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fromconnotea	411
motif	178
discovery	130
duplicates	59
synteny	57
scanning	57
enhancer	56
tandem	53
syntenypaper	52
enhancerprediction	43
molecularbiologytechniques	41
combination	37
cns-differences	34
factors	32
cns	32
geneorder	30
cross-species-enhancer	28
noalignment	28
wnt	26
review	24
ncrna	23
conserved	22
phylogenomics	21
phylogeny	20
chipchip	20
ultraconserved	19
alignment	19
transcription	18
promoter	17
notconserved	16
rennes	16
repeated	16
otx	15
cis-trans	15
tools	14
genome	14
whole	14
pcr	14
enhancerpromotercompatibility	13
cluster	12
insulator	12
pwm	11
ciona	11
disease	11
websites	11
randombreakage	10
pwmimprovement	10
cns-enhancer-screen	10
mirna	10
chromatin	10
cns-collaboration	10
cns-ranking	10
dna	9
thermodynamicmodels	9
3dstructure	8
genome-papers	8
genomicregulatoryblocks	8
pitx	8
promoters	8
cns-similarity	8
snp	7
redundancy	7
pwmcomparison	7
application	7
conservation	7
genes	7
genomeregulatoryblocks	7
syntenytools	7
promoterprediction	7
chipseq	7
bidirectionalpromoters	6
orthology	6
long-range	6
position	6
enhanceosome	6
textmining	6
enhancer-vertebrate-invertebrate	6
enhancer-screen	6
phenotype	6
validated	5
expression	5
enhancersharing	5
enhancerdistances	5
enhancer-and-repeats	5
microrna	5
comparative	5
genecoregulation	5
methylation	5
similarity	5
structure	5
footprinting	4
enhancer-prediction	4
recognition	4
interaction	4
wholegenomescanning	4
enhancerincodingregion	4
interchromosomal	4
otxpaper	4
silencer	4
antisensetranscription	4
region	4
competition	4
comparison	4
introns	4
mutations	3
genometrees	3
replicationorigins	3
regulatory	3
tf	3
evoluation	3
matrix	3
model-species	3
mirnaenhancer	3
encode	3
enhancer-stage-specificity	3
regions	3
factorclass	3
promoter-minimal	3
rna-binding	3
composition	3
phylotypicstage	3
ncrnas	3
syntenyorientation	3
trainingset	3
cionapopulationgenetics	3
copy-number-variation	3
inter-cns-distances	3
myarticles	3
go	3
coding	3
term_recognition	3
coexpression	2
jshypotheses	2
mammals	2
tfsynergy	2
spacing	2
genomiccontext	2
ascidians	2
protocols	2
ultraconserveddefinition	2
drosophila	2
microarray	2
factorinteractions	2
cns-database	2
molecularbiologytools	2
pluripotency	2
histones	2
of	2
3putr	2
gene_expression_databases	2
polymorphism	2
binding	2
bullshitarticles	2
strengthofmatch	2
ncrna-long	2
cellsortingbasedanalysis	2
networks	2
codingconservation	2
core	2
regulatory-flexibility	2
site-prediction	2
pvalue-multiplicity	2
ciona-gene-annotation	2
pituitary	2
assayscisregwetlab	2
prediction	2
whyconserved	2
grn	2
rearrangement	2
bioinformatics	1
transgenesis	1
positiveselection	1
arx	1
cns-enhancer	1
element	1
intra-primate	1
enhancer-contextanalysis	1
microarray-analysis	1
duplicatese	1
nucleosome	1
generegulatorynetworks	1
grns	1
syntenypapers	1
applicationbioinf	1
cns-enhance	1
autoregulation	1
smarts	1
cell-cultures	1
tr-reviews	1
impossible	1
turnover	1
cns-difference	1
drosphila	1
phylogenytools	1
notconservedfunction	1
gibbs	1
doublets	1
books	1
genefamilyfootprinting	1
pax6	1
olfactoryreceptors	1
fugu	1
decoy	1
fastindexing	1
hmm	1
nomotif	1
sites	1
dlx	1
writing	1
drosophia	1
blast	1
genomeregulatoryblock	1
insertionsdeletions	1
kernel	1
primers	1
igh	1
statistics	1
suppressor	1
generalregulation	1
genemodels	1
noaccess	1
cisregdatabase	1
degeneratesites	1
screening	1
ciona-gene-annotations	1
factorsclass	1
word	1
purificationfromdna	1