Publications

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Names of current and former members of the Bulyk Lab appear in boldface.

Original Research

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Preprints Peer-reviewed Preprints 2023 2022 2021 2020 2019 2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005-2002 pre-2002

Preprints

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• Julie A. Jurgens, Paola M. Matos Ruiz, Jessica King, Emma E. Foster, Lindsay Berube, Wai-Man Chan, Brenda J. Barry, Raehoon Jeong, Elisabeth Rothman, Mary C. Whitman, Sarah MacKinnon, Cristina Rivera-Quiles, Brandon M. Pratt, Teresa Easterbrooks, Fiona M. Mensching, Silvio Alessandro Di Gioia, Lynn Pais, Eleina M. England, Teresa de Berardinis, Adriano Magli, Feray Koc, Kazuhide Asakawa, Koichi Kawakami, Anne O'Donnell-Luria, David G. Hunter, Caroline D. Robson, Martha L. Bulyk, Elizabeth C. Engle. Gene identification for ocular congenital cranial motor neuron disorders using human sequencing, zebrafish screening, and protein binding microarrays. bioRxiv. September 2024.
• Luca Mariani, Xiao Liu, Kwangwoon Lee, Stephen S Gisselbrecht, P. A. Cole, Martha L Bulyk. DNA flexibility regulates transcription factor binding to nucleosomes. bioRxiv. September 2024.
• Luke Lambourne, Kaia Mattioli, Clarissa Santoso, Gloria Sheynkman, Sachi Inukai, Babita Kaundal, Anna Berenson, Kerstin Spirohn-Fitzgerald, Anukana Bhattacharjee, Elisabeth Rothman, Shaleen Shrestha, Florent Laval, Zhipeng Yang, Deepa Bisht, Jared A. Sewell, Guangyuan Li, Anisa Prasad, Sabrina Phanor, Ryan Lane, Devlin M. Campbell, Toby Hunt, Dawit Balcha, Marinella Gebbia, Jean-Claude Twizere, Tong Hao, Adam Frankish, Josh A. Riback, Nathan Salomonis, Michael A. Calderwood, David E. Hill, Nidhi Sahni, Marc Vidal, Martha L. Bulyk, Juan I. Fuxman Bass. Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms. bioRxiv. March 2024.
• Shubham Khetan, Martha L. Bulyk. Overlapping binding sites underlie TF genomic occupancy. bioRxiv. March 2024.
• D’Souza E, Weinand K, Hosage E, Gisselbrecht SS, Markstein V, Markstein P, Martha L. Bulyk, Markstein M. GA-repeats on mammalian X chromosomes support Ohno’s hypothesis of dosage compensation by transcriptional upregulation. bioRxiv. Apr 2019.

Peer-reviewed Preprints

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• Raehoon Jeong, Martha L. Bulyk. Chromatin accessibility variation provides insights into missing regulation underlying immune-mediated diseases. eLife. June 19, 2024.

2024

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• Kock KH, Kimes PK, Gisselbrecht SS, Inukai S, Phanor SK, Anderson JL, Ramakrishnan GL, Lipper CH, Song D, Kurland JV, Rogers JM, Jeong R, Blacklow S, Irizarry RA, Bulyk ML. DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues. Nature Communications. April 2024.

2023

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• Stevenson MJ, Phanor SK, Patel U, Gisselbrecht SS, Bulyk ML, O’Brien LL. Altered binding affinity of SIX1-Q177R correlates with enhanced WNT5A and WNT pathway effector expression in Wilms tumor. Disease Models & Mechanisms. 2023 Nov 1;16(11):dmm050208.
• Jeong R and Bulyk ML. Blood cell traits’ GWAS loci colocalization with variation in PU.1 genomic occupancy prioritizes causal noncoding regulatory variants. Cell Genomics. 2023 Jul 12; 3(7): 100327.
• Becht DC, Klein BJ, Kanai A, Jang SM, Cox KL, Zhou B-R, Phanor SK, Zhang Y, Lachance C, 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. Nature Communications. 2023 Feb 8;14(1):697.
• Masih KE, Gardner RA, Chou H-C, 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 A T-C, 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 Non-Response to CD19 CAR T-cells in Pediatric ALL. Blood Advances. (in press).

