-
1
-
-
49949117302
-
Widespread changes in protein synthesis induced by microRNAs
-
Selbach, M., Schwanhusser, 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
Schwanhusser, B.2
Thierfelder, N.3
Fang, Z.4
Khanin, R.5
Rajewsky, N.6
-
2
-
-
1642374097
-
Specificity of microRNA target selection in translational repression
-
Doench, J.G., Sharp, P.A. (2004) Specificity of microRNA target selection in translational repression. Genes Dev., 18, 504-511.
-
(2004)
Genes Dev.
, vol.18
, pp. 504-511
-
-
Doench, J.G.1
Sharp, P.A.2
-
3
-
-
84867499417
-
Computational analysis of target hub gene repression regulated by multiple and cooperative miRNAs
-
Lai, X., Schmitz, U., Gupta, S.K., Bhattacharya, A., Kunz, M., Wolkenhauer, O., Vera, J. (2012) Computational analysis of target hub gene repression regulated by multiple and cooperative miRNAs. Nucleic Acids Res., 40, 8818-8834.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 8818-8834
-
-
Lai, X.1
Schmitz, U.2
Gupta, S.K.3
Bhattacharya, A.4
Kunz, M.5
Wolkenhauer, O.6
Vera, J.7
-
4
-
-
34547555796
-
Global and local architecture of the mammalian microRNA-transcription factor regulatory network
-
Shalgi, R., Lieber, D., Oren, M., Pilpel, Y. (2007) Global and local architecture of the mammalian microRNA-transcription factor regulatory network. PLoS Comput. Biol., 3, e131.
-
(2007)
PLoS Comput. Biol.
, vol.3
-
-
Shalgi, R.1
Lieber, D.2
Oren, M.3
Pilpel, Y.4
-
5
-
-
84934439280
-
Working together: Combinatorial regulation by microRNAs
-
Schmitz, U., Wolkenhauer, O., Vera, J. (eds.) Springer, Netherlands, Dordrecht
-
Friedman, Y., Balaga, O., Linial, M. (2013) Working together: combinatorial regulation by microRNAs. In: Schmitz, U., Wolkenhauer, O., Vera, J. (eds.), MicroRNACancer Regulation. Vol. 774. Springer, Netherlands, Dordrecht, pp. 317-337.
-
(2013)
MicroRNACancer Regulation
, vol.774
, pp. 317-337
-
-
Friedman, Y.1
Balaga, O.2
Linial, M.3
-
6
-
-
84934438006
-
MicroRNA-regulated networks: The perfect storm for classical molecular biology, the ideal scenario for systems biology
-
Vera, J., Lai, X., Schmitz, U., Wolkenhauer, O. (2013) MicroRNA-regulated networks: the perfect storm for classical molecular biology, the ideal scenario for systems biology. Adv Exp Med Biol.774:55-76.
-
(2013)
Adv Exp Med Biol.
, vol.774
, pp. 55-76
-
-
Vera, J.1
Lai, X.2
Schmitz, U.3
Wolkenhauer, O.4
-
7
-
-
58149179989
-
MiR2Disease: A manually curated database for microRNA deregulation in human disease
-
Jiang, Q., Wang, Y., Hao, Y., Juan, L., Teng, M., Zhang, X., Li, M., Wang, G., Liu, Y. (2009) miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res., 37, D98-D104.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Jiang, Q.1
Wang, Y.2
Hao, Y.3
Juan, L.4
Teng, M.5
Zhang, X.6
Li, M.7
Wang, G.8
Liu, Y.9
-
8
-
-
53349177819
-
Characterization of microRNAs in serum: A novel class of biomarkers for diagnosis of cancer and other diseases
-
Chen, X., Ba, Y., Ma, L., Cai, X., Yin, Y., Wang, K., Guo, J., Zhang, Y., Chen, J., Guo, X. et al. (2008) Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res., 18, 997-1006.
-
(2008)
Cell Res.
, vol.18
, pp. 997-1006
-
-
Chen, X.1
Ba, Y.2
Ma, L.3
Cai, X.4
Yin, Y.5
Wang, K.6
Guo, J.7
Zhang, Y.8
Chen, J.9
Guo, X.10
-
9
-
-
48749122914
-
Circulating microRNAs as stable blood-based markers for cancer detection
-
Mitchell, P.S., Parkin, R.K., Kroh, E.M., Fritz, B.R., Wyman, S.K., Pogosova-Agadjanyan, E.L., Peterson, A., Noteboom, J., O'Briant, K.C., Allen, A. et al. (2008) Circulating microRNAs as stable blood-based markers for cancer detection. Proc. Natl. Acad. Sci., 105, 10513-10518.
