Martha L. Bulyk - Publications

Genetics Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States 
transcriptional regulation

130 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Mizeracka K, Rogers JM, Rumley JD, Shaham S, Bulyk ML, Murray JI, Heiman MG. Lineage-specific control of convergent differentiation by a Forkhead repressor. Development (Cambridge, England). PMID 34423346 DOI: 10.1242/dev.199493  1
2021 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, et al. The SAM domain-containing protein 1 (SAMD1) acts as a repressive chromatin regulator at unmethylated CpG islands. Science Advances. 7. PMID 33980486 DOI: 10.1126/sciadv.abf2229  0.04
2021 Segert JA, Gisselbrecht SS, Bulyk ML. Transcriptional Silencers: Driving Gene Expression with the Brakes On. Trends in Genetics : Tig. PMID 33712326 DOI: 10.1016/j.tig.2021.02.002  1
2021 Afanasiev O, Berghout J, Brenner SE, Bulyk ML, Crawford DC, Chen JH, Daneshjou R, Kidziński Ł. Computational Challenges and Artificial Intelligence in Precision Medicine. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 26: 166-171. PMID 33691014  0.04
2021 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, et al. Zinc Finger Protein SALL4 Functions through an AT-Rich Motif to Regulate Gene Expression. Cell Reports. 34: 108574. PMID 33406418 DOI: 10.1016/j.celrep.2020.108574  0.01
2020 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, ... ... Bulyk ML, et al. Common variants in signaling transcription-factor-binding sites drive phenotypic variability in red blood cell traits. Nature Genetics. PMID 33230299 DOI: 10.1038/s41588-020-00738-2  1
2020 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. Proceedings of the National Academy of Sciences of the United States of America. PMID 32601179 DOI: 10.1073/Pnas.1922692117  1
2020 Mariani L, Weinand K, Gisselbrecht SS, Bulyk ML. MEDEA: analysis of transcription factor binding motifs in accessible chromatin. Genome Research. 30: 736-748. PMID 32424069 DOI: 10.1101/Gr.260877.120  1
2020 Brenner SE, Bulyk ML, Crawford DC, Morgan AA, Radivojac P, Tatonetti NP. Precision Medicine: Addressing the Challenges of Sharing, Analysis, and Privacy at Scale. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 25: 547-550. PMID 31797626  0.04
2019 Anderson JT, Rogers JM, Barrera LA, Bulyk ML. Context and number of non-canonical repeat variable diresidues (RVDs) impede the design of TALE proteins with improved DNA targeting. Protein Science : a Publication of the Protein Society. PMID 31833142 DOI: 10.1002/Pro.3801  1
2019 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. Molecular Cell. PMID 31704182 DOI: 10.1016/J.Molcel.2019.10.004  1
2019 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. Proceedings of the National Academy of Sciences of the United States of America. PMID 31262815 DOI: 10.1073/Pnas.1821863116  0.08
2019 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 Reports. 27: 955-970.e7. PMID 30995488 DOI: 10.1016/J.Celrep.2019.03.071  1
2019 Berghout J, Lussier YA, Vitali F, Bulyk ML, Kann MG, Moore JH. Workshop during the Pacific Symposium of Biocomputing, Jan 3-7, 2019: Reading between the genes: interpreting non-coding DNA in high-throughput. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 24: 444-448. PMID 30864345  0.01
2019 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. Molecular Cell. PMID 30826165 DOI: 10.1016/J.Molcel.2019.01.019  1
2019 Hafner A, Bulyk ML, Jambhekar A, Lahav G. The multiple mechanisms that regulate p53 activity and cell fate. Nature Reviews. Molecular Cell Biology. PMID 30824861 DOI: 10.1038/S41580-019-0110-X  0.01
2018 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. 7. PMID 30298815 DOI: 10.7554/Elife.34594  1
2018 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 & Development. PMID 29764918 DOI: 10.1101/Gad.311985.118  1
