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	Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster [My Copy] Bioinformatics, Vol. 25, No. 19. (1 October 2009), pp. 2473-2477. by Antonio Marco, Charlotte Konikoff, Timothy L. Karr, Sudhir Kumar posted to combination enhancerprediction noalignment by maximilianh on 2009-08-06 21:35:59 as along with 8 people and 1 group Garamonfok TRHvidsten djkt rdiaz natstreet nuin sebastien_vigneau isimpson Jarman Lab
	Organization of developmental enhancers in the Drosophila embryo [My Copy] Nucl. Acids Res., Vol. 37, No. 17. (1 September 2009), pp. 5665-5677. by Dmitri Papatsenko, Yury Goltsev, Michael Levine posted to cns-differences combination enhancerprediction noalignment notconserved regulatory-flexibility by maximilianh on 2009-08-05 22:03:48 as along with 3 people and 1 group inesdesantiago bmajoros al2na Journal picks
	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 cluster combination by maximilianh on 2009-07-28 17:57:22 as along with 11 people and 2 groups venancio aalibes fenghezi idonaldson daveGerrard megraw scjparker djkt isimpson Stew druvus BergmanLab Bioinformatics - CRUK
	Detection of cis -element clusters in higher eukaryotic DNA [My Copy] Bioinformatics, Vol. 17, No. 10. (1 October 2001), pp. 878-889. by Martin C. Frith, Ulla Hansen, Zhiping Weng posted to combination motif by maximilianh on 2009-04-28 13:29:14 as along with 2 people and 2 groups daveGerrard indigoviolet BergmanLab EisenLab
	A probabilistic method to detect regulatory modules. [My Copy] Bioinformatics, Vol. 19 Suppl 1 (2003) by S. Sinha, E. van Nimwegen, E. D. Siggia posted to combination motif scanning by maximilianh on 2009-04-28 13:27:41 as along with 4 people and 2 groups indigoviolet dquest lusk cisevol EisenLab cis-regulatory-evolution
	ModuleDigger: an itemset mining framework for the detection of cis-regulatory modules. [My Copy] BMC bioinformatics, Vol. 10 Suppl 1 (2009) by H. Sun, T. De Bie, V. Storms, et al.Q. Fu, T. Dhollander, K. Lemmens, A. Verstuyf, B. De Moor, K. Marchal posted to combination by maximilianh on 2009-04-09 12:57:32 as along with 1 person idonaldson
	Homotypic regulatory clusters in Drosophila. [My Copy] Genome Res, Vol. 13, No. 4. (April 2003), pp. 579-588. by A. P. Lifanov, V. J. Makeev, A. G. Nazina, D. A. Papatsenko posted to cluster combination motif by maximilianh on 2009-04-02 16:27:21 as along with 3 people and 1 group isimpson indigoviolet tresch EisenLab
	Compo: composite motif discovery using discrete models [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008) by Geir K. Sandve, Osman Abul, Finn Drablos posted to combination discovery motif by maximilianh on 2008-12-10 12:24:43 as along with 5 people wowalz magusina nuin lptolik druvus
	Ab initio identification of functionally interacting pairs of cis-regulatory elements. [My Copy] Genome research, Vol. 18, No. 10. (October 2008), pp. 1643-1651. by B. A. Friedman, M. B. Stadler, N. Shomron, Y. Ding, C. B. Burge posted to combination discovery motif by maximilianh on 2008-11-29 20:54:23 as along with 2 people dandaman jfr
	PlantPAN: Plant Promoter Analysis Navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups [My Copy] BMC Genomics, Vol. 9 (26 November 2008), 561. by Wen-Chi, Rong-Long Pan posted to combination motif scanning websites by maximilianh on 2008-11-29 13:28:39 as along with 3 people tg150 lptolik agustinarce
	Evolutionary computation for discovery of composite transcription factor binding sites [My Copy] Nucl. Acids Res., Vol. 36, No. 21. (1 December 2008), e142. by Gary B. Fogel, V. William Porto, Gabor Varga, et al.Ernst R. Dow, Andrew M. Craven, David M. Powers, Harry B. Harlow, Eric W. Su, Jude E. Onyia, Chen Su posted to combination motif by maximilianh on 2008-10-16 13:43:54 as along with 5 people nklee wowalz lptolik idonaldson davfre
