-
1
-
-
44249084514
-
Proteogenomics: needs and roles to be filled by proteomics in genome annotation
-
Ansong C., Purvine S.O., Adkins J.N., Lipton M.S., Smith R.D. Proteogenomics: needs and roles to be filled by proteomics in genome annotation. Brief Funct Genomic Proteomic 2008, 7(1):50-62.
-
(2008)
Brief Funct Genomic Proteomic
, vol.7
, Issue.1
, pp. 50-62
-
-
Ansong, C.1
Purvine, S.O.2
Adkins, J.N.3
Lipton, M.S.4
Smith, R.D.5
-
2
-
-
0029083530
-
The turning point in genome research
-
Boguski M.S. The turning point in genome research. Trends Biochem Sci 1995, 20(8):295-296.
-
(1995)
Trends Biochem Sci
, vol.20
, Issue.8
, pp. 295-296
-
-
Boguski, M.S.1
-
3
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
Mortazavi A., Williams B.A., McCue K., Schaeffer L., Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5(7):621-628.
-
(2008)
Nat Methods
, vol.5
, Issue.7
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
4
-
-
19944365069
-
Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform
-
Pan Q., et al. Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Mol Cell 2004, 16(6):929-941.
-
(2004)
Mol Cell
, vol.16
, Issue.6
, pp. 929-941
-
-
Pan, Q.1
-
5
-
-
0035166979
-
The comprehensive microbial resource
-
Peterson J.D., Umayam L.A., Dickinson T., Hickey E.K., White O. The comprehensive microbial resource. Nucleic Acids Res 2001, 29(1):123-125.
-
(2001)
Nucleic Acids Res
, vol.29
, Issue.1
, pp. 123-125
-
-
Peterson, J.D.1
Umayam, L.A.2
Dickinson, T.3
Hickey, E.K.4
White, O.5
-
6
-
-
0037561991
-
GenDB - an open source genome annotation system for prokaryote genomes
-
Meyer F., et al. GenDB - an open source genome annotation system for prokaryote genomes. Nucleic Acids Res 2003, 31(8):2187-2195.
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.8
, pp. 2187-2195
-
-
Meyer, F.1
-
7
-
-
23144467676
-
BASys: a web server for automated bacterial genome annotation
-
(Web Server issue)
-
Van Domselaar G.H., et al. BASys: a web server for automated bacterial genome annotation. Nucleic Acids Res 2005, 33:W455-W459. (Web Server issue).
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Van Domselaar, G.H.1
-
8
-
-
77955876447
-
Mass spectrometry-based proteomics in cell biology
-
Walther T.C., Mann M. Mass spectrometry-based proteomics in cell biology. J Cell Biol 2010, 190(4):491-500.
-
(2010)
J Cell Biol
, vol.190
, Issue.4
, pp. 491-500
-
-
Walther, T.C.1
Mann, M.2
-
9
-
-
34247254351
-
Novel peptide identification from tandem mass spectra using ESTs and sequence database compression
-
Edwards N.J. Novel peptide identification from tandem mass spectra using ESTs and sequence database compression. Mol Syst Biol 2007, 3:102.
-
(2007)
Mol Syst Biol
, vol.3
, pp. 102
-
-
Edwards, N.J.1
-
10
-
-
60849111947
-
A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data
-
Mo F., et al. A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data. BMC Bioinformatics 2008, 9:537.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 537
-
-
Mo, F.1
-
11
-
-
58549101102
-
Discovery and revision of Arabidopsis genes by proteogenomics
-
Castellana N.E., et al. Discovery and revision of Arabidopsis genes by proteogenomics. Proc Natl Acad Sci U S A 2008, 105(52):21034-21038.
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, Issue.52
, pp. 21034-21038
-
-
Castellana, N.E.1
-
12
-
-
33846884410
-
Improving gene annotation using peptide mass spectrometry
-
Tanner S., et al. Improving gene annotation using peptide mass spectrometry. Genome Res 2007, 17(2):231-239.
-
(2007)
Genome Res
, vol.17
, Issue.2
, pp. 231-239
-
-
Tanner, S.1
-
13
-
-
53549100731
-
Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations
-
Merrihew G.E., et al. Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations. Genome Res 2008, 18(10):1660-1669.