2022

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• Weber L, Jia Y, Stielow B, Gisselbrecht SS, Cao Y, Ren Y, Rohner Iris, Forné I, King J, Rothman E, Fischer S, Simon C, 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 Research. 2023 Jan 25;51(2):574-594.
• 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. Molecular Systems Biology 2022 Aug;18(8):e10473.
• 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 Apr 8;25(5):104231.
• *†Durbin AD, *Wang T, Wimalasena VK, Zimmerman MW, Li D, Dharia NV, Mariani L, Nance S, Park PPM, Sigua LH, Morita K, Conway AS, Robichaud AL, Perez-Atayde A, Bikowitz M, Quinn T, Wiest O, Schönbrunn E, Bulyk ML, Abraham BJ, †Stegmaier K, †Look TA, †Qi J. EP300 selectively controls the enhancer landscape of high-risk neuroblastoma. Cancer Discovery. 2022 Mar 1;12(3):730-751. (*co-1st authors, †co-corresponding authors)

2021

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• *Waters CT, *Gisselbrecht SS, Sytnikova YA, Cafarelli TM, Hill DE, Bulyk ML. Quantitative-enhancer-FACS-seq (QeFS) reveals epistatic interactions among motifs within transcriptional enhancers in developing Drosophila tissue. Genome Biology. 2021 Dec 20;22(1):348. (*co-1st authors)
• Mizeracka K, Rogers JM, Rumley JD, Shaham S, Bulyk ML, Murray JI, Heiman MG. Lineage-specific control of convergent cell identity by a Forkhead repressor. Development. 2021 Sept 28;148(19):dev199493.
• 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, Shaw AP, Novitzky K, McAnarney E, Keogh M-C, Shilatifard A, Basu U, †Bulyk ML, †Pugh BF. Screening of PCRP transcription factor antibodies in biochemical assays. Genome Research. 2021 Sep;31(9):1663-1679. (†co-corresponding authors)
  Supplementary Figures
  Read a perspective of this paper in Science Advances.
• 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. Science Advances. 2021 May 12;7(20):eabf2229.
• Kong NR, Bassal MA, Tan HK, Kurland JV, Yong KJ, Young JJ, Yang Y, Li F, Lee J, 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 Reports. 2021 Jan 5; 34(1)

2020

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• *Choudhuri A, *Trompouki E, *Abraham BJ, Colli LM, Kock KH, Mallard W, Yang M-L, 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 S, Rinn J, Bulyk ML, Chanock SJ, Young RA, Zon LI. Common variants in signaling transcription factor binding sites drive the majority of red blood cell traits. Nature Genetics, 2020 Nov 23;52:1333–1345.
• *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 promoters. Proc. Natl. Acad. Sci. USA, 2020. 117(28):16516–16526. Epub June 29, 2020. (*co-1st authors, †co-corresponding authors)
• Mariani L*, Weinand K*, Gisselbrecht SS, Bulyk ML. MEDEA: analysis of transcription factor binding motifs in accessible chromatin. Genome Research. 2020 May;30(5):736-748.
• 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. 2020 Feb;29(2):606-616. Epub 2019 Dec 24.
• 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. 2020 Jan 16;77(2):324-337.
  Read the highlight of this paper in Trends in Genetics.

2019

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• 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. PNAS. 2019 Jul 16;116(29):14614-14619. doi: 10.1073/pnas.1821863116. Epub 2019 Jul 1.
• 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. 2019 Apr 18; 74(2):245-253.e6
• Shokri L*, Inukai S*, Hafner A, Weinand K, Hens K, Vedenko A, Gisselbrecht SS, Dainese R, Bischof J, Furger E, Feuz J-D, Basler K, †Deplancke B, †Bulyk ML. A comprehensive Drosophila melanogaster transcription factor interactome. Cell Reports. 2019 Apr 16; 27(3):955-970.e7 (*co-1st authors, †co-corresponding authors)

