-
1
-
-
79955036679
-
Experimental strategies for studying transcription factor-DNA binding specificities
-
Geertz, M. and Maerkl, S.J. (2010) Experimental strategies for studying transcription factor-DNA binding specificities. Brief. Funct. Genomics, 9, 362-373.
-
(2010)
Brief. Funct. Genomics
, vol.9
, pp. 362-373
-
-
Geertz, M.1
Maerkl, S.J.2
-
2
-
-
70349312354
-
ChIP-seq: Advantages and challenges of a maturing technology
-
Park, P.J. (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat. Rev. Genet., 10, 669-680.
-
(2009)
Nat. Rev. Genet.
, vol.10
, pp. 669-680
-
-
Park, P.J.1
-
3
-
-
67649982744
-
Diversity and complexity in DNA recognition by transcription factors
-
Badis, G., Berger, M.F., Philippakis, A.A., Talukder, S., Gehrke, A.R., Jaeger, S.A., Chan, E.T., Metzler, G., Vedenko, A., Chen, X. et al. (2009) Diversity and complexity in DNA recognition by transcription factors. Science, 324, 1720-1723.
-
(2009)
Science
, vol.324
, pp. 1720-1723
-
-
Badis, G.1
Berger, M.F.2
Philippakis, A.A.3
Talukder, S.4
Gehrke, A.R.5
Jaeger, S.A.6
Chan, E.T.7
Metzler, G.8
Vedenko, A.9
Chen, X.10
-
4
-
-
74549209548
-
Inferring binding energies from selected binding sites
-
Zhao, Y., Granas, D. and Stormo, G.D. (2009) Inferring binding energies from selected binding sites. PLoS Comp. Biol., 5, e1000590.
-
(2009)
PLoS Comp. Biol.
, vol.5
-
-
Zhao, Y.1
Granas, D.2
Stormo, G.D.3
-
5
-
-
77953006022
-
Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities
-
10.101/gr.100552.109
-
Jolma, A., Kivioja, T., Toivonen, J., Cheng, L., Wei, G., Enge, M., Taipale, M., Vaquerizas, J.M., Yan, J., Sillanpaa, M.J. et al. (2010) Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Res, 20, 861-873, 10.101/gr.100552.109.
-
(2010)
Genome Res
, vol.20
, pp. 861-873
-
-
Jolma, A.1
Kivioja, T.2
Toivonen, J.3
Cheng, L.4
Wei, G.5
Enge, M.6
Taipale, M.7
Vaquerizas, J.M.8
Yan, J.9
Sillanpaa, M.J.10
-
6
-
-
79960277492
-
Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument
-
10.038/ nbt.1882
-
Nutiu, R., Friedman, R.C., Luo, S., Khrebtukova, I., Silva, D., Li, R., Zhang, L., Schroth, G.P. and Burge, C.B. (2011) Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument. Nat. Biotechnol., 29, 659-664, 10.038/ nbt.1882.
-
(2011)
Nat. Biotechnol.
, vol.29
, pp. 659-664
-
-
Nutiu, R.1
Friedman, R.C.2
Luo, S.3
Khrebtukova, I.4
Silva, D.5
Li, R.6
Zhang, L.7
Schroth, G.P.8
Burge, C.B.9
-
7
-
-
33846467150
-
A systems approach to measuring the binding energy landscapes of transcription factors
-
Maerkl, S.J. and Quake, S.R. (2007) A systems approach to measuring the binding energy landscapes of transcription factors. Science, 315, 233-237.
-
(2007)
Science
, vol.315
, pp. 233-237
-
-
Maerkl, S.J.1
Quake, S.R.2
-
8
-
-
0029809862
-
Reverse two-hybrid and one-hybrid systems to detect dissociation of protein-protein and DNA-protein interactions
-
Vidal, M., Brachmann, R.K., Fattaey, A., Harlow, E. and Boeke, J.D. (1996) Reverse two-hybrid and one-hybrid systems to detect dissociation of protein-protein and DNA-protein interactions. Proc. Natl Acad. Sci. USA, 93, 10315-10320.
-
(1996)
Proc. Natl Acad. Sci. USA
, vol.93
, pp. 10315-10320
-
-
Vidal, M.1
Brachmann, R.K.2
Fattaey, A.3
Harlow, E.4
Boeke, J.D.5
-
9
-
-
82355191645
-
Automated protein-DNA interaction screening of Drosophila regulatory elements
-
Hens, K., Feuz, J.-D., Isakova, A., Iagovitina, A., Massouras, A., Bryois, J., Callaerts, P., Celniker, S.E. and Deplancke, B. (2011) Automated protein-DNA interaction screening of Drosophila regulatory elements. Nat. Methods, 8, 1065-1070.
-
(2011)
Nat. Methods
, vol.8
, pp. 1065-1070
-
-
Hens, K.1
Feuz, J.-D.2
Isakova, A.3
Iagovitina, A.4
Massouras, A.5
Bryois, J.6
Callaerts, P.7
Celniker, S.E.8
Deplancke, B.9
-
10
-
-
63849338777
-
Experimental advances in the characterization of metazoan gene regulatory networks
-
Deplancke, B. (2009) Experimental advances in the characterization of metazoan gene regulatory networks. Brief. Funct. Genomic. Proteomic., 8, 12.
