-
1
-
-
84901599553
-
A draft map of the human proteome
-
Kim, M. S.; Pinto, S. M.; Getnet, D.; Nirujogi, R. S.; Manda, S. S.; Chaerkady, R.; Madugundu, A. K.; Kelkar, D. S.; Isserlin, R.; Jain, S.; Thomas, J. K.; Muthusamy, B.; Leal-Rojas, P.; Kumar, P.; Sahasrabuddhe, N. A.; Balakrishnan, L.; Advani, J.; George, B.; Renuse, S.; Selvan, L. D.; Patil, A. H.; Nanjappa, V.; Radhakrishnan, A.; Prasad, S.; Subbannayya, T.; Raju, R.; Kumar, M.; Sreenivasamurthy, S. K.; Marimuthu, A.; Sathe, G. J.; Chavan, S.; Datta, K. K.; Subbannayya, Y.; Sahu, A.; Yelamanchi, S. D.; Jayaram, S.; Rajagopalan, P.; Sharma, J.; Murthy, K. R.; Syed, N.; Goel, R.; Khan, A. A.; Ahmad, S.; Dey, G.; Mudgal, K.; Chatterjee, A.; Huang, T. C.; Zhong, J.; Wu, X.; Shaw, P. G.; Freed, D.; Zahari, M. S.; Mukherjee, K. K.; Shankar, S.; Mahadevan, A.; Lam, H.; Mitchell, C. J.; Shankar, S. K.; Satishchandra, P.; Schroeder, J. T.; Sirdeshmukh, R.; Maitra, A.; Leach, S. D.; Drake, C. G.; Halushka, M. K.; Prasad, T. S.; Hruban, R. H.; Kerr, C. L.; Bader, G. D.; Iacobuzio-Donahue, C. A.; Gowda, H.; Pandey, A. A draft map of the human proteome Nature 2014, 509, 575-581 10.1038/nature13302
-
(2014)
Nature
, vol.509
, pp. 575-581
-
-
Kim, M.S.1
Pinto, S.M.2
Getnet, D.3
Nirujogi, R.S.4
Manda, S.S.5
Chaerkady, R.6
Madugundu, A.K.7
Kelkar, D.S.8
Isserlin, R.9
Jain, S.10
Thomas, J.K.11
Muthusamy, B.12
Leal-Rojas, P.13
Kumar, P.14
Sahasrabuddhe, N.A.15
Balakrishnan, L.16
Advani, J.17
George, B.18
Renuse, S.19
Selvan, L.D.20
Patil, A.H.21
Nanjappa, V.22
Radhakrishnan, A.23
Prasad, S.24
Subbannayya, T.25
Raju, R.26
Kumar, M.27
Sreenivasamurthy, S.K.28
Marimuthu, A.29
Sathe, G.J.30
Chavan, S.31
Datta, K.K.32
Subbannayya, Y.33
Sahu, A.34
Yelamanchi, S.D.35
Jayaram, S.36
Rajagopalan, P.37
Sharma, J.38
Murthy, K.R.39
Syed, N.40
Goel, R.41
Khan, A.A.42
Ahmad, S.43
Dey, G.44
Mudgal, K.45
Chatterjee, A.46
Huang, T.C.47
Zhong, J.48
Wu, X.49
Shaw, P.G.50
Freed, D.51
Zahari, M.S.52
Mukherjee, K.K.53
Shankar, S.54
Mahadevan, A.55
Lam, H.56
Mitchell, C.J.57
Shankar, S.K.58
Satishchandra, P.59
Schroeder, J.T.60
Sirdeshmukh, R.61
Maitra, A.62
Leach, S.D.63
Drake, C.G.64
Halushka, M.K.65
Prasad, T.S.66
Hruban, R.H.67
Kerr, C.L.68
Bader, G.D.69
Iacobuzio-Donahue, C.A.70
Gowda, H.71
Pandey, A.72
more..
-
2
-
-
84901611036
-
Mass-spectrometry-based draft of the human proteome
-
Wilhelm, M.; Schlegl, J.; Hahne, H.; Gholami, A. M.; Lieberenz, M.; Savitski, M. M.; Ziegler, E.; Butzmann, L.; Gessulat, S.; Marx, H.; Mathieson, T.; Lemeer, S.; Schnatbaum, K.; Reimer, U.; Wenschuh, H.; Mollenhauer, M.; Slotta-Huspenina, J.; Boese, J. H.; Bantscheff, M.; Gerstmair, A.; Faerber, F.; Kuster, B. Mass-spectrometry-based draft of the human proteome Nature 2014, 509, 582-587 10.1038/nature13319
-
(2014)
Nature
, vol.509
, pp. 582-587
-
-
WIlhelm, M.1
Schlegl, J.2
Hahne, H.3
Gholami, A.M.4
Lieberenz, M.5
Savitski, M.M.6
Ziegler, E.7
Butzmann, L.8
Gessulat, S.9
Marx, H.10
Mathieson, T.11
Lemeer, S.12
Schnatbaum, K.13
Reimer, U.14
Wenschuh, H.15
Mollenhauer, M.16
Slotta-Huspenina, J.17
Boese, J.H.18
Bantscheff, M.19
Gerstmair, A.20
Faerber, F.21
Kuster, B.22
more..
-
3
-
-
84920269464
-
Proteomics. Tissue-based map of the human proteome
-
Uhlen, M.; Fagerberg, L.; Hallstrom, B. M.; Lindskog, C.; Oksvold, P.; Mardinoglu, A.; Sivertsson, A.; Kampf, C.; Sjostedt, E.; Asplund, A.; Olsson, I.; Edlund, K.; Lundberg, E.; Navani, S.; Szigyarto, C. A.; Odeberg, J.; Djureinovic, D.; Takanen, J. O.; Hober, S.; Alm, T.; Edqvist, P. H.; Berling, H.; Tegel, H.; Mulder, J.; Rockberg, J.; Nilsson, P.; Schwenk, J. M.; Hamsten, M.; von Feilitzen, K.; Forsberg, M.; Persson, L.; Johansson, F.; Zwahlen, M.; von Heijne, G.; Nielsen, J.; Ponten, F. Proteomics. Tissue-based map of the human proteome Science (Washington, DC, U. S.) 2015, 347, 1260419 10.1126/science.1260419
-
(2015)
Science (Washington, DC, U. S.)