2018

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• Liu Q*, Onal P*, Datta R*, 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 Oct 9; 7:e34594 (*co-1st authors)
• 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 between Bicoid and Orthodenticle Regulates the Timing of Embryonic Patterning in Drosophila. Genes & Development. 2018 May 1;32(9-10):723-736.
• 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. 2018 Mar 20;22(12):3227-3239 (*co-1st authors)
• Liu N*, Hargreaves VV*, Zhu Q*, Kurland JV, Hong J, Kim W, Sher F, Macias-Trevino C, Rogers JM, Kurita R, Nakamura Y, Yuan G-C, Bauer DE, Xu J, Bulyk ML, Orkin SH. Direct promoter repression by BCL11A controls the fetal to adult hemoglobin switch. Cell. 2018 Apr 19;173:1–13. (*co-1st authors)

2017

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• 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 Sep 14;549(7671):287-291
• Hafner A, Stewart-Ornstein J, Purvis J, Forrester W, Bulyk ML, Lahav G. p53 pulses lead to distinct patterns of gene expression albeit similar DNA binding dynamics. Nature Structural and Molecular Biology. 2017 Oct;24(10):840-847
• Mariani L, Weinand K, Vedenko A, Barrera LA, Bulyk ML. Identification of human lineage-specific transcriptional co-regulators enabled by a glossary of binding modules and tunable genomic backgrounds. Cell Systems. 2017 Sep 27;5(3):187–201

2016

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• 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 Sep 29;17(1):201.
• Kuzu G*, Kaye EG*, Chery J, Siggers T, Yang L, Dobson J, 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. 2016 Jul 14;12(7) (*co-1st authors)
• 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(6280):1450-1454. (*co-2nd authors)
  Abstract
  Reprint
  Full text
  Read the Cell Systems Calls highlight of this paper in Cell Systems.

2015

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• Cui H, Schlesinger J, Schoenhals S, Tönjes M, Dunkel I, Meierhofer, 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) 44(6):2538-53. Epub 17 Nov 2015.
• Nishi Y, Zhang X, Jeong J, Peterson K, Vedenko A, Bulyk M, Hide W, McMahon A. A direct fate exclusion mechanism by Sonic Hedgehog-regulated transcriptional repressors. Development (2015) 142(19):3286-93. Epub 20 Aug 2015.
• Menke C, Cionni M, Siggers T, Bulyk ML, Beier DR, Stottmann RW. Grhl2 is required in non-neural tissues for neural progenitor survival and forebrain development. Genesis (2015) 53:573-582. Epub 2015 Jul 14.
• Satterstrom FK, Swindell WR, Laurent G, Vyas S, Bulyk ML, Haigis MC. Nuclear respiratory factor 2 induces SIRT3 expression. Aging Cell (2015) 14(5):818-25. Epub 24 Jun 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 (2015) 6:7440. Epub Jun 11.

2014

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• 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 (2015) 43(Database issue):D117-22. Epub Nov. 5, 2014.
• Zhao B*, Barrera LA*, Ersing I, Willox B, Schmidt S, Greenfeld H, Zhou H, Mollo S, Shi T, Takasaki K, Cahir-McFarland E, Kellis M, Bulyk ML**, Kieff E**, Gewurz B**  The NF-kappaB genomic landscape in lymphoblastoid B-cells. Cell Reports (2014) 8(5):1595-606. Epub Aug 21, 2014.
  * Co-first authors
  ** Co-corresponding authors
• 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 (2014) 31(10):2672-88. Epub 2014 Jul 12.
  Read the Editor’s Choice highlight of this paper in Science.
• Siggers T**, Reddy J, Barron B, Bulyk ML**. Diversification of transcription factor paralogs via noncanonical modularity in C2H2 zinc finger DNA binding. Molecular Cell (2014) 55(4):640-8. Available online 17 July 2014.
  ** Co-corresponding authors
• 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(4):878-88. * Co-first authors
• 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 modifier in hypertrophic cardiomyopathy. The Journal of Clinical Investigation (2014). Epub Feb 10, 2014.

