-
1
-
-
0347444723
-
MicroRNAs: Genomics, biogenesis, mechanism, and function
-
Bartel DP.(2004).MicroRNAs: genomics, biogenesis, mechanism, and function.Cell 116:281-297
-
(2004)
Cell
, vol.116
, pp. 281-297
-
-
Bartel, D.P.1
-
2
-
-
74049108922
-
BLAST+: Architecture and applications
-
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL.(2009).BLAST+: architecture and applications.BMC Bioinformatics 10:421
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 421
-
-
Camacho, C.1
Coulouris, G.2
Avagyan, V.3
Ma, N.4
Papadopoulos, J.5
Bealer, K.6
Madden, T.L.7
-
3
-
-
30744432134
-
Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals
-
Chamary JV, Hurst LD.(2005).Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals.Genome Biol.6:R75
-
(2005)
Genome Biol
, vol.6
, pp. R75
-
-
Chamary, J.V.1
Hurst, L.D.2
-
4
-
-
84860581983
-
Genome-wide analysis of long noncoding RNA stability
-
Clark MB, Johnston RL, Inostroza-Ponta M, Fox AH, Fortini E, Moscato P, Dinger ME, Mattick JS.(2012).Genome-wide analysis of long noncoding RNA stability.Genome Res.22:885-898
-
(2012)
Genome Res
, vol.22
, pp. 885-898
-
-
Clark, M.B.1
Johnston, R.L.2
Inostroza-Ponta, M.3
Fox, A.H.4
Fortini, E.5
Moscato, P.6
Dinger, M.E.7
Mattick, J.S.8
-
5
-
-
84893427735
-
In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features
-
Ding Y, Tang Y, Kwok CK, Zhang Y, Bevilacqua PC, Assmann SM.(2014).In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features.Nature 505:696-700
-
(2014)
Nature
, vol.505
, pp. 696-700
-
-
Ding, Y.1
Tang, Y.2
Kwok, C.K.3
Zhang, Y.4
Bevilacqua, P.C.5
Assmann, S.M.6
-
6
-
-
47549097539
-
Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution
-
Drummond DA, Wilke CO.(2008).Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution.Cell 134:341-352
-
(2008)
Cell
, vol.134
, pp. 341-352
-
-
Drummond, D.A.1
Wilke, C.O.2
-
7
-
-
84891768365
-
Ensembl 2014
-
Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, et al.(2014).Ensembl 2014.Nucleic Acids Res.42:D749-D755
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D749-D755
-
-
Flicek, P.1
Amode, M.R.2
Barrell, D.3
Beal, K.4
Billis, K.5
Brent, S.6
Carvalho-Silva, D.7
Clapham, P.8
Coates, G.9
Fitzgerald, S.10
-
8
-
-
54149095553
-
Biological principles of microRNAmediated regulation: Shared themes amid diversity
-
Flynt AS, Lai EC.(2008).Biological principles of microRNAmediated regulation: shared themes amid diversity.Nat Rev Genet.9:831-842
-
(2008)
Nat Rev Genet
, vol.9
, pp. 831-842
-
-
Flynt, A.S.1
Lai, E.C.2
-
9
-
-
84886252113
-
RNA in unexpected places: Long non-coding RNA functions in diverse cellular contexts
-
Geisler S, Coller J.(2013).RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts.Nat Rev Mol Cell Biol.14: 699-712
-
(2013)
Nat Rev Mol Cell Biol
, vol.14
, pp. 699-712
-
-
Geisler, S.1
Coller, J.2
-
10
-
-
77649198142
-
A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes
-
Gu W, Zhou T, Wilke CO.(2010).A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes.PLoS Comput Biol.6:e1000664
-
(2010)
PLoS Comput Biol
, vol.6
, pp. e1000664
-
-
Gu, W.1
Zhou, T.2
Wilke, C.O.3
-
11
-
-
84879969127
-
Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins
-
Guttman M, Russell P, Ingolia NT, Weissman JS, Lander ES.(2013).Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins.Cell 154:240-251
-
(2013)
Cell
