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Results: 1 to 20 of 78

References for PMC Articles for PubMed (Select 21470963)

1.

Stochastic relaxation, gibbs distributions, and the bayesian restoration of images.

Geman S, Geman D.

IEEE Trans Pattern Anal Mach Intell. 1984 Jun;6(6):721-41.

PMID:
22499653
2.

Regulating the regulators: modulators of transcription factor activity.

Everett L, Hansen M, Hannenhalli S.

Methods Mol Biol. 2010;674:297-312. doi: 10.1007/978-1-60761-854-6_19.

PMID:
20827600
3.

Discovering modulators of gene expression.

Babur O, Demir E, Gönen M, Sander C, Dogrusoz U.

Nucleic Acids Res. 2010 Sep;38(17):5648-56. doi: 10.1093/nar/gkq287. Epub 2010 May 13.

4.

Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs.

Mok J, Kim PM, Lam HY, Piccirillo S, Zhou X, Jeschke GR, Sheridan DL, Parker SA, Desai V, Jwa M, Cameroni E, Niu H, Good M, Remenyi A, Ma JL, Sheu YJ, Sassi HE, Sopko R, Chan CS, De Virgilio C, Hollingsworth NM, Lim WA, Stern DF, Stillman B, Andrews BJ, Gerstein MB, Snyder M, Turk BE.

Sci Signal. 2010 Feb 16;3(109):ra12. doi: 10.1126/scisignal.2000482.

5.

Mimosa: mixture model of co-expression to detect modulators of regulatory interaction.

Hansen M, Everett L, Singh L, Hannenhalli S.

Algorithms Mol Biol. 2010 Jan 4;5:4. doi: 10.1186/1748-7188-5-4.

6.
7.

Genome-wide identification of post-translational modulators of transcription factor activity in human B cells.

Wang K, Saito M, Bisikirska BC, Alvarez MJ, Lim WK, Rajbhandari P, Shen Q, Nemenman I, Basso K, Margolin AA, Klein U, Dalla-Favera R, Califano A.

Nat Biotechnol. 2009 Sep;27(9):829-39. doi: 10.1038/nbt.1563. Epub 2009 Sep 9.

8.

Transcriptional regulatory circuits: predicting numbers from alphabets.

Kim HD, Shay T, O'Shea EK, Regev A.

Science. 2009 Jul 24;325(5939):429-32. doi: 10.1126/science.1171347. Review.

9.

Extracting transcription factor targets from ChIP-Seq data.

Tuteja G, White P, Schug J, Kaestner KH.

Nucleic Acids Res. 2009 Sep;37(17):e113. doi: 10.1093/nar/gkp536. Epub 2009 Jun 24.

10.

Protein microarrays.

Fasolo J, Snyder M.

Methods Mol Biol. 2009;548:209-22. doi: 10.1007/978-1-59745-540-4_12.

PMID:
19521827
11.

Protein acetylation microarray reveals that NuA4 controls key metabolic target regulating gluconeogenesis.

Lin YY, Lu JY, Zhang J, Walter W, Dang W, Wan J, Tao SC, Qian J, Zhao Y, Boeke JD, Berger SL, Zhu H.

Cell. 2009 Mar 20;136(6):1073-84. doi: 10.1016/j.cell.2009.01.033.

12.

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls.

Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB.

Nat Biotechnol. 2009 Jan;27(1):66-75. doi: 10.1038/nbt.1518. Epub 2009 Jan 4.

13.

A predictive model of the oxygen and heme regulatory network in yeast.

Kundaje A, Xin X, Lan C, Lianoglou S, Zhou M, Zhang L, Leslie C.

PLoS Comput Biol. 2008 Nov;4(11):e1000224. doi: 10.1371/journal.pcbi.1000224. Epub 2008 Nov 14.

14.

STRING 8--a global view on proteins and their functional interactions in 630 organisms.

Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C.

Nucleic Acids Res. 2009 Jan;37(Database issue):D412-6. doi: 10.1093/nar/gkn760. Epub 2008 Oct 21.

15.

PTM-Switchboard--a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes.

Everett L, Vo A, Hannenhalli S.

Nucleic Acids Res. 2009 Jan;37(Database issue):D66-71. doi: 10.1093/nar/gkn731. Epub 2008 Oct 15.

16.

Yeast Yak1 kinase, a bridge between PKA and stress-responsive transcription factors, Hsf1 and Msn2/Msn4.

Lee P, Cho BR, Joo HS, Hahn JS.

Mol Microbiol. 2008 Nov;70(4):882-95. doi: 10.1111/j.1365-2958.2008.06450.x. Epub 2008 Sep 11.

PMID:
18793336
17.

Inferring condition-specific modulation of transcription factor activity in yeast through regulon-based analysis of genomewide expression.

Boorsma A, Lu XJ, Zakrzewska A, Klis FM, Bussemaker HJ.

PLoS One. 2008 Sep 3;3(9):e3112. doi: 10.1371/journal.pone.0003112.

18.

The Predikin webserver: improved prediction of protein kinase peptide specificity using structural information.

Saunders NF, Kobe B.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W286-90. doi: 10.1093/nar/gkn279. Epub 2008 May 13.

19.

Eukaryotic transcription factor binding sites--modeling and integrative search methods.

Hannenhalli S.

Bioinformatics. 2008 Jun 1;24(11):1325-31. doi: 10.1093/bioinformatics/btn198. Epub 2008 Apr 21. Review.

20.

From promoter analysis to transcriptional regulatory network prediction using PAINT.

Gonye GE, Chakravarthula P, Schwaber JS, Vadigepalli R.

Methods Mol Biol. 2007;408:49-68. doi: 10.1007/978-1-59745-547-3_4.

PMID:
18314577
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