2013

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• Gisselbrecht SS, Barrera LA, Porsch M, Aboukhalil A, Estep PW 3rd, 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 (2013) 10(8):774-780. Epub July 14, 2013.
  
  Read the News and Views highlight of this paper in Nature Methods.
  High resolution version of figures S5 and S9.
  
• Soruco MML, 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 (2013) 27:1551–1556.
• *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 USA. (2013) 110(30):12349-54 Epub July 8, 2013. (*co-1st authors; **co-corresponding authors)
  Read the Editor’s Choice highlight of this paper in Science.
  
• 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
• 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) 29(11):1390-1398. Epub April 4, 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 (2013) 3:1093-1104 Epub April 4, 2013. (*co-2nd authors; **co-corresponding authors )
  Winner of a Top Ten Paper Award at the 2013 RECOMB/ISCB Regulatory and Systems Genomics meeting.
• Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S, DREAM5 Consortium, Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, Hughes TR. Evaluation of methods for modeling transcription-factor sequence specificity. Nature Biotechnology (2013) 31(2):126-34.

2012

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• 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 & Development (2012) 26: 2802-2816
• 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. PNAS (2012) 109(50):20768-73. Epub 2012 Nov 26
• 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 (2012) 47(2):183-192.
• Jumlongras D, Lachke SA, O.Connell DJ, Aboukhalil A , Li X, Choe SE, Ho JWK, 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. Epub 2012 Jun 12.
• 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 (2012) 90(1):46-52.
• Aboukhalil A, Bulyk ML. LOESS correction for length variation in gene set-based genomic sequence analysis. Bioinformatics (2012) 28(11):1446-54. Epub 2012 Apr 5.
• 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. Epub Mar 7 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 (2012) 139: 1457-1466. Epub Feb 29, 2012.
• Sakabe NJ, Aneas I, Shen T, Shokri L, Bulyk ML, Evans SM, Nobrega MA. Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function. Human Molecular Genetics. (2012) 21(10):2194-204. Epub Feb 10 2012.
• Lachke SA, Ho JWK, Kryukov GV, O’Connell DH, Aboukhalil A, Bulyk ML, Park PJ, Maas RL. iSyTE: integrated Systems Tool for Eye gene discovery. Investigative Ophthalmology and Visual Science. (2012) 53(3):1617-1627. Epub Feb 8 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 (*co-1st authors; †co-corresponding authors )(2012) 139:1164-1174. Epub Feb 6 2012.
• *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-kB family DNA binding. Nature Immunology (2012) 13(1):95-102 (*co-1st authors) Supplementary Text and Figures, Supplementary Spreadsheet 1.
  A Faculty of 1000 Recommended.
  Click here to access the NF-kB PBM data and search tools.
• Guo X, *Bulyk ML,*Hartemink AJ. Intrinsic disorder within and flanking the DNA-binding domains of human transcription factors. Pacific Symposium on Biocomputing (2012) 17:104-115 (*co-corresponding authors)
• *Gordân R, *Pyne S, *Bulyk ML Identification of cell cycle-regulated putative hyphal genes in Candida albicans. Pacific Symposium on Biocomputing (2012) 17:299-310 (*co-corresponding authors)

2011

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• *Gordân R, *Murphy K, 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 2011, 12:R125 Epub Dec. 21, 2011 (*co-1st authors)
• Siggers T, Duyzend M, Reddy J, Kahn S, Bulyk ML. Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex. Molecular Systems Biology (2011) 7:555.
  
  Read the highlight of this paper in Nature Reviews Genetics.
• McCord RP, Zhou V, Yuh T, Bulyk ML. Distant cis regulatory elements in human skeletal muscle differentiation. Genomics (2011) 98(6):401-11. Epub 2011 Aug 23.
• Wong D, Teixeira A, Oikonomopoulos S, Humburg P, Lone IN, Saliba D, Siggers T, Bulyk ML, Angelov D, Dimitrov S, Udalova I, Ragoussis J. Extensive characterization of NF-kB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits. Genome Biology. (2011), Epub 2011 Jul 29;12(7):R70.
• *Lachke SA, *Alkuraya FS, *Kneeland SC, Ohn T, Aboukhalil A, Howell GR, Saadi I, Cavallesco R, Yue Y, Tsai AC, Nair S, Cosma MI, Smith RS, Hodges E, Al-Fadhli SM, Al-Hajeri A, Shamseldin HE, Behbehani A, Hannon GJ, Bulyk ML, Drack AV, Anderson PJ, John SWM, Maas RL. Mutations in the RNA granule component gene TDRD7 cause cataract and glaucoma. Science (2011) 311:1571-1576. (*co-1st authors)
  A Faculty of 1000 Recommended.
  Read the Research Highlight of this paper in Nature Reviews Genetics.


