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Martha L. Bulyk, PhD

Publications

  • Ahmad SM, Busser BW, Huang D, Cozart EJ, Michaud S, Zhu X, Jeffries N, Aboukhalil A, Bulyk ML, Ovcharenko I, Michelson AM.Machine learning classification of cell-specific cardiac enhancers uncovers developmental subnetworks regulating progenitor cell division and cell fate specification.Development. 2014 Feb;141(4):878-88.
    24496624
  • Busser BW, Gisselbrecht SS, Shokri L, Tansey TR, Gamble CE, Bulyk ML, Michelson AM.Contribution of distinct homeodomain DNA binding specificities to Drosophila embryonic mesodermal cell-specific gene expression programs.PLoS ONE. 2013;8(7):e69385.
    23922708
  • Gisselbrecht SS, Barrera LA, Porsch M, Aboukhalil A, Estep PW, Vedenko A, Palagi A, Kim Y, Zhu X, Busser BW, Gamble CE, Iagovitina A, Singhania A, Michelson AM, Bulyk ML.Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos.Nat Methods. 2013 Aug;10(8):774-80.
    23852450
  • Nakagawa S, Gisselbrecht SS, Rogers JM, Hartl DL, Bulyk ML.DNA-binding specificity changes in the evolution of forkhead transcription factors.Proc Natl Acad Sci U S A. 2013 Jul 23;110(30):12349-54.
    23836653
  • 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.The CLAMP protein links the MSL complex to the X chromosome during Drosophila dosage compensation.Genes Dev. 2013 Jul 15;27(14):1551-6.
    23873939
  • Gordân R, Shen N, Dror I, Zhou T, Horton J, Rohs R, Bulyk ML.Genomic Regions Flanking E-Box Binding Sites Influence DNA Binding Specificity of bHLH Transcription Factors through DNA Shape.Cell Rep. 2013 Apr 4.
    23562153
  • Jiang B, Liu JS, Bulyk ML.Bayesian hierarchical model of protein binding microarray k-mer data reduces noise and identifies transcription factor subclasses and preferred k-mers.Bioinformatics. 2013 Apr 4.
    23559638
  • Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S, , Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, Hughes TR.Evaluation of methods for modeling transcription factor sequence specificity.Nat Biotechnol. 2013 Feb;31(2):126-34.
    23354101
  • Busser BW, Huang D, Rogacki KR, Lane EA, Shokri L, Ni T, Gamble CE, Gisselbrecht SS, Zhu J, Bulyk ML, Ovcharenko I, Michelson AM.Integrative analysis of the zinc finger transcription factor Lame duck in the Drosophila myogenic gene regulatory network.Proc Natl Acad Sci U S A. 2012 Dec 11;109(50):20768-73.
    23184988
  • Charoensawan V, Janga SC, Bulyk ML, Babu MM, Teichmann SA.DNA sequence preferences of transcriptional activators correlate more strongly than repressors with nucleosomes.Mol Cell. 2012 Jul 27;47(2):183-92.
    22841002
  • De Masi F, Grove CA, Vedenko A, Alibés A, Gisselbrecht SS, Serrano L, Bulyk ML, Walhout AJ.Using a structural and logics systems approach to infer bHLH-DNA binding specificity determinants.Nucleic Acids Res. 2011 Feb 18.
    21335608
  • Helfer A, Nusinow DA, Chow BY, Gehrke AR, Bulyk ML, Kay SA.LUX ARRHYTHMO encodes a nighttime repressor of circadian gene expression in the Arabidopsis core clock.Curr Biol. 2011 Jan 25;21(2):126-33.
    21236673
  • Robasky K, Bulyk ML.UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions.Nucleic Acids Res. 2011 Jan;39(Database issue):D124-8.
    21037262
  • Santos MA, Turinsky AL, Ong S, Tsai J, Berger MF, Badis G, Talukder S, Gehrke AR, Bulyk ML, Hughes TR, Wodak SJ.Objective sequence-based subfamily classifications of mouse homeodomains reflect their in vitro DNA-binding preferences.Nucleic Acids Res. 2010 Dec 1;38(22):7927-42.
    20705649
  • Del Bianco C, Vedenko A, Choi SH, Berger MF, Shokri L, Bulyk ML, Blacklow SC.Notch and MAML-1 complexation do not detectably alter the dna binding specificity of the transcription factor CSL.PLoS ONE. 2010;5(11):e15034.
