-
1
-
-
0035106351
-
Large-scale analysis of the yeast proteome by multidimensional protein identification technology
-
10.1038/85686 11231557
-
Washburn MP Wolters D Yates JR III Large-scale analysis of the yeast proteome by multidimensional protein identification technology Nat Biotechnol 2001, 19:242-247 10.1038/85686 11231557
-
(2001)
Nat Biotechnol
, vol.19
, pp. 242-247
-
-
Washburn, M.P.1
Wolters, D.2
Yates III, J.R.3
-
2
-
-
30744476222
-
Performance of a linear ion trap-Orbitrap hybrid for peptide analysis
-
10.1021/ac0514624 16408932
-
Yates JR Cociorva D Liao L Zabrouskov V Performance of a linear ion trap-Orbitrap hybrid for peptide analysis Anal Chem 2006, 78:493-500 10.1021/ac0514624 16408932
-
(2006)
Anal Chem
, vol.78
, pp. 493-500
-
-
Yates, J.R.1
Cociorva, D.2
Liao, L.3
Zabrouskov, V.4
-
3
-
-
0037015602
-
A proteomic view of the Plasmodium falciparum life cycle
-
10.1038/nature01107 12368866
-
Florens L Washburn MP Raine JD Anthony RM Grainger M Haynes JD Moch JK Muster N Sacci JB Tabb DL Witney AA Wolters D Wu Y Gardner MJ Holder AA Sinden RE Yates JR Carucci DJ A proteomic view of the Plasmodium falciparum life cycle Nature 2002, 419:520-526 10.1038/nature01107 12368866
-
(2002)
Nature
, vol.419
, pp. 520-526
-
-
Florens, L.1
Washburn, M.P.2
Raine, J.D.3
Anthony, R.M.4
Grainger, M.5
Haynes, J.D.6
Moch, J.K.7
Muster, N.8
Sacci, J.B.9
Tabb, D.L.10
Witney, A.A.11
Wolters, D.12
Wu, Y.13
Gardner, M.J.14
Holder, A.A.15
Sinden, R.E.16
Yates, J.R.17
Carucci, D.J.18
-
5
-
-
10744233766
-
Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards
-
10.1021/ac026468x 14674459
-
Wang W Zhou H Lin H Roy S Shaler TA Hill LR Norton S Kumar P Anderle M Becker CH Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards Anal Chem 2003, 75:4818-4826 10.1021/ac026468x 14674459
-
(2003)
Anal Chem
, vol.75
, pp. 4818-4826
-
-
Wang, W.1
Zhou, H.2
Lin, H.3
Roy, S.4
Shaler, T.A.5
Hill, L.R.6
Norton, S.7
Kumar, P.8
Anderle, M.9
Becker, C.H.10
-
6
-
-
3242731195
-
A model for random sampling and estimation of relative protein abundance in shotgun proteomics
-
10.1021/ac0498563 15253663
-
Liu H Sadygov RG Yates JR III A model for random sampling and estimation of relative protein abundance in shotgun proteomics Anal Chem 2004, 76:4193-4201 10.1021/ac0498563 15253663
-
(2004)
Anal Chem
, vol.76
, pp. 4193-4201
-
-
Liu, H.1
Sadygov, R.G.2
Yates III, J.R.3
-
7
-
-
0034069495
-
Gene ontology: Tool for the unification of biology
-
The Gene Ontology Consortium 10.1038/75556 10802651
-
Ashburner M Ball CA Blake JA Botstein D Butler H Cherry JM Davis AP Dolinski K Dwight SS Eppig JT Harris MA Hill DP Tarver LI Kasarskis A Lewis S Matese JC Richardson JE Ringwald M Rubin GM Sherlock G Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium Nat Genet 2000, 25:25-29 10.1038/75556 10802651
-
(2000)
Nat Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
Harris, M.A.11
Hill, D.P.12
Tarver, L.I.13
Kasarskis, A.14
Lewis, S.15
Matese, J.C.16
Richardson, J.E.17
Ringwald, M.18
Rubin, G.M.19
Sherlock, G.20
more..
