-
1
-
-
45449115390
-
Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences
-
[Medline]
-
Berger MF, Badis G, Gehrke AR, Talukder S, Philippakis AA, Pena-Castillo L, Alleyne TM, Mnaimneh S, Botvinnik OB, Chan ET, et al. 2008. Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell 133: 1266-1276.[Medline]
-
(2008)
Cell
, vol.133
, pp. 1266-1276
-
-
Berger, M.F.1
Badis, G.2
Gehrke, A.R.3
Talukder, S.4
Philippakis, A.A.5
Pena-Castillo, L.6
Alleyne, T.M.7
Mnaimneh, S.8
Botvinnik, O.B.9
Chan, E.T.10
-
2
-
-
71049156699
-
Identification of novel serological biomarkers for inflammatory bowel disease using Escherichia coli proteome chip
-
[Abstract/Free Full Text]
-
Chen CS, Sullivan S, Anderson T, Tan AC, Alex PJ, Brant SR, Cuffari C, Bayless TM, Talor MV, Burek CL, et al. 2009. Identification of novel serological biomarkers for inflammatory bowel disease using Escherichia coli proteome chip. Mol Cell Proteomics 8: 1765-1776.[Abstract/Free Full Text]
-
(2009)
Mol Cell Proteomics
, vol.8
, pp. 1765-1776
-
-
Chen, C.S.1
Sullivan, S.2
Anderson, T.3
Tan, A.C.4
Alex, P.J.5
Brant, S.R.6
Cuffari, C.7
Bayless, T.M.8
Talor, M.V.9
Burek, C.L.10
-
3
-
-
7444267933
-
A gateway-compatible yeast one-hybrid system
-
[Abstract/Free Full Text]
-
Deplancke B, Dupuy D, Vidal M, Walhout AJ. 2004. A gateway-compatible yeast one-hybrid system. Genome Res 14: 2093-2101.[Abstract/Free Full Text]
-
(2004)
Genome Res
, vol.14
, pp. 2093-2101
-
-
Deplancke, B.1
Dupuy, D.2
Vidal, M.3
Walhout, A.J.4
-
4
-
-
33744972290
-
A gene-centered C. Elegans protein-DNA interaction network
-
[Medline]
-
Deplancke B, Mukhopadhyay A, Ao W, Elewa AM, Grove CA, Martinez NJ, Sequerra R, Doucette-Stamm L, Reece-Hoyes JS, Hope IA, et al. 2006. A gene-centered C. elegans protein-DNA interaction network. Cell 125: 1193-1205.[Medline]
-
(2006)
Cell
, vol.125
, pp. 1193-1205
-
-
Deplancke, B.1
Mukhopadhyay, A.2
Ao, W.3
Elewa, A.M.4
Grove, C.A.5
Martinez, N.J.6
Sequerra, R.7
Doucette-Stamm, L.8
Reece-Hoyes, J.S.9
Hope, I.A.10
-
5
-
-
33747064917
-
How does DNA sequence motif discovery work?
-
[Medline]
-
D'Haeseleer P. 2006. How does DNA sequence motif discovery work? Nat Biotechnol 24: 959-961.[Medline]
-
(2006)
Nat Biotechnol
, vol.24
, pp. 959-961
-
-
D'haeseleer, P.1
-
6
-
-
73149086161
-
A protein microarray-based analysis of S-nitrosylation
-
[Abstract/Free Full Text]
-
Foster MW, Forrester MT, Stamler JS. 2009. A protein microarray-based analysis of S-nitrosylation. Proc Natl Acad Sci 106: 18948-18953.[Abstract/Free Full Text]
-
(2009)
Proc Natl Acad Sci
, vol.106
, pp. 18948-18953
-
-
Foster, M.W.1
Forrester, M.T.2
Stamler, J.S.3
-
7
-
-
5644229499
-
Regulation of gene expression by a metabolic enzyme
-
[Abstract/Free Full Text]
-
Hall DA, Zhu H, Zhu X, Royce T, Gerstein M, Snyder M. 2004. Regulation of gene expression by a metabolic enzyme. Science 306: 482-484.[Abstract/Free Full Text]
-
(2004)
Science
, vol.306
, pp. 482-484
-
-
Hall, D.A.1
Zhu, H.2
Zhu, X.3
Royce, T.4
Gerstein, M.5
Snyder, M.6
-
8
-
-
30344439849
-
Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity
-
[Medline]
-
Hallikas O, Palin K, Sinjushina N, Rautiainen R, Partanen J, Ukkonen E, Taipale J. 2006. Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity. Cell 124: 47-59.[Medline]
-
(2006)
Cell
, vol.124
, pp. 47-59
-
-
Hallikas, O.1
Palin, K.2
Sinjushina, N.3
Rautiainen, R.4
Partanen, J.5
Ukkonen, E.6
Taipale, J.7
-
9
-
-
33745614618
-
Linking DNA-binding proteins to their recognition sequences by using protein microarrays
-
[Abstract/Free Full Text]
-
Ho SW, Jona G, Chen CT, Johnston M, Snyder M. 2006. Linking DNA-binding proteins to their recognition sequences by using protein microarrays. Proc Natl Acad Sci 103: 9940-9945.[Abstract/Free Full Text]
-
(2006)
Proc Natl Acad Sci
, vol.103
, pp. 9940-9945
-
-
Ho, S.W.1
Jona, G.2
Chen, C.T.3
Johnston, M.4
Snyder, M.5
-
10
-
-
34447557663
-
A protein chip approach for high-throughput antigen identification and characterization
-
[Medline]
-
Hu S, Li Y, Liu G, Song Q, Wang L, Han Y, Zhang Y, Song Y, Yao X, Tao Y, et al. 2007. A protein chip approach for high-throughput antigen identification and characterization. Proteomics 7: 2151-2161.[Medline]
-
(2007)
Proteomics
, vol.7
, pp. 2151-2161
-
-
Hu, S.1
Li, Y.2
Liu, G.3
Song, Q.4
Wang, L.5
Han, Y.6
Zhang, Y.7
Song, Y.8
Yao, X.9
Tao, Y.10
-
11
-
-
70350340058
-
Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling
-
[Medline]
-
Hu S, Xie Z, Onishi A, Yu X, Jiang L, Lin J, Rho HS, Woodard C, Wang H, Jeong JS, et al. 2009. Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling. Cell 139: 610-622.[Medline]
-
(2009)
Cell
, vol.139
, pp. 610-622
-
-
Hu, S.1
Xie, Z.2
Onishi, A.3
Yu, X.4
Jiang, L.5
Lin, J.6
Rho, H.S.7
Woodard, C.8
Wang, H.9
Jeong, J.S.10
-
12
-
-
9344247454
-
Finding new components of the target of rapamycin (TOR) signaling network through chemical genetics and proteome chips
-
[Abstract/Free Full Text]
-
Huang J, Zhu H, Haggarty SJ, Spring DR, Hwang H, Jin F, Snyder M, Schreiber SL. 2004. Finding new components of the target of rapamycin (TOR) signaling network through chemical genetics and proteome chips. Proc Natl Acad Sci 101: 16594-16599.[Abstract/Free Full Text]
-
(2004)
Proc Natl Acad Sci
, vol.101
, pp. 16594-16599
-
-
Huang, J.1
Zhu, H.2
Haggarty, S.J.3
Spring, D.R.4
Hwang, H.5
Jin, F.6
Snyder, M.7
Schreiber, S.L.8
-
13
-
-
30544449081
-
A quantitative protein interaction network for the ErbB receptors using protein microarrays
-
[Medline]
-
Jones RB, Gordus A, Krall JA, MacBeath G. 2006. A quantitative protein interaction network for the ErbB receptors using protein microarrays. Nature 439: 168-174.[Medline]
-
(2006)
Nature
, vol.439
, pp. 168-174
-
-
Jones, R.B.1
Gordus, A.2
Krall, J.A.3
Macbeath, G.4
-
14
-
-
70349333832
-
Global analysis of the glycoproteome in Saccharomyces cerevisiae reveals new roles for protein glycosylation in eukaryotes
-
doi: 10.1038/msb.2009.64.[Medline]
-
Kung LA, Tao SC, Qian J, Smith MG, Snyder M, Zhu H. 2009. Global analysis of the glycoproteome in Saccharomyces cerevisiae reveals new roles for protein glycosylation in eukaryotes. Mol Syst Biol 5: 308. doi: 10.1038/msb.2009.64.[Medline]
