idonaldson's chip-chip [26 articles] Export

Recent papers added to idonaldson's library classified by the tag chip-chip. You can also see everyone's chip-chip.

	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 12 people and 2 groups bsamal venancio aalibes fenghezi daveGerrard megraw scjparker maximilianh djkt isimpson Stew druvus BergmanLab Bioinformatics - CRUK
	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 tool chip-seq chip-chip by idonaldson on 2009-08-24 10:26:34 as along with 6 people bsamal maximilianh druvus ewilban1 guhjy nuin
	Distinguishing direct versus indirect transcription factor-DNA interactions. [My Copy] Genome research, Vol. 19, No. 11. (3 November 2009), pp. 2090-2100. by Raluca Gordân, Alexander J. Hartemink, Martha L. Bulyk posted to chip-chip indirect by idonaldson on 2009-08-10 09:54:47 as along with 13 people roys sebastien_vigneau oannes nklee djkt vingron venancio owhitney tmmurali emptyhb maximilianh jbhiatt frohike
	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
	Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data [My Copy] Bioinformatics (Oxford, England) In Bioinformatics, Vol. 25, No. 14. (15 July 2009), pp. 1715-1721. by Hyungwon Choi, Alexey I. Nesvizhskii, Debashis Ghosh, Zhaohui S. Qin posted to chip-chip chip-seq hmm by idonaldson on 2009-05-26 10:32:31 as along with 13 people and 1 group bsamal jfr tonamswish rdiaz fpattyn jcbarret guhjy hendrik85 inesdesantiago nklee polivares ewilban1 humburg Journal picks
	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 tool by idonaldson on 2009-04-08 09:22:55 as along with 11 people and 1 group ashishanand siebert mcm rgottardo GeeSharpMinor kengg nicholso talponer caseybrown bertelsen bozdagd Plantandetc
	Visualization of genomic data with the Hilbert curve [My Copy] Bioinformatics, Vol. 25, No. 10. (15 May 2009), pp. 1231-1235. by Simon Anders posted to chip-chip chip-seq genomic tool visualisation by idonaldson on 2009-03-23 17:05:05 as along with 15 people and 1 group Yanno jfr jandot ewilban1 polivares inesdesantiago djkt behindtherabbit guhjy humburg Thaverkamp svenrahmann jmeppley rdiaz paszkows BergmanLab
	Genome-wide analysis of histone H3 lysine 27 trimethylation by ChIP-chip in gastric cancer patients [My Copy] Journal of Gastroenterology by Li Zhang, Keli Zhong, Yong Dai, Hanxin Zhou posted to cancer chip-chip gastric methylation by idonaldson on 2009-03-16 10:39:03 as
	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 expression gene method by idonaldson on 2009-03-16 10:37:04 as along with 5 people fpattyn ewilban1 guhjy inesdesantiago sebastien_vigneau
	A Bayesian Hidden Markov Model for Motif Discovery Through Joint Modeling of Genomic Sequence and ChIP-Chip Data [My Copy] Biometrics, Vol. 9999, No. 9999. (2009) by Jonathan A. L. Gelfond, Mayetri Gupta, Joseph G. Ibrahim posted to bayesian chip-chip motif-discovery by idonaldson on 2009-02-16 09:02:57 as along with 2 people wowalz maximilianh
	Extracting transcription factor binding sites from unaligned gene sequences with statistical models. [My Copy] BMC bioinformatics, Vol. 9 Suppl 12 (2008) by C. C. Lu, W. H. Yuan, T. M. Chen posted to chip-chip tfbs tool by idonaldson on 2009-01-15 09:56:34 as along with 3 people and 1 group stajich kristallreiner maximilianh Mycology
	Genome-wide analysis of BP1 transcriptional targets in breast cancer cell line Hs578T. [My Copy] International journal of biological sciences, Vol. 5, No. 1. (2009), pp. 1-12. by Y. Song, C. Dang, Y. Fu, et al.Y. Lian, J. Hottel, X. Li, T. McCaffrey, S. W. Fu posted to cancer chip-chip by idonaldson on 2009-01-05 09:29:51 as
	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 tool by idonaldson on 2008-11-10 09:21:39 as along with 25 people and 3 groups bsamal hzoltan fpattyn stubrown isimpson huali tonamswish ewilban1 sebastien_vigneau jfr kmdaily cassj bryankr malcook rschulz mcm behindtherabbit psique renatomilani polivares guhjy inesdesantiago pengchy kengg bais Neuroblastoma SIMR bioinformatics BenosLab
	PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale. [My Copy] Genes & development, Vol. 22, No. 21. (1 November 2008), pp. 2941-2952. by M. I. Lefterova, Y. Zhang, D. J. Steger, et al.M. Schupp, J. Schug, A. Cristancho, D. Feng, D. Zhuo, C. J. Stoeckert, X. S. Liu, M. A. Lazar posted to chip-chip by idonaldson on 2008-11-07 10:20:38 as