	Sepsid even-skipped Enhancers Are Functionally Conserved in Drosophila Despite Lack of Sequence Conservation [My Copy] PLoS Genet, Vol. 4, No. 6. (27 June 2008), e1000106. by Emily E. Hare, Brant K. Peterson, Venky N. Iyer, Rudolf Meier, Michael B. Eisen posted to cns-differences cns-similarity combination composition cross-species-enhancer drosophila noalignment notconserved by maximilianh on 2008-09-05 10:47:36 as along with 8 people and 2 groups lusk Stew emptyhb djkt stajich pradiptaray cisevol caseybrown Mycology cis-regulatory-evolution
	Determining physical constraints in transcriptional initiation complexes using DNA sequence analysis. [My Copy] PLoS ONE, Vol. 2, No. 11. (2007) by R. K. Shultzaberger, D. Y. Chiang, A. M. Moses, M. B. Eisen posted to cns-similarity combination pwm by maximilianh on 2008-08-25 15:03:56 as
	Differential binding of quadruplex structures of muscle-specific genes regulatory sequences by MyoD, MRF4 and myogenin [My Copy] Nucl. Acids Res. (29 May 2008), gkn340. by Anat Yafe, Jeny Shklover, Pnina Weisman-Shomer, Eyal Bengal, Michael Fry posted to combination motif trainingset by maximilianh on 2008-08-14 08:47:27 as along with 2 people and 1 group nklee jmrivort G-quadruplex
	Modeling Promoter Grammars with Evolving Hidden Markov Models. [My Copy] Bioinformatics (Oxford, England) (5 June 2008) by Kyoung-Jae J. Won, Albin Sandelin, Troels Torben T. Marstrand, Anders Krogh posted to combination motif by maximilianh on 2008-07-22 00:06:04 as along with 2 people lusk niallhaslam
	MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs [My Copy] Nucl. Acids Res. (7 July 2008), gkn407. by Jianfei Hu, Haiyan Hu, Xiaoman Li posted to cns-similarity combination motif noalignment scanning by maximilianh on 2008-07-07 17:15:10 as along with 2 people fenghezi wowalz
	Expression-Guided In Silico Evaluation of Candidate Cis Regulatory Codes for Drosophila Muscle Founder Cells [My Copy] PLoS Computational Biology, Vol. 2, No. 5. (1 May 2006), e53. by Anthony A. Philippakis, Brian W. Busser, Stephen S. Gisselbrecht, et al.Fangxue S. He, Beatriz Estrada, Alan M. Michelson, Martha L. Bulyk posted to combination enhancerprediction by maximilianh on 2008-06-16 23:40:34 as along with 2 people and 1 group maximilianh_otx emilyhare EisenLab
	Detecting cis-regulatory binding sites for cooperatively binding proteins [My Copy] Nucl. Acids Res., Vol. 36, No. 8. (1 May 2008), e46. by Liesbeth van Oeffelen, Pierre Cornelis, Wouter Van Delm, Fedor De Ridder, Bart De Moor, Yves Moreau posted to combination motif scanning by maximilianh on 2008-05-06 15:27:19 as along with 3 people tmmurali idonaldson isimpson
	Nuclear Dvl, c-Jun, beta-catenin, and TCF form a complex leading to stabilization of beta-catenin-TCF interaction. [My Copy] The Journal of cell biology, Vol. 180, No. 6. (24 March 2008), pp. 1087-1100. by X. Q. Gan, J. Y. Wang, Y. Xi, Z. L. Wu, Y. P. Li, L. Li posted to combination factorinteractions factors by maximilianh on 2008-05-01 09:25:57 as
	Implementing arithmetic and other analytic operations by transcriptional regulation. [My Copy] PLoS computational biology, Vol. 4, No. 4. (April 2008) by S. M. Cory, T. J. Perkins posted to combination factors transcription by maximilianh on 2008-04-28 18:07:18 as along with 6 people and 1 group balabu bayesian jjray eskay dquest dbikard SynBioSys
	ModuleMiner: improved computational detection of cis-regulatory modules. Different modes of gene regulation in embryonic development and adult tissues? [My Copy] Genome Biology, Vol. 9, No. 4. (2008) by Peter Van Loo, Stein Aerts, Bernard Thienpont, Bart De Moor, Yves Moreau, Peter Marynen posted to combination discovery motif promoters by maximilianh on 2008-04-09 07:41:36 as along with 5 people heliopais brant djkt natstreet phoenixzxl
	Statistical modeling of transcription factor binding affinities predicts regulatory interactions. [My Copy] PLoS Comput Biol, Vol. 4, No. 3. (March 2008) by T. Manke, H. G. Roider, M. Vingron posted to combination scanning tfsynergy by maximilianh on 2008-03-30 18:52:53 as along with 2 people jjray eskay
	Discovering functional transcription-factor combinations in the human cell cycle [My Copy] Genome Res., Vol. 15, No. 6. (1 June 2005), pp. 848-855. by Zhou Zhu, Jay Shendure, George M. Church posted to applicationbioinf combination by maximilianh on 2008-03-15 18:29:23 as
