Tag chip-chip [181 articles] Export

Recent papers classified by the tag chip-chip.

	The Euchromatic and Heterochromatic Landscapes Are Shaped by Antagonizing Effects of Transcription on H2A.Z Deposition [My Copy] PLoS Genet, Vol. 5, No. 10. (16 October 2009), e1000687. by Sara Hardy, Pierre-Étienne Jacques, Nicolas Gévry, et al.Audrey Forest, Marie-Ève Fortin, Liette Laflamme, Luc Gaudreau, François Robert posted to histone expression chromatin chip-chip by djkt on 2009-11-02 19:05:27 as
	Distinguishing direct versus indirect transcription factorâDNA interactions [My Copy] Genome Research, Vol. 19, No. 11. (3 November 2009), pp. 2090-2100. by Raluca GordÃ¢n, Alexander J. Hartemink, Martha L. Bulyk posted to tf motif chip-chip by djkt on 2009-11-02 18:17:10 as along with 9 people vingron venancio owhitney tmmurali emptyhb idonaldson maximilianh jbhiatt frohike
	Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data [My Copy] Bioinformatics, Vol. 25, No. 14. (15 July 2009), pp. 1715-1721. by Hyungwon Choi, Alexey I. Nesvizhskii, Debashis Ghosh, Zhaohui S. Qin posted to hmm chip-seq chip-chip bioinfo by tonamswish on 2009-10-27 02:15:59 as along with 11 people and 1 group rdiaz fpattyn jcbarret guhjy hendrik85 inesdesantiago nklee polivares ewilban1 idonaldson humburg Journal picks
	Bayesian modeling of ChIP-chip data using latent variables [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 352. by Mingqi Wu, Faming Liang, Yanan Tian posted to chip-chip bioinfo bayesian_models bayesian by tonamswish on 2009-10-26 21:21:50 as
	ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data [My Copy] Genome Biology, Vol. 6, No. 11. (2005), R97. by Michael Buck, Andrew Nobel, Jason Lieb posted to chip-chip by ashishanand on 2009-10-13 15:34:39 as along with 3 people and 1 group humburg antonkratz kengg Plantandetc
	Model-based analysis of tiling-arrays for ChIP-chip [My Copy] Proceedings of the National Academy of Sciences, Vol. 103, No. 33. (15 August 2006), pp. 12457-12462. by W. Evan Johnson, Wei Li, Clifford A. Meyer, et al.Raphael Gottardo, Jason S. Carroll, Myles Brown, X. Shirley Liu posted to chip-chip by ashishanand on 2009-10-13 15:34:08 as along with 11 people and 1 group idonaldson siebert mcm rgottardo GeeSharpMinor kengg nicholso talponer caseybrown bertelsen bozdagd Plantandetc
	Meta-analysis based on control of false discovery rate: combining yeast ChIP-chip datasets [My Copy] Bioinformatics, Vol. 22, No. 20. (15 October 2006), pp. 2516-2522. by Saumyadipta Pyne, Bruce Futcher, Steve Skiena posted to chip-chip by ashishanand on 2009-10-09 14:39:44 as
	Double error shrinkage method for identifying protein binding sites observed by tiling arrays with limited replication [My Copy] Bioinformatics, Vol. 25, No. 19. (1 October 2009), pp. 2486-2491. by Youngchul Kim, Stefan Bekiranov, Jae K. Lee, Taesung Park posted to chip-chip by djkt on 2009-09-28 19:25:59 as along with 1 person humburg
	Integrative analysis of HIF binding and transactivation reveals its role in maintaining histone methylation homeostasis. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 11. (17 March 2009), pp. 4260-4265. by Xiaobo Xia, Madeleine E. Lemieux, Wei Li, et al.Jason S. Carroll, Myles Brown, X. Shirley Liu, Andrew L. Kung posted to methylation ma hif chip-chip by guhjy on 2009-09-24 10:18:05 as