-
(2008)
Proc. Natl. Acad. Sci.
, vol.105
, pp. 10513-10518
-
-
Mitchell, P.S.1
Parkin, R.K.2
Kroh, E.M.3
Fritz, B.R.4
Wyman, S.K.5
Pogosova-Agadjanyan, E.L.6
Peterson, A.7
Noteboom, J.8
O'Briant, K.C.9
Allen, A.10
-
10
-
-
77954386183
-
The road toward microRNA therapeutics
-
Seto, A.G. (2010) The road toward microRNA therapeutics. Intl. J. Biochem. Cell Biol., 42, 1298-1305.
-
(2010)
Intl. J. Biochem. Cell Biol.
, vol.42
, pp. 1298-1305
-
-
Seto, A.G.1
-
11
-
-
81855224576
-
MicroRNAs en route to the clinic: Progress in validating and targeting microRNAs for cancer therapy
-
Kasinski, A.L., Slack, F.J. (2011) MicroRNAs en route to the clinic: progress in validating and targeting microRNAs for cancer therapy. Nat. Rev. Cancer, 11, 849-864.
-
(2011)
Nat. Rev. Cancer
, vol.11
, pp. 849-864
-
-
Kasinski, A.L.1
Slack, F.J.2
-
12
-
-
0942301280
-
The C elegans microRNA let-7 binds to imperfect let-7 complementary sites from the lin-41 3'UTR
-
Vella, M.C., Choi, E-Y, Lin, S-Y, Reinert, K., Slack, F.J. (2004) The C. elegans microRNA let-7 binds to imperfect let-7 complementary sites from the lin-41 3'UTR. Genes Dev., 18, 132-137.
-
(2004)
Genes Dev.
, vol.18
, pp. 132-137
-
-
Vella, M.C.1
Choi, E.-Y.2
Lin, S.-Y.3
Reinert, K.4
Slack, F.J.5
-
13
-
-
34249856066
-
Distance constraints between microRNA target sites dictate efficacy and cooperativity
-
Saetrom, P., Heale, B.S.E., Sne, O., Aagaard, L., Alluin, J., Rossi, J.J. (2007) Distance constraints between microRNA target sites dictate efficacy and cooperativity. Nucleic Acids Res., 35, 2333-2342.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 2333-2342
-
-
Saetrom, P.1
Heale, B.S.E.2
Sne, O.3
Aagaard, L.4
Alluin, J.5
Rossi, J.J.6
-
14
-
-
37349050790
-
The roles of binding site arrangement and combinatorial targeting in microRNA repression of gene expression
-
Hon, L.S., Zhang, Z. (2007) The roles of binding site arrangement and combinatorial targeting in microRNA repression of gene expression. Genome Biol., 8, R166.
-
(2007)
Genome Biol.
, vol.8
-
-
Hon, L.S.1
Zhang, Z.2
-
15
-
-
84890019107
-
A systems' biology approach to study microRNA-mediated gene regulatory networks
-
Lai, X., Bhattacharya, A., Schmitz, U., Kunz, M., Vera, J., Wolkenhauer, O.(2013) A systems' biology approach to study microRNA-mediated gene regulatory networks. Biomed Res Int. 2013:703849.
-
(2013)
Biomed Res Int.
, vol.2013
, pp. 703849
-
-
Lai, X.1
Bhattacharya, A.2
Schmitz, U.3
Kunz, M.4
Vera, J.5
Wolkenhauer, O.6
-
16
-
-
77955963884
-
Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites
-
Betel, D., Koppal, A., Agius, P., Sander, C., Leslie, C. (2010) Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol., 11, R90.
-
(2010)
Genome Biol.
, vol.11
-
-
Betel, D.1
Koppal, A.2
Agius, P.3
Sander, C.4
Leslie, C.5
-
17
-
-
77954664186
-
A viral microRNA down-regulates multiple cell cycle genes through mRNA 5'UTRs
-
Grey, F., Tirabassi, R., Meyers, H., Wu, G., McWeeney, S., Hook, L., Nelson, J.A. (2010) A viral microRNA down-regulates multiple cell cycle genes through mRNA 5'UTRs. PLoS Pathogens, 6, e1000967.
