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Items: 1 to 50 of 111

1.

Interspecies analysis of MYC targets identifies tRNA synthetases as mediators of growth and survival in MYC-overexpressing cells.

Zirin J, Ni X, Sack LM, Yang-Zhou D, Hu Y, Brathwaite R, Bulyk ML, Elledge SJ, Perrimon N.

Proc Natl Acad Sci U S A. 2019 Jul 16;116(29):14614-14619. doi: 10.1073/pnas.1821863116. Epub 2019 Jul 1. Erratum in: Proc Natl Acad Sci U S A. 2019 Aug 12;:.

PMID:
31262815
2.

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.

3.
4.

Bispecific Forkhead Transcription Factor FoxN3 Recognizes Two Distinct Motifs with Different DNA Shapes.

Rogers JM, Waters CT, Seegar TCM, Jarrett SM, Hallworth AN, Blacklow SC, Bulyk ML.

Mol Cell. 2019 Apr 18;74(2):245-253.e6. doi: 10.1016/j.molcel.2019.01.019. Epub 2019 Feb 27.

PMID:
30826165
5.

The multiple mechanisms that regulate p53 activity and cell fate.

Hafner A, Bulyk ML, Jambhekar A, Lahav G.

Nat Rev Mol Cell Biol. 2019 Apr;20(4):199-210. doi: 10.1038/s41580-019-0110-x. Review.

PMID:
30824861
6.

Ancient mechanisms for the evolution of the bicoid homeodomain's function in fly development.

Liu Q, Onal P, Datta RR, Rogers JM, Schmidt-Ott U, Bulyk ML, Small S, Thornton JW.

Elife. 2018 Oct 9;7. pii: e34594. doi: 10.7554/eLife.34594.

7.

A feed-forward relay integrates the regulatory activities of Bicoid and Orthodenticle via sequential binding to suboptimal sites.

Datta RR, Ling J, Kurland J, Ren X, Xu Z, Yucel G, Moore J, Shokri L, Baker I, Bishop T, Struffi P, Levina R, Bulyk ML, Johnston RJ Jr, Small S.

Genes Dev. 2018 May 1;32(9-10):723-736. doi: 10.1101/gad.311985.118. Epub 2018 May 15.

8.

Diversification of transcription factor-DNA interactions and the evolution of gene regulatory networks.

Rogers JM, Bulyk ML.

Wiley Interdiscip Rev Syst Biol Med. 2018 Apr 25:e1423. doi: 10.1002/wsbm.1423. [Epub ahead of print] Review.

PMID:
29694718
9.

Direct Promoter Repression by BCL11A Controls the Fetal to Adult Hemoglobin Switch.

Liu N, Hargreaves VV, Zhu Q, Kurland JV, Hong J, Kim W, Sher F, Macias-Trevino C, Rogers JM, Kurita R, Nakamura Y, Yuan GC, Bauer DE, Xu J, Bulyk ML, Orkin SH.

Cell. 2018 Apr 5;173(2):430-442.e17. doi: 10.1016/j.cell.2018.03.016. Epub 2018 Mar 29.

10.

Differential Occupancy of Two GA-Binding Proteins Promotes Targeting of the Drosophila Dosage Compensation Complex to the Male X Chromosome.

Kaye EG, Booker M, Kurland JV, Conicella AE, Fawzi NL, Bulyk ML, Tolstorukov MY, Larschan E.

Cell Rep. 2018 Mar 20;22(12):3227-3239. doi: 10.1016/j.celrep.2018.02.098.

11.

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.

12.

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.

13.

Polycomb-like proteins link the PRC2 complex to CpG islands.

Li H, Liefke R, Jiang J, Kurland JV, Tian W, Deng P, Zhang W, He Q, Patel DJ, Bulyk ML, Shi Y, Wang Z.

Nature. 2017 Sep 14;549(7671):287-291. doi: 10.1038/nature23881. Epub 2017 Sep 6.

14.

p53 pulses lead to distinct patterns of gene expression albeit similar DNA-binding dynamics.

Hafner A, Stewart-Ornstein J, Purvis JE, Forrester WC, Bulyk ML, Lahav G.

Nat Struct Mol Biol. 2017 Oct;24(10):840-847. doi: 10.1038/nsmb.3452. Epub 2017 Aug 21.

15.

Transcription factor-DNA binding: beyond binding site motifs.

Inukai S, Kock KH, Bulyk ML.

Curr Opin Genet Dev. 2017 Apr;43:110-119. doi: 10.1016/j.gde.2017.02.007. Epub 2017 Mar 27. Review.

16.

CellMapper: rapid and accurate inference of gene expression in difficult-to-isolate cell types.

Nelms BD, Waldron L, Barrera LA, Weflen AW, Goettel JA, Guo G, Montgomery RK, Neutra MR, Breault DT, Snapper SB, Orkin SH, Bulyk ML, Huttenhower C, Lencer WI.

