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Martha Leonia Bulyk, Ph.D.

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Institution
Department

Mentoring
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
The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
  1. U01CA232161 (VIDAL, MARC) Sep 17, 2018 - Aug 31, 2023
    NIH/NCI
    Rewiring of regulatory networks in breast cancer by transcription factor isoforms
    Role: Co-Principal Investigator
  2. R21HG010200 (BULYK, MARTHA L) Aug 20, 2018 - May 31, 2021
    NIH/NHGRI
    AVATAR: highly parallel analysis of variation in transcription factors and their DNA binding sites
    Role: Principal Investigator
  3. R01HG009723 (BULYK, MARTHA L) Aug 1, 2017 - May 31, 2021
    NIH/NHGRI
    Transcriptional silencers inDrosophila
    Role: Principal Investigator
  4. R21HG009268 (BULYK, MARTHA L) Sep 28, 2016 - Jul 31, 2019
    NIH/NHGRI
    Surveying transcription factor pioneer interactions with nucleosomal DNA
    Role: Principal Investigator
  5. R21HG007573 (BULYK, MARTHA L) Sep 4, 2014 - Aug 31, 2016
    NIH/NHGRI
    Analysis of TALE-DNA Recognition
    Role: Principal Investigator
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
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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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Liu Q, Onal P, Datta RR, Rogers JM, Schmidt-Ott U, Bulyk ML, Small S, Thornton JW. Ancient mechanisms for the evolution of the bicoid homeodomain's function in fly development. Elife. 2018 10 09; 7. PMID: 30298815.
    Citations:    Fields:    Translation:Animals
  2. 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, Small S. A feed-forward relay integrates the regulatory activities of Bicoid and Orthodenticle via sequential binding to suboptimal sites. Genes Dev. 2018 05 01; 32(9-10):723-736. PMID: 29764918.
    Citations:    Fields:    Translation:AnimalsCells
  3. Rogers JM, Bulyk ML. Diversification of transcription factor-DNA interactions and the evolution of gene regulatory networks. Wiley Interdiscip Rev Syst Biol Med. 2018 Apr 25; e1423. PMID: 29694718.
    Citations:    Fields:    
  4. 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. Direct Promoter Repression by BCL11A Controls the Fetal to Adult Hemoglobin Switch. Cell. 2018 04 05; 173(2):430-442.e17. PMID: 29606353.
    Citations: 4     Fields:    
  5. Kaye EG, Booker M, Kurland JV, Conicella AE, Fawzi NL, Bulyk ML, Tolstorukov MY, Larschan E. Differential Occupancy of Two GA-Binding Proteins Promotes Targeting of the Drosophila Dosage Compensation Complex to the Male X Chromosome. Cell Rep. 2018 Mar 20; 22(12):3227-3239. PMID: 29562179.
    Citations:    Fields:    
  6. Mariani L, Weinand K, Vedenko A, Barrera LA, Bulyk ML. Identification of Human Lineage-Specific Transcriptional Coregulators Enabled by a Glossary of Binding Modules and Tunable Genomic Backgrounds. Cell Syst. 2017 Dec 27; 5(6):654. PMID: 29284131.
    Citations:    Fields:    
  7. Mariani L, Weinand K, Vedenko A, Barrera LA, Bulyk ML. Identification of Human Lineage-Specific Transcriptional Coregulators Enabled by a Glossary of Binding Modules and Tunable Genomic Backgrounds. Cell Syst. 2017 Sep 27; 5(3):187-201.e7. PMID: 28957653.
    Citations: 2     Fields:    
  8. Li H, Liefke R, Jiang J, Kurland JV, Tian W, Deng P, Zhang W, He Q, Patel DJ, Bulyk ML, Shi Y, Wang Z. Polycomb-like proteins link the PRC2 complex to CpG islands. Nature. 2017 09 14; 549(7671):287-291. PMID: 28869966.
    Citations: 7     Fields:    Translation:HumansAnimalsCells
  9. Hafner A, Stewart-Ornstein J, Purvis JE, Forrester WC, Bulyk ML, Lahav G. p53 pulses lead to distinct patterns of gene expression albeit similar DNA-binding dynamics. Nat Struct Mol Biol. 2017 Oct; 24(10):840-847. PMID: 28825732.
    Citations: 1     Fields:    Translation:HumansCells
  10. Inukai S, Kock KH, Bulyk ML. Transcription factor-DNA binding: beyond binding site motifs. Curr Opin Genet Dev. 2017 Apr; 43:110-119. PMID: 28359978.