-
(2008)
Genome Res
, vol.18
, Issue.10
, pp. 1660-1669
-
-
Merrihew, G.E.1
-
14
-
-
0030751012
-
Identifying the major proteome components of Haemophilus influenzae type-strain NCTC 8143
-
Link A.J., Hays L.G., Carmack E.B., Yates J.R. Identifying the major proteome components of Haemophilus influenzae type-strain NCTC 8143. Electrophoresis 1997, 18(8):1314-1334.
-
(1997)
Electrophoresis
, vol.18
, Issue.8
, pp. 1314-1334
-
-
Link, A.J.1
Hays, L.G.2
Carmack, E.B.3
Yates, J.R.4
-
15
-
-
36549015654
-
Mass spectrometry-based prokaryote gene annotation
-
Ishino Y., Okada H., Ikeuchi M., Taniguchi H. Mass spectrometry-based prokaryote gene annotation. Proteomics 2007, 7(22):4053-4065.
-
(2007)
Proteomics
, vol.7
, Issue.22
, pp. 4053-4065
-
-
Ishino, Y.1
Okada, H.2
Ikeuchi, M.3
Taniguchi, H.4
-
16
-
-
77749282896
-
An integrated mass-spectrometry pipeline identifies novel protein coding-regions in the human genome
-
Bitton D.A., Smith D.L., Connolly Y., Scutt P.J., Miller C.J. An integrated mass-spectrometry pipeline identifies novel protein coding-regions in the human genome. PLoS One 2010, 5(1):e8949.
-
(2010)
PLoS One
, vol.5
, Issue.1
-
-
Bitton, D.A.1
Smith, D.L.2
Connolly, Y.3
Scutt, P.J.4
Miller, C.J.5
-
17
-
-
75549090999
-
The Mouse Genome Database: enhancements and updates
-
(Database issue) D586-592
-
Bult C.J., Kadin J.A., Richardson J.E., Blake J.A., Eppig J.T. The Mouse Genome Database: enhancements and updates. Nucleic Acids Res 2010, 38. (Database issue) D586-592.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Bult, C.J.1
Kadin, J.A.2
Richardson, J.E.3
Blake, J.A.4
Eppig, J.T.5
-
18
-
-
75549089335
-
Ensembl's 10th year
-
(Database issue) D557-562
-
Flicek P., et al. Ensembl's 10th year. Nucleic Acids Res 2010, 38. (Database issue) D557-562.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Flicek, P.1
-
19
-
-
79955555530
-
Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome
-
Brosch M. Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome. Genome Res 2011, 21(5):756-767.
-
(2011)
Genome Res
, vol.21
, Issue.5
, pp. 756-767
-
-
Brosch, M.1
-
20
-
-
58149178579
-
NCBI Reference Sequences: current status, policy and new initiatives
-
(Database issue)
-
Pruitt K.D., Tatusova T., Klimke W., Maglott D.R. NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res 2009, 37:D32-D36. (Database issue).
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Pruitt, K.D.1
Tatusova, T.2
Klimke, W.3
Maglott, D.R.4
-
21
-
-
3042818018
-
The International Protein Index: an integrated database for proteomics experiments
-
Kersey P.J., et al. The International Protein Index: an integrated database for proteomics experiments. Proteomics 2004, 4(7):1985-1988.
-
(2004)
Proteomics
, vol.4
, Issue.7
, pp. 1985-1988
-
-
Kersey, P.J.1
-
22
-
-
33846610475
-
Protein phosphorylation and expression profiling by Yin-yang multidimensional liquid chromatography (Yin-yang MDLC) mass spectrometry
-
Dai J., et al. Protein phosphorylation and expression profiling by Yin-yang multidimensional liquid chromatography (Yin-yang MDLC) mass spectrometry. J Proteome Res 2007, 6(1):250-262.
-
(2007)
J Proteome Res
, vol.6
, Issue.1
, pp. 250-262
-
-
Dai, J.1
-
23
-
-
70449392251
-
Effect of peptide-to-TiO2 beads ratio on phosphopeptide enrichment selectivity
-
Li Q.R., Ning Z.B., Tang J.S., Nie S., Zeng R. Effect of peptide-to-TiO2 beads ratio on phosphopeptide enrichment selectivity. J Proteome Res 2009, 8(11):5375-5381.
-
(2009)
J Proteome Res
, vol.8
, Issue.11
, pp. 5375-5381
-
-
Li, Q.R.1
Ning, Z.B.2
Tang, J.S.3
Nie, S.4
Zeng, R.5
-
24
-
-
75749101460
-
Phosphoproteomics for the masses
-
Grimsrud P.A., Swaney D.L., Wenger C.D., Beauchene N.A., Coon J.J. Phosphoproteomics for the masses. ACS Chem Biol 2010, 5(1):105-119.
