-
1
-
-
84865757142
-
Landscape of transcription in human cells
-
Djebali, S., Davis, C.A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F. et al. (2012) Landscape of transcription in human cells. Nature, 489, 101-108.
-
(2012)
Nature
, vol.489
, pp. 101-108
-
-
Djebali, S.1
Davis, C.A.2
Merkel, A.3
Dobin, A.4
Lassmann, T.5
Mortazavi, A.6
Tanzer, A.7
Lagarde, J.8
Lin, W.9
Schlesinger, F.10
-
2
-
-
41349116135
-
The eukaryotic genome as an RNA machine
-
Amaral, P.P., Dinger, M.E., Mercer, T.R., Mattick, J.S. (2008) The eukaryotic genome as an RNA machine. Science., 319, 1787-1789.
-
(2008)
Science
, vol.319
, pp. 1787-1789
-
-
Amaral, P.P.1
Dinger, M.E.2
Mercer, T.R.3
Mattick, J.S.4
-
3
-
-
84875183056
-
Structure and function of long noncoding RNAs in epigenetic regulation
-
Mercer, T.R., Mattick, J.S. (2013) Structure and function of long noncoding RNAs in epigenetic regulation. Nat. Struct. Mol. Biol., 20, 300-307.
-
(2013)
Nat. Struct. Mol. Biol
, vol.20
, pp. 300-307
-
-
Mercer, T.R.1
Mattick, J.S.2
-
4
-
-
85011941303
-
Computational prediction of sRNAs and their targets in bacteriA
-
Backofen, R., Hess, W.R. (2010) Computational prediction of sRNAs and their targets in bacteriA. RNA Biol., 7, 33-42.
-
(2010)
RNA Biol
, vol.7
, pp. 33-42
-
-
Backofen, R.1
Hess, W.R.2
-
5
-
-
84897742116
-
Common features of microRNA target prediction tools
-
Peterson, S.M., Thompson, J.A., Ufkin, M.L., Sathyanarayana, P., Liaw, L., Congdon, C.B. (2014) Common features of microRNA target prediction tools. Front. Genet., 5, 1-10.
-
(2014)
Front. Genet
, vol.5
, pp. 1-10
-
-
Peterson, S.M.1
Thompson, J.A.2
Ufkin, M.L.3
Sathyanarayana, P.4
Liaw, L.5
Congdon, C.B.6
-
6
-
-
44949145107
-
Predicting novel RNA-RNA interactions
-
Meyer, I.M. (2008) Predicting novel RNA-RNA interactions. Curr. Opin. Struc. Biol., 18, 387-393.
-
(2008)
Curr. Opin. Struc. Biol
, vol.18
, pp. 387-393
-
-
Meyer, I.M.1
-
7
-
-
78651415661
-
PETcofold: Predicting conserved interactions and structures of two multiple alignments of RNA sequences
-
Seemann, S.E., Richter, A.S., Gesell, T., Backofen, R., Gorodkin, J. (2011) PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences. Bioinformatics, 27, 211-219.
-
(2011)
Bioinformatics
, vol.27
, pp. 211-219
-
-
Seemann, S.E.1
Richter, A.S.2
Gesell, T.3
Backofen, R.4
Gorodkin, J.5
-
8
-
-
82055164092
-
ViennaRNA Package 2.0
-
Lorenz, R., Bernhart, S.H., Höner Zu Siederdissen, C., Tafer, H., Flamm, C., Stadler, P.F., Hofacker, I.L. (2011) ViennaRNA Package 2.0. Algorithms Mol. Biol., 6, 26.
-
(2011)
Algorithms Mol. Biol
, vol.6
, pp. 26
-
-
Lorenz, R.1
Bernhart, S.H.2
Höner, Zu.3
Siederdissen, C.4
Tafer, H.5
Flamm, C.6
Stadler, P.F.7
Hofacker, I.L.8
-
9
-
-
55749083578
-
RNAplex: A fast tool for RNA-RNA interaction search
-
Tafer, H., Hofacker, I.L. (2008) RNAplex: a fast tool for RNA-RNA interaction search. Bioinformatics, 24, 2657-2663.
