Photo of Martha L. Bulyk,   PhD

Martha L. Bulyk, PhD

Brigham And Women's Hospital

Brigham And Women's Hospital
Phone: (617) 525-4725


mlbulyk@genetics.med.harvard.edu

Martha L. Bulyk, PhD

Brigham And Women's Hospital

EDUCATIONAL TITLES

  • Professor, Medicine, Harvard Medical School
  • Professor, Pathology, Harvard Medical School
  • Principal Investigator, Bulyk Laboratory, Division of Genetics, Brigham And Women's Hospital
  • Co-Chair, Biophysics Graduate Program, Committee on Higher Degrees in Biophysics, Harvard University

DF/HCC PROGRAM AFFILIATION

Research Abstract

Although numerous eukaryotic genomes have been sequenced, much still remains to be understood about how the genes in those genomes are regulated. The interactions between transcription factors (TFs) and their DNA binding sites are an integral part of the regulatory networks within cells. We employ numerous combined experimental and computational strategies in studying these regulatory interactions, to discover cis regulatory codes in the genome.

To permit a genome-wide scan of all possible TF binding sites in a given genome, we developed universal protein binding microarrays (PBMs), a DNA microarray-based technology that allows rapid, high-throughput characterization of the DNA binding site sequence specificities of proteins. We are using PBMs to study hundreds of TFs in Drosophila and mammals, so that we may predict sets of co-regulatory TFs acting together at candidate transcriptional cis regulatory modules, such as transcriptional enhancers. We are examining the effects of protein-protein interactions in DNA binding. We are also investigating divergence within TF families and how different members of a TF family gain distinct regulatory roles. We are investigating the effects of mutations and naturally occurring genetic variation on human TFs. We are combining sequence, evolutionary, structural, and PBM data to understand the molecular determinants of protein-DNA binding specificity and its evolution. We have developed computational strategies that employ comparative genomics methods for prediction of tissue-specific transcriptional enhancers in fly, and separately in mammals. Many of these predicted enhancers recently have been validated in vivo. In our analyses, we infer each TF’s relative importance for a given cell-type-specific gene expression pattern. We are interested in understanding the quantitative nature of information encoded within transcriptional enhancers, as it pertains to spatiotemporal specificity of enhancer activity. Technology development projects include novel approaches for high-throughput, experimental identification of tissue/cell-type-specific enhancers. The results of these experiments and analyses aim for a better understanding of the functions, locations and organization of DNA regulatory elements, and their evolution.