	Genome-wide analysis of estrogen receptor binding sites [My Copy] Nature Genetics, Vol. 38, No. 11. (01 October 2006), pp. 1289-1297. by Jason S. Carroll, Clifford A. Meyer, Jun Song, et al.Wei Li, Timothy R. Geistlinger, Jerome Eeckhoute, Alexander S. Brodsky, Erika K. Keeton, Kirsten C. Fertuck, Giles F. Hall, Qianben Wang, Stefan Bekiranov, Victor Sementchenko, Edward A. Fox, Pamela A. Silver, Thomas R. Gingeras, X. Shirley Liu, Myles Brown posted to era_target era er chip-chip by tonamswish on 2009-09-21 14:29:08 as along with 3 people jfr olympos bozdagd
	Genome-Wide Identification of Estrogen Receptor alpha-Binding Sites in Mouse Liver [My Copy] Mol Endocrinol, Vol. 22, No. 1. (1 January 2008), pp. 10-22. by Hui Gao, Susann Falt, Albin Sandelin, Jan-Ake Gustafsson, Karin Dahlman-Wright posted to era chip-chip bioinfo by tonamswish on 2009-09-17 21:42:51 as along with 2 people guhjy yevishere
	Learning module networks from genome-wide location and expression data [My Copy] FEBS Letters, Vol. 578, No. 3. (17 December 2004), pp. 297-304. by Xiaojiang Xu, Lianshui Wang, Dafu Ding posted to network module expression cls-anton chip-chip by ptrobajo on 2009-09-13 20:55:36 as
	ChIP-chip: Data, Model, and Analysis [My Copy] Biometrics, Vol. 63, No. 3. (September 2007), pp. 787-796. by Ming Zheng, Leah O. Barrera, Bing Ren, Ying N. Wu posted to tiling-array tf microarray chip-chip algorithm by humburg on 2009-09-10 08:07:10 as along with 3 people huali guhjy caseybrown
	CEAS: cis-regulatory element annotation system [My Copy] Bioinformatics, Vol. 25, No. 19. (1 October 2009), pp. 2605-2606. by Hyunjin Shin, Tao Liu, Arjun K. Manrai, X. Shirley Liu posted to software chip-seq chip-chip by guhjy on 2009-09-04 14:07:48 as along with 5 people maximilianh druvus ewilban1 idonaldson nuin
	High-resolution computational models of genome binding events [My Copy] Nat Biotech, Vol. 24, No. 8. (09 August 2006), pp. 963-970. by Yuan Qi, Alex Rolfe, Kenzie D. Macisaac, et al.Georg K. Gerber, Dmitry Pokholok, Julia Zeitlinger, Timothy Danford, Robin D. Dowell, Ernest Fraenkel, Tommi S. Jaakkola, Richard A. Young, David K. Gifford posted to tiling-array microarray chip-chip algorithm by humburg on 2009-09-02 07:22:55 as along with 9 people and 1 group arsyed Scis0000002 siebert Stew jfr wnpx ccr caseybrown inesdesantiago Bioinformatics - CRUK
	Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions [My Copy] Genome Biology, Vol. 10, No. 7. (23 July 2009), R80. by Stewart MacArthur, Xiao Y. Li, Jingyi Li, et al.James Brown, Hou C. Chu, Lucy Zeng, Brandi Grondona, Aaron Hechmer, Lisa Simirenko, Soile Keranen, David Knowles, Mark Stapleton, Peter Bickel, Mark Biggin, Michael Eisen posted to tfbs drosophila chip-chip by idonaldson on 2009-09-01 11:18:15 as along with 11 people and 2 groups venancio aalibes fenghezi daveGerrard megraw scjparker maximilianh djkt isimpson Stew druvus BergmanLab Bioinformatics - CRUK
	Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization [My Copy] Genome Biology, Vol. 6, No. 11. (2005), R96. by Francis Gibbons, Markus Proft, Kevin Struhl, Frederick Roth posted to tiling-array microarray chip-chip algorithm by humburg on 2009-09-01 05:30:46 as along with 3 people and 1 group nklee oelemento blobbybirdman Myxo group
