-
3
-
-
33748849648
-
Machine learning in bioinformatics
-
Larranaga P et al. (2006) Machine learning in bioinformatics. Brief Bioinform 7, 86 112.
-
(2006)
Brief Bioinform
, vol.7
, pp. 86-112
-
-
Larranaga, P.1
-
6
-
-
0004019973
-
-
Technical Report UCSCCRL -99-10. Baskin School of Engineering, University of California, Santa Cruz, CA.
-
Haussler D (1999) Convolution Kernels on Discrete Structures. Technical Report UCSCCRL -99-10. Baskin School of Engineering, University of California, Santa Cruz, CA.
-
(1999)
Convolution Kernels on Discrete Structures.
-
-
Haussler, D.1
-
7
-
-
0034818556
-
Gene functional classification from heterogeneous data
-
In. pp. ACM Press, Montreal.
-
Pavlidis P, Weston J, Cai J Grundy WN (2001) Gene functional classification from heterogeneous data. In Proceedings of the Fifth Annual International Conference on Computational Biology, pp. 249 255. ACM Press, Montreal.
-
(2001)
Proceedings of the Fifth Annual International Conference on Computational Biology
, pp. 249-255
-
-
Pavlidis, P.1
Weston, J.2
Cai, J.3
Grundy, W.N.4
-
8
-
-
2942549190
-
PreBIND and Textomy - Mining the biomedical literature for protein-protein interactions using a support vector machine
-
Donaldson I et al. (2003) PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machine. BMC Bioinformatics 4, 11.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 11
-
-
Donaldson, I.1
-
9
-
-
0037423845
-
Vertebrate microRNA genes
-
Lim LP, Glasner ME, Yekta S, Burge CB Bartel DP (2003) Vertebrate microRNA genes. Science 299, 1540.
-
(2003)
Science
, vol.299
, pp. 1540
-
-
Lim, L.P.1
Glasner, M.E.2
Yekta, S.3
Burge, C.B.4
Bartel, D.P.5
-
10
-
-
11444251652
-
New human and mouse microRNA genes found by homology search
-
Weber MJ (2005) New human and mouse microRNA genes found by homology search. FEBS J 272, 59 73.
-
(2005)
FEBS J
, vol.272
, pp. 59-73
-
-
Weber, M.J.1
-
11
-
-
0037447334
-
The microRNAs of Caenorhabditis elegans
-
Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB Bartel DP (2003) The microRNAs of Caenorhabditis elegans. Genes Dev 17, 991 1008.
-
(2003)
Genes Dev
, vol.17
, pp. 991-1008
-
-
Lim, L.P.1
Lau, N.C.2
Weinstein, E.G.3
Abdelhakim, A.4
Yekta, S.5
Rhoades, M.W.6
Burge, C.B.7
Bartel, D.P.8
-
13
-
-
0038054470
-
Computational and experimental identification of C. elegans microRNAs
-
Grad Y, Aach J, Hayes GD, Reinhart BJ, Church GM, Ruvkun G Kim J (2003) Computational and experimental identification of C. elegans microRNAs. Mol Cell 11, 1253.
-
(2003)
Mol Cell
, vol.11
, pp. 1253
-
-
Grad, Y.1
Aach, J.2
Hayes, G.D.3
Reinhart, B.J.4
Church, G.M.5
Ruvkun, G.6
Kim, J.7
-
14
-
-
0347444723
-
MicroRNAs: Genomics, biogenesis, mechanism, and function
-
Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281.
-
(2004)
Cell
, vol.116
, pp. 281
-
-
Bartel, D.P.1
-
15
-
-
0035955374
-
Identification of novel genes coding for small expressed RNAs
-
Lagos-Quintana M, Rauhut R, Lendeckel W Tuschl T (2001) Identification of novel genes coding for small expressed RNAs. Science 294, 853 858.
-
(2001)
Science
, vol.294
, pp. 853-858
-
-
Lagos-Quintana, M.1
Rauhut, R.2
Lendeckel, W.3
Tuschl, T.4
-
16
-
-
0035955361
-
An abundant class of tiny rnas with probable regulatory roles in Caenorhabditis elegans
-
Lau NC, Lim LP, Weinstein EG Bartel DP (2001) An abundant class of tiny rnas with probable regulatory roles in Caenorhabditis elegans. Science 294, 858 862.
-
(2001)
Science
, vol.294
, pp. 858-862
-
-
Lau, N.C.1
Lim, L.P.2
Weinstein, E.G.3
Bartel, D.P.4
-
17
-
-
0035955366
-
An extensive class of small rnas in Caenorhabditis elegans
-
Lee RC Ambros V (2001) An extensive class of small rnas in Caenorhabditis elegans. Science 294, 862 864.
