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Keywords
Last Name
Institution

Martha Leonia Bulyk, PH.D.

TitleProfessor of Medicine
InstitutionBrigham and Women's Hospital
DepartmentMedicine
AddressBrigham and Women
New Research Bldg, Rm. 466D
77 Ave Louis Pasteur
Boston MA 02115
Phone617/525-4725
Fax617/525-4705
Other Positions
TitleAssociate Professor of Pathology
InstitutionBrigham and Women's Hospital
DepartmentPathology


 Mentoring 
 completed student projects
Transcription factor binding sites in eucaryotic DNA
Summer, 06/23/03 - 08/31/03
Identification of Transcription Factor Binding Sites within Eukaryotic Noncoding DNA
Summer, 06/01/02 - 08/30/02
Identifying Transcription Factor Binding Sites in Eucaryotic Genomes
Summer, 07/01/03 - 08/31/03
Computational Analysis of Human Transcription Factor Binding Sites
Summer, 06/01/02 - 09/01/02

 Research 
 research resources
This researcher has shared information about their research resources
in the eagle-i Network. To update or add resource records, contact
eagle-i@hms.harvard.edu.
Bulyk Laboratory - Databases (1) and Software (6)

 Bibliographic 
 selected publications
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. 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.
    View in: PubMed
  2. 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.
    View in: PubMed
  3. 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.
    View in: PubMed
  4. 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.
    View in: PubMed
  5. 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 Jun 1; 29(11):1390-8.
    View in: PubMed
  6. 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 25; 3(4):1093-104.
    View in: PubMed
  7. Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S, Agius P, Arvey A, Bucher P, Callan CG, Chang CW, Chen CY, Chen YS, Chu YW, Grau J, Grosse I, Jagannathan V, Keilwagen J, Kielbasa SM, Kinney JB, Klein H, Kursa MB, Lähdesmäki H, Laurila K, Lei C, Leslie C, Linhart C, Murugan A, Myšicková A, Noble WS, Nykter M, Orenstein Y, Posch S, Ruan J, Rudnicki WR, Schmid CD, Shamir R, Sung WK, Vingron M, Zhang Z, Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, Hughes TR. Evaluation of methods for modeling transcription factor sequence specificity. Nat Biotechnol. 2013 Jan 27; 31(2):126-34.
    View in: PubMed
  8. 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. Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning. Genes Dev. 2012 Dec 15; 26(24):2802-16.
    View in: PubMed
  9. 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.
    View in: PubMed
  10. 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.
    View in: PubMed
  11. 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. An evolutionarily conserved enhancer regulates Bmp4 expression in developing incisor and limb bud. PLoS One. 2012; 7(6):e38568.
    View in: PubMed
  12. Nowak-Lovato KL, Hickmott AJ, Maity TS, Bulyk ML, Dunbar J, Hong-Geller E. DNA binding site analysis of Burkholderia thailandensis response regulators. J Microbiol Methods. 2012 Jul; 90(1):46-52.
    View in: PubMed
  13. Aboukhalil A, Bulyk ML. LOESS correction for length variation in gene set-based genomic sequence analysis. Bioinformatics. 2012 Jun 1; 28(11):1446-54.
    View in: PubMed
  14. Lachke SA, Ho JW, Kryukov GV, O'Connell DJ, Aboukhalil A, Bulyk ML, Park PJ, Maas RL. iSyTE: integrated Systems Tool for Eye gene discovery. Invest Ophthalmol Vis Sci. 2012 Mar; 53(3):1617-27.
    View in: PubMed
  15. Swindell WR, Johnston A, Sun L, Xing X, Fisher GJ, Bulyk ML, Elder JT, Gudjonsson JE. Meta-profiles of gene expression during aging: limited similarities between mouse and human and an unexpectedly decreased inflammatory signature. PLoS One. 2012; 7(3):e33204.
    View in: PubMed
  16. Zhu X, Ahmad SM, Aboukhalil A, Busser BW, Kim Y, Tansey TR, Haimovich A, Jeffries N, Bulyk ML, Michelson AM. Differential regulation of mesodermal gene expression by Drosophila cell type-specific Forkhead transcription factors. Development. 2012 Apr; 139(8):1457-66.
    View in: PubMed
  17. Sakabe NJ, Aneas I, Shen T, Shokri L, Park SY, Bulyk ML, Evans SM, Nobrega MA. Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function. Hum Mol Genet. 2012 May 15; 21(10):2194-204.
    View in: PubMed
  18. Busser BW, Shokri L, Jaeger SA, Gisselbrecht SS, Singhania A, Berger MF, Zhou B, Bulyk ML, Michelson AM. Molecular mechanism underlying the regulatory specificity of a Drosophila homeodomain protein that specifies myoblast identity. Development. 2012 Mar; 139(6):1164-74.
    View in: PubMed
  19. Gordân R, Pyne S, Bulyk ML. Identification of cell cycle-regulated, putative hyphal genes in Candida albicans. Pac Symp Biocomput. 2012; 299-310.