	Nucleosome positioning in human HOX gene clusters [My Copy] Genome Research, Vol. 18, No. 10. (22 October 2008), pp. 1554-1561. by Peter V. Kharchenko, Caroline J. Woo, Michael Y. Tolstorukov, Robert E. Kingston, Peter J. Park posted to tiling-array nucleosomes microarray chromatin-structure chip-chip by humburg on 2009-08-28 05:06:31 as along with 2 people inesdesantiago aalibes
	Chromosomal Distribution of PcG Proteins during Drosophila Development [My Copy] PLoS Biol, Vol. 4, No. 6. (20 April 2006), e170. by Nicolas Nègre, Jérôme Hennetin, Ling V. Sun, et al.Sergey Lavrov, Michel Bellis, Kevin P. White, Giacomo Cavalli posted to drosophila chromatin-structure chip-chip by humburg on 2009-08-28 04:54:20 as along with 1 person johncumbers
	Genome-Scale Identification of Nucleosome Positions in S. cerevisiae [My Copy] Science, Vol. 309, No. 5734. (22 July 2005), pp. 626-630. by Guo-Cheng Yuan, Yuen-Jong Liu, Michael F. Dion, et al.Michael D. Slack, Lani F. Wu, Steven J. Altschuler, Oliver J. Rando posted to tiling-array nucleosomes microarray chromatin-structure chip-chip by humburg on 2009-08-26 01:48:47 as along with 8 people hagechouchin443 ilyashl aalibes koller olympos redfish99213 epigenetics elzodw
	Global nucleosome occupancy in yeast [My Copy] Genome Biology, Vol. 5, No. 9. (2004), R62. by Bradley Bernstein, Chih Liu, Emily Humphrey, Ethan Perlstein, Stuart Schreiber posted to yeast microarray chip-chip by humburg on 2009-08-26 01:43:39 as along with 4 people and 2 groups hagechouchin443 shantanu nucleosome kengg Plantandetc Chromatin
	A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells [My Copy] Cell, Vol. 125, No. 2. (21 April 2006), pp. 315-326. by B. Bernstein, T. Mikkelsen, X. Xie, et al.M. Kamal, D. Huebert, J. Cuff, B. Fry, A. Meissner, M. Wernig, K. Plath posted to chromatin-structure chip-chip by humburg on 2009-08-24 07:51:50 as along with 5 people gderwin inesdesantiago tuck olympos jasonflannick
	Insights from genomic profiling of transcription factors [My Copy] Nat Rev Genet, Vol. 10, No. 9. (11 August 2009), pp. 605-616. by Peggy J. Farnham posted to transcription factor chip-seq chip-chip by mkiyer to the group Chinnaiyan Lab on 2009-08-18 21:36:35 as along with 16 people and 1 group inesdesantiago fenghezi nklee samanthacooper fpattyn druvus frohike stubrown qayub megraw TRHvidsten ericrpaquet ilyashl jbhiatt idonaldson danmaclean Journal picks
	TileProbe: modeling tiling array probe effects using publicly available data [My Copy] Bioinformatics (9 July 2009), btp425. by Jennifer T. Judy, Hongkai Ji posted to chip-chip probe-effect tiling-array by humburg on 2009-08-10 23:30:46 as
	Mixture Modeling for Genome-Wide Localization of Transcription Factors [My Copy] Biometrics, Vol. 63, No. 1. (March 2007), pp. 10-21. by F. Sündüz Kele015 posted to chip-chip mixture-model stat-gen transcription-factors by jmstat on 2009-08-05 20:04:48 as along with 1 person caseybrown
	An integrative ChIP-chip and gene expression profiling to model SMAD regulatory modules. [My Copy] BMC systems biology, Vol. 3, No. 1. (17 July 2009), 73. by Huaxia Qin, Michael W. Chan, Sandya Liyanarachchi, et al.Curtis Balch, Dustin Potter, Irene J. Souriraj, Alfred S. Cheng, Francisco J. Agosto-Perez, Elena V. Nikonova, Pearlly S. Yan, Huey-Jen J. Lin, Kenneth P. Nephew, Joel H. Saltz, Louise C. Showe, Tim H. Huang, Ramana V. Davuluri posted to smad ma chip-chip by guhjy on 2009-07-31 13:49:47 as along with 1 person and 1 group dswan Bioinformatics