-
8
-
-
0038005018
-
DAVID: Database for Annotation, Visualization, and Integrated Discovery
-
10.1186/gb-2003-4-5-p3
-
Dennis G Jr Sherman BT Hosack DA Yang J Gao W Lane HC Lempicki RA DAVID: Database for Annotation, Visualization, and Integrated Discovery Genome Biol 2003, 4:3 10.1186/gb-2003-4-5-p3
-
(2003)
Genome Biol
, vol.4
, pp. 3
-
-
Dennis Jr., G.1
Sherman, B.T.2
Hosack, D.A.3
Yang, J.4
Gao, W.5
Lane, H.C.6
Lempicki, R.A.7
-
9
-
-
0038175144
-
GoMiner: A resource for biological interpretation of genomic and proteomic data
-
154579 12702209 10.1186/gb-2003-4-4-r28
-
Zeeberg BR Feng W Wang G Wang MD Fojo AT Sunshine M Narasimhan S Jane DW Reinhold WC Lababidi S Bussey KJ Riss J Barret JC Weinstein JN GoMiner: a resource for biological interpretation of genomic and proteomic data Genome Biol 2003, 4:R28 154579 12702209 10.1186/gb-2003-4-4-r28
-
(2003)
Genome Biol
, vol.4
-
-
Zeeberg, B.R.1
Feng, W.2
Wang, G.3
Wang, M.D.4
Fojo, A.T.5
Sunshine, M.6
Narasimhan, S.7
Jane, D.W.8
Reinhold, W.C.9
Lababidi, S.10
Bussey, K.J.11
Riss, J.12
Barret, J.C.13
Weinstein, J.N.14
-
10
-
-
0242585492
-
GoFish finds genes with combinations of Gene Ontology attributes
-
10.1093/bioinformatics/btg088 12691998
-
Berriz GF White JV King OD Roth FP GoFish finds genes with combinations of Gene Ontology attributes Bioinformatics 2003, 19:788-789 10.1093/ bioinformatics/btg088 12691998
-
(2003)
Bioinformatics
, vol.19
, pp. 788-789
-
-
Berriz, G.F.1
White, J.V.2
King, O.D.3
Roth, F.P.4
-
11
-
-
9744260518
-
Development of gene ontology tool for biological interpretation of genomic and proteomic data
-
8-12 November Washington, DC Musen M
-
Feng W Wang G Zeeberg BR Guo K Fojo AT Kane DW Reinhold WC Lababidi S Weinstein JN Wang MD Development of gene ontology tool for biological interpretation of genomic and proteomic data Proceedings of the AMIA Annual Symposium: 8-12 November 2003; Washington, DC Musen M 2003 839
-
(2003)
Proceedings of the AMIA Annual Symposium
, pp. 839
-
-
Feng, W.1
Wang, G.2
Zeeberg, B.R.3
Guo, K.4
Fojo, A.T.5
Kane, D.W.6
Reinhold, W.C.7
Lababidi, S.8
Weinstein, J.N.9
Wang, M.D.10
-
12
-
-
36549027355
-
GSEA-P: A desktop application for Gene Set Enrichment Analysis
-
10.1093/bioinformatics/btm369 17644558
-
Subramanian A Kuehn H Gould J Tamayo P Mesirov JP GSEA-P: A desktop application for Gene Set Enrichment Analysis Bioinformatics 2007, 23:3251-3253 10.1093/bioinformatics/btm369 17644558
-
(2007)
Bioinformatics
, vol.23
, pp. 3251-3253
-
-
Subramanian, A.1
Kuehn, H.2
Gould, J.3
Tamayo, P.4
Mesirov, J.P.5
-
14
-
-
0141925956
-
Anti-leukemia effect of perillyl alcohol in Bcr/Abl-transformed cells indirectly inhibits signaling through Mek in a Ras- and Raf-independent fashion
-
14555523
-
Clark SS Zhong L Filiault D Perman S Ren Z Gould M Yang X Anti-leukemia effect of perillyl alcohol in Bcr/Abl-transformed cells indirectly inhibits signaling through Mek in a Ras- and Raf-independent fashion Clin Cancer Res 2003, 9:4494-4504 14555523
-
(2003)
Clin Cancer Res
, vol.9
, pp. 4494-4504
-
-
Clark, S.S.1
Zhong, L.2
Filiault, D.3
Perman, S.4
Ren, Z.5
Gould, M.6
Yang, X.7
-
15
-
-
0036172970
-