    21124806
  • Alibés A, Nadra AD, De Masi F, Bulyk ML, Serrano L, Stricher F.Using protein design algorithms to understand the molecular basis of disease caused by protein-DNA interactions: the Pax6 example.Nucleic Acids Res. 2010 Nov 1;38(21):7422-31.
    20685816
  • Iliopoulos D, Jaeger SA, Hirsch HA, Bulyk ML, Struhl K.STAT3 activation of miR-21 and miR-181b-1 via PTEN and CYLD are part of the epigenetic switch linking inflammation to cancer.Mol Cell. 2010 Aug 27;39(4):493-506.
    20797623
  • Wei GH, Badis G, Berger MF, Kivioja T, Palin K, Enge M, Bonke M, Jolma A, Varjosalo M, Gehrke AR, Yan J, Talukder S, Turunen M, Taipale M, Stunnenberg HG, Ukkonen E, Hughes TR, Bulyk ML, Taipale J.Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo.EMBO J. 2010 Jul 7;29(13):2147-60.
    20517297
  • Rowan S, Siggers T, Lachke SA, Yue Y, Bulyk ML, Maas RL.Precise temporal control of the eye regulatory gene Pax6 via enhancer-binding site affinity.Genes Dev. 2010 May 15;24(10):980-5.
    20413611
  • Hirsch HA, Iliopoulos D, Joshi A, Zhang Y, Jaeger SA, Bulyk M, Tsichlis PN, Shirley Liu X, Struhl K.A transcriptional signature and common gene networks link cancer with lipid metabolism and diverse human diseases.Cancer Cell. 2010 Apr 13;17(4):348-61.
    20385360
  • Jaeger SA, Chan ET, Berger MF, Stottmann R, Hughes TR, Bulyk ML.Conservation and regulatory associations of a wide affinity range of mouse transcription factor binding sites.Genomics. 2010 Apr;95(4):185-95.
    20079828
  • Giorgetti L, Siggers T, Tiana G, Caprara G, Notarbartolo S, Corona T, Pasparakis M, Milani P, Bulyk ML, Natoli G.Noncooperative interactions between transcription factors and clustered DNA binding sites enable graded transcriptional responses to environmental inputs.Mol Cell. 2010 Feb 12;37(3):418-28.
    20159560
  • Enriquez J, Boukhatmi H, Dubois L, Philippakis AA, Bulyk ML, Michelson AM, Crozatier M, Vincent A.Multi-step control of muscle diversity by Hox proteins in the Drosophila embryo.Development. 2010 Feb;137(3):457-66.
    20056681
  • Bulyk ML, Levine M.Genomes and evolution: advances in deciphering the genomics of gene regulation in evolution.Curr Opin Genet Dev. 2009 Dec;19(6):533-4.
    19932611
  • Gordân R, Hartemink AJ, Bulyk ML.Distinguishing direct versus indirect transcription factor-DNA interactions.Genome Res. 2009 Nov;19(11):2090-100.
    19652015
  • Grove CA, De Masi F, Barrasa MI, Newburger DE, Alkema MJ, Bulyk ML, Walhout AJ.A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors.Cell. 2009 Jul 23;138(2):314-27.
    19632181
  • 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.Diversity and Complexity in DNA Recognition by Transcription Factors.Science. 2009 Jun 26;324(5935):1720-3.
    19443739
  • Estep PW 3rd,Warner JB,Bulyk ML.Short-term calorie restriction in male mice feminizes gene expression and alters key regulators of conserved aging regulatory pathways.PLoS ONE. 2009;4(4):e5242.
    19370158
  • Berger MF,Bulyk ML.Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors.Nat Protoc. 2009;4(3):393-411.
    19265799
  • Lesch BJ,Gehrke AR,Bulyk ML,Bargmann CI.Transcriptional regulation and stabilization of left-right neuronal identity in C. elegans.Genes Dev. 2009 Feb 1;23(3):345-58.
    19204119
  • Scharer CD,McCabe CD,Ali-Seyed M,Berger MF,Bulyk ML,Moreno CS.Genome-wide promoter analysis of the SOX4 transcriptional network in prostate cancer cells.Cancer Res. 2009 Jan 15;69(2):709-17.
