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Ключевое слово chip-chip [71 articles]

Recent papers classified by the tag chip-chip.
  • Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
    Genome Res. (7 February 2008), gr.7080508.
    by David S Johnson, Wei Li, Benjamin D Gordon, Arindam Bhattacharjee, Bo Curry, Jayati Ghosh, Leonardo Brizuela, Jason S Carroll, Myles Brown, Paul Flicek, Christopher M Koch, Ian Dunham, Mark Bieda, Xiaoqin Xu, Peggy J Farnham, Philipp Kapranov, David A Nix, Thomas R Gingeras, Xinmin Zhang, Heather Holster, Nan Jiang, Roland Green, Jun S Song, Scott A Mccuine, Elizabeth Anton, Loan Nguyen, Nathan D Trinklein, Zhen Ye, Keith Ching, David Hawkins, Bing Ren, Peter C Scacheri, Joel Rozowsky, Alexander Karpikov, Ghia Euskirchen, Sherman Weissman, Mark Gerstein, Michael Snyder, Annie Yang, Zarmik Moqtaderi, Heather Hirsch, Hennady P Shulha, Yutao Fu, Zhiping Weng, Kevin Struhl, Richard M Myers, Jason D Lieb, Shirley X Liu
  • Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data.
    BMC Bioinformatics, Vol. 5 (18 March 2004)
    by F Gao, BC Foat, HJ Bussemaker
  • Polycomb complexes repress developmental regulators in murine embryonic stem cells
    Nature (19 April 2006)
    by Laurie A Boyer, Kathrin Plath, Julia Zeitlinger, Tobias Brambrink, Lea A Medeiros, Tong I Lee, Stuart S Levine, Marius Wernig, Adriana Tajonar, Mridula K Ray, George W Bell, Arie P Otte, Miguel Vidal, David K Gifford, Richard A Young, Rudolf Jaenisch
  • Control of developmental regulators by polycomb in human embryonic stem cells.
    Cell, Vol. 125, No. 2. (21 April 2006), pp. 301-313.
    by TI Lee, RG Jenner, LA Boyer, MG Guenther, SS Levine, RM Kumar, B Chevalier, SE Johnstone, MF Cole, K Isono, H Koseki, T Fuchikami, K Abe, HL Murray, JP Zucker, B Yuan, GW Bell, E Herbolsheimer, NM Hannett, K Sun, DT Odom, AP Otte, TL Volkert, DP Bartel, DA Melton, DK Gifford, R Jaenisch, RA Young
  • Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4
    Nature, Vol. 441, No. 7090., pp. 173-178.
    by Mark Gilchrist, Vesteinn Thorsson, Bin Li, Alistair G Rust, Martin Korb, Kathleen Kennedy, Tsonwin Hai, Hamid Bolouri, Alan Aderem
    posted to chip-chip network transcription by tuck on 2006-05-16 03:42:43 as ** along with 2 people biozhang2001 miguel
  • Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution
    Science, Vol. 308, No. 5725. (20 May 2005), pp. 1149-1154.
    by Jill Cheng, Philipp Kapranov, Jorg Drenkow, Sujit Dike, Shane Brubaker, Sandeep Patel, Jeffrey Long, David Stern, Hari Tammana, Gregg Helt, Victor Sementchenko, Antonio Piccolboni, Stefan Bekiranov, Dione K Bailey, Madhavan Ganesh, Srinka Ghosh, Ian Bell, Daniela S Gerhard, Thomas R Gingeras
  • A supervised hidden Markov model framework for efficiently segmenting tiling array data in transcriptional and ChIP-chip experiments: systematically incorporating validated biological knowledge.
    Bioinformatics (12 October 2006)
    by Jiang Du, Joel S S Rozowsky, Jan O O Korbel, Zhengdong D D Zhang, Thomas E E Royce, Martin H H Schultz, Michael Snyder, Mark Gerstein
  • Devising transcriptional regulatory networks operating during the cell cycle and differentiation using ChIP-on-chip
    Chromosome Research, Vol. 13, No. 3. (January 2005), pp. 275-288.
    by Alexandre Blais, Brian Dynlacht
    posted to chip-chip network regulatory transcriptional by tabu on 2006-01-17 14:23:03 as **
  • Identification of Promoters Bound by c-Jun/ATF2 during Rapid Large-Scale Gene Activation following Genotoxic Stress
    Molecular Cell, Vol. 16, No. 4. (19 November 2004), pp. 521-535.
    by Jun Hayakawa, Shalu Mittal, Yipeng Wang, Kemal S Korkmaz, Eileen Adamson, Christopher English, Masahide Omichi, Michael Mcclelland, Dan Mercola
    posted to chip-chip by tabu on 2006-02-01 10:03:34 as **
  • Core transcriptional regulatory circuitry in human embryonic stem cells.