    Citations: 5     Fields:    Translation:Cells
  11. 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. CellMapper: rapid and accurate inference of gene expression in difficult-to-isolate cell types. Genome Biol. 2016 09 29; 17(1):201. PMID: 27687735.
    Citations: 4     Fields:    Translation:HumansAnimalsCells
  12. 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. Expansion of GA Dinucleotide Repeats Increases the Density of CLAMP Binding Sites on the X-Chromosome to Promote Drosophila Dosage Compensation. PLoS Genet. 2016 07; 12(7):e1006120. PMID: 27414415; PMCID: PMC4945028.
    Citations: 9     Fields:    Translation:AnimalsCells
  13. 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. Survey of variation in human transcription factors reveals prevalent DNA binding changes. Science. 2016 Mar 25; 351(6280):1450-1454. PMID: 27013732; PMCID: PMC4825693.
    Citations: 27     Fields:    Translation:HumansCells
  14. 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. Phosphorylation of the chromatin remodeling factor DPF3a induces cardiac hypertrophy through releasing HEY repressors from DNA. Nucleic Acids Res. 2016 Apr 07; 44(6):2538-53. PMID: 26582913.
    Citations: 7     Fields:    Translation:HumansAnimalsCells
  15. Nishi Y, Zhang X, Jeong J, Peterson KA, Vedenko A, Bulyk ML, Hide WA, McMahon AP. A direct fate exclusion mechanism by Sonic hedgehog-regulated transcriptional repressors. Development. 2015 Oct 01; 142(19):3286-93. PMID: 26293298; PMCID: PMC4631756.
    Citations: 15     Fields:    Translation:HumansCells
  16. Menke C, Cionni M, Siggers T, Bulyk ML, Beier DR, Stottmann RW. Grhl2 is required in nonneural tissues for neural progenitor survival and forebrain development. Genesis. 2015 Sep; 53(9):573-582. PMID: 26177923.
    Citations: 2     Fields:    
  17. Satterstrom FK, Swindell WR, Laurent G, Vyas S, Bulyk ML, Haigis MC. Nuclear respiratory factor 2 induces SIRT3 expression. Aging Cell. 2015 Oct; 14(5):818-25. PMID: 26109058.
    Citations: 8     Fields:    Translation:HumansAnimalsCells
  18. Rogers JM, Barrera LA, Reyon D, Sander JD, Kellis M, Joung JK, Bulyk ML. Context influences on TALE-DNA binding revealed by quantitative profiling. Nat Commun. 2015 Jun 11; 6:7440. PMID: 26067805; PMCID: PMC4467457.
    Citations: 4     Fields:    Translation:Cells
  19. Hume MA, Barrera LA, Gisselbrecht SS, Bulyk ML. UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions. Nucleic Acids Res. 2015 Jan; 43(Database issue):D117-22. PMID: 25378322; PMCID: PMC4383892.
    Citations: 62     Fields:    Translation:Cells
  20. 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. The NF-?B genomic landscape in lymphoblastoid B cells. Cell Rep. 2014 Sep 11; 8(5):1595-606. PMID: 25159142; PMCID: PMC4163118.
    Citations: 47     Fields:    Translation:HumansCells
  21. Siggers T, Reddy J, Barron B, Bulyk ML. Diversification of transcription factor paralogs via noncanonical modularity in C2H2 zinc finger DNA binding. Mol Cell. 2014 Aug 21; 55(4):640-8. PMID: 25042805; PMCID: PMC4142112.
    Citations: 9     Fields:    Translation:AnimalsCells
  22. Cheatle Jarvela AM, Brubaker L, Vedenko A, Gupta A, Armitage BA, Bulyk ML, Hinman VF. Modular evolution of DNA-binding preference of a Tbrain transcription factor provides a mechanism for modifying gene regulatory networks. Mol Biol Evol. 2014 Oct; 31(10):2672-88. PMID: 25016582; PMCID: PMC4166925.
    Citations: 7     Fields:    Translation:AnimalsCells
  23. 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. 5'RNA-Seq identifies Fhl1 as a genetic modifier in cardiomyopathy. J Clin Invest. 2014 Mar; 124(3):1364-70. PMID: 24509080; PMCID: PMC3934171.
    Citations: 13     Fields:    Translation:HumansAnimalsCells
  24. 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. PMID: 24496624; PMCID: PMC3912831.
    Citations: 11     Fields:    Translation:AnimalsCells
  25. 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. PMID: 23922708; PMCID: PMC3724861.
