-
1
-
-
27744567556
-
Interactome: gateway into systems biology
-
Cusick ME, Klitgord N, Vidal M, Hill DE, (2005) Interactome: gateway into systems biology. Hum Mol Genet 14 Spec No. 2: R171-181.
-
(2005)
Hum Mol Genet
, vol.14
, Issue.SPEC. 2
-
-
Cusick, M.E.1
Klitgord, N.2
Vidal, M.3
Hill, D.E.4
-
3
-
-
27144530248
-
Towards a proteome-scale map of the human protein-protein interaction network
-
Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, et al. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437: 1173-1178.
-
(2005)
Nature
, vol.437
, pp. 1173-1178
-
-
Rual, J.F.1
Venkatesan, K.2
Hao, T.3
Hirozane-Kishikawa, T.4
Dricot, A.5
-
4
-
-
78650373804
-
Network medicine: a network-based approach to human disease
-
Barabasi AL, Gulbahce N, Loscalzo J, (2011) Network medicine: a network-based approach to human disease. Nat Rev Genet 12: 56-68.
-
(2011)
Nat Rev Genet
, vol.12
, pp. 56-68
-
-
Barabasi, A.L.1
Gulbahce, N.2
Loscalzo, J.3
-
6
-
-
33645453254
-
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
-
Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440: 637-643.
-
(2006)
Nature
, vol.440
, pp. 637-643
-
-
Krogan, N.J.1
Cagney, G.2
Yu, H.3
Zhong, G.4
Guo, X.5
-
7
-
-
79952474742
-
Protein complexes are central in the yeast genetic landscape
-
Michaut M, Baryshnikova A, Costanzo M, Myers CL, Andrews BJ, et al. (2011) Protein complexes are central in the yeast genetic landscape. PLoS Comput Biol 7: e1001092.
-
(2011)
PLoS Comput Biol
, vol.7
-
-
Michaut, M.1
Baryshnikova, A.2
Costanzo, M.3
Myers, C.L.4
Andrews, B.J.5
-
8
-
-
75549091794
-
CORUM: the comprehensive resource of mammalian protein complexes-2009
-
Ruepp A, Waegele B, Lechner M, Brauner B, Dunger-Kaltenbach I, et al. (2010) CORUM: the comprehensive resource of mammalian protein complexes-2009. Nucleic Acids Res 38: D497-501.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Ruepp, A.1
Waegele, B.2
Lechner, M.3
Brauner, B.4
Dunger-Kaltenbach, I.5
-
9
-
-
84867742082
-
Community of protein complexes impacts disease association
-
Wang Q, Liu W, Ning S, Ye J, Huang T, et al. (2012) Community of protein complexes impacts disease association. Eur J Hum Genet 20: 1162-1167.
-
(2012)
Eur J Hum Genet
, vol.20
, pp. 1162-1167
-
-
Wang, Q.1
Liu, W.2
Ning, S.3
Ye, J.4
Huang, T.5
-
10
-
-
76749134818
-
Associating genes and protein complexes with disease via network propagation
-
Vanunu O, Magger O, Ruppin E, Shlomi T, Sharan R, (2010) Associating genes and protein complexes with disease via network propagation. PLoS Comput Biol 6: e1000641.
-
(2010)
PLoS Comput Biol
, vol.6
-
-
Vanunu, O.1
Magger, O.2
Ruppin, E.3
Shlomi, T.4
Sharan, R.5
-
11
-
-
84859611662
-
Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data
-
Ning K, Fermin D, Nesvizhskii AI, (2012) Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data. J Proteome Res 11: 2261-2271.
-
(2012)
J Proteome Res
, vol.11
, pp. 2261-2271
-
-
Ning, K.1
Fermin, D.2
Nesvizhskii, A.I.3
-
12
-
-
80855128254
-
Deep proteome and transcriptome mapping of a human cancer cell line
-
Nagaraj N, Wisniewski JR, Geiger T, Cox J, Kircher M, et al. (2011) Deep proteome and transcriptome mapping of a human cancer cell line. Mol Syst Biol 7: 548.
-
(2011)
Mol Syst Biol
, vol.7
, pp. 548
-
-
Nagaraj, N.1
Wisniewski, J.R.2
Geiger, T.3
Cox, J.4
Kircher, M.5
-
13
-
-
79956322553
-
Global quantification of mammalian gene expression control
-
Schwanhausser B, Busse D, Li N, Dittmar G, Schuchhardt J, et al. (2011) Global quantification of mammalian gene expression control. Nature 473: 337-342.
