-
1
-
-
0034303643
-
Molecular profiling of human cancer
-
Liotta, L. & Petricoin, E. Molecular profiling of human cancer. Nat. Rev. Genet. 1, 48-56 (2000).
-
(2000)
Nat. Rev. Genet
, vol.1
, pp. 48-56
-
-
Liotta, L.1
Petricoin, E.2
-
2
-
-
18244409687
-
Gene expression profiling predicts clinical outcome of breast cancer
-
van 't Veer, L.J. et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature 415, 530-536 (2002).
-
(2002)
Nature
, vol.415
, pp. 530-536
-
-
Van'T Veer, L.J.1
-
3
-
-
60849097255
-
Gene-expression signatures in breast cancer
-
Sotiriou, C. & Pusztai, L. Gene-expression signatures in breast cancer. N. Engl. J. Med. 360, 790-800 (2009).
-
(2009)
N. Engl. J. Med
, vol.360
, pp. 790-800
-
-
Sotiriou, C.1
Pusztai, L.2
-
4
-
-
58149182724
-
NCBI GEO: Archive for high-throughput functional genomic data
-
Barrett, T. et al. NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res. 37, D885-D890 (2009).
-
(2009)
Nucleic Acids Res
, vol.37
, pp. D885-D890
-
-
Barrett, T.1
-
5
-
-
84946040120
-
COSMIC: Exploring the world's knowledge of somatic mutations in human cancer
-
Forbes, S.A. et al. COSMIC: exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Res. 43, D805-D811 (2015).
-
(2015)
Nucleic Acids Res
, vol.43
, pp. D805-D811
-
-
Forbes, S.A.1
-
6
-
-
84884994218
-
The Cancer Genome Atlas Pan-Cancer analysis project
-
Cancer Genome Atlas Research Network
-
Cancer Genome Atlas Research Network, Weinstein, J.N. et al. The Cancer Genome Atlas Pan-Cancer analysis project. Nat. Genet. 45, 1113-1120 (2013).
-
(2013)
Nat. Genet
, vol.45
, pp. 1113-1120
-
-
Weinstein, J.N.1
-
7
-
-
20444460289
-
MicroRNA expression profiles classify human cancers
-
Lu, J. et al. MicroRNA expression profiles classify human cancers. Nature 435, 834-838 (2005).
-
(2005)
Nature
, vol.435
, pp. 834-838
-
-
Lu, J.1
-
8
-
-
60149091657
-
Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression
-
Sreekumar, A. et al. Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature 457, 910-914 (2009).
-
(2009)
Nature
, vol.457
, pp. 910-914
-
-
Sreekumar, A.1
-
9
-
-
0031822837
-
Tissue microarrays for high-throughput molecular profiling of tumor specimens
-
Kononen, J. et al. Tissue microarrays for high-throughput molecular profiling of tumor specimens. Nat. Med. 4, 844-847 (1998).
-
(1998)
Nat. Med
, vol.4
, pp. 844-847
-
-
Kononen, J.1
-
10
-
-
17844386055
-
Antibody arrays in cancer research
-
Haab, B.B. Antibody arrays in cancer research. Mol. Cell Proteomics 4, 377-383 (2005).
-
(2005)
Mol. Cell Proteomics
, vol.4
, pp. 377-383
-
-
Haab, B.B.1
-
11
-
-
77954523086
-
Options and considerations when selecting a quantitative proteomics strategy
-
Domon, B. & Aebersold, R. Options and considerations when selecting a quantitative proteomics strategy. Nat. Biotechnol. 28, 710-721 (2010).
-
(2010)
Nat. Biotechnol
, vol.28
, pp. 710-721
-
-
Domon, B.1
Aebersold, R.2
-
12
-
-
84861860481
-
Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: A new concept for consistent and accurate proteome analysis
-
O111016717
-
Gillet, L.C. et al. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol. Cell. Proteomics 11, O111.016717 (2012).
-
(2012)
Mol. Cell. Proteomics
, vol.11
-
-
Gillet, L.C.1
-
13
-
-
84876337044
-
Quantitative measurements of N-linked glycoproteins in human plasma by SWATH-MS
-
Liu, Y. et al. Quantitative measurements of N-linked glycoproteins in human plasma by SWATH-MS. Proteomics 13, 1247-1256 (2013).
-
(2013)
Proteomics
, vol.13
, pp. 1247-1256
-
-
Liu, Y.1
-
14
-
-
84888858053
-
Quantifying protein interaction dynamics by SWATH mass spectrometry: Application to the 14-3-3 system
-
Collins, B.C. et al. Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system. Nat. Methods 10, 1246-1253 (2013).