    Citations: 6     Fields:    Translation:AnimalsCells
  26. 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. PMID: 23873939; PMCID: PMC3731544.
    Citations: 33     Fields:    Translation:AnimalsCells
  27. 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. PMID: 23852450; PMCID: PMC3733245.
    Citations: 19     Fields:    Translation:AnimalsCells
  28. 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. PMID: 23836653.
    Citations: 42     Fields:    Translation:AnimalsCells
  29. 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 01; 29(11):1390-8. PMID: 23559638; PMCID: PMC3661050.
    Citations: 7     Fields:    Translation:Cells
  30. 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. PMID: 23562153; PMCID: PMC3640701.
    Citations: 100     Fields:    Translation:AnimalsCells
  31. 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. PMID: 23354101; PMCID: PMC3687085.
    Citations: 107     Fields:    Translation:AnimalsCells
  32. 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. PMID: 23249739; PMCID: PMC3533082.
    Citations: 52     Fields:    Translation:AnimalsCells
  33. 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. PMID: 23184988; PMCID: PMC3528522.
    Citations: 15     Fields:    Translation:AnimalsCells
  34. 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. PMID: 22841002; PMCID: PMC3566590.
    Citations: 14     Fields:    Translation:AnimalsCells
  35. 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. PMID: 22701669.
    Citations: 6     Fields:    Translation:AnimalsCells
  36. 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. PMID: 22521922.
    Citations: 1     Fields:    Translation:Cells
  37. Aboukhalil A, Bulyk ML. LOESS correction for length variation in gene set-based genomic sequence analysis. Bioinformatics. 2012 Jun 01; 28(11):1446-54. PMID: 22492312; PMCID: PMC3356840.
    Citations: 2     Fields:    Translation:AnimalsCells
  38. 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. PMID: 22323457.
    Citations: 39     Fields:    Translation:Animals
  39. 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. PMID: 22413003; PMCID: PMC3296693.
    Citations: 20     Fields:    Translation:HumansAnimalsCells
  40. 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. PMID: 22378636; PMCID: PMC3308180.
    Citations: 11     Fields:    Translation:AnimalsCells
  41. 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. PMID: 22328084.
    Citations: 29     Fields:    Translation:AnimalsCells
  42. 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. PMID: 22296846; PMCID: PMC3283125.
    Citations: 17     Fields:    Translation:AnimalsCells
  43. Gordân R, Pyne S, Bulyk ML. Identification of cell cycle-regulated, putative hyphal genes in Candida albicans. Pac Symp Biocomput. 2012; 299-310. PMID: 22174285; PMCID: PMC3331874.
    Citations: 1     Fields:    Translation:HumansAnimalsCells
  44. 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. PMID: 22174267; PMCID: PMC3327284.
    Citations: 9     Fields:    Translation:HumansCells
  45. 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 Dec 21; 12(12):R125. PMID: 22189060.
    Citations: 47     Fields:    Translation:AnimalsCells
  46. 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 Dec 06; 7:555. PMID: 22146299; PMCID: PMC3737730.
    Citations: 44     Fields:    Translation:AnimalsCells
  47. 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. 2011 Nov 20; 13(1):95-102. PMID: 22101729.
    Citations: 72     Fields:    Translation:HumansAnimalsCells
  48. McCord RP, Zhou VW, Yuh T, Bulyk ML. Distant cis-regulatory elements in human skeletal muscle differentiation. Genomics. 2011 Dec; 98(6):401-11. PMID: 21907276; PMCID: PMC3229301.
    Citations: 6     Fields:    Translation:HumansCells
  49. 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 Jul 29; 12(7):R70. PMID: 21801342.
    Citations: 49     Fields:    Translation:HumansCells
  50. Morris Q, Bulyk ML, Hughes TR. Jury remains out on simple models of transcription factor specificity. Nat Biotechnol. 2011 Jun 07; 29(6):483-4. PMID: 21654663; PMCID: PMC4409134.
    Citations: 13     Fields:    Translation:Humans
  51. 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. PMID: 21436445.
    Citations: 67     Fields:    Translation:HumansAnimalsCells
  52. 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. PMID: 21335608.
    Citations: 28     Fields:    Translation:Cells
  53. 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. PMID: 21236673; PMCID: PMC3057456.
    Citations: 76     Fields:    Translation:AnimalsCells
  54. 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 Nov 24; 5(11):e15034. PMID: 21124806; PMCID: PMC2991368.