-
(2011)
Nature
, vol.473
, pp. 337-342
-
-
Schwanhausser, B.1
Busse, D.2
Li, N.3
Dittmar, G.4
Schuchhardt, J.5
-
14
-
-
78650642557
-
Defining the transcriptome and proteome in three functionally different human cell lines
-
Lundberg E, Fagerberg L, Klevebring D, Matic I, Geiger T, et al. (2010) Defining the transcriptome and proteome in three functionally different human cell lines. Mol Syst Biol 6: 450.
-
(2010)
Mol Syst Biol
, vol.6
, pp. 450
-
-
Lundberg, E.1
Fagerberg, L.2
Klevebring, D.3
Matic, I.4
Geiger, T.5
-
15
-
-
79959812980
-
Comparative analysis of proteome and transcriptome variation in mouse
-
Ghazalpour A, Bennett B, Petyuk VA, Orozco L, Hagopian R, et al. (2011) Comparative analysis of proteome and transcriptome variation in mouse. PLoS Genet 7: e1001393.
-
(2011)
PLoS Genet
, vol.7
-
-
Ghazalpour, A.1
Bennett, B.2
Petyuk, V.A.3
Orozco, L.4
Hagopian, R.5
-
16
-
-
72949089708
-
Global signatures of protein and mRNA expression levels
-
de Sousa Abreu R, Penalva LO, Marcotte EM, Vogel C, (2009) Global signatures of protein and mRNA expression levels. Mol Biosyst 5: 1512-1526.
-
(2009)
Mol Biosyst
, vol.5
, pp. 1512-1526
-
-
de Sousa Abreu, R.1
Penalva, L.O.2
Marcotte, E.M.3
Vogel, C.4
-
17
-
-
71149108056
-
Correlation of mRNA and protein in complex biological samples
-
Maier T, Guell M, Serrano L, (2009) Correlation of mRNA and protein in complex biological samples. FEBS Lett 583: 3966-3973.
-
(2009)
FEBS Lett
, vol.583
, pp. 3966-3973
-
-
Maier, T.1
Guell, M.2
Serrano, L.3
-
18
-
-
33845790070
-
Correlation of mRNA expression and protein abundance affected by multiple sequence features related to translational efficiency in Desulfovibrio vulgaris: a quantitative analysis
-
Nie L, Wu G, Zhang W, (2006) Correlation of mRNA expression and protein abundance affected by multiple sequence features related to translational efficiency in Desulfovibrio vulgaris: a quantitative analysis. Genetics 174: 2229-2243.
-
(2006)
Genetics
, vol.174
, pp. 2229-2243
-
-
Nie, L.1
Wu, G.2
Zhang, W.3
-
19
-
-
0037453060
-
Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae
-
Washburn MP, Koller A, Oshiro G, Ulaszek RR, Plouffe D, et al. (2003) Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 100: 3107-3112.
-
(2003)
Proc Natl Acad Sci U S A
, vol.100
, pp. 3107-3112
-
-
Washburn, M.P.1
Koller, A.2
Oshiro, G.3
Ulaszek, R.R.4
Plouffe, D.5
-
20
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B, (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621-628.
-
(2008)
Nat Methods
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
21
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28: 511-515.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.4
Kwan, G.5
-
22
-
-
79957842166
-
Computational methods for transcriptome annotation and quantification using RNA-seq
-
Garber M, Grabherr MG, Guttman M, Trapnell C, (2011) Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Methods 8: 469-477.
-
(2011)
Nat Methods
, vol.8
, pp. 469-477
-
-
Garber, M.1
Grabherr, M.G.2
Guttman, M.3
Trapnell, C.4
-
23
-
-
78751570979
-
RNA sequencing: advances, challenges and opportunities
-
Ozsolak F, Milos PM, (2011) RNA sequencing: advances, challenges and opportunities. Nat Rev Genet 12: 87-98.
-
(2011)
Nat Rev Genet
, vol.12
, pp. 87-98
-
-
Ozsolak, F.1
Milos, P.M.2
-
24
-
-
82355183893
-
Comparative analysis of human protein-coding and noncoding RNAs between brain and 10 mixed cell lines by RNA-Seq
-
Chen G, Yin K, Shi L, Fang Y, Qi Y, et al. (2011) Comparative analysis of human protein-coding and noncoding RNAs between brain and 10 mixed cell lines by RNA-Seq. PLoS One 6: e28318.