	Predicting rules on organization of cis-regulatory elements, taking the order of elements into account. [My Copy] Bioinformatics, Vol. 20, No. 7. (1 May 2004), pp. 1119-1128. by G. Terai, T. Takagi posted to combination by maximilianh on 2008-03-15 18:26:14 as
	Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining [My Copy] BMC Bioinformatics, Vol. 8, No. 1. (2007) by Xochitl Morgan, Shulin Ni, Daniel Miranker, Vishwanath Iyer posted to combination motif by maximilianh on 2008-03-15 18:06:50 as along with 4 people barriot idonaldson dps sconlan
	Functional Architecture and Evolution of Transcriptional Elements That Drive Gene Coexpression [My Copy] Science, Vol. 317, No. 5844. (14 September 2007), pp. 1557-1560. by Christopher D. Brown, David S. Johnson, Arend Sidow posted to ciona cis-trans cluster cns-differences combination enhanceosome pwm by maximilianh on 2008-02-29 17:27:57 as along with 10 people and 2 groups pradiptaray dpollard djkt joepickrell zwang Garamonfok Stew mimulus_99 cisevol emptyhb EisenLab cis-regulatory-evolution
	Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs. [My Copy] Genome biology, Vol. 9, No. 1. (28 January 2008) by Andra Ivan, Marc S. Halfon, Saurabh Sinha posted to trainingset motif enhancerprediction discovery combination by maximilianh on 2008-02-29 16:39:34 as along with 2 people and 1 group cisevol csdhwang cis-regulatory-evolution
	Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model. [My Copy] Genome Res, Vol. 12, No. 7. (July 2002), pp. 1019-1028. by M. S. Halfon, Y. Grad, G. M. Church, A. M. Michelson posted to combination conserved enhancerprediction motif scanning by maximilianh on 2008-02-29 13:02:28 as along with 2 people maximilianh_otx isimpson
	Statistical methods to infer cooperative binding among transcription factors in Saccharomyces cerevisiae [My Copy] Bioinformatics, Vol. 24, No. 4. (15 February 2008), pp. 545-552. by Debayan Datta, Hongyu Zhao posted to combination motif by maximilianh on 2008-02-13 16:05:26 as
	Identification of a new binding motif for the paired domain of Pax-3 and unusual characteristics of spacing of bipartite recognition elements on binding and transcription activation. [My Copy] J Biol Chem, Vol. 273, No. 30. (24 July 1998), pp. 19153-19159. by S. A. Phelan, M. R. Loeken posted to combination spacing by maximilianh on 2008-02-12 15:37:11 as
	Grammatical model of the regulation of gene expression. [My Copy] Proc Natl Acad Sci U S A, Vol. 89, No. 20. (15 October 1992), pp. 9405-9409. by J. Collado-Vides posted to combination enhanceosome motif promoter by maximilianh on 2008-02-02 09:29:27 as along with 3 people and 1 group irenas andytseng discreteonyxorb dbk-lab
	Predicting and understanding transcription factor interactions based on sequence level determinants of combinatorial control [My Copy] Bioinformatics, Vol. 24, No. 1. (1 January 2008), pp. 26-33. by A. D. J. van Dijk, Ter, R. G. Immink, G. C. Angenent, R. C. H. J. van Ham posted to combination factors scanning by maximilianh on 2008-01-18 14:20:23 as along with 3 people heliopais idonaldson isimpson
	Structural relationships between diverse cis-acting elements are critical for the functional properties of a rbcS minimal light regulatory unit. [My Copy] J Exp Bot, Vol. 58, No. 15-16. (2007), pp. 4397-4406. by L. López-Ochoa, G. Acevedo-Hernández, A. Martínez-Hernández, G. Argüello-Astorga, L. Herrera-Estrella posted to combination enhanceosome spacing by maximilianh on 2008-01-12 11:13:47 as along with 2 people JustinCrocker lusk
	Predicting Gene Expression from Sequence: A Reexamination [My Copy] PLoS Comput Biol, Vol. 3, No. 11. (30 November 2007), e243. by Yuan Yuan, Lei Guo, Lei Shen, Jun S. Liu posted to combination motif by maximilianh on 2007-12-08 15:04:41 as along with 4 people roys Ema phoenixzxl ptrobajo
