My NCBISign In
Model-based analysis of two-color arrays (MA2C)
Jun S Song, W Evan Johnson, Xiaopeng Zhu, Xinmin Zhang, Wei Li, Arjun K Manrai, Jun S Liu, Runsheng Chen, X Shirley Liu
Genome Biol. 2007; 8(8): R178. Published online 2007 August 29. doi: 10.1186/gb-2007-8-8-r178
PMCID:
PMC2375008
Abstract Full Text PDF–1.0M

Is Cited by the Following 47 Articles in this Archive:

Caenorhabditis elegans Dosage Compensation Regulates Histone H4 Chromatin State on X Chromosomes
Michael B. Wells, Martha J. Snyder, Laura M. Custer, Gyorgyi Csankovszki
Mol Cell Biol. 2012 May; 32(9): 1710–1719. doi: 10.1128/MCB.06546-11
PMCID:
PMC3347233
Free in PMC on 2012/11/01
Dynamic Changes in Nucleosome Occupancy Are Not Predictive of Gene Expression Dynamics but Are Linked to Transcription and Chromatin Regulators
Dana J. Huebert, Pei-Fen Kuan, Sündüz Keleş, Audrey P. Gasch
Mol Cell Biol. 2012 May; 32(9): 1645–1653. doi: 10.1128/MCB.06170-11
PMCID:
PMC3347246
Free in PMC on 2012/11/01
An evaluation of two-channel ChIP-on-chip and DNA methylation microarray normalization strategies
Michiel E Adriaens, Magali Jaillard, Lars MT Eijssen, Claus-Dieter Mayer, Chris TA Evelo
BMC Genomics. 2012; 13: 42. Published online 2012 January 25. doi: 10.1186/1471-2164-13-42
PMCID:
PMC3293711
Abstract Full Text PDF–2.0M Supplementary Material
Identification and characterization of Hoxa9 binding sites in hematopoietic cells
Yongsheng Huang, Kajal Sitwala, Joel Bronstein, Daniel Sanders, Monisha Dandekar, Cailin Collins, Gordon Robertson, James MacDonald, Timothee Cezard, Misha Bilenky, Nina Thiessen, Yongjun Zhao, Thomas Zeng, Martin Hirst, Alfred Hero, Steven Jones, Jay L. Hess
Blood. 2012 January 12; 119(2): 388–398. Prepublished online 2011 November 9. doi: 10.1182/blood-2011-03-341081
PMCID:
PMC3257007
Free in PMC on 2013/01/12
Developmental control of gene copy number by repression of replication initiation and fork progression
Noa Sher, George W. Bell, Sharon Li, Jared Nordman, Thomas Eng, Matthew L. Eaton, David M. MacAlpine, Terry L. Orr-Weaver
Genome Res. 2012 January; 22(1): 64–75. doi: 10.1101/gr.126003.111
PMCID:
PMC3246207
Abstract Full Text PDF–954K
Analysis of Biological Features Associated with Meiotic Recombination Hot and Cold Spots in Saccharomyces cerevisiae
Loren Hansen, Nak-Kyeong Kim, Leonardo Mariño-Ramírez, David Landsman
PLoS One. 2011; 6(12): e29711. Published online 2011 December 29. doi: 10.1371/journal.pone.0029711
PMCID:
PMC3248464
Abstract Full Text PDF–746K Supplementary Material
Euchromatic Subdomains in Rice Centromeres Are Associated with Genes and Transcription
Yufeng Wu, Shinji Kikuchi, Huihuang Yan, Wenli Zhang, Heidi Rosenbaum, A. Leonardo Iniguez, Jiming Jiang
Plant Cell. 2011 November; 23(11): 4054–4064. Published online 2011 November 11. doi: 10.1105/tpc.111.090043
PMCID:
PMC3246336
Free in PMC on 2012/11/01