Publications from Harvard Catalyst Profiles

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  • Bulyk ML, Drouin J, Harrison MM, Taipale J, Zaret KS. Pioneer factors - key regulators of chromatin and gene expression. Nat Rev Genet 2023. PubMed
  • Jeong R, Bulyk ML. Blood cell traits' GWAS loci colocalization with variation in PU.1 genomic occupancy prioritizes causal noncoding regulatory variants. Cell Genom 2023; 3:100327. PubMed
  • Becht DC, Klein BJ, Kanai A, Jang SM, Cox KL, Zhou BR, Phanor SK, Zhang Y, Chen RW, Ebmeier CC, Lachance C, Galloy M, Fradet-Turcotte A, Bulyk ML, Bai Y, Poirier MG, Côté J, Yokoyama A, Kutateladze TG. MORF and MOZ acetyltransferases target unmethylated CpG islands through the winged helix domain. Nat Commun 2023; 14:697. PubMed
  • Weber LM, Jia Y, Stielow B, Gisselbrecht SS, Cao Y, Ren Y, Rohner I, King J, Rothman E, Fischer S, Simon C, Forné I, Nist A, Stiewe T, Bulyk ML, Wang Z, Liefke R. The histone acetyltransferase KAT6A is recruited to unmethylated CpG islands via a DNA binding winged helix domain. Nucleic Acids Res 2023; 51:574-594. PubMed
  • Masih KE, Gardner RA, Chou HC, Abdelmaksoud A, Song YK, Mariani L, Gangalapudi V, Gryder BE, Wilson AL, Adebola SO, Stanton BZ, Wang C, Milewski D, Kim YY, Tian M, Cheuk AT, Wen X, Zhang Y, Altan-Bonnet G, Kelly MC, Wei JS, Bulyk ML, Jensen MC, Orentas RJ, Khan J. A stem cell epigenome is associated with primary nonresponse to CD19 CAR T-cells in pediatric acute lymphoblastic leukemia. Blood Adv 2023. PubMed
  • Ibarra IL, Ratnu VS, Gordillo L, Hwang IY, Mariani L, Weinand K, Hammarén HM, Heck J, Bulyk ML, Savitski MM, Zaugg JB, Noh KM. Comparative chromatin accessibility upon BDNF stimulation delineates neuronal regulatory elements. Mol Syst Biol 2022; 18:e10473. PubMed
  • Terakawa A, Hu Y, Kokaji T, Yugi K, Morita K, Ohno S, Pan Y, Bai Y, Parkhitko AA, Ni X, Asara JM, Bulyk ML, Perrimon N, Kuroda S. Trans-omics analysis of insulin action reveals a cell growth subnetwork which co-regulates anabolic processes. iScience 2022; 25:104231. PubMed
  • Durbin AD, Wang T, Wimalasena VK, Zimmerman MW, Li D, Dharia NV, Mariani L, Shendy NAM, Nance S, Patel AG, Shao Y, Mundada M, Maxham L, Park PMC, Sigua LH, Morita K, Saur Conway A, Robichaud AL, Perez-Atayde AR, Bikowitz MJ, Quinn TR, Wiest OG, Easton J, Schonbrunn E, Bulyk ML, Abraham BJ, Stegmaier K, Look AT, Qi J. EP300 selectively controls the enhancer landscape of MYCN-amplified neuroblastoma. 2021. PubMed
  • Lai WKM, Mariani L, Rothschild G, Smith ER, Venters BJ, Blanda TR, Kuntala PK, Bocklund K, Mairose J, Dweikat SN, Mistretta K, Rossi MJ, James D, Anderson JT, Phanor SK, Zhang W, Zhao Z, Shah AP, Novitzky K, McAnarney E, Keogh MC, Shilatifard A, Basu U, Bulyk ML, Pugh BF. A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells. Genome Res 2021; 31:1663-1679. PubMed
  • Segert JA, Gisselbrecht SS, Bulyk ML. Transcriptional Silencers: Driving Gene Expression with the Brakes On. Trends Genet 2021; 37:514-527. PubMed
  • Stielow B, Zhou Y, Cao Y, Simon C, Pogoda HM, Jiang J, Ren Y, Phanor SK, Rohner I, Nist A, Stiewe T, Hammerschmidt M, Shi Y, Bulyk ML, Wang Z, Liefke R. The SAM domain-containing protein 1 (SAMD1) acts as a repressive chromatin regulator at unmethylated CpG islands. Sci Adv 2021. PubMed
  • Kong NR, Bassal MA, Tan HK, Kurland JV, Yong KJ, Young JJ, Yang Y, Li F, Lee JD, Liu Y, Wu CS, Stein A, Luo HR, Silberstein LE, Bulyk ML, Tenen DG, Chai L. Zinc Finger Protein SALL4 Functions through an AT-Rich Motif to Regulate Gene Expression. Cell Rep 2021; 34:108574. PubMed
  • Tao T, Shi H, Mariani L, Abraham BJ, Durbin AD, Zimmerman MW, Powers JT, Missios P, Ross KN, Perez-Atayde AR, Bulyk ML, Young RA, Daley GQ, Look AT. LIN28B regulates transcription and potentiates MYCN-induced neuroblastoma through binding to ZNF143 at target gene promotors. Proc Natl Acad Sci U S A 2020. PubMed
  • Mariani L, Weinand K, Gisselbrecht SS, Bulyk ML. MEDEA: analysis of transcription factor binding motifs in accessible chromatin. Genome Res 2020; 30:736-748. PubMed
  • Choudhuri A, Trompouki E, Abraham BJ, Colli LM, Kock KH, Mallard W, Yang ML, Vinjamur DS, Ghamari A, Sporrij A, Hoi K, Hummel B, Boatman S, Chan V, Tseng S, Nandakumar SK, Yang S, Lichtig A, Superdock M, Grimes SN, Bowman TV, Zhou Y, Takahashi S, Joehanes R, Cantor AB, Bauer DE, Ganesh SK, Rinn J, Albert PS, Bulyk ML, Chanock SJ, Young RA, Zon LI. Common variants in signaling transcription-factor-binding sites drive phenotypic variability in red blood cell traits. Nat Genet 2020; 52:1333-1345. PubMed
  • Anderson JT, Rogers JM, Barrera LA, Bulyk ML. Context and number of noncanonical repeat variable diresidues impede the design of TALE proteins with improved DNA targeting. Protein Sci 2019. PubMed
  • Gisselbrecht SS, Palagi A, Kurland JV, Rogers JM, Ozadam H, Zhan Y, Dekker J, Bulyk ML. Transcriptional Silencers in Drosophila Serve a Dual Role as Transcriptional Enhancers in Alternate Cellular Contexts. Mol Cell 2019. PubMed
  • Zirin J, Ni X, Sack LM, Yang-Zhou D, Hu Y, Brathwaite R, Bulyk ML, Elledge SJ, Perrimon N. Interspecies analysis of MYC targets identifies tRNA synthetases as mediators of growth and survival in MYC-overexpressing cells. Proc Natl Acad Sci U S A 2019. PubMed
  • 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. A Comprehensive Drosophila melanogaster Transcription Factor Interactome. Cell Rep 2019; 27:955-970.e7. PubMed
  • Hafner A, Bulyk ML, Jambhekar A, Lahav G. The multiple mechanisms that regulate p53 activity and cell fate. Nat Rev Mol Cell Biol 2019; 20:199-210. PubMed
  • Rogers JM, Waters CT, Seegar TCM, Jarrett SM, Hallworth AN, Blacklow SC, Bulyk ML. Bispecific Forkhead Transcription Factor FoxN3 Recognizes Two Distinct Motifs with Different DNA Shapes. Mol Cell 2019. PubMed