, vol.347
, pp. 1260419
-
-
Uhlen, M.1
Fagerberg, L.2
Hallstrom, B.M.3
Lindskog, C.4
Oksvold, P.5
Mardinoglu, A.6
Sivertsson, A.7
Kampf, C.8
Sjostedt, E.9
Asplund, A.10
Olsson, I.11
Edlund, K.12
Lundberg, E.13
Navani, S.14
Szigyarto, C.A.15
Odeberg, J.16
Djureinovic, D.17
Takanen, J.O.18
Hober, S.19
Alm, T.20
Edqvist, P.H.21
Berling, H.22
Tegel, H.23
Mulder, J.24
Rockberg, J.25
Nilsson, P.26
Schwenk, J.M.27
Hamsten, M.28
Von Feilitzen, K.29
Forsberg, M.30
Persson, L.31
Johansson, F.32
Zwahlen, M.33
Von Heijne, G.34
Nielsen, J.35
Ponten, F.36
more..
-
4
-
-
84941060754
-
The neXtProt knowledgebase on human proteins: Current status
-
Gaudet, P.; Michel, P. A.; Zahn-Zabal, M.; Cusin, I.; Duek, P. D.; Evalet, O.; Gateau, A.; Gleizes, A.; Pereira, M.; Teixeira, D.; Zhang, Y.; Lane, L.; Bairoch, A. The neXtProt knowledgebase on human proteins: current status Nucleic Acids Res. 2015, 43, D764-770 10.1093/nar/gku1178
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. 764-770
-
-
Gaudet, P.1
Michel, P.A.2
Zahn-Zabal, M.3
Cusin, I.4
Duek, P.D.5
Evalet, O.6
Gateau, A.7
Gleizes, A.8
Pereira, M.9
Teixeira, D.10
Zhang, Y.11
Lane, L.12
Bairoch, A.13
-
5
-
-
84891818310
-
Metrics for the human proteome project 2013-2014 and strategies for finding missing proteins
-
Lane, L.; Bairoch, A.; Beavis, R. C.; Deutsch, E. W.; Gaudet, P.; Lundberg, E.; Omenn, G. S. Metrics for the human proteome project 2013-2014 and strategies for finding missing proteins J. Proteome Res. 2014, 13, 15-20 10.1021/pr401144x
-
(2014)
J. Proteome Res.
, vol.13
, pp. 15-20
-
-
Lane, L.1
Bairoch, A.2
Beavis, R.C.3
Deutsch, E.W.4
Gaudet, P.5
Lundberg, E.6
Omenn, G.S.7
-
6
-
-
84924359564
-
Prediction of a missing protein expression map in the context of the human proteome project
-
Guruceaga, E.; Sanchez Del Pino, M. M.; Corrales, F. J.; Segura, V. Prediction of a missing protein expression map in the context of the human proteome project J. Proteome Res. 2015, 14, 1350-1360 10.1021/pr500850u
-
(2015)
J. Proteome Res.
, vol.14
, pp. 1350-1360
-
-
Guruceaga, E.1
Sanchez Del Pino, M.M.2
Corrales, F.J.3
Segura, V.4
-
7
-
-
84891806707
-
Deciphering the human brain proteome: Characterization of the anterior temporal lobe and corpus callosum as part of the Chromosome 15-centric Human Proteome Project
-
Martins-de-Souza, D.; Carvalho, P. C.; Schmitt, A.; Junqueira, M.; Nogueira, F. C.; Turck, C. W.; Domont, G. B. Deciphering the human brain proteome: characterization of the anterior temporal lobe and corpus callosum as part of the Chromosome 15-centric Human Proteome Project J. Proteome Res. 2014, 13, 147-157 10.1021/pr4009157
-
(2014)
J. Proteome Res.
, vol.13
, pp. 147-157
-
-
Martins-de-Souza, D.1
Carvalho, P.C.2
Schmitt, A.3
Junqueira, M.4
Nogueira, F.C.5
Turck, C.W.6
Domont, G.B.7
-
8
-
-
84891792618
-
Proteogenomic analysis of human chromosome 9-encoded genes from human samples and lung cancer tissues
-
Ahn, J. M.; Kim, M. S.; Kim, Y. I.; Jeong, S. K.; Lee, H. J.; Lee, S. H.; Paik, Y. K.; Pandey, A.; Cho, J. Y. Proteogenomic analysis of human chromosome 9-encoded genes from human samples and lung cancer tissues J. Proteome Res. 2014, 13, 137-146 10.1021/pr400792p
-
(2014)
J. Proteome Res.
, vol.13
, pp. 137-146
-
-
Ahn, J.M.1
Kim, M.S.2
Kim, Y.I.3
Jeong, S.K.4
Lee, H.J.5
Lee, S.H.6
Paik, Y.K.7
Pandey, A.8
Cho, J.Y.9
-
9
-
-
84879390233
-
Identification of missing proteins in the neXtProt database and unregistered phosphopeptides in the PhosphoSitePlus database as part of the Chromosome-centric Human Proteome Project
-
Shiromizu, T.; Adachi, J.; Watanabe, S.; Murakami, T.; Kuga, T.; Muraoka, S.; Tomonaga, T. Identification of missing proteins in the neXtProt database and unregistered phosphopeptides in the PhosphoSitePlus database as part of the Chromosome-centric Human Proteome Project J. Proteome Res. 2013, 12, 2414-2421 10.1021/pr300825v
-
(2013)
