Publications

Jump down to Review articles, commentaries, and book chapters

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

Original Research

• *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). 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.

• *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.

• 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.

• Yanhui Hu, Andreas Rolfs, Bhupinder Bhullar, Tellamraju V. S. Murthy, Cong Zhu, Michael F. Berger, Anamaria A. Camargo, Fontina Kelley, Seamus McCarron, Daniel Jepson, Aaron Richardson, Jacob Raphael, Donna Moreira, Elena Taycher, Dongmei Zuo, Stephanie Mohr, Michael F. Kane, Janice Williamson, Andrew Simpson, Martha L. Bulyk, Edward Harlow, Gerald Marsischky, Richard D. Kolodner and Joshua LaBaer. 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): in press. (* AAP and AMQ contributed equally to this work)

• *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. (* these authors contributed equally to this work) 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, Volume 2, Issue 5, 2006. (AA Philippakis and B Busser contributed equally to this work)

• 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.

• Philippakis AA, He FS, Bulyk ML.  ModuleFinder: a tool for computational discovery of cis regulatory modules.  Pacific Symposium on Biocomputing.  2005; p. 519-530.  (AA Philippakis and FS He contributed equally to this work)
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.  (S Mukherjee and MF Berger contributed equally to this work)  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. (ML Bulyk and AM McGuire contributed equally to this work)

• 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.

• 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.

Review articles, commentaries, book chapters, etc.

• 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. Determining DNA binding specificity using microarrays.   Chapter 15 in DNA "Microarrays Part A: Array Platforms and Wet-Bench Protocols" 2006, volume 411, pages 276-296, 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.)

Patents

• 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.

This page was last updated on March 2nd, 2008