-
1
-
-
33646483032
-
The abundance of short proteins in the mammalian proteome
-
Frith, M.C. et al. The abundance of short proteins in the mammalian proteome. PLoS Genet. 2, e52 (2006).
-
(2006)
PLoS Genet.
, vol.2
-
-
Frith, M.C.1
-
2
-
-
81055155799
-
Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes
-
Ingolia, N.T., Lareau, L.F. & Weissman, J.S. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147, 789-802 (2011).
-
(2011)
Cell
, vol.147
, pp. 789-802
-
-
Ingolia, N.T.1
Lareau, L.F.2
Weissman, J.S.3
-
3
-
-
79955575834
-
An upstream ORF with non-AUG start codon is translated in vivo but dispensable for translational control of GCN4 mRNA
-
Zhang, F. & Hinnebusch, A.G. An upstream ORF with non-AUG start codon is translated in vivo but dispensable for translational control of GCN4 mRNA. Nucleic Acids Res. 39, 3128-3140 (2011).
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 3128-3140
-
-
Zhang, F.1
Hinnebusch, A.G.2
-
4
-
-
66149118241
-
Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans
-
Calvo, S.E., Pagliarini, D.J. & Mootha, V.K. Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans. Proc. Natl. Acad. Sci. USA 106, 7507-7512 (2009).
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 7507-7512
-
-
Calvo, S.E.1
Pagliarini, D.J.2
Mootha, V.K.3
-
5
-
-
0025728532
-
A quantitative model for translational control of the GCN4 gene of Saccharomyces cerevisiae
-
Abastado, J.P., Miller, P.F. & Hinnebusch, A.G. A quantitative model for translational control of the GCN4 gene of Saccharomyces cerevisiae. New Biol. 3, 511-524 (1991).
-
(1991)
New Biol.
, vol.3
, pp. 511-524
-
-
Abastado, J.P.1
Miller, P.F.2
Hinnebusch, A.G.3
-
6
-
-
0023054773
-
Bifunctional messenger RNAs in eukaryotes
-
Kozak, M. Bifunctional messenger RNAs in eukaryotes. Cell 47, 481-483 (1986).
-
(1986)
Cell
, vol.47
, pp. 481-483
-
-
Kozak, M.1
-
7
-
-
0028145741
-
The peptide product of a 5′ leader cistron in the β2 adrenergic receptor mRNA inhibits receptor synthesis
-
Parola, A.L. & Kobilka, B.K. The peptide product of a 5′ leader cistron in the β2 adrenergic receptor mRNA inhibits receptor synthesis. J. Biol. Chem. 269, 4497-4505 (1994).
-
(1994)
J. Biol. Chem.
, vol.269
, pp. 4497-4505
-
-
Parola, A.L.1
Kobilka, B.K.2
-
8
-
-
0023659507
-
The leader peptide of yeast gene CPA1 is essential for the translational repression of its expression
-
Werner, M., Feller, A. & Messenguy, F. The leader peptide of yeast gene CPA1 is essential for the translational repression of its expression. Cell 49, 805-813 (1987).
-
(1987)
Cell
, vol.49
, pp. 805-813
-
-
Werner, M.1
Feller, A.2
Messenguy, F.3
-
9
-
-
38049115217
-
A dual function for a bacterial small RNA: SgrS performs base pairing-dependent regulation and encodes a functional polypeptide
-
Wadler, C.S. & Vanderpool, C.K. A dual function for a bacterial small RNA: SgrS performs base pairing-dependent regulation and encodes a functional polypeptide. Proc. Natl. Acad. Sci. USA 104, 20454-20459 (2007).
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 20454-20459
-
-
Wadler, C.S.1
Vanderpool, C.K.2
-
10
-
-
0019410218
-
Identification of the SV40 agnogene product: A DNA binding protein
-
Jay, G., Nomura, S., Anderson, C.W. & Khoury, G. Identification of the SV40 agnogene product: a DNA binding protein. Nature 8, 346-349 (1981).