2018 Rogers JM, Bulyk ML. Diversification of transcription factor-DNA interactions and the evolution of gene regulatory networks. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. e1423. PMID 29694718 DOI: 10.1002/Wsbm.1423  1
2018 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, et al. Direct Promoter Repression by BCL11A Controls the Fetal to Adult Hemoglobin Switch. Cell. PMID 29606353 DOI: 10.1016/J.Cell.2018.03.016  1
2018 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 Reports. 22: 3227-3239. PMID 29562179 DOI: 10.1016/J.Celrep.2018.02.098  1
2018 Liu Q, Onal P, Datta RR, Rogers JM, Schmidt-Ott U, Bulyk ML, Small S, Thornton JW. Author response: Ancient mechanisms for the evolution of the bicoid homeodomain's function in fly development Elife. DOI: 10.7554/Elife.34594.023  1
2017 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 Systems. 5: 654. PMID 29284131 DOI: 10.1016/J.Cels.2017.12.011  1
2017 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 Systems. 5: 187-201.e7. PMID 28957653 DOI: 10.1016/j.cels.2017.06.015  1
2017 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. PMID 28869966 DOI: 10.1038/Nature23881  0.08
2017 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. Nature Structural & Molecular Biology. PMID 28825732 DOI: 10.1038/Nsmb.3452  0.08
2017 Inukai S, Kock KH, Bulyk ML. Transcription factor-DNA binding: beyond binding site motifs. Current Opinion in Genetics & Development. 43: 110-119. PMID 28359978 DOI: 10.1016/J.Gde.2017.02.007  0.01
2016 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 Biology. 17: 201. PMID 27687735 DOI: 10.1186/S13059-016-1062-5  1
2016 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 Genetics. 12: e1006120. PMID 27414415 DOI: 10.1371/Journal.Pgen.1006120  1
2016 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, ... ... Bulyk ML, et al. Survey of variation in human transcription factors reveals prevalent DNA binding changes. Science (New York, N.Y.). 351: 1450-4. PMID 27013732 DOI: 10.1126/Science.Aad2257  1
2015 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 Research. PMID 26582913 DOI: 10.1093/Nar/Gkv1244  1
2015 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 (Cambridge, England). 142: 3286-93. PMID 26293298 DOI: 10.1242/Dev.124636  1
2015 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 (New York, N.Y. : 2000). PMID 26177923 DOI: 10.1002/Dvg.22875  1
2015 Satterstrom FK, Swindell WR, Laurent G, Vyas S, Bulyk ML, Haigis MC. Nuclear respiratory factor 2 induces SIRT3 expression. Aging Cell. PMID 26109058 DOI: 10.1111/Acel.12360  1
2015 Rogers JM, Barrera LA, Reyon D, Sander JD, Kellis M, Joung JK, Bulyk ML. Context influences on TALE-DNA binding revealed by quantitative profiling. Nature Communications. 6: 7440. PMID 26067805 DOI: 10.1038/Ncomms8440  1
2015 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 Research. 43: D117-22. PMID 25378322 DOI: 10.1093/Nar/Gku1045  1
2015 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. DOI: 10.1002/dvg.22875  1
2014 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, et al. The NF-κB genomic landscape in lymphoblastoid B cells. Cell Reports. 8: 1595-606. PMID 25159142 DOI: 10.1016/J.Celrep.2014.07.037  1
2014 Siggers T, Reddy J, Barron B, Bulyk ML. Diversification of transcription factor paralogs via noncanonical modularity in C2H2 zinc finger DNA binding. Molecular Cell. 55: 640-8. PMID 25042805 DOI: 10.1016/J.Molcel.2014.06.019  1
2014 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. Molecular Biology and Evolution. 31: 2672-88. PMID 25016582 DOI: 10.1093/Molbev/Msu213  1
2014 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, ... ... Bulyk ML, et al. 5'RNA-Seq identifies Fhl1 as a genetic modifier in cardiomyopathy. The Journal of Clinical Investigation. 124: 1364-70. PMID 24509080 DOI: 10.1172/Jci70108  1
