
-
13
-
-
39049169222
-
Ab initio identification of human microRNAs based on structure motifs
-
10.1186/1471-2105-8-478, 2238772, 18088431
-
Brameier M, Wiuf C. Ab initio identification of human microRNAs based on structure motifs. BMC Bioinformatics 2007, 8. 10.1186/1471-2105-8-478, 2238772, 18088431.
-
(2007)
BMC Bioinformatics
, vol.8
-
-
Brameier, M.1
Wiuf, C.2
-
14
-
-
34447309058
-
De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures
-
10.1093/bioinformatics/btm026, 17267435
-
Kwang Loong S, Mishra SK. De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures. Bioinformatics 2007, 23(11):1321-1330. 10.1093/bioinformatics/btm026, 17267435.
-
(2007)
Bioinformatics
, vol.23
, Issue.11
, pp. 1321-1330
-
-
Kwang Loong, S.1
Mishra, S.K.2
-
15
-
-
57649207899
-
Using a kernel density estimation based classifier to predict species-specific microRNA precursors
-
Chang DTH, Wang CC, Chen JW. Using a kernel density estimation based classifier to predict species-specific microRNA precursors. BMC Bioinformatics 2008, 9.
-
(2008)
BMC Bioinformatics
, vol.9
-
-
Chang, D.T.H.1
Wang, C.C.2
Chen, J.W.3
-
16
-
-
0033013683
-
Estimating the contributions of selection and self-organization in RNA secondary structure
-
10.1007/PL00006536, 10368436
-
Schultes EA, Hraber PT, LaBean TH. Estimating the contributions of selection and self-organization in RNA secondary structure. J Mol Evol 1999, 49(1):76-83. 10.1007/PL00006536, 10368436.
-
(1999)
J Mol Evol
, vol.49
, Issue.1
, pp. 76-83
-
-
Schultes, E.A.1
Hraber, P.T.2
LaBean, T.H.3
-
17
-
-
30744468557
-
Evidence that miRNAs are different from other RNAs
-
10.1007/s00018-005-5467-7, 16395542
-
Zhang BH, Pan XP, Cox SB, Cobb GP, Anderson TA. Evidence that miRNAs are different from other RNAs. Cell Mol Life Sci 2006, 63(2):246-254. 10.1007/s00018-005-5467-7, 16395542.
-
(2006)
Cell Mol Life Sci
, vol.63
, Issue.2
, pp. 246-254
-
-
Zhang, B.H.1
Pan, X.P.2
Cox, S.B.3
Cobb, G.P.4
Anderson, T.A.5
-
19
-
-
3042542464
-
RAG: RNA-As-Graphs database - concepts, analysis, and features
-
10.1093/bioinformatics/bth084, 14962931
-
Gan HH, Fera D, Zorn J, Shiffeldrim N, Tang M, Laserson U, Kim N, Schlick T. RAG: RNA-As-Graphs database - concepts, analysis, and features. Bioinformatics 2004, 20(8):1285-1291. 10.1093/bioinformatics/bth084, 14962931.
-
(2004)
Bioinformatics
, vol.20
, Issue.8
, pp. 1285-1291
-
-
Gan, H.H.1
Fera, D.2
Zorn, J.3
Shiffeldrim, N.4
Tang, M.5
Laserson, U.6
Kim, N.7
Schlick, T.8
-
20
-
-
21844477027
-
Human microRNA prediction through a probabilistic co-learning model of sequence and structure
-
10.1093/nar/gki668, 1159118, 15987789
-
Nam JW, Shin KR, Han JJ, Lee Y, Kim VN, Zhang BT. Human microRNA prediction through a probabilistic co-learning model of sequence and structure. Nucleic Acids Res 2005, 33(11):3570-3581. 10.1093/nar/gki668, 1159118, 15987789.