-
(2013)
Nat. Methods
, vol.10
, pp. 1246-1253
-
-
Collins, B.C.1
-
15
-
-
84866444879
-
Pressure cycling technology in systems biology
-
Powell, B.S., Lazarev, A.V., Carlson, G., Ivanov, A.R. & Rozak, D.A. Pressure cycling technology in systems biology. Methods Mol. Biol. 881, 27-62 (2012).
-
(2012)
Methods Mol. Biol
, vol.881
, pp. 27-62
-
-
Powell, B.S.1
Lazarev, A.V.2
Carlson, G.3
Ivanov, A.R.4
Rozak, D.A.5
-
16
-
-
53049107743
-
Application of pressurized solvents for ultrafast trypsin hydrolysis in proteomics: Proteomics on the fly
-
López-Ferrer, D. et al. Application of pressurized solvents for ultrafast trypsin hydrolysis in proteomics: proteomics on the fly. J. Proteome Res. 7, 3276-3281 (2008).
-
(2008)
J. Proteome Res
, vol.7
, pp. 3276-3281
-
-
López-Ferrer, D.1
-
17
-
-
84868327851
-
Large-scale quantitative assessment of different in-solution protein digestion protocols reveals superior cleavage efficiency of tandem Lys-C/trypsin proteolysis over trypsin digestion
-
Glatter, T. et al. Large-scale quantitative assessment of different in-solution protein digestion protocols reveals superior cleavage efficiency of tandem Lys-C/trypsin proteolysis over trypsin digestion. J. Proteome Res. 11, 5145-5156 (2012).
-
(2012)
J. Proteome Res
, vol.11
, pp. 5145-5156
-
-
Glatter, T.1
-
18
-
-
84898665956
-
OpenSWATH: Automated, targeted analysis of mass spectrometric data generated by data-independent acquisition
-
Röst, H. et al. OpenSWATH: Automated, targeted analysis of mass spectrometric data generated by data-independent acquisition. Nat. Biotechnol. 32, 219-223 (2014).
-
(2014)
Nat. Biotechnol
, vol.32
, pp. 219-223
-
-
Röst, H.1
-
19
-
-
84907030818
-
ALFQ: An R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data
-
Rosenberger, G., Ludwig, C., Rost, H.L., Aebersold, R. & Malmstrom, L. aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data. Bioinformatics 30, 2511-2513 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 2511-2513
-
-
Rosenberger, G.1
Ludwig, C.2
Rost, H.L.3
Aebersold, R.4
Malmstrom, L.5
-
20
-
-
68749094119
-
Full dynamic range proteome analysis of S. Cerevisiae by targeted proteomics
-
Picotti, P., Bodenmiller, B., Mueller, L.N., Domon, B. & Aebersold, R. Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell 138, 795-806 (2009).
-
(2009)
Cell
, vol.138
, pp. 795-806
-
-
Picotti, P.1
Bodenmiller, B.2
Mueller, L.N.3
Domon, B.4
Aebersold, R.5
-
21
-
-
80052264424
-
Current pathology keys of renal cell carcinoma
-
Algaba, F. et al. Current pathology keys of renal cell carcinoma. Eur. Urol. 60, 634-643 (2011).
-
(2011)
Eur. Urol
, vol.60
, pp. 634-643
-
-
Algaba, F.1
-
22
-
-
84900393064
-
Renal tumors: Diagnostic and prognostic biomarkers
-
Tan, P.H. et al. Renal tumors: diagnostic and prognostic biomarkers. Am. J. Surg. Pathol. 37, 1518-1531 (2013).
-
(2013)
Am. J. Surg. Pathol
, vol.37
, pp. 1518-1531
-
-
Tan, P.H.1
-
23
-
-
21744435622
-
Scoring proteomes with proteotypic peptide probes
-
Kuster, B., Schirle, M., Mallick, P. & Aebersold, R. Scoring proteomes with proteotypic peptide probes. Nat. Rev. Mol. Cell Biol. 6, 577-583 (2005).
-
(2005)
Nat. Rev. Mol. Cell Biol
, vol.6
, pp. 577-583
-
-
Kuster, B.1
Schirle, M.2
Mallick, P.3
Aebersold, R.4
-
24
-
-
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
-
25
-
-
84872685287
-
Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma
-
Wi͆niewski, J.R. et al. Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma. Mol. Syst. Biol. 8, 611 (2012).
-
(2012)
Mol. Syst. Biol
, vol.8
, pp. 611
-
-
Wis̈niewski, J.R.1
-
26
-
-
67650564834
-
Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma
-
Addona, T.A. et al. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat. Biotechnol. 27, 633-641 (2009).
-
(2009)
Nat. Biotechnol
, vol.27
, pp. 633-641
-
-
Addona, T.A.1
-
27
-
-
84887433583
-
Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories
-
't Hoen, P.A. et al. Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. Nat. Biotechnol. 31, 1015-1022 (2013).
