-
1
-
-
2942683220
-
Evolutionary rate depends on number of protein-protein interactions independently of gene expression level: Response
-
Bloom JD, Adami C. 2004. Evolutionary rate depends on number of protein-protein interactions independently of gene expression level: response. BMC Evol Biol. 4:14.
-
(2004)
BMC Evol Biol
, vol.4
, pp. 14
-
-
Bloom, J.D.1
Adami, C.2
-
2
-
-
64349094767
-
Tissue specificity and the human protein interaction network
-
Bossi A, Lehner B. 2009. Tissue specificity and the human protein interaction network. Mol Syst Biol. 5:260.
-
(2009)
Mol Syst Biol
, vol.5
, pp. 260
-
-
Bossi, A.1
Lehner, B.2
-
3
-
-
77249102545
-
Comparing models of evolution for ordered and disordered proteins
-
Brown CJ, Johnson AK, Daughdrill GW. 2010. Comparing models of evolution for ordered and disordered proteins. Mol Biol Evol. 27:609-621.
-
(2010)
Mol Biol Evol
, vol.27
, pp. 609-621
-
-
Brown, C.J.1
Johnson, A.K.2
Daughdrill, G.W.3
-
4
-
-
0036017388
-
Evolutionary rate heterogeneity in proteins with long disordered regions
-
DOI 10.1007/s00239-001-2309-6
-
Brown CJ, Takayama S, Campen AM, Vise P, Marshall TW, Oldfield CJ, Williams CJ, Dunker AK. 2002. Evolutionary rate heterogeneity in proteins with long disordered regions. J Mol Evol. 55:104-110. (Pubitemid 34634364)
-
(2002)
Journal of Molecular Evolution
, vol.55
, Issue.1
, pp. 104-110
-
-
Brown, C.J.1
Takayama, S.2
Campen, A.M.3
Vise, P.4
Marshall, T.W.5
Oldfield, C.J.6
Williams, C.J.7
Keith Dunker, A.8
-
5
-
-
77955012237
-
Gene family size conservation is a good indicator of evolutionary rates
-
Chen FC, Chen CJ, Li WH, Chuang TJ. 2010. Gene family size conservation is a good indicator of evolutionary rates. Mol Biol Evol. 27:1750-1758.
-
(2010)
Mol Biol Evol
, vol.27
, pp. 1750-1758
-
-
Chen, F.C.1
Chen, C.J.2
Li, W.H.3
Chuang, T.J.4
-
6
-
-
34548245376
-
The effects of multiple features of alternatively spliced exons on the K(A)/K(S) ratio test
-
Chen FC, Chuang TJ. 2006. The effects of multiple features of alternatively spliced exons on the K(A)/K(S) ratio test. BMC Bioinformatics. 7:259.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 259
-
-
Chen, F.C.1
Chuang, T.J.2
-
7
-
-
48249119102
-
Protein structure protection commits gene expression patterns
-
Chen J, Liang H, Fernandez A. 2008. Protein structure protection commits gene expression patterns. Genome Biol. 9:R107.
-
(2008)
Genome Biol
, vol.9
-
-
Chen, J.1
Liang, H.2
Fernandez, A.3
-
8
-
-
77958118308
-
Phosphorylated and non-phosphorylated serine and threonine residues evolve at different rates in mammals
-
Chen SC, Chen FC, Li WH. 2010. Phosphorylated and non-phosphorylated serine and threonine residues evolve at different rates in mammals. Mol Biol Evol. 27:2548-2554.
-
(2010)
Mol Biol Evol
, vol.27
, pp. 2548-2554
-
-
Chen, S.C.1
Chen, F.C.2
Li, W.H.3
-
9
-
-
70350469040
-
The relationship between the evolution of microRNA targets and the length of their UTRs
-
Cheng C, Bhardwaj N, Gerstein M. 2009. The relationship between the evolution of microRNA targets and the length of their UTRs. BMC Genomics. 10:431.