J. Proteome Res.
, vol.12
, pp. 2414-2421
-
-
Shiromizu, T.1
Adachi, J.2
Watanabe, S.3
Murakami, T.4
Kuga, T.5
Muraoka, S.6
Tomonaga, T.7
-
10
-
-
84891765115
-
Systematic analysis of missing proteins provides clues to help define all of the protein-coding genes on human chromosome 1
-
Zhang, C.; Li, N.; Zhai, L.; Xu, S.; Liu, X.; Cui, Y.; Ma, J.; Han, M.; Jiang, J.; Yang, C.; Fan, F.; Li, L.; Qin, P.; Yu, Q.; Chang, C.; Su, N.; Zheng, J.; Zhang, T.; Wen, B.; Zhou, R.; Lin, L.; Lin, Z.; Zhou, B.; Zhang, Y.; Yan, G.; Liu, Y.; Yang, P.; Guo, K.; Gu, W.; Chen, Y.; Zhang, G.; He, Q. Y.; Wu, S.; Wang, T.; Shen, H.; Wang, Q.; Zhu, Y.; He, F.; Xu, P. Systematic analysis of missing proteins provides clues to help define all of the protein-coding genes on human chromosome 1 J. Proteome Res. 2014, 13, 114-125 10.1021/pr400900j
-
(2014)
J. Proteome Res.
, vol.13
, pp. 114-125
-
-
Zhang, C.1
Li, N.2
Zhai, L.3
Xu, S.4
Liu, X.5
Cui, Y.6
Ma, J.7
Han, M.8
Jiang, J.9
Yang, C.10
Fan, F.11
Li, L.12
Qin, P.13
Yu, Q.14
Chang, C.15
Su, N.16
Zheng, J.17
Zhang, T.18
Wen, B.19
Zhou, R.20
Lin, L.21
Lin, Z.22
Zhou, B.23
Zhang, Y.24
Yan, G.25
Liu, Y.26
Yang, P.27
Guo, K.28
Gu, W.29
Chen, Y.30
Zhang, G.31
He, Q.Y.32
Wu, S.33
Wang, T.34
Shen, H.35
Wang, Q.36
Zhu, Y.37
He, F.38
Xu, P.39
more..
-
11
-
-
84924931361
-
Found in translation: Functions and evolution of a recently discovered alternative proteome
-
Landry, C. R.; Zhong, X.; Nielly-Thibault, L.; Roucou, X. Found in translation: functions and evolution of a recently discovered alternative proteome Curr. Opin. Struct. Biol. 2015, 32, 74-80 10.1016/j.sbi.2015.02.017
-
(2015)
Curr. Opin. Struct. Biol.
, vol.32
, pp. 74-80
-
-
Landry, C.R.1
Zhong, X.2
Nielly-Thibault, L.3
Roucou, X.4
-
12
-
-
84891816492
-
Systematic analyses of the transcriptome, translatome, and proteome provide a global view and potential strategy for the C-HPP
-
Chang, C.; Li, L.; Zhang, C.; Wu, S.; Guo, K.; Zi, J.; Chen, Z.; Jiang, J.; Ma, J.; Yu, Q.; Fan, F.; Qin, P.; Han, M.; Su, N.; Chen, T.; Wang, K.; Zhai, L.; Zhang, T.; Ying, W.; Xu, Z.; Zhang, Y.; Liu, Y.; Liu, X.; Zhong, F.; Shen, H.; Wang, Q.; Hou, G.; Zhao, H.; Li, G.; Liu, S.; Gu, W.; Wang, G.; Wang, T.; Zhang, G.; Qian, X.; Li, N.; He, Q. Y.; Lin, L.; Yang, P.; Zhu, Y.; He, F.; Xu, P. Systematic analyses of the transcriptome, translatome, and proteome provide a global view and potential strategy for the C-HPP J. Proteome Res. 2014, 13, 38-49 10.1021/pr4009018
-
(2014)
J. Proteome Res.
, vol.13
, pp. 38-49
-
-
Chang, C.1
Li, L.2
Zhang, C.3
Wu, S.4
Guo, K.5
Zi, J.6
Chen, Z.7
Jiang, J.8
Ma, J.9
Yu, Q.10
Fan, F.11
Qin, P.12
Han, M.13
Su, N.14
Chen, T.15
Wang, K.16
Zhai, L.17
Zhang, T.18
Ying, W.19
Xu, Z.20
Zhang, Y.21
Liu, Y.22
Liu, X.23
Zhong, F.24
Shen, H.25
Wang, Q.26
Hou, G.27
Zhao, H.28
Li, G.29
Liu, S.30
Gu, W.31
Wang, G.32
Wang, T.33
Zhang, G.34
Qian, X.35
Li, N.36
He, Q.Y.37
Lin, L.38
Yang, P.39
Zhu, Y.40
He, F.41
Xu, P.42
more..
-
13
-
-
80855128111
-
The quantitative proteome of a human cell line
-
Beck, M.; Schmidt, A.; Malmstroem, J.; Claassen, M.; Ori, A.; Szymborska, A.; Herzog, F.; Rinner, O.; Ellenberg, J.; Aebersold, R. The quantitative proteome of a human cell line Mol. Syst. Biol. 2011, 7, 549 10.1038/msb.2011.82
-
(2011)
Mol. Syst. Biol.
, vol.7
, pp. 549
-
-
Beck, M.1
Schmidt, A.2
Malmstroem, J.3
Claassen, M.4
Ori, A.5
Szymborska, A.6
Herzog, F.7
Rinner, O.8
Ellenberg, J.9
Aebersold, R.10
-
14
-
-
10944249586
-
Hiding behind hydrophobicity: Transmembrane segments in mass spectrometry
-
Eichacker, L. A.; Granvogl, B.; Mirus, O.; Müller, B. C.; Miess, C.; Schleiff, E. Hiding behind hydrophobicity: transmembrane segments in mass spectrometry J. Biol. Chem. 2004, 279, 50915-50922 10.1074/jbc.M405875200
-
(2004)
J. Biol. Chem.
, vol.279
, pp. 50915-50922
-
-
Eichacker, L.A.1
Granvogl, B.2
Mirus, O.3
Müller, B.C.4
Miess, C.5
Schleiff, E.6
-
15
-
-
84911444179
-
Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes
-
Ezkurdia, I.; Juan, D.; Rodriguez, J. M.; Frankish, A.; Diekhans, M.; Harrow, J.; Vazquez, J.; Valencia, A.; Tress, M. L. Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes Hum. Mol. Genet. 2014, 23, 5866-5878 10.1093/hmg/ddu309
-
(2014)
Hum. Mol. Genet.