-
(1981)
Nature
, vol.8
, pp. 346-349
-
-
Jay, G.1
Nomura, S.2
Anderson, C.W.3
Khoury, G.4
-
11
-
-
0036670296
-
The POLARIS gene of Arabidopsis encodes a predicted peptide required for correct root growth and leaf vascular patterning
-
Casson, S.A. et al. The POLARIS gene of Arabidopsis encodes a predicted peptide required for correct root growth and leaf vascular patterning. Plant Cell 14, 1705-1721 (2002).
-
(2002)
Plant Cell
, vol.14
, pp. 1705-1721
-
-
Casson, S.A.1
-
12
-
-
0037133258
-
Soybean ENOD40 encodes two peptides that bind to sucrose synthase
-
Rohrig, H., Schmidt, J., Miklashevichs, E., Schell, J. & John, M. Soybean ENOD40 encodes two peptides that bind to sucrose synthase. Proc. Natl. Acad. Sci. USA 99, 1915-1920 (2002).
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 1915-1920
-
-
Rohrig, H.1
Schmidt, J.2
Miklashevichs, E.3
Schell, J.4
John, M.5
-
13
-
-
33644641676
-
Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae
-
Kastenmayer, J.P. et al. Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae. Genome Res. 16, 365-373 (2006).
-
(2006)
Genome Res.
, vol.16
, pp. 365-373
-
-
Kastenmayer, J.P.1
-
14
-
-
43549119321
-
Silencing a candidate nematode effector gene corresponding to the tomato resistance gene Mi-1 leads to acquisition of virulence
-
Gleason, C.A., Liu, Q.L. & Williamson, V.M. Silencing a candidate nematode effector gene corresponding to the tomato resistance gene Mi-1 leads to acquisition of virulence. Mol. Plant Microbe Interact. 21, 576-585 (2008).
-
(2008)
Mol. Plant Microbe Interact.
, vol.21
, pp. 576-585
-
-
Gleason, C.A.1
Liu, Q.L.2
Williamson, V.M.3
-
15
-
-
34249021370
-
Peptides encoded by short ORFs control development and define a new eukaryotic gene family
-
Galindo, M.I., Pueyo, J.I., Fouix, S., Bishop, S.A. & Couso, J.P. Peptides encoded by short ORFs control development and define a new eukaryotic gene family. PLoS Biol. 5, e106 (2007).
-
(2007)
PLoS Biol.
, vol.5
-
-
Galindo, M.I.1
Pueyo, J.I.2
Fouix, S.3
Bishop, S.A.4
Couso, J.P.5
-
16
-
-
34447573973
-
Small peptide regulators of actin-based cell morphogenesis encoded by a polycistronic mRNA
-
Kondo, T. et al. Small peptide regulators of actin-based cell morphogenesis encoded by a polycistronic mRNA. Nat. Cell Biol. 9, 660-665 (2007).
-
(2007)
Nat. Cell Biol.
, vol.9
, pp. 660-665
-
-
Kondo, T.1
-
17
-
-
4243333514
-
A rescue factor abolishing neuronal cell death by a wide spectrum of familial Alzheimer′s disease genes and Aβ
-
Hashimoto, Y. et al. A rescue factor abolishing neuronal cell death by a wide spectrum of familial Alzheimer′s disease genes and Aβ. Proc. Natl. Acad. Sci. USA 98, 6336-6341 (2001).
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 6336-6341
-
-
Hashimoto, Y.1
-
18
-
-
56749151013
-
Small membrane proteins found by comparative genomics and ribosome binding site models
-
Hemm, M.R., Paul, B.J., Schneider, T.D., Storz, G. & Rudd, K.E. Small membrane proteins found by comparative genomics and ribosome binding site models. Mol. Microbiol. 70, 1487-1501 (2008).
-
(2008)
Mol. Microbiol.