2014 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 (Cambridge, England). 141: 878-88. PMID 24496624 DOI: 10.1242/Dev.101709  1
2013 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. 8: e69385. PMID 23922708 DOI: 10.1371/Journal.Pone.0069385  1
2013 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 & Development. 27: 1551-6. PMID 23873939 DOI: 10.1101/Gad.214585.113  1
2013 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. Nature Methods. 10: 774-80. PMID 23852450 DOI: 10.1038/Nmeth.2558  1
2013 Nakagawa S, Gisselbrecht SS, Rogers JM, Hartl DL, Bulyk ML. DNA-binding specificity changes in the evolution of forkhead transcription factors. Proceedings of the National Academy of Sciences of the United States of America. 110: 12349-54. PMID 23836653 DOI: 10.1073/Pnas.1310430110  1
2013 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 Reports. 3: 1093-104. PMID 23562153 DOI: 10.1016/J.Celrep.2013.03.014  1
2013 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 (Oxford, England). 29: 1390-8. PMID 23559638 DOI: 10.1093/Bioinformatics/Btt152  1
2013 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, et al. Evaluation of methods for modeling transcription factor sequence specificity. Nature Biotechnology. 31: 126-34. PMID 23354101 DOI: 10.1038/Nbt.2486  1
2013 Bulyk ML, Walhout AJM. Gene Regulatory Networks Handbook of Systems Biology. 65-88. DOI: 10.1016/B978-0-12-385944-0.00004-6  1
2012 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, et al. Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning. Genes & Development. 26: 2802-16. PMID 23249739 DOI: 10.1101/Gad.207142.112  1
2012 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. Proceedings of the National Academy of Sciences of the United States of America. 109: 20768-73. PMID 23184988 DOI: 10.1073/Pnas.1210415109  1
2012 Charoensawan V, Janga SC, Bulyk ML, Babu MM, Teichmann SA. DNA sequence preferences of transcriptional activators correlate more strongly than repressors with nucleosomes. Molecular Cell. 47: 183-92. PMID 22841002 DOI: 10.1016/J.Molcel.2012.06.028  1
2012 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. 7: e38568. PMID 22701669 DOI: 10.1371/Journal.Pone.0038568  1
2012 Nowak-Lovato KL, Hickmott AJ, Maity TS, Bulyk ML, Dunbar J, Hong-Geller E. DNA binding site analysis of Burkholderia thailandensis response regulators. Journal of Microbiological Methods. 90: 46-52. PMID 22521922 DOI: 10.1016/J.Mimet.2012.03.019  1
2012 Aboukhalil A, Bulyk ML. LOESS correction for length variation in gene set-based genomic sequence analysis. Bioinformatics (Oxford, England). 28: 1446-54. PMID 22492312 DOI: 10.1093/Bioinformatics/Bts155  1
2012 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. 7: e33204. PMID 22413003 DOI: 10.1371/Journal.Pone.0033204  1
2012 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 (Cambridge, England). 139: 1457-66. PMID 22378636 DOI: 10.1242/Dev.069005  1
2012 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. Human Molecular Genetics. 21: 2194-204. PMID 22328084 DOI: 10.1093/Hmg/Dds034  1
2012 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. Investigative Ophthalmology & Visual Science. 53: 1617-27. PMID 22323457 DOI: 10.1167/Iovs.11-8839  1
2012 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 (Cambridge, England). 139: 1164-74. PMID 22296846 DOI: 10.1242/Dev.077362  1
2012 Gordân R, Pyne S, Bulyk ML. Identification of cell cycle-regulated, putative hyphal genes in Candida albicans. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 299-310. PMID 22174285  1
2012 Guo X, Bulyk ML, Hartemink AJ. Intrinsic disorder within and flanking the DNA-binding domains of human transcription factors. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 104-15. PMID 22174267  1
2011 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 Biology. 12: R125. PMID 22189060 DOI: 10.1186/Gb-2011-12-12-R125  1
