-
1
-
-
0035895505
-
The sequence of the human genome
-
Venter J.C., Adams M.D., Myers E.W., Li P.W., Mural R.J., Sutton G.G., Smith H.O., Yandell M., Evans C.A., Holt R.A.et al. The sequence of the human genome. Science. 291:2001;1304-1351.
-
(2001)
Science
, vol.291
, pp. 1304-1351
-
-
Venter, J.C.1
Adams, M.D.2
Myers, E.W.3
Li, P.W.4
Mural, R.J.5
Sutton, G.G.6
Smith, H.O.7
Yandell, M.8
Evans, C.A.9
Holt, R.A.10
-
2
-
-
2042437650
-
Initial sequencing and analysis of the human genome
-
Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W.et al. Initial sequencing and analysis of the human genome. Nature. 409:2001;860-921.
-
(2001)
Nature
, vol.409
, pp. 860-921
-
-
Lander, E.S.1
Linton, L.M.2
Birren, B.3
Nusbaum, C.4
Zody, M.C.5
Baldwin, J.6
Devon, K.7
Dewar, K.8
Doyle, M.9
FitzHugh, W.10
-
3
-
-
0034659815
-
Proteomics to study genes and genomes
-
Pandey A., Mann M. Proteomics to study genes and genomes. Nature. 405:2000;837-846.
-
(2000)
Nature
, vol.405
, pp. 837-846
-
-
Pandey, A.1
Mann, M.2
-
4
-
-
0034628508
-
A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
-
Uetz P., Giot L., Cagney G., Mansfield T.A., Judson R.S., Knight J.R., Lockshon D., Narayan V., Srinivasan M., Pochart P.et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature. 403:2000;623-627.
-
(2000)
Nature
, vol.403
, pp. 623-627
-
-
Uetz, P.1
Giot, L.2
Cagney, G.3
Mansfield, T.A.4
Judson, R.S.5
Knight, J.R.6
Lockshon, D.7
Narayan, V.8
Srinivasan, M.9
Pochart, P.10
-
5
-
-
0033974688
-
Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins
-
Ito T., Tashiro K., Muta S., Ozawa R., Chiba T., Nishizawa M., Yamamoto K., Kuhara S., Sakaki Y. Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc. Natl. Acad. Sci. U.S.A. 97:2000;1143-1147.
-
(2000)
Proc. Natl. Acad. Sci. U.S.A.
, vol.97
, pp. 1143-1147
-
-
Ito, T.1
Tashiro, K.2
Muta, S.3
Ozawa, R.4
Chiba, T.5
Nishizawa, M.6
Yamamoto, K.7
Kuhara, S.8
Sakaki, Y.9
-
6
-
-
0035836765
-
A comprehensive two-hybrid analysis to explore the yeast protein interactome
-
Ito T., Chiba T., Ozawa R., Yoshida M., Hattori M., Sakaki Y. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. U.S.A. 98:2001;4569-4574.
-
(2001)
Proc. Natl. Acad. Sci. U.S.A.
, vol.98
, pp. 4569-4574
-
-
Ito, T.1
Chiba, T.2
Ozawa, R.3
Yoshida, M.4
Hattori, M.5
Sakaki, Y.6
-
7
-
-
0035212065
-
Is there a bias in proteome research?
-
Mrowka R., Patzak A., Herzel H. Is there a bias in proteome research? Genome. Res. 11:2001;1971-1973.
-
(2001)
Genome. Res.
, vol.11
, pp. 1971-1973
-
-
Mrowka, R.1
Patzak, A.2
Herzel, H.3
-
8
-
-
0030895921
-
A comparison of selected mRNA and protein abundances in human liver
-
Anderson L., Seilhamer J. A comparison of selected mRNA and protein abundances in human liver. Electrophoresis. 18:1997;533-537.
-
(1997)
Electrophoresis
, vol.18
, pp. 533-537
-
-
Anderson, L.1
Seilhamer, J.2
-
10
-
-
0034772403
-
The role of separation science in proteomics research
-
Issaq H.J. The role of separation science in proteomics research. Electrophoresis. 22:2001;3629-3638.
-
(2001)
Electrophoresis
, vol.22
, pp. 3629-3638
-
-
Issaq, H.J.1
-
12
-
-
0034662907
-
Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology
-
Gygi S.P., Corthals G.L., Zhang Y., Rochon Y., Aebersold R. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc. Natl. Acad. Sci. U.S.A. 97:2000;9390-9395.
-
(2000)
Proc. Natl. Acad. Sci. U.S.A.
, vol.97
, pp. 9390-9395
-
-
Gygi, S.P.1
Corthals, G.L.2
Zhang, Y.3
Rochon, Y.4
Aebersold, R.5
-
13
-
-
0034923505
-
Analysis of proteins and proteomes by mass spectrometry
-
Mann M., Hendrickson R.C., Pandey A. Analysis of proteins and proteomes by mass spectrometry. Annu. Rev. Biochem. 70:2001;437-473.