, vol.70
, pp. 1487-1501
-
-
Hemm, M.R.1
Paul, B.J.2
Schneider, T.D.3
Storz, G.4
Rudd, K.E.5
-
19
-
-
34347392057
-
Diversity of translation start sites may define increased complexity of the human short ORFeome
-
Oyama, M. et al. Diversity of translation start sites may define increased complexity of the human short ORFeome. Mol. Cell. Proteomics 6, 1000-1006 (2007).
-
(2007)
Mol. Cell. Proteomics
, vol.6
, pp. 1000-1006
-
-
Oyama, M.1
-
20
-
-
77949821699
-
Expanding the dipeptidyl peptidase 4-regulated peptidome via an optimized peptidomics platform
-
Tinoco, A.D., Tagore, D.M. & Saghatelian, A. Expanding the dipeptidyl peptidase 4-regulated peptidome via an optimized peptidomics platform. J. Am. Chem. Soc. 132, 3819-3830 (2010).
-
(2010)
J. Am. Chem. Soc.
, vol.132
, pp. 3819-3830
-
-
Tinoco, A.D.1
Tagore, D.M.2
Saghatelian, A.3
-
21
-
-
0042140649
-
Peptidomics-based discovery of novel neuropeptides
-
Svensson, M., Skold, K., Svenningsson, P. & Andren, P.E. Peptidomics-based discovery of novel neuropeptides. J. Proteome Res. 2, 213-219 (2003).
-
(2003)
J. Proteome Res.
, vol.2
, pp. 213-219
-
-
Svensson, M.1
Skold, K.2
Svenningsson, P.3
Andren, P.E.4
-
22
-
-
57749105226
-
Peptidase substrates via global peptide profiling
-
Tagore, D.M. et al. Peptidase substrates via global peptide profiling. Nat. Chem. Biol. 5, 23-25 (2009).
-
(2009)
Nat. Chem. Biol.
, vol.5
, pp. 23-25
-
-
Tagore, D.M.1
-
23
-
-
77949786295
-
Value of using multiple proteases for large-scale mass spectrometry-based proteomics
-
Swaney, D.L., Wenger, C.D. & Coon, J.J. Value of using multiple proteases for large-scale mass spectrometry-based proteomics. J. Proteome Res. 9, 1323-1329 (2010).
-
(2010)
J. Proteome Res.
, vol.9
, pp. 1323-1329
-
-
Swaney, D.L.1
Wenger, C.D.2
Coon, J.J.3
-
24
-
-
0000857494
-
An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
-
Eng, J.K., McCormack, A.L. & Yates Iii, J.R. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5, 976-989 (1994).
-
(1994)
J. Am. Soc. Mass Spectrom.
, vol.5
, pp. 976-989
-
-
Eng, J.K.1
McCormack, A.L.2
Yates Iii, J.R.3
-
25
-
-
0029644596
-
Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database
-
Yates, J.R. III, Eng, J.K., McCormack, A.L. & Schieltz, D. Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal. Chem. 67, 1426-1436 (1995).
-
(1995)
Anal. Chem.
, vol.67
, pp. 1426-1436
-
-
Yates III, J.R.1
Eng, J.K.2
McCormack, A.L.3
Schieltz, D.4
-
26
-
-
40749099894
-
Pyruvate kinase M2 is a phosphotyrosine-binding protein
-
Christofk, H.R., Vander Heiden, M.G., Wu, N., Asara, J.M. & Cantley, L.C. Pyruvate kinase M2 is a phosphotyrosine-binding protein. Nature 452, 181-186 (2008).
-
(2008)
Nature
, vol.452
, pp. 181-186
-
-
Christofk, H.R.1
Vander Heiden, M.G.2
Wu, N.3
Asara, J.M.4
Cantley, L.C.5
-
27
-
-
80052978224
-
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
-
Cabili, M.N. et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 25, 1915-1927 (2011).