-
(2013)
Nat. Biotechnol
, vol.31
, pp. 1015-1022
-
-
T'Hoen, P.A.1
-
28
-
-
84880384052
-
Targeted proteomics reveals strain-specific changes in the mouse insulin and central metabolic pathways after a sustained high-fat diet
-
Sabidó, E. et al. Targeted proteomics reveals strain-specific changes in the mouse insulin and central metabolic pathways after a sustained high-fat diet. Mol. Syst. Biol. 16, 681 (2013).
-
(2013)
Mol. Syst. Biol
, vol.16
, pp. 681
-
-
Sabidó, E.1
-
29
-
-
84860869167
-
Using iRT, a normalized retention time for more targeted measurement of peptides
-
Escher, C. et al. Using iRT, a normalized retention time for more targeted measurement of peptides. Proteomics 12, 1111-1121 (2012).
-
(2012)
Proteomics
, vol.12
, pp. 1111-1121
-
-
Escher, C.1
-
30
-
-
84857966803
-
Expanding the chemical cross-linking toolbox by the use of multiple proteases and enrichment by size exclusion chromatography
-
M111014126
-
Leitner, A. et al. Expanding the chemical cross-linking toolbox by the use of multiple proteases and enrichment by size exclusion chromatography. Mol. Cell. Proteomics 11, M111.014126 (2012).
-
(2012)
Mol. Cell. Proteomics
, vol.11
-
-
Leitner, A.1
-
31
-
-
33750979860
-
General framework for developing and evaluating database scoring algorithms using the TANDEM search engine
-
MacLean, B., Eng, J.K., Beavis, R.C. & McIntosh, M. General framework for developing and evaluating database scoring algorithms using the TANDEM search engine. Bioinformatics 22, 2830-2832 (2006).
-
(2006)
Bioinformatics
, vol.22
, pp. 2830-2832
-
-
Maclean, B.1
Eng, J.K.2
Beavis, R.C.3
McIntosh, M.4
-
32
-
-
7044246160
-
Open mass spectrometry search algorithm
-
Geer, L.Y. et al. Open mass spectrometry search algorithm. J. Proteome Res. 3, 958-964 (2004).
-
(2004)
J. Proteome Res
, vol.3
, pp. 958-964
-
-
Geer, L.Y.1
-
33
-
-
77949676526
-
A guided tour of the Trans-Proteomic Pipeline
-
Deutsch, E.W. et al. A guided tour of the Trans-Proteomic Pipeline. Proteomics 10, 1150-1159 (2010).
-
(2010)
Proteomics
, vol.10
, pp. 1150-1159
-
-
Deutsch, E.W.1
-
34
-
-
84922875582
-
IPortal: The Swiss Grid Proteomics Portal: Requirements and new features based on experience and usability considerations
-
Kunszt, P. et al. iPortal: the Swiss Grid Proteomics Portal: requirements and new features based on experience and usability considerations. Concurrency and Computation: Practice and Experience 27, 433-445 (2015).
-
(2015)
Concurrency and Computation: Practice and Experience
, vol.27
, pp. 433-445
-
-
Kunszt, P.1
-
35
-
-
54949129419
-
ProteoWizard: Open source software for rapid proteomics tools development
-
Kessner, D., Chambers, M., Burke, R., Agus, D. & Mallick, P. ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics 24, 2534-2536 (2008).
-
(2008)
Bioinformatics
, vol.24
, pp. 2534-2536
-
-
Kessner, D.1
Chambers, M.2
Burke, R.3
Agus, D.4
Mallick, P.5
-
36
-
-
42249108173
-
OpenMS: An open-source software framework for mass spectrometry
-
Sturm, M. et al. OpenMS: an open-source software framework for mass spectrometry. BMC Bioinformatics 9, 163 (2008).
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 163
-
-
Sturm, M.1
-
37
-
-
84874762979
-
The PRoteomics IDEntifications (PRIDE) database and associated tools: Status in 2013
-
Vizcaíno, J.A. et al. The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res. 41, D1063-D1069 (2013).
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D1063-D1069
-
-
Vizcaíno, J.A.1
-
38
-
-
11244346557
-
Variance stabilization applied to microarray data calibration and to the quantification of differential expression
-
Huber, W., von Heydebreck, A., Sultmann, H., Poustka, A. & Vingron, M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 18 (suppl. 1), S96-S104 (2002).
-
(2002)
Bioinformatics
, vol.18
, pp. S96-S104
-
-
Huber, W.1
Von Heydebreck, A.2
Sultmann, H.3
Poustka, A.4
Vingron, M.5
-
39
-
-
0037316303
-
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
-
Bolstad, B.M., Irizarry, R.A., Astrand, M. & Speed, T.P. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19, 185-193 (2003).
-
(2003)
Bioinformatics
, vol.19
, pp. 185-193
-
-
Bolstad, B.M.1
Irizarry, R.A.2
Astrand, M.3
Speed, T.P.4
|