-
(2008)
Bioinformatics
, vol.24
, pp. 2657-2663
-
-
Tafer, H.1
Hofacker, I.L.2
-
10
-
-
84867300120
-
RIsearch: Fast RNA-RNA interaction search using a simplified nearest-neighbor energy model
-
Wenzel, A., Akbasli, E., Gorodkin, J. (2012) RIsearch: fast RNA-RNA interaction search using a simplified nearest-neighbor energy model. Bioinformatics, 28, 2738-2746.
-
(2012)
Bioinformatics
, vol.28
, pp. 2738-2746
-
-
Wenzel, A.1
Akbasli, E.2
Gorodkin, J.3
-
11
-
-
33645103560
-
GUUGle: A utility for fast exact matching under RNA complementary rules including G-U base pairing
-
Gerlach, W., Giegerich, R. (2006) GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing. Bioinformatics, 22, 762-764.
-
(2006)
Bioinformatics
, vol.22
, pp. 762-764
-
-
Gerlach, W.1
Giegerich, R.2
-
12
-
-
0025264854
-
The equilibrium partition function and base pair binding probabilities for RNA secondary structure
-
McCaskill, J.S. (1990) The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers, 29, 1105-1119.
-
(1990)
Biopolymers
, vol.29
, pp. 1105-1119
-
-
McCaskill, J.S.1
-
13
-
-
79952345068
-
RNA Accessibility in cubic time
-
Bernhart, S.H., Mückstein, U., Hofacker, I.L. (2011) RNA Accessibility in cubic time. Algorithms Mol. Biol., 6, 3.
-
(2011)
Algorithms Mol. Biol
, vol.6
, pp. 3
-
-
Bernhart, S.H.1
Mückstein, U.2
Hofacker, I.L.3
-
14
-
-
33646877072
-
Thermodynamics of RNA-RNA binding
-
Mückstein, U., Tafer, H., Hackerm uller, 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
-
-
Mückstein, U.1
Tafer, H.2
Hackerm, J.3
Bernhart, S.H.4
Stadler, P.F.5
Hofacker, I.L.6
-
15
-
-
57249083988
-
IntaRNA: Efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions
-
Busch, A., Richter, A.S., Backofen, R. (2008) IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics, 24, 2849-2856.
-
(2008)
Bioinformatics
, vol.24
, pp. 2849-2856
-
-
Busch, A.1
Richter, A.S.2
Backofen, R.3
-
16
-
-
79959933227
-
Fast accessibility-based prediction of RNA-RNA interactions
-
Tafer, H., Amman, F., Eggenhofer, F., Stadler, P.F., Hofacker, I.L. (2011) Fast accessibility-based prediction of RNA-RNA interactions. Bioinformatics, 27, 1934-1940.
-
(2011)
Bioinformatics
, vol.27
, pp. 1934-1940
-
-
Tafer, H.1
Amman, F.2
Eggenhofer, F.3
Stadler, P.F.4
Hofacker, I.L.5
-
17
-
-
0019876473
-
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
-
Zuker, M., Stiegler, P. (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res., 9, 133-148.
-
(1981)
Nucleic Acids Res
, vol.9
, pp. 133-148
-
-
Zuker, M.1
Stiegler, P.2
-
18
-
-
34249772381
-
Fast folding and comparison of RNA secondary structures
-
Hofacker, I.L., Fontana, W., Stadler, P.F., Bonhoeffer, L.S., Tacker, M., Schuster, P. (1994) Fast folding and comparison of RNA secondary structures. Monatsh. Chem., 125, 167-188.
-
(1994)
Monatsh. Chem
, vol.125
, pp. 167-188
-
-
Hofacker, I.L.1
Fontana, W.2
Stadler, P.F.3
Bonhoeffer, L.S.4
Tacker, M.5
Schuster, P.6
-
19
-
-
11844254846
-
Secondary structure prediction of interacting RNA molecules
-
19.,ronescu, M., Zhang, Z.C., Condon, A. (2005) Secondary structure prediction of interacting RNA molecules. J. Mol. Biol., 345, 987-1001.
-
(2005)
J. Mol. Biol
, vol.345
, pp. 987-1001
-
-
Ronescu, M.1
Zhang, Z.C.2
Condon, A.3
-
20
-
-
33744979613
-
Partition function and base pairing probabilities of RNA heterodimers
-
Bernhart, S.H., Tafer, H., Mückstein, U., Flamm, C., Stadler, P.F., Hofacker, I.L. (2006) Partition function and base pairing probabilities of RNA heterodimers. Algorithms Mol. Biol., 1, 3.
