454 Life Sciences

Epigenomic analysis of Alu repeats in human ependymomas  Xie H, Wang M, Bonaldo MD, Rajaram V, Stellpflug W, Smith C, Arndt K, Goldman S, Tomita T, Soares MB. (3/29/2010) PNAS 107(15): 6952-7.
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LEDGF hybrids efficiently retarget lentiviral integration into heterochromatin.  Gijsbers R, Ronen K, Vets S, Malani N, De Rijck J, McNeely M, Bushman FD, Debyser Z. (3/1/2010) Molecular Therapy 18(3): 552-60.
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Comparison of bisulfite sequencing PCR with pyrosequencing for measuring differences in DNA methylation.  Reed K, Poulin ML, Yan L, Parissenti AM. (2/1/2010) Analytical Biochemistry 397(1): 96-106.
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Massive parallel bisulfite sequencing of CG-rich DNA fragments reveals that methylation of many X-chromosomal CpG islands in female blood DNA is incomplete.  Zeschnigk M, Martin M, Betzl G, Kalbe A, Sirsch C, Buiting K, Gross S, Fritzilas E, Frey B, Rahmann S, Horsthemke B. (4/15/2009) Human Molecular Genetics 18(8): 1439-48.
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NA-Seq: a discovery tool for the analysis of chromatin structure and dynamics during differentiation.  Gargiulo G, Levy S, Bucci G, Romanenghi M, Fornasari L, Beeson KY, Goldberg SM, Cesaroni M, Ballarini M, Santoro F, Bezman N, Frigè G, Gregory PD, Holmes MC, Strausberg RL, Pelicci PG, Urnov FD, Minucci S. (3/1/2009) Dev Cell 16(3): 466-81.
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RNA cytosine methylation analysis by bisulfite sequencing.  Schaefer M, Pollex T, Hanna K, Lyko F. (2/1/2009) Nucleic Acids Research 37(2): e12
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Genome-wide histone methylation profile for heart failure.  Kaneda R, Takada S, Yamashita Y, Choi YL, Nonaka-Sarukawa M, Soda M, Misawa Y, Isomura T, Shimada K, Mano H. (1/1/2009) Genes to Cells 14(1): 69-77
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Intergenic locations of rice centromeric chromatin.  Yan H, Talbert PB, Lee HR, Jett J, Henikoff S, Chen F, Jiang J. (11/25/2008) PLoS Biology 6: e286
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A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome  Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, Qi J, Schuster SC, Albert I, Pugh BF (6/12/2008) Genome Research :
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Nucleosome organization in the Drosophila genome  Mavrich TN, Jiang C, Ioshikhes IP, Li X, Venters BJ, Zanton SJ, Tomsho LP, Qi J, Glaser RL, Schuster SC, Gilmour DS, Albert I, Pugh BF (4/18/2008) Nature 453: 358-362
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Using RNase sequence specificity to refine the identification of RNA-protein binding regions  Xin Wang, Guohua Wang, Changyu Shen, Lang Li, Xinguo Wang, Sean D Mooney, Howard J Edenberg, Jeremy R Sanford and Yunlong Liu (3/20/2008) BMC Genomics 9:
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High-Resolution Mapping and Characterization of Open Chromatin across the Genome  Alan P. Boyle, Sean Davis, Hennady P. Shulha, Paul Meltzer, Elliott H. Margulies, Zhiping Weng, Terrence S. Furey, and Gregory E. Crawford (1/25/2008) Cell 132: 311–322
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Identification of Novel High-Frequency DNA Methylation Changes in Breast Cancer  Jared M. Ordway, Muhammad A. Budiman, Yulia Korshunova, Rebecca K. Maloney, Joseph A. Bedell, Robert W. Citek, Blaire Bacher, Seth Peterson, Tracy Rohlfing, Jacqueline Hall, Robert Brown, Nathan Lakey, Rebecca W. Doerge, Robert A. Martienssen, Jorge Leon, John D. McPherson, Jeffrey A. Jeddeloh (12/1/2007) PLoS ONE 12:
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Massively parallel bisulphite pyrosequencing reveals the molecular complexity of breast cancer-associated cytosine-methylation patterns obtained from tissue and serum DNA  Korshunova Y, Maloney RK, Lakey N, Citek RW, Bacher B, Budiman A, Ordway JM, McCombie WR, Leon J, Jeddeloh JA, McPherson JD (9/21/2007) Genome Research :
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Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing  Taylor KH, Kramer RS, Davis JW, Guo J, Duff DJ, Xu D, Caldwell CW, Shi H (9/15/2007) Cancer Research 67: 8511-8518
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Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE)  Akshay A. Bhinge, Jonghwan Kim, Ghia M. Euskirchen, Michael Snyder and Vishwanath R. Iyer (6/17/2007) Genome Research 17: 910-916
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HIV integration site selection: Analysis by massively parallel pyrosequencing reveals association with epigenetic modifications  Gary P. Wang, Angela Ciuffi, Jeremy Leipzig, Charles C. Berry and Frederic D. Bushman (6/1/2007) Genome Research :
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Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome  Istvan Albert, Travis N. Mavrich, Lynn P. Tomsho, Ji Qi, Sara J. Zanton, Stephan C. Schuster & B. Franklin Pugh (3/29/2007) Nature 446: 572-576
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Activation of TLX3 and NKX2-5 in t(5;14)(q35;q32) T-Cell Acute Lymphoblastic Leukemia by Remote 3’-BCL11B Enhancers and Coregulation by PU.1 and HMGA1  Stefan Nagel, Michaela Scherr, Alexander Kel, Klaus Hornischer, Gregory E. Crawford, Maren Kaufmann, Corinna Meyer, Hans G. Drexler, and Roderick A.F. MacLeod (2/15/2007) Cancer Research 67: 1461-1471

Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin  Steven M. Johnson, Frederick J. Tan, Heather L. McCullough, Daniel P. Riordan, and Andrew Z. Fire (12/1/2006) Genome Research 16: 1505 - 1516
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Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements  Josée Dostie, Todd A. Richmond, Ramy A. Arnaout, Rebecca R. Selzer, William L. Lee, Tracey A. Honan, Eric D. Rubio, Anton Krumm, Justin Lamb, Chad Nusbaum, Roland D. Green and Job Dekker (9/5/2006) Genome Research 16: 1299-1309
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