-
1
-
-
53849145298
-
Mass spectrometry for proteomics
-
Han, X., Aslanian, A., Yates, J. R., III, Mass spectrometry for proteomics. Curr. Opin. Chem. Biol. 2008, 12, 483-490.
-
(2008)
Curr. Opin. Chem. Biol.
, vol.12
, pp. 483-490
-
-
Han, X.1
Aslanian, A.2
Yates III, J.R.3
-
2
-
-
84864031015
-
PRIDE: quality control in a proteomics data repository
-
doi: 10.1093/database/bas004.
-
Csordas, A., Ovelleiro, D., Wang, R., Foster, J. M. et al., PRIDE: quality control in a proteomics data repository. Database 2012, 2012, doi: 10.1093/database/bas004.
-
(2012)
Database
, vol.2012
-
-
Csordas, A.1
Ovelleiro, D.2
Wang, R.3
Foster, J.M.4
-
3
-
-
84874762979
-
The Proteomics Identifications (PRIDE) database and associated tools: status in 2013
-
Vizcaino, J. A., Cote, R. G., Csordas, A., Dianes, J. A. et al., The Proteomics Identifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res. 2013, 41, D1063-D1069.
-
(2013)
Nucleic Acids Res.
, vol.41
-
-
Vizcaino, J.A.1
Cote, R.G.2
Csordas, A.3
Dianes, J.A.4
-
4
-
-
84872341102
-
Solving hard computational problems efficiently: asymptotic parametric complexity 3-coloring algorithm
-
Martín, H., Solving hard computational problems efficiently: asymptotic parametric complexity 3-coloring algorithm. PLoS One 2013, 8, e53437.
-
(2013)
PLoS One
, vol.8
-
-
Martín, H.1
-
5
-
-
84896764422
-
Toward the commoditization of translational genomic research: design and implementation features of the Galaxy genomic workbench
-
Lazarus, R., Taylor, J., Qiu, W., Nekrutenko, A., Toward the commoditization of translational genomic research: design and implementation features of the Galaxy genomic workbench. Summit on Translat. Bioinforma. 2008, 2008, 56-60.
-
(2008)
Summit on Translat. Bioinforma.
, vol.2008
, pp. 56-60
-
-
Lazarus, R.1
Taylor, J.2
Qiu, W.3
Nekrutenko, A.4
-
6
-
-
84862943903
-
Cramming more components onto integrated circuits, Reprinted from Electronics, volume 38, number 8, April 19, 1965, pp. 114 ff
-
Moore, G. E., Cramming more components onto integrated circuits, Reprinted from Electronics, volume 38, number 8, April 19, 1965, pp. 114 ff. IEEE Solid-State Circuits Soc. Newsl. 2006, 11, 33-35.
-
(2006)
IEEE Solid-State Circuits Soc. Newsl.
, vol.11
, pp. 33-35
-
-
Moore, G.E.1
-
7
-
-
84942018952
-
-
Springer, Berlin, Heidelberg
-
Missbach, M., Stelzel, J., Gardiner, C., Anderson, G., Tempes, M., SAP Cloud, Springer, Berlin, Heidelberg 2013, pp. 1-13.
-
(2013)
SAP Cloud
, pp. 1-13
-
-
Missbach, M.1
Stelzel, J.2
Gardiner, C.3
Anderson, G.4
Tempes, M.5
-
8
-
-
0036894068
-
Future of supercomputing
-
Oyanagi, Y., Future of supercomputing. J. Comput. Appl. Math. 2002, 149, 147-153.
-
(2002)
J. Comput. Appl. Math.
, vol.149
, pp. 147-153
-
-
Oyanagi, Y.1
-
9
-
-
80054028420
-
-
SuperStar Virgo, Singapore
-
Sadashiv, N., Kumar, S. M. D., 2011 6th International Conference on Computer Science and Education (ICCSE), SuperStar Virgo, Singapore 2011, pp. 477-482.
-
(2011)
2011 6th International Conference on Computer Science and Education (ICCSE)
, pp. 477-482
-
-
Sadashiv, N.1
Kumar, S.M.D.2
-
10
-
-
35148880815
-
Towards highly available and scalable high performance clusters
-
Boukerche, A., Al-Shaikh, R. A., Notare, M. S. M. A., Towards highly available and scalable high performance clusters. J. Comput. Syst. Sci. 2007, 73, 1240-1251.
-
(2007)
J. Comput. Syst. Sci.
, vol.73
, pp. 1240-1251
-
-
Boukerche, A.1
Al-Shaikh, R.A.2
Notare, M.S.M.A.3
-
11
-
-
0003982659
-
-
Elsevier, Morgan Kaufmann, San Francisco, California
-
Foster, I., Kesselman, C., The Grid 2: Blueprint for a New Computing Infrastructure, Elsevier, Morgan Kaufmann, San Francisco, California, 2003.