	Improved ChIP-chip analysis by a mixture model approach. [My Copy] BMC bioinformatics, Vol. 10, No. 1. (2009), 173. by W. Sun, M. J. Buck, M. Patel, I. J. Davis posted to chip-chip stats by guhjy on 2009-07-26 09:26:16 as along with 1 person humburg
	CoCAS: a ChIP-on-chip analysis suite. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 7. (1 April 2009), pp. 954-955. by Touati Benoukraf, Pierre Cauchy, Romain Fenouil, et al.Adrien Jeanniard, Frederic Koch, Sébastien Jaeger, Denis Thieffry, Jean Imbert, Jean-Christophe C. Andrau, Salvatore Spicuglia, Pierre Ferrier posted to chip-chip software by guhjy on 2009-07-26 09:25:08 as along with 6 people and 1 group Eduvernois jfr dswan Stew siebert sebastien_vigneau Bioinformatics - CRUK
	Using ChIP-chip and ChIP-seq to study the regulation of gene expression: genome-wide localization studies reveal widespread regulation of transcription elongation. [My Copy] Methods (San Diego, Calif.), Vol. 48, No. 4. (9 August 2009), pp. 398-408. by Daniel A. Gilchrist, David C. Fargo, Karen Adelman posted to chip-chip chip-seq by guhjy on 2009-07-26 09:24:04 as along with 5 people fpattyn ewilban1 inesdesantiago sebastien_vigneau idonaldson
	Distinctive chromatin in human sperm packages genes for embryo development [My Copy] Nature, Vol. 460, No. 7254. (23 July 2009), pp. 473-478. by Saher S. Hammoud, David A. Nix, Haiying Zhang, Jahnvi Purwar, Douglas T. Carrell, Bradley R. Cairns posted to chip-chip chip-seq chromatin-structure high-throughput-sequencing human tiling-array by humburg on 2009-07-22 23:36:23 as along with 6 people absterga jd222 leliavski fenghezi djkt dchughes
	Epigenetic profiling at mouse imprinted gene clusters reveals novel epigenetic and genetic features at differentially methylated regions. [My Copy] Genome research, Vol. 19, No. 8. (19 August 2009), pp. 1374-1383. by Scott V. Dindot, Richard Person, Mark Strivens, Rejinaldo Garcia, Arthur L. Beaudet posted to cgi chip-chip cpg epigenetics h3k4me3 h3k9me3 imprinting microarray tiling-array by rschulz on 2009-07-15 09:33:18 as along with 3 people inesdesantiago clearbluespring taylor73
	Predicting functionality of protein-DNA interactions by integrating diverse evidence [My Copy] Bioinformatics, Vol. 25, No. 12. (15 June 2009), pp. i137-144. by Duygu Ucar, Andreas Beyer, Srinivasan Parthasarathy, Christopher T. Workman posted to data_integrationinteraction_protein-dna chip-chip by ashishanand on 2009-06-20 06:30:50 as along with 3 people dquest TRHvidsten scjparker
	Identification of Yeast Transcriptional Regulation Networks Using Multivariate Random Forests [My Copy] PLoS Comput Biol, Vol. 5, No. 6. (19 June 2009), e1000414. by Yuanyuan Xiao, Mark R. Segal posted to chip-chip expression motif prediction sysbio yeast by djkt on 2009-06-19 16:22:10 as along with 2 people ptrobajo TRHvidsten
	Computational epigenetics [My Copy] Bioinformatics, Vol. 24, No. 1. (1 January 2008), pp. 1-10. by Christoph Bock, Thomas Lengauer posted to chip-chip by huali to the group SIMR bioinformatics on 2009-06-17 21:23:23 as along with 17 people and 1 group operon iris42 pawelsobko suizifish mmartin sebastien_vigneau ealloza djkt frohike timflutre cjeans epigenetics cabbagezs barriot Ema Thomasah guhjy Bioinformatics