    Cell, Vol. 122, No. 6. (23 September 2005), pp. 947-956.
    by LA Boyer, TI Lee, MF Cole, SE Johnstone, SS Levine, JP Zucker, MG Guenther, RM Kumar, HL Murray, RG Jenner, DK Gifford, DA Melton, R Jaenisch, RA Young
  • Temporal ChIP-on-chip reveals Biniou as a universal regulator of the visceral muscle transcriptional network.
    Genes Dev, Vol. 21, No. 19. (1 October 2007), pp. 2448-2460.
    posted to chip-chip by Stew on 2007-10-04 23:31:08 as ***** along with 1 person and 1 group dpollard EisenLab
  • Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo.
    Genes Dev, Vol. 21, No. 4. (15 February 2007), pp. 385-390.
    by J Zeitlinger, RP Zinzen, A Stark, M Kellis, H Zhang, RA Young, M Levine
  • Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array
    Proceedings of the National Academy of Sciences, Vol. 103, No. 34. (22 August 2006), pp. 12763-12768.
    by Frederic Biemar, David A Nix, Jessica Piel, Brant Peterson, Matthew Ronshaugen, Victor Sementchenko, Ian Bell, Robert J Manak, Michael S Levine
  • Association of cohesin and Nipped-B with transcriptionally active regions of the Drosophila melanogaster genome.
    Chromosoma (27 October 2007)
    by Ziva Misulovin, Yuri B Schwartz, Xiao-Yong Y Li, Tatyana G Kahn, Maria Gause, Stewart Macarthur, Justin C Fay, Michael B Eisen, Vincenzo Pirrotta, Mark D Biggin, Dale Dorsett
    posted to chip-chip chromatin drosophila nipped-b by Stew on 2007-12-03 18:20:44 as **
  • RNA polymerase is poised for activation across the genome
    Nature Genetics, Vol. 39, No. 12. (11 November 2007), pp. 1507-1511.
    by Ginger W Muse, Daniel A Gilchrist, Sergei Nechaev, Ruchir Shah, Joel S Parker, Sherry F Grissom, Julia Zeitlinger, Karen Adelman
  • Epigenetic characterization of hematopoietic stem cell differentiation using miniChIP and bisulfite sequencing analysis
    PNAS (18 July 2007), 0704468104.
    by Joanne L Attema, Peter Papathanasiou, Camilla E Forsberg, Jian Xu, Stephen T Smale, Irving L Weissman
  • The Binding Sites for the Chromatin Insulator Protein CTCF Map to DNA Methylation-Free Domains Genome-Wide
    Genome Res., Vol. 14, No. 8. (1 August 2004), pp. 1594-1602.
    by Rituparna Mukhopadhyay, Wenqiang Yu, Joanne Whitehead, Junwang Xu, Magda Lezcano, Svetlana Pack, Chandrasekhar Kanduri, Meena Kanduri, Vasudeva Ginjala, Alexander Vostrov, Wolfgang Quitschke, Igor Chernukhin, Elena Klenova, Victor Lobanenkov, Rolf Ohlsson
  • Genome-Wide Analysis of Protein-DNA Interactions.
    Annu Rev Genomics Hum Genet, Vol. 7 (2006), pp. 81-102.
    by TH Kim, B Ren
  • CTCF Interacts with and Recruits the Largest Subunit of RNA Polymerase II to CTCF Target Sites Genome-Wide
    Mol. Cell. Biol., Vol. 27, No. 5. (1 March 2007), pp. 1631-1648.
    by Igor Chernukhin, Shaharum Shamsuddin, Sung Y Kang, Rosita Bergstrom, Yoo-Wook Kwon, Wenqiang Yu, Joanne Whitehead, Rituparna Mukhopadhyay, France Docquier, Dawn Farrar, Ian Morrison, Marc Vigneron, Shwu-Yuan Wu, Cheng-Ming Chiang, Dmitri Loukinov, Victor Lobanenkov, Rolf Ohlsson, Elena Klenova
  • A physical model for tiling array analysis.
    Bioinformatics, Vol. 23, No. 13. (1 July 2007)
    by HR Chung, D Kostka, M Vingron
  • Transcriptional regulatory code of a eukaryotic genome
    Nature, Vol. 431, No. 7004. (2004), pp. 99-104.
    by Christopher T Harbison, Benjamin D Gordon, Tong I Lee, Nicola J Rinaldi, Kenzie D Macisaac, Timothy W Danford, Nancy M Hannett, Jean-Bosco Tagne, David B Reynolds, Jane Yoo, Ezra G Jennings, Julia Zeitlinger, Dmitry K Pokholok, Manolis Kellis, Alex P Rolfe, Ken T Takusagawa, Eric S Lander, David K Gifford, Ernest Fraenkel, Richard A Young
  • Computational discovery of gene modules and regulatory networks.