• *De Masi F, *Grove CA, Vedenko A, Alibés A, Gisselbrecht SS, Serrano L, †Bulyk ML, †Walhout AJM. Using a structural and logics systems approach to infer bHLH DNA binding specificity determinants. Nucleic Acids Research. Jul 29;12(7):R70. (*co-1st authors; †co-corresponding authors)
• Helfer A, Nusinow DA, Chow BY, Gehrke AR, Bulyk ML, Kay SA. LUX ARRHYTHMO Encodes a night time repressor of circadian gene expression in the Arabidopsis core clock. Current Biology (2011), Jan 25;21(2):126-33.
  A Faculty of 1000 Recommended.
• 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 (2011) Jan;39(Database issue):D124-8. Epub 2010 Oct 30.

2010

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• Del Bianco C, Vedenko A, Choi S-H, 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. (†co-corresponding authors)
• Iliopoulos D, Jaeger SA, Hirsch H, 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 (2010) Aug 27;39(4):493-506.
• 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 classification of mouse homeodomains reflects their in vitro DNA binding preferences. Nucleic Acids Res. Epub (2010) Aug 12.
• 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) Aug 4. [Epub ahead of print]
• Wei G-H, Badis G, Berger MF, Kivioja T, Palin K, Enge M, Bonke M, Jolma A, Varjosalo M, Gehrke AR, Yan J, Talukder S, Turunen M, Taipale M, Stunnenberg HG, Ukkonen E, Hughes TR, Bulyk ML, Taipale J. Genome-wide analysis of ETS family DNA-binding in vitro and in vivo. EMBO J. (2010) Jul 7;29(13):2147-60. Epub 2010 Jun 1.
• *Rowan S, *Siggers T, Lachke S, Yue Y, †Bulyk ML, †Maas RL. Precise temporal control of the eye regulatory gene Pax6 via enhancer binding site affinity. Genes & Development. (2010) 24:980-985. (*co-1st authors; †co-corresponding authors). Supplemental information.
• *Hirsch HA, *Iliopoulos D, *Joshi A, Zhang Y, Jaeger SA, Bulyk ML, Tsichlis PN, Liu XS, 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. (*co-1st authors)
  A Faculty of 1000 Exceptional.
• Giorgetti L, Siggers T, Tiana G, Caprara G, Notarbartolo S, Corona T, Pasparakis M, Milani P, Bulyk ML, Natoli G. Non-cooperative interactions between transcription factors and clustered DNA binding sites enable graded transcriptional responses to environmental inputs. Molecular Cell (2010) Feb 12;37(3):418-28. Supplemental information.
  Read a highlight of this paper from Nature Reviews Genetics.
• 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. Epub (2010) Jan 15.
• 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):457-466. Epub 2010 Jan 7.

