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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
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 Is Cited by the Following 39 Articles in this Archive:
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
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
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
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
Waved aCGH: to smooth or not to smooth
F. Leprêtre, C. Villenet, S. Quief, O. Nibourel, C. Jacquemin, X. Troussard, F. Jardin, F. Gibson, J. P. Kerckaert, C. Roumier, M. Figeac
Nucleic Acids Res. 2010 April; 38(7): e94. Published online 2010 April. doi: 10.1093/nar/gkp1215
PMCID:
PMC2853126
Abstract Full Text PDF–6.6M
Chromatin signature of embryonic pluripotency is established during genome activation
Nadine L. Vastenhouw, Yong Zhang, Ian G. Woods, Farhad Imam, Aviv Regev, X. Shirley Liu, John Rinn, Alexander F. Schier
Nature. Author manuscript; available in PMC 2011 April 8.
Published in final edited form as: Nature. 2010 April 8; 464(7290): 922–926. Published online 2010 March 24. doi: 10.1038/nature08866
PMCID:
PMC2874748
Abstract Full Text PDF–922K Supplementary Material
Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading
Heather K. MacAlpine, Raluca Gordân, Sara K. Powell, Alexander J. Hartemink, David M. MacAlpine
Genome Res. 2010 February; 20(2): 201–211. doi: 10.1101/gr.097873.109
PMCID:
PMC2813476
Abstract Full Text PDF–766K
A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data
Desmond S Lun, Ashley Sherrid, Brian Weiner, David R Sherman, James E Galagan
Genome Biol. 2009; 10(12): R142. Published online 2009 December 22. doi: 10.1186/gb-2009-10-12-r142
PMCID:
PMC2812949
Abstract Full Text PDF–1.2M
Double error shrinkage method for identifying protein binding sites observed by tiling arrays with limited replication
Youngchul Kim, Stefan Bekiranov, Jae K. Lee, Taesung Park
Bioinformatics. 2009 October 1; 25(19): 2486–2491. Published online 2009 August 10. doi: 10.1093/bioinformatics/btp471
PMCID:
PMC2800349
Abstract Full Text PDF–349K Supplementary Material
Comparison of sequence-dependent tiling array normalization approaches
Ho-Ryun Chung, Martin Vingron
BMC Bioinformatics. 2009; 10: 204. Published online 2009 June 30. doi: 10.1186/1471-2105-10-204
PMCID:
PMC2753852
Abstract Full Text PDF–479K
Improved ChIP-chip analysis by a mixture model approach
Wei Sun, Michael J Buck, Mukund Patel, Ian J Davis
BMC Bioinformatics. 2009; 10: 173. Published online 2009 June 7. doi: 10.1186/1471-2105-10-173
PMCID:
PMC2700807
Abstract Full Text PDF–995K Supplementary Material
Histone Modifications at Human Enhancers Reflect Global Cell Type-Specific Gene Expression
Nathaniel D. Heintzman, Gary C. Hon, R. David Hawkins, Pouya Kheradpour, Alexander Stark, Lindsey F. Harp, Zhen Ye, Leonard K. Lee, Rhona K. Stuart, Christina W. Ching, Keith A. Ching, Jessica E. Antosiewicz, Hui Liu, Xinmin Zhang, Roland D. Green, Ron Stewart, James A. Thomson, Gregory E. Crawford, Manolis Kellis, Bing Ren
Nature. Author manuscript; available in PMC 2010 July 27.
Published in final edited form as: Nature. 2009 May 7; 459(7243): 108–112. Published online 2009 March 18. doi: 10.1038/nature07829
PMCID:
PMC2910248
Abstract Full Text PDF–2.7M Supplementary Material
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