Antileukemia activity of perillyl alcohol (POH): Uncoupling apoptosis from G0/G1 arrest suggests that the primary effect of POH on Bcr/ Abl-transformed cells is to induce growth arrest
-
10.1038/sj.leu.2402369 11840288
-
Clark SS Perman SM Sahin MB Jenkins GJ Elegbede JA Antileukemia activity of perillyl alcohol (POH): Uncoupling apoptosis from G0/G1 arrest suggests that the primary effect of POH on Bcr/Abl-transformed cells is to induce growth arrest Leukemia 2002, 16:213-222 10.1038/sj.leu.2402369 11840288
-
(2002)
Leukemia
, vol.16
, pp. 213-222
-
-
Clark, S.S.1
Perman, S.M.2
Sahin, M.B.3
Jenkins, G.J.4
Elegbede, J.A.5
-
16
-
-
0036870653
-
Effects of the isoprenoids perillyl alcohol and farnesol on apoptosis biomarkers in pancreatic cancer chemoprevention
-
12530055
-
Burke YD Ayoubi AS Werner SR McFarland BC Heilman DK Ruggeri BA Crowell PL Effects of the isoprenoids perillyl alcohol and farnesol on apoptosis biomarkers in pancreatic cancer chemoprevention Anticancer Res 2002, 22:3127-3134 12530055
-
(2002)
Anticancer Res
, vol.22
, pp. 3127-3134
-
-
Burke, Y.D.1
Ayoubi, A.S.2
Werner, S.R.3
McFarland, B.C.4
Heilman, D.K.5
Ruggeri, B.A.6
Crowell, P.L.7
-
17
-
-
35148831822
-
Perillyl alcohol and perillic acid induced cell cycle arrest and apoptosis in non small cell lung cancer cells
-
10.1016/j.canlet.2007.07.020 17888568
-
Yeruva L Pierre KJ Elegbede A Wang RC Carper SW Perillyl alcohol and perillic acid induced cell cycle arrest and apoptosis in non small cell lung cancer cells Cancer Lett 2007, 257:216-226 10.1016/ j.canlet.2007.07.020 17888568
-
(2007)
Cancer Lett
, vol.257
, pp. 216-226
-
-
Yeruva, L.1
Pierre, K.J.2
Elegbede, A.3
Wang, R.C.4
Carper, S.W.5
-
18
-
-
33644891059
-
Perillyl alcohol induces c-Myc-dependent apoptosis in Bcr/ Abl-transformed leukemia cells
-
10.1159/000091181 16439861
-
Clark SS Perillyl alcohol induces c-Myc-dependent apoptosis in Bcr/ Abl-transformed leukemia cells Oncology 2006, 70:13-18 10.1159/000091181 16439861
-
(2006)
Oncology
, vol.70
, pp. 13-18
-
-
Clark, S.S.1
-
19
-
-
33646509454
-
Perillyl alcohol inhibits the expression and function of the androgen receptor in human prostate cancer cells
-
10.1016/j.canlet.2005.05.023 16029925
-
Chung BH Lee HY Lee JS Young CY Perillyl alcohol inhibits the expression and function of the androgen receptor in human prostate cancer cells Cancer Lett 2006, 236:222-228 10.1016/j.canlet.2005.05.023 16029925
-
(2006)
Cancer Lett
, vol.236
, pp. 222-228
-
-
Chung, B.H.1
Lee, H.Y.2
Lee, J.S.3
Young, C.Y.4
-
20
-
-
1842482587
-
Perillyl alcohol inhibits human breast cancer cell growth in vitro and in vivo
-
10.1023/B:BREA.0000019966.97011.4d 15026623
-
Yuri T Danbara N Tsujita-Kyutoku M Kiyozuka Y Senzaki H Shikata N Kanzaki H Tsubura A Perillyl alcohol inhibits human breast cancer cell growth in vitro and in vivo Breast Cancer Res Treat 2004, 84:251-260 10.1023/B:BREA.0000019966.97011.4d 15026623
-
(2004)
Breast Cancer Res Treat
, vol.84
, pp. 251-260
-
-
Yuri, T.1
Danbara, N.2
Tsujita-Kyutoku, M.3
Kiyozuka, Y.4
Senzaki, H.5
Shikata, N.6
Kanzaki, H.7
Tsubura, A.8
-
22
-
-
34547232157
-
Optimization of mass spectrometry-compatible surfactants for shotgun proteomics