-
(2009)
Mol Syst Biol
, vol.5
, pp. 308
-
-
Kung, L.A.1
Tao, S.C.2
Qian, J.3
Smith, M.G.4
Snyder, M.5
Zhu, H.6
-
15
-
-
0033388858
-
In vivo cross-linking and immunoprecipitation for studying dynamic Protein: DNA associations in a chromatin environment
-
[Medline]
-
Kuo MH, Allis CD. 1999. In vivo cross-linking and immunoprecipitation for studying dynamic Protein:DNA associations in a chromatin environment. Methods 19: 425-433.[Medline]
-
(1999)
Methods
, vol.19
, pp. 425-433
-
-
Kuo, M.H.1
Allis, C.D.2
-
16
-
-
62149143727
-
Protein acetylation microarray reveals that NuA4 controls key metabolic target regulating gluconeogenesis
-
[Medline]
-
Lin YY, Lu JY, Zhang J, Walter W, Dang W, Wan J, Tao SC, Qian J, Zhao Y, Boeke JD, et al. 2009. Protein acetylation microarray reveals that NuA4 controls key metabolic target regulating gluconeogenesis. Cell 136: 1073-1084.[Medline]
-
(2009)
Cell
, vol.136
, pp. 1073-1084
-
-
Lin, Y.Y.1
Lu, J.Y.2
Zhang, J.3
Walter, W.4
Dang, W.5
Wan, J.6
Tao, S.C.7
Qian, J.8
Zhao, Y.9
Boeke, J.D.10
-
17
-
-
39049148016
-
Functional dissection of a HECT ubiquitin E3 ligase
-
[Abstract/Free Full Text]
-
Lu JY, Lin YY, Qian J, Tao SC, Zhu J, Pickart C, Zhu H. 2008. Functional dissection of a HECT ubiquitin E3 ligase. Mol Cell Proteomics 7: 35-45.[Abstract/Free Full Text]
-
(2008)
Mol Cell Proteomics
, vol.7
, pp. 35-45
-
-
Lu, J.Y.1
Lin, Y.Y.2
Qian, J.3
Tao, S.C.4
Zhu, J.5
Pickart, C.6
Zhu, H.7
-
18
-
-
39549092828
-
Glycomics: Towards bioinformatic approaches to understanding glycosylation
-
[Medline]
-
Mahal LK. 2008. Glycomics: Towards bioinformatic approaches to understanding glycosylation. Anticancer Agents Med Chem 8: 37-51.[Medline]
-
(2008)
Anticancer Agents Med Chem
, vol.8
, pp. 37-51
-
-
Mahal, L.K.1
-
19
-
-
23444446753
-
A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors
-
[Medline]
-
Meng X, Brodsky MH, Wolfe SA. 2005. A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors. Nat Biotechnol 23: 988-994.[Medline]
-
(2005)
Nat Biotechnol
, vol.23
, pp. 988-994
-
-
Meng, X.1
Brodsky, M.H.2
Wolfe, S.A.3
-
20
-
-
45449111373
-
Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites
-
[Medline]
-
Noyes MB, Christensen RG, Wakabayashi A, Stormo GD, Brodsky MH, Wolfe SA. 2008. Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell 133: 1277-1289.[Medline]
-
(2008)
Cell
, vol.133
, pp. 1277-1289
-
-
Noyes, M.B.1
Christensen, R.G.2
Wakabayashi, A.3
Stormo, G.D.4
Brodsky, M.H.5
Wolfe, S.A.6
-
21
-
-
33846393568
-
Chip-based analysis of SUMO (small ubiquitin-like modifier) conjugation to a target protein
-
[Medline]
-
Oh YH, Hong MY, Jin Z, Lee T, Han MK, Park S, Kim HS. 2007. Chip-based analysis of SUMO (small ubiquitin-like modifier) conjugation to a target protein. Biosens Bioelectron 22: 1260-1267.[Medline]
-
(2007)
Biosens Bioelectron
, vol.22
, pp. 1260-1267
-
-
Oh, Y.H.1
Hong, M.Y.2
Jin, Z.3
Lee, T.4
Han, M.K.5
Park, S.6
Kim, H.S.7
-
22
-
-
28444460297
-
Global analysis of protein phosphorylation in yeast
-
[Medline]
-
