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