2009

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• Gordân R, Hartemink AJ, Bulyk ML. Distinguishing direct versus indirect transcription factor-DNA interactions. Genome Research. (2009) Nov;19(11):2090-100. Epub 2009 Aug 3.
• *Grove CA, *de Masi F, Barrasa MI, Newburger DE, Alkema MJ, †Bulyk ML, †Walhout AJM. A multi-parameter network reveals extensive divergence between C. elegans bHLH transcription factors. Cell (2009) 138:314-327 (*co-1st authors; †co-corresponding authors).
  A Faculty of 1000 Exceptional.
• *Badis G, *Berger MF, *Philippakis AA, *Talukder S, *Gehrke AR, *Jaeger SA, *Chan ET, Metzler G, Vedenko A, Chen X, Kuznetsov H, Wang C-F, Coburn D, Newburger D, Morris QD, †Hughes TR, †Bulyk ML. Diversity and complexity in DNA recognition by transcription factors. Science (2009) 324:1720-1723. [Epub 2009 May 14.] (*co-1st authors; †co-corresponding authors).
  Abstract
  Reprint
  Full text
  Supplemental Information
  Read the summary of this paper in Nature Biotechnology
  A Faculty of 1000 Must Read
• †Estep PW III, 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- (†corresponding author: pestep@post.harvard.edu)
• Lesch BJ, Gehrke AR, Bulyk ML, Bargmann CI. Transcriptional regulation and stabilization of left-right neuronal identity in C. elegans. Genes and Development (2009) 23(3):345-58.
• *Zhu C, *Byers K, *McCord RP, Shi Z, Berger MF, Newburger D, Saulrieta K, Smith Z, Shah M, Radhakrishnan M, Philippakis AA, Hu Y, De Masi F, Pacek M, Rolfs A , Murthy TVS, LaBaer J, Bulyk ML. High-Resolution DNA Binding Specificity Analysis of Yeast Transcription Factors. Genome Research. 2009 Apr;19(4):556-66. Epub 2009 Jan 21. doi:10.1101/gr.090233.108 (*co-1st authors). Supplemental Information
• Berger MF and Bulyk ML. Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors. Nature Protocols. (2009) 4(3):393-411
• 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. Epub 2008 Dec 16.
• 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. Cancer Research. January 15, 2009. 69(2). Supplemental Information
• Viiri KM, Janis J, Siggers T, Heinonen TY, Valjakka J, Bulyk ML, Maki M, Lohi O. DNA-binding and -bending activities of SAP30L and SAP30 are mediated by a zinc-dependent module and monophosphoinositides. Mol Cell Biol. 2009 Jan;29(2):342-56. Epub 2008 Nov 17.
  



2008

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• Newburger DE and Bulyk ML. UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. Nucl. Acids Res. 2009 37: D77-D82; doi:10.1093/nar/gkn660. Epub October 8, 2008. Click here to access the UniPROBE database.
  
• Pompeani AJ, Irgon JJ, Berger MF, Bulyk ML, Wingreen NS, and 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. (2008) 70(1):76-88.
  A Faculty of 1000 Recommended. Supplemental Information
  
• *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 June 27, 2008; 133:1266-1276 (doi:10.1016/j.cell.2008.05.024) (*co-1st authors; †co-corresponding authors). Supplemental Data. Additional Supplementary Information. Click here to access the mouse homeodomains PBM database.
  
• De Silva EK, Gehrke AR, Olszewki K, Leon I, Chahal JS, Bulyk ML, Llinas M. Specific DNA-binding by Apicomplexan AP2 transcription factors. Proc. Natl. Acad. Sci. USA. June 17, 2008; vol. 105, no. 24, 8393-8398 (10.1073/pnas.0801993105).
  A Faculty of 1000 Must Read.Supplemental Information
  
• *Warner JB, *Philippakis AA, *Jaeger SA, He FS, Lin J, Bulyk ML. Systematic identification of mammalian regulatory motifs' target genes and functions. Nature Methods. 2008 Apr; 5(4):347-53. Epub 2008 Mar 2 (10.1038/nmeth.1188) (* co-1st authors) Supplementary Information. Read the News and Views highlight of this paper in Nature Methods.
  
• McCord RP and Bulyk ML.  Functional trends in structural classes of the DNA binding domains of regulatory transcription factors. Pacific Symposium on Biocomputing 13:441-452 (2008). Supplementary Information.
  



2007

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• Choi Y, Qin Y, Berger MF, Ballow DJ, Bulyk ML, Rajkovic A.  Microarray Analyses of Newborn Mouse Ovaries Lacking Nobox. Biology of Reproduction 2007 Jul;77(2):312-9. Epub 2007 May 9.
  
• McCord RP, Berger MF, Philippakis AA, Bulyk ML.  Inferring condition-specific transcription factor function from DNA binding and gene expression. Molecular Systems Biology, 2007; 3:100. Supplemental Information.
  