-
2570269 17530876 10.1021/pr060682a
-
Chen EI Cociorva D Norris JL Yates JR III Optimization of mass spectrometry-compatible surfactants for shotgun proteomics J Proteome Res 2007, 6:2529-2538 2570269 17530876 10.1021/pr060682a
-
(2007)
J Proteome Res
, vol.6
, pp. 2529-2538
-
-
Chen, E.I.1
Cociorva, D.2
Norris, J.L.3
Yates III, J.R.4
-
23
-
-
24744455665
-
Automatic quality assessment of peptide tandem mass spectra
-
10.1093/bioinformatics/bth947 15262780
-
Bern M Goldberg D McDonald WH Yates JR III Automatic quality assessment of peptide tandem mass spectra Bioinformatics 2004, 20(Suppl 1):i49-i54 10.1093/bioinformatics/bth947 15262780
-
(2004)
Bioinformatics
, vol.20
, Issue.SUPPL. 1
-
-
Bern, M.1
Goldberg, D.2
McDonald, W.H.3
Yates III, J.R.4
-
24
-
-
3042818018
-
The International Protein Index: An integrated database for proteomics experiments
-
10.1002/pmic.200300721 15221759
-
Kersey PJ Duarte J Williams A Karavidopoulou Y Birney E Apweiler R The International Protein Index: An integrated database for proteomics experiments Proteomics 2004, 4:1985-1988 10.1002/pmic.200300721 15221759
-
(2004)
Proteomics
, vol.4
, pp. 1985-1988
-
-
Kersey, P.J.1
Duarte, J.2
Williams, A.3
Karavidopoulou, Y.4
Birney, E.5
Apweiler, R.6
-
25
-
-
0037277179
-
Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: The yeast proteome
-
10.1021/pr025556v 12643542
-
Peng J Elias JE Thoreen CC Licklider LJ Gygi SP Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: The yeast proteome J Proteome Res 2003, 2:43-50 10.1021/pr025556v 12643542
-
(2003)
J Proteome Res
, vol.2
, pp. 43-50
-
-
Peng, J.1
Elias, J.E.2
Thoreen, C.C.3
Licklider, L.J.4
Gygi, S.P.5
-
26
-
-
0031814022
-
Database searching using mass spectrometry data
-
10.1002/elps.1150190604 9638935
-
Yates JR III Database searching using mass spectrometry data Electrophoresis 1998, 19:893-900 10.1002/elps.1150190604 9638935
-
(1998)
Electrophoresis
, vol.19
, pp. 893-900
-
-
Yates III, J.R.1
-
27
-
-
0036393898
-
DTASelect and Contrast: Tools for assembling and comparing protein identifications from shotgun proteomics
-
10.1021/pr015504q 12643522
-
Tabb DL McDonald WH Yates JR III DTASelect and Contrast: Tools for assembling and comparing protein identifications from shotgun proteomics J Proteome Res 2002, 1:21-26 10.1021/pr015504q 12643522
-
(2002)
J Proteome Res
, vol.1
, pp. 21-26
-
-
Tabb, D.L.1
McDonald, W.H.2
Yates III, J.R.3
-
28
-
-
0030681260
-
The significance of digital gene expression profiles
-
9331369
-
Audic S Claverie JM The significance of digital gene expression profiles Genome Res 1997, 7:986-995 9331369
-
(1997)
Genome Res
, vol.7
, pp. 986-995
-
-
Audic, S.1
Claverie, J.M.2
-
29
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini Y Hochberg Y Controlling the false discovery rate: A practical and powerful approach to multiple testing J R Stat Soc Ser B 1995, 57:289-300
-
(1995)
J R Stat Soc Ser B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
30
-
-
0030771026
-
Signal transduction pathways and their relevance in human astrocytomas
-
10.1023/A:1005800114912 9440022
-