-
(2003)
The Grid 2: Blueprint for a New Computing Infrastructure
-
-
Foster, I.1
Kesselman, C.2
-
12
-
-
0033954256
-
The Protein Data Bank
-
Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G. et al., The Protein Data Bank. Nucleic Acids Res. 2000, 28, 235-242.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
-
13
-
-
0345059376
-
Announcing the worldwide Protein Data Bank
-
Berman, H., Henrick, K., Nakamura, H., Announcing the worldwide Protein Data Bank. Nat. Struct. Mol. Biol. 2003, 10, 980.
-
(2003)
Nat. Struct. Mol. Biol.
, vol.10
, pp. 980
-
-
Berman, H.1
Henrick, K.2
Nakamura, H.3
-
14
-
-
84876039482
-
Trendspotting in the Protein Data Bank
-
Berman, H. M., Coimbatore Narayanan, B., Costanzo, L. D., Dutta, S. et al., Trendspotting in the Protein Data Bank. FEBS Lett. 2013, 587, 1036-1045.
-
(2013)
FEBS Lett.
, vol.587
, pp. 1036-1045
-
-
Berman, H.M.1
Coimbatore Narayanan, B.2
Costanzo, L.D.3
Dutta, S.4
-
15
-
-
0031182215
-
The first years of the Protein Data Bank
-
Meyer, E. F., The first years of the Protein Data Bank. Protein Sci. 1997, 6, 1591-1597.
-
(1997)
Protein Sci.
, vol.6
, pp. 1591-1597
-
-
Meyer, E.F.1
-
16
-
-
50249097395
-
Proteopedia-a scientific "wiki" bridging the rift between three-dimensional structure and function of biomacromolecules
-
Hodis, E., Prilusky, J., Martz, E., Silman, I. et al., Proteopedia-a scientific "wiki" bridging the rift between three-dimensional structure and function of biomacromolecules. Genome Biol. 2008, 9, R121.
-
(2008)
Genome Biol.
, vol.9
-
-
Hodis, E.1
Prilusky, J.2
Martz, E.3
Silman, I.4
-
17
-
-
13444280419
-
PDB_TM: selection and membrane localization of transmembrane proteins in the Protein Data Bank
-
Tusnády, G. E., Dosztányi, Z., Simon, I., PDB_TM: selection and membrane localization of transmembrane proteins in the Protein Data Bank. Nucleic Acids Res. 2005, 33, D275-D278.
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Tusnády, G.E.1
Dosztányi, Z.2
Simon, I.3
-
18
-
-
1842424944
-
The need for a public proteomics repository
-
Prince, J. T., Carlson, M. W., Wang, R., Lu, P., Marcotte, E. M., The need for a public proteomics repository. Nat. Biotechnol. 2004, 22, 471-472.
-
(2004)
Nat. Biotechnol.
, vol.22
, pp. 471-472
-
-
Prince, J.T.1
Carlson, M.W.2
Wang, R.3
Lu, P.4
Marcotte, E.M.5
-
19
-
-
23944440436
-
Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories
-
Martens, L., Nesvizhskii, A. I., Hermjakob, H., Adamski, M. et al., Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories. Proteomics 2005, 5, 3501-3505.
-
(2005)
Proteomics
, vol.5
, pp. 3501-3505
-
-
Martens, L.1
Nesvizhskii, A.I.2
Hermjakob, H.3
Adamski, M.4
-
20
-
-
0033434080
-
Probability-based protein identification by searching sequence databases using mass spectrometry data
-
Perkins, D. N., Pappin, D. J., Creasy, D. M., Cottrell, J. S., Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20, 3551-3567.
-
(1999)
Electrophoresis
, vol.20
, pp. 3551-3567
-
-
Perkins, D.N.1
Pappin, D.J.2
Creasy, D.M.3
Cottrell, J.S.4
-
21
-
-
0037442649
-
A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes
-
Fenyö, D., Beavis, R. C., A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. Anal. Chem. 2003, 75, 768-774.
-
(2003)
Anal. Chem.
, vol.75
, pp. 768-774
-
-
Fenyö, D.1
Beavis, R.C.2
-
22
-
-
7044246160
-
Open mass spectrometry search algorithm
-
Geer, L. Y., Markey, S. P., Kowalak, J. A., Wagner, L. et al., Open mass spectrometry search algorithm. J. Proteome Res. 2004, 3, 958-964.
-
(2004)
J. Proteome Res.
, vol.3
, pp. 958-964
-
-
Geer, L.Y.1
Markey, S.P.2
Kowalak, J.A.3
Wagner, L.4
-
23
-
-
82755182013
-
Universal and confident phosphorylation site localization using phosphoRS
-
Taus, T., Köcher, T., Pichler, P., Paschke, C. et al., Universal and confident phosphorylation site localization using phosphoRS. J. Proteome Res. 2011, 10, 5354-5362.