• Hu Y, Rolfs A, Bhullar B, Murthy TVS, 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 and LaBaer J. Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae. Genome Research 2007 Apr;17(4):536-43.Epub 2007 Feb 23.
  
• *Philippakis AA, *Qureshi A, Berger MF, Bulyk ML. Design of Compact, Universal DNA Microarrays for Protein Binding Microarray Experiments. RECOMB 2007, published in Journal of Computational Biology (2008) 15(7):655-665, doi: 10.1089/cmb.2007.0114 (* co-1st authors)
  



2006

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• *Berger MF, *Philippakis AA, Qureshi A, He FS, Estep PW 3rd, Bulyk ML. Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nature Biotechnology 2006 Nov;24(11):1429-1435. Epub 2006 Sept 24. (* co-1st authors) Supplemental Information.
  
• *Philippakis AA, *Busser B, 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, (2006) 2(5):e53. (* co-1st authors)
  
• Huber BR and Bulyk ML.  Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data. BMC Bioinformatics. 2006; 7:229.
  Click here to get MultiFinder software.
  



2005-2002

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• *Philippakis AA, *He FS, Bulyk ML. ModuleFinder: a tool for computational discovery of cis regulatory modules.  Pacific Symposium on Biocomputing.  2005; p. 519-530.  (* co-1st authors)
  Click here to get ModuleFinder software.
  
• *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.  2004 Dec; 36(12):1331-1339.  Epub 2004 Nov 14.  (* co-1st authors)  Supplemental Information. Read the highlight of this paper in Nature Methods.
  Faculty of 1000 Recommended.
  
• *Bulyk ML, *McGuire AM, Masuda N, Church GM.  A motif co-occurrence approach for genome-wide prediction of transcription factor binding sites in E. coli.  Genome Research. 2004; 14(2):201-208. (* co-1st authors)
• Lee M-LT, Bulyk ML, Whitmore GA, Church GM. A statistical model for investigating binding probabilities of DNA nucleotide sequences using microarrays. Biometrics. 2002 Dec; 58(4):981-988.
• Benos P, Bulyk ML, Stormo GD. Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Research. 2002; 30(20):4442-4451.
• Bulyk ML, Johnson PLF, Church GM. Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Research 2002 Mar 1; 30(5):1255-1261. Supplemental data.



pre-2002

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• Bulyk ML, Huang XH, Choo Y, Church GM.  Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc. Natl. Acad. Sci. U.S.A. 2001 Jun 12; 98(13):7158-7163. Supplemental data.  (News & Comment in Trends in Genetics)
• Aach J, Bulyk ML, Church GM, Comander J, Derti A, Shendure J.  Comparison of systematic computations on the human genome. Nature 2001 Feb 15; 409:856-9.
• Bulyk ML, Gentalen E, Lockhart DJ, Church GM.  Quantifying DNA-protein interactions by double-stranded DNA arrays. Nature Biotechnology 1999 Jun; 17(6):573-7.
• 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 1996 Nov 1; 56(21):5023-32.

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Review articles, commentaries, book chapters, etc.