, vol.154
, pp. 240-251
-
-
Guttman, M.1
Russell, P.2
Ingolia, N.T.3
Weissman, J.S.4
Lander, E.S.5
-
12
-
-
84878082656
-
Mutations within lncRNAs are effectively selected against in fruitfly but not in human
-
Haerty W, Ponting CP.(2013).Mutations within lncRNAs are effectively selected against in fruitfly but not in human.Genome Biol.14:R49
-
(2013)
Genome Biol
, vol.14
, pp. R49
-
-
Haerty, W.1
Ponting, C.P.2
-
13
-
-
84856397817
-
Analysis of energy-based algorithms for RNA secondary structure prediction
-
Hajiaghayi M, Condon A, Hoos HH.(2012).Analysis of energy-based algorithms for RNA secondary structure prediction.BMC Bioinformatics 13:22
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 22
-
-
Hajiaghayi, M.1
Condon, A.2
Hoos, H.H.3
-
14
-
-
84899833919
-
Elements and machinery of noncoding RNAs: Toward their taxonomy
-
Hirose T, Mishima Y, Tomari Y.(2014).Elements and machinery of noncoding RNAs: toward their taxonomy.EMBO Rep.15:489-507
-
(2014)
EMBO Rep
, vol.15
, pp. 489-507
-
-
Hirose, T.1
Mishima, Y.2
Tomari, Y.3
-
15
-
-
0141519339
-
Widespread selection for local RNA secondary structure in coding regions of bacterial genes
-
Katz L, Burge CB.(2003).Widespread selection for local RNA secondary structure in coding regions of bacterial genes.Genome Res.13: 2042-2051
-
(2003)
Genome Res
, vol.13
, pp. 2042-2051
-
-
Katz, L.1
Burge, C.B.2
-
16
-
-
34748821761
-
The role of site accessibility in microRNA target recognition
-
Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E.(2007).The role of site accessibility in microRNA target recognition.Nat Genet.39: 1278-1284
-
(2007)
Nat Genet
, vol.39
, pp. 1278-1284
-
-
Kertesz, M.1
Iovino, N.2
Unnerstall, U.3
Gaul, U.4
Segal, E.5
-
17
-
-
77956306662
-
Genome-wide measurement of RNA secondary structure in yeast
-
Kertesz M, Wan Y, Mazor E, Rinn JL, Nutter RC, Chang HY, Segal E.(2010).Genome-wide measurement of RNA secondary structure in yeast.Nature 467:103-107
-
(2010)
Nature
, vol.467
, pp. 103-107
-
-
Kertesz, M.1
Wan, Y.2
Mazor, E.3
Rinn, J.L.4
Nutter, R.C.5
Chang, H.Y.6
Segal, E.7
-
18
-
-
26444450722
-
Prediction of pathogenic mutations in mitochondrially encoded human tRNAs
-
Kondrashov FA.(2005).Prediction of pathogenic mutations in mitochondrially encoded human tRNAs.Hum Mol Genet.14: 2415-2419
-
(2005)
Hum Mol Genet
, vol.14
, pp. 2415-2419
-
-
Kondrashov, F.A.1
-
20
-
-
64849114915
-
Coding-sequence determinants of gene expression in Escherichia coli
-
Kudla G, Murray AW, Tollervey D, Plotkin JB.(2009).Coding-sequence determinants of gene expression in Escherichia coli.Science 324: 255-258
-
(2009)
Science
, vol.324
, pp. 255-258
-
-
Kudla, G.1
Murray, A.W.2
Tollervey, D.3
Plotkin, J.B.4
-
21
-
-
84864629645
-
Rapid turnover of long noncoding RNAs and the evolution of gene expression
-
Kutter C, Watt S, Stefflova K, Wilson MD, Goncalves A, Ponting CP, Odom DT, Marques AC.(2012).Rapid turnover of long noncoding RNAs and the evolution of gene expression.PLoS Genet.8:e1002841
-
(2012)
PLoS Genet
, vol.8
, pp. e1002841
-
-
Kutter, C.1
Watt, S.2
Stefflova, K.3
Wilson, M.D.4
Goncalves, A.5
Ponting, C.P.6
Odom, D.T.7
Marques, A.C.8
-
22
-
-
84863200501
-
Global or local?.Predicting secondary structure and accessibility in mRNAs
-
Lange SJ, Maticzka D, Mohl M, Gagnon JN, Brown CM, Backofen R.(2012).Global or local?.Predicting secondary structure and accessibility in mRNAs.Nucleic Acids Res.40:5215-5226