-
(2011)
J. Proteome Res.
, vol.10
, pp. 5354-5362
-
-
Taus, T.1
Köcher, T.2
Pichler, P.3
Paschke, C.4
-
24
-
-
84896754701
-
Proteome discovery pipeline for mass spectrometry-based proteomics
-
Gough, E., Oh, C., He, J., Riley, C. P. et al., Proteome discovery pipeline for mass spectrometry-based proteomics. BMC Bioinformatics 2008, 9, P21.
-
(2008)
BMC Bioinformatics
, vol.9
-
-
Gough, E.1
Oh, C.2
He, J.3
Riley, C.P.4
-
25
-
-
26844556940
-
Parallel tandem: a program for parallel processing of tandem mass spectra using PVM or MPI and X!Tandem
-
Duncan, D. T., Craig, R., Link, A. J., Parallel tandem: a program for parallel processing of tandem mass spectra using PVM or MPI and X!Tandem. J. Proteome Res. 2005, 4, 1842-1847.
-
(2005)
J. Proteome Res.
, vol.4
, pp. 1842-1847
-
-
Duncan, D.T.1
Craig, R.2
Link, A.J.3
-
26
-
-
34948899345
-
On the predictability of protein database search complexity and its relevance to optimization of distributed searches
-
Deciu, C., Sun, J., Wall, M. A., On the predictability of protein database search complexity and its relevance to optimization of distributed searches. J. Proteome Res. 2007, 6, 3443-3448.
-
(2007)
J. Proteome Res.
, vol.6
, pp. 3443-3448
-
-
Deciu, C.1
Sun, J.2
Wall, M.A.3
-
27
-
-
38649110750
-
X!!Tandem, an improved method for running X!Tandem in parallel on collections of commodity computers
-
Bjornson, R. D., Carriero, N. J., Colangelo, C., Shifman, M. et al., X!!Tandem, an improved method for running X!Tandem in parallel on collections of commodity computers. J. Proteome Res. 2008, 7, 293-299.
-
(2008)
J. Proteome Res.
, vol.7
, pp. 293-299
-
-
Bjornson, R.D.1
Carriero, N.J.2
Colangelo, C.3
Shifman, M.4
-
28
-
-
77449158584
-
De novo sequencing methods in proteomics
-
Hughes, C., Ma, B., Lajoie, G. A., De novo sequencing methods in proteomics. Methods Mol. Biol. 2010, 604, 105-121.
-
(2010)
Methods Mol. Biol.
, vol.604
, pp. 105-121
-
-
Hughes, C.1
Ma, B.2
Lajoie, G.A.3
-
29
-
-
80054760698
-
Algorithms for the de novo sequencing of peptides from tandem mass spectra
-
Allmer, J., Algorithms for the de novo sequencing of peptides from tandem mass spectra. Expert Rev. Proteomics 2011, 8, 645-657.
-
(2011)
Expert Rev. Proteomics
, vol.8
, pp. 645-657
-
-
Allmer, J.1
-
30
-
-
84870596405
-
Current methods for global proteome identification
-
Vaudel, M., Sickmann, A., Martens, L., Current methods for global proteome identification. Expert Rev. Proteomics 2012, 9, 519-532.
-
(2012)
Expert Rev. Proteomics
, vol.9
, pp. 519-532
-
-
Vaudel, M.1
Sickmann, A.2
Martens, L.3
-
31
-
-
33751068791
-
Performance evaluation of existing de novo sequencing algorithms
-
Pevtsov, S., Fedulova, I., Mirzaei, H., Buck, C., Zhang, X., Performance evaluation of existing de novo sequencing algorithms. J. Proteome Res. 2006, 5, 3018-3028.
-
(2006)
J. Proteome Res.
, vol.5
, pp. 3018-3028
-
-
Pevtsov, S.1
Fedulova, I.2
Mirzaei, H.3
Buck, C.4
Zhang, X.5
-
32
-
-
55249118638
-
DirecTag: accurate sequence tags from peptide MS/MS through statistical scoring
-
Tabb, D. L., Ma, Z.-Q., Martin, D. B., Ham, A.-J. L., Chambers, M. C., DirecTag: accurate sequence tags from peptide MS/MS through statistical scoring. J. Proteome Res. 2008, 7, 3838-3846.
-
(2008)
J. Proteome Res.
, vol.7
, pp. 3838-3846
-
-
Tabb, D.L.1
Ma, Z.-Q.2
Martin, D.B.3
Ham, A.-J.L.4
Chambers, M.C.5
-
33
-
-
77953889259
-
GPU computing for systems biology
-
Dematté, L., Prandi, D., GPU computing for systems biology. Brief. Bioinform. 2010, 11, 323-333.