, vol.23
, pp. 5866-5878
-
-
Ezkurdia, I.1
Juan, D.2
Rodriguez, J.M.3
Frankish, A.4
Diekhans, M.5
Harrow, J.6
Vazquez, J.7
Valencia, A.8
Tress, M.L.9
-
16
-
-
84874092250
-
In-depth membrane proteomic study of breast cancer tissues for the generation of a chromosome-based protein list
-
Muraoka, S.; Kume, H.; Adachi, J.; Shiromizu, T.; Watanabe, S.; Masuda, T.; Ishihama, Y.; Tomonaga, T. In-depth membrane proteomic study of breast cancer tissues for the generation of a chromosome-based protein list J. Proteome Res. 2013, 12, 208-213 10.1021/pr300824m
-
(2013)
J. Proteome Res.
, vol.12
, pp. 208-213
-
-
Muraoka, S.1
Kume, H.2
Adachi, J.3
Shiromizu, T.4
Watanabe, S.5
Masuda, T.6
Ishihama, Y.7
Tomonaga, T.8
-
17
-
-
74049131716
-
High-throughput generation of selected reaction-monitoring assays for proteins and proteomes
-
Picotti, P.; Rinner, O.; Stallmach, R.; Dautel, F.; Farrah, T.; Domon, B.; Wenschuh, H.; Aebersold, R. High-throughput generation of selected reaction-monitoring assays for proteins and proteomes Nat. Methods 2010, 7, 43-46 10.1038/nmeth.1408
-
(2010)
Nat. Methods
, vol.7
, pp. 43-46
-
-
Picotti, P.1
Rinner, O.2
Stallmach, R.3
Dautel, F.4
Farrah, T.5
Domon, B.6
Wenschuh, H.7
Aebersold, R.8
-
18
-
-
84924144429
-
Challenges facing complete human proteome analysis
-
Iwasaki, M.; Ishihama, Y. Challenges facing complete human proteome analysis Chromatography 2014, 35, 73-80 10.15583/jpchrom.2014.013
-
(2014)
Chromatography
, vol.35
, pp. 73-80
-
-
Iwasaki, M.1
Ishihama, Y.2
-
19
-
-
84862660669
-
Recent advances in peptide separation by multidimensional liquid chromatography for proteome analysis
-
Di Palma, S.; Hennrich, M. L.; Heck, A. J. R.; Mohammed, S. Recent advances in peptide separation by multidimensional liquid chromatography for proteome analysis J. Proteomics 2012, 75, 3791-3813 10.1016/j.jprot.2012.04.033
-
(2012)
J. Proteomics
, vol.75
, pp. 3791-3813
-
-
Di Palma, S.1
Hennrich, M.L.2
Heck, A.J.R.3
Mohammed, S.4
-
20
-
-
31644438577
-
Large scale protein profiling by combination of protein fractionation and multidimensional protein identification technology (MudPIT)
-
Chen, E. I.; Hewel, J.; Felding-Habermann, B.; Yates, J. R., 3rd. Large scale protein profiling by combination of protein fractionation and multidimensional protein identification technology (MudPIT) Mol. Cell. Proteomics 2006, 5, 53-56 10.1074/mcp.T500013-MCP200
-
(2006)
Mol. Cell. Proteomics
, vol.5
, pp. 53-56
-
-
Chen, E.I.1
Hewel, J.2
Felding-Habermann, B.3
Yates, J.R.4
-
21
-
-
84859622404
-
Standard guidelines for the chromosome-centric human proteome project
-
Paik, Y. K.; Omenn, G. S.; Uhlen, M.; Hanash, S.; Marko-Varga, G.; Aebersold, R.; Bairoch, A.; Yamamoto, T.; Legrain, P.; Lee, H. J.; Na, K.; Jeong, S. K.; He, F.; Binz, P. A.; Nishimura, T.; Keown, P.; Baker, M. S.; Yoo, J. S.; Garin, J.; Archakov, A.; Bergeron, J.; Salekdeh, G. H.; Hancock, W. S. Standard guidelines for the chromosome-centric human proteome project J. Proteome Res. 2012, 11, 2005-2013 10.1021/pr200824a
-
(2012)
J. Proteome Res.
, vol.11
, pp. 2005-2013
-
-
Paik, Y.K.1
Omenn, G.S.2
Uhlen, M.3
Hanash, S.4
Marko-Varga, G.5
Aebersold, R.6
Bairoch, A.7
Yamamoto, T.8
Legrain, P.9
Lee, H.J.10
Na, K.11
Jeong, S.K.12
He, F.13
Binz, P.A.14
Nishimura, T.15
Keown, P.16
Baker, M.S.17
Yoo, J.S.18
Garin, J.19
Archakov, A.20
Bergeron, J.21
Salekdeh, G.H.22
Hancock, W.S.23
more..
-
22
-
-
84898739772
-
Screening of missing proteins in the human liver proteome by improved MRM-approach-based targeted proteomics
-
Chen, C.; Liu, X.; Zheng, W.; Zhang, L.; Yao, J.; Yang, P. Screening of missing proteins in the human liver proteome by improved MRM-approach-based targeted proteomics J. Proteome Res. 2014, 13, 1969-1978 10.1021/pr4010986
-
(2014)