-
(2005)
Nucleic Acids Res
, vol.33
, Issue.11
, pp. 3570-3581
-
-
Nam, J.W.1
Shin, K.R.2
Han, J.J.3
Lee, Y.4
Kim, V.N.5
Zhang, B.T.6
-
21
-
-
36249010340
-
MiRRim: A novel system to find conserved miRNAs with high sensitivity and specificity
-
Terai G, Komori T, Asai K, Kin T. miRRim: A novel system to find conserved miRNAs with high sensitivity and specificity. RNA-a Publication of the RNA Society 2007, 13(12):2081-2090.
-
(2007)
RNA-a Publication of the RNA Society
, vol.13
, Issue.12
, pp. 2081-2090
-
-
Terai, G.1
Komori, T.2
Asai, K.3
Kin, T.4
-
22
-
-
57649174704
-
MiRTif: a support vector machine-based microRNA target interaction filter
-
Yang YC, Wang YP, Li KB. MiRTif: a support vector machine-based microRNA target interaction filter. BMC Bioinformatics 2008, 9.
-
(2008)
BMC Bioinformatics
, vol.9
-
-
Yang, Y.C.1
Wang, Y.P.2
Li, K.B.3
-
23
-
-
64549116289
-
MicroPred: effective classification of pre-miRNAs for human miRNA gene prediction
-
10.1093/bioinformatics/btp107, 19233894
-
Batuwita R, Palade V. microPred: effective classification of pre-miRNAs for human miRNA gene prediction. Bioinformatics 2009, 25(8):989-995. 10.1093/bioinformatics/btp107, 19233894.
-
(2009)
Bioinformatics
, vol.25
, Issue.8
, pp. 989-995
-
-
Batuwita, R.1
Palade, V.2
-
25
-
-
34447338865
-
IPTREE-STAB: interpretable decision tree based method for predicting protein stability changes upon mutations
-
10.1093/bioinformatics/btm100, 17379687
-
Huang LT, Gromiha MM, Ho SY. iPTREE-STAB: interpretable decision tree based method for predicting protein stability changes upon mutations. Bioinformatics 2007, 23(10):1292-1293. 10.1093/bioinformatics/btm100, 17379687.
-
(2007)
Bioinformatics
, vol.23
, Issue.10
, pp. 1292-1293
-
-
Huang, L.T.1
Gromiha, M.M.2
Ho, S.Y.3
-
26
-
-
34047234690
-
Characterization and identification of microRNA core promoters in four model species
-
Zhou XF, Ruan JH, Wang GD, Zhang WX. Characterization and identification of microRNA core promoters in four model species. PLoS Comput Biol 2007, 3(3):412-423.
-
(2007)
PLoS Comput Biol
, vol.3
, Issue.3
, pp. 412-423
-
-
Zhou, X.F.1
Ruan, J.H.2
Wang, G.D.3
Zhang, W.X.4
-
27
-
-
33747067136
-
Interpretable gene expression classifier with an accurate and compact fuzzy rule base for microarray data analysis
-
10.1016/j.biosystems.2006.01.002, 16490299
-
Ho SY, Hsieh CH, Chen HM, Huang HL. Interpretable gene expression classifier with an accurate and compact fuzzy rule base for microarray data analysis. Biosystems 2006, 85(3):165-176. 10.1016/j.biosystems.2006.01.002, 16490299.
-
(2006)
Biosystems
, vol.85
, Issue.3
, pp. 165-176
-
-
Ho, S.Y.1
Hsieh, C.H.2
Chen, H.M.3
Huang, H.L.4
-
28
-
-
33646152515
-
Recognizing names in biomedical texts using mutual information independence model and SVM plus sigmoid
-
Zhou GD. Recognizing names in biomedical texts using mutual information independence model and SVM plus sigmoid. Int J Med Inf 2006, 75(6):456-467.
-
(2006)
Int J Med Inf
, vol.75
, Issue.6
, pp. 456-467
-
-
Zhou, G.D.1
-
30
-
-
33947728394
-
RNA stem-loops: To be or not to be cleaved by RNAse III
-
10.1261/rna.366507, 1831864, 17299129
-
Ritchie W, Legendre M, Gautheret D. RNA stem-loops: To be or not to be cleaved by RNAse III. RNA 2007, 13(4):457-462. 10.1261/rna.366507, 1831864, 17299129.