    Nat Biotechnol, Vol. 21, No. 11. (November 2003), pp. 1337-1342.
    by Z Bar-Joseph, GK Gerber, TI Lee, NJ Rinaldi, JY Yoo, F Robert, DB Gordon, E Fraenkel, TS Jaakkola, RA Young, DK Gifford
  • PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny.
    PLoS Comput Biol, Vol. 1, No. 7. (December 2005)
  • Integrated assessment and prediction of transcription factor binding.
    PLoS Comput Biol, Vol. 2, No. 6. (16 June 2006)
  • Target hub proteins serve as master regulators of development in yeast.
    Genes Dev, Vol. 20, No. 4. (15 February 2006), pp. 435-448.
  • Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarrays.
    J Bacteriol, Vol. 187, No. 17. (September 2005), pp. 6166-6174.
    by CD Herring, M Raffaelle, TE Allen, EI Kanin, R Landick, AZ Ansari, BØ Palsson
    posted to chip-chip ecoli by nickluscombe on 2006-08-17 19:20:04 as ** along with 1 group EBI-regulation
  • Global histone acetylation induces functional genomic reorganization at mammalian nuclear pore complexes
    Genes Dev., Vol. 22, No. 5. (1 March 2008), pp. 627-639.
    by Christopher R Brown, Caleb J Kennedy, Valerie A Delmar, Douglass J Forbes, Pamela A Silver
    posted to chip-chip by kengg on 2008-03-12 20:48:39 as ** along with 1 person sunhwan
  • A core transcriptional network for early mesoderm development in Drosophila melanogaster.
    Genes Dev, Vol. 21, No. 4. (15 February 2007), pp. 436-449.
  • Comparison of sample preparation methods for ChIP-chip assays.
    Biotechniques, Vol. 41, No. 5. (November 2006), pp. 577-580.
    by H O'Geen, CM Nicolet, K Blahnik, R Green, PJ Farnham
    posted to chip-chip technique by kengg on 2007-12-27 15:39:53 as ** along with 1 person kristallreiner
  • Sensitive ChIP-DSL technology reveals an extensive estrogen receptor alpha-binding program on human gene promoters.
    Proc Natl Acad Sci U S A, Vol. 104, No. 12. (20 March 2007), pp. 4852-4857.
    by YS Kwon, I Garcia-Bassets, KR Hutt, CS Cheng, M Jin, D Liu, C Benner, D Wang, Z Ye, M Bibikova, JB Fan, L Duan, CK Glass, MG Rosenfeld, XD Fu
    posted to chip chip-chip by kengg on 2007-12-22 03:40:26 as ** along with 1 person jfr
  • The role of AtMSH2 in homologous recombination in Arabidopsis thaliana
    EMBO Reports, Vol. aop, No. current. (25 November 2005)
    by Eyal Emmanuel, Elizabeth Yehuda, Cathy Melamed-Bessudo, Naomi Avivi-Ragolsky, Avraham A Levy
    posted to chip-chip microarray by kengg on 2007-10-19 14:31:13 as **
  • The impact of sequence divergence and DNA mismatch repair on homeologous recombination in Arabidopsis
    The Plant Journal, Vol. 45, No. 6. (March 2006), pp. 908-916.
    by Liangliang Li, Martine Jean, Francois Belzile
    posted to chip-chip microarray by kengg on 2007-10-19 14:28:32 as **
  • Impact of the loss of AtMSH2 on double-strand break-induced recombination between highly diverged homeologous sequences in Arabidopsis thaliana germinal tissues.
    Plant Mol Biol, Vol. 63, No. 6. (April 2007), pp. 833-846.
    posted to chip-chip microarray by kengg on 2007-10-19 14:26:21 as **
  • DISTORTED3/SCAR2 is a putative arabidopsis WAVE complex subunit that activates the Arp2/3 complex and is required for epidermal morphogenesis.
    Plant Cell, Vol. 17, No. 2. (February 2005), pp. 502-524.
    by D Basu, J Le, Sel-D El-Essal, S Huang, C Zhang, EL Mallery, G Koliantz, CJ Staiger, DB Szymanski
    posted to arabidopsis chip-chip tfs trichome by kengg on 2008-01-30 21:01:28 as **
  • Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm
    PLoS Biology, Vol. 6, No. 2. (1 February 2008), e27.
    by Xiao-Yong Li, Stewart Macarthur, Richard Bourgon, David Nix, Daniel A Pollard, Venky N Iyer, Aaron Hechmer, Lisa Simirenko, Mark Stapleton, Cris L Hendriks, Hou C Chu, Nobuo Ogawa, William Inwood, Victor Sementchenko, Amy Beaton, Richard Weiszmann, Susan E Celniker, David W Knowles, Tom Gingeras, Terence P Speed, Michael B Eisen, Mark D Biggin
  • Two Arabidopsis metacaspases AtMCP1b and AtMCP2b are arginine/lysine-specific cysteine proteases and activate apoptosis-like cell death in yeast.