-
(2011)
PLoS One
, vol.6
-
-
Chen, G.1
Yin, K.2
Shi, L.3
Fang, Y.4
Qi, Y.5
-
25
-
-
84862914469
-
Overview of available methods for diverse RNA-Seq data analyses
-
Chen G, Wang C, Shi T, (2011) Overview of available methods for diverse RNA-Seq data analyses. Sci China Life Sci 54: 1121-1128.
-
(2011)
Sci China Life Sci
, vol.54
, pp. 1121-1128
-
-
Chen, G.1
Wang, C.2
Shi, T.3
-
26
-
-
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
-
27
-
-
47649124124
-
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome
-
Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, et al. (2008) A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321: 956-960.
-
(2008)
Science
, vol.321
, pp. 956-960
-
-
Sultan, M.1
Schulz, M.H.2
Richard, H.3
Magen, A.4
Klingenhoff, A.5
-
28
-
-
77957663917
-
Alternative expression analysis by RNA sequencing
-
Griffith M, Griffith OL, Mwenifumbo J, Goya R, Morrissy AS, et al. (2010) Alternative expression analysis by RNA sequencing. Nat Methods 7: 843-847.
-
(2010)
Nat Methods
, vol.7
, pp. 843-847
-
-
Griffith, M.1
Griffith, O.L.2
Mwenifumbo, J.3
Goya, R.4
Morrissy, A.S.5
-
29
-
-
80051567157
-
Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development
-
Pal S, Gupta R, Kim H, Wickramasinghe P, Baubet V, et al. (2011) Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development. Genome Res 21: 1260-1272.
-
(2011)
Genome Res
, vol.21
, pp. 1260-1272
-
-
Pal, S.1
Gupta, R.2
Kim, H.3
Wickramasinghe, P.4
Baubet, V.5
-
30
-
-
56549101959
-
Alternative isoform regulation in human tissue transcriptomes
-
Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, et al. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456: 470-476.
-
(2008)
Nature
, vol.456
, pp. 470-476
-
-
Wang, E.T.1
Sandberg, R.2
Luo, S.3
Khrebtukova, I.4
Zhang, L.5
-
31
-
-
84858221706
-
Ensembl 2012
-
Flicek P, Amode MR, Barrell D, Beal K, Brent S, et al. (2012) Ensembl 2012. Nucleic Acids Res 40: D84-90.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Flicek, P.1
Amode, M.R.2
Barrell, D.3
Beal, K.4
Brent, S.5
-
32
-
-
84865760395
-
GENCODE: the reference human genome annotation for The ENCODE Project
-
Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, et al. (2012) GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res 22: 1760-1774.
-
(2012)
Genome Res
, vol.22
, pp. 1760-1774
-
-
Harrow, J.1
Frankish, A.2
Gonzalez, J.M.3
Tapanari, E.4
Diekhans, M.5
-
33
-
-
84856528270
-
Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer
-
Hon GC, Hawkins RD, Caballero OL, Lo C, Lister R, et al. (2012) Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res 22: 246-258.
-
(2012)
Genome Res
, vol.22
, pp. 246-258
-
-
Hon, G.C.1
Hawkins, R.D.2
Caballero, O.L.3
Lo, C.4
Lister, R.5
-
34
-
-
79957822290
-
Characterizing the impact of smoking and lung cancer on the airway transcriptome using RNA-Seq
-
Beane J, Vick J, Schembri F, Anderlind C, Gower A, et al. (2011) Characterizing the impact of smoking and lung cancer on the airway transcriptome using RNA-Seq. Cancer Prev Res (Phila) 4: 803-817.
-
(2011)
Cancer Prev Res (Phila)
, vol.4
, pp. 803-817
-
-
Beane, J.1
Vick, J.2
Schembri, F.3
Anderlind, C.4
Gower, A.5
-
35
-
-
84862777104
-
RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings
-
Ren S, Peng Z, Mao JH, Yu Y, Yin C, et al. (2012) RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings. Cell Res 22: 806-821.
-
(2012)
Cell Res
, vol.22
, pp. 806-821
-
-
Ren, S.1
Peng, Z.2
Mao, J.H.3
Yu, Y.4
Yin, C.5
-
36
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead B, Trapnell C, Pop M, Salzberg SL, (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
-
(2009)
Genome Biol
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
37
-
-
79751531332
-
Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads
-
Turro E, Su SY, Goncalves A, Coin LJ, Richardson S, et al. (2011) Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads. Genome Biol 12: R13.