-
(2010)
PLoS Pathogens
, vol.6
-
-
Grey, F.1
Tirabassi, R.2
Meyers, H.3
Wu, G.4
McWeeney, S.5
Hook, L.6
Nelson, J.A.7
-
18
-
-
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., Jungkamp, A.-C., Munschauer, M. et al. (2010) Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cel, 141, 129-141.
-
(2010)
Cel
, 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, M.8
Jungkamp, A.-C.9
Munschauer, M.10
-
19
-
-
78651266827
-
MiRTarBase: A database curates experimentally validated microRNA-target interactions
-
Hsu, S.-D., Lin, F.-M., Wu, W.-Y., Liang, C., Huang, W.-C., Chan, W.-L., Tsai, W.-T., Chen, G.-Z., Lee, C.-J., Chiu, C.-M. et al. (2011) miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res., 39, D163-D169.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Hsu, S.-D.1
Lin, F.-M.2
Wu, W.-Y.3
Liang, C.4
Huang, W.-C.5
Chan, W.-L.6
Tsai, W.-T.7
Chen, G.-Z.8
Lee, C.-J.9
Chiu, C.-M.10
-
20
-
-
84875404794
-
The UCSC Genome Browser database: Extensions and updates 2013
-
Meyer, L.R., Zweig, A.S., Hinrichs, A.S., Karolchik, D., Kuhn, R.M., Wong, M., Sloan, C.A., Rosenbloom, K.R., Roe, G., Rhead, B. et al. (2012) The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res., 41, D64-D69.
-
(2012)
Nucleic Acids Res.
, vol.41
-
-
Meyer, L.R.1
Zweig, A.S.2
Hinrichs, A.S.3
Karolchik, D.4
Kuhn, R.M.5
Wong, M.6
Sloan, C.A.7
Rosenbloom, K.R.8
Roe, G.9
Rhead, B.10
-
21
-
-
33644750115
-
MiRBase: MicroRNA sequences, targets and gene nomenclature
-
Griffiths-Jones, S., Grocock, R.J., Dongen, S., van Bateman, A., Enright, A.J. (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
Dongen, S.3
Van Bateman, A.4
Enright, A.J.5
-
22
-
-
78149355812
-
NUPACK: Analysis and design of nucleic acid systems
-
Zadeh, J.N., Steenberg, C.D., Bois, J.S., Wolfe, B.R., Pierce, M.B., Khan, A.R., Dirks, R.M., Pierce, N.A. (2011) NUPACK: analysis and design of nucleic acid systems. J. Comput. Chem., 32, 170-173.
-
(2011)
J. Comput. Chem.
, vol.32
, pp. 170-173
-
-
Zadeh, J.N.1
Steenberg, C.D.2
Bois, J.S.3
Wolfe, B.R.4
Pierce, M.B.5
Khan, A.R.6
Dirks, R.M.7
Pierce, N.A.8
-
23
-
-
67650727366
-
VARNA: Interactive drawing and editing of the RNA secondary structure
-
Darty, K., Denise, A., Ponty, Y. (2009) VARNA: interactive drawing and editing of the RNA secondary structure. Bioinformatics, 25, 1974-1975.
-
(2009)
Bioinformatics
, vol.25
, pp. 1974-1975
-
-
Darty, K.1
Denise, A.2
Ponty, Y.3
-
24
-
-
84863624199
-
The structure of human Argonaute-2 in complex with miR-20a
-
Elkayam, E., Kuhn, C-D, Tocilj, A., Haase, A.D., Greene, E.M., Hannon, G.J., Joshua-Tor, L. (2012) The structure of human Argonaute-2 in complex with miR-20a. Cell, 150, 100-110.
-
(2012)
Cell
, vol.150
, pp. 100-110
-
-
Elkayam, E.1
Kuhn, C.-D.2
Tocilj, A.3
Haase, A.D.4
Greene, E.M.5
Hannon, G.J.6
Joshua-Tor, L.7
-
25
-
-
21644476468
-
PatchDock and SymmDock: Servers for rigid and symmetric docking
-
Schneidman-Duhovny, D., Inbar, Y., Nussinov, R., Wolfson, H.J. (2005) PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res., 33, W363-W367.