-
(2010)
Brief. Bioinform.
, vol.11
, pp. 323-333
-
-
Dematté, L.1
Prandi, D.2
-
34
-
-
67650733220
-
Highly accelerated feature detection in proteomics data sets using modern graphics processing units
-
Hussong, R., Gregorius, B., Tholey, A., Hildebrandt, A., Highly accelerated feature detection in proteomics data sets using modern graphics processing units. Bioinformatics 2009, 25, 1937-1943.
-
(2009)
Bioinformatics
, vol.25
, pp. 1937-1943
-
-
Hussong, R.1
Gregorius, B.2
Tholey, A.3
Hildebrandt, A.4
-
35
-
-
79958191849
-
Fast parallel tandem mass spectral library searching using GPU hardware acceleration
-
Baumgardner, L. A., Shanmugam, A. K., Lam, H., Eng, J. K., Martin, D. B., Fast parallel tandem mass spectral library searching using GPU hardware acceleration. J. Proteome Res. 2011, 10, 2882-2888.
-
(2011)
J. Proteome Res.
, vol.10
, pp. 2882-2888
-
-
Baumgardner, L.A.1
Shanmugam, A.K.2
Lam, H.3
Eng, J.K.4
Martin, D.B.5
-
36
-
-
33947366516
-
Development and validation of a spectral library searching method for peptide identification from MS/MS
-
Lam, H., Deutsch, E. W., Eddes, J. S., Eng, J. K. et al., Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics 2007, 7, 655-667.
-
(2007)
Proteomics
, vol.7
, pp. 655-667
-
-
Lam, H.1
Deutsch, E.W.2
Eddes, J.S.3
Eng, J.K.4
-
37
-
-
84863624493
-
Tempest: GPU-CPU computing for high-throughput database spectral matching
-
Milloy, J. A., Faherty, B. K., Gerber, S. A., Tempest: GPU-CPU computing for high-throughput database spectral matching. J. Proteome Res. 2012, 11, 3581-3591.
-
(2012)
J. Proteome Res.
, vol.11
, pp. 3581-3591
-
-
Milloy, J.A.1
Faherty, B.K.2
Gerber, S.A.3
-
38
-
-
10644290213
-
ProteomeGRID: towards a high-throughput proteomics pipeline through opportunistic cluster image computing for two-dimensional gel electrophoresis
-
Dowsey, A. W., Dunn, M. J., Yang, G.-Z., ProteomeGRID: towards a high-throughput proteomics pipeline through opportunistic cluster image computing for two-dimensional gel electrophoresis. Proteomics 2004, 4, 3800-3812.
-
(2004)
Proteomics
, vol.4
, pp. 3800-3812
-
-
Dowsey, A.W.1
Dunn, M.J.2
Yang, G.-Z.3
-
39
-
-
84870375666
-
Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework
-
Lewis, S., Csordas, A., Killcoyne, S., Hermjakob, H. et al., Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework. BMC Bioinformatics 2012, 13, 324.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 324
-
-
Lewis, S.1
Csordas, A.2
Killcoyne, S.3
Hermjakob, H.4
-
40
-
-
77949732319
-
From proteome lists to biological impact-tools and strategies for the analysis of large MS data sets
-
Malik, R., Dulla, K., Nigg, E. A., Körner, R., From proteome lists to biological impact-tools and strategies for the analysis of large MS data sets. Proteomics 2010, 10, 1270-1283.
-
(2010)
Proteomics
, vol.10
, pp. 1270-1283
-
-
Malik, R.1
Dulla, K.2
Nigg, E.A.3
Körner, R.4
-
41
-
-
84865612411
-
Towards a human proteomics atlas
-
Gonnelli, G., Hulstaert, N., Degroeve, S., Martens, L., Towards a human proteomics atlas. Anal. Bioanal. Chem. 2012, 404, 1069-1077.
-
(2012)
Anal. Bioanal. Chem.
, vol.404
, pp. 1069-1077
-
-
Gonnelli, G.1
Hulstaert, N.2
Degroeve, S.3
Martens, L.4
-
42
-
-
84864474310
-
Reanalysis of phosphoproteomics data uncovers ADP-ribosylation sites
-
Matic, I., Ahel, I., Hay, R. T., Reanalysis of phosphoproteomics data uncovers ADP-ribosylation sites. Nat. Methods 2012, 9, 771-772.