-
(2007)
RNA
, vol.13
, Issue.4
, pp. 457-462
-
-
Ritchie, W.1
Legendre, M.2
Gautheret, D.3
-
31
-
-
23144462493
-
MEDock: a web server for efficient prediction of ligand binding sites based on a novel optimization algorithm
-
10.1093/nar/gki586, 1160262, 15991337
-
Chang DTH, Oyang YJ, Lin JH. MEDock: a web server for efficient prediction of ligand binding sites based on a novel optimization algorithm. Nucleic Acids Res 2005, 33:W233-W238. 10.1093/nar/gki586, 1160262, 15991337.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Chang, D.T.H.1
Oyang, Y.J.2
Lin, J.H.3
-
32
-
-
13844266749
-
Data classification with radial basis function networks based on a novel kernel density estimation algorithm
-
10.1109/TNN.2004.836229, 15732402
-
Oyang YJ, Hwang SC, Ou YY, Chen CY, Chen ZW. Data classification with radial basis function networks based on a novel kernel density estimation algorithm. IEEE Transactions on Neural Networks 2005, 16(1):225-236. 10.1109/TNN.2004.836229, 15732402.
-
(2005)
IEEE Transactions on Neural Networks
, vol.16
, Issue.1
, pp. 225-236
-
-
Oyang, Y.J.1
Hwang, S.C.2
Ou, Y.Y.3
Chen, C.Y.4
Chen, Z.W.5
-
33
-
-
1242274331
-
Prediction of RNA-binding proteins from primary sequence by a support vector machine approach
-
10.1261/rna.5890304, 1370931, 14970381
-
Han LY, Cai CZ, Lo SL, Chung MCM, Chen YZ. Prediction of RNA-binding proteins from primary sequence by a support vector machine approach. RNA 2004, 10(3):355-368. 10.1261/rna.5890304, 1370931, 14970381.
-
(2004)
RNA
, vol.10
, Issue.3
, pp. 355-368
-
-
Han, L.Y.1
Cai, C.Z.2
Lo, S.L.3
Chung, M.C.M.4
Chen, Y.Z.5
-
34
-
-
16344396421
-
Accurate identification of alternatively spliced exons using support vector machine
-
10.1093/bioinformatics/bti132, 15531599
-
Dror G, Sorek R, Shamir R. Accurate identification of alternatively spliced exons using support vector machine. Bioinformatics 2005, 21(7):897-901. 10.1093/bioinformatics/bti132, 15531599.
-
(2005)
Bioinformatics
, vol.21
, Issue.7
, pp. 897-901
-
-
Dror, G.1
Sorek, R.2
Shamir, R.3
-
35
-
-
0003500248
-
C4.5: Programs for Machine Learning
-
San Francisco: Morgan Kaufmann
-
Quinlan JR. C4.5: Programs for Machine Learning. 1993, San Francisco: Morgan Kaufmann.
-
(1993)
-
-
Quinlan, J.R.1
-
37
-
-
0001884644
-
Individual Comparisons by Ranking Methods
-
Wilcoxon F. Individual Comparisons by Ranking Methods. Biometrics Bulletin 1945, 1(6):80-83.
-
(1945)
Biometrics Bulletin
, vol.1
, Issue.6
, pp. 80-83
-
-
Wilcoxon, F.1
-
38
-
-
0004238551
-
Probability and statistical inference
-
Upper Saddle River, NJ: Pearson Prentice Hall, 7
-
Hogg RV, Tanis EA. Probability and statistical inference. 2006, Upper Saddle River, NJ: Pearson Prentice Hall, 7.
-
(2006)
-
-
Hogg, R.V.1
Tanis, E.A.2
-
39
-
-
0033119454
-
MRNAs have greater negative folding free energies than shuffled or codon choice randomized sequences
-
10.1093/nar/27.7.1578, 148359, 10075987
-
Seffens W, Digby D. mRNAs have greater negative folding free energies than shuffled or codon choice randomized sequences. Nucleic Acids Res 1999, 27(7):1578-1584. 10.1093/nar/27.7.1578, 148359, 10075987.