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 5215-5226
-
-
Lange, S.J.1
Maticzka, D.2
Mohl, M.3
Gagnon, J.N.4
Brown, C.M.5
Backofen, R.6
-
23
-
-
84871069553
-
Epigenetic regulation by long noncoding RNAs
-
Lee JT.(2012).Epigenetic regulation by long noncoding RNAs.Science 338: 1435-1439
-
(2012)
Science
, vol.338
, pp. 1435-1439
-
-
Lee, J.T.1
-
24
-
-
82055164092
-
Viennarna package 20
-
Lorenz R, Bernhart SH, Honer Zu Siederdissen C, Tafer H, Flamm C, Stadler PF, Hofacker IL.(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
Honer, Z.U.3
Siederdissen, C.4
Tafer, H.5
Flamm, C.6
Stadler, P.F.7
Hofacker, I.L.8
-
25
-
-
84858798657
-
Negative correlation between expression level and evolutionary rate of long intergenic noncoding RNAs
-
Managadze D, Rogozin IB, Chernikova D, Shabalina SA, Koonin EV.(2011).Negative correlation between expression level and evolutionary rate of long intergenic noncoding RNAs.Genome Biol Evol.3: 1390-1404
-
(2011)
Genome Biol Evol
, vol.3
, pp. 1390-1404
-
-
Managadze, D.1
Rogozin, I.B.2
Chernikova, D.3
Shabalina, S.A.4
Koonin, E.V.5
-
26
-
-
33746320475
-
Revolutions in RNA secondary structure prediction
-
Mathews DH.(2006).Revolutions in RNA secondary structure prediction.J Mol Biol.359:526-532
-
(2006)
J Mol Biol
, vol.359
, pp. 526-532
-
-
Mathews, D.H.1
-
27
-
-
7444244924
-
Assigning pathogenicity to mitochondrial tRNA mutations: When "definitely maybe"is not good enough
-
McFarland R, Elson JL, Taylor RW, Howell N, Turnbull DM.(2004).Assigning pathogenicity to mitochondrial tRNA mutations: when "definitely maybe" is not good enough.Trends Genet.20: 591-596
-
(2004)
Trends Genet
, vol.20
, pp. 591-596
-
-
McFarland, R.1
Elson, J.L.2
Taylor, R.W.3
Howell, N.4
Turnbull, D.M.5
-
28
-
-
84895908120
-
The evolution of lncRNA repertoires and expression patterns in tetrapods
-
Necsulea A, Soumillon M, Warnefors M, Liechti A, Daish T, Zeller U, Baker JC, Grutzner F, Kaessmann H.(2014).The evolution of lncRNA repertoires and expression patterns in tetrapods.Nature 505: 635-640
-
(2014)
Nature
, vol.505
, pp. 635-640
-
-
Necsulea, A.1
Soumillon, M.2
Warnefors, M.3
Liechti, A.4
Daish, T.5
Zeller, U.6
Baker, J.C.7
Grutzner, F.8
Kaessmann, H.9
-
29
-
-
84883214592
-
Sizing up long noncoding RNAs: Do lncRNAs have secondary and tertiary structure?
-
Novikova IV, Hennelly SP, Sanbonmatsu KY.(2012).Sizing up long noncoding RNAs: do lncRNAs have secondary and tertiary structure?.Bioarchitecture 2:189-199
-
(2012)
Bioarchitecture
, vol.2
, pp. 189-199
-
-
Novikova, I.V.1
Hennelly, S.P.2
Sanbonmatsu, K.Y.3
-
30
-
-
84866449925
-
Prediction of variable translation rate effects on cotranslational protein folding
-
OBrien EP, Vendruscolo M, Dobson CM.(2012).Prediction of variable translation rate effects on cotranslational protein folding.Nat Commun.3:868
-
(2012)
Nat Commun
, vol.3
, pp. 868
-
-
O'Brien, E.P.1
Vendruscolo, M.2
Dobson, C.M.3
-
31
-
-
84874250754
-
Differential requirements for mRNA folding partially explain why highly expressed proteins evolve slowly
-
Park C, Chen X, Yang JR, Zhang J.(2013).Differential requirements for mRNA folding partially explain why highly expressed proteins evolve slowly.Proc Natl Acad Sci U S A.110:E678-E686
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