-
(2001)
Science
, vol.294
, pp. 862-864
-
-
Lee, R.C.1
Ambros, V.2
-
18
-
-
0034597777
-
Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA
-
Pasquinelli AE et al. (2000) Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408, 86.
-
(2000)
Nature
, vol.408
, pp. 86
-
-
Pasquinelli, A.E.1
-
19
-
-
24644476482
-
MicroRNA identification based on sequence and structure alignment
-
Wang X, Zhang J, Li F, Gu J, He T, Zhang X Li Y (2005) MicroRNA identification based on sequence and structure alignment. Bioinformatics 21, 3610 3614.
-
(2005)
Bioinformatics
, vol.21
, pp. 3610-3614
-
-
Wang, X.1
Zhang, J.2
Li, F.3
Gu, J.4
He, T.5
Zhang, X.6
Li, Y.7
-
20
-
-
21844477027
-
Human microRNA prediction through a probabilistic co-learning model of sequence and structure
-
Nam J-W, Shin K-R, Han J, Lee Y, Kim VN Zhang B-T (2005) Human microRNA prediction through a probabilistic co-learning model of sequence and structure. Nucleic Acids Res 33, 3570 3581.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 3570-3581
-
-
Nam, J.-W.1
Shin, K.-R.2
Han, J.3
Lee, Y.4
Kim, V.N.5
Zhang, B.-T.6
-
21
-
-
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 M et al. (2005) Identification of microRNAs of the herpesvirus family. Nat Meth 2, 269 276.
-
(2005)
Nat Meth
, 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.10
-
22
-
-
27844508214
-
Identification of clustered microRNAs using an ab initio prediction method
-
Sewer A et al. (2005) Identification of clustered microRNAs using an ab initio prediction method. BMC Bioinformatics 6, 267.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 267
-
-
Sewer, A.1
-
23
-
-
33745594057
-
Combining multi-species genomic data for microRNA identification using a Naive Bayes classifier
-
Yousef M, Nebozhyn M, Shatkay H, Kanterakis S, Showe LC Showe MK (2006) Combining multi-species genomic data for microRNA identification using a Naive Bayes classifier. Bioinformatics 22, 1325 1334.
-
(2006)
Bioinformatics
, vol.22
, pp. 1325-1334
-
-
Yousef, M.1
Nebozhyn, M.2
Shatkay, H.3
Kanterakis, S.4
Showe, L.C.5
Showe, M.K.6
-
24
-
-
33646168051
-
A combined computational and microarray-based approach identifies novel microRNAs encoded by human gamma-herpesviruses
-
Grundhoff A, Sullivan CS Ganem D (2006) A combined computational and microarray-based approach identifies novel microRNAs encoded by human gamma-herpesviruses. RNA 12, 733 750.
-
(2006)
RNA
, vol.12
, pp. 733-750
-
-
Grundhoff, A.1
Sullivan, C.S.2
Ganem, D.3
-
25
-
-
33747871855
-
Hairpins in a Haystack: Recognizing microRNA precursors in comparative genomics data
-
Hertel J Stadler PF (2006) Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data. Bioinformatics 22, e197 e202.
-
(2006)
Bioinformatics
, vol.22
-
-
Hertel, J.1
Stadler, P.F.2
-
26
-
-
41549152081
-
Mammalian microRNA prediction through a support vector machine model of sequence and structure
-
Sheng Y, Engstrom PG Lenhard B (2007) Mammalian microRNA prediction through a support vector machine model of sequence and structure. PLoS ONE 2, e946.
-
(2007)
PLoS ONE
, vol.2
-
-
Sheng, Y.1
Engstrom, P.G.2
Lenhard, B.3
-
27
-
-
43949125230
-
Learning from positive examples when the negative class is undetermined - MicroRNA gene idenification
-
doi:.
-
Yousef M, Jung S, Showe L Showe M (2008) Learning from positive examples when the negative class is undetermined - microRNA gene idenification. Algorithms Mol Biol doi :.
-
(2008)
Algorithms Mol Biol
-
-
Yousef, M.1
Jung, S.2
Showe, L.3
Showe, M.4
-
28
-
-
30344447264
-
Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine
-
Xue C, Li F, He T, Liu G-P, Li Y Zhang X (2005) Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine. BMC Bioinformatics 6, 310.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 310
-
-
Xue, C.1
Li, F.2
He, T.3
Liu, G.-P.4
Li, Y.5
Zhang, X.6
-
29
-
-
44849106063
-
A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach
-
Glazov EA, Cottee PA, Barris WC, Moore RJ, Dalrymple BP Tizard ML (2008) A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. Genome Res 18, 957 964.