  • 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. PubMed
  • Rogers JM, Bulyk ML. Diversification of transcription factor-DNA interactions and the evolution of gene regulatory networks. 2018. PubMed
  • 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. PubMed
  • 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; 22:3227-3239. PubMed
  • 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; 32:723-736. PubMed
  • 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; 24:840-847. PubMed
  • 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; 5:187-201.e7. PubMed
  • 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; 549:287-291. PubMed
  • Inukai S, Kock KH, Bulyk ML. Transcription factor-DNA binding: beyond binding site motifs. Curr Opin Genet Dev 2017; 43:110-119. PubMed
  • 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; 12:e1006120. PubMed
  • 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; 351:1450-4. PubMed
  • 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; 142:3286-93. PubMed
  • Satterstrom FK, Swindell WR, Laurent G, Vyas S, Bulyk ML, Haigis MC. Nuclear respiratory factor 2 induces SIRT3 expression. Aging Cell 2015. PubMed
  • 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. PubMed
  • 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; 6:7440. PubMed
  • 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; 43:D117-22. PubMed
  • 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; 31:2672-88. PubMed
  • 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-κB genomic landscape in lymphoblastoid B cells. Cell Rep 2014; 8:1595-606. PubMed
  • 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; 55:640-8. PubMed
  • 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; 141:878-88. PubMed
  • 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; 10:774-80. PubMed
  • 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; 110:12349-54. PubMed
  • 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; 27:1551-6. PubMed
  • 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. PubMed
  • 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. PubMed
  • 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; 31:126-34. PubMed
  • 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:e69385. PubMed
  • 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; 109:20768-73. PubMed
  • 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; 47:183-92. PubMed
  • 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. PubMed
  • 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; 21:126-33. PubMed
  • 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; 39:D124-8. PubMed
  • 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; 38:7927-42. PubMed
  • 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; 38:7422-31. PubMed
  • 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; 39:493-506. PubMed
  • 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; 29:2147-60. PubMed
  • 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; 24:980-5. PubMed
  • 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; 17:348-61. PubMed
  • 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; 95:185-95. PubMed
  • 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; 37:418-28. PubMed
  • 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; 137:457-66. PubMed
  • 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:e15034. PubMed
  • Bulyk ML, Levine M. Genomes and evolution: advances in deciphering the genomics of gene regulation in evolution. Curr Opin Genet Dev 2009; 19:533-4. PubMed
  • Gordân R, Hartemink AJ, Bulyk ML. Distinguishing direct versus indirect transcription factor-DNA interactions. Genome Res 2009; 19:2090-100. PubMed
  • 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; 138:314-27. PubMed
  • 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; 324:1720-3. PubMed
  • 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; 25:1012-8. PubMed
  • Lesch BJ,Gehrke AR,Bulyk ML,Bargmann CI. Transcriptional regulation and stabilization of left-right neuronal identity in C. elegans. Genes Dev 2009; 23:345-58. PubMed
  • 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; 69:709-17. PubMed
  • 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:e5242. PubMed
  • 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; 29:342-56. PubMed
  • Newburger DE,Bulyk ML. UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Res 2009; 37:D77-82. PubMed
  • Berger MF,Bulyk ML. Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors. Nat Protoc 2009; 4:393-411. PubMed
  • Busser BW,Bulyk ML,Michelson AM. Toward a systems-level understanding of developmental regulatory networks. Curr Opin Genet Dev 2008; 18:521-9. PubMed
  • 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; 70:76-88. PubMed
  • Philippakis AA,Qureshi AM,Berger MF,Bulyk ML. Design of compact, universal DNA microarrays for protein binding microarray experiments. J Comput Biol 2008; 15:655-65. PubMed
  • 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; 133:1266-76. PubMed
  • 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; 105:8393-8. PubMed
  • 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; 5:347-53. PubMed
  • McCord RP, Bulyk ML. Functional trends in structural classes of the DNA binding domains of regulatory transcription factors. Pac Symp Biocomput 2008. PubMed
  • 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; 114:1-15. PubMed
  • 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 ; 17:201. PubMed
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