Systems Analysis of ATF3 in Stress Response and Cancer Reveals Opposing Effects on Pro-Apoptotic Genes in p53 Pathway
Yujiro Tanaka, Aya Nakamura, Masaki Suimye Morioka, Shoko Inoue, Mimi Tamamori-Adachi, Kazuhiko Yamada, Kenji Taketani, Junya Kawauchi, Miki Tanaka-Okamoto, Jun Miyoshi, Hiroshi Tanaka, Shigetaka Kitajima
PLoS One. 2011; 6(10): e26848. Published online 2011 October 26. doi: 10.1371/journal.pone.0026848
PMCID:
PMC3202577
Abstract Full Text PDF–1.1M Supplementary Material
Cistrome: an integrative platform for transcriptional regulation studies
Tao Liu, Jorge A Ortiz, Len Taing, Clifford A Meyer, Bernett Lee, Yong Zhang, Hyunjin Shin, Swee S Wong, Jian Ma, Ying Lei, Utz J Pape, Michael Poidinger, Yiwen Chen, Kevin Yeung, Myles Brown, Yaron Turpaz, X Shirley Liu
Genome Biol. 2011; 12(8): R83. Published online 2011 August 22. doi: 10.1186/gb-2011-12-8-r83
PMCID:
PMC3245621
Abstract Full Text PDF–2.1M Supplementary Material
The SKP1-Cul1-F-box and Leucine-rich Repeat Protein 4 (SCF-FbxL4) Ubiquitin Ligase Regulates Lysine Demethylase 4A (KDM4A)/Jumonji Domain-containing 2A (JMJD2A) Protein
Capucine Van Rechem, Joshua C. Black, Tarek Abbas, Andrew Allen, Claire A. Rinehart, Guo-Cheng Yuan, Anindya Dutta, Johnathan R. Whetstine
J Biol Chem. 2011 September 2; 286(35): 30462–30470. Published online 2011 July 8. doi: 10.1074/jbc.M111.273508
PMCID:
PMC3162406
Abstract Full Text
Integrative analysis of gene amplification in Drosophila follicle cells: parameters of origin activation and repression
Jane C. Kim, Jared Nordman, Fang Xie, Helena Kashevsky, Thomas Eng, Sharon Li, David M. MacAlpine, Terry L. Orr-Weaver
Genes Dev. 2011 July 1; 25(13): 1384–1398. doi: 10.1101/gad.2043111
PMCID:
PMC3134082
Abstract Full Text PDF–1.1M
Significance analysis and statistical dissection of variably methylated regions
Andrew E. Jaffe, Andrew P. Feinberg, Rafael A. Irizarry, Jeffrey T. Leek
Biostatistics. 2012 January; 13(1): 166–178. Published online 2011 June 17. doi: 10.1093/biostatistics/kxr013
PMCID:
PMC3276267
Free in PMC on 2013/01/01
Chromosome-Biased Binding and Gene Regulation by the Caenorhabditis elegans DRM Complex
Tomoko M. Tabuchi, Bart Deplancke, Naoki Osato, Lihua J. Zhu, M. Inmaculada Barrasa, Melissa M. Harrison, H. Robert Horvitz, Albertha J. M. Walhout, Kirsten A. Hagstrom
PLoS Genet. 2011 May; 7(5): e1002074. Published online 2011 May 12. doi: 10.1371/journal.pgen.1002074
PMCID:
PMC3093354
Abstract Full Text PDF–3.2M Supplementary Material
An Epigenetic Signature for Monoallelic Olfactory Receptor Expression
Angeliki Magklara, Angela Yen, Bradley M. Colquitt, E. Josephine Clowney, William Allen, Eirene Markenscoff-Papadimitriou, Zoe A. Evans, Pouya Kheradpour, George Mountoufaris, Catriona Carey, Gilad Barnea, Manolis Kellis, Stavros Lomvardas
Cell. Author manuscript; available in PMC 2012 May 13.