-
(2011)
Genome Biol
, vol.12
-
-
Turro, E.1
Su, S.Y.2
Goncalves, A.3
Coin, L.J.4
Richardson, S.5
-
38
-
-
83055192078
-
Differential expression in RNA-seq: a matter of depth
-
Tarazona S, Garcia-Alcalde F, Dopazo J, Ferrer A, Conesa A, (2011) Differential expression in RNA-seq: a matter of depth. Genome Res 21: 2213-2223.
-
(2011)
Genome Res
, vol.21
, pp. 2213-2223
-
-
Tarazona, S.1
Garcia-Alcalde, F.2
Dopazo, J.3
Ferrer, A.4
Conesa, A.5
-
39
-
-
0038168025
-
Mechanistic studies of human molybdopterin synthase reaction and characterization of mutants identified in group B patients of molybdenum cofactor deficiency
-
Leimkuhler S, Freuer A, Araujo JA, Rajagopalan KV, Mendel RR, (2003) Mechanistic studies of human molybdopterin synthase reaction and characterization of mutants identified in group B patients of molybdenum cofactor deficiency. J Biol Chem 278: 26127-26134.
-
(2003)
J Biol Chem
, vol.278
, pp. 26127-26134
-
-
Leimkuhler, S.1
Freuer, A.2
Araujo, J.A.3
Rajagopalan, K.V.4
Mendel, R.R.5
-
40
-
-
16844363315
-
Modularity and evolutionary constraint on proteins
-
Fraser HB, (2005) Modularity and evolutionary constraint on proteins. Nat Genet 37: 351-352.
-
(2005)
Nat Genet
, vol.37
, pp. 351-352
-
-
Fraser, H.B.1
-
41
-
-
33845875196
-
Relating three-dimensional structures to protein networks provides evolutionary insights
-
Kim PM, Lu LJ, Xia Y, Gerstein MB, (2006) Relating three-dimensional structures to protein networks provides evolutionary insights. Science 314: 1938-1941.
-
(2006)
Science
, vol.314
, pp. 1938-1941
-
-
Kim, P.M.1
Lu, L.J.2
Xia, Y.3
Gerstein, M.B.4
-
42
-
-
24944460598
-
Shelterin: the protein complex that shapes and safeguards human telomeres
-
de Lange T, (2005) Shelterin: the protein complex that shapes and safeguards human telomeres. Genes Dev 19: 2100-2110.
-
(2005)
Genes Dev
, vol.19
, pp. 2100-2110
-
-
de Lange, T.1
-
43
-
-
33947095027
-
A human phenome-interactome network of protein complexes implicated in genetic disorders
-
Lage K, Karlberg EO, Storling ZM, Olason PI, Pedersen AG, et al. (2007) A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol 25: 309-316.
-
(2007)
Nat Biotechnol
, vol.25
, pp. 309-316
-
-
Lage, K.1
Karlberg, E.O.2
Storling, Z.M.3
Olason, P.I.4
Pedersen, A.G.5
-
45
-
-
82455162834
-
Revealing the missing expressed genes beyond the human reference genome by RNA-Seq
-
Chen G, Li R, Shi L, Qi J, Hu P, et al. (2011) Revealing the missing expressed genes beyond the human reference genome by RNA-Seq. BMC Genomics 12: 590.
-
(2011)
BMC Genomics
, vol.12
, pp. 590
-
-
Chen, G.1
Li, R.2
Shi, L.3
Qi, J.4
Hu, P.5
-
46
-
-
84865757142
-
Landscape of transcription in human cells
-
Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, 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
-
47
-
-
84875418427
-
Incorporating the human gene annotations in different databases significantly improved transcriptomic and genetic analyses
-
Chen G, Wang C, Shi L, Qu X, Chen J, et al. (2013) Incorporating the human gene annotations in different databases significantly improved transcriptomic and genetic analyses. RNA 19: 479-489.
-
(2013)
RNA
, vol.19
, pp. 479-489
-
-
Chen, G.1
Wang, C.2
Shi, L.3
Qu, X.4
Chen, J.5
-
48
-
-
84880918628
-
Comprehensively identifying and characterizing the missing gene sequences in human reference genome with integrated analytic approaches
-
(Accepted)
-
Chen G, Wang C, Shi L, Tong W, Qu X, et al. (2013) Comprehensively identifying and characterizing the missing gene sequences in human reference genome with integrated analytic approaches. Hum Genet (Accepted).
-
(2013)
Hum Genet
-
-
Chen, G.1
Wang, C.2
Shi, L.3
Tong, W.4
Qu, X.5
|