J. Proteome Res.
, vol.13
, pp. 1969-1978
-
-
Chen, C.1
Liu, X.2
Zheng, W.3
Zhang, L.4
Yao, J.5
Yang, P.6
-
23
-
-
84891809959
-
Surfing transcriptomic landscapes. A step beyond the annotation of chromosome 16 proteome
-
Segura, V.; Medina-Aunon, J. A.; Mora, M. I.; Martinez-Bartolome, S.; Abian, J.; Aloria, K.; Antunez, O.; Arizmendi, J. M.; Azkargorta, M.; Barcelo-Batllori, S.; Beaskoetxea, J.; Bech-Serra, J. J.; Blanco, F.; Monteiro, M. B.; Caceres, D.; Canals, F.; Carrascal, M.; Casal, J. I.; Clemente, F.; Colome, N.; Dasilva, N.; Diaz, P.; Elortza, F.; Fernandez-Puente, P.; Fuentes, M.; Gallardo, O.; Gharbi, S. I.; Gil, C.; Gonzalez-Tejedo, C.; Hernaez, M. L.; Lombardia, M.; Lopez-Lucendo, M.; Marcilla, M.; Mato, J. M.; Mendes, M.; Oliveira, E.; Orera, I.; Pascual-Montano, A.; Prieto, G.; Ruiz-Romero, C.; Sanchez del Pino, M. M.; Tabas-Madrid, D.; Valero, M. L.; Vialas, V.; Villanueva, J.; Albar, J. P.; Corrales, F. J. Surfing transcriptomic landscapes. A step beyond the annotation of chromosome 16 proteome J. Proteome Res. 2014, 13, 158-172 10.1021/pr400721r
-
(2014)
J. Proteome Res.
, vol.13
, pp. 158-172
-
-
Segura, V.1
Medina-Aunon, J.A.2
Mora, M.I.3
Martinez-Bartolome, S.4
Abian, J.5
Aloria, K.6
Antunez, O.7
Arizmendi, J.M.8
Azkargorta, M.9
Barcelo-Batllori, S.10
Beaskoetxea, J.11
Bech-Serra, J.J.12
Blanco, F.13
Monteiro, M.B.14
Caceres, D.15
Canals, F.16
Carrascal, M.17
Casal, J.I.18
Clemente, F.19
Colome, N.20
Dasilva, N.21
Diaz, P.22
Elortza, F.23
Fernandez-Puente, P.24
Fuentes, M.25
Gallardo, O.26
Gharbi, S.I.27
Gil, C.28
Gonzalez-Tejedo, C.29
Hernaez, M.L.30
Lombardia, M.31
Lopez-Lucendo, M.32
Marcilla, M.33
Mato, J.M.34
Mendes, M.35
Oliveira, E.36
Orera, I.37
Pascual-Montano, A.38
Prieto, G.39
Ruiz-Romero, C.40
Sanchez Del Pino, M.M.41
Tabas-Madrid, D.42
Valero, M.L.43
Vialas, V.44
Villanueva, J.45
Albar, J.P.46
Corrales, F.J.47
more..
-
24
-
-
84941064833
-
Rapid high-pH reverse phase StageTip for sensitive small-scale membrane proteomic profiling
-
manuscript submitted.
-
Dimayacyac-Esleta, B. R. T.; Tsai, C.-F.; Kitata, R. B.; Lin, P.-Y.; Choong, W.-K.; Weng, S.-H.; Yang, P.-C.; Arco, S. D.; Sung, T.-Y.; Chen, Y.-J. Rapid high-pH reverse phase StageTip for sensitive small-scale membrane proteomic profiling. Anal. Chem. manuscript submitted.
-
Anal. Chem.
-
-
Dimayacyac-Esleta, B.R.T.1
Tsai, C.-F.2
Kitata, R.B.3
Lin, P.-Y.4
Choong, W.-K.5
Weng, S.-H.6
Yang, P.-C.7
Arco, S.D.8
Sung, T.-Y.9
Chen, Y.-J.10
-
25
-
-
55049129918
-
A multiplexed quantitative strategy for membrane proteomics: Opportunities for mining therapeutic targets for autosomal dominant polycystic kidney disease
-
Han, C. L.; Chien, C. W.; Chen, W. C.; Chen, Y. R.; Wu, C. P.; Li, H.; Chen, Y. J. A multiplexed quantitative strategy for membrane proteomics: opportunities for mining therapeutic targets for autosomal dominant polycystic kidney disease Mol. Cell. Proteomics 2008, 7, 1983-1997 10.1074/mcp.M800068-MCP200
-
(2008)
Mol. Cell. Proteomics
, vol.7
, pp. 1983-1997
-
-
Han, C.L.1
Chien, C.W.2
Chen, W.C.3
Chen, Y.R.4
Wu, C.P.5
Li, H.6
Chen, Y.J.7
-
26
-
-
34548183872
-
Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips
-
Rappsilber, J.; Mann, M.; Ishihama, Y. Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips Nat. Protoc. 2007, 2, 1896-1906 10.1038/nprot.2007.261
-
(2007)
Nat. Protoc.
, vol.2
, pp. 1896-1906
-
-
Rappsilber, J.1
Mann, M.2
Ishihama, Y.3
-
27
-
-
84891796097
-
ProteomeXchange provides globally coordinated proteomics data submission and dissemination
-
Vizcaino, J. A.; Deutsch, E. W.; Wang, R.; Csordas, A.; Reisinger, F.; Rios, D.; Dianes, J. A.; Sun, Z.; Farrah, T.; Bandeira, N.; Binz, P.-A.; Xenarios, I.; Eisenacher, M.; Mayer, G.; Gatto, L.; Campos, A.; Chalkley, R. J.; Kraus, H.-J.; Albar, J. P.; Martinez-Bartolome, S.; Apweiler, R.; Omenn, G. S.; Martens, L.; Jones, A. R.; Hermjakob, H. ProteomeXchange provides globally coordinated proteomics data submission and dissemination Nat. Biotechnol. 2014, 32, 223-226 10.1038/nbt.2839
-
(2014)
Nat. Biotechnol.
, vol.32
, pp. 223-226
-
-
Vizcaino, J.A.1
Deutsch, E.W.2
Wang, R.3
Csordas, A.4
Reisinger, F.5
Rios, D.6
Dianes, J.A.7
Sun, Z.8
Farrah, T.9
Bandeira, N.10
Binz, P.-A.11
Xenarios, I.12
Eisenacher, M.13
Mayer, G.14
Gatto, L.15
Campos, A.16
Chalkley, R.J.17
Kraus, H.-J.18
Albar, J.P.19
Martinez-Bartolome, S.20
Apweiler, R.21
Omenn, G.S.22
Martens, L.23
Jones, A.R.24
Hermjakob, H.25
more..