	An integrated software system for analyzing ChIP-chip and ChIP-seq data. [My Copy] Nature biotechnology, Vol. 26, No. 11. (02 November 2008), pp. 1293-1300. by Hongkai Ji, Hui Jiang, Wenxiu Ma, David S. Johnson, Richard M. Myers, Wing H. Wong posted to chip-chip chip-seq by huali to the group SIMR bioinformatics on 2009-06-17 21:10:42 as along with 23 people and 2 groups fpattyn stubrown isimpson tonamswish ewilban1 sebastien_vigneau jfr kmdaily cassj bryankr malcook rschulz mcm behindtherabbit psique renatomilani polivares guhjy inesdesantiago pengchy kengg bais idonaldson Neuroblastoma BenosLab
	Model-based Analysis of 2-Color Arrays (MA2C) [My Copy] Genome Biology, Vol. 8 (29 August 2007), R178. by Jun S. Song, Evan W. Johnson, Xiaopeng Zhu, et al.Xinmin Zhang, Wei Li, Arjun K. Manrai, Jun S. Liu, Runsheng Chen, Shirley X. Liu posted to chip-chip by huali on 2009-06-17 21:08:14 as along with 2 people jfr caseybrown
	ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 1. (6 January 2009), pp. 244-249. by A. A. Margolin, T. Palomero, P. Sumazin, A. Califano, A. A. Ferrando, G. Stolovitzky posted to chip-chip by huali on 2009-06-17 20:46:59 as along with 1 person guhjy
	A Gibbs sampler for the identification of gene expression and network connectivity consistency [My Copy] Bioinformatics, Vol. 22, No. 24. (15 December 2006), pp. 3040-3046. by Brynildsen, P. Mark, Tran, M. Linh, Liao, C. James posted to chip-chip consistency gene-expression gibbs microarray network by bertelsen on 2009-06-13 11:49:16 as along with 1 person wenhan
	Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana [My Copy] Genome Biology, Vol. 10, No. 6. (2009), R62. by Xiaoyu Zhang, Yana Bernatavichute, Shawn Cokus, Matteo Pellegrini, Steven Jacobsen posted to arabidopsis chip-chip chromatin-structure tiling-array by humburg on 2009-06-10 07:48:36 as along with 3 people megraw lptolik vinithepooh
	Genome-Wide Analysis of Protein-DNA Interactions [My Copy] Annual Review of Genomics and Human Genetics, Vol. 7, No. 1. (2006), pp. 81-102. by Tae H. Kim, Bing Ren posted to chip-chip by cabbagezs on 2009-06-03 19:35:47 as along with 5 people darian ewilban1 sebastien_vigneau epigenetics waraz
	NTAP: for NimbleGen tiling array ChIP-chip data analysis [My Copy] Bioinformatics, Vol. 25, No. 14. (15 July 2009), pp. 1838-1840. by Kun He, Xueyong Li, Junli Zhou, Xing-Wang Deng, Hongyu Zhao, Jingchu Luo posted to chip-chip nimblegen tool by idonaldson on 2009-06-01 09:16:25 as along with 3 people and 1 group ashishanand dswan rschulz Bioinformatics
	Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. [My Copy] Nucleic acids research, Vol. 36, No. 16. (6 September 2008), pp. 5221-5231. by R. Jothi, S. Cuddapah, A. Barski, K. Cui, K. Zhao posted to bioinfo chip-chip chip-seq tool by tonamswish on 2009-05-27 15:33:17 as along with 10 people talponer ewilban1 polivares guhjy mcm Eroslavochka inesdesantiago mdperry sebastien_vigneau idonaldson
