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ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data
Michael J Buck, Andrew B Nobel, Jason D Lieb
Genome Biol. 2005; 6(11): R97. Published online 2005 October 19. doi: 10.1186/gb-2005-6-11-r97
PMCID:
PMC1297653
Abstract Full Text PDF–320K Supplementary Material
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 Is Cited by the Following 47 Articles in this Archive:
Tup1 stabilizes promoter nucleosome positioning and occupancy at transcriptionally plastic genes
Jason M. Rizzo, Piotr A. Mieczkowski, Michael J. Buck
Nucleic Acids Res. 2011 November; 39(20): 8803–8819. Published online 2011 July 23. doi: 10.1093/nar/gkr557
PMCID:
PMC3203618
Abstract Full Text PDF–4.8M Supplementary Material
Identification of Novel Targets of CSL-Dependent Notch Signaling in Hematopoiesis
Habib Hamidi, Derek Gustafason, Matteo Pellegrini, Judith Gasson
PLoS One. 2011; 6(5): e20022. Published online 2011 May 26. doi: 10.1371/journal.pone.0020022
PMCID:
PMC3102675
Abstract Full Text PDF–601K Supplementary Material
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
The Stress Response Factors Yap6, Cin5, Phd1, and Skn7 Direct Targeting of the Conserved Co-Repressor Tup1-Ssn6 in S. cerevisiae
Sean E. Hanlon, Jason M. Rizzo, Deirdre C. Tatomer, Jason D. Lieb, Michael J. Buck
PLoS One. 2011; 6(4): e19060. Published online 2011 April 28. doi: 10.1371/journal.pone.0019060
PMCID:
PMC3084262
Abstract Full Text PDF–1.2M Supplementary Material
Important Characteristics of Sequence-Specific Recombination Hotspots in Schizosaccharomyces pombe
Walter W. Steiner, Peter A. Davidow, Andrew T. M. Bagshaw
Genetics. 2011 February; 187(2): 385–396. doi: 10.1534/genetics.110.124636
PMCID:
PMC3030484
Abstract Full Text PDF–1.1M
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
The Histone H3K36 Methyltransferase MES-4 Acts Epigenetically to Transmit the Memory of Germline Gene Expression to Progeny
Andreas Rechtsteiner, Sevinc Ercan, Teruaki Takasaki, Taryn M. Phippen, Thea A. Egelhofer, Wenchao Wang, Hiroshi Kimura, Jason D. Lieb, Susan Strome
PLoS Genet. 2010 September; 6(9): e1001091. Published online 2010 September 2. doi: 10.1371/journal.pgen.1001091
PMCID:
PMC2932692
Abstract Full Text PDF–2.3M Supplementary Material
Application of machine learning methods to histone methylation ChIP-Seq data reveals H4R3me2 globally represses gene expression
Xiaojiang Xu, Stephen Hoang, Marty W Mayo, Stefan Bekiranov
BMC Bioinformatics. 2010; 11: 396. Published online 2010 July 23. doi: 10.1186/1471-2105-11-396
PMCID:
PMC2928206
Abstract Full Text PDF–2.2M Supplementary Material
Evaluation of Algorithm Performance in ChIP-Seq Peak Detection
Elizabeth G. Wilbanks, Marc T. Facciotti
PLoS One. 2010; 5(7): e11471. Published online 2010 July 8. doi: 10.1371/journal.pone.0011471
PMCID:
PMC2900203
Abstract Full Text PDF–1.9M Supplementary Material
The conserved bromo-adjacent homology domain of yeast Orc1 functions in the selection of DNA replication origins within chromatin
Philipp Müller, Sookhee Park, Erika Shor, Dana J. Huebert, Christopher L. Warren, Aseem Z. Ansari, Michael Weinreich, Matthew L. Eaton, David M. MacAlpine, Catherine A. Fox
Genes Dev. 2010 July 1; 24(13): 1418–1433. doi: 10.1101/gad.1906410
PMCID:
PMC2895200
Abstract Full Text PDF–1.0M
A map of open chromatin in human pancreatic islets
Kyle J. Gaulton, Takao Nammo, Lorenzo Pasquali, Jeremy M. Simon, Paul G. Giresi, Marie P. Fogarty, Tami M. Panhuis, Piotr Mieczkowski, Antonio Secchi, Domenico Bosco, Thierry Berney, Eduard Montanya, Karen L. Mohlke, Jason D. Lieb, Jorge Ferrer
Nat Genet. Author manuscript; available in PMC 2010 September 1.