	Chromatin immunoprecipitation on microarray analysis of Smad2/3 binding sites reveals roles of ETS1 and TFAP2A in transforming growth factor beta signaling. [My Copy] Molecular and cellular biology, Vol. 29, No. 1. (27 January 2009), pp. 172-186. by Daizo Koinuma, Shuichi Tsutsumi, Naoko Kamimura, et al.Hirokazu Taniguchi, Keiji Miyazawa, Makoto Sunamura, Takeshi Imamura, Kohei Miyazono, Hiroyuki Aburatani posted to chip-chip smad by idonaldson on 2008-11-03 09:16:27 as along with 3 people guhjy heliopais KaminskiLab
	E2F in vivo binding specificity: Comparison of consensus versus nonconsensus binding sites [My Copy] Genome Research, Vol. 18, No. 11. (3 November 2008), pp. 1763-1777. by Alina Rabinovich, Victor X. Jin, Roman Rabinovich, Xiaoqin Xu, Peggy J. Farnham posted to binding chip-chip specificity tfbs by idonaldson on 2008-10-13 09:21:25 as along with 1 person fenghezi
	Parameter estimation for robust HMM analysis of ChIP-chip data [My Copy] BMC Bioinformatics, Vol. 9 (18 August 2008), 343. by Peter Humburg, David Bulger, Glenn Stone posted to chip-chip by idonaldson on 2008-08-28 09:46:40 as along with 1 person dakelley
	ChIPping away at gene regulation. [My Copy] EMBO reports, Vol. 9, No. 4. (April 2008), pp. 337-343. by C. E. Massie, I. G. Mills posted to chip-chip review by idonaldson on 2008-07-08 10:53:50 as along with 1 person yoonk
	W-AlignACE: an improved Gibbs sampling algorithm based on more accurate position weight matrices learned from sequence and gene expression/ChIP-chip data [My Copy] Bioinformatics In Bioinformatics, Vol. 24, No. 9. (1 May 2008), pp. 1121-1128. by Xin Chen, Lingqiong Guo, Zhaocheng Fan, Tao Jiang posted to chip-chip motif-discovery tool by idonaldson on 2008-04-25 14:11:01 as along with 4 people bsamal cassj maximilianh isimpson
	Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies [My Copy] Genome Res., Vol. 17, No. 6. (1 June 2007), pp. 898-909. by Ghia M. Euskirchen, Joel S. Rozowsky, Chia-Lin Wei, et al.Wah H. Lee, Zhengdong D. Zhang, Stephen Hartman, Olof Emanuelsson, Viktor Stolc, Sherman Weissman, Mark B. Gerstein, Yijun Ruan, Michael Snyder posted to chip-chip chip-seq comparison by idonaldson on 2008-02-20 14:32:15 as along with 6 people and 4 groups kengg jtaylor ghattem epigenetics blobbybirdman isimpson Bioinformatics Plantandetc UH - Computational Biology BergmanLab
	Genome-scale ChIP-chip analysis using 10,000 human cells. [My Copy] Biotechniques, Vol. 43, No. 6. (December 2007), pp. 791-797. by L. G. Acevedo, A. L. Iniguez, H. L. Holster, X. Zhang, R. Green, P. J. Farnham posted to chip-chip method by idonaldson on 2008-02-12 17:08:47 as along with 2 people Petersarkies guhjy
	Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets [My Copy] Genome Research, Vol. 18, No. 3. (7 March 2008), pp. 393-403. by David S. Johnson, Wei Li, D. Benjamin Gordon, et al.Arindam Bhattacharjee, Bo Curry, Jayati Ghosh, Leonardo Brizuela, Jason S. Carroll, Myles Brown, Paul Flicek, Christoph 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 D. 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, X. Shirley Liu posted to chip-chip comparison by idonaldson on 2008-02-12 17:07:30 as along with 12 people and 2 groups fenghezi jfr kengg djkt xiaobeizhao cabbagezs caseybrown magusina lp2 stajich gracio gdb BergmanLab Mycology
	CMARRT: a tool for the analysis of ChIP-chip data from tiling arrays by incorporating the correlation structure. [My Copy] Pac Symp Biocomput (2008), pp. 515-526. by P. F. Kuan, H. Chun, S. Keleş posted to chip-chip tool by idonaldson on 2008-02-04 13:14:00 as along with 1 person jfr
	Model-based deconvolution of genome-wide DNA binding. [My Copy] Bioinformatics (1 December 2007) by David J J. Reiss, Marc T T. Facciotti, Nitin S S. Baliga posted to chip-chip deconvolution tfbs by idonaldson on 2008-01-31 11:10:21 as along with 5 people djkt yevishere guhjy vega isimpson
	Lyl1 Interacts with CREB1 and Alters Expression of CREB1 Target Genes. [My Copy] Biochim Biophys Acta (7 December 2007) by Serban San-Marina, Youqi Han, Fernando Suarez Saiz, Michael R R. Trus, Mark D D. Minden posted to chip-chip creb lyl by idonaldson on 2008-01-03 12:01:49 as
	A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray dataâA case study using E2F1 [My Copy] Genome Res In Genome Research, Vol. 16, No. 12. (19 December 2006), pp. 1585-1595. by Victor X. Jin, Alina Rabinovich, Sharon L. Squazzo, Roland Green, Peggy J. Farnham posted to chip-chip crm tfbs tool by idonaldson on 2007-11-08 08:50:56 as along with 3 people bsamal aprasad jfr

