bigram

This is a table of type bigram and their frequencies. Use it to search & browse the list to learn more about your study carrel.

bigram	frequency
ribosomal frameshifting	286
nucleic acids	172
stop codon	146
nucleic acid	145
specific amplification	138
rna polymerase	133
reading frame	126
gene expression	124
supplementary table	111
secondary structure	106
immunodeficiency virus	94
frameshift efficiency	91
human immunodeficiency	91
amino acid	87
slippery sequence	83
virus type	81
viral rna	78
escherichia coli	78
rna synthesis	77
sf asf	75
dependent rna	75
rna pseudoknot	73
supplementary data	68
amino acids	67
rna viruses	67
rna binding	65
frameshifting efficiency	64
sukh superfamily	63
cord uid	62
acids res	62
doc id	62
res doi	62
mm nacl	60
previously described	60
programmed ribosomal	60
firefly luciferase	58
mg ml	58
crystal structure	58
rf signals	58
saccharomyces cerevisiae	57
time pcr	57
respiratory syndrome	56
rna structure	56
viral genome	55
highly conserved	55
small molecules	55
site trna	53
binding site	52
frameshift site	51
copy number	51
secondary structures	50
bloom filter	49
cell lines	49
acute respiratory	49
stranded rna	49
pol ii	49
sg mrna	49
base pairs	48
exon skipping	48
severe acute	47
sars coronavirus	47
room temperature	46
ribosomal frameshift	46
mm tris	46
recombination events	46
cell death	46
rna secondary	45
human genome	45
active site	45
virus rna	44
binding protein	43
viral proteins	43
gel electrophoresis	43
described previously	43
thermodynamic stability	43
small molecule	43
site loop	43
viral replication	42
total rna	42
mm hepes	42
slippery site	42
translational frameshifting	41
binding sites	41
performed using	40
viral genomes	40
mm mgcl	40
negative control	39
virus genome	39
antisense oligonucleotides	39
csl exosome	39
positional clustering	39
amplification events	39
reverse transcriptase	38
rna pseudoknots	38
infected cells	38
rna interference	37
alternative splicing	37
interest statement	37
wild type	37
acids research	37
rna virus	37
genomic rna	36
nar online	36
luciferase reporter	36
ge healthcare	36
primer extension	36
rna samples	36
none declared	35
oxidative stress	35
loop structure	35
chemical probes	35
base pairing	35
mammalian cells	34
virus variation	34
genomic dna	34
cell line	34
ribosomal rna	34
sequence analysis	33
false positives	33
terminal domain	33
structural basis	33
breast cancer	33
mm edta	33
luciferase activity	33
open reading	33
previous studies	33
stranded dna	32
sequence data	32
protein synthesis	32
frameshift signal	31
frameshifting signal	31
ebola virus	31
ltr promoter	31
virus replication	31
zinc finger	31
rrna degradation	30
shift site	30
strand rna	30
dna polymerase	30
molecular beacons	30
may also	30
base pair	29
single nucleotide	29
target genes	29
messenger rna	29
rna replication	29
sequence alignment	29
rna integrity	29
digital array	29
cleavage site	29
containing mm	29
reverse transcription	29
complex formation	29
renilla luciferase	29
antiviral activity	28
rna chaperone	28
acid sequence	28
cov nsp	28
probe design	28
gibbs sampling	28
structural proteins	27
bloom filters	27
quadruplex structures	27
directed mutagenesis	27
mutational analysis	27
isothermal amplification	27
syndrome coronavirus	27
rna structures	27
frame maintenance	27
uga codon	26
leukemia virus	26
unfolded protein	26
multiple sequence	26
influenza virus	26
ifn induction	26
expression levels	26
helicase activity	26
mm dtt	26
western blot	26
open access	26
thermo fisher	26
protein response	26
west nile	26
polyacrylamide gel	26
acetic acid	26
data sets	25
fisher scientific	25
quality control	25
surveyor tm	25
zero frame	25
kcal mol	25
pcr products	25
nucleotide sequence	25
multiplex pcr	25
mm kcl	25
reference sequence	25
final concentration	25
labeled rna	25
cell culture	25
fusion protein	25
infectious bronchitis	25
stop codons	24
sequence database	24
rna interactions	24
dengue virus	24
ifn activation	24
cells expressing	24