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Schneidman-Duhovny, D.1
Inbar, Y.2
Nussinov, R.3
Wolfson, H.J.4
-
26
-
-
84864953710
-
Automated 3D structure composition for large RNAs
-
Popenda, M., Szachniuk, M., Antczak, M., Purzycka, K.J., Lukasiak, P., Bartol, N., Blazewicz, J., Adamiak, R.W. (2012) Automated 3D structure composition for large RNAs. Nucleic Acids Res., 40, e112-e112.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Popenda, M.1
Szachniuk, M.2
Antczak, M.3
Purzycka, K.J.4
Lukasiak, P.5
Bartol, N.6
Blazewicz, J.7
Adamiak, R.W.8
-
27
-
-
0348244547
-
All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data
-
Foloppe, N., MacKerell, A.D. Jr. (2000) All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data. J. Comput. Chem., 21, 86-104.
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 86-104
-
-
Foloppe, N.1
MacKerell Jr., A.D.2
-
28
-
-
33947424813
-
MicroTar: Predicting microRNA targets from RNA duplexes
-
Thadani, R., Tammi, M. (2006) MicroTar: predicting microRNA targets from RNA duplexes. BMC Bioinformat., 7, S20.
-
(2006)
BMC Bioinformat.
, vol.7
-
-
Thadani, R.1
Tammi, M.2
-
29
-
-
0000214231
-
All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution
-
MacKerell, A.D., Banavali, N.K. (2000) All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution. J. Comput. Chem., 21, 105-120.
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 105-120
-
-
Mackerell, A.D.1
Banavali, N.K.2
-
30
-
-
17844373551
-
Molecular dynamics simulations and free energy calculations of base flipping in dsRNA
-
Hart, K., Nystrm, B., Ohman, M., Nilsson, L. (2005) Molecular dynamics simulations and free energy calculations of base flipping in dsRNA. RNA, 11, 609-618.
-
(2005)
RNA
, vol.11
, pp. 609-618
-
-
Hart, K.1
Nystr-M, B.2
Ohman, M.3
Nilsson, L.4
-
31
-
-
70349270612
-
Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM
-
Bans, P., Jurecka, P., Walter, N.G., Sponer, J., Otyepka, M. (2009) Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM. Methods, 49, 202-216.
-
(2009)
Methods
, vol.49
, pp. 202-216
-
-
Bans, P.1
Jurecka, P.2
Walter, N.G.3
Sponer, J.4
Otyepka, M.5
-
32
-
-
70350741850
-
Molecular dynamics study of the RNA ring nanostructure: A phenomenon of self-stabilization
-
Paliy, M., Melnik, R., Shapiro, B.A. (2009) Molecular dynamics study of the RNA ring nanostructure: a phenomenon of self-stabilization. Phys. Biol., 6, 046003.
-
(2009)
Phys. Biol.
, vol.6
, pp. 046003
-
-
Paliy, M.1
Melnik, R.2
Shapiro, B.A.3
-
33
-
-
0141956090
-
Generalized born model with a simple smoothing function
-
Im, W., Lee, M.S., Brooks, C.L. 3rd. (2003) Generalized born model with a simple smoothing function. J. Comput. Chem., 24, 1691-1702.
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1691-1702
-
-
Im, W.1
Lee, M.S.2
Brooks III, C.L.3
-
34
-
-
0031167555
-
Atomic radii for continuum electrostatics calculations based on molecular dynamics free energy simulations
-
Nina, M., Beglov, D., Roux, B. (1997) Atomic radii for continuum electrostatics calculations based on molecular dynamics free energy simulations. J. Phys. Chem. B, 101, 5239-5248.
-
(1997)
J. Phys. Chem. B
, vol.101
, pp. 5239-5248
-
-
Nina, M.1
Beglov, D.2
Roux, B.3
-
35
-
-
33845368513
-
COPASI-a COmplex PAthway SImulator
-
Hoops, S., Sahle, S., Gauges, R., Lee, C., Pahle, J., Simus, N., Singhal, M., Xu, L., Mendes, P., Kummer, U. (2006) COPASI-a COmplex PAthway SImulator. Bioinformatics, 22, 3067-3074.
-
(2006)
Bioinformatics
, vol.22
, pp. 3067-3074
-
-
Hoops, S.1
Sahle, S.2
Gauges, R.3
Lee, C.4
Pahle, J.5
Simus, N.6
Singhal, M.7
Xu, L.8
Mendes, P.9
Kummer, U.10
-
36
-
-
33750318273
-
A guide through present computational approaches for the identification of mammalian microRNA targets
-
Sethupathy, P., Megraw, M., Hatzigeorgiou, A.G. (2006) A guide through present computational approaches for the identification of mammalian microRNA targets. Nat. Methods, 3, 881-886.