-
28
-
-
0033434080
-
Probability-based protein identification by searching sequence databases using mass spectrometry data
-
Perkins, D. N.; Pappin, D. J. C.; Creasy, D. M.; Cottrell, J. S. Probability-based protein identification by searching sequence databases using mass spectrometry data Electrophoresis 1999, 20, 3551-3567 10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2
-
(1999)
Electrophoresis
, vol.20
, pp. 3551-3567
-
-
Perkins, D.N.1
Pappin, D.J.C.2
Creasy, D.M.3
Cottrell, J.S.4
-
29
-
-
3142702204
-
TANDEM: Matching proteins with tandem mass spectra
-
Craig, R.; Beavis, R. C. TANDEM: matching proteins with tandem mass spectra Bioinformatics 2004, 20, 1466-1467 10.1093/bioinformatics/bth092
-
(2004)
Bioinformatics
, vol.20
, pp. 1466-1467
-
-
Craig, R.1
Beavis, R.C.2
-
30
-
-
84872371907
-
Comet: An open-source MS/MS sequence database search tool
-
Eng, J. K.; Jahan, T. A.; Hoopmann, M. R. Comet: an open-source MS/MS sequence database search tool Proteomics 2013, 13, 22-24 10.1002/pmic.201200439
-
(2013)
Proteomics
, vol.13
, pp. 22-24
-
-
Eng, J.K.1
Jahan, T.A.2
Hoopmann, M.R.3
-
31
-
-
84867345063
-
A cross-platform toolkit for mass spectrometry and proteomics
-
Chambers, M. C.; Maclean, B.; Burke, R.; Amodei, D.; Ruderman, D. L.; Neumann, S.; Gatto, L.; Fischer, B.; Pratt, B.; Egertson, J.; Hoff, K.; Kessner, D.; Tasman, N.; Shulman, N.; Frewen, B.; Baker, T. A.; Brusniak, M.-Y.; Paulse, C.; Creasy, D.; Flashner, L.; Kani, K.; Moulding, C.; Seymour, S. L.; Nuwaysir, L. M.; Lefebvre, B.; Kuhlmann, F.; Roark, J.; Rainer, P.; Detlev, S.; Hemenway, T.; Huhmer, A.; Langridge, J.; Connolly, B.; Chadick, T.; Holly, K.; Eckels, J.; Deutsch, E. W.; Moritz, R. L.; Katz, J. E.; Agus, D. B.; MacCoss, M.; Tabb, D. L.; Mallick, P. A cross-platform toolkit for mass spectrometry and proteomics Nat. Biotechnol. 2012, 30, 918-920 10.1038/nbt.2377
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 918-920
-
-
Chambers, M.C.1
MacLean, B.2
Burke, R.3
Amodei, D.4
Ruderman, D.L.5
Neumann, S.6
Gatto, L.7
Fischer, B.8
Pratt, B.9
Egertson, J.10
Hoff, K.11
Kessner, D.12
Tasman, N.13
Shulman, N.14
Frewen, B.15
Baker, T.A.16
Brusniak, M.-Y.17
Paulse, C.18
Creasy, D.19
Flashner, L.20
Kani, K.21
Moulding, C.22
Seymour, S.L.23
Nuwaysir, L.M.24
Lefebvre, B.25
Kuhlmann, F.26
Roark, J.27
Rainer, P.28
Detlev, S.29
Hemenway, T.30
Huhmer, A.31
Langridge, J.32
Connolly, B.33
Chadick, T.34
Holly, K.35
Eckels, J.36
Deutsch, E.W.37
Moritz, R.L.38
Katz, J.E.39
Agus, D.B.40
MacCoss, M.41
Tabb, D.L.42
Mallick, P.43
more..
-
32
-
-
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 2008, 24, 2534-2536 10.1093/bioinformatics/btn323
-
(2008)
Bioinformatics
, vol.24
, pp. 2534-2536
-
-
Kessner, D.1
Chambers, M.2
Burke, R.3
Agus, D.4
Mallick, P.5
-
33
-
-
84923897273
-
PeptideShaker enables reanalysis of MS-derived proteomics data sets
-
Vaudel, M.; Burkhart, J. M.; Zahedi, R. P.; Oveland, E.; Berven, F. S.; Sickmann, A.; Martens, L.; Barsnes, H. PeptideShaker enables reanalysis of MS-derived proteomics data sets Nat. Biotechnol. 2015, 33, 22-24 10.1038/nbt.3109
-
(2015)
Nat. Biotechnol.
, vol.33
, pp. 22-24
-
-
Vaudel, M.1
Burkhart, J.M.2
Zahedi, R.P.3
Oveland, E.4
Berven, F.S.5
Sickmann, A.6
Martens, L.7
Barsnes, H.8
-
34
-
-
0037108887
-
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
-
Keller, A.; Nesvizhskii, A. I.; Kolker, E.; Aebersold, R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search Anal. Chem. 2002, 74, 5383-5392 10.1021/ac025747h
-
(2002)
Anal. Chem.