-
(2009)
Brief. Funct. Genomic. Proteomic.
, vol.8
, pp. 12
-
-
Deplancke, B.1
-
11
-
-
70350340058
-
Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling
-
Hu, S.S., Xie, Z.Z., Onishi, A.A., Yu, X.X., Jiang, L.L., Lin, J.J., Rho, H.-S.H., Woodard, C.C., Wang, H.H., Jeong, J.S.J. et al. (2009) Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling. Cell, 139, 610-622.
-
(2009)
Cell
, vol.139
, pp. 610-622
-
-
Hu, S.S.1
Xie, Z.Z.2
Onishi, A.A.3
Yu, X.X.4
Jiang, L.L.5
Lin, J.J.6
Rho, H.-S.H.7
Woodard, C.C.8
Wang, H.H.9
Jeong, J.S.J.10
-
12
-
-
44449102838
-
Next-generation high-density self-assembling functional protein arrays
-
Ramachandran, N., Raphael, J.V., Hainsworth, E., Demirkan, G., Fuentes, M.G., Rolfs, A., Hu, Y. and Labaer, J. (2008) Next-generation high-density self-assembling functional protein arrays. Nat. Methods, 5, 535-538.
-
(2008)
Nat. Methods
, vol.5
, pp. 535-538
-
-
Ramachandran, N.1
Raphael, J.V.2
Hainsworth, E.3
Demirkan, G.4
Fuentes, M.G.5
Rolfs, A.6
Hu, Y.7
Labaer, J.8
-
13
-
-
84867372779
-
Massively parallel measurements of molecular interaction kinetics on a microfluidic platform
-
Geertz, M., Shore, D. and Maerkl, S.J. (2012) Massively parallel measurements of molecular interaction kinetics on a microfluidic platform. Proc. Natl Acad. Sci., 109, 16540-16545.
-
(2012)
Proc. Natl Acad. Sci.
, vol.109
, pp. 16540-16545
-
-
Geertz, M.1
Shore, D.2
Maerkl, S.J.3
-
14
-
-
77956654773
-
De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis
-
Fordyce, P.M., Gerber, D., Tran, D., Zheng, J., Li, H., Derisi, J.L. and Quake, S.R. (2010) De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis. Nat. Biotechnol., 28, 970-975.
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 970-975
-
-
Fordyce, P.M.1
Gerber, D.2
Tran, D.3
Zheng, J.4
Li, H.5
Derisi, J.L.6
Quake, S.R.7
-
15
-
-
73249134379
-
Experimental determination of the evolvability of a transcription factor
-
Maerkl, S.J. and Quake, S.R. (2009) Experimental determination of the evolvability of a transcription factor. Proc. Natl Acad. Sci. USA, 106, 18650-18655.
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 18650-18655
-
-
Maerkl, S.J.1
Quake, S.R.2
-
16
-
-
58149229162
-
An in vitro microfluidic approach to generating protein-interaction networks
-
Gerber, D., Maerkl, S.J. and Quake, S.R. (2009) An in vitro microfluidic approach to generating protein-interaction networks. Nat. Methods, 6, 71-74.
-
(2009)
Nat. Methods
, vol.6
, pp. 71-74
-
-
Gerber, D.1
Maerkl, S.J.2
Quake, S.R.3
-
17
-
-
69249191551
-
Highly parallel measurements of interaction kinetic constants with a microfabricated optomechanical device
-
Bates, S.R. and Quake, S.R. (2009) Highly parallel measurements of interaction kinetic constants with a microfabricated optomechanical device. Appl. Phys. Lett., 95, 73705-73705.
-
(2009)
Appl. Phys. Lett.
, vol.95
, pp. 73705-73705
-
-
Bates, S.R.1
Quake, S.R.2
-
18
-
-
77951259297
-
Challenges for modeling global gene regulatory networks during development: Insights from Drosophila
-
Wilczynski, B. and Furlong, E.E. (2010) Challenges for modeling global gene regulatory networks during development: insights from Drosophila. Dev. Biol., 340, 161-169.
-
(2010)
Dev. Biol.
, vol.340
, pp. 161-169
-
-
Wilczynski, B.1
Furlong, E.E.2
-
19
-
-
45449088853
-
Design of compact universal DNA microarrays for protein binding microarray experiments
-
Philippakis, A.A., Qureshi, A.M., Berger, M.F. and Bulyk, M.L. (2008) Design of compact, universal DNA microarrays for protein binding microarray experiments. J. Comput. Biol., 15, 655-665.