-
(2009)
BMC Genomics
, vol.10
, pp. 431
-
-
Cheng, C.1
Bhardwaj, N.2
Gerstein, M.3
-
10
-
-
0034383949
-
The regulation of protein function by multisite phosphorylation-a 25 year update
-
Cohen P. 2000. The regulation of protein function by multisite phosphorylation-a 25 year update. Trends Biochem Sci. 25:596-601.
-
(2000)
Trends Biochem Sci
, vol.25
, pp. 596-601
-
-
Cohen, P.1
-
11
-
-
38549092088
-
Phospho.ELM: A database of phosphorylation sites - Update 2008
-
DOI 10.1093/nar/gkm772
-
Diella F, Gould CM, Chica C, Via A, Gibson TJ. 2008. Phospho.ELM: a database of phosphorylation sites-update 2008. Nucleic Acids Res. 36:D240-D244. (Pubitemid 351149729)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.SUPPL. 1
-
-
Diella, F.1
Gould, C.M.2
Chica, C.3
Via, A.4
Gibson, T.J.5
-
12
-
-
26444621352
-
Why highly expressed proteins evolve slowly
-
DOI 10.1073/pnas.0504070102
-
Drummond DA, Bloom JD, Adami C, Wilke CO, Arnold FH. 2005. Why highly expressed proteins evolve slowly. Proc Natl Acad Sci USA. 102:14338-14343. (Pubitemid 41429699)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.40
, pp. 14338-14343
-
-
Drummond, D.A.1
Bloom, J.D.2
Adami, C.3
Wilke, C.O.4
Arnold, F.H.5
-
13
-
-
47549097539
-
Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution
-
DOI 10.1016/j.cell.2008.05.042, PII S0092867408007058
-
Drummond DA, Wilke CO. 2008. Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134:341-352. (Pubitemid 352010328)
-
(2008)
Cell
, vol.134
, Issue.2
, pp. 341-352
-
-
Drummond, D.A.1
Wilke, C.O.2
-
14
-
-
66749163093
-
Insights into the regulation of intrinsically disordered proteins in the human proteome by analyzing sequence and gene expression data
-
Edwards YJ, Lobley AE, Pentony MM, Jones DT. 2009. Insights into the regulation of intrinsically disordered proteins in the human proteome by analyzing sequence and gene expression data. Genome Biol. 10:R50.
-
(2009)
Genome Biol
, vol.10
-
-
Edwards, Y.J.1
Lobley, A.E.2
Pentony, M.M.3
Jones, D.T.4
-
15
-
-
73249153595
-
Human capacitance to dosage imbalance: Coping with inefficient selection
-
Fernandez A, Chen J. 2009. Human capacitance to dosage imbalance: coping with inefficient selection. Genome Res. 19:2185-2192.
-
(2009)
Genome Res
, vol.19
, pp. 2185-2192
-
-
Fernandez, A.1
Chen, J.2
-
16
-
-
2942678187
-
Evolutionary rate depends on number of protein-protein interactions independently of gene expression level
-
Fraser HB, Hirsh AE. 2004. Evolutionary rate depends on number of protein-protein interactions independently of gene expression level. BMC Evol Biol. 4:13.