, vol.74
, pp. 5383-5392
-
-
Keller, A.1
Nesvizhskii, A.I.2
Kolker, E.3
Aebersold, R.4
-
35
-
-
80053387432
-
IProphet: Multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates
-
007690
-
Shteynberg, D.; Deutsch, E. W.; Lam, H.; Eng, J. K.; Sun, Z.; Tasman, N.; Mendoza, L.; Moritz, R. L.; Aebersold, R.; Nesvizhskii, A. I. iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates Mol. Cell. Proteomics 2011, 10, M111 007690 10.1074/mcp.M111.007690
-
(2011)
Mol. Cell. Proteomics
, vol.10
, pp. 111
-
-
Shteynberg, D.1
Deutsch, E.W.2
Lam, H.3
Eng, J.K.4
Sun, Z.5
Tasman, N.6
Mendoza, L.7
Moritz, R.L.8
Aebersold, R.9
Nesvizhskii, A.I.10
-
36
-
-
77949676526
-
A guided tour of the Trans-Proteomic Pipeline
-
Deutsch, E. W.; Mendoza, L.; Shteynberg, D.; Farrah, T.; Lam, H.; Tasman, N.; Sun, Z.; Nilsson, E.; Pratt, B.; Prazen, B.; Eng, J. K.; Martin, D. B.; Nesvizhskii, A. I.; Aebersold, R. A guided tour of the Trans-Proteomic Pipeline Proteomics 2010, 10, 1150-1159 10.1002/pmic.200900375
-
(2010)
Proteomics
, vol.10
, pp. 1150-1159
-
-
Deutsch, E.W.1
Mendoza, L.2
Shteynberg, D.3
Farrah, T.4
Lam, H.5
Tasman, N.6
Sun, Z.7
Nilsson, E.8
Pratt, B.9
Prazen, B.10
Eng, J.K.11
Martin, D.B.12
Nesvizhskii, A.I.13
Aebersold, R.14
-
37
-
-
72149093828
-
Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry
-
Reiter, L.; Claassen, M.; Schrimpf, S. P.; Jovanovic, M.; Schmidt, A.; Buhmann, J. M.; Hengartner, M. O.; Aebersold, R. Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry Mol. Cell. Proteomics 2009, 8, 2405-2417 10.1074/mcp.M900317-MCP200
-
(2009)
Mol. Cell. Proteomics
, vol.8
, pp. 2405-2417
-
-
Reiter, L.1
Claassen, M.2
Schrimpf, S.P.3
Jovanovic, M.4
Schmidt, A.5
Buhmann, J.M.6
Hengartner, M.O.7
Aebersold, R.8
-
38
-
-
33846041078
-
The Universal Protein Resource (UniProt)
-
Uniprot Consortium
-
Uniprot Consortium The Universal Protein Resource (UniProt) Nucleic Acids Res. 2007, 35, D193-197 10.1093/nar/gkl929
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 193-197
-
-
-
39
-
-
84862187489
-
NeXtProt: A knowledge platform for human proteins
-
Lane, L.; Argoud-Puy, G.; Britan, A.; Cusin, I.; Duek, P. D.; Evalet, O.; Gateau, A.; Gaudet, P.; Gleizes, A.; Masselot, A.; Zwahlen, C.; Bairoch, A. neXtProt: a knowledge platform for human proteins Nucleic Acids Res. 2012, 40, D76-D83 10.1093/nar/gkr1179
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 76-D83
-
-
Lane, L.1
Argoud-Puy, G.2
Britan, A.3
Cusin, I.4
Duek, P.D.5
Evalet, O.6
Gateau, A.7
Gaudet, P.8
Gleizes, A.9
Masselot, A.10
Zwahlen, C.11
Bairoch, A.12
-
40
-
-
80054026316
-
The Human Protein Atlas as a proteomic resource for biomarker discovery
-
Pontén, F.; Schwenk, J. M.; Asplund, A.; Edqvist, P. H. D. The Human Protein Atlas as a proteomic resource for biomarker discovery J. Intern. Med. 2011, 270, 428-446 10.1111/j.1365-2796.2011.02427.x
-
(2011)
J. Intern. Med.
, vol.270
, pp. 428-446
-
-
Pontén, F.1
Schwenk, J.M.2
Asplund, A.3
Edqvist, P.H.D.4
-
41
-
-
0000515372
-
InterPro: An integrated documentation resource for protein families, domains and functional sites
-
Mulder, N. J.; Apweiler, R.; Attwood, T. K.; Bairoch, A.; Bateman, A.; Binns, D.; Biswas, M.; Bradley, P.; Bork, P.; Bucher, P.; Copley, R.; Courcelle, E.; Durbin, R.; Falquet, L.; Fleischmann, W.; Gouzy, J.; Griffith-Jones, S.; Haft, D.; Hermjakob, H.; Hulo, N.; Kahn, D.; Kanapin, A.; Krestyaninova, M.; Lopez, R.; Letunic, I.; Orchard, S.; Pagni, M.; Peyruc, D.; Ponting, C. P.; Servant, F.; Sigrist, C. J. InterPro: an integrated documentation resource for protein families, domains and functional sites Briefings Bioinf 2002, 3, 225-235 10.1093/bib/3.3.225
-
(2002)
Briefings Bioinf
, vol.3
, pp. 225-235
-
-
Mulder, N.J.1
Apweiler, R.2
Attwood, T.K.3
Bairoch, A.4
Bateman, A.5
Binns, D.6
Biswas, M.7
Bradley, P.8
Bork, P.9
Bucher, P.10
Copley, R.11
Courcelle, E.12
Durbin, R.13
Falquet, L.14
Fleischmann, W.15
Gouzy, J.16
Griffith-Jones, S.17
Haft, D.18
Hermjakob, H.19
Hulo, N.20
Kahn, D.21
Kanapin, A.22
Krestyaninova, M.23
Lopez, R.24
Letunic, I.25
Orchard, S.26
Pagni, M.27
Peyruc, D.28
Ponting, C.P.29
Servant, F.30
Sigrist, C.J.31
more..
-
42
-
-
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 10.1038/embor.2008.56
-
(2008)
EMBO Rep.
, vol.9
, pp. 429-434
-
-
Deutsch, E.W.1
Lam, H.2
Aebersold, R.3
-
43
-
-
84863900597
-
A computational tool to detect and avoid redundancy in selected reaction monitoring
-
Rost, H.; Malmstrom, L.; Aebersold, R. A computational tool to detect and avoid redundancy in selected reaction monitoring Mol. Cell. Proteomics 2012, 11, 540-549 10.1074/mcp.M111.013045
-
(2012)
Mol. Cell. Proteomics
, vol.11
, pp. 540-549
-
-
Rost, H.1
Malmstrom, L.2
Aebersold, R.3
-
44
-
-
77951965920
-
Skyline: An open source document editor for creating and analyzing targeted proteomics experiments
-
MacLean, B.; Tomazela, D. M.; Shulman, N.; Chambers, M.; Finney, G. L.; Frewen, B.; Kern, R.; Tabb, D. L.; Liebler, D. C.; MacCoss, M. J. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments Bioinformatics 2010, 26, 966-968 10.1093/bioinformatics/btq054
-
(2010)
Bioinformatics
, vol.26
, pp. 966-968
-
-
MacLean, B.1
Tomazela, D.M.2
Shulman, N.3
Chambers, M.4
Finney, G.L.5
Frewen, B.6
Kern, R.7
Tabb, D.L.8
Liebler, D.C.9
MacCoss, M.J.10
-
45
-
-
84855792427
-
Cancer statistics, 2012
-
Siegel, R.; Naishadham, D.; Jemal, A. Cancer statistics, 2012 Ca-Cancer J. Clin. 2012, 62, 10-29 10.3322/caac.20138
-
(2012)
Ca-Cancer J. Clin.