-
(1915)
Genes Dev.
, vol.25
, pp. 2011
-
-
Cabili, M.N.1
-
28
-
-
66349086264
-
Identifying novel constrained elements by exploiting biased substitution patterns
-
Garber, M. et al. Identifying novel constrained elements by exploiting biased substitution patterns. Bioinformatics 25, i54-i62 (2009).
-
(2009)
Bioinformatics
, vol.25
-
-
Garber, M.1
-
29
-
-
0022552131
-
Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes
-
Kozak, M. Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. Cell 44, 283-292 (1986).
-
(1986)
Cell
, vol.44
, pp. 283-292
-
-
Kozak, M.1
-
30
-
-
49549113643
-
Global mapping of the topography and magnitude of proteolytic events in apoptosis
-
Dix, M.M., Simon, G.M. & Cravatt, B.F. Global mapping of the topography and magnitude of proteolytic events in apoptosis. Cell 134, 679-691 (2008).
-
(2008)
Cell
, vol.134
, pp. 679-691
-
-
Dix, M.M.1
Simon, G.M.2
Cravatt, B.F.3
-
31
-
-
83055176451
-
Mapping intact protein isoforms in discovery mode using top-down proteomics
-
Tran, J.C. et al. Mapping intact protein isoforms in discovery mode using top-down proteomics. Nature 480, 254-258 (2011).
-
(2011)
Nature
, vol.480
, pp. 254-258
-
-
Tran, J.C.1
-
32
-
-
80054865417
-
A mass spectrometry-guided genome mining approach for natural product peptidogenomics
-
Kersten, R.D. et al. A mass spectrometry-guided genome mining approach for natural product peptidogenomics. Nat. Chem. Biol. 7, 794-802 (2011).
-
(2011)
Nat. Chem. Biol.
, vol.7
, pp. 794-802
-
-
Kersten, R.D.1
-
33
-
-
38349068918
-
Quantitative multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution
-
Keshishian, H., Addona, T., Burgess, M., Kuhn, E. & Carr, S.A. Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution. Mol. Cell. Proteomics 6, 2212-2229 (2007).
-
(2007)
Mol. Cell. Proteomics
, vol.6
, pp. 2212-2229
-
-
Keshishian, H.1
Addona, T.2
Burgess, M.3
Kuhn, E.4
Carr, S.A.5
-
34
-
-
55249096894
-
Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast
-
de Godoy, L.M. et al. Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 455, 1251-1254 (2008).
-
(2008)
Nature
, vol.455
, pp. 1251-1254
-
-
De Godoy, L.M.1
-
35
-
-
79956322553
-
Global quantification of mammalian gene expression control
-
Schwanhäusser, B. et al. Global quantification of mammalian gene expression control. Nature 473, 337-342 (2011).
-
(2011)
Nature
, vol.473
, pp. 337-342
-
-
Schwanhäusser, B.1
-
36
-
-
80855128111
-
The quantitative proteome of a human cell line
-
Beck, M. et al. The quantitative proteome of a human cell line. Mol. Syst. Biol. 7, 549 (2011).
-
(2011)
Mol. Syst. Biol.
, vol.7
, pp. 549
-
-
Beck, M.1
-
37
-
-
33846057724
-
NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins
-
Pruitt, K.D., Tatusova, T. & Maglott, D.R. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 35, D61-D65 (2007).
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Pruitt, K.D.1
Tatusova, T.2
Maglott, D.R.3
-
38
-
-
80052742721
-
Molecular mechanism of scanning and start codon selection in eukaryotes
-
Hinnebusch, A.G. Molecular mechanism of scanning and start codon selection in eukaryotes. Microbiol. Mol. Biol. Rev. 75, 434-467 (2011).
-
(2011)
Microbiol. Mol. Biol. Rev.