-
(2006)
Nat. Methods
, vol.3
, pp. 881-886
-
-
Sethupathy, P.1
Megraw, M.2
Hatzigeorgiou, A.G.3
-
37
-
-
84904019403
-
MicroRNA target prediction and validation
-
Schmitz, U., Wolkenhauer, O., Vera, J. (eds.) Springer, Netherlands, Dordrecht
-
Ritchie, W., Rasko, J.E.J., Flamant, S. (2013) MicroRNA Target Prediction and Validation. In: Schmitz, U., Wolkenhauer, O., Vera, J. (eds.), MicroRNACancer Regulation. Vol. 774. Springer, Netherlands, Dordrecht, pp. 189-224.
-
(2013)
MicroRNACancer Regulation
, vol.774
, pp. 189-224
-
-
Ritchie, W.1
Rasko, J.E.J.2
Flamant, S.3
-
38
-
-
84885680575
-
MicroRNA target identification-experimental approaches
-
Martinez-Sanchez, A., Murphy, C. (2013) MicroRNA target identification-experimental approaches. Biology, 2, 189-205.
-
(2013)
Biology
, vol.2
, pp. 189-205
-
-
Martinez-Sanchez, A.1
Murphy, C.2
-
39
-
-
57749206034
-
Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex
-
Wang, Y., Juranek, S., Li, H., Sheng, G., Tuschl, T., Patel, D.J. (2008) Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex. Nature, 456, 921-926.
-
(2008)
Nature
, vol.456
, pp. 921-926
-
-
Wang, Y.1
Juranek, S.2
Li, H.3
Sheng, G.4
Tuschl, T.5
Patel, D.J.6
-
40
-
-
84875466989
-
Tertiary structure-based analysis of microRNA-target interactions
-
Gan, H.H., Gunsalus, K.C. (2013) Tertiary structure-based analysis of microRNA-target interactions. RNA, 19, 539-551.
-
(2013)
RNA
, vol.19
, pp. 539-551
-
-
Gan, H.H.1
Gunsalus, K.C.2
-
41
-
-
4644237189
-
Fast and effective prediction of microRNA/target duplexes
-
Rehmsmeier, M., Steffen, P., Hochsmann, 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
Hochsmann, M.3
Giegerich, R.4
-
42
-
-
33745248430
-
MicroRNA target predictions in animals
-
Rajewsky, N. (2006) microRNA target predictions in animals. Nat. Genet., 38 , S8-S13.
-
(2006)
Nat. Genet.
, vol.38
-
-
Rajewsky, N.1
-
43
-
-
80255140476
-
RNA and protein 3D structure modeling: Similarities and differences
-
Rother, K., Rother, M., Boniecki, M., Puton, T., Bujnicki, J.M. (2011) RNA and protein 3D structure modeling: similarities and differences. J. Mol. Model., 17, 2325-2336.
-
(2011)
J. Mol. Model.
, vol.17
, pp. 2325-2336
-
-
Rother, K.1
Rother, M.2
Boniecki, M.3
Puton, T.4
Bujnicki, J.M.5
-
44
-
-
33847609597
-
Thermodynamic analysis of interacting nucleic acid strands
-
Dirks, R.M., Bois, J.S., Schaeffer, J.M., Winfree, E., Pierce, N.A. (2007) Thermodynamic analysis of interacting nucleic acid strands. SIAM Rev., 49, 65-88.
-
(2007)
SIAM Rev.
, vol.49
, pp. 65-88
-
-
Dirks, R.M.1
Bois, J.S.2
Schaeffer, J.M.3
Winfree, E.4
Pierce, N.A.5
-
45
-
-
14044251458
-
Human microRNA targets
-
John, B., Enright, A.J., Aravin, A., Tuschl, T., Sander, C., Marks, D.S. (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
-
46
-
-
60149095444
-
Most mammalian mRNAs are conserved targets of microRNAs
-
Friedman, R.C., Farh, K.K.-H., Burge, C.B., Bartel, D.P. (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res., 19, 92-105.
-
(2009)
Genome Res.