-
(2012)
Nat. Methods
, vol.9
, pp. 771-772
-
-
Matic, I.1
Ahel, I.2
Hay, R.T.3
-
43
-
-
84867167595
-
Discovery of O-GlcNAc-modified proteins in published large-scale proteome data
-
Hahne, H., Moghaddas Gholami, A., Kuster, B., Discovery of O-GlcNAc-modified proteins in published large-scale proteome data. Mol. Cell. Proteomics 2012, 11, 843-850.
-
(2012)
Mol. Cell. Proteomics
, vol.11
, pp. 843-850
-
-
Hahne, H.1
Moghaddas Gholami, A.2
Kuster, B.3
-
45
-
-
77950673061
-
Practically useful: what the Rosetta protein modeling suite can do for you
-
Kaufmann, K. W., Lemmon, G. H., DeLuca, S. L., Sheehan, J. H., Meiler, J., Practically useful: what the Rosetta protein modeling suite can do for you. Biochemistry 2010, 49, 2987-2998.
-
(2010)
Biochemistry
, vol.49
, pp. 2987-2998
-
-
Kaufmann, K.W.1
Lemmon, G.H.2
DeLuca, S.L.3
Sheehan, J.H.4
Meiler, J.5
-
46
-
-
1642464839
-
-
Brand, L., Johnson, M. L. Academic Press, Salt Lake City, Utah
-
Rohl, C. A., Strauss, C. E. M., Misura, K. M. S., Baker, D., in: Brand, L., Johnson, M. L. (Eds.), Methods in Enzymology, Vol. 383, Academic Press, Salt Lake City, Utah, 2004, pp. 66-93.
-
(2004)
Methods in Enzymology
, vol.383
, pp. 66-93
-
-
Rohl, C.A.1
Strauss, C.E.M.2
Misura, K.M.S.3
Baker, D.4
-
47
-
-
0035782925
-
Review: protein secondary structure prediction continues to rise
-
Rost, B., Review: protein secondary structure prediction continues to rise. J. Struct. Biol. 2001, 134, 204-218.
-
(2001)
J. Struct. Biol.
, vol.134
, pp. 204-218
-
-
Rost, B.1
-
48
-
-
84869761071
-
The protein-folding problem, 50 years on
-
Dill, K. A., MacCallum, J. L., The protein-folding problem, 50 years on. Science 2012, 338, 1042-1046.
-
(2012)
Science
, vol.338
, pp. 1042-1046
-
-
Dill, K.A.1
MacCallum, J.L.2
-
49
-
-
84896755264
-
-
The NIST Definition of Cloud Computing n.d.
-
Mell, P., Grance, T., The NIST Definition of Cloud Computing n.d. http://csrc.nist.gov/publications/nistpubs/800-145/SP800-145.pdf.
-
-
-
Mell, P.1
Grance, T.2
-
50
-
-
67049134015
-
Low cost, scalable proteomics data analysis using Amazon's cloud computing services and open source search algorithms
-
Halligan, B. D., Geiger, J. F., Vallejos, A. K., Greene, A. S., Twigger, S. N., Low cost, scalable proteomics data analysis using Amazon's cloud computing services and open source search algorithms. J. Proteome Res. 2009, 8, 3148-3153.
-
(2009)
J. Proteome Res.
, vol.8
, pp. 3148-3153
-
-
Halligan, B.D.1
Geiger, J.F.2
Vallejos, A.K.3
Greene, A.S.4
Twigger, S.N.5
-
51
-
-
84867441831
-
Cloud parallel processing of tandem mass spectrometry based proteomics data
-
Mohammed, Y., Mostovenko, E., Henneman, A. A., Marissen, R. J. et al., Cloud parallel processing of tandem mass spectrometry based proteomics data. J. Proteome Res. 2012, 11, 5101-5108.
-
(2012)
J. Proteome Res.
, vol.11
, pp. 5101-5108
-
-
Mohammed, Y.1
Mostovenko, E.2
Henneman, A.A.3
Marissen, R.J.4
-
52
-
-
77949676526
-
A guided tour of the Trans-Proteomic Pipeline
-
Deutsch, E. W., Mendoza, L., Shteynberg, D., Farrah, T. et al., A guided tour of the Trans-Proteomic Pipeline. Proteomics 2010, 10, 1150-1159.
-
(2010)
Proteomics
, vol.10
, pp. 1150-1159
-
-
Deutsch, E.W.1
Mendoza, L.2
Shteynberg, D.3
Farrah, T.4
-
53
-
-
33747833111
-
Taverna: a tool for building and running workflows of services
-
Hull, D., Wolstencroft, K., Stevens, R., Goble, C. et al., Taverna: a tool for building and running workflows of services. Nucleic Acids Res. 2006, 34, W729-W732.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Hull, D.1
Wolstencroft, K.2
Stevens, R.3
Goble, C.4
-
54
-
-
84896760748
-
The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud
-
Wolstencroft, K., Haines, R., Fellows, D., Williams, A. et al., The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud. Nucleic Acids Res. 2013, 34, 729-732.