-
(2006)
Algorithms Mol. Biol
, vol.1
, pp. 3
-
-
Bernhart, S.H.1
Tafer, H.2
Mückstein, U.3
Flamm, C.4
Stadler, P.F.5
Hofacker, I.L.6
-
21
-
-
77956503102
-
RactIP: Fast and accurate prediction of RNA-RNA interaction using integer programming
-
Kato, Y., Sato, K., Hamada, M., Watanabe, Y., Asai, K., Akutsu, T. (2010) RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming. Bioinformatics, 26, i460-i466.
-
(2010)
Bioinformatics
, vol.26
, pp. i460-i466
-
-
Kato, Y.1
Sato, K.2
Hamada, M.3
Watanabe, Y.4
Asai, K.5
Akutsu, T.6
-
22
-
-
0043123155
-
Pfold: RNA secondary structure prediction using stochastic context-free grammars
-
Knudsen, B. (2003) Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res., 31, 3423-3428.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3423-3428
-
-
Knudsen, B.1
-
23
-
-
58249121729
-
RNAalifold: Improved consensus structure prediction for RNA alignments
-
Bernhart, S.H., Hofacker, I.L., Will, S., Gruber, A.R., Stadler, P.F. (2008) RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics, 9, 474.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 474
-
-
Bernhart, S.H.1
Hofacker, I.L.2
Will, S.3
Gruber, A.R.4
Stadler, P.F.5
-
24
-
-
49949116902
-
The impact of microRNAs on protein output
-
Baek, D., Villén, J., Shin, C., Camargo, F.D., Gygi, S.P., Bartel, D.P. (2008) The impact of microRNAs on protein output. Nature, 455, 64-71.
-
(2008)
Nature
, vol.455
, pp. 64-71
-
-
Baek, D.1
Villén, J.2
Shin, C.3
Camargo, F.D.4
Gygi, S.P.5
Bartel, D.P.6
-
25
-
-
74049088856
-
Lost in translation: An assessment and perspective for computational microrna target identification
-
Alexiou, P., Maragkakis, M., Papadopoulos, G.L., Reczko, M., Hatzigeorgiou, A.G. (2009) Lost in translation: An assessment and perspective for computational microrna target identification. Bioinformatics, 25, 3049-3055.
-
(2009)
Bioinformatics
, vol.25
, pp. 3049-3055
-
-
Alexiou, P.1
Maragkakis, M.2
Papadopoulos, G.L.3
Reczko, M.4
Hatzigeorgiou, A.G.5
-
26
-
-
79959937873
-
RNApredator: Fast accessibility-based prediction of sRNA targets
-
Eggenhofer, F., Tafer, H., Stadler, P.F., Hofacker, I.L. (2011) RNApredator: fast accessibility-based prediction of sRNA targets. Nucleic Acids Res., 39, W149-W154.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. W149-W154
-
-
Eggenhofer, F.1
Tafer, H.2
Stadler, P.F.3
Hofacker, I.L.4
-
27
-
-
84883772639
-
Comparative genomics boosts target prediction for bacterial small RNAs
-
Wright, P.R., Richter, A.S., Papenfort, K., Mann, M., Vogel, J., Hess, W.R., Backofen, R., Georg, J. (2013) Comparative genomics boosts target prediction for bacterial small RNAs. Proc. Natl. Acad. Sci. U.S.A., 110, E3487-E3496.
-
(2013)
Proc. Natl. Acad. Sci. U.S.A
, vol.110
, pp. E3487-E3496
-
-
Wright, P.R.1
Richter, A.S.2
Papenfort, K.3
Mann, M.4
Vogel, J.5
Hess, W.R.6
Backofen, R.7
Georg, J.8
-
28
-
-
84939288737
-
An assessment of bacterial small RNA target prediction programs
-
Pain, A., Ott, A., Amine, H., Rochat, T., Bouloc, P., Gautheret, D. (2015) An assessment of bacterial small RNA target prediction programs. RNA Biol., 12, 509-513.