	HeliCis: a DNA motif discovery tool for colocalized motif pairs with periodic spacing. [My Copy] BMC bioinformatics, Vol. 8 (28 October 2007), 418. by Erik Larsson, Per Lindahl, Petter Mostad posted to combination discovery motif by maximilianh on 2007-10-31 13:49:41 as along with 2 people idonaldson isimpson
	SMOTIF: efficient structured pattern and profile motif search. [My Copy] Algorithms for molecular biology : AMB, Vol. 1 (xx 2006), pp. 22-22. by Yongqiang Zhang, Mohammed Zaki posted to combination fromconnotea by maximilianh on 2007-09-23 12:59:14 as

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fromconnotea	411
motif	169
discovery	122
duplicates	59
scanning	57
enhancer	55
synteny	54
tandem	53
syntenypaper	52
enhancerprediction	43
molecularbiologytechniques	41
combination	36
cns-differences	34
factors	32
cns	31
geneorder	29
cross-species-enhancer	27
noalignment	27
wnt	26
review	23
ncrna	22
conserved	21
phylogenomics	21
alignment	19
phylogeny	18
transcription	18
chipchip	17
promoter	17
ultraconserved	17
notconserved	16
rennes	16
repeated	16
otx	15
cis-trans	14
genome	14
pcr	14
whole	14
cluster	12
enhancerpromotercompatibility	12
insulator	12
disease	11
pwm	11
chromatin	10
ciona	10
cns-enhancer-screen	10
cns-ranking	10
mirna	10
pwmimprovement	10
randombreakage	10
websites	10
cns-collaboration	9
dna	9
tools	9
3dstructure	8
cns-similarity	8
genome-papers	8
pitx	8
promoters	8
application	7
conservation	7
genes	7
genomeregulatoryblocks	7
genomicregulatoryblocks	7
pwmcomparison	7
bidirectionalpromoters	6
enhanceosome	6
enhancer-screen	6
enhancer-vertebrate-invertebrate	6
long-range	6
orthology	6
phenotype	6
position	6
promoterprediction	6
redundancy	6
snp	6
syntenytools	6
comparative	5
enhancer-and-repeats	5
enhancerdistances	5
genecoregulation	5
methylation	5
microrna	5
similarity	5
structure	5
textmining	5
validated	5
antisensetranscription	4
chipseq	4
comparison	4
competition	4
enhancersharing	4
expression	4
footprinting	4
interchromosomal	4
introns	4
otxpaper	4
recognition	4
region	4
silencer	4
wholegenomescanning	4
cionapopulationgenetics	3
coding	3
composition	3
copy-number-variation	3
encode	3
enhancerincodingregion	3
evoluation	3
factorclass	3
genometrees	3
go	3
interaction	3
inter-cns-distances	3
matrix	3
mirnaenhancer	3
model-species	3
mutations	3
myarticles	3
ncrnas	3
phylotypicstage	3
promoter-minimal	3
regions	3
regulatory	3
rna-binding	3
syntenyorientation	3
term_recognition	3
tf	3
thermodynamicalmodels	3
trainingset	3
3putr	2
ascidians	2
assayscisregwetlab	2
binding	2
bullshitarticles	2
cellsortingbasedanalysis	2
ciona-gene-annotation	2
cns-database	2
core	2
drosophila	2
enhancer-prediction	2
enhancer-stage-specificity	2
factorinteractions	2
genomiccontext	2
grn	2
histones	2
jshypotheses	2
mammals	2
microarray	2
molecularbiologytools	2
ncrna-long	2
networks	2
of	2
pituitary	2
pluripotency	2
polymorphism	2
prediction	2
protocols	2
pvalue-multiplicity	2
rearrangement	2
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replicationorigins	2
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whyconserved	2
applicationbioinf	1
arx	1
autoregulation	1
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books	1
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cisregdatabase	1
cns-difference	1
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decoy	1
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dlx	1
doublets	1
drosophia	1
drosphila	1
duplicatese	1
element	1
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factorsclass	1
fastindexing	1
fugu	1
genefamilyfootprinting	1
genemodels	1
generalregulation	1
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gibbs	1
grns	1
hmm	1
igh	1
impossible	1
insertionsdeletions	1
intra-primate	1
kernel	1
noaccess	1
nomotif	1
notconservedfunction	1
nucleosome	1
olfactoryreceptors	1
pax6	1
phylogenytools	1
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primers	1
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sites	1
smarts	1
statistics	1
suppressor	1
syntenypapers	1
transgenesis	1
tr-reviews	1
turnover	1
word	1
writing	1

maximilianh's combination [36 articles] Export

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