-
(2001)
Annu. Rev. Biochem.
, vol.70
, pp. 437-473
-
-
Mann, M.1
Hendrickson, R.C.2
Pandey, A.3
-
14
-
-
0032875697
-
Quantitative analysis of complex protein mixtures using isotope-coded affinity tags
-
Gygi S.P., Rist B., Gerber S.A., Turecek F., Gelb M.H., Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17:1999;994-999.
-
(1999)
Nat. Biotechnol.
, vol.17
, pp. 994-999
-
-
Gygi, S.P.1
Rist, B.2
Gerber, S.A.3
Turecek, F.4
Gelb, M.H.5
Aebersold, R.6
-
15
-
-
0035106351
-
Large-scale analysis of the yeast proteome by multidimensional protein identification technology
-
Washburn M.P., Wolters D., Yates J.R. III Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19:2001;242-247.
-
(2001)
Nat. Biotechnol.
, vol.19
, pp. 242-247
-
-
Washburn, M.P.1
Wolters, D.2
Yates J.R. III3
-
16
-
-
0034677966
-
Drug discovery: A historical perspective
-
Drews J. Drug discovery: a historical perspective. Science. 287:2000;1960-1964.
-
(2000)
Science
, vol.287
, pp. 1960-1964
-
-
Drews, J.1
-
17
-
-
0001426432
-
Chemical strategies for functional proteomics
-
This is an excellent review of the broader functional proteomics landscape and the use of a variety of chemical approaches to fractionate the proteome in functionally useful ways.
-
Adam G.C., Sorensen E.J., Cravatt B.F. Chemical strategies for functional proteomics. Mol. Cell Proteomics. 1:2002;781-790 This is an excellent review of the broader functional proteomics landscape and the use of a variety of chemical approaches to fractionate the proteome in functionally useful ways.
-
(2002)
Mol. Cell Proteomics.
, vol.1
, pp. 781-790
-
-
Adam, G.C.1
Sorensen, E.J.2
Cravatt, B.F.3
-
18
-
-
0033636862
-
Chemical strategies for the global analysis of protein function
-
Cravatt B.F., Sorensen E.J. Chemical strategies for the global analysis of protein function. Curr. Opin. Chem. Biol. 4:2000;663-668.
-
(2000)
Curr. Opin. Chem. Biol.
, vol.4
, pp. 663-668
-
-
Cravatt, B.F.1
Sorensen, E.J.2
-
20
-
-
0035469599
-
Direct visualization of serine hydroalse activities in complex proteomes using fluorescent active site-directed probes
-
This paper describes the useful development of fluorescent serine hydrolase probes that are valuable for high-throughput protein detection and quantification.
-
Patricelli M.P., Giang D.K., Stamp L.M., Burbaum J.J. Direct visualization of serine hydroalse activities in complex proteomes using fluorescent active site-directed probes. Proteomics. 1:2001;1067-1071 This paper describes the useful development of fluorescent serine hydrolase probes that are valuable for high-throughput protein detection and quantification.
-
(2001)
Proteomics
, vol.1
, pp. 1067-1071
-
-
Patricelli, M.P.1
Giang, D.K.2
Stamp, L.M.3
Burbaum, J.J.4
-
21
-
-
0001047320
-
Trifunctional chemical probes for the consolidated detection and identification of enzyme activities from complex proteomes
-
Adam G.C., Sorensen E.J., Cravatt B.F. Trifunctional chemical probes for the consolidated detection and identification of enzyme activities from complex proteomes. Mol. Cell Proteomics. 1:2002;828-835.
-
(2002)
Mol. Cell Proteomics.
, vol.1
, pp. 828-835
-
-
Adam, G.C.1
Sorensen, E.J.2
Cravatt, B.F.3
-
22
-
-
0034054576
-
Selective targeting of lysosomal cysteine proteases with radiolabeled electrophilic substrate analogs
-
This paper demonstrates the utility of a variety of cathepsin reactive probes albeit in the limited setting of radioisotopic analysis.
-
Bogyo M., Verhelst S., Bellingard-Dubouchaud V., Toba S., Greenbaum D. Selective targeting of lysosomal cysteine proteases with radiolabeled electrophilic substrate analogs. Chem. Biol. 7:2000;27-38 This paper demonstrates the utility of a variety of cathepsin reactive probes albeit in the limited setting of radioisotopic analysis.
-
(2000)
Chem. Biol.