-
(2013)
Nucleic Acids Res.
, vol.34
, pp. 729-732
-
-
Wolstencroft, K.1
Haines, R.2
Fellows, D.3
Williams, A.4
-
55
-
-
84870926630
-
Cloud CPFP: a shotgun proteomics data analysis pipeline using cloud and high performance computing
-
Trudgian, D. C., Mirzaei, H., Cloud CPFP: a shotgun proteomics data analysis pipeline using cloud and high performance computing. J. Proteome Res. 2012, 11, 6282-6290.
-
(2012)
J. Proteome Res.
, vol.11
, pp. 6282-6290
-
-
Trudgian, D.C.1
Mirzaei, H.2
-
56
-
-
84893419172
-
ProteoCloud: a full-featured open source proteomics cloud computing pipeline
-
Muth, T., Peters, J., Blackburn, J., Rapp, E., Martens, L., ProteoCloud: a full-featured open source proteomics cloud computing pipeline. J. Proteomics 2013, 88, 104-108.
-
(2013)
J. Proteomics
, vol.88
, pp. 104-108
-
-
Muth, T.1
Peters, J.2
Blackburn, J.3
Rapp, E.4
Martens, L.5
-
57
-
-
27544511899
-
InsPecT: identification of posttranslationally modified peptides from tandem mass spectra
-
Tanner, S., Shu, H., Frank, A., Wang, L.-C. et al., InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Anal. Chem. 2005, 77, 4626-4639.
-
(2005)
Anal. Chem.
, vol.77
, pp. 4626-4639
-
-
Tanner, S.1
Shu, H.2
Frank, A.3
Wang, L.-C.4
-
58
-
-
13844319908
-
PepNovo: de novo peptide sequencing via probabilistic network modeling
-
Frank, A., Pevzner, P., PepNovo: de novo peptide sequencing via probabilistic network modeling. Anal. Chem. 2005, 77, 964-973.
-
(2005)
Anal. Chem.
, vol.77
, pp. 964-973
-
-
Frank, A.1
Pevzner, P.2
-
59
-
-
63549095080
-
QVALITY: non-parametric estimation of q-values and posterior error probabilities
-
Käll, L., Storey, J. D., Noble, W. S., QVALITY: non-parametric estimation of q-values and posterior error probabilities. Bioinformatics 2009, 25, 964-966.
-
(2009)
Bioinformatics
, vol.25
, pp. 964-966
-
-
Käll, L.1
Storey, J.D.2
Noble, W.S.3
-
60
-
-
84875147845
-
Cloud-based solution to identify statistically significant MS peaks differentiating sample categories
-
Ji, J., Ling, J., Jiang, H., Wen, Q. et al., Cloud-based solution to identify statistically significant MS peaks differentiating sample categories. BMC Res. Notes 2013, 6, 109.
-
(2013)
BMC Res. Notes
, vol.6
, pp. 109
-
-
Ji, J.1
Ling, J.2
Jiang, H.3
Wen, Q.4
-
61
-
-
0242653640
-
Clinical proteomics: written in blood
-
Liotta, L. A., Ferrari, M., Petricoin, E., Clinical proteomics: written in blood. Nature 2003, 425, 905-905.
-
(2003)
Nature
, vol.425
, pp. 905-905
-
-
Liotta, L.A.1
Ferrari, M.2
Petricoin, E.3
-
62
-
-
33746211196
-
OMICS-driven biomarker discovery in nutrition and health
-
Kussmann, M., Raymond, F., Affolter, M., OMICS-driven biomarker discovery in nutrition and health. J. Biotechnol. 2006, 124, 758-787.
-
(2006)
J. Biotechnol.
, vol.124
, pp. 758-787
-
-
Kussmann, M.1
Raymond, F.2
Affolter, M.3
-
63
-
-
0036523738
-
Biomarker discovery in urine by proteomics
-
Pang, J. X., Ginanni, N., Dongre, A. R., Hefta, S. A., Opiteck, G. J., Biomarker discovery in urine by proteomics. J. Proteome Res. 2002, 1, 161-169.
-
(2002)
J. Proteome Res.
, vol.1
, pp. 161-169
-
-
Pang, J.X.1
Ginanni, N.2
Dongre, A.R.3
Hefta, S.A.4
Opiteck, G.J.5
-
64
-
-
84880973546
-
Crowdsourcing for bioinformatics
-
Good, B. M., Su, A. I., Crowdsourcing for bioinformatics. Bioinformatics 2013, 29, 1925-1933.