2011 Siggers T, Duyzend MH, Reddy J, Khan S, Bulyk ML. Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex. Molecular Systems Biology. 7: 555. PMID 22146299 DOI: 10.1038/Msb.2011.89  1
2011 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-κB family DNA binding. Nature Immunology. 13: 95-102. PMID 22101729 DOI: 10.1038/Ni.2151  1
2011 McCord RP, Zhou VW, Yuh T, Bulyk ML. Distant cis-regulatory elements in human skeletal muscle differentiation. Genomics. 98: 401-11. PMID 21907276 DOI: 10.1016/J.Ygeno.2011.08.003  1
2011 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-κB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits Genome Biology. 12. PMID 21801342 DOI: 10.1186/Gb-2011-12-7-R70  1
2011 Morris Q, Bulyk ML, Hughes TR. Jury remains out on simple models of transcription factor specificity. Nature Biotechnology. 29: 483-4. PMID 21654663 DOI: 10.1038/Nbt.1892  1
2011 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, ... ... Bulyk ML, et al. Mutations in the RNA granule component TDRD7 cause cataract and glaucoma. Science (New York, N.Y.). 331: 1571-6. PMID 21436445 DOI: 10.1126/Science.1195970  1
2011 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 Research. 39: 4553-63. PMID 21335608 DOI: 10.1093/Nar/Gkr070  1
2011 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. Current Biology : Cb. 21: 126-33. PMID 21236673 DOI: 10.1016/J.Cub.2010.12.021  1
2011 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 Research. 39: D124-8. PMID 21037262 DOI: 10.1093/Nar/Gkq992  1
2010 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. 5: e15034. PMID 21124806 DOI: 10.1371/Journal.Pone.0015034  1
2010 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. Molecular Cell. 39: 493-506. PMID 20797623 DOI: 10.1016/J.Molcel.2010.07.023  1
2010 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 Research. 38: 7927-42. PMID 20705649 DOI: 10.1093/Nar/Gkq714  1
2010 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 Research. 38: 7422-31. PMID 20685816 DOI: 10.1093/Nar/Gkq683  1
2010 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, ... ... Bulyk ML, et al. Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo. The Embo Journal. 29: 2147-60. PMID 20517297 DOI: 10.1038/Emboj.2010.106  1
2010 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 & Development. 24: 980-5. PMID 20413611 DOI: 10.1101/Gad.1890410  1
2010 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. 17: 348-61. PMID 20385360 DOI: 10.1016/J.Ccr.2010.01.022  1
2010 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. Molecular Cell. 37: 418-28. PMID 20159560 DOI: 10.1016/J.Molcel.2010.01.016  1
2010 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. 95: 185-95. PMID 20079828 DOI: 10.1016/J.Ygeno.2010.01.002  1
2010 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 (Cambridge, England). 137: 457-66. PMID 20056681 DOI: 10.1242/Dev.045286  1
2009 Bulyk ML, Levine M. Genomes and evolution: advances in deciphering the genomics of gene regulation in evolution. Current Opinion in Genetics & Development. 19: 533-4. PMID 19932611 DOI: 10.1016/J.Gde.2009.11.003  1
2009 Gordân R, Hartemink AJ, Bulyk ML. Distinguishing direct versus indirect transcription factor-DNA interactions. Genome Research. 19: 2090-100. PMID 19652015 DOI: 10.1101/Gr.094144.109  1
2009 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. 138: 314-27. PMID 19632181 DOI: 10.1016/J.Cell.2009.04.058  1
2009 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, ... ... Bulyk ML, et al. Diversity and complexity in DNA recognition by transcription factors. Science (New York, N.Y.). 324: 1720-3. PMID 19443739 DOI: 10.1126/Science.1162327  1
2009 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. 4: e5242. PMID 19370158 DOI: 10.1371/Journal.Pone.0005242  1