    View in: PubMed
  20. Guo X, Bulyk ML, Hartemink AJ. Intrinsic disorder within and flanking the DNA-binding domains of human transcription factors. Pac Symp Biocomput. 2012; 104-15.
    View in: PubMed
  21. Gordân R, Murphy KF, McCord RP, Zhu C, Vedenko A, Bulyk ML. Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights. Genome Biol. 2011; 12(12):R125.
    View in: PubMed
  22. Siggers T, Duyzend MH, Reddy J, Khan S, Bulyk ML. Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex. Mol Syst Biol. 2011; 7:555.
    View in: PubMed
  23. Siggers T, Chang AB, Teixeira A, Wong D, Williams KJ, Ahmed B, Ragoussis J, Udalova IA, Smale ST, Bulyk ML. Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-?B family DNA binding. Nat Immunol. 2012 Jan; 13(1):95-102.
    View in: PubMed
  24. McCord RP, Zhou VW, Yuh T, Bulyk ML. Distant cis-regulatory elements in human skeletal muscle differentiation. Genomics. 2011 Dec; 98(6):401-11.
    View in: PubMed
  25. Wong D, Teixeira A, Oikonomopoulos S, Humburg P, Lone IN, Saliba D, Siggers T, Bulyk M, Angelov D, Dimitrov S, Udalova IA, Ragoussis J. Extensive characterization of NF-?B binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits. Genome Biol. 2011; 12(7):R70.
    View in: PubMed
  26. Morris Q, Bulyk ML, Hughes TR. Jury remains out on simple models of transcription factor specificity. Nat Biotechnol. 2011 Jun; 29(6):483-4.
    View in: PubMed
  27. Lachke SA, Alkuraya FS, Kneeland SC, Ohn T, Aboukhalil A, Howell GR, Saadi I, Cavallesco R, Yue Y, Tsai AC, Nair KS, Cosma MI, Smith RS, Hodges E, Alfadhli SM, Al-Hajeri A, Shamseldin HE, Behbehani A, Hannon GJ, Bulyk ML, Drack AV, Anderson PJ, John SW, Maas RL. Mutations in the RNA granule component TDRD7 cause cataract and glaucoma. Science. 2011 Mar 25; 331(6024):1571-6.
    View in: PubMed
  28. 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 Jun; 39(11):4553-63.
    View in: PubMed
  29. 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.
    View in: PubMed
  30. 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.
    View in: PubMed
  31. 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.
    View in: PubMed
  32. 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.
    View in: PubMed
  33. 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; 38(22):7927-42.
    View in: PubMed
  34. 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; 38(21):7422-31.
    View in: PubMed
  35. 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.
    View in: PubMed
  36. 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.
    View in: PubMed
  37. 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.
    View in: PubMed
  38. 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.
    View in: PubMed
  39. 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.
    View in: PubMed
  40. 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.
    View in: PubMed
  41. 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.
    View in: PubMed
  42. Gordân R, Hartemink AJ, Bulyk ML. Distinguishing direct versus indirect transcription factor-DNA interactions. Genome Res. 2009 Nov; 19(11):2090-100.
    View in: PubMed
  43. 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.
    View in: PubMed
  44. 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.
    View in: PubMed
  45. Estep PW, 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.
    View in: PubMed
  46. 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.
    View in: PubMed
  47. Zhu C, Byers KJ, McCord RP, Shi Z, Berger MF, Newburger DE, Saulrieta K, Smith Z, Shah MV, Radhakrishnan M, Philippakis AA, Hu Y, De Masi F, Pacek M, Rolfs A, Murthy T, Labaer J, Bulyk ML. High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res. 2009 Apr; 19(4):556-66.
    View in: PubMed
  48. 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.
    View in: PubMed
  49. 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.
    View in: PubMed
  50. Alleyne TM, Peña-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.
    View in: PubMed
  51. Viiri KM, Jänis J, Siggers T, Heinonen TY, Valjakka J, Bulyk ML, Mäki 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.
    View in: PubMed
  52. 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.
    View in: PubMed
  53. 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.
    View in: PubMed
  54. 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.
    View in: PubMed
  55. 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.
    View in: PubMed
  56. Berger MF, Badis G, Gehrke AR, Talukder S, Philippakis AA, Peña-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.