-
(2004)
BMC Evol Biol
, vol.4
, pp. 13
-
-
Fraser, H.B.1
Hirsh, A.E.2
-
17
-
-
0037177560
-
Evolutionary rate in the protein interaction network
-
DOI 10.1126/science.1068696
-
Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW. 2002. Evolutionary rate in the protein interaction network. Science 296:750-752. (Pubitemid 34442006)
-
(2002)
Science
, vol.296
, Issue.5568
, pp. 750-752
-
-
Fraser, H.B.1
Hirsh, A.E.2
Steinmetz, L.M.3
Scharfe, C.4
Feldman, M.W.5
-
18
-
-
0032979568
-
Importance of long-range interactions in protein folding
-
DOI 10.1016/S0301-4622(99)00010-1, PII S0301462299000101
-
Gromiha MM, Selvaraj S. 1999. Importance of long-range interactions in protein folding. Biophys Chem. 77:49-68. (Pubitemid 29117295)
-
(1999)
Biophysical Chemistry
, vol.77
, Issue.1
, pp. 49-68
-
-
Gromiha, M.M.1
Selvaraj, S.2
-
19
-
-
1842464687
-
Inter-residue interactions in protein folding and stability
-
DOI 10.1016/j.pbiomolbio.2003.09.003, PII S0079610703000816
-
Gromiha MM, Selvaraj S. 2004. Inter-residue interactions in protein folding and stability. Prog Biophys Mol Biol. 86:235-277. (Pubitemid 39027234)
-
(2004)
Progress in Biophysics and Molecular Biology
, vol.86
, Issue.2
, pp. 235-277
-
-
Gromiha, M.M.1
Selvaraj, S.2
-
20
-
-
57149116929
-
Tight regulation of unstructured proteins: From transcript synthesis to protein degradation
-
DOI 10.1126/science.1163581
-
Gsponer J, Futschik ME, Teichmann SA, Babu MM. 2008. Tight regulation of unstructured proteins: from transcript synthesis to protein degradation. Science 322:1365-1368. (Pubitemid 352775246)
-
(2008)
Science
, vol.322
, Issue.5906
, pp. 1365-1368
-
-
Gsponer, J.1
Futschik, M.E.2
Teichmann, S.A.3
Babu, M.M.4
-
21
-
-
77955644289
-
Mammalian microRNAs predominantly act to decrease target mRNA levels
-
Guo H, Ingolia NT, Weissman JS, Bartel DP. 2010. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466:835-840.
-
(2010)
Nature
, vol.466
, pp. 835-840
-
-
Guo, H.1
Ingolia, N.T.2
Weissman, J.S.3
Bartel, D.P.4
-
22
-
-
31544433157
-
Serine/arginine-rich splicing factors belong to a class of intrinsically disordered proteins
-
DOI 10.1093/nar/gkj424
-
Haynes C, Iakoucheva LM. 2006. Serine/arginine-rich splicing factors belong to a class of intrinsically disordered proteins. Nucleic Acids Res. 34:305-312. (Pubitemid 43160053)
-
(2006)
Nucleic Acids Research
, vol.34
, Issue.1
, pp. 305-312
-
-
Haynes, C.1
Iakoucheva, L.M.2
-
23
-
-
33748074139
-
Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes
-
Haynes C, Oldfield CJ, Ji F, Klitgord N, Cusick ME, Radivojac P, Uversky VN, Vidal M, Iakoucheva LM. 2006. Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes. PLoS Comput Biol. 2:e100.
-
(2006)
PLoS Comput Biol
, vol.2
-
-
Haynes, C.1
Oldfield, C.J.2
Ji, F.3
Klitgord, N.4
Cusick, M.E.5
Radivojac, P.6
Uversky, V.N.7
Vidal, M.8
Iakoucheva, L.M.9
-
24
-
-
33747817940
-
Toward a molecular understanding of pleiotropy
-
DOI 10.1534/genetics.106.060269
-
He X, Zhang J. 2006. Toward a molecular understanding of pleiotropy. Genetics 173:1885-1891. (Pubitemid 44285670)