-
(2013)
Bioinformatics
, vol.29
, pp. 1925-1933
-
-
Good, B.M.1
Su, A.I.2
-
65
-
-
84876692278
-
Crowdsourcing in proteomics: public resources lead to better experiments
-
Barsnes, H., Martens, L., Crowdsourcing in proteomics: public resources lead to better experiments. Amino Acids 2013, 44, 1129-1137.
-
(2013)
Amino Acids
, vol.44
, pp. 1129-1137
-
-
Barsnes, H.1
Martens, L.2
-
66
-
-
80455154956
-
Crystal structure of a monomeric retroviral protease solved by protein folding game players
-
Foldit Contenders Group, Foldit Void Crushers Group
-
Khatib, F., DiMaio, F., Foldit Contenders Group, Foldit Void Crushers Group et al., Crystal structure of a monomeric retroviral protease solved by protein folding game players. Nat. Struct. Mol. Biol. 2011, 18, 1175-1177.
-
(2011)
Nat. Struct. Mol. Biol.
, vol.18
, pp. 1175-1177
-
-
Khatib, F.1
DiMaio, F.2
-
67
-
-
84856723541
-
Increased Diels-Alderase activity through backbone remodeling guided by Foldit players
-
Eiben, C. B., Siegel, J. B., Bale, J. B., Cooper, S. et al., Increased Diels-Alderase activity through backbone remodeling guided by Foldit players. Nat. Biotechnol. 2012, 30, 190-192.
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 190-192
-
-
Eiben, C.B.1
Siegel, J.B.2
Bale, J.B.3
Cooper, S.4
-
68
-
-
77955491294
-
Predicting protein structures with a multiplayer online game
-
Cooper, S., Khatib, F., Treuille, A., Barbero, J. et al., Predicting protein structures with a multiplayer online game. Nature 2010, 466, 756-760.
-
(2010)
Nature
, vol.466
, pp. 756-760
-
-
Cooper, S.1
Khatib, F.2
Treuille, A.3
Barbero, J.4
-
69
-
-
85060036181
-
-
ACM, New York, NY, USA
-
Amdahl, G. M., Proceedings of the Spring Joint Computer Conference, April 18-20, 1967, ACM, New York, NY, USA 1967, pp. 483-485.
-
(1967)
Proceedings of the Spring Joint Computer Conference, April 18-20, 1967
, pp. 483-485
-
-
Amdahl, G.M.1
-
70
-
-
48249118853
-
Amdahl's law in the multicore era
-
Hill, M. D., Marty, M. R., Amdahl's law in the multicore era. Computer 2008, 41, 33-38.
-
(2008)
Computer
, vol.41
, pp. 33-38
-
-
Hill, M.D.1
Marty, M.R.2
-
71
-
-
33845951476
-
Parallel processing of large datasets from NanoLC-FTICR-MS measurements
-
Van der Burgt, Y. E. M., Taban, I. M., Konijnenburg, M., Biskup, M. et al., Parallel processing of large datasets from NanoLC-FTICR-MS measurements. J. Am. Soc. Mass Spectrom. 2007, 18, 152-161.
-
(2007)
J. Am. Soc. Mass Spectrom.
, vol.18
, pp. 152-161
-
-
Van der Burgt, Y.E.M.1
Taban, I.M.2
Konijnenburg, M.3
Biskup, M.4
-
72
-
-
84896745799
-
SoyProDB: a database for the identification of soybean seed proteins
-
Tavakolan, M., Alkharouf, N. W., Khan, F. H., Natarajan, S., SoyProDB: a database for the identification of soybean seed proteins. Bioinformation 2013, 9, 165-167.
-
(2013)
Bioinformation
, vol.9
, pp. 165-167
-
-
Tavakolan, M.1
Alkharouf, N.W.2
Khan, F.H.3
Natarajan, S.4
-
73
-
-
61949346123
-
EPIC-DB: a proteomics database for studying Apicomplexan organisms
-
Madrid-Aliste, C. J., Dybas, J. M., Angeletti, R. H., Weiss, L. M. et al., EPIC-DB: a proteomics database for studying Apicomplexan organisms. BMC Genomics 2009, 10, 38.
-
(2009)
BMC Genomics
, vol.10
, pp. 38
-
-
Madrid-Aliste, C.J.1
Dybas, J.M.2
Angeletti, R.H.3
Weiss, L.M.4
-
74
-
-
84894422156
-
Validation of the curation pipeline of UniCarb-DB: building a global glycan reference MS/MS repository
-
doi:pii: S1570-9639(13)00172-6.
-
Campbell, M. P., Nguyen-Khuong, T., Hayes, C. A., Flowers, S. A. et al., Validation of the curation pipeline of UniCarb-DB: building a global glycan reference MS/MS repository. Bio-chim. Biophys. Acta 2013, doi:pii: S1570-9639(13)00172-6.