Published in final edited form as: Nat Genet. 2010 March; 42(3): 255–259. Published online 2010 January 31. doi: 10.1038/ng.530
PMCID:
PMC2828505
Abstract Full Text PDF–2.1M Supplementary Material
Computational Epigenetics: the new scientific paradigm
Shen Jean Lim, Tin Wee Tan, Joo Chuan Tong
Bioinformation. 2010; 4(7): 331–337. Published online 2010 January 23.
PMCID:
PMC2957762
Abstract Full Text PDF–241K Supplementary Material
The Origin Recognition Complex Interacts with a Subset of Metabolic Genes Tightly Linked to Origins of Replication
Erika Shor, Christopher L. Warren, Joshua Tietjen, Zhonggang Hou, Ulrika Müller, Ilaria Alborelli, Florence H. Gohard, Adrian I. Yemm, Lev Borisov, James R. Broach, Michael Weinreich, Conrad A. Nieduszynski, Aseem Z. Ansari, Catherine A. Fox
PLoS Genet. 2009 December; 5(12): e1000755. Published online 2009 December 4. doi: 10.1371/journal.pgen.1000755
PMCID:
PMC2778871
Abstract Full Text PDF–1015K Supplementary Material
A positive but complex association between meiotic double-strand break hotspots and open chromatin in Saccharomyces cerevisiae
Luke E. Berchowitz, Sean E. Hanlon, Jason D. Lieb, Gregory P. Copenhaver
Genome Res. 2009 December; 19(12): 2245–2257. doi: 10.1101/gr.096297.109
PMCID:
PMC2792181
Abstract Full Text PDF–1.6M
A Bayesian hidden Markov model for motif discovery through joint modeling of genomic sequence and ChIP-chip data
Jonathan A. L. Gelfond, Mayetri Gupta, Joseph G. Ibrahim
Biometrics. Author manuscript; available in PMC 2009 December 17.
Published in final edited form as: Biometrics. 2009 December; 65(4): 1087–1095. doi: 10.1111/j.1541-0420.2008.01180.x
PMCID:
PMC2794970
Abstract Full Text PDF–1.3M Supplementary Material
Strategies for analyzing highly enriched IP-chip datasets
Simon RV Knott, Christopher J Viggiani, Oscar M Aparicio, Simon Tavaré
BMC Bioinformatics. 2009; 10: 305. Published online 2009 September 22. doi: 10.1186/1471-2105-10-305
PMCID:
PMC2759964
Abstract Full Text PDF–2.3M Supplementary Material
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
DNA-binding specificity and in vivo targets of Caenorhabditis elegans nuclear factor I
Christina M. Whittle, Elena Lazakovitch, Richard M. Gronostajski, Jason D. Lieb
Proc Natl Acad Sci U S A. 2009 July 21; 106(29): 12049–12054. Published online 2009 July 7. doi: 10.1073/pnas.0812894106
Correction in:
Proc Natl Acad Sci U S A. 2009 September 8; 106(36): 15514.
PMCID:
PMC2715542
Abstract Full Text PDF–1.0M Supplementary Material Correction
Highly transcribed RNA polymerase II genes are impediments to replication fork progression in Saccharomyces cerevisiae
Anna Azvolinsky, Paul G. Giresi, Jason D. Lieb, Virginia A. Zakian
Mol Cell. Author manuscript; available in PMC 2010 June 26.