-
(2015)
RNA Biol
, vol.12
, pp. 509-513
-
-
Pain, A.1
Ott, A.2
Amine, H.3
Rochat, T.4
Bouloc, P.5
Gautheret, D.6
-
29
-
-
84903223681
-
RNA-RNA interaction prediction using genetic algorithm
-
Montaseri, S., Zare-Mirakabad, F., Moghadam-Charkari, N. (2014) RNA-RNA interaction prediction using genetic algorithm. Algorithms Mol. Biol., 9, 17.
-
(2014)
Algorithms Mol. Biol
, vol.9
, pp. 17
-
-
Montaseri, S.1
Zare-Mirakabad, F.2
Moghadam-Charkari, N.3
-
30
-
-
78049479577
-
Time and space efficient RNA-RNA interaction prediction via sparse folding
-
Salari, R., Mathias, M., Will, S. (2010) Time and space efficient RNA-RNA interaction prediction via sparse folding. Lect. Notes Comput. Sci., 6044, 473-490.
-
(2010)
Lect. Notes Comput. Sci
, vol.6044
, pp. 473-490
-
-
Salari, R.1
Mathias, M.2
Will, S.3
-
31
-
-
70349984002
-
Partition function and base pairing probabilities for RNA-RNA interaction prediction
-
Huang, F.W.D., Qin, J., Reidys, C.M., Stadler, P.F. (2009) Partition function and base pairing probabilities for RNA-RNA interaction prediction. Bioinformatics, 25, 2646-2654.
-
(2009)
Bioinformatics
, vol.25
, pp. 2646-2654
-
-
Huang, F.W.D.1
Qin, J.2
Reidys, C.M.3
Stadler, P.F.4
-
32
-
-
79951537034
-
RNA-RNA interaction prediction based on multiple sequence alignments
-
Li, A.X., Marz, M., Qin, J., Reidys, C.M. (2011) RNA-RNA interaction prediction based on multiple sequence alignments. Bioinformatics, 27, 456-463.
-
(2011)
Bioinformatics
, vol.27
, pp. 456-463
-
-
Li, A.X.1
Marz, M.2
Qin, J.3
Reidys, C.M.4
-
33
-
-
84937543518
-
Evaluating the accuracy and efficiency of multiple sequence alignment methods
-
Pervez, M.T., Babar, M., Nadeem, A., Aslam, M., Awan, A., Aslam, N., Hussain, T., Naveed, N., Qadri, S., Waheed, U. et al. (2014) Evaluating the accuracy and efficiency of multiple sequence alignment methods. Evol. Bioinform., 10, 205-217.
-
(2014)
Evol. Bioinform
, vol.10
, pp. 205-217
-
-
Pervez, M.T.1
Babar, M.2
Nadeem, A.3
Aslam, M.4
Awan, A.5
Aslam, N.6
Hussain, T.7
Naveed, N.8
Qadri, S.9
Waheed, U.10
-
34
-
-
84899491312
-
Assessing the efficiency of multiple sequence alignment programs
-
Pais, F.S.M., Ruy, P.D.C., Oliveira, G., Coimbra, R.S. (2014) Assessing the efficiency of multiple sequence alignment programs. Algorithm. Mol. Biol., 9, 4.
-
(2014)
Algorithm. Mol. Biol
, vol.9
, pp. 4
-
-
Pais, F.S.M.1
Ruy, P.D.C.2
Oliveira, G.3
Coimbra, R.S.4
-
35
-
-
84875619226
-
MAFFT multiple sequence alignment software version 7: Improvements in performance and usability
-
Katoh, K., Standley, D.M. (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol., 30, 772-780.
-
(2013)
Mol. Biol. Evol
, vol.30
, pp. 772-780
-
-
Katoh, K.1
Standley, D.M.2
-
36
-
-
14644430471
-
ProbCons: Probabilistic consistency-based multiple sequence alignment
-
Do, C.B. (2005) ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome. Res., 15, 330-340.
-
(2005)
Genome. Res
, vol.15
, pp. 330-340
-
-
Do, C.B.1
-
37
-
-
34247598415
-
Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering
-
Will, S., Reiche, K., Hofacker, I.L., Stadler, P.F., Backofen, R. (2007) Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering. PLoS Comput. Biol., 3, e65.
-
(2007)
PLoS Comput. Biol
, vol.3
, pp. e65
-
-
Will, S.1
Reiche, K.2
Hofacker, I.L.3
Stadler, P.F.4
Backofen, R.5
-
38
-
-
84943606050
-
SPARSE: Quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics
-
Will, S., Otto, C., Miladi, M., Möhl, M., Backofen, R. (2015) SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics. Bioinformatics, 31, 2489-2496.