Ptacek J, Devgan G, Michaud G, Zhu H, Zhu X, Fasolo J, Guo H, Jona G, Breitkreutz A, Sopko R, et al. 2005. Global analysis of protein phosphorylation in yeast. Nature 438: 679-684.[Medline]
-
(2005)
Nature
, vol.438
, pp. 679-684
-
-
Ptacek, J.1
Devgan, G.2
Michaud, G.3
Zhu, H.4
Zhu, X.5
Fasolo, J.6
Guo, H.7
Jona, G.8
Breitkreutz, A.9
Sopko, R.10
-
23
-
-
0034704248
-
Genome-wide location and function of DNA binding proteins
-
[Abstract/Free Full Text]
-
Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E, et al. 2000. Genome-wide location and function of DNA binding proteins. Science 290: 2306-2309.[Abstract/Free Full Text]
-
(2000)
Science
, vol.290
, pp. 2306-2309
-
-
Ren, B.1
Robert, F.2
Wyrick, J.J.3
Aparicio, O.4
Jennings, E.G.5
Simon, I.6
Zeitlinger, J.7
Schreiber, J.8
Hannett, N.9
Kanin, E.10
-
24
-
-
34547633677
-
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
-
[Medline]
-
Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, et al. 2007. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 4: 651-657.[Medline]
-
(2007)
Nat Methods
, vol.4
, pp. 651-657
-
-
Robertson, G.1
Hirst, M.2
Bainbridge, M.3
Bilenky, M.4
Zhao, Y.5
Zeng, T.6
Euskirchen, G.7
Bernier, B.8
Varhol, R.9
Delaney, A.10
-
25
-
-
0036022523
-
High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites
-
[Medline]
-
Roulet E, Busso S, Camargo AA, Simpson AJ, Mermod N, Bucher P. 2002. High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites. Nat Biotechnol 20: 831-835.[Medline]
-
(2002)
Nat Biotechnol
, vol.20
, pp. 831-835
-
-
Roulet, E.1
Busso, S.2
Camargo, A.A.3
Simpson, A.J.4
Mermod, N.5
Bucher, P.6
-
26
-
-
44649091314
-
Identification of novel substrates for Cdk5 and new targets for Cdk5 inhibitors using high-density protein microarrays
-
[Medline]
-
Schnack C, Hengerer B, Gillardon F. 2008. Identification of novel substrates for Cdk5 and new targets for Cdk5 inhibitors using high-density protein microarrays. Proteomics 8: 1980-1986.[Medline]
-
(2008)
Proteomics
, vol.8
, pp. 1980-1986
-
-
Schnack, C.1
Hengerer, B.2
Gillardon, F.3
-
27
-
-
73649129599
-
Novel autoimmune hepatitis-specific autoantigens identified using protein microarray technology
-
[Medline]
-
Song Q, Liu G, Hu S, Zhang Y, Tao Y, Han Y, Zeng H, Huang W, Li F, Chen P, et al. 2010. Novel autoimmune hepatitis-specific autoantigens identified using protein microarray technology. J Proteome Res 9: 30-39.[Medline]
-
(2010)
J Proteome Res
, vol.9
, pp. 30-39
-
-
Song, Q.1
Liu, G.2
Hu, S.3
Zhang, Y.4
Tao, Y.5
Han, Y.6
Zeng, H.7
Huang, W.8
Li, F.9
Chen, P.10
-
29
-
-
53049096773
-
Lectin microarrays identify cell-specific and functionally significant cell surface glycan markers
-
[Abstract/Free Full Text]
-
Tao SC, Li Y, Zhou J, Qian J, Schnaar RL, Zhang Y, Goldstein IJ, Zhu H, Schneck JP. 2008. Lectin microarrays identify cell-specific and functionally significant cell surface glycan markers. Glycobiology 18: 761-769.[Abstract/Free Full Text]
-
(2008)
Glycobiology
, vol.18
, pp. 761-769
-
-
Tao, S.C.1
Li, Y.2
Zhou, J.3
Qian, J.4
Schnaar, R.L.5
Zhang, Y.6
Goldstein, I.J.7
Zhu, H.8
Schneck, J.P.9
-
30
-
-