-
(2008)
Genome Res
, vol.18
, pp. 957-964
-
-
Glazov, E.A.1
Cottee, P.A.2
Barris, W.C.3
Moore, R.J.4
Dalrymple, B.P.5
Tizard, M.L.6
-
30
-
-
33749377869
-
Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis
-
Berezikov E, van Tetering G, Verheul M, van de Belt J, van Laake L, Vos J, Verloop R, van de Wetering M, Gurvey V, Takada S et al. (2006) Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis. Genome Res 16, 1289 1298.
-
(2006)
Genome Res
, vol.16
, pp. 1289-1298
-
-
Berezikov, E.1
Van Tetering, G.2
Verheul, M.3
Van De Belt, J.4
Van Laake, L.5
Vos, J.6
Verloop, R.7
Van De Wetering, M.8
Gurvey, V.9
Takada, S.10
-
32
-
-
34547441263
-
Target mRNAs are repressed as efficiently by microRNA-binding sites in the 5′ UTR as in the 3′ UTR
-
Lytle JR, Yario TA Steitz JA (2007) Target mRNAs are repressed as efficiently by microRNA-binding sites in the 5′ UTR as in the 3′ UTR. Proc Natl Acad Sci 104, 9667 9672.
-
(2007)
Proc Natl Acad Sci
, vol.104
, pp. 9667-9672
-
-
Lytle, J.R.1
Yario, T.A.2
Steitz, J.A.3
-
33
-
-
2442672918
-
A combined computational-experimental approach predicts human microRNA targets
-
Kiriakidou M, Nelson PT, Kouranov A, Fitziev P, Bouyioukos C, Mourelatos Z Hatzigeorgiou A (2004) A combined computational-experimental approach predicts human microRNA targets. Genes Dev 18, 1165 1178.
-
(2004)
Genes Dev
, vol.18
, pp. 1165-1178
-
-
Kiriakidou, M.1
Nelson, P.T.2
Kouranov, A.3
Fitziev, P.4
Bouyioukos, C.5
Mourelatos, Z.6
Hatzigeorgiou, A.7
-
34
-
-
19544390155
-
Predicting and validating microRNA targets
-
Lai E (2004) Predicting and validating microRNA targets. Genome Biol 5, 115.
-
(2004)
Genome Biol
, vol.5
, pp. 115
-
-
Lai, E.1
-
35
-
-
14044251458
-
Human microRNA targets
-
John B, Enright AJ, Aravin A, Tuschl T, Sander C Marks DS (2004) Human microRNA targets. PLoS Biol 2, e363.
-
(2004)
PLoS Biol
, vol.2
-
-
John, B.1
Enright, A.J.2
Aravin, A.3
Tuschl, T.4
Sander, C.5
Marks, D.S.6
-
36
-
-
38549124383
-
The microRNA.org resource: Targets and expression
-
Betel D, Wilson M, Gabow A, Marks DS Sander C (2008) The microRNA.org resource: targets and expression. Nucleic Acids Res 36, D149 D153.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Betel, D.1
Wilson, M.2
Gabow, A.3
Marks, D.S.4
Sander, C.5
-
37
-
-
4644237189
-
Fast and effective prediction of microRNA/target duplexes
-
Rehmsmeier M, Steffen P, H.-Chsmann M Giegerich R (2004) Fast and effective prediction of microRNA/target duplexes. RNA 10, 1507 1517.
-
(2004)
RNA
, vol.10
, pp. 1507-1517
-
-
Rehmsmeier, M.1
Steffen, P.2
H.-Chsmann, M.3
Giegerich, R.4
-
38
-
-
33747849920
-
RNAhybrid: MicroRNA target prediction easy, fast and flexible
-
Kruger J Rehmsmeier M (2006) RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Res 34, W451 W454.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Kruger, J.1
Rehmsmeier, M.2
-
39
-
-
0042121256
-
Mfold web server for nucleic acid folding and hybridization prediction
-
Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31 (13 3406 3415.
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.13
, pp. 3406-3415
-
-
Zuker, M.1
-
41
-
-
34047259186
-
Improving the prediction of human microRNA target genes by using ensemble algorithm
-
Yan X et al. (2007) Improving the prediction of human microRNA target genes by using ensemble algorithm. FEBS Lett 581, 1587.
-
(2007)
FEBS Lett
, vol.581
, pp. 1587
-
-
Yan, X.1
-
42
-
-
0346094457
-
Prediction of mammalian microRNA targets
-
Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP Burge CB (2003) Prediction of mammalian microRNA targets. Cell 115, 787.