• Bulyk ML, Drouin J, Harrison MM, Taipale J, Zaret KS. Pioneer factors - key regulators of chromatin and gene expression. Nature Reviews Genetics. 2023 Sep 22.
• Lead authors: Fowler DM, Gloyn AL, Hurles M. Additional co-authors: Adams DJ, Hahn WC, Marks DS, Neal JT, Roth FP, Rubin AF, Starita LM. Bulyk ML is among the contributing authors in the Acknowledgements section of the paper. An Atlas of Variant Effects to understand the genome at nucleotide resolution. Genome Biology. 2023 Jul; 24(1):147.
• Nora EP, Aerts S, Wittkopp PJ, Bussemaker HJ, Bulyk ML, Sinha S, Zeitlinger J, Crocker J, Fuxman Bass JI. Emerging questions in transcriptional regulation. Cell Systems. 2023 Apr;14(4):247-251.
• *Segert JA, *Gisselbrecht SS, Bulyk ML. Transcriptional silencers: driving gene expression with the brakes on. Trends in Genetics. 2021 Jun;37(6):514-527.
• Hafner A, Bulyk ML, Jambhekar A, Galit L. The multiple mechanisms that regulate p53 activity and cell fate. Nature Reviews Molecular Cell Biology. 2019 Mar 1. 20:199-210.
• Rogers JM, Bulyk ML. Diversification of TF-DNA interactions and the evolution of gene regulatory networks. WIREs Systems Biology and Medicine. 2018 Apr 25:e1423.
• Inukai S*, Kock KH*, Bulyk ML. Transcription factor-DNA binding: beyond binding site motifs. Current Opinion in Genetics & Development (2017) 43:110-119
• Bulyk ML and Walhout A.J.M. Chapter 4, “Gene Regulatory Networks”, in "Handbook of Systems Biology: Concepts and Insights”, 2012, pages 65-88, Elsevier Inc. Edited by Albertha J.M. Walhout, Marc Vidal, and Job Dekker
• Morris Q, Bulyk ML, Hughes TR. Jury remains out on simple models of transcription factor specificity. Nat Biotechnol. (2011) Jun 7;29(6):483-4.
• †Bulyk ML, Levine M.  Genomes and evolution: advances in deciphering the genomics of gene regulation in evolution. Current Opinion in Genetics & Development. (2009) 19(6):533-534. (†corresponding author)
• Busser BW, †Bulyk ML, †Michelson AM.   Toward a systems-level understanding of developmental regulatory networks. Current Opinion in Genetics & Development. (2008) 18:521-529. Epub 2008 Oct 9 (†co-corresponding authors)
• Bulyk ML.   DNA microarray technologies for measuring protein-DNA interactions. Current Opinion in Biotechnology. 2006 July 11; 17(4)
• Bulyk ML. Protein binding microarrays for the characterization of protein-DNA interactions. Chapter in   "Analytics of protein-DNA interactions", 2007, volume 104, pages 65-85, Advances in Biochemical Engineering / Biotechnology.Springer-Verlag, Inc. Edited by Harald Steitz.
• 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 (2006)
• Michelson AM and Bulyk ML.  Biological code breaking in the 21st century. Molecular Systems Biology. 2006; 2:2006.0018. Epub 2006 May 2 (News & Views).
• Berger MF and Bulyk ML. Protein binding microarrays (PBMs) for the rapid, high-throughout characterization of the sequence specificities of DNA binding proteins.   Chapter 13 in "Gene mapping, discovery, and expression", 2006; Volume 338, pages 245-260, Methods in Molecular Biology. The Humana Press, Inc. Edited by Minou Bina.
• Bulyk ML. Analysis of the Sequence Specificities of DNA Binding Proteins with Protein Binding Microarrays.   Chapter 13 in DNA "Microarrays Part A: Array Platforms and Wet-Bench Protocols" 2006, volume 410, pages 276-299, Methods in Enzymology. Elsevier Life Sciences. Edited by Brian Oliver and Alan Kimmel.
• Bulyk ML.   Discovering DNA regulatory elements with bacteria. Nature Biotechnology. 2005 Aug; 23(8):942-4. (News & Views)
• Bulyk ML. Integrative functional genomics. Genome Biology. 2004; 5:331.  (Meeting Report)
  
• Bulyk ML.  Computational prediction of transcription-factor binding site locations.  Genome Biology. 2003; 5(1):201.  (Click here for the abridged version.)

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Patents

• United States Patent 8,530,638. Bulyk ML, Philippakis AA, Estep PW. "Space efficient polymer sets". September 10, 2013.
• United States Patent 6,548,021. Church GM and Bulyk ML. "Surface-bound, double-stranded DNA protein arrays". April 15, 2003.
• International Patent Application No. WO 02/18648 A2. Church GM, Bulyk ML, and Choo Y. "Analysis of Binding Interactions". March 7, 2002.
• United States Patent 6,326,489. Church GM and Bulyk ML" Surface-bound, bimolecular, double-stranded DNA arrays". December 4, 2001.