, vol.62
, pp. 10-29
-
-
Siegel, R.1
Naishadham, D.2
Jemal, A.3
-
46
-
-
79751494680
-
EGFR mutations and lung cancer
-
da Cunha Santos, G.; Shepherd, F. A.; Tsao, M. S. EGFR mutations and lung cancer Annu. Rev. Pathol.: Mech. Dis. 2011, 6, 49-69 10.1146/annurev-pathol-011110-130206
-
(2011)
Annu. Rev. Pathol.: Mech. Dis.
, vol.6
, pp. 49-69
-
-
Da Cunha Santos, G.1
Shepherd, F.A.2
Tsao, M.S.3
-
47
-
-
84905366894
-
Acquired resistance to TKIs in solid tumours: Learning from lung cancer
-
Camidge, D. R.; Pao, W.; Sequist, L. V. Acquired resistance to TKIs in solid tumours: learning from lung cancer Nat. Rev. Clin. Oncol. 2014, 11, 473-481 10.1038/nrclinonc.2014.104
-
(2014)
Nat. Rev. Clin. Oncol.
, vol.11
, pp. 473-481
-
-
Camidge, D.R.1
Pao, W.2
Sequist, L.V.3
-
48
-
-
27644555055
-
Interpretation of shotgun proteomic data: The protein inference problem
-
Nesvizhskii, A. I.; Aebersold, R. Interpretation of shotgun proteomic data: the protein inference problem Mol. Cell. Proteomics 2005, 4, 1419-1440 10.1074/mcp.R500012-MCP200
-
(2005)
Mol. Cell. Proteomics
, vol.4
, pp. 1419-1440
-
-
Nesvizhskii, A.I.1
Aebersold, R.2
-
49
-
-
84884363278
-
Combining results of multiple search engines in proteomics
-
Shteynberg, D.; Nesvizhskii, A. I.; Moritz, R. L.; Deutsch, E. W. Combining results of multiple search engines in proteomics Mol. Cell. Proteomics 2013, 12, 2383-2393 10.1074/mcp.R113.027797
-
(2013)
Mol. Cell. Proteomics
, vol.12
, pp. 2383-2393
-
-
Shteynberg, D.1
Nesvizhskii, A.I.2
Moritz, R.L.3
Deutsch, E.W.4
-
50
-
-
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 10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2
-
(1999)
Electrophoresis
, vol.20
, pp. 3551-3567
-
-
Perkins, D.N.1
Pappin, D.J.2
Creasy, D.M.3
Cottrell, J.S.4
-
51
-
-
84891810621
-
Large-Scale Quantification of Single Amino-Acid Variations by a Variation-Associated Database Search Strategy
-
Song, C.; Wang, F.; Cheng, K.; Wei, X.; Bian, Y.; Wang, K.; Tan, Y.; Wang, H.; Ye, M.; Zou, H. Large-Scale Quantification of Single Amino-Acid Variations by a Variation-Associated Database Search Strategy J. Proteome Res. 2014, 13, 241-248 10.1021/pr400544j
-
(2014)
J. Proteome Res.
, vol.13
, pp. 241-248
-
-
Song, C.1
Wang, F.2
Cheng, K.3
Wei, X.4
Bian, Y.5
Wang, K.6
Tan, Y.7
Wang, H.8
Ye, M.9
Zou, H.10
-
52
-
-
84941031116
-
The State of the Human Proteome in 2014/2015 as viewed through PeptideAtlas: Enhancing accuracy and coverage through the AtlasProphet
-
Deutsch, E. W.; Sun, Z.; Campbell, D.; Kusebauch, U.; Chu, C. S.; Mendoza, L.; Shteynberg, D.; Omenn, G. S.; Moritz, R. L. The State of the Human Proteome in 2014/2015 as viewed through PeptideAtlas: enhancing accuracy and coverage through the AtlasProphet J. Proteome Res. 2015, 150703045314008 10.1021/acs.jproteome.5b00500
-
(2015)
J. Proteome Res.
-
-
Deutsch, E.W.1
Sun, Z.2
Campbell, D.3
Kusebauch, U.4
Chu, C.S.5
Mendoza, L.6
Shteynberg, D.7
Omenn, G.S.8
Moritz, R.L.9
-
53
-
-
84908540871
-
Proteogenomics: Concepts, applications and computational strategies
-
Nesvizhskii, A. I. Proteogenomics: concepts, applications and computational strategies Nat. Methods 2014, 11, 1114-1125 10.1038/nmeth.3144
-
(2014)
Nat. Methods
, vol.11
, pp. 1114-1125
-
-
Nesvizhskii, A.I.1
-
54
-
-
66249144426
-
The structure and function of G-protein-coupled receptors
-
Rosenbaum, D. M.; Rasmussen, S. G. F.; Kobilka, B. K. The structure and function of G-protein-coupled receptors Nature 2009, 459, 356-363 10.1038/nature08144
-
(2009)
Nature
, vol.459
, pp. 356-363
-
-
Rosenbaum, D.M.1
Rasmussen, S.G.F.2
Kobilka, B.K.3
-
55
-
-
54049090766
-
Selected reaction monitoring for quantitative proteomics: A tutorial
-
Lange, V.; Picotti, P.; Domon, B.; Aebersold, R. Selected reaction monitoring for quantitative proteomics: a tutorial Mol. Syst. Biol. 2008, 4, 222-222 10.1038/msb.2008.61
-
(2008)
Mol. Syst. Biol.
, vol.4
, pp. 222-222
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Lange, V.1
Picotti, P.2
Domon, B.3
Aebersold, R.4
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