-
(2015)
Bioinformatics
, vol.31
, pp. 2489-2496
-
-
Will, S.1
Otto, C.2
Miladi, M.3
Möhl, M.4
Backofen, R.5
-
39
-
-
52049083257
-
RNA STRAND: The RNA secondary structure and statistical analysis database
-
39.,ronescu, M., Bereg, V., Hoos, H.H., Condon, A. (2008) RNA STRAND: the RNA secondary structure and statistical analysis database. BMC Bioinformatics, 9, 340.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 340
-
-
Ronescu, M.1
Bereg, V.2
Hoos, H.H.3
Condon, A.4
-
40
-
-
84874266637
-
Rfam 11.0: 10 years of RNA families
-
Burge, S.W., Daub, J., Eberhardt, R., Tate, J., Barquist, L., Nawrocki, E.P., Eddy, S.R., Gardner, P.P., Bateman, A. (2013) Rfam 11.0: 10 years of RNA families. Nucleic Acids Res., 41, D226-D232.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D226-D232
-
-
Burge, S.W.1
Daub, J.2
Eberhardt, R.3
Tate, J.4
Barquist, L.5
Nawrocki, E.P.6
Eddy, S.R.7
Gardner, P.P.8
Bateman, A.9
-
41
-
-
1842453716
-
Controlling mRNA stability and translation with small noncoding RNAs
-
Storz, G., Opdyke, J.A., Zhang, A. (2004) Controlling mRNA stability and translation with small, noncoding RNAs. Curr. Opin. Microbiol., 7, 140-144.
-
(2004)
Curr. Opin. Microbiol
, vol.7
, pp. 140-144
-
-
Storz, G.1
Opdyke, J.A.2
Zhang, A.3
-
42
-
-
66349105749
-
A partition function algorithm for interacting nucleic acid strands
-
Chitsaz, H., Salari, R., Sahinalp, S.C., Backofen, R. (2009) A partition function algorithm for interacting nucleic acid strands. Bioinformatics, 25, i365-i373.
-
(2009)
Bioinformatics
, vol.25
, pp. i365-i373
-
-
Chitsaz, H.1
Salari, R.2
Sahinalp, S.C.3
Backofen, R.4
-
43
-
-
79952786136
-
Accessibility and evolutionary conservation mark bacterial small-RNA target-binding regions
-
Peer, A., Margalit, H. (2011) Accessibility and evolutionary conservation mark bacterial small-rna target-binding regions. J. Bacteriol., 193, 1690-1701.
-
(2011)
J. Bacteriol
, vol.193
, pp. 1690-1701
-
-
Peer, A.1
Margalit, H.2
-
44
-
-
84865302975
-
Accessibility and conservation: General features of bacterial small RNA-mRNA interactions
-
Richter, A.S., Backofen, R. (2012) Accessibility and conservation: general features of bacterial small RNA-mRNA interactions? RNA Biol., 9, 954-965.
-
(2012)
RNA Biol
, vol.9
, pp. 954-965
-
-
Richter, A.S.1
Backofen, R.2
-
45
-
-
78149343511
-
SRNATarBase: A comprehensive database of bacterial sRNA targets verified by experiments
-
Cao, Y., Wu, J., Liu, Q., Zhao, Y., Ying, X., Cha, L., Wang, L., Li, W. (2010) sRNATarBase: a comprehensive database of bacterial sRNA targets verified by experiments. RNA, 16, 2051-2057.
-
(2010)
RNA
, vol.16
, pp. 2051-2057
-
-
Cao, Y.1
Wu, J.2
Liu, Q.3
Zhao, Y.4
Ying, X.5
Cha, L.6
Wang, L.7
Li, W.8
-
46
-
-
84941102229
-
Update on RefSeq microbial genomes resources
-
Tatusova, T., Ciufo, S., Federhen, S., Fedorov, B., McVeigh, R., O'Neill, K., Tolstoy, I., Zaslavsky, L. (2014) Update on RefSeq microbial genomes resources. Nucleic Acids Res., 43, D599-D605.