Genome Biol. 2016 Sep 29;17(1):201.

17.

Expansion of GA Dinucleotide Repeats Increases the Density of CLAMP Binding Sites on the X-Chromosome to Promote Drosophila Dosage Compensation.

Kuzu G, Kaye EG, Chery J, Siggers T, Yang L, Dobson JR, Boor S, Bliss J, Liu W, Jogl G, Rohs R, Singh ND, Bulyk ML, Tolstorukov MY, Larschan E.

PLoS Genet. 2016 Jul 14;12(7):e1006120. doi: 10.1371/journal.pgen.1006120. eCollection 2016 Jul.

18.

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.

19.

Phosphorylation of the chromatin remodeling factor DPF3a induces cardiac hypertrophy through releasing HEY repressors from DNA.

Cui H, Schlesinger J, Schoenhals S, Tönjes M, Dunkel I, Meierhofer D, Cano E, Schulz K, Berger MF, Haack T, Abdelilah-Seyfried S, Bulyk ML, Sauer S, Sperling SR.

Nucleic Acids Res. 2016 Apr 7;44(6):2538-53. doi: 10.1093/nar/gkv1244. Epub 2015 Nov 17.

20.

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.

21.

Grhl2 is required in nonneural tissues for neural progenitor survival and forebrain development.

Menke C, Cionni M, Siggers T, Bulyk ML, Beier DR, Stottmann RW.

Genesis. 2015 Sep;53(9):573-582. doi: 10.1002/dvg.22875. Epub 2015 Jul 22.

22.

Nuclear respiratory factor 2 induces SIRT3 expression.

Satterstrom FK, Swindell WR, Laurent G, Vyas S, Bulyk ML, Haigis MC.

Aging Cell. 2015 Oct;14(5):818-25. doi: 10.1111/acel.12360. Epub 2015 Jun 24.

23.

Context influences on TALE-DNA binding revealed by quantitative profiling.

Rogers JM, Barrera LA, Reyon D, Sander JD, Kellis M, Joung JK, Bulyk ML.

Nat Commun. 2015 Jun 11;6:7440. doi: 10.1038/ncomms8440.

24.

UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions.

Hume MA, Barrera LA, Gisselbrecht SS, Bulyk ML.

Nucleic Acids Res. 2015 Jan;43(Database issue):D117-22. doi: 10.1093/nar/gku1045. Epub 2014 Nov 5.

25.

The NF-κB genomic landscape in lymphoblastoid B cells.

Zhao B, Barrera LA, Ersing I, Willox B, Schmidt SC, Greenfeld H, Zhou H, Mollo SB, Shi TT, Takasaki K, Jiang S, Cahir-McFarland E, Kellis M, Bulyk ML, Kieff E, Gewurz BE.

Cell Rep. 2014 Sep 11;8(5):1595-606. doi: 10.1016/j.celrep.2014.07.037. Epub 2014 Aug 21.

26.

Diversification of transcription factor paralogs via noncanonical modularity in C2H2 zinc finger DNA binding.

Siggers T, Reddy J, Barron B, Bulyk ML.

Mol Cell. 2014 Aug 21;55(4):640-8. doi: 10.1016/j.molcel.2014.06.019. Epub 2014 Jul 17.

27.

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.

28.

5'RNA-Seq identifies Fhl1 as a genetic modifier in cardiomyopathy.

Christodoulou DC, Wakimoto H, Onoue K, Eminaga S, Gorham JM, DePalma SR, Herman DS, Teekakirikul P, Conner DA, McKean DM, Domenighetti AA, Aboukhalil A, Chang S, Srivastava G, McDonough B, De Jager PL, Chen J, Bulyk ML, Muehlschlegel JD, Seidman CE, Seidman JG.

J Clin Invest. 2014 Mar;124(3):1364-70. doi: 10.1172/JCI70108. Epub 2014 Feb 10.

29.

Machine learning classification of cell-specific cardiac enhancers uncovers developmental subnetworks regulating progenitor cell division and cell fate specification.

Ahmad SM, Busser BW, Huang D, Cozart EJ, Michaud S, Zhu X, Jeffries N, Aboukhalil A, Bulyk ML, Ovcharenko I, Michelson AM.

Development. 2014 Feb;141(4):878-88. doi: 10.1242/dev.101709.

30.

Contribution of distinct homeodomain DNA binding specificities to Drosophila embryonic mesodermal cell-specific gene expression programs.

Busser BW, Gisselbrecht SS, Shokri L, Tansey TR, Gamble CE, Bulyk ML, Michelson AM.

PLoS One. 2013 Jul 26;8(7):e69385. doi: 10.1371/journal.pone.0069385. Print 2013.

31.

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.

32.

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.

33.

DNA-binding specificity changes in the evolution of forkhead transcription factors.

Nakagawa S, Gisselbrecht SS, Rogers JM, Hartl DL, Bulyk ML.