-
(2006)
Genetics
, vol.173
, Issue.4
, pp. 1885-1891
-
-
He, X.1
Zhang, J.2
-
25
-
-
2342473198
-
The importance of intrinsic disorder for protein phosphorylation
-
DOI 10.1093/nar/gkh253
-
Iakoucheva LM, Radivojac P, Brown CJ, O'Connor TR, Sikes JG, Obradovic Z, Dunker AK. 2004. The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Res. 32:1037-1049. (Pubitemid 38854704)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.3
, pp. 1037-1049
-
-
Iakoucheva, L.M.1
Radivojac, P.2
Brown, C.J.3
O'Connor, T.R.4
Sikes, J.G.5
Obradovic, Z.6
Dunker, A.K.7
-
27
-
-
41149119083
-
The role of disorder in interaction networks: A structural analysis
-
DOI 10.1038/msb.2008.16, PII MSB200816
-
Kim PM, Sboner A, Xia Y, Gerstein M. 2008. The role of disorder in interaction networks: a structural analysis. Mol Syst Biol. 4:179. (Pubitemid 351441045)
-
(2008)
Molecular Systems Biology
, vol.4
, pp. 179
-
-
Kim, P.M.1
Sboner, A.2
Xia, Y.3
Gerstein, M.4
-
28
-
-
34548339681
-
MicroRNA regulation of human protein-protein interaction network
-
DOI 10.1261/rna.634607
-
Liang H, Li WH. 2007. MicroRNA regulation of human protein protein interaction network. RNA 13:1402-1408. (Pubitemid 47347411)
-
(2007)
RNA
, vol.13
, Issue.9
, pp. 1402-1408
-
-
Liang, H.1
Li, W.-H.2
-
29
-
-
33749579409
-
Impacts of gene essentiality, expression pattern, and gene compactness on the evolutionary rate of mammalian proteins
-
DOI 10.1093/molbev/msl076
-
Liao BY, Scott NM, Zhang J. 2006. Impacts of gene essentiality, expression pattern, and gene compactness on the evolutionary rate of mammalian proteins. Mol Biol Evol. 23:2072-2080. (Pubitemid 44536815)
-
(2006)
Molecular Biology and Evolution
, vol.23
, Issue.11
, pp. 2072-2080
-
-
Liao, B.-Y.1
Scott, N.M.2
Zhang, J.3
-
30
-
-
77958489829
-
Impact of extracellularity on the evolutionary rate of mammalian proteins
-
Liao BY, Weng MP, Zhang J. 2010. Impact of extracellularity on the evolutionary rate of mammalian proteins. Genome Biol Evol. 2:39-43.
-
(2010)
Genome Biol Evol
, vol.2
, pp. 39-43
-
-
Liao, B.Y.1
Weng, M.P.2
Zhang, J.3
-
31
-
-
33750460897
-
Phosphorylation-dependent ubiquitination of cyclin D1 by the SCF(FBX4-alphaB crystallin) complex
-
DOI 10.1016/j.molcel.2006.09.007, PII S1097276506006356
-
Lin DI, Barbash O, Kumar KG, Weber JD, Harper JW, Klein-Szanto AJ, Rustgi A, Fuchs SY, Diehl JA. 2006. Phosphorylation-dependent ubiquitination of cyclin D1 by the SCF(FBX4-alphaB crystallin) complex. Mol Cell. 24:355-366. (Pubitemid 44647901)
-
(2006)
Molecular Cell
, vol.24
, Issue.3
, pp. 355-366
-
-
Lin, D.I.1
Barbash, O.2
Kumar, K.G.S.3
Weber, J.D.4
Harper, J.W.5
Klein-Szanto, A.J.6
Rustgi, A.7
Fuchs, S.Y.8
Diehl, J.A.9
-
32
-
-
64049086247
-
Topological and organizational properties of the products of house-keeping and tissue-specific genes in protein-protein interaction networks
-
Lin WH, Liu WC, Hwang MJ. 2009. Topological and organizational properties of the products of house-keeping and tissue-specific genes in protein-protein interaction networks. BMC Syst Biol. 3:32.