, vol.19
, pp. 92-105
-
-
Friedman, R.C.1
Farh, K.K.-H.2
Burge, C.B.3
Bartel, D.P.4
-
47
-
-
23744458086
-
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
-
Siepel, A., Bejerano, G., Pedersen, J.S., Hinrichs, A.S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L.W., Richards, S. et al. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res., 15, 1034-1050.
-
(2005)
Genome Res.
, vol.15
, pp. 1034-1050
-
-
Siepel, A.1
Bejerano, G.2
Pedersen, J.S.3
Hinrichs, A.S.4
Hou, M.5
Rosenbloom, K.6
Clawson, H.7
Spieth, J.8
Hillier, L.W.9
Richards, S.10
-
48
-
-
33646877072
-
Thermodynamics of RNA-RNA binding
-
Muckstein, U., Tafer, H., Hackermuller, J., Bernhart, S.H., Stadler, P.F., Hofacker, I.L. (2006) Thermodynamics of RNA-RNA binding. Bioinformatics, 22, 1177-1182.
-
(2006)
Bioinformatics
, vol.22
, pp. 1177-1182
-
-
Muckstein, U.1
Tafer, H.2
Hackermuller, J.3
Bernhart, S.H.4
Stadler, P.F.5
Hofacker, I.L.6
-
49
-
-
4243170045
-
Identification of Drosophila microRNA targets
-
Stark, A., Brennecke, J., Russell, R.B., Cohen, S.M. (2003) Identification of Drosophila microRNA targets. PLoS Biol., 1, E60.
-
(2003)
PLoS Biol.
, vol.1
-
-
Stark, A.1
Brennecke, J.2
Russell, R.B.3
Cohen, S.M.4
-
50
-
-
0035656688
-
Non-coding RNA genes and the modern RNA world
-
Eddy, S.R. (2001) Non-coding RNA genes and the modern RNA world. Nat. Rev. Genet., 2, 919-929.
-
(2001)
Nat. Rev. Genet.
, vol.2
, pp. 919-929
-
-
Eddy, S.R.1
-
51
-
-
51349085880
-
A story of growing confusion: Genes and their regulation
-
Prohaska, S.J., Stadler, P.F. (2008) A story of growing confusion: genes and their regulation. Biophys. Rev. Lett., 03, 285-302.
-
(2008)
Biophys. Rev. Lett.
, vol.3
, pp. 285-302
-
-
Prohaska, S.J.1
Stadler, P.F.2
-
52
-
-
3042767202
-
MicroRNAs: Small RNAs with a big role in gene regulation
-
He, L., Hannon, G.J. (2004) MicroRNAs: small RNAs with a big role in gene regulation. Nat. Rev. Genet., 5, 522-531.
-
(2004)
Nat. Rev. Genet.
, vol.5
, pp. 522-531
-
-
He, L.1
Hannon, G.J.2
-
53
-
-
34047259186
-
Improving the prediction of human microRNA target genes by using ensemble algorithm
-
Yan, X., Chao, T., Tu, K., Zhang, Y., Xie, L., Gong, Y., Yuan, J., Qiang, B., Peng, X. (2007) Improving the prediction of human microRNA target genes by using ensemble algorithm. FEBS Lett., 581, 1587-1593.
-
(2007)
FEBS Lett.
, vol.581
, pp. 1587-1593
-
-
Yan, X.1
Chao, T.2
Tu, K.3
Zhang, Y.4
Xie, L.5
Gong, Y.6
Yuan, J.7
Qiang, B.8
Peng, X.9
-
54
-
-
84876935138
-
Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding
-
Helwak, A., Kudla, G., Dudnakova, T., Tollervey, D. (2013) Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Cell, 153, 654-665.
-
(2013)
Cell
, vol.153
, pp. 654-665
-
-
Helwak, A.1
Kudla, G.2
Dudnakova, T.3
Tollervey, D.4
-
55
-
-
79959946169
-
Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast
-
Kudla, G., Granneman, S., Hahn, D., Beggs, J.D., Tollervey, D. (2011) Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast. Proc. Natl. Acad. Sci., 108, 10010-10015.
-
(2011)
Proc. Natl. Acad. Sci.
, vol.108
, pp. 10010-10015
-
-
Kudla, G.1
Granneman, S.2
Hahn, D.3
Beggs, J.D.4
Tollervey, D.5
-
56
-
-
15244354492
-
Incorporating structure to predict microRNA targets
-
Robins, H., Li, Y., Padgett, R.W. (2005) Incorporating structure to predict microRNA targets. Proc. Natl. Acad. Sci. U.S.A., 102, 4006-4009.