2009 Berger MF, Bulyk ML. Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors. Nature Protocols. 4: 393-411. PMID 19265799 DOI: 10.1038/Nprot.2008.195  1
2009 Lesch BJ, Gehrke AR, Bulyk ML, Bargmann CI. Transcriptional regulation and stabilization of left-right neuronal identity in C. elegans. Genes & Development. 23: 345-58. PMID 19204119 DOI: 10.1101/Gad.1763509  1
2009 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, ... ... Bulyk ML, et al. High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Research. 19: 556-66. PMID 19158363 DOI: 10.1101/Gr.090233.108  1
2009 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 Research. 69: 709-17. PMID 19147588 DOI: 10.1158/0008-5472.Can-08-3415  1
2009 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 (Oxford, England). 25: 1012-8. PMID 19088121 DOI: 10.1093/Bioinformatics/Btn645  1
2009 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. Molecular and Cellular Biology. 29: 342-56. PMID 19015240 DOI: 10.1128/Mcb.01213-08  1
2009 Newburger DE, Bulyk ML. UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Research. 37: D77-82. PMID 18842628 DOI: 10.1093/Nar/Gkn660  1
2008 Busser BW, Bulyk ML, Michelson AM. Toward a systems-level understanding of developmental regulatory networks. Current Opinion in Genetics & Development. 18: 521-9. PMID 18848887 DOI: 10.1016/J.Gde.2008.09.003  1
2008 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. Molecular Microbiology. 70: 76-88. PMID 18681939 DOI: 10.1111/J.1365-2958.2008.06389.X  1
2008 Philippakis AA, Qureshi AM, Berger MF, Bulyk ML. Design of compact, universal DNA microarrays for protein binding microarray experiments. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 15: 655-65. PMID 18651798 DOI: 10.1089/Cmb.2007.0114  1
2008 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, et al. Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell. 133: 1266-76. PMID 18585359 DOI: 10.1016/J.Cell.2008.05.024  1
2008 De Silva EK, Gehrke AR, Olszewski K, León I, Chahal JS, Bulyk ML, Llinás M. Specific DNA-binding by apicomplexan AP2 transcription factors. Proceedings of the National Academy of Sciences of the United States of America. 105: 8393-8. PMID 18541913 DOI: 10.1073/Pnas.0801993105  1
2008 Warner JB, Philippakis AA, Jaeger SA, He FS, Lin J, Bulyk ML. Systematic identification of mammalian regulatory motifs' target genes and functions. Nature Methods. 5: 347-53. PMID 18311145 DOI: 10.1038/Nmeth.1188  1
2008 McCord RP, Bulyk ML. Functional trends in structural classes of the DNA binding domains of regulatory transcription factors. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 441-52. PMID 18229706  1
2008 Choi Y, Qin Y, Berger MF, Ballow DJ, Bulyk ML, Rajkovic A. Microarray analyses of newborn mouse ovaries lacking nobox (Biology of Reproduction (2007) 77, (312-319) DOI: 10.1095/biolreprod.107.060459) Biology of Reproduction. 78: 378. DOI: biolreprod/2007/066670  1
2008 Bulyk ML, Hartemink AJ, Fraenkel E, Mandel-Gutfreund Y. Protein-nucleic acid interactions: Integrating structure, sequence, and function Pacific Symposium On Biocomputing 2008, Psb 2008. 438-440.  1
2007 Choi Y, Qin Y, Berger MF, Ballow DJ, Bulyk ML, Rajkovic A. Microarray analyses of newborn mouse ovaries lacking Nobox. Biology of Reproduction. 77: 312-9. PMID 17494914 DOI: 10.1095/Biolreprod.107.060459  1
2007 McCord RP, Berger MF, Philippakis AA, Bulyk ML. Inferring condition-specific transcription factor function from DNA binding and gene expression data. Molecular Systems Biology. 3: 100. PMID 17437025 DOI: 10.1038/Msb4100140  1
2007 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, ... ... Bulyk ML, et al. Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae. Genome Research. 17: 536-43. PMID 17322287 DOI: 10.1101/Gr.6037607  1
2007 Bulyk ML. Protein binding microarrays for the characterization of DNA-protein interactions. Advances in Biochemical Engineering/Biotechnology. 104: 65-85. PMID 17290819 DOI: 10.1007/10_025  1