, vol.7
, pp. 27-38
-
-
Bogyo, M.1
Verhelst, S.2
Bellingard-Dubouchaud, V.3
Toba, S.4
Greenbaum, D.5
-
23
-
-
0035799319
-
Profiling serine hydrolase activities in complex proteomes
-
This important paper introduces several specificity and kinetic issues that must be carefully considered in the evaluation of activity probes for proteomic analysis. In addition, the breadth of detection and identification of serine hydrolases in cytosol and membranes is nicely highlighted, as is the potential for drug selectivity analysis by kinetic modulation of the probe reactivity.
-
Kidd D., Liu Y., Cravatt B.F. Profiling serine hydrolase activities in complex proteomes. Biochemistry. 40:2001;4005-4015 This important paper introduces several specificity and kinetic issues that must be carefully considered in the evaluation of activity probes for proteomic analysis. In addition, the breadth of detection and identification of serine hydrolases in cytosol and membranes is nicely highlighted, as is the potential for drug selectivity analysis by kinetic modulation of the probe reactivity.
-
(2001)
Biochemistry
, vol.40
, pp. 4005-4015
-
-
Kidd, D.1
Liu, Y.2
Cravatt, B.F.3
-
24
-
-
0036678119
-
Enzyme activity profiles of the secreted and membrane proteome that depict cancer cell invasiveness
-
This impressive paper interprets the serine hydrolase activity profiles of a panel of breast and melanoma cell lines by cluster analysis. The broad-based analysis integrates activity, subcellular distribution and glycosylation state to identify a cluster of serine hydrolases that distinguish cell line based upon tissue of origin. A unique set of hydrolases was determined to be highly correlated to invasiveness. The potential for the diagnosis and treatment of cancers by an activity-based approach is clearly demonstrated.
-
Jessani N., Liu Y., Humphrey M., Cravatt B.F. Enzyme activity profiles of the secreted and membrane proteome that depict cancer cell invasiveness. Proc. Natl. Acad. Sci. U.S.A. 99:2002;10335-10340 This impressive paper interprets the serine hydrolase activity profiles of a panel of breast and melanoma cell lines by cluster analysis. The broad-based analysis integrates activity, subcellular distribution and glycosylation state to identify a cluster of serine hydrolases that distinguish cell line based upon tissue of origin. A unique set of hydrolases was determined to be highly correlated to invasiveness. The potential for the diagnosis and treatment of cancers by an activity-based approach is clearly demonstrated.
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 10335-10340
-
-
Jessani, N.1
Liu, Y.2
Humphrey, M.3
Cravatt, B.F.4
-
25
-
-
0032103006
-
Substrate binding and sequence preference of the proteasome revealed by active-site-directed affinity probes
-
Bogyo M., Shin S., McMaster J.S., Ploegh H. Substrate binding and sequence preference of the proteasome revealed by active-site-directed affinity probes. Chem. Biol. 5:1998;307-320.
-
(1998)
Chem. Biol.
, vol.5
, pp. 307-320
-
-
Bogyo, M.1
Shin, S.2
McMaster, J.S.3
Ploegh, H.4
-
26
-
-
0033835372
-
Epoxide electrophiles as activity-dependent cysteine protease profiling and discovery tools
-
This paper nicely demonstrates the utility of libraries of epoxide affinity probes for cysteine proteases for obtaining detailed information on the function and inhibitor specificity without the need for prior purification or identification of proteins.
-
Greenbaum D., Medzihradszky K.F., Burlingame A., Bogyo M. Epoxide electrophiles as activity-dependent cysteine protease profiling and discovery tools. Chem. Biol. 7:2000;569-581 This paper nicely demonstrates the utility of libraries of epoxide affinity probes for cysteine proteases for obtaining detailed information on the function and inhibitor specificity without the need for prior purification or identification of proteins.
-
(2000)
Chem. Biol.
, vol.7
, pp. 569-581
-
-
Greenbaum, D.1
Medzihradszky, K.F.2
Burlingame, A.3
Bogyo, M.4
-
27
-
-
0036051482
-
Chemical approaches for functionally probing the proteome
-
This paper continues a detailed study of the cathepsins using activity-based fluorescent probes and introduces their use with positional scanning libraries of peptide inhibitors to assess target protein specificity.
-
Greenbaum D., Baruch A., Hayrapetian L., Darula Z., Burlingame A., Medzihradszky K.F., Bogyo M. Chemical approaches for functionally probing the proteome. Mol. Cell Proteomics. 1:2002;60-68 This paper continues a detailed study of the cathepsins using activity-based fluorescent probes and introduces their use with positional scanning libraries of peptide inhibitors to assess target protein specificity.
-
(2002)
Mol. Cell Proteomics.
, vol.1
, pp. 60-68
-
-
Greenbaum, D.1
Baruch, A.2
Hayrapetian, L.3
Darula, Z.4
Burlingame, A.5
Medzihradszky, K.F.6
Bogyo, M.7
-
28
-
-
0037143705
-
Profiling protein function with small molecule arrays
-
This paper reports an interesting application of microarray technology with small libraries of specific probes to cysteine proteases for the capture, quantitation and identification of target proteins.