Published in final edited form as: Mol Cell. 2009 June 26; 34(6): 722–734. doi: 10.1016/j.molcel.2009.05.022
PMCID:
PMC2728070
Abstract Full Text PDF–2.5M Supplementary Material
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
Systematic Identification of Balanced Transposition Polymorphisms in Saccharomyces cerevisiae
Dina A. Faddah, Eric W. Ganko, Caroline McCoach, Joseph K. Pickrell, Sean E. Hanlon, Frederick G. Mann, Joanna O. Mieczkowska, Corbin D. Jones, Jason D. Lieb, Todd J. Vision
PLoS Genet. 2009 June; 5(6): e1000502. Published online 2009 June 5. doi: 10.1371/journal.pgen.1000502
PMCID:
PMC2682701
Abstract Full Text PDF–1.6M Supplementary Material
Features of Mammalian microRNA Promoters Emerge from Polymerase II Chromatin Immunoprecipitation Data
David L. Corcoran, Kusum V. Pandit, Ben Gordon, Arindam Bhattacharjee, Naftali Kaminski, Panayiotis V. Benos
PLoS ONE. 2009; 4(4): e5279. Published online 2009 April 23. doi: 10.1371/journal.pone.0005279
PMCID:
PMC2668758
Abstract Full Text PDF–258K
Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)
Paul G. Giresi, Jason D. Lieb
Methods. Author manuscript; available in PMC 2010 July 1.
Published in final edited form as: Methods. 2009 July; 48(3): 233–239. Published online 2009 March 18. doi: 10.1016/j.ymeth.2009.03.003
PMCID:
PMC2710428
Abstract Full Text PDF–796K
Relics of repeat-induced point mutation direct heterochromatin formation in Neurospora crassa
Zachary A. Lewis, Shinji Honda, Tamir K. Khlafallah, Jennifer K. Jeffress, Michael Freitag, Fabio Mohn, Dirk Schübeler, Eric U. Selker
Genome Res. 2009 March; 19(3): 427–437. doi: 10.1101/gr.086231.108
PMCID:
PMC2661801
Abstract Full Text PDF–999K
H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome
Florian M. Pauler, Mathew A. Sloane, Ru Huang, Kakkad Regha, Martha V. Koerner, Ido Tamir, Andreas Sommer, Andras Aszodi, Thomas Jenuwein, Denise P. Barlow
Genome Res. 2009 February; 19(2): 221–233. doi: 10.1101/gr.080861.108
PMCID:
PMC2652204
Abstract Full Text PDF–2.3M
A Multi-Factorial Signature of DNA Sequence and Polycomb Binding Predicts Aberrant CpG Island Methylation
Michael T. McCabe, Eva K. Lee, Paula M. Vertino
Cancer Res. Author manuscript; available in PMC 2010 January 1.
Published in final edited form as: Cancer Res. 2009 January 1; 69(1): 282–291. doi: 10.1158/0008-5472.CAN-08-3274
PMCID:
PMC2653261
Abstract Full Text PDF–2.0M Supplementary Material
ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes
Adam A. Margolin, Teresa Palomero, Pavel Sumazin, Andrea Califano, Adolfo A. Ferrando, Gustavo Stolovitzky
Proc Natl Acad Sci U S A. 2009 January 6; 106(1): 244–249. Published online 2008 December 31. doi: 10.1073/pnas.0806445106
PMCID:
PMC2613038
Abstract Full Text PDF–765K Supplementary Material
Analyzing ChIP-chip Data Using Bioconductor
Joern Toedling, Wolfgang Huber
PLoS Comput Biol. 2008 November; 4(11): e1000227. Published online 2008 November 28. doi: 10.1371/journal.pcbi.1000227
PMCID:
PMC2582686
Full Text PDF–283K Supplementary Material
Indistinguishable Landscapes of Meiotic DNA Breaks in rad50+ and rad50S Strains of Fission Yeast Revealed by a Novel rad50+ Recombination Intermediate
Randy W. Hyppa, Gareth A. Cromie, Gerald R. Smith
PLoS Genet. 2008 November; 4(11): e1000267. Published online 2008 November 21. doi: 10.1371/journal.pgen.1000267
PMCID:
PMC2580034
Abstract Full Text PDF–567K Supplementary Material
Technical Considerations in using DNA Microarrays to Define Regulons
Virgil A. Rhodius, Joseph T. Wade
Methods. Author manuscript; available in PMC 2010 January 1.
Published in final edited form as: Methods. 2009 January; 47(1): 63–72. Published online 2008 October 26. doi: 10.1016/j.ymeth.2008.10.017
PMCID:
PMC2637246
Abstract Full Text PDF–255K
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