    View in: PubMed
  57. De Silva EK, Gehrke AR, Olszewski K, León I, Chahal JS, Bulyk ML, Llinás M. Specific DNA-binding by apicomplexan AP2 transcription factors. Proc Natl Acad Sci U S A. 2008 Jun 17; 105(24):8393-8.
    View in: PubMed
  58. 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.
    View in: PubMed
  59. McCord RP, Bulyk ML. Functional trends in structural classes of the DNA binding domains of regulatory transcription factors. Pac Symp Biocomput. 2008; 441-52.
    View in: PubMed
  60. Choi Y, Qin Y, Berger MF, Ballow DJ, Bulyk ML, Rajkovic A. Microarray analyses of newborn mouse ovaries lacking Nobox. Biol Reprod. 2007 Aug; 77(2):312-9.
    View in: PubMed
  61. McCord RP, Berger MF, Philippakis AA, Bulyk ML. Inferring condition-specific transcription factor function from DNA binding and gene expression data. Mol Syst Biol. 2007; 3:100.
    View in: PubMed
  62. Hu Y, Rolfs A, Bhullar B, Murthy TV, Zhu C, Berger MF, Camargo AA, Kelley F, McCarron S, Jepson D, Richardson A, Raphael J, Moreira D, Taycher E, Zuo D, Mohr S, Kane MF, Williamson J, Simpson A, Bulyk ML, Harlow E, Marsischky G, Kolodner RD, LaBaer J. Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae. Genome Res. 2007 Apr; 17(4):536-43.
    View in: PubMed
  63. Bulyk ML. Protein binding microarrays for the characterization of DNA-protein interactions. Adv Biochem Eng Biotechnol. 2007; 104:65-85.
    View in: PubMed
  64. Berger MF, Philippakis AA, Qureshi AM, He FS, Estep PW, Bulyk ML. Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat Biotechnol. 2006 Nov; 24(11):1429-35.
    View in: PubMed
  65. Bulyk ML. DNA microarray technologies for measuring protein-DNA interactions. Curr Opin Biotechnol. 2006 Aug; 17(4):422-30.
    View in: PubMed
  66. Philippakis AA, Busser BW, Gisselbrecht SS, He FS, Estrada B, Michelson AM, Bulyk ML. Expression-guided in silico evaluation of candidate cis regulatory codes for Drosophila muscle founder cells. PLoS Comput Biol. 2006 May; 2(5):e53.
    View in: PubMed
  67. Michelson AM, Bulyk ML. Biological code breaking in the 21st century. Mol Syst Biol. 2006; 2:2006.0018.
    View in: PubMed
  68. Huber BR, Bulyk ML. Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data. BMC Bioinformatics. 2006; 7:229.
    View in: PubMed
  69. Berger MF, Bulyk ML. Protein binding microarrays (PBMs) for rapid, high-throughput characterization of the sequence specificities of DNA binding proteins. Methods Mol Biol. 2006; 338:245-60.
    View in: PubMed
  70. Bulyk ML. Analysis of sequence specificities of DNA-binding proteins with protein binding microarrays. Methods Enzymol. 2006; 410:279-99.
    View in: PubMed
  71. 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.
    View in: PubMed
  72. Bulyk ML. Discovering DNA regulatory elements with bacteria. Nat Biotechnol. 2005 Aug; 23(8):942-4.
    View in: PubMed
  73. Philippakis AA, He FS, Bulyk ML. Modulefinder: a tool for computational discovery of cis regulatory modules. Pac Symp Biocomput. 2005; 519-30.
    View in: PubMed
  74. 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.
    View in: PubMed
  75. Bulyk ML. Integrative functional genomics. Genome Biol. 2004; 5(7):331.
    View in: PubMed
  76. 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.
    View in: PubMed
  77. Bulyk ML. Computational prediction of transcription-factor binding site locations. Genome Biol. 2003; 5(1):201.
    View in: PubMed
  78. Lee ML, Bulyk ML, Whitmore GA, Church GM. A statistical model for investigating binding probabilities of DNA nucleotide sequences using microarrays. Biometrics. 2002 Dec; 58(4):981-8.
    View in: PubMed
  79. Benos PV, Bulyk ML, Stormo GD. Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Res. 2002 Oct 15; 30(20):4442-51.
    View in: PubMed
  80. 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.
    View in: PubMed
  81. 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.
    View in: PubMed
  82. Aach J, Bulyk ML, Church GM, Comander J, Derti A, Shendure J. Computational comparison of two draft sequences of the human genome. Nature. 2001 Feb 15; 409(6822):856-9.
    View in: PubMed
  83. Bulyk ML, Gentalen E, Lockhart DJ, Church GM. Quantifying DNA-protein interactions by double-stranded DNA arrays. Nat Biotechnol. 1999 Jun; 17(6):573-7.
    View in: PubMed
  84. Flores JF, Walker GJ, Glendening JM, Haluska FG, Castresana JS, Rubio MP, Pastorfide GC, Boyer LA, Kao WH, Bulyk ML, Barnhill RL, Hayward NK, Housman DE, Fountain JW. Loss of the p16INK4a and p15INK4b genes, as well as neighboring 9p21 markers, in sporadic melanoma. Cancer Res. 1996 Nov 1; 56(21):5023-32.
    View in: PubMed
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