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, pp. 4006-4009
-
-
Robins, H.1
Li, Y.2
Padgett, R.W.3
-
57
-
-
50849141708
-
MirWIP: MicroRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts
-
Hammell, M., Long, D., Zhang, L., Lee, A., Carmack, C.S., Han, M., Ding, Y., Ambros, V. (2008) mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts. Nat. Methods 5, 813-819.
-
(2008)
Nat. Methods
, vol.5
, pp. 813-819
-
-
Hammell, M.1
Long, D.2
Zhang, L.3
Lee, A.4
Carmack, C.S.5
Han, M.6
Ding, Y.7
Ambros, V.8
-
58
-
-
38849145861
-
Prediction of both conserved and nonconserved microRNA targets in animals
-
Wang, X., El Naqa, I.M. (2007) Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics, 24, 325-332.
-
(2007)
Bioinformatics
, vol.24
, pp. 325-332
-
-
Wang, X.1
El Naqa, I.M.2
-
59
-
-
0033709625
-
RNA pseudoknot prediction in energy-based models
-
Lyngs?R.B., Pedersen, C.N.S. (2000) RNA pseudoknot prediction in energy-based models. J. Comput. Biol., 7, 409-427.
-
(2000)
J. Comput. Biol.
, vol.7
, pp. 409-427
-
-
Lyngs, R.B.1
Pedersen, C.N.S.2
-
60
-
-
40449139010
-
The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data
-
Parisien, M., Major, F. (2008) The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature, 452, 51-55.
-
(2008)
Nature
, vol.452
, pp. 51-55
-
-
Parisien, M.1
Major, F.2
-
61
-
-
80255140294
-
A molecular dynamics study of a miRNA:mRNA interaction
-
Paciello, G., Acquaviva, A., Ficarra, E., Deriu, M.A., Macii, E. (2011) A molecular dynamics study of a miRNA:mRNA interaction. J. Mol. Model., 17, 2895-2906.
-
(2011)
J. Mol. Model.
, vol.17
, pp. 2895-2906
-
-
Paciello, G.1
Acquaviva, A.2
Ficarra, E.3
Deriu, M.A.4
Macii, E.5
-
62
-
-
84875466989
-
Tertiary structure-based analysis of microRNA-target interactions
-
Gan, H.H., Gunsalus, K.C. (2013) Tertiary structure-based analysis of microRNA-target interactions. RNA, 19, 539-551.
-
(2013)
RNA
, vol.19
, pp. 539-551
-
-
Gan, H.H.1
Gunsalus, K.C.2
-
63
-
-
66449110287
-
DOCK 6: Combining techniques to model RNA-small molecule complexes
-
Lang, P.T., Brozell, S.R., Mukherjee, S., Pettersen, E.F., Meng, E.C., Thomas, V., Rizzo, R.C., Case, D.A., James, T.L., Kuntz, I.D. (2009) DOCK 6: combining techniques to model RNA-small molecule complexes. RNA, 15, 1219-1230.
-
(2009)
RNA
, vol.15
, pp. 1219-1230
-
-
Lang, P.T.1
Brozell, S.R.2
Mukherjee, S.3
Pettersen, E.F.4
Meng, E.C.5
Thomas, V.6
Rizzo, R.C.7
Case, D.A.8
James, T.L.9
Kuntz, I.D.10
-
64
-
-
33748774659
-
Implicit solvent simulations of DNA and DNA-protein complexes: Agreement with explicit solvent vs experiment
-
Chocholousov, J., Feig, M. (2006) Implicit solvent simulations of DNA and DNA-protein complexes: agreement with explicit solvent vs experiment. J. Phys. Chem. B, 110, 17240-17251.
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 17240-17251
-
-
Chocholousov, J.1
Feig, M.2
-
65
-
-
33847318371
-
Molecular dynamics simulations of RNA: Anin silico single molecule approach
-
McDowell, S.E., Spackov, N., Sponer, J., Walter, N.G. (2007) Molecular dynamics simulations of RNA: Anin silico single molecule approach. Biopolymers, 85, 169-184.