Published in final edited form as: Cell. 2011 May 13; 145(4): 555–570. Published online 2011 April 28. doi: 10.1016/j.cell.2011.03.040
PMCID:
PMC3094500
Abstract Full Text PDF–2.5M Supplementary Material
Statistical Approaches for the Analysis of DNA Methylation Microarray Data
Kimberly D. Siegmund
Hum Genet. Author manuscript; available in PMC 2012 June 1.
Published in final edited form as: Hum Genet. 2011 June; 129(6): 585–595. Published online 2011 April 26. doi: 10.1007/s00439-011-0993-x
PMCID:
PMC3166559
Free in PMC on 2012/06/01
Chromatin Organization in Sperm May Be the Major Functional Consequence of Base Composition Variation in the Human Genome
Tanya Vavouri, Ben Lehner
PLoS Genet. 2011 April; 7(4): e1002036. Published online 2011 April 7. doi: 10.1371/journal.pgen.1002036
PMCID:
PMC3072381
Abstract Full Text PDF–1.4M Supplementary Material
PU.1 and C/EBPα synergistically program distinct response to NF-κB activation through establishing monocyte specific enhancers
Fulai Jin, Yan Li, Bing Ren, Rama Natarajan
Proc Natl Acad Sci U S A. 2011 March 29; 108(13): 5290–5295. Published online 2011 March 14. doi: 10.1073/pnas.1017214108
PMCID:
PMC3069155
Abstract Full Text PDF–1.1M Supplementary Material
ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis
Joshua WK Ho, Eric Bishop, Peter V Karchenko, Nicolas Nègre, Kevin P White, Peter J Park
BMC Genomics. 2011; 12: 134. Published online 2011 February 28. doi: 10.1186/1471-2164-12-134
PMCID:
PMC3053263
Abstract Full Text PDF–522K Supplementary Material
Tiling array data analysis: a multiscale approach using wavelets
Alexander Karpikov, Joel Rozowsky, Mark Gerstein
BMC Bioinformatics. 2011; 12: 57. Published online 2011 February 21. doi: 10.1186/1471-2105-12-57
PMCID:
PMC3055839
Abstract Full Text PDF–3.4M Supplementary Material
Broad chromosomal domains of histone modification patterns in C. elegans
Tao Liu, Andreas Rechtsteiner, Thea A. Egelhofer, Anne Vielle, Isabel Latorre, Ming-Sin Cheung, Sevinc Ercan, Kohta Ikegami, Morten Jensen, Paulina Kolasinska-Zwierz, Heidi Rosenbaum, Hyunjin Shin, Scott Taing, Teruaki Takasaki, A. Leonardo Iniguez, Arshad Desai, Abby F. Dernburg, Hiroshi Kimura, Jason D. Lieb, Julie Ahringer, Susan Strome, X. Shirley Liu
Genome Res. 2011 February; 21(2): 227–236. doi: 10.1101/gr.115519.110
PMCID:
PMC3032926
Abstract Full Text PDF–1.3M
MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data
Yiwen Chen, Clifford A Meyer, Tao Liu, Wei Li, Jun S Liu, Xiaole Shirley Liu
Genome Biol. 2011; 12(2): R11. Published online 2011 February 1. doi: 10.1186/gb-2011-12-2-r11
PMCID:
PMC3188793
Abstract Full Text PDF–643K Supplementary Material
Activation-induced cytidine deaminase induces reproducible DNA breaks at many non-Ig loci in activated B cells
Ori Staszewski, Richard E. Baker, Anna J. Ucher, Raygene Martier, Janet Stavnezer, Jeroen E.J. Guikema
Mol Cell. Author manuscript; available in PMC 2012 January 21.