-
(2014)
Nucleic Acids Res
, vol.43
, pp. D599-D605
-
-
Tatusova, T.1
Ciufo, S.2
Federhen, S.3
Fedorov, B.4
McVeigh, R.5
O'Neill, K.6
Tolstoy, I.7
Zaslavsky, L.8
-
47
-
-
0036703184
-
The expanding snoRNA world
-
Bachellerie, J.P., Cavaillé, J., Hüttenhofer, A. (2002) The expanding snoRNA world. Biochimie., 84, 775-790.
-
(2002)
Biochimie
, vol.84
, pp. 775-790
-
-
Bachellerie, J.P.1
Cavaillé, J.2
Hüttenhofer, A.3
-
48
-
-
75249094684
-
RNAsnoop: Efficient target prediction for H/ACA snoRNAs
-
Tafer, H., Kehr, S., Hertel, J., Hofacker, I.L., Stadler, P.F. (2010) RNAsnoop: efficient target prediction for H/ACA snoRNAs. Bioinformatics, 26, 610-616.
-
(2010)
Bioinformatics
, vol.26
, pp. 610-616
-
-
Tafer, H.1
Kehr, S.2
Hertel, J.3
Hofacker, I.L.4
Stadler, P.F.5
-
49
-
-
0033582628
-
A computational screen for methylation guide snoRNAs in yeast
-
Lowe, T.M., Eddy, S.R. (1999) A computational screen for methylation guide snoRNAs in yeast. Science, 283, 1168-1171.
-
(1999)
Science
, vol.283
, pp. 1168-1171
-
-
Lowe, T.M.1
Eddy, S.R.2
-
50
-
-
33847270751
-
New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA
-
Piekna-Przybylska, D., Decatur, W.A., Fournier, M.J. (2007) New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA. RNA, 13, 305-312.
-
(2007)
RNA
, vol.13
, pp. 305-312
-
-
Piekna-Przybylska, D.1
Decatur, W.A.2
Fournier, M.J.3
-
51
-
-
84858588614
-
Saccharomyces Genome Database: The genomics resource of budding yeast
-
Cherry, J.M., Hong, E.L., Amundsen, C., Balakrishnan, R., Binkley, G., Chan, E.T., Christie, K.R., Costanzo, M.C., Dwight, S.S., Engel, S.R. et al. (2012) Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res., 40, D700-D705.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. D700-D705
-
-
Cherry, J.M.1
Hong, E.L.2
Amundsen, C.3
Balakrishnan, R.4
Binkley, G.5
Chan, E.T.6
Christie, K.R.7
Costanzo, M.C.8
Dwight, S.S.9
Engel, S.R.10
-
52
-
-
84858983547
-
KEGG for integration and interpretation of large-scale molecular data sets
-
Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res., 40, D109-D114.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. D109-D114
-
-
Kanehisa, M.1
Goto, S.2
Sato, Y.3
Furumichi, M.4
Tanabe, M.5
-
53
-
-
63249120880
-
Non-coding RNA annotation of the genome of Trichoplax adhaerens
-
Hertel, J., de Jong, D., Marz, M., Rose, D., Tafer, H., Tanzer, A., Schierwater, B., Stadler, P.F. (2009) Non-coding RNA annotation of the genome of Trichoplax adhaerens. Nucleic Acids Res., 37, 1602-1615.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 1602-1615
-
-
Hertel, J.1
De Jong, D.2
Marz, M.3
Rose, D.4
Tafer, H.5
Tanzer, A.6
Schierwater, B.7
Stadler, P.F.8
-
54
-
-
84863192000
-
R-CHIE: A web server and R package for visualizing RNA secondary structures
-
Lai, D., Proctor, J.R., Zhu, J.Y.A., Meyer, I.M. (2012) R-CHIE: a web server and R package for visualizing RNA secondary structures. Nucleic Acids Res., 40, e95.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. e95
-
-
Lai, D.1
Proctor, J.R.2
Zhu, J.Y.A.3
Meyer, I.M.4
-
55
-
-
13344262673
-
A comprehensive comparison of comparative RNA structure prediction approaches
-
Gardner, P.P., Giegerich, R. (2004) A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics, 5, 140.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 140
-
-
Gardner, P.P.1
Giegerich, R.2
-
56
-
-
0016772212
-
Comparison of the predicted and observed secondary structure of T4 phage lysozyme
-
Matthews, B.W. (1975) Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Acta., 405, 442-451.