    Citations: 14     Fields:    Translation:HumansCells
  55. 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. PMID: 21037262.
    Citations: 77     Fields:    Translation:HumansAnimalsCells
  56. 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. PMID: 20797623; PMCID: PMC2929389.
    Citations: 306     Fields:    Translation:HumansAnimalsCells
  57. 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. PMID: 20705649.
    Citations: 1     Fields:    Translation:Animals
  58. 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. PMID: 20685816.
    Citations: 23     Fields:    Translation:HumansCells
  59. 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 07; 29(13):2147-60. PMID: 20517297; PMCID: PMC2905244.
    Citations: 231     Fields:    Translation:HumansAnimalsCells
  60. 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. PMID: 20413611; PMCID: PMC2867212.
    Citations: 48     Fields:    Translation:AnimalsCells
  61. 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. PMID: 20385360; PMCID: PMC2854678.
    Citations: 104     Fields:    Translation:HumansCells
  62. 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. PMID: 20159560.
    Citations: 62     Fields:    Translation:HumansCells
  63. 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. PMID: 20079828; PMCID: PMC2848887.
    Citations: 20     Fields:    Translation:HumansAnimalsCells
  64. 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. PMID: 20056681; PMCID: PMC2858909.
    Citations: 12     Fields:    Translation:AnimalsCells
  65. 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. PMID: 19932611; PMCID: PMC2799937.
    Citations:    Fields:    Translation:AnimalsCells
  66. Gordân R, Hartemink AJ, Bulyk ML. Distinguishing direct versus indirect transcription factor-DNA interactions. Genome Res. 2009 Nov; 19(11):2090-100. PMID: 19652015; PMCID: PMC2775597.
    Citations: 71     Fields:    Translation:AnimalsCells
  67. 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. PMID: 19632181; PMCID: PMC2774807.
    Citations: 115     Fields:    Translation:AnimalsCells
  68. 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. PMID: 19443739; PMCID: PMC2905877.
    Citations: 391     Fields:    Translation:HumansAnimalsCells
  69. 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. PMID: 19370158; PMCID: PMC2667255.
    Citations: 31     Fields:    Translation:AnimalsCells
  70. Lesch BJ, Gehrke AR, Bulyk ML, Bargmann CI. Transcriptional regulation and stabilization of left-right neuronal identity in C. elegans. Genes Dev. 2009 Feb 01; 23(3):345-58. PMID: 19204119; PMCID: PMC2648548.
    Citations: 23     Fields:    Translation:AnimalsCells
  71. 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. PMID: 19158363; PMCID: PMC2665775.
    Citations: 207     Fields:    Translation:AnimalsCells
  72. 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. PMID: 19147588; PMCID: PMC2629396.
    Citations: 71     Fields:    Translation:HumansCells
  73. 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. PMID: 19265799; PMCID: PMC2908410.
    Citations: 116     Fields:    Translation:Cells
  74. 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. PMID: 19088121; PMCID: PMC2666811.
    Citations: 16     Fields:    Translation:Cells
  75. 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. PMID: 19015240; PMCID: PMC2612513.
    Citations: 18     Fields:    Translation:HumansCells
  76. 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. PMID: 18848887; PMCID: PMC2704888.
    Citations: 20     Fields:    Translation:AnimalsCells
  77. 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. PMID: 18842628.
    Citations: 192     Fields:    Translation:HumansAnimalsCells
  78. 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. PMID: 18651798.
    Citations: 23     Fields:    Translation:Cells
  79. 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. PMID: 18681939; PMCID: PMC2628434.
    Citations: 52     Fields:    Translation:Cells
  80. 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. PMID: 18585359; PMCID: PMC2531161.
    Citations: 272     Fields:    Translation:AnimalsCells
  81. 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. PMID: 18541913; PMCID: PMC2423414.
    Citations: 118     Fields:    Translation:AnimalsCells
  82. 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. PMID: 18311145; PMCID: PMC2708972.
    Citations: 49     Fields:    Translation:HumansAnimalsCells
  83. McCord RP, Bulyk ML. Functional trends in structural classes of the DNA binding domains of regulatory transcription factors. Pac Symp Biocomput. 2008; 441-52. PMID: 18229706; PMCID: PMC2757920.
    Citations: 2     Fields:    Translation:AnimalsCells
  84. 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. PMID: 17494914.
    Citations: 46     Fields:    Translation:AnimalsCells
  85. 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. PMID: 17437025; PMCID: PMC1865582.