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tool	112
tfbs	54
motif-discovery	31
chip-chip	26
chip-seq	25
cis-regulation	25
ngs	22
crm	22
motif	19
review	15
conserved	15
mapping	14
short-read	13
promoter	13
yeast	11
visualisation	10
networks	10
nucleosome	9
me	9
prediction	8
expression	8
comparison	7
matrix	7
human	7
method	7
te	7
regulation	7
tissue-specific	6
transcription-factor	6
gene	6
go	6
alignment	5
binding	5
forkhead	5
tss	5
position	5
genome	5
text-mining	4
chromatin	4
cancer	4
statistics	4
combinatorial	4
analysis	4
microarray	4
gene-set	4
sequence	4
gottgens	4
network	3
srf	3
primer	3
scanning	3
histone	3
rna-seq	3
database	3
modification	3
mouse	3
genome_browser	3
orthologues	3
comparative_genomics	3
bayesian	2
creb	2
cooperative	2
mirna	2
hmm	2
exon-array	2
structural	2
distribution	2
regulatory_elements	2
nfr	2
discovery	2
3c	2
multiple	2
re1	2
evolution	2
haematopoiesis	2
list	2
spacing	2
browser	2
cpg	1
roc	1
non-coding	1
rsat	1
bro	1
halo-chip-chip	1
5c	1
pbm	1
chromosome-territory	1
snp	1
smad	1
enrichment	1
protein-coding	1
mps	1
retrieve	1
neighbouring	1
protein-array	1
kinase	1
organisation	1
polymerase	1
methylation	1
ssr	1
ensembl	1
ccds	1
ncrna	1
nactem	1
periodicity	1
ebox	1
nimblegen	1
artefact	1
chimp	1
procedure	1
over-optimism	1
drosophila	1
dna-interactions	1
pathway	1
motifs	1
ctcf	1
error	1
phosphorylation	1
housekeeping	1
specificity	1
name	1
ribosome	1
yy1	1
functional	1
peak_detection	1
chromosome-kissing	1
journal	1
fdr	1
phylogenetic	1
plasmodium	1
carg	1
muscle	1
random	1
gastric	1
promoter-sharing	1
evolutionary_constraint	1
galaxy	1
indirect	1
transgenic	1
g4	1
sumoylation	1
transcription	1
p53	1
myod	1
deconvolution	1
apoptosis	1
topology	1
ucsc	1
5utr	1
enhancer	1
transposon-free-regions	1
annotation	1
compression	1
footprint	1
lyl	1
genomic	1
scoring	1
protein	1
stem-cells	1
interaction	1
chromosome	1
assembler	1
ecm	1
fungi	1
insulator	1

idonaldson's chip-chip [26 articles] Export

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