-
(1975)
Biochim. Biophys. Acta
, vol.405
, pp. 442-451
-
-
Matthews, B.W.1
-
57
-
-
0035873307
-
Discovering common stem-loop motifs in unaligned RNA sequences
-
Gorodkin, J., Stricklin, S.L., Stormo, G.D. (2001) Discovering common stem-loop motifs in unaligned RNA sequences. Nucleic Acids Res., 29, 2135-2144.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 2135-2144
-
-
Gorodkin, J.1
Stricklin, S.L.2
Stormo, G.D.3
-
58
-
-
79951860125
-
Ggplot2 Wiley interdiscip
-
Wickham, H. (2011) ggplot2. Wiley Interdiscip. Rev. Comput. Stat., 3, 180-185.
-
(2011)
Rev. Comput. Stat
, vol.3
, pp. 180-185
-
-
Wickham, H.1
-
59
-
-
0036301332
-
Secondary structure prediction for aligned RNA sequences
-
Hofacker, I.L., Fekete, M., Stadler, P.F. (2002) Secondary structure prediction for aligned RNA sequences. J. Mol. Biol., 319, 1059-1066.
-
(2002)
J. Mol. Biol
, vol.319
, pp. 1059-1066
-
-
Hofacker, I.L.1
Fekete, M.2
Stadler, P.F.3
-
60
-
-
2942571539
-
The comparative RNA web (CRW) site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs
-
Cannone, J.J., Subramanian, S., Schnare, M.N., Collett, J.R., D'Souza, L.M., Du, Y., Feng, B., Lin, N., Madabusi, L.V., Müller, K.M. et al. (2002) The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics, 3, 2.
-
(2002)
BMC Bioinformatics
, vol.3
, pp. 2
-
-
Cannone, J.J.1
Subramanian, S.2
Schnare, M.N.3
Collett, J.R.4
D'Souza, L.M.5
Du, Y.6
Feng, B.7
Lin, N.8
Madabusi, L.V.9
Müller, K.M.10
-
61
-
-
61449135227
-
Multiperm: Shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies
-
Anandam, P., Torarinsson, E., Ruzzo, W.L. (2009) Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies. Bioinformatics, 25, 668-669.
-
(2009)
Bioinformatics
, vol.25
, pp. 668-669
-
-
Anandam, P.1
Torarinsson, E.2
Ruzzo, W.L.3
-
62
-
-
0019797407
-
Evolutionary trees from DNA sequences: A maximum likelihood approach
-
Felsenstein, J. (1981) Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol., 17, 368-376.
-
(1981)
J. Mol. Evol
, vol.17
, pp. 368-376
-
-
Felsenstein, J.1
-
63
-
-
47649093396
-
Compensatory evolution in RNA secondary structures increases substitution rate variation among sites
-
Knies, J.L., Dang, K.K., Vision, T.J., Hoffman, N.G., Swanstrom, R., Burch, C.L. (2008) Compensatory evolution in RNA secondary structures increases substitution rate variation among sites. Mol. Biol. Evol., 25, 1778-1787.
-
(2008)
Mol. Biol. Evol
, vol.25
, pp. 1778-1787
-
-
Knies, J.L.1
Dang, K.K.2
Vision, T.J.3
Hoffman, N.G.4
Swanstrom, R.5
Burch, C.L.6
-
64
-
-
78651416809
-
PLEXY: Efficient target prediction for box C/D snoRNAs
-
Kehr, S., Bartschat, S., Stadler, P.F., Tafer, H. (2011) PLEXY: efficient target prediction for box C/D snoRNAs. Bioinformatics, 27, 279-280.
-
(2011)
Bioinformatics
, vol.27
, pp. 279-280
-
-
Kehr, S.1
Bartschat, S.2
Stadler, P.F.3
Tafer, H.4
-
65
-
-
84895493169
-
Mapping the miRNA interactome by cross-linking ligation and sequencing of hybrids (CLASH)
-
Helwak, A., Tollervey, D. (2014) Mapping the miRNA interactome by cross-linking ligation and sequencing of hybrids (CLASH). Nat. Protoc., 9, 711-728.
-
(2014)
Nat. Protoc
, vol.9
, pp. 711-728
-
-
Helwak, A.1
Tollervey, D.2
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