Feldkamp MM Lau N Guha A Signal transduction pathways and their relevance in human astrocytomas J Neurooncol 1997, 35:223-248 10.1023/ A:1005800114912 9440022
-
(1997)
J Neurooncol
, vol.35
, pp. 223-248
-
-
Feldkamp, M.M.1
Lau, N.2
Guha, A.3
-
31
-
-
0028343655
-
Structure-activity relationships among monoterpene inhibitors of protein isoprenylation and cell proliferation
-
10.1016/0006-2952(94)90341-7 8185648
-
Crowell PL Ren Z Lin S Vedejs E Gould MN Structure-activity relationships among monoterpene inhibitors of protein isoprenylation and cell proliferation Biochem Pharmacol 1994, 47:1405-1415 10.1016/ 0006-2952(94)90341-7 8185648
-
(1994)
Biochem Pharmacol
, vol.47
, pp. 1405-1415
-
-
Crowell, P.L.1
Ren, Z.2
Lin, S.3
Vedejs, E.4
Gould, M.N.5
-
32
-
-
33748676444
-
RhoA protein expression correlates positively with degree of malignancy in astrocytomas
-
10.1016/j.neulet.2006.08.032 16978776
-
Yan B Chour HH Peh BK Lim C Salto-Tellez M RhoA protein expression correlates positively with degree of malignancy in astrocytomas Neurosci Lett 2006, 407:124-126 10.1016/j.neulet.2006.08.032 16978776
-
(2006)
Neurosci Lett
, vol.407
, pp. 124-126
-
-
Yan, B.1
Chour, H.H.2
Peh, B.K.3
Lim, C.4
Salto-Tellez, M.5
-
33
-
-
62549101517
-
RhoB regulates TNFalpha-induced Akt activation and angiogenesis
-
10.1016/j.vph.2006.08.187
-
Fernandez-Borja M RhoB regulates TNFalpha-induced Akt activation and angiogenesis Vascular Pharmacology 45:e44 10.1016/j.vph.2006.08.187
-
Vascular Pharmacology
, vol.45
-
-
Fernandez-Borja, M.1
-
35
-
-
0035163845
-
Transcriptional regulation and function during the human cell cycle
-
11137997
-
Cho RJ Huang M Campbell MJ Dong H Steinmetz L Sapinoso L Hampton G Elledge SJ Davis RW Lockhart DJ Transcriptional regulation and function during the human cell cycle Nat Genet 2001, 27:48-54 11137997
-
(2001)
Nat Genet
, vol.27
, pp. 48-54
-
-
Cho, R.J.1
Huang, M.2
Campbell, M.J.3
Dong, H.4
Steinmetz, L.5
Sapinoso, L.6
Hampton, G.7
Elledge, S.J.8
Davis, R.W.9
Lockhart, D.J.10
-
36
-
-
0034352940
-
POWER_SAGE: Comparing statistical tests for SAGE experiments
-
10.1093/bioinformatics/16.11.953 11159306
-
Man MZ Wang X Wang Y POWER_SAGE: Comparing statistical tests for SAGE experiments Bioinformatics 2000, 16:953-959 10.1093/bioinformatics/ 16.11.953 11159306
-
(2000)
Bioinformatics
, vol.16
, pp. 953-959
-
-
Man, M.Z.1
Wang, X.2
Wang, Y.3
-
37
-
-
24644470505
-
Ontological analysis of gene expression data: Current tools, limitations, and open problems
-
2435250 15994189 10.1093/bioinformatics/bti565
-
Khatri P Draghici S Ontological analysis of gene expression data: current tools, limitations, and open problems Bioinformatics 2005, 21:3587-3595 2435250 15994189 10.1093/bioinformatics/bti565
-
(2005)
Bioinformatics
, vol.21
, pp. 3587-3595
-
-
Khatri, P.1
Draghici, S.2
-
38
-
-
36448946146
-
Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysis
-
10.1093/bioinformatics/btm440 17848398
-
Grossmann S Bauer S Robinson PN Vingron M Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysis Bioinformatics 2007, 23:3024-3031 10.1093/bioinformatics/btm440 17848398
-
(2007)
Bioinformatics
, vol.23
, pp. 3024-3031
-
-
Grossmann, S.1
Bauer, S.2
Robinson, P.N.3
Vingron, M.4
|