, vol.75
, pp. 434-467
-
-
Hinnebusch, A.G.1
-
39
-
-
3042521098
-
Improved prediction of signal peptides: SignalP 3.0
-
Bendtsen, J.D., Nielsen, H., von Heijne, G. & Brunak, S. Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol. 340, 783-795 (2004).
-
(2004)
J. Mol. Biol.
, vol.340
, pp. 783-795
-
-
Bendtsen, J.D.1
Nielsen, H.2
Von Heijne, G.3
Brunak, S.4
-
40
-
-
0345270035
-
Messenger RNA editing in mammals: New members of the APOBEC family seeking roles in the family business
-
Wedekind, J.E., Dance, G.S., Sowden, M.P. & Smith, H.C. Messenger RNA editing in mammals: new members of the APOBEC family seeking roles in the family business. Trends Genet. 19, 207-216 (2003).
-
(2003)
Trends Genet.
, vol.19
, pp. 207-216
-
-
Wedekind, J.E.1
Dance, G.S.2
Sowden, M.P.3
Smith, H.C.4
-
41
-
-
62249133709
-
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
-
Guttman, M. et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458, 223-227 (2009).
-
(2009)
Nature
, vol.458
, pp. 223-227
-
-
Guttman, M.1
-
42
-
-
60349120914
-
Long non-coding RNAs: Insights into functions
-
Mercer, T.R., Dinger, M.E. & Mattick, J.S. Long non-coding RNAs: insights into functions. Nat. Rev. Genet. 10, 155-159 (2009).
-
(2009)
Nat. Rev. Genet.
, vol.10
, pp. 155-159
-
-
Mercer, T.R.1
Dinger, M.E.2
Mattick, J.S.3
-
43
-
-
77952148742
-
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
-
Guttman, M. et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotechnol. 28, 503-510 (2010).
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 503-510
-
-
Guttman, M.1
-
44
-
-
67650921949
-
Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression
-
Khalil, A.M. et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl. Acad. Sci. USA 106, 11667-11672 (2009).
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 11667-11672
-
-
Khalil, A.M.1
-
45
-
-
79961212595
-
Improvements in proteomic metrics of low abundance proteins through proteome equalization using ProteoMiner prior to MudPIT
-
Fonslow, B.R. et al. Improvements in proteomic metrics of low abundance proteins through proteome equalization using ProteoMiner prior to MudPIT. J. Proteome Res. 10, 3690-3700 (2011).
-
(2011)
J. Proteome Res.
, vol.10
, pp. 3690-3700
-
-
Fonslow, B.R.1
-
46
-
-
41149110237
-
Electrostatic repulsion hydrophilic interaction chromatography for isocratic separation of charged solutes and selective isolation of phosphopeptides
-
Alpert, A.J. Electrostatic repulsion hydrophilic interaction chromatography for isocratic separation of charged solutes and selective isolation of phosphopeptides. Anal. Chem. 80, 62-76 (2008).
-
(2008)
Anal. Chem.
, vol.80
, pp. 62-76
-
-
Alpert, A.J.1
-
47
-
-
77954368187
-
Novel application of electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) in shotgun proteomics: Comprehensive profiling of rat kidney proteome
-
Hao, P. et al. Novel application of electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) in shotgun proteomics: comprehensive profiling of rat kidney proteome. J. Proteome Res. 9, 3520-3526 (2010).
-
(2010)
J. Proteome Res.
, vol.9
, pp. 3520-3526
-
-
Hao, P.1
-
48
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511-515 (2010).
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
-
49
-
-
77956340995
-
Comprehensive comparative analysis of strand-specific RNA sequencing methods
-
Levin, J.Z. et al. Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat. Methods 7, 709-715 (2010).
-
(2010)
Nat. Methods
, vol.7
, pp. 709-715
-
-
Levin, J.Z.1
-
50
-
-
65449136284
-
TopHat: Discovering splice junctions with RNA-Seq
-
Trapnell, C., Pachter, L. & Salzberg, S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
|