, pp. E678-E686
-
-
Park, C.1
Chen, X.2
Yang, J.R.3
Zhang, J.4
-
32
-
-
84901850307
-
Cell biology Lengthy RNAs earn respect as cellular players
-
Pennisi E.(2014).Cell biology.Lengthy RNAs earn respect as cellular players.Science 344:1072
-
(2014)
Science
, vol.344
, pp. 1072
-
-
Pennisi, E.1
-
33
-
-
34248162440
-
Functionality or transcriptional noise?.Evidence for selection within long noncoding RNAs
-
Ponjavic J, Ponting CP, Lunter G.(2007).Functionality or transcriptional noise?.Evidence for selection within long noncoding RNAs.Genome Res.17:556-565
-
(2007)
Genome Res
, vol.17
, pp. 556-565
-
-
Ponjavic, J.1
Ponting, C.P.2
Lunter, G.3
-
34
-
-
79959676389
-
The ribosome uses two active mechanisms to unwind messenger RNA during translation
-
Qu X, Wen JD, Lancaster L, Noller HF, Bustamante C, Tinoco I Jr.(2011).The ribosome uses two active mechanisms to unwind messenger RNA during translation.Nature 475:118-121
-
(2011)
Nature
, vol.475
, pp. 118-121
-
-
Qu, X.1
Wen, J.D.2
Lancaster, L.3
Noller, H.F.4
Bustamante, C.5
Tinoco, I.6
-
35
-
-
84893351549
-
Genomewide probing of RNA structure reveals active unfolding of mRNA structures in vivo
-
Rouskin S, Zubradt M, Washietl S, Kellis M, Weissman JS.(2014).Genomewide probing of RNA structure reveals active unfolding of mRNA structures in vivo.Nature 505:701-705
-
(2014)
Nature
, vol.505
, pp. 701-705
-
-
Rouskin, S.1
Zubradt, M.2
Washietl, S.3
Kellis, M.4
Weissman, J.S.5
-
36
-
-
84964315393
-
Purifying selection on splice-related motifs, not expression level nor RNA folding, explains nearly all constraint on human lincRNAs
-
Schuler A, Ghanbarian AT, Hurst LD.(2014).Purifying selection on splice-related motifs, not expression level nor RNA folding, explains nearly all constraint on human lincRNAs.Mol Biol Evol.31: 3164-3183
-
(2014)
Mol Biol Evol
, vol.31
, pp. 3164-3183
-
-
Schuler, A.1
Ghanbarian, A.T.2
Hurst, L.D.3
-
37
-
-
84864116955
-
RNA structure prediction: An overview of methods
-
Seetin MG, Mathews DH.(2012).RNA structure prediction: an overview of methods.Methods Mol Biol.905:99-122
-
(2012)
Methods Mol Biol
, vol.905
, pp. 99-122
-
-
Seetin, M.G.1
Mathews, D.H.2
-
39
-
-
80155213999
-
Composite effects of gene determinants on the translation speed and density of ribosomes
-
Tuller T, Veksler-Lublinsky I, Gazit N, Kupiec M, Ruppin E, Ziv-Ukelson M.(2011).Composite effects of gene determinants on the translation speed and density of ribosomes.Genome Biol.12:R110
-
(2011)
Genome Biol
, vol.12
, pp. R110
-
-
Tuller, T.1
Veksler-Lublinsky, I.2
Gazit, N.3
Kupiec, M.4
Ruppin, E.5
Ziv-Ukelson, M.6
-
40
-
-
77649245858
-
Translation efficiency is determined by both codon bias and folding energy
-
Tuller T, Waldman YY, Kupiec M, Ruppin E.(2010).Translation efficiency is determined by both codon bias and folding energy.Proc Natl Acad Sci U S A.107:3645-3650
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 3645-3650
-
-
Tuller, T.1
Waldman, Y.Y.2
Kupiec, M.3
Ruppin, E.4
-
41
-
-
84879987789
-
LincRNAs: Genomics, evolution, and mechanisms
-
Ulitsky I, Bartel DP.(2013).lincRNAs: genomics, evolution, and mechanisms.Cell 154:26-46
-
(2013)
Cell
, vol.154
, pp. 26-46
-
-
Ulitsky, I.1
Bartel, D.P.2
-
42
-
-
84875530540
-
LNCipedia: A database for annotated human lncRNA transcript sequences and structures
-