-
(2010)
ACS Chem Biol
, vol.5
, Issue.1
, pp. 105-119
-
-
Grimsrud, P.A.1
Swaney, D.L.2
Wenger, C.D.3
Beauchene, N.A.4
Coon, J.J.5
-
25
-
-
3142702204
-
TANDEM: matching proteins with tandem mass spectra
-
Craig R., Beavis R.C. TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004, 20(9):1466-1467.
-
(2004)
Bioinformatics
, vol.20
, Issue.9
, pp. 1466-1467
-
-
Craig, R.1
Beavis, R.C.2
-
26
-
-
77449146854
-
Target-decoy search strategy for mass spectrometry-based proteomics
-
Elias J.E., Gygi S.P. Target-decoy search strategy for mass spectrometry-based proteomics. Methods Mol Biol 2010, 604:55-71.
-
(2010)
Methods Mol Biol
, vol.604
, pp. 55-71
-
-
Elias, J.E.1
Gygi, S.P.2
-
27
-
-
78650466243
-
A tissue-specific atlas of mouse protein phosphorylation and expression
-
Huttlin E.L., et al. A tissue-specific atlas of mouse protein phosphorylation and expression. Cell 2010, 143(7):1174-1189.
-
(2010)
Cell
, vol.143
, Issue.7
, pp. 1174-1189
-
-
Huttlin, E.L.1
-
28
-
-
33745054329
-
Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics
-
Fermin D., et al. Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics. Genome Biol 2006, 7(4):R35.
-
(2006)
Genome Biol
, vol.7
, Issue.4
-
-
Fermin, D.1
-
29
-
-
33747830848
-
AUGUSTUS: ab initio prediction of alternative transcripts
-
(Web Server issue)
-
Stanke M., et al. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res 2006, 34:W435-439. (Web Server issue).
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Stanke, M.1
-
30
-
-
77957237701
-
Proteogenomics to discover the full coding content of genomes: a computational perspective
-
Castellana N., Bafna V. Proteogenomics to discover the full coding content of genomes: a computational perspective. J Proteomics 2010, 73(11):2124-2135.
-
(2010)
J Proteomics
, vol.73
, Issue.11
, pp. 2124-2135
-
-
Castellana, N.1
Bafna, V.2
-
31
-
-
0034800374
-
InterProScan - an integration platform for the signature-recognition methods in InterPro
-
Zdobnov E.M., Apweiler R. InterProScan - an integration platform for the signature-recognition methods in InterPro. Bioinformatics 2001, 17(9):847-848.
-
(2001)
Bioinformatics
, vol.17
, Issue.9
, pp. 847-848
-
-
Zdobnov, E.M.1
Apweiler, R.2
-
32
-
-
75149160944
-
Concurrent quantification of proteome and phosphoproteome to reveal system-wide association of protein phosphorylation and gene expression
-
Wu Y.B., et al. Concurrent quantification of proteome and phosphoproteome to reveal system-wide association of protein phosphorylation and gene expression. Mol Cell Proteomics 2009, 8(12):2809-2826.
-
(2009)
Mol Cell Proteomics
, vol.8
, Issue.12
, pp. 2809-2826
-
-
Wu, Y.B.1
-
33
-
-
59449094729
-
Adipogenesis licensing and execution are disparately linked to cell proliferation
-
Guo W., et al. Adipogenesis licensing and execution are disparately linked to cell proliferation. Cell Res 2009, 19(2):216-223.
-
(2009)
Cell Res
, vol.19
, Issue.2
, pp. 216-223
-
-
Guo, W.1
-
34
-
-
80053951579
-
Large-scale phosphoproteome profiles comprehensive features of mouse embryonic stem cells
-
M110.001750
-
Li Q.R., et al. Large-scale phosphoproteome profiles comprehensive features of mouse embryonic stem cells. Mol Cell Proteomics 2010, M110.001750.
-
(2010)
Mol Cell Proteomics
-
-
Li, Q.R.1
-
35
-
-
77951770756
-
BEDTools: a flexible suite of utilities for comparing genomic features
-
Quinlan A.R., Hall I.M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010, 26(6):841-842.
-
(2010)
Bioinformatics
, vol.26
, Issue.6
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
|