62549128139
-
A census of human transcription factors: Function, expression and evolution
-
[Medline]
-
Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM. 2009. A census of human transcription factors: Function, expression and evolution. Nat Rev Genet 10: 252-263.[Medline]
-
(2009)
Nat Rev Genet
, vol.10
, pp. 252-263
-
-
Vaquerizas, J.M.1
Kummerfeld, S.K.2
Teichmann, S.A.3
Luscombe, N.M.4
-
31
-
-
77950472891
-
hPDI: A database of experimental human protein-DNA interactions
-
[Abstract/Free Full Text]
-
Xie Z, Hu S, Blackshaw S, Zhu H, Qian J. 2010. hPDI: A database of experimental human protein-DNA interactions. Bioinformatics 26: 287-289.[Abstract/Free Full Text]
-
(2010)
Bioinformatics
, vol.26
, pp. 287-289
-
-
Xie, Z.1
Hu, S.2
Blackshaw, S.3
Zhu, H.4
Qian, J.5
-
32
-
-
0033768106
-
Analysis of yeast protein kinases using protein chips
-
[Medline]
-
Zhu H, Klemic JF, Chang S, Bertone P, Casamayor A, Klemic KG, Smith D, Gerstein M, Reed MA, Snyder M. 2000. Analysis of yeast protein kinases using protein chips. Nat Genet 26: 283-289.[Medline]
-
(2000)
Nat Genet
, vol.26
, pp. 283-289
-
-
Zhu, H.1
Klemic, J.F.2
Chang, S.3
Bertone, P.4
Casamayor, A.5
Klemic, K.G.6
Smith, D.7
Gerstein, M.8
Reed, M.A.9
Snyder, M.10
-
33
-
-
0035860499
-
Global analysis of protein activities using proteome chips
-
[Abstract/Free Full Text]
-
Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, Bertone P, Lan N, Jansen R, Bidlingmaier S, Houfek T, et al. 2001. Global analysis of protein activities using proteome chips. Science 293: 2101-2105.[Abstract/Free Full Text]
-
(2001)
Science
, vol.293
, pp. 2101-2105
-
-
Zhu, H.1
Bilgin, M.2
Bangham, R.3
Hall, D.4
Casamayor, A.5
Bertone, P.6
Lan, N.7
Jansen, R.8
Bidlingmaier, S.9
Houfek, T.10
-
34
-
-
33645225281
-
Severe acute respiratory syndrome diagnostics using a coronavirus protein microarray
-
[Abstract/Free Full Text]
-
Zhu H, Hu S, Jona G, Zhu X, Kreiswirth N, Willey BM, Mazzulli T, Liu G, Song Q, Chen P, et al. 2006a. Severe acute respiratory syndrome diagnostics using a coronavirus protein microarray. Proc Natl Acad Sci 103: 4011-4016.[Abstract/Free Full Text]
-
(2006)
Proc Natl Acad Sci
, vol.103
, pp. 4011-4016
-
-
Zhu, H.1
Hu, S.2
Jona, G.3
Zhu, X.4
Kreiswirth, N.5
Willey, B.M.6
Mazzulli, T.7
Liu, G.8
Song, Q.9
Chen, P.10
-
35
-
-
33847705714
-
ProCAT: A data analysis approach for protein microarrays
-
doi: 10.1186/gb-2006-7-11-r110.[Medline]
-
Zhu X, Gerstein M, Snyder M. 2006b. ProCAT: A data analysis approach for protein microarrays. Genome Biol 7: R110. doi: 10.1186/gb-2006-7-11-r110.[Medline]
-
(2006)
Genome Biol
, vol.7
-
-
Zhu, X.1
Gerstein, M.2
Snyder, M.3
-
36
-
-
33847655582
-
RNA-binding proteins that inhibit RNA virus infection
-
[Abstract/Free Full Text]
-
Zhu J, Gopinath K, Murali A, Yi G, Hayward SD, Zhu H, Kao C. 2007. RNA-binding proteins that inhibit RNA virus infection. Proc Natl Acad Sci 104: 3129-3134.[Abstract/Free Full Text]
-
(2007)
Proc Natl Acad Sci
, vol.104
, pp. 3129-3134
-
-
Zhu, J.1
Gopinath, K.2
Murali, A.3
Yi, G.4
Hayward, S.D.5
Zhu, H.6
Kao, C.7
|