-
Winssinger N., Ficarro S., Schultz P.G., Harris J.L. Profiling protein function with small molecule arrays. Proc. Natl. Acad. Sci. U.S.A. 99:2002;11139-11144 This paper reports an interesting application of microarray technology with small libraries of specific probes to cysteine proteases for the capture, quantitation and identification of target proteins.
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 11139-11144
-
-
Winssinger, N.1
Ficarro, S.2
Schultz, P.G.3
Harris, J.L.4
-
29
-
-
0035113229
-
Profiling the specific reactivity of the proteome with non-directed activity-based probes
-
This is the first report of the use of libraries of probes that explore recognition and electrophilic design features to identify probes with interesting and specific proteomic targeting capabilities.
-
Adam G.C., Cravatt B.F., Sorensen E.J. Profiling the specific reactivity of the proteome with non-directed activity-based probes. Chem. Biol. 8:2001;81-95 This is the first report of the use of libraries of probes that explore recognition and electrophilic design features to identify probes with interesting and specific proteomic targeting capabilities.
-
(2001)
Chem. Biol.
, vol.8
, pp. 81-95
-
-
Adam, G.C.1
Cravatt, B.F.2
Sorensen, E.J.3
-
30
-
-
0036022519
-
Proteomic profiling of mechanistically distinct enzyme classes using a common chemotype
-
This excellent paper further develops the concepts underlying the non-directed approach to probe design.
-
Adam G.C., Sorensen E.J., Cravatt B.F. Proteomic profiling of mechanistically distinct enzyme classes using a common chemotype. Nat. Biotechnol. 20:2002;805-809 This excellent paper further develops the concepts underlying the non-directed approach to probe design.
-
(2002)
Nat. Biotechnol.
, vol.20
, pp. 805-809
-
-
Adam, G.C.1
Sorensen, E.J.2
Cravatt, B.F.3
-
31
-
-
0036775490
-
Chemistry-based functional proteomics reveals novel members of the deubiquitinating enzyme family
-
This paper reports on a novel application of intein-based chemical ligation to generate a library of electrophilic probes for the family of deubiquitinating enzymes, demonstrating the breadth of design approaches and protein families that are under investigation with activity-based probes.
-
Borodovsky A., Ovaa H., Kolli N., Gan-Erdene T., Wilkinson K.D., Ploegh H.L., Kessler B.M. Chemistry-based functional proteomics reveals novel members of the deubiquitinating enzyme family. Chem. Biol. 9:2002;1149-1159 This paper reports on a novel application of intein-based chemical ligation to generate a library of electrophilic probes for the family of deubiquitinating enzymes, demonstrating the breadth of design approaches and protein families that are under investigation with activity-based probes.
-
(2002)
Chem. Biol.
, vol.9
, pp. 1149-1159
-
-
Borodovsky, A.1
Ovaa, H.2
Kolli, N.3
Gan-Erdene, T.4
Wilkinson, K.D.5
Ploegh, H.L.6
Kessler, B.M.7
-
32
-
-
0028863679
-
4-(Fluoromethyl)phenyl phosphate acts as a mechanism-based inhibitor of calcineurin
-
Born T.L., Myers J.K., Widlanski T.S., Rusnak F. 4-(Fluoromethyl)phenyl phosphate acts as a mechanism-based inhibitor of calcineurin. J. Biol. Chem. 270:1995;25651-25655.
-
(1995)
J. Biol. Chem.
, vol.270
, pp. 25651-25655
-
-
Born, T.L.1
Myers, J.K.2
Widlanski, T.S.3
Rusnak, F.4
-
33
-
-
0027729415
-
Mechanism-based inactivation of prostatic acid phosphatase
-
Myers J.K., Widlanski T.S. Mechanism-based inactivation of prostatic acid phosphatase. Science. 262:1993;1451-1453.
-
(1993)
Science
, vol.262
, pp. 1451-1453
-
-
Myers, J.K.1
Widlanski, T.S.2
-
35
-
-
0030932349
-
Chemical arrows for enzymatic targets
-
Colman R.F. Chemical arrows for enzymatic targets. FASEB J. 11:1997;217-226.
-
(1997)
FASEB J.
, vol.11
, pp. 217-226
-
-
Colman, R.F.1
-
36
-
-
0031428787
-
Affinity labels for NAD(P)-specific sites
-
Colman R.F. Affinity labels for NAD(P)-specific sites. Methods Enzymol. 280:1997;186-203.
-
(1997)
Methods Enzymol.
, vol.280
, pp. 186-203
-
-
Colman, R.F.1
|