    Citations: 16     Fields:    Translation:Animals
  86. 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. PMID: 17322287; PMCID: PMC1832101.
    Citations: 55     Fields:    Translation:AnimalsCells
  87. Bulyk ML. Protein binding microarrays for the characterization of DNA-protein interactions. Adv Biochem Eng Biotechnol. 2007; 104:65-85. PMID: 17290819; PMCID: PMC2727742.
    Citations: 14     Fields:    Translation:Cells
  88. 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. PMID: 16998473; PMCID: PMC4419707.
    Citations: 259     Fields:    Translation:HumansAnimalsCells
  89. Bulyk ML. DNA microarray technologies for measuring protein-DNA interactions. Curr Opin Biotechnol. 2006 Aug; 17(4):422-30. PMID: 16839757; PMCID: PMC2727741.
    Citations: 43     Fields:    Translation:HumansAnimalsCells
  90. 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. PMID: 16733548; PMCID: PMC1464814.
    Citations: 44     Fields:    Translation:AnimalsCells
  91. Michelson AM, Bulyk ML. Biological code breaking in the 21st century. Mol Syst Biol. 2006; 2:2006.0018. PMID: 16738563; PMCID: PMC1681494.
    Citations: 4     Fields:    Translation:Cells
  92. Huber BR, Bulyk ML. Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data. BMC Bioinformatics. 2006 Apr 27; 7:229. PMID: 16643658; PMCID: PMC1522027.
    Citations: 13     Fields:    Translation:HumansAnimalsCells
  93. 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. PMID: 16888363; PMCID: PMC2690637.
    Citations: 33     Fields:    Translation:AnimalsCells
  94. Bulyk ML. Analysis of sequence specificities of DNA-binding proteins with protein binding microarrays. Methods Enzymol. 2006; 410:279-99. PMID: 16938556; PMCID: PMC2747587.
    Citations: 13     Fields:    Translation:HumansAnimals
  95. 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. PMID: 16717444; PMCID: PMC2734277.
    Citations: 18     Fields:    Translation:Humans
  96. Bulyk ML. Discovering DNA regulatory elements with bacteria. Nat Biotechnol. 2005 Aug; 23(8):942-4. PMID: 16082362; PMCID: PMC2720157.
    Citations: 7     Fields:    Translation:Cells
  97. Philippakis AA, He FS, Bulyk ML. Modulefinder: a tool for computational discovery of cis regulatory modules. Pac Symp Biocomput. 2005; 519-30. PMID: 15759656; PMCID: PMC2692613.
    Citations: 22     Fields:    Translation:HumansAnimalsCells
  98. 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. PMID: 15543148; PMCID: PMC2692596.
    Citations: 157     Fields:    Translation:AnimalsCells
  99. Bulyk ML. Integrative functional genomics. Genome Biol. 2004; 5(7):331. PMID: 15239826; PMCID: PMC463286.
    Citations: 2     Fields:    Translation:HumansAnimals
  100. 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. PMID: 14762058; PMCID: PMC327095.
    Citations: 31     Fields:    Translation:Cells
  101. Bulyk ML. Computational prediction of transcription-factor binding site locations. Genome Biol. 2003; 5(1):201. PMID: 14709165; PMCID: PMC395725.
    Citations: 100     Fields:    Translation:HumansAnimalsCells
  102. 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. PMID: 12495153.
    Citations: 16     Fields:    Translation:Cells
  103. 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. PMID: 12384591; PMCID: PMC137142.
    Citations: 146     Fields:    Translation:AnimalsCells
  104. 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 01; 30(5):1255-61. PMID: 11861919; PMCID: PMC101241.
    Citations: 130     Fields:    Translation:AnimalsCells
  105. 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. PMID: 11404456; PMCID: PMC34639.
    Citations: 101     Fields:    Translation:Cells
  106. 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. PMID: 11237010.
    Citations: 16     Fields:    Translation:HumansCells
  107. 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. PMID: 10385322.
    Citations: 63     Fields:    Translation:Cells
  108. 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 01; 56(21):5023-32. PMID: 8895759.
    Citations: 21     Fields:    Translation:HumansCells
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Funded by the NIH/NCATS Clinical and Translational Science Award (CTSA) program, grant number UL1TR001102, and through institutional support from Harvard University, Harvard Medical School, Harvard T.H. Chan School of Public Health, Beth Israel Deaconess Medical Center, Boston Children's Hospital, Brigham and Women's Hospital, Massachusetts General Hospital and the Dana Farber Cancer Institute.