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fromconnotea	411
motif	175
discovery	128
duplicates	59
scanning	57
synteny	56
enhancer	55
tandem	53
syntenypaper	52
enhancerprediction	43
molecularbiologytechniques	41
combination	36
cns-differences	34
factors	32
cns	31
geneorder	30
cross-species-enhancer	28
noalignment	28
wnt	26
review	23
ncrna	22
phylogenomics	21
conserved	21
alignment	19
chipchip	19
phylogeny	18
transcription	18
promoter	17
ultraconserved	17
notconserved	16
repeated	16
rennes	16
cis-trans	15
otx	15
whole	14
genome	14
pcr	14
enhancerpromotercompatibility	12
insulator	12
cluster	12
tools	11
pwm	11
websites	11
disease	11
randombreakage	10
mirna	10
ciona	10
cns-ranking	10
chromatin	10
pwmimprovement	10
cns-enhancer-screen	10
dna	9
cns-collaboration	9
genome-papers	8
promoters	8
cns-similarity	8
3dstructure	8
genomicregulatoryblocks	8
pitx	8
genes	7
syntenytools	7
pwmcomparison	7
genomeregulatoryblocks	7
application	7
conservation	7
long-range	6
enhancer-screen	6
orthology	6
snp	6
phenotype	6
position	6
enhanceosome	6
promoterprediction	6
enhancer-vertebrate-invertebrate	6
bidirectionalpromoters	6
redundancy	6
enhancer-and-repeats	5
chipseq	5
validated	5
methylation	5
structure	5
genecoregulation	5
microrna	5
enhancerdistances	5
similarity	5
comparative	5
textmining	5
competition	4
interaction	4
enhancersharing	4
enhancerincodingregion	4
comparison	4
introns	4
region	4
silencer	4
enhancer-prediction	4
interchromosomal	4
wholegenomescanning	4
otxpaper	4
expression	4
antisensetranscription	4
footprinting	4
recognition	4
ncrnas	3
phylotypicstage	3
copy-number-variation	3
go	3
replicationorigins	3
regulatory	3
thermodynamicalmodels	3
regions	3
coding	3
matrix	3
mutations	3
model-species	3
mirnaenhancer	3
promoter-minimal	3
cionapopulationgenetics	3
genometrees	3
rna-binding	3
term_recognition	3
tf	3
evoluation	3
inter-cns-distances	3
composition	3
factorclass	3
trainingset	3
syntenyorientation	3
myarticles	3
encode	3
whyconserved	2
core	2
ultraconserveddefinition	2
binding	2
polymorphism	2
3putr	2
cellsortingbasedanalysis	2
histones	2
factorinteractions	2
drosophila	2
cns-database	2
of	2
pluripotency	2
tfsynergy	2
bullshitarticles	2
strengthofmatch	2
codingconservation	2
mammals	2
ciona-gene-annotation	2
microarray	2
enhancer-stage-specificity	2
molecularbiologytools	2
assayscisregwetlab	2
networks	2
spacing	2
regulatory-flexibility	2
rearrangement	2
site-prediction	2
prediction	2
pvalue-multiplicity	2
ncrna-long	2
genomiccontext	2
jshypotheses	2
protocols	2
pituitary	2
grn	2
ascidians	2
syntenypapers	1
coexpression	1
microarray-analysis	1
arx	1
purificationfromdna	1
smarts	1
word	1
factorsclass	1
genomeregulatoryblock	1
cell-cultures	1
degeneratesites	1
bioinformatics	1
drosphila	1
transgenesis	1
positiveselection	1
cns-enhancer	1
element	1
intra-primate	1
duplicatese	1
genefamilyfootprinting	1
generegulatorynetworks	1
grns	1
decoy	1
applicationbioinf	1
cns-enhance	1
autoregulation	1
phylogenytools	1
hmm	1
pax6	1
tr-reviews	1
impossible	1
turnover	1
cns-difference	1
nomotif	1
notconservedfunction	1
gibbs	1
sites	1
doublets	1
books	1
dlx	1
olfactoryreceptors	1
fugu	1
fastindexing	1
writing	1
drosophia	1
statistics	1
insertionsdeletions	1
kernel	1
primers	1
generalregulation	1
igh	1
suppressor	1
genemodels	1
noaccess	1
cisregdatabase	1
ciona-gene-annotations	1
enhancer-contextanalysis	1
nucleosome	1

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