Volders PJ, Helsens K, Wang X, Menten B, Martens L, Gevaert K, Vandesompele J, Mestdagh P.(2013).LNCipedia: a database for annotated human lncRNA transcript sequences and structures.Nucleic Acids Res.41:D246-D251
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D246-D251
-
-
Volders, P.J.1
Helsens, K.2
Wang, X.3
Menten, B.4
Martens, L.5
Gevaert, K.6
Vandesompele, J.7
Mestdagh, P.8
-
43
-
-
84893358533
-
Landscape and variation of RNA secondary structure across the human transcriptome
-
Wan Y, Qu K, Zhang QC, Flynn RA, Manor O, Ouyang Z, Zhang J, Spitale RC, Snyder MP, Segal E, et al.(2014).Landscape and variation of RNA secondary structure across the human transcriptome.Nature 505: 706-709
-
(2014)
Nature
, vol.505
, pp. 706-709
-
-
Wan, Y.1
Qu, K.2
Zhang, Q.C.3
Flynn, R.A.4
Manor, O.5
Ouyang, Z.6
Zhang, J.7
Spitale, R.C.8
Snyder, M.P.9
Segal, E.10
-
44
-
-
68449092202
-
Architecture and secondary structure of an entire HIV-1 RNA genome
-
Watts JM, Dang KK, Gorelick RJ, Leonard CW, Bess JW Jr, Swanstrom R, Burch CL, Weeks KM.(2009).Architecture and secondary structure of an entire HIV-1 RNA genome.Nature 460:711-716
-
(2009)
Nature
, vol.460
, pp. 711-716
-
-
Watts, J.M.1
Dang, K.K.2
Gorelick, R.J.3
Leonard, C.W.4
Bess, J.W.5
Swanstrom, R.6
Burch, C.L.7
Weeks, K.M.8
-
45
-
-
84901611036
-
Mass-spectrometry-based draft of the human proteome
-
Wilhelm M, Schlegl J, Hahne H, Moghaddas Gholami A, Lieberenz M, Savitski MM, Ziegler E, Butzmann L, Gessulat S, Marx H, et al.(2014).Mass-spectrometry-based draft of the human proteome.Nature 509:582-587
-
(2014)
Nature
, vol.509
, pp. 582-587
-
-
Wilhelm, M.1
Schlegl, J.2
Hahne, H.3
Moghaddas Gholami, A.4
Lieberenz, M.5
Savitski, M.M.6
Ziegler, E.7
Butzmann, L.8
Gessulat, S.9
Marx, H.10
-
46
-
-
0346743541
-
Impact of disease-related mitochondrial mutations on tRNA structure and function
-
Wittenhagen LM, Kelley SO.(2003).Impact of disease-related mitochondrial mutations on tRNA structure and function.Trends Biochem Sci.28:605-611
-
(2003)
Trends Biochem Sci
, vol.28
, pp. 605-611
-
-
Wittenhagen, L.M.1
Kelley, S.O.2
-
47
-
-
84905375893
-
Codon-by-codon modulation of translational speed and accuracy via mRNA folding
-
Yang JR, Chen X, Zhang J.(2014).Codon-by-codon modulation of translational speed and accuracy via mRNA folding.PLoS Biol.12:e1001910
-
(2014)
PLoS Biol
, vol.12
, pp. e1001910
-
-
Yang, J.R.1
Chen, X.2
Zhang, J.3
-
48
-
-
84859473329
-
Protein misinteraction avoidance causes highly expressed proteins to evolve slowly
-
Yang JR, Liao BY, Zhuang SM, Zhang J.(2012).Protein misinteraction avoidance causes highly expressed proteins to evolve slowly.Proc Natl Acad Sci U S A.109:E831-E840
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, pp. E831-E840
-
-
Yang, J.R.1
Liao, B.Y.2
Zhuang, S.M.3
Zhang, J.4
-
49
-
-
0000616205
-
RNA secondary structures and their prediction
-
Zuker M, Sankoff D.(1984).RNA secondary structures and their prediction.Bull Math Biol.46:591-621
-
(1984)
Bull Math Biol
, vol.46
, pp. 591-621
-
-
Zuker, M.1
Sankoff, D.2
-
50
-
-
84857770146
-
Strong association between mRNA folding strength and protein abundance in Scerevisiae
-
Zur H, Tuller T.(2012).Strong association between mRNA folding strength and protein abundance in Scerevisiae.EMBO Rep.13: 272-277
-
(2012)
EMBO Rep
, vol.13
, pp. 272-277
-
-
Zur, H.1
Tuller, T.2
|