-
(2007)
Biopolymers
, vol.85
, pp. 169-184
-
-
McDowell, S.E.1
Spackov, N.2
Sponer, J.3
Walter, N.G.4
-
66
-
-
80052020054
-
Molecular dynamics simulation and binding energy calculation for estimation of oligonucleotide duplex thermostability in RNA-based therapeutics
-
Shen, L., Johnson, T.L., Clugston, S., Huang, H., Butenhof, K.J., Stanton, R.V. (2011) Molecular dynamics simulation and binding energy calculation for estimation of oligonucleotide duplex thermostability in RNA-based therapeutics. J. Chem. Informat. Model., 51, 1957-1965.
-
(2011)
J. Chem. Informat. Model.
, vol.51
, pp. 1957-1965
-
-
Shen, L.1
Johnson, T.L.2
Clugston, S.3
Huang, H.4
Butenhof, K.J.5
Stanton, R.V.6
-
67
-
-
36849064251
-
Target-specific and global effectors in gene regulation by MicroRNA
-
Levine, E., Jacob, E.B., Levine, H. (2007) Target-specific and global effectors in gene regulation by MicroRNA. Biophys. J., 93, L52-L54.
-
(2007)
Biophys. J.
, vol.93
-
-
Levine, E.1
Jacob, E.B.2
Levine, H.3
-
68
-
-
47949097974
-
Computational analysis of miRNA-mediated repression of translation: Implications for models of translation initiation inhibition
-
Nissan, T., Parker, R. (2008) Computational analysis of miRNA-mediated repression of translation: implications for models of translation initiation inhibition. RNA, 14, 1480-1491.
-
(2008)
RNA
, vol.14
, pp. 1480-1491
-
-
Nissan, T.1
Parker, R.2
-
69
-
-
84934444801
-
Mathematical modeling of microRNA-mediated mechanisms of translation repression
-
Schmitz, U., Wolkenhauer, O., Vera, J. (eds.) Springer, Netherlands, Dordrecht
-
Zinovyev, A., Morozova, N., Gorban, A.N., Harel-Belan, A. (2013) Mathematical modeling of microRNA-mediated mechanisms of translation repression. In: Schmitz, U., Wolkenhauer, O., Vera, J. (eds.). MicroRNA Cancer Regulation. Vol. 774. Springer , Netherlands, Dordrecht, pp. 189-224.
-
(2013)
MicroRNA Cancer Regulation
, vol.774
, pp. 189-224
-
-
Zinovyev, A.1
Morozova, N.2
Gorban, A.N.3
Harel-Belan, A.4
-
70
-
-
61449172037
-
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
-
Huang, D.W., Sherman, B.T., Lempicki, R.A. (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc., 4, 44-57.
-
(2009)
Nat. Protoc.
, vol.4
, pp. 44-57
-
-
Huang, D.W.1
Sherman, B.T.2
Lempicki, R.A.3
-
71
-
-
33646242293
-
Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes
-
Rigoutsos, I. (2006) Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes. Proc. Natl. Acad. Sci., 103, 6605-6610.
-
(2006)
Proc. Natl. Acad. Sci.
, vol.103
, pp. 6605-6610
-
-
Rigoutsos, I.1
-
72
-
-
34247278567
-
Combinatorial RNAi: A winning strategy for the race against evolving targets? Mol
-
Grimm, D., Kay, M.A. (2007) Combinatorial RNAi: a winning strategy for the race against evolving targets? Mol. Therapy, 15, 878-888.
-
(2007)
Therapy
, vol.15
, pp. 878-888
-
-
Grimm, D.1
Kay, M.A.2
-
73
-
-
77953934646
-
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
-
Li, C., Donizelli, M., Rodriguez, N., Dharuri, H., Endler, L., Chelliah, V., Li, L., He, E., Henry, A., Stefan, M.I. et al. (2010) BioModels Database: an enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst. Biol., 4, 92.
-
(2010)
BMC Syst. Biol.
, vol.4
, pp. 92
-
-
Li, C.1
Donizelli, M.2
Rodriguez, N.3
Dharuri, H.4
Endler, L.5
Chelliah, V.6
Li, L.7
He, E.8
Henry, A.9
Stefan, M.I.10
-
74
-
-
0037246950
-
DSMM: A Database of Simulated Molecular Motions
-
Finocchiaro, G. (2003) DSMM: a Database of Simulated Molecular Motions. Nucleic Acids Res., 31, 456-457.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 456-457
-
-
Finocchiaro, G.1
|