-
(2009)
BMC Syst Biol
, vol.3
, pp. 32
-
-
Lin, W.H.1
Liu, W.C.2
Hwang, M.J.3
-
33
-
-
33744961763
-
Intrinsic disorder in transcription factors
-
DOI 10.1021/bi0602718
-
Liu J, Perumal NB, Oldfield CJ, Su EW, Uversky VN, Dunker AK. 2006. Intrinsic disorder in transcription factors. Biochemistry 45:6873-6888. (Pubitemid 43856673)
-
(2006)
Biochemistry
, vol.45
, Issue.22
, pp. 6873-6888
-
-
Liu, J.1
Perumal, N.B.2
Oldfield, C.J.3
Su, E.W.4
Uversky, V.N.5
Dunker, A.K.6
-
34
-
-
33644909094
-
The evolutionary rate of a protein is influenced by features of the interacting partners
-
Makino T, Gojobori T. 2006. The evolutionary rate of a protein is influenced by features of the interacting partners. Mol Biol Evol. 23:784-789.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 784-789
-
-
Makino, T.1
Gojobori, T.2
-
35
-
-
60949085866
-
Evolutionary constraints on hub and non-hub proteins in human protein interaction network: Insight from protein connectivity and intrinsic disorder
-
Manna B, Bhattacharya T, Kahali B, Ghosh TC. 2009. Evolutionary constraints on hub and non-hub proteins in human protein interaction network: insight from protein connectivity and intrinsic disorder. Gene 434:50-55.
-
(2009)
Gene
, vol.434
, pp. 50-55
-
-
Manna, B.1
Bhattacharya, T.2
Kahali, B.3
Ghosh, T.C.4
-
36
-
-
36749042541
-
Critical assessment of methods of protein structure prediction - Round VII
-
DOI 10.1002/prot.21767
-
Moult J, Fidelis K, Kryshtafovych A, Rost B, Hubbard T, Tramontano A. 2007. Critical assessment of methods of protein structure prediction-Round VII. Proteins 69(Suppl 8):3-9. (Pubitemid 350210108)
-
(2007)
Proteins: Structure, Function and Genetics
, vol.69
, Issue.SUPPL. 8
, pp. 3-9
-
-
Moult, J.1
Fidelis, K.2
Kryshtafovych, A.3
Rost, B.4
Hubbard, T.5
Tramontano, A.6
-
37
-
-
33646182934
-
An integrated view of protein evolution
-
Pal C, Papp B, Lercher MJ. 2006. An integrated view of protein evolution. Nat Rev Genet. 7:337-348.
-
(2006)
Nat Rev Genet
, vol.7
, pp. 337-348
-
-
Pal, C.1
Papp, B.2
Lercher, M.J.3
-
38
-
-
77955223565
-
Expression breadth and expression abundance behave differently in correlations with evolutionary rates
-
Park SG, Choi SS. 2010. Expression breadth and expression abundance behave differently in correlations with evolutionary rates. BMC Evol Biol. 10:241.
-
(2010)
BMC Evol Biol
, vol.10
, pp. 241
-
-
Park, S.G.1
Choi, S.S.2
-
39
-
-
11144358198
-
A gene atlas of the mouse and human protein-encoding transcriptomes
-
DOI 10.1073/pnas.0400782101
-
Su AI, Wiltshire T, Batalov S, et al. (13 co-authors). 2004. A gene atlas of the mouse and human protein-encoding transcrip-tomes. Proc Natl Acad Sci USA. 101:6062-6067. (Pubitemid 38520528)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.16
, pp. 6062-6067
-
-
Su, A.I.1
Wiltshire, T.2
Batalov, S.3
Lapp, H.4
Ching, K.A.5
Block, D.6
Zhang, J.7
Soden, R.8
Hayakawa, M.9
Kreiman, G.10
Cooke, M.P.11
Walker, J.R.12
Hogenesch, J.B.13
-
40
-
-
25144472591
-
Showing your ID: Intrinsic disorder as an ID for recognition, regulation and cell signaling
-
DOI 10.1002/jmr.747
-
Uversky VN, Oldfield CJ, Dunker AK. 2005. Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling. J Mol Recognit. 18:343-384. (Pubitemid 41341287)
-
(2005)
Journal of Molecular Recognition
, vol.18
, Issue.5
, pp. 343-384
-
-
Uversky, V.N.1
Oldfield, C.J.2
Dunker, A.K.3
-
41
-
-
48249097986
-
Intrinsically disordered proteins in human diseases: Introducing the D2 concept
-
Uversky VN, Oldfield CJ, Dunker AK. 2008. Intrinsically disordered proteins in human diseases: introducing the D2 concept. Annu Rev Biophys. 37:215-246.