-
(2008)
J. Comput. Biol.
, vol.15
, pp. 655-665
-
-
Philippakis, A.A.1
Qureshi, A.M.2
Berger, M.F.3
Bulyk, M.L.4
-
20
-
-
80555129262
-
MITOMI: A microfluidic platform for in vitro characterization of transcription factor-DNA interaction
-
Rockel, S., Geertz, M. and Maerkl, S.J. (2012) MITOMI: a microfluidic platform for in vitro characterization of transcription factor-DNA interaction. Methods Mol. Biol., 786, 97-114.
-
(2012)
Methods Mol. Biol.
, vol.786
, pp. 97-114
-
-
Rockel, S.1
Geertz, M.2
Maerkl, S.J.3
-
21
-
-
33748191291
-
Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE
-
Foat, B.C., Foat, B.C., Morozov, A.V., Morozov, A.V., Bussemaker, H.J. and Bussemaker, H.J. (2006) Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE. Bioinformatics, 22, e141-e149.
-
(2006)
Bioinformatics
, vol.22
-
-
Foat, B.C.1
Foat, B.C.2
Morozov, A.V.3
Morozov, A.V.4
Bussemaker, H.J.5
Bussemaker, H.J.6
-
22
-
-
79959359483
-
Integrated approaches reveal determinants of genome-wide binding and function of the transcription factor Pho4
-
Zhou, X. and O'Shea, E.K. (2011) Integrated approaches reveal determinants of genome-wide binding and function of the transcription factor Pho4. Mol. Cell, 42, 826-836.
-
(2011)
Mol. Cell
, vol.42
, pp. 826-836
-
-
Zhou, X.1
O'shea, E.K.2
-
23
-
-
0031468348
-
Regulation of the twist target gene tinman by modular cis-regulatory elements during early mesoderm development
-
Yin, Z., Yin, Z., Xu, X.L., Xu, X.L., Frasch, M. and Frasch, M. (1997) Regulation of the twist target gene tinman by modular cis-regulatory elements during early mesoderm development. Development, 124, 4971-4982.
-
(1997)
Development
, vol.124
, pp. 4971-4982
-
-
Yin, Z.1
Yin, Z.2
Xu, X.L.3
Xu, X.L.4
Frasch, M.5
Frasch, M.6
-
24
-
-
0030872367
-
Drosophila Mad binds to DNA and directly mediates activation of vestigial by Decapentaplegic
-
Kim, J., Johnson, K., Chen, H.J., Carroll, S. and Laughon, A. (1997) Drosophila Mad binds to DNA and directly mediates activation of vestigial by Decapentaplegic. Nature, 388, 304-308.
-
(1997)
Nature
, vol.388
, pp. 304-308
-
-
Kim, J.1
Johnson, K.2
Chen, H.J.3
Carroll, S.4
Laughon, A.5
-
25
-
-
82355175168
-
Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping
-
Reece-Hoyes, J.S., Diallo, A., Lajoie, B., Kent, A., Shrestha, S., Kadreppa, S., Pesyna, C., Dekker, J., Myers, C.L. and Walhout, A.J. (2011) Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping. Nat. Methods, 8, 1059-1064.
-
(2011)
Nat. Methods
, vol.8
, pp. 1059-1064
-
-
Reece-Hoyes, J.S.1
Diallo, A.2
Lajoie, B.3
Kent, A.4
Shrestha, S.5
Kadreppa, S.6
Pesyna, C.7
Dekker, J.8
Myers, C.L.9
Walhout, A.J.10
-
26
-
-
84859241581
-
Probing the Informational and regulatory plasticity of a transcription factor DNA-binding domain
-
Shultzaberger, R.K., Maerkl, S.J., Kirsch, J.F. and Eisen, M.B. (2012) Probing the Informational and regulatory plasticity of a transcription factor DNA-binding domain. PLoS Genet., 8, e1002614.
-
(2012)
PLoS Genet.
, vol.8
-
-
Shultzaberger, R.K.1
Maerkl, S.J.2
Kirsch, J.F.3
Eisen, M.B.4
-
27
-
-
82355181929
-
A high-throughput microfluidic method for generating and characterizing transcription factor mutant libraries
-
Geertz, M., Rockel, S. and Maerkl, S.J. (2012) A high-throughput microfluidic method for generating and characterizing transcription factor mutant libraries. Methods Mol. Biol., 813, 107-123.
-
(2012)
Methods Mol. Biol.
, vol.813
, pp. 107-123
-
-
Geertz, M.1
Rockel, S.2
Maerkl, S.J.3
-
28
-
-
84875566370
-
Topology and dynamics of the Zebrafish segmentation clock core circuit
-
Schrö ter, C., Ares, S., Morelli, L.G., Isakova, A., Hens, K., Soroldoni, D., Gajewski, M., Jülicher, F., Maerkl, S.J., Deplancke, B. et al. (2012) Topology and dynamics of the Zebrafish segmentation clock core circuit. PLoS Biol., 10, e1001364.
-
(2012)
PLoS Biol.
, vol.10
-
-
Schröter, C.1
Ares, S.2
Morelli, L.G.3
Isakova, A.4
Hens, K.5
Soroldoni, D.6
Gajewski, M.7
Jülicher, F.8
Maerkl, S.J.9
Deplancke, B.10
|