2007 Bulyk ML, Hartemink AJ, Fraenkel E, Stormo G. DNA-protein interactions: Integrating structure, sequence, and function Pacific Symposium On Biocomputing 2007, Psb 2007. 470-471.  1
2006 Berger MF, Philippakis AA, Qureshi AM, He FS, Estep PW, Bulyk ML. Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nature Biotechnology. 24: 1429-35. PMID 16998473 DOI: 10.1038/Nbt1246  1
2006 Bulyk ML. Analysis of sequence specificities of DNA-binding proteins with protein binding microarrays. Methods in Enzymology. 410: 279-99. PMID 16938556 DOI: 10.1016/S0076-6879(06)10013-0  1
2006 Berger MF, Bulyk ML. Protein binding microarrays (PBMs) for rapid, high-throughput characterization of the sequence specificities of DNA binding proteins. Methods in Molecular Biology (Clifton, N.J.). 338: 245-60. PMID 16888363 DOI: 10.1385/1-59745-097-9:245  1
2006 Bulyk ML. DNA microarray technologies for measuring protein-DNA interactions. Current Opinion in Biotechnology. 17: 422-30. PMID 16839757 DOI: 10.1016/J.Copbio.2006.06.015  1
2006 Michelson AM, Bulyk ML. Biological code breaking in the 21st century. Molecular Systems Biology. 2: 2006.0018. PMID 16738563 DOI: 10.1038/Msb4100062  1
2006 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 Computational Biology. 2: e53. PMID 16733548 DOI: 10.1371/Journal.Pcbi.0020053  1
2006 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. Cytogenetic and Genome Research. 114: 1-15. PMID 16717444 DOI: 10.1159/000091922  1
2006 Huber BR, Bulyk ML. Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data. Bmc Bioinformatics. 7: 229. PMID 16643658 DOI: 10.1186/1471-2105-7-229  1
2005 Bulyk ML. Discovering DNA regulatory elements with bacteria. Nature Biotechnology. 23: 942-4. PMID 16082362 DOI: 10.1038/Nbt0805-942  1
2005 Philippakis AA, He FS, Bulyk ML. Modulefinder: a tool for computational discovery of cis regulatory modules. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 519-30. PMID 15759656  1
2004 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. Nature Genetics. 36: 1331-9. PMID 15543148 DOI: 10.1038/Ng1473  1
2004 Bulyk ML. Integrative functional genomics. Genome Biology. 5: 331. PMID 15239826 DOI: 10.1186/Gb-2004-5-7-331  1
2004 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 Research. 14: 201-8. PMID 14762058 DOI: 10.1101/Gr.1448004  1
2003 Bulyk ML. Computational prediction of transcription-factor binding site locations. Genome Biology. 5: 201. PMID 14709165 DOI: 10.1186/Gb-2003-5-1-201  1
2002 Lee ML, Bulyk ML, Whitmore GA, Church GM. A statistical model for investigating binding probabilities of DNA nucleotide sequences using microarrays. Biometrics. 58: 981-8. PMID 12495153 DOI: 10.1111/J.0006-341X.2002.00981.X  1
2002 Benos PV, Bulyk ML, Stormo GD. Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Research. 30: 4442-51. PMID 12384591 DOI: 10.1093/Nar/Gkf578  1
2002 Bulyk ML, Johnson PL, Church GM. Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Research. 30: 1255-61. PMID 11861919 DOI: 10.1093/Nar/30.5.1255  1
2001 Bulyk ML, Huang X, Choo Y, Church GM. Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proceedings of the National Academy of Sciences of the United States of America. 98: 7158-63. PMID 11404456 DOI: 10.1073/Pnas.111163698  1
2001 Aach J, Bulyk ML, Church GM, Comander J, Derti A, Shendure J. Computational comparison of two draft sequences of the human genome. Nature. 409: 856-9. PMID 11237010 DOI: 10.1038/35057055  1
1999 Bulyk ML, Gentalen E, Lockhart DJ, Church GM. Quantifying DNA-protein interactions by double-stranded DNA arrays. Nature Biotechnology. 17: 573-7. PMID 10385322 DOI: 10.1038/9878  1
1996 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 Research. 56: 5023-32. PMID 8895759  1
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