    19147588
  • Alleyne TM,Pena-Castillo L,Badis G,Talukder S,Berger MF,Gehrke AR,Philippakis AA,Bulyk ML,Morris QD,Hughes TR.Predicting the binding preference of transcription factors to individual DNA k-mers.Bioinformatics. 2009 Apr 15;25(8):1012-8.
    19088121
  • Viiri KM,Janis J,Siggers T,Heinonen TY,Valjakka J,Bulyk ML,Maki M,Lohi O.DNA-binding and -bending activities of SAP30L and SAP30 are mediated by a zinc-dependent module and monophosphoinositides.Mol Cell Biol. 2009 Jan;29(2):342-56.
    19015240
  • Busser BW,Bulyk ML,Michelson AM.Toward a systems-level understanding of developmental regulatory networks.Curr Opin Genet Dev. 2008 Dec;18(6):521-9. Review.
    18848887
  • Newburger DE,Bulyk ML.UniPROBE: an online database of protein binding microarray data on protein-DNA interactions.Nucleic Acids Res. 2009 Jan;37(Database issue):D77-82.
    18842628
  • Pompeani AJ,Irgon JJ,Berger MF,Bulyk ML,Wingreen NS,Bassler BL.The Vibrio harveyi master quorum-sensing regulator, LuxR, a TetR-type protein is both an activator and a repressor: DNA recognition and binding specificity at target promoters.Mol Microbiol. 2008 Oct;70(1):76-88.
    18681939
  • Philippakis AA,Qureshi AM,Berger MF,Bulyk ML.Design of compact, universal DNA microarrays for protein binding microarray experiments.J Comput Biol. 2008 Sep;15(7):655-65.
    18651798
  • Berger MF,Badis G,Gehrke AR,Talukder S,Philippakis AA,Pena-Castillo L,Alleyne TM,Mnaimneh S,Botvinnik OB,Chan ET,Khalid F,Zhang W,Newburger D,Jaeger SA,Morris QD,Bulyk ML,Hughes TR.Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences.Cell. 2008 Jun 27;133(7):1266-76.
    18585359
  • De Silva EK,Gehrke AR,Olszewski K,Leon I,Chahal JS,Bulyk ML,Llinas M.Specific DNA-binding by apicomplexan AP2 transcription factors.Proc Natl Acad Sci U S A. 2008 Jun 17;105(24):8393-8.
    18541913
  • Warner JB, Philippakis AA, Jaeger SA, He FS, Lin J, Bulyk ML.Systematic identification of mammalian regulatory motifs' target genes and functions.Nat Methods. 2008 Apr;5(4):347-53.
    18311145
  • McCord RP, Bulyk ML.Functional trends in structural classes of the DNA binding domains of regulatory transcription factors.Pac Symp Biocomput. 2008:441-52.
    18229706
  • Lieb JD, Beck S, Bulyk ML, Farnham P, Hattori N, Henikoff S, Liu XS, Okumura K, Shiota K, Ushijima T, Greally JM.Applying whole-genome studies of epigenetic regulation to study human disease.Cytogenet Genome Res. 2006;114(1):1-15. Review.
    16717444
  • Bulyk ML.Discovering DNA regulatory elements with bacteria.Nat Biotechnol. 2005 Aug;23(8):942-4.
    16082362
  • Philippakis AA, He FS, Bulyk ML.Modulefinder: a tool for computational discovery of cis regulatory modules.Nat Biotechnol. 2005:519-30.
    15759656
  • Mukherjee S, Berger MF, Jona G, Wang XS, Muzzey D, Snyder M, Young RA, Bulyk ML.Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays.Nat Genet. 2004 Dec;36(12):1331-9.
    15543148
  • Bulyk ML.Integrative functional genomics.Genome Biol. 2004;5(7):331.
    15239826
  • Bulyk ML, McGuire AM, Masuda N, Church GM.A motif co-occurrence approach for genome-wide prediction of transcription-factor-binding sites in Escherichia coli.Genome Res. 2004 Feb;14(2):201-8.
    14762058
  • Bulyk ML, Johnson PL, Church GM.Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors.Nucleic Acids Res. 2002 Mar 1;30(5):1255-61.
    11861919
  • Bulyk ML, Huang X, Choo Y, Church GM.Exploring the DNA-binding specificities of zinc fingers with DNA microarrays.Proc Natl Acad Sci U S A. 2001 Jun 19;98(13):7158-63.
    11404456