-
(2008)
Annu Rev Biophys
, vol.37
, pp. 215-246
-
-
Uversky, V.N.1
Oldfield, C.J.2
Dunker, A.K.3
-
42
-
-
67649635978
-
Intrinsic protein disorder and interaction promiscuity are widely associated with dosage sensitivity
-
Vavouri T, Semple JI, Garcia-Verdugo R, Lehner B. 2009. Intrinsic protein disorder and interaction promiscuity are widely associated with dosage sensitivity. Cell 138:198-208.
-
(2009)
Cell
, vol.138
, pp. 198-208
-
-
Vavouri, T.1
Semple, J.I.2
Garcia-Verdugo, R.3
Lehner, B.4
-
43
-
-
1542358787
-
Prediction and Functional Analysis of Native Disorder in Proteins from the Three Kingdoms of Life
-
DOI 10.1016/j.jmb.2004.02.002, PII S0022283604001482
-
Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF, Jones DT. 2004. Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol. 337:635-645. (Pubitemid 38326883)
-
(2004)
Journal of Molecular Biology
, vol.337
, Issue.3
, pp. 635-645
-
-
Ward, J.J.1
Sodhi, J.S.2
McGuffin, L.J.3
Buxton, B.F.4
Jones, D.T.5
-
44
-
-
34548076977
-
Assessing the conservation of mammalian gene expression using high-density exon arrays
-
DOI 10.1093/molbev/msm061
-
Xing Y, Ouyang Z, Kapur K, Scott MP, Wong WH. 2007. Assessing the conservation of mammalian gene expression using high-density exon arrays. Mol Biol Evol. 24:1283-1285. (Pubitemid 47343944)
-
(2007)
Molecular Biology and Evolution
, vol.24
, Issue.6
, pp. 1283-1285
-
-
Xing, Y.1
Ouyang, Z.2
Kapur, K.3
Scott, M.P.4
Wong, W.H.5
-
45
-
-
20144376345
-
Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification
-
DOI 10.1093/bioinformatics/bti042
-
Yanai I, Benjamin H, Shmoish M, et al. (12 co-authors). 2005. Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 21:650-659. (Pubitemid 40424791)
-
(2005)
Bioinformatics
, vol.21
, Issue.5
, pp. 650-659
-
-
Yanai, I.1
Benjamin, H.2
Shmoish, M.3
Chalifa-Caspi, V.4
Shklar, M.5
Ophir, R.6
Bar-Even, A.7
Horn-Saban, S.8
Safran, M.9
Domany, E.10
Lancet, D.11
Shmueli, O.12
-
46
-
-
77958577844
-
Impact of translational error-induced and error-free misfolding on the rate of protein evolution
-
Yang JR, Zhuang SM, Zhang J. 2010. Impact of translational error-induced and error-free misfolding on the rate of protein evolution. Mol Syst Biol. 6:421.
-
(2010)
Mol Syst Biol.
, vol.6
, pp. 421
-
-
Yang, J.R.1
Zhuang, S.M.2
Zhang, J.3
-
47
-
-
78049295254
-
Long-range interaction networks in the function and fidelity of poliovirus RNA-dependent RNA polymerase studied by nuclear magnetic resonance
-
Yang X, Welch JL, Arnold JJ, Boehr DD. 2010. Long-range interaction networks in the function and fidelity of poliovirus RNA-dependent RNA polymerase studied by nuclear magnetic resonance. Biochemistry 49:9361-9371.
-
(2010)
Biochemistry
, vol.49
, pp. 9361-9371
-
-
Yang, X.1
Welch, J.L.2
Arnold, J.J.3
Boehr, D.D.4
|