-
(2003)
Cell
, vol.115
, pp. 787
-
-
Lewis, B.P.1
Shih, I.H.2
Jones-Rhoades, M.W.3
Bartel, D.P.4
Burge, C.B.5
-
43
-
-
20944450160
-
Combinatorial microRNA target predictions
-
Krek A et al. (2005) Combinatorial microRNA target predictions. Nat Genet 37, 495 500.
-
(2005)
Nat Genet
, vol.37
, pp. 495-500
-
-
Krek, A.1
-
44
-
-
27344456287
-
MicroRNA target predictions across seven Drosophila species and comparison to mammalian targets
-
Grun D, Wang Y-L, Langenberger D, Gunsalus KC Rajewsky N (2005) microRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLoS Comput Biol 1, e13.
-
(2005)
PLoS Comput Biol
, vol.1
-
-
Grun, D.1
Wang, Y.-L.2
Langenberger, D.3
Gunsalus, K.C.4
Rajewsky, N.5
-
45
-
-
22244447130
-
Weighted sequence motifs as an improved seeding step in microRNA target prediction algorithms
-
SaeTrom OLA, Snove OJ SaeTrom PAL (2005) Weighted sequence motifs as an improved seeding step in microRNA target prediction algorithms. RNA 11, 995 1003.
-
(2005)
RNA
, vol.11
, pp. 995-1003
-
-
Saetrom, O.L.A.1
Snove, O.J.2
Saetrom, P.A.L.3
-
46
-
-
43949133761
-
A Kernel method for microRNA target prediction using sensible data and position-based features
-
In. pp. CIBCB, La Jolla, CA.
-
Sung-Kyu K, Jin-Wu N, Wha-Jin L Byoung-Tak Z (2005) A Kernel method for microRNA target prediction using sensible data and position-based features. In Proceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, pp. 46 52. CIBCB, La Jolla, CA.
-
(2005)
Proceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology
, pp. 46-52
-
-
Sung-Kyu, K.1
Jin-Wu, N.2
Wha-Jin, L.3
Byoung-Tak, Z.4
-
47
-
-
33947424813
-
MicroTar: Predicting microRNA targets from RNA duplexes
-
Thadani R Tammi M (2006) MicroTar: predicting microRNA targets from RNA duplexes. BMC Bioinformatics 7, S20.
-
(2006)
BMC Bioinformatics
, vol.7
-
-
Thadani, R.1
Tammi, M.2
-
48
-
-
33748587841
-
A pattern-based method for the identification of microRNA binding sites and their corresponding heteroduplexes
-
Miranda KC, Huynh T, Tay Y, Ang Y-S, Tam W-L, Thomson AM, Lim B Rigoutsos I (2006) A pattern-based method for the identification of microRNA binding sites and their corresponding heteroduplexes. Cell 126, 1203 1217.
-
(2006)
Cell
, vol.126
, pp. 1203-1217
-
-
Miranda, K.C.1
Huynh, T.2
Tay, Y.3
Ang, Y.-S.4
Tam, W.-L.5
Thomson, A.M.6
Lim, B.7
Rigoutsos, I.8
-
49
-
-
36448982458
-
Naive Bayes for microRNA target predictions - Machine learning for microRNA targets
-
Yousef M, Jung S, Kossenkov AV, Showe LC Showe MK (2007) Naive Bayes for microRNA target predictions - machine learning for microRNA targets. Bioinformatics 23, 2987 2992.
-
(2007)
Bioinformatics
, vol.23
, pp. 2987-2992
-
-
Yousef, M.1
Jung, S.2
Kossenkov, A.V.3
Showe, L.C.4
Showe, M.K.5
-
50
-
-
31044444975
-
TarBase: A comprehensive database of experimentally supported animal microRNA targets
-
Sethupathy P, Corda B Hatzigeorgiou AG (2006) TarBase: a comprehensive database of experimentally supported animal microRNA targets. RNA 12, 192 197.
-
(2006)
RNA
, vol.12
, pp. 192-197
-
-
Sethupathy, P.1
Corda, B.2
Hatzigeorgiou, A.G.3
-
51
-
-
33644878178
-
Argonaute - A database for gene regulation by mammalian microRNAs
-
Shahi P et al. (2006) Argonaute - a database for gene regulation by mammalian microRNAs. Nucleic Acids Res 34, D115 D118.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Shahi, P.1
-
52
-
-
58149186499
-
MiRecords: An integrated resource for microRNA-target interactions
-
Xiao F, Zuo Z, Cai G, Kang S, Gao X Li T (2009) miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res 37, D105 D110.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Xiao, F.1
Zuo, Z.2
Cai, G.3
Kang, S.4
Gao, X.5
Li, T.6
|