Buck Lab: Publications

Publications Buck Lab members underlined
Rizzo, J.M., Buck, M.J. (2012) Key principles and clinical applications of "next-generation" DNA sequencing. Cancer Prevention Research, 2012 Jun 6.
Rizzo, J.M., Bard, J.E., Buck, M.J. (2012) Standardization of the collection and analysis of MNase-seq experiments. BMC Molecular Biology, 2012 May 6;13(1):15.
Givens, R., Lai, W., Rizzo, J.M., Mieczkowski, P.A., Bard, J.E., Leatherwood, J., Huberman, J., Buck, M.J. (2012) Chromatin architectures at fission yeast transcriptional promoters and replication origins. Nucleic Acids Research. 2012 May 9.
Lai, W., Bard, J.E., Buck, M.J. (2012) ArchTEx: accurate extraction and visualization of Next-Generation Sequence data. Bioinformatics, 2012 Apr 1;28(7):1021-3.
Givens, R., Mesner, L.D., Hamlin, J.L., Buck, M.J., Huberman, J. (2011) Integrity of chromatin and replicating DNA in nuclei released from fission yeast by semi-automated grinding in liquid nitrogen. BMC Research Notes, Nov 16;4(1):499.
Rizzo, J.M., Mieczkowski, P.A., Buck, M.J. (2011). Tup1 stabilizes promoter nucleosome positioning and occupancy at transcriptionally plastic genes. Nucleic Acids Research. 2011 Jul 23. Epub ahead of print
Hanlon, S.E., Rizzo, J.M., Tatomer, D.C, Lieb, JD, and Buck, M.J. (2011). The stress response factors Yap6, Cin5, Phd1, and Skn7 direct targeting of the conserved co-repressor Tup1-Ssn6 in S. cerevisiae. PLOS One, 6(4): e19060.
Lai, W., and Buck, M.J. (2010). ArchAlign: Coordinate-free alignment of chromatin datasets reveals novel architectures. Genome Biology 11:R126. Highly Accessed
Rizzo, J. and Buck, M.J. (2011). All things ChIP: ChIP-chip, ChIP-Seq, ChIP-PCR. Encyclopedia of Molecular Cell Biology and Molecular Medicine, In press.
Mutiu, A.I, Hoke S.M., Genereaux, J., Buck, M.J., Yu, M., and Brandl, C.J. (2010). Mutational analysis of the C-terminal FATC domain of Saccharomyces cerevisiae Tra1. Current Genetics Jul 16.
Escamilla-Hernadez, R., Chakrabarti, R., Romano, R-A, Smalley, K., Zhu, Q., Lai, W., Halfon, M.S., Buck, M.J., Sinha, S. (2010). Genome-wide search identifies Ccnd2 as a direct transcriptional target of Elf5 in mouse mammary gland. BMC Molecular Biology Sep 10;11(1):68.
Sun, W., Buck, M.J., Patel, M., Davis, I.J. (2009) Improved ChIP-chip analysis by a mixture model approach. BMC Bioinformatics 10:173. Highly Accessed
Before UB
Mieczkowski, P.A., Dominska, M., Buck, M.J., Lieb, J.D., and Petes, T.D. (2007). Loss of a histone deacetylase dramatically alters the genomic distribution of Spo11p-catalyzed DNA breaks in Saccharomyces cerevisiae. PNAS Mar 6;104(10):3955-60.
Xiao, T., Shibata, Y., Rao, B., Laribee, R.N., O'Rourke, R., Buck, M.J., Greenblatt, J.F., Krogan, N.J., Lieb, J.D., Strahl, B.D. (2007). The RNA Pol II kinase Ctk1 regulates positioning of a 5' histone methylation boundary along genes. Molecular Cell Biology Jan; 27(2)721-31. F1000 Recommended
Buck, M.J., and Lieb, J.D. (2006). A chromatin-mediated mechanism for specification of conditional transcription factor targets. Nature Genetics Dec; 38(12): 1446-51. F1000 Recommended
Mieczkowski, P.A., Dominska, M., Buck, M.J., Gerton, J.L., Lieb, J.D., Petes, T.D. (2006). A global analysis of the relationship between the binding of the Bas1p transcription factor and meiotic recombination activity in Saccharomyces cerevisiae. Molecular Cell Biology Feb; 26(3): 1014-27.
Buck, M.J., Nobel, A.B., and Lieb, J.D. (2005). ChIPOTle: A user-friendly tool for the analysis of ChIP-chip data. Genome Biology 6: R97. Highly Accessed
Buck, M.J., and Atchley, W.R. (2005). Networks of coevolving sites in structural and functional domains of serpin proteins. Molecular Biology and Evolution Jul; 22(7):1627-34.
Buck, M.J., and Lieb, J.D. (2004). ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics Mar; 83(3): 349-60. Highly Accessed
Buck, M.J., and Atchley, W.R. (2003). Phylogenetic analysis of plant basic Helix-Loop-Helix proteins. Journal of Molecular Evolution Jun; 56(6): 742-50.
Buck, M.J., Squire, T.L., and Andrews, M.T. (2002). Coordinate expression of the PDK4 gene: a means of regulating fuel selection in a hibernating mammal. Physiological Genomics Feb; 8(1): 5-13.