	GeneTrack--a genomic data processing and visualization framework [My Copy] Bioinformatics, Vol. 24, No. 10. (15 May 2008), pp. 1305-1306. by Istvan Albert, Shinichiro Wachi, Cizhong Jiang, B. Franklin Pugh posted to bioinfo chip-chip chip-seq tool by tonamswish on 2009-05-27 15:31:32 as along with 6 people ewilban1 cassj zhouyu wisdom_love guhjy inesdesantiago
	Analyzing ChIP-chip Data Using Bioconductor [My Copy] PLoS Comput Biol, Vol. 4, No. 11. (28 November 2008), e1000227. by Joern Toedling, Wolfgang Huber posted to bioconductor bioinfo chip-chip review by tonamswish on 2009-05-27 15:25:15 as along with 9 people and 1 group phoenixzxl jfr bertelsen cabbagesofdoom antonkratz guhjy barry ghattem dswan SIMR bioinformatics
	CARPET: a web-based package for the analysis of ChIP-chip and expression tiling data. [My Copy] Bioinformatics (Oxford, England), Vol. 24, No. 24. (15 December 2008), pp. 2918-2920. by M. Cesaroni, D. Cittaro, A. Brozzi, P. G. Pelicci, L. Luzi posted to bioinfo chip-chip tool by tonamswish on 2009-05-27 15:21:44 as along with 1 person jfr
	Utilizing gene pair orientations for HMM-based analysis of promoter array ChIP-chip data [My Copy] Bioinformatics (28 April 2009), btp276. by Michael Seifert, Jens Keilwagen, Marc Strickert, Ivo Grosse posted to algorithm arabidopsis chip-chip hmm tf tiling-array yeast by humburg on 2009-05-19 00:24:37 as
	Multi-scale correlations in continuous genomic data. [My Copy] Pac Symp Biocomput (2008), pp. 201-215. by R. E. Thurman, W. S. Noble, J. A. Stamatoyannopoulos posted to chip-chip chip-seq chromatin encode genome-wide heterochromatin signature by sebastien_vigneau on 2009-05-18 01:19:03 as along with 5 people and 1 group timflutre Eroslavochka guhjy operon dpollard EisenLab
	caBIG VISDA: modeling, visualization, and discovery for cluster analysis of genomic data [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008) by Yitan Zhu, Huai Li, David Miller, et al.Zuyi Wang, Jianhua Xuan, Robert Clarke, Eric Hoffman, Yue Wang posted to chip chip-chip chip-seq cluster clustering heatmap software by sebastien_vigneau on 2009-05-17 13:57:59 as along with 3 people operon rdiaz nuin
	The Arabidopsis LHP1 protein colocalizes with histone H3 Lys27 trimethylation [My Copy] Nature Structural & Molecular Biology, Vol. 14, No. 9. (05 August 2007), pp. 869-871. by Xiaoyu Zhang, Sophie Germann, Bartlomiej J. Blus, Sepideh Khorasanizadeh, Valerie Gaudin, Steven E. Jacobsen posted to chip-chip chromatin histone methylation by kengg on 2009-05-07 01:30:47 as along with 1 person rjlawren
	Histone modifications at human enhancers reflect global cell-type-specific gene expression. [My Copy] Nature, Vol. 459, No. 7243. (7 May 2009), pp. 108-112. by Nathaniel D. Heintzman, Gary C. Hon, R. David Hawkins, et al.Pouya Kheradpour, Alexander Stark, Lindsey F. Harp, Zhen Ye, Leonard K. Lee, Rhona K. Stuart, Christina W. Ching, Keith A. Ching, Jessica E. Antosiewicz-Bourget, Hui Liu, Xinmin Zhang, Roland D. Green, Victor V. Lobanenkov, Ron Stewart, James A. Thomson, Gregory E. Crawford, Manolis Kellis, Bing Ren posted to chip-chip chromatin-structure tiling-array by humburg on 2009-05-04 02:40:15 as along with 15 people and 2 groups suizifish RyuOgawa inesdesantiago gdb djkt tonamswish t08681mn akundaje leliavski scjparker fenghezi TRHvidsten frohike idonaldson sebastien_vigneau Epigenetics CTCF

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