-
(2013)
Bio-chim. Biophys. Acta
-
-
Campbell, M.P.1
Nguyen-Khuong, T.2
Hayes, C.A.3
Flowers, S.A.4
-
75
-
-
33644876912
-
The PeptideAtlas project
-
Desiere, F., Deutsch, E. W., King, N. L., Nesvizhskii, A. I. et al., The PeptideAtlas project. Nucleic Acids Res. 2006, 34, D655-D658.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Desiere, F.1
Deutsch, E.W.2
King, N.L.3
Nesvizhskii, A.I.4
-
76
-
-
43049127826
-
PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows
-
Deutsch, E. W., Lam, H., Aebersold, R., PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep. 2008, 9, 429-434.
-
(2008)
EMBO Rep.
, vol.9
, pp. 429-434
-
-
Deutsch, E.W.1
Lam, H.2
Aebersold, R.3
-
77
-
-
61649083057
-
BioMart-biological queries made easy
-
Smedley, D., Haider, S., Ballester, B., Holland, R. et al., BioMart-biological queries made easy. BMC Genomics 2009, 10, 22.
-
(2009)
BMC Genomics
, vol.10
, pp. 22
-
-
Smedley, D.1
Haider, S.2
Ballester, B.3
Holland, R.4
-
78
-
-
84855410433
-
BioMart: a data federation framework for large collaborative projects
-
bar038
-
Zhang, J., Haider, S., Baran, J., Cros, A. et al., BioMart: a data federation framework for large collaborative projects. Database 2011, 2011, bar038.
-
(2011)
Database
, vol.2011
-
-
Zhang, J.1
Haider, S.2
Baran, J.3
Cros, A.4
-
79
-
-
84858314394
-
BioMart: driving a paradigm change in biological data management
-
bar049
-
Kasprzyk, A., BioMart: driving a paradigm change in biological data management. Database 2011, 2011, bar049.
-
(2011)
Database
, vol.2011
-
-
Kasprzyk, A.1
-
80
-
-
84855386495
-
BioMart Central Portal: an open database network for the biological community
-
bar041
-
Guberman, J. M., Ai, J., Arnaiz, O., Baran, J. et al., BioMart Central Portal: an open database network for the biological community. Database 2011, 2011, bar041.
-
(2011)
Database
, vol.2011
-
-
Guberman, J.M.1
Ai, J.2
Arnaiz, O.3
Baran, J.4
-
81
-
-
27544446224
-
The International HapMap Project Web site
-
Thorisson, G. A., Smith, A. V., Krishnan, L., Stein, L. D., The International HapMap Project Web site. Genome Res. 2005, 15, 1592-1593.
-
(2005)
Genome Res.
, vol.15
, pp. 1592-1593
-
-
Thorisson, G.A.1
Smith, A.V.2
Krishnan, L.3
Stein, L.D.4
-
82
-
-
0346494826
-
WormBase: a multi-species resource for nematode biology and genomics
-
Harris, T. W., Chen, N., Cunningham, F., Tello-Ruiz, M. et al., WormBase: a multi-species resource for nematode biology and genomics. Nucleic Acids Res. 2004, 32, D411-D417.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Harris, T.W.1
Chen, N.2
Cunningham, F.3
Tello-Ruiz, M.4
-
83
-
-
79952201997
-
Gramene database: a hub for comparative plant genomics
-
Jaiswal, P., Gramene database: a hub for comparative plant genomics. Methods Mol. Biol. 2011, 678, 247-275.
-
(2011)
Methods Mol. Biol.
, vol.678
, pp. 247-275
-
-
Jaiswal, P.1
-
84
-
-
0347125228
-
dictyBase: a new Dictyostelium discoideum genome database
-
Kreppel, L., Fey, P., Gaudet, P., Just, E. et al., dictyBase: a new Dictyostelium discoideum genome database. Nucleic Acids Res. 2004, 32, D332-D333.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Kreppel, L.1
Fey, P.2
Gaudet, P.3
Just, E.4
-
85
-
-
84855731050
-
Ensembl BioMarts: a hub for data retrieval across taxonomic space
-
bar030
-
Kinsella, R. J., Kähäri, A., Haider, S., Zamora, J. et al., Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database 2011, 2011, bar030.
-
(2011)
Database
, vol.2011
-
-
Kinsella, R.J.1
Kähäri, A.2
Haider, S.3
Zamora, J.4
-
86
-
-
9144232912
-
UniProt: the Universal Protein knowledgebase
-
Apweiler, R., Bairoch, A., Wu, C. H., Barker, W. C. et al., UniProt: the Universal Protein knowledgebase. Nucleic Acids Res. 2004, 32, D115-D119.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Apweiler, R.1
Bairoch, A.2
Wu, C.H.3
Barker, W.C.4
|