-
(1999)
Nucleic Acids Res
, vol.27
, Issue.7
, pp. 1578-1584
-
-
Seffens, W.1
Digby, D.2
-
40
-
-
0034125274
-
Metrics on RNA secondary structures
-
10.1089/10665270050081522, 10890402
-
Moulton V, Zuker M, Steel M, Pointon R, Penny D. Metrics on RNA secondary structures. J Comput Biol 2000, 7(1-2):277-292. 10.1089/10665270050081522, 10890402.
-
(2000)
J Comput Biol
, vol.7
, Issue.1-2
, pp. 277-292
-
-
Moulton, V.1
Zuker, M.2
Steel, M.3
Pointon, R.4
Penny, D.5
-
41
-
-
13244289884
-
RAG: RNA-As-Graphs web resource
-
10.1186/1471-2105-5-88, 471545, 15238163
-
Fera D, Kim N, Shiffeldrim N, Zorn J, Laserson U, Gan HH, Schlick T. RAG: RNA-As-Graphs web resource. BMC Bioinformatics 2004, 5. 10.1186/1471-2105-5-88, 471545, 15238163.
-
(2004)
BMC Bioinformatics
, vol.5
-
-
Fera, D.1
Kim, N.2
Shiffeldrim, N.3
Zorn, J.4
Laserson, U.5
Gan, H.H.6
Schlick, T.7
-
42
-
-
0003912423
-
An Introduction to Mathematical Statistics and Its Applications
-
Prentice Hall, 3
-
Larsen RJ, Marx ML. An Introduction to Mathematical Statistics and Its Applications. 2005, Prentice Hall, 3.
-
(2005)
-
-
Larsen, R.J.1
Marx, M.L.2
-
43
-
-
33644750115
-
MiRBase: microRNA sequences, targets and gene nomenclature
-
10.1093/nar/gkj112, 1347474, 16381832
-
Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 2006, 34:D140-D144. 10.1093/nar/gkj112, 1347474, 16381832.
-
(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
-
44
-
-
0035162594
-
RefSeq and LocusLink: NCBI gene-centered resources
-
10.1093/nar/29.1.137, 29787, 11125071
-
Pruitt KD, Maglott DR. RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res 2001, 29(1):137-140. 10.1093/nar/29.1.137, 29787, 11125071.
-
(2001)
Nucleic Acids Res
, vol.29
, Issue.1
, pp. 137-140
-
-
Pruitt, K.D.1
Maglott, D.R.2
-
45
-
-
0037250168
-
The UCSC Genome Browser Database
-
10.1093/nar/gkg129, 165576, 12519945
-
Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, et al. The UCSC Genome Browser Database. Nucleic Acids Res 2003, 31(1):51-54. 10.1093/nar/gkg129, 165576, 12519945.
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.1
, pp. 51-54
-
-
Karolchik, D.1
Baertsch, R.2
Diekhans, M.3
Furey, T.S.4
Hinrichs, A.5
Lu, Y.T.6
Roskin, K.M.7
Schwartz, M.8
Sugnet, C.W.9
Thomas, D.J.10
-
46
-
-
0043123153
-
Vienna RNA secondary structure server
-
10.1093/nar/gkg599, 169005, 12824340
-
Hofacker IL. Vienna RNA secondary structure server. Nucleic Acids Res 2003, 31(13):3429-3431. 10.1093/nar/gkg599, 169005, 12824340.
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.13
, pp. 3429-3431
-
-
Hofacker, I.L.1
-
47
-
-
0003710380
-
LIBSVM: a library for support vector machines
-
Chang CC, Lin CJ. LIBSVM: a library for support vector machines. 2001, , http://www.csie.ntu.edu.tw/~cjlin/libsvm
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(2001)
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Chang, C.C.1
Lin, C.J.2
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