Proc Natl Acad Sci U S A. 2013 Jul 23;110(30):12349-54. doi: 10.1073/pnas.1310430110. Epub 2013 Jul 8.

34.

Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape.

Gordân R, Shen N, Dror I, Zhou T, Horton J, Rohs R, Bulyk ML.

Cell Rep. 2013 Apr 25;3(4):1093-104. doi: 10.1016/j.celrep.2013.03.014. Epub 2013 Apr 4.

35.

Bayesian hierarchical model of protein-binding microarray k-mer data reduces noise and identifies transcription factor subclasses and preferred k-mers.

Jiang B, Liu JS, Bulyk ML.

Bioinformatics. 2013 Jun 1;29(11):1390-8. doi: 10.1093/bioinformatics/btt152. Epub 2013 Apr 4.

36.

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.

37.

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.

38.

Integrative analysis of the zinc finger transcription factor Lame duck in the Drosophila myogenic gene regulatory network.

Busser BW, Huang D, Rogacki KR, Lane EA, Shokri L, Ni T, Gamble CE, Gisselbrecht SS, Zhu J, Bulyk ML, Ovcharenko I, Michelson AM.

Proc Natl Acad Sci U S A. 2012 Dec 11;109(50):20768-73. doi: 10.1073/pnas.1210415109. Epub 2012 Nov 26.

39.

DNA sequence preferences of transcriptional activators correlate more strongly than repressors with nucleosomes.

Charoensawan V, Janga SC, Bulyk ML, Babu MM, Teichmann SA.

Mol Cell. 2012 Jul 27;47(2):183-92. doi: 10.1016/j.molcel.2012.06.028.

40.

An evolutionarily conserved enhancer regulates Bmp4 expression in developing incisor and limb bud.

Jumlongras D, Lachke SA, O'Connell DJ, Aboukhalil A, Li X, Choe SE, Ho JW, Turbe-Doan A, Robertson EA, Olsen BR, Bulyk ML, Amendt BA, Maas RL.

PLoS One. 2012;7(6):e38568. doi: 10.1371/journal.pone.0038568. Epub 2012 Jun 12.

41.

DNA binding site analysis of Burkholderia thailandensis response regulators.

Nowak-Lovato KL, Hickmott AJ, Maity TS, Bulyk ML, Dunbar J, Hong-Geller E.

J Microbiol Methods. 2012 Jul;90(1):46-52. doi: 10.1016/j.mimet.2012.03.019. Epub 2012 Apr 13.

PMID:
22521922
42.

LOESS correction for length variation in gene set-based genomic sequence analysis.

Aboukhalil A, Bulyk ML.

Bioinformatics. 2012 Jun 1;28(11):1446-54. doi: 10.1093/bioinformatics/bts155. Epub 2012 Apr 5.

43.

Meta-profiles of gene expression during aging: limited similarities between mouse and human and an unexpectedly decreased inflammatory signature.

Swindell WR, Johnston A, Sun L, Xing X, Fisher GJ, Bulyk ML, Elder JT, Gudjonsson JE.

PLoS One. 2012;7(3):e33204. doi: 10.1371/journal.pone.0033204. Epub 2012 Mar 7.

44.

Differential regulation of mesodermal gene expression by Drosophila cell type-specific Forkhead transcription factors.

Zhu X, Ahmad SM, Aboukhalil A, Busser BW, Kim Y, Tansey TR, Haimovich A, Jeffries N, Bulyk ML, Michelson AM.

Development. 2012 Apr;139(8):1457-66. doi: 10.1242/dev.069005. Epub 2012 Feb 29.

45.

Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function.

Sakabe NJ, Aneas I, Shen T, Shokri L, Park SY, Bulyk ML, Evans SM, Nobrega MA.

Hum Mol Genet. 2012 May 15;21(10):2194-204. doi: 10.1093/hmg/dds034. Epub 2012 Feb 10.

46.

iSyTE: integrated Systems Tool for Eye gene discovery.

Lachke SA, Ho JW, Kryukov GV, O'Connell DJ, Aboukhalil A, Bulyk ML, Park PJ, Maas RL.

Invest Ophthalmol Vis Sci. 2012 Mar 21;53(3):1617-27. doi: 10.1167/iovs.11-8839. Print 2012 Mar.

47.

Molecular mechanism underlying the regulatory specificity of a Drosophila homeodomain protein that specifies myoblast identity.

Busser BW, Shokri L, Jaeger SA, Gisselbrecht SS, Singhania A, Berger MF, Zhou B, Bulyk ML, Michelson AM.

Development. 2012 Mar;139(6):1164-74. doi: 10.1242/dev.077362. Epub 2012 Feb 1.

48.

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.

49.

Identification of cell cycle-regulated, putative hyphal genes in Candida albicans.

Gordân R, Pyne S, Bulyk ML.

Pac Symp Biocomput. 2012:299-310.

50.

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