    J Biol Chem, Vol. 280, No. 15. (15 April 2005), pp. 14691-14699.
    by N Watanabe, E Lam
    posted to chip-chip microarray by kengg on 2007-10-19 14:38:59 as **
  • Rapid accumulation of mutations during seed-to-seed propagation of mismatch-repair-defective Arabidopsis.
    Genes Dev, Vol. 18, No. 21. (1 November 2004), pp. 2676-2685.
    by PD Hoffman, JM Leonard, GE Lindberg, SR Bollmann, JB Hays
    posted to chip-chip microarray msh by kengg on 2007-10-19 14:33:47 as **
  • Transcriptional regulatory networks in Saccharomyces cerevisiae.
    Science, Vol. 298, No. 5594. (25 October 2002), pp. 799-804.
    by TI Lee, NJ Rinaldi, F Robert, DT Odom, Z Bar-Joseph, GK Gerber, NM Hannett, CT Harbison, CM Thompson, I Simon, J Zeitlinger, EG Jennings, HL Murray, DB Gordon, B Ren, JJ Wyrick, JB Tagne, TL Volkert, E Fraenkel, DK Gifford, RA Young
  • Genome-wide analysis of chromatin status using tiling microarrays.
    Methods, Vol. 41, No. 3. (March 2007), pp. 304-311.
    by S Shivaswamy, VR Iyer
  • A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--A case study using E2F1.
    Genome Res (19 October 2006)
    by Victor X X Jin, Alina Rabinovich, Sharon L L Squazzo, Roland Green, Peggy J J Farnham
    posted to chip-chip regulation by jfr on 2006-11-08 09:52:38 as ** along with 2 people aprasad idonaldson
  • Identifying synergistic regulation involving c-Myc and sp1 in human tissues.
    Nucleic Acids Res, Vol. 35, No. 4. (2007), pp. 1098-1107.
    by F Parisi, P Wirapati, F Naef
    posted to regulation integration gene_expression chip-chip by jfr on 2008-05-04 23:42:17 as **
  • Inferring transcriptional modules from ChIP-chip, motif and microarray data.
    Genome Biol, Vol. 7, No. 5. (2006)
  • Ringo - an R/Bioconductor package for analyzing ChIP-chip readouts
    BMC Bioinformatics, Vol. 8 (26 June 2007), 221.
    by Joern Toedling, Oleg Sklyar, Wolfgang Huber
  • GSE: a comprehensive database system for the representation, retrieval, and analysis of microarray data.
    Pac Symp Biocomput (2008), pp. 539-550.
    by T Danford, A Rolfe, D Gifford
    posted to software database chip-chip by jfr on 2008-04-30 16:53:52 as ** along with 2 people jyuh idonaldson
  • BoCaTFBS: a boosted cascade learner to refine the binding sites suggested by ChIP-chip experiments
    Genome Biology, Vol. 7 (01 November 2006), R102.
    by Lu-Yong Wang, Michael Snyder, Mark Gerstein
  • Rank-statistics based enrichment-site prediction algorithm developed for chromatin immunoprecipitation on chip experiments.
    BMC Bioinformatics, Vol. 7 (05 October 2006), 434.
    by Srinka Ghosh, Heather A Hirsch, Edward Sekinger, Kevin Struhl, Thomas R Gingeras
    posted to methodology chip-chip by jfr on 2007-01-12 16:45:14 as ** along with 1 person olympos
  • CMARRT: a tool for the analysis of ChIP-chip data from tiling arrays by incorporating the correlation structure.
    Pac Symp Biocomput (2008), pp. 515-526.
    by PF Kuan, H Chun, S Keleş
    posted to software chip-chip by jfr on 2008-05-05 11:10:00 as ** along with 1 person idonaldson
  • ChIP-chip Comes of Age for Genome-wide Functional Analysis
    Cancer Res, Vol. 66, No. 14. (15 July 2006), pp. 6899-6902.
    by Jiejun Wu, Laura T Smith, Christoph Plass, Tim H Huang
  • W-AlignACE: An improved Gibbs sampling algorithm based on more accurate position weight matrices learned from sequence and gene expression/ChIP-chip data.
    Bioinformatics (5 March 2008)
    by Xin Chen, Lingqiong Guo, Zhaocheng Fan, Tao Jiang
  • ChIPping away at gene regulation.
    EMBO reports, Vol. 9, No. 4. (April 2008), pp. 337-343.
    by CE Massie, IG Mills
    posted to review chip-on-chip chip-chip by idonaldson on 2008-07-08 10:53:50 as ***
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