Published in final edited form as: Mol Cell. 2011 January 21; 41(2): 232–242. doi: 10.1016/j.molcel.2011.01.007
PMCID:
PMC3044441
Abstract Full Text PDF–2.2M Supplementary Material
Caenorhabditis elegans chromosome arms are anchored to the nuclear membrane via discontinuous association with LEM-2
Kohta Ikegami, Thea A Egelhofer, Susan Strome, Jason D Lieb
Genome Biol. 2010; 11(12): R120. Published online 2010 December 23. doi: 10.1186/gb-2010-11-12-r120
PMCID:
PMC3046480
Abstract Full Text PDF–1.6M Supplementary Material
Pre-replication complex proteins assemble at regions of low nucleosome occupancy within the Chinese hamster dihydrofolate reductase initiation zone
Yoav Lubelsky, Takayo Sasaki, Marjorie A. Kuipers, Isabelle Lucas, Michelle M. Le Beau, Sandra Carignon, Michelle Debatisse, Joseph A. Prinz, Jonathan H. Dennis, David M. Gilbert
Nucleic Acids Res. 2011 April; 39(8): 3141–3155. Published online 2010 December 9. doi: 10.1093/nar/gkq1276
PMCID:
PMC3082903
Abstract Full Text PDF–14M Supplementary Material
Gene expression profiling of human breast tissue samples using SAGE-Seq
Zhenhua Jeremy Wu, Clifford A. Meyer, Sibgat Choudhury, Michail Shipitsin, Reo Maruyama, Marina Bessarabova, Tatiana Nikolskaya, Saraswati Sukumar, Armin Schwartzman, Jun S. Liu, Kornelia Polyak, X. Shirley Liu
Genome Res. 2010 December; 20(12): 1730–1739. doi: 10.1101/gr.108217.110
PMCID:
PMC2989999
Abstract Full Text PDF–888K
Sensitive and accurate identification of protein–DNA binding events in ChIP-chip assays using higher order derivative analysis
Christian L. Barrett, Byung-Kwan Cho, Bernhard O. Palsson
Nucleic Acids Res. 2011 March; 39(5): 1656–1665. Published online 2010 November 4. doi: 10.1093/nar/gkq848
PMCID:
PMC3061075
Abstract Full Text PDF–3.3M
Role for the nuclear receptor-binding SET domain protein 1 (NSD1) methyltransferase in coordinating lysine 36 methylation at histone 3 with RNA polymerase II function
Agda Karina Lucio-Eterovic, Melissa M. Singh, Jeffrey E. Gardner, Chendhore S. Veerappan, Judd C. Rice, Phillip B. Carpenter
Proc Natl Acad Sci U S A. 2010 September 28; 107(39): 16952–16957. Published online 2010 September 13. doi: 10.1073/pnas.1002653107
PMCID:
PMC2947892
Abstract Full Text PDF–543K Supplementary Material
A Data Integration Approach to Mapping OCT4 Gene Regulatory Networks Operative in Embryonic Stem Cells and Embryonal Carcinoma Cells
Marc Jung, Hedi Peterson, Lukas Chavez, Pascal Kahlem, Hans Lehrach, Jaak Vilo, James Adjaye
PLoS One. 2010; 5(5): e10709. Published online 2010 May 21. doi: 10.1371/journal.pone.0010709
PMCID:
PMC2873957
Abstract Full Text PDF–1.8M Supplementary Material
Modeling non-uniformity in short-read rates in RNA-Seq data
Jun Li, Hui Jiang, Wing Hung Wong
Genome Biol. 2010; 11(5): R50. Published online 2010 May 11. doi: 10.1186/gb-2010-11-5-r50
PMCID:
PMC2898062
Abstract Full Text PDF–1.0M Supplementary Material
An extended set of PRDM1/BLIMP1 target genes links binding motif type to dynamic repression
Gina M. Doody, Matthew A. Care, Nicholas J. Burgoyne, James R. Bradford, Maria Bota, Constanze Bonifer, David R. Westhead, Reuben M. Tooze
Nucleic Acids Res. 2010 September; 38(16): 5336–5350. Published online 2010 April 26. doi: 10.1093/nar/gkq268
PMCID:
PMC2938208
Abstract Full Text PDF–4.1M Supplementary Material
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