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Items: 15

1.

A Comprehensive Drosophila melanogaster Transcription Factor Interactome.

Shokri L, Inukai S, Hafner A, Weinand K, Hens K, Vedenko A, Gisselbrecht SS, Dainese R, Bischof J, Furger E, Feuz JD, Basler K, Deplancke B, Bulyk ML.

Cell Rep. 2019 Apr 16;27(3):955-970.e7. doi: 10.1016/j.celrep.2019.03.071.

2.

Identification of Human Lineage-Specific Transcriptional Coregulators Enabled by a Glossary of Binding Modules and Tunable Genomic Backgrounds.

Mariani L, Weinand K, Vedenko A, Barrera LA, Bulyk ML.

Cell Syst. 2017 Dec 27;5(6):654. doi: 10.1016/j.cels.2017.12.011. No abstract available.

3.

Identification of Human Lineage-Specific Transcriptional Coregulators Enabled by a Glossary of Binding Modules and Tunable Genomic Backgrounds.

Mariani L, Weinand K, Vedenko A, Barrera LA, Bulyk ML.

Cell Syst. 2017 Sep 27;5(3):187-201.e7. doi: 10.1016/j.cels.2017.06.015. Erratum in: Cell Syst. 2017 Dec 27;5(6):654.

4.

Cardiac Cell Therapy 3.0: The Beginning of the End or the End of the Beginning?

Hatzistergos KE, Vedenko A.

Circ Res. 2017 Jul 7;121(2):95-97. doi: 10.1161/CIRCRESAHA.117.311293. No abstract available.

5.

Survey of variation in human transcription factors reveals prevalent DNA binding changes.

Barrera LA, Vedenko A, Kurland JV, Rogers JM, Gisselbrecht SS, Rossin EJ, Woodard J, Mariani L, Kock KH, Inukai S, Siggers T, Shokri L, Gordân R, Sahni N, Cotsapas C, Hao T, Yi S, Kellis M, Daly MJ, Vidal M, Hill DE, Bulyk ML.

Science. 2016 Mar 25;351(6280):1450-1454. doi: 10.1126/science.aad2257. Epub 2016 Mar 24.

6.

A direct fate exclusion mechanism by Sonic hedgehog-regulated transcriptional repressors.

Nishi Y, Zhang X, Jeong J, Peterson KA, Vedenko A, Bulyk ML, Hide WA, McMahon AP.

Development. 2015 Oct 1;142(19):3286-93. doi: 10.1242/dev.124636. Epub 2015 Aug 20.

7.

Modular evolution of DNA-binding preference of a Tbrain transcription factor provides a mechanism for modifying gene regulatory networks.

Cheatle Jarvela AM, Brubaker L, Vedenko A, Gupta A, Armitage BA, Bulyk ML, Hinman VF.

Mol Biol Evol. 2014 Oct;31(10):2672-88. doi: 10.1093/molbev/msu213. Epub 2014 Jul 12.

8.

The CLAMP protein links the MSL complex to the X chromosome during Drosophila dosage compensation.

Soruco MM, Chery J, Bishop EP, Siggers T, Tolstorukov MY, Leydon AR, Sugden AU, Goebel K, Feng J, Xia P, Vedenko A, Bulyk ML, Park PJ, Larschan E.

Genes Dev. 2013 Jul 15;27(14):1551-6. doi: 10.1101/gad.214585.113.

9.

Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos.

Gisselbrecht SS, Barrera LA, Porsch M, Aboukhalil A, Estep PW 3rd, Vedenko A, Palagi A, Kim Y, Zhu X, Busser BW, Gamble CE, Iagovitina A, Singhania A, Michelson AM, Bulyk ML.

Nat Methods. 2013 Aug;10(8):774-80. doi: 10.1038/nmeth.2558. Epub 2013 Jul 14.

10.

Evaluation of methods for modeling transcription factor sequence specificity.

Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S; DREAM5 Consortium, Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, Hughes TR.

Nat Biotechnol. 2013 Feb;31(2):126-34. doi: 10.1038/nbt.2486. Epub 2013 Jan 27.

11.

Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning.

Peterson KA, Nishi Y, Ma W, Vedenko A, Shokri L, Zhang X, McFarlane M, Baizabal JM, Junker JP, van Oudenaarden A, Mikkelsen T, Bernstein BE, Bailey TL, Bulyk ML, Wong WH, McMahon AP.

Genes Dev. 2012 Dec 15;26(24):2802-16. doi: 10.1101/gad.207142.112.

12.

Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights.

Gordân R, Murphy KF, McCord RP, Zhu C, Vedenko A, Bulyk ML.

Genome Biol. 2011 Dec 21;12(12):R125. doi: 10.1186/gb-2011-12-12-r125.

13.

Using a structural and logics systems approach to infer bHLH-DNA binding specificity determinants.

De Masi F, Grove CA, Vedenko A, Alibés A, Gisselbrecht SS, Serrano L, Bulyk ML, Walhout AJ.

Nucleic Acids Res. 2011 Jun;39(11):4553-63. doi: 10.1093/nar/gkr070. Epub 2011 Feb 18.

14.

Notch and MAML-1 complexation do not detectably alter the DNA binding specificity of the transcription factor CSL.

Del Bianco C, Vedenko A, Choi SH, Berger MF, Shokri L, Bulyk ML, Blacklow SC.

PLoS One. 2010 Nov 24;5(11):e15034. doi: 10.1371/journal.pone.0015034.

15.

Diversity and complexity in DNA recognition by transcription factors.

Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, Chan ET, Metzler G, Vedenko A, Chen X, Kuznetsov H, Wang CF, Coburn D, Newburger DE, Morris Q, Hughes TR, Bulyk ML.

Science. 2009 Jun 26;324(5935):1720-3. doi: 10.1126/science.1162327. Epub 2009 May 14.

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