local stability	24
results showed	24
protein interactions	24
reading frames	24
polymerase ii	24
transfected cells	24
tissue culture	24
point mutations	24
free energy	24
dual luciferase	24
applied biosystems	24
eav nsp	23
sequencing data	23
bronchitis virus	23
ribosomal pausing	23
determine whether	23
genome sequences	23
ribosomal protein	23
fs product	23
assay system	23
blot analysis	23
dna replication	23
variation resource	23
copy numbers	23
nucleotide sequences	23
trna sec	23
mrna transcription	23
codon readthrough	23
reference genome	23
viral sequences	23
frameshift products	22
chain reaction	22
nucleocapsid protein	22
catalytic domain	22
also observed	22
incomplete translocation	22
polymerase chain	22
hash functions	22
stress response	22
host proteins	22
length cd	22
northern blot	22
minigenome rna	22
mass spectrometry	22
destabilizing activity	22
site effect	21
data indicate	21
ft cells	21
positive control	21
rna quality	21
binding pocket	21
antisense oligonucleotide	21
archaeal dnag	21
rna degradation	21
transcription factor	21
genome replication	21
rna dimerization	21
maximum rate	21
promoter activity	21
supplementary figures	21
three times	21
coronavirus ribosomal	21
nuclease toxins	21
wide range	20
hepes ph	20
generated using	20
rna helix	20
expression vector	20
termination codon	20
muscular dystrophy	20
viral infection	20
see supplementary	20
class i	20
toprim domain	20
cell lysates	20
statistically significant	20
rna adp	20
trna slippage	20
rf signal	20
lentiviral vector	20
stimulatory rna	20
dna sequencing	20
est mrna	20
line probing	20
life cycle	20
locked nucleic	20
mediated isothermal	20
frameshift proteins	20
terminal segment	20
bovine serum	19
pathway i	19
mutation scanning	19
prf activity	19
molecular beacon	19
protein sequences	19
protein sequence	19
side chain	19
rna polymerases	19
truncated cd	19
target effects	19
described earlier	19
conserved residues	19
viral transcription	19
large number	19
coronavirus genome	19
reference sequences	19
pcr amplification	19
binding activity	19
near cognate	19
hcl ph	19
small interfering	19
previously reported	18
quadruplex dna	18
mrna stability	18
luciferase assay	18
important role	18
iii iv	18
using bst	18
rna substrates	18
prf stimulator	18
xxy yyz	18
cellular uptake	18
protein products	18
translational readthrough	18
dna fragments	18
rna genome	18
side chains	18
cells treated	18
mrna decay	18
immunity proteins	18
molecular biology	18
sukh domain	18
frameshift product	18
pcr product	18
two different	18
programmed translational	18
specific products	18
error rate	18
yeast cells	18
rna elements	18
taken together	18
mdx mice	17
even though	17
buffer containing	17
frameshift signals	17
sense strand	17
translation initiation	17
false positive	17
host cell	17
inhibitory effect	17
terminal region	17
sequence alignments	17
forming sequences	17
untranslated region	17
immune response	17
protease inhibitor	17
ri rna	17
sequence similarity	17
sox binding	17
mosaic virus	17
test whether	17
least one	17
time rt	17
dna damage	17
crystal structures	17
luciferase gene	17
lysis buffer	17
first step	17
rna chaperones	17
nt spacer	17
genome sequence	17
nile virus	17
agarose gel	17
recoding events	17
smi knr	17
binding domain	17
exterior surface	17
lacz gene	16
human cytomegalovirus	16
orf ab	16
antisense strand	16
hepatitis virus	16
generation sequencing	16
trna arg	16
data set	16
mechanical strength	16
binding peptides	16
ii iii	16
western blotting	16
data structure	16
coding sequences	16
also found	16
vitro transcription	16
spacer length	16
loop kissing	16
human cells	16
commonly used	16
rna processing	16
endoplasmic reticulum	16
increasing concentrations	16
binding motifs	16
nmr spectroscopy	16
stalled ribosomes	16
results indicate	16
elongation factor	16
toxin systems	16
curve analysis	16
palindromic sequence	16
coding region	16
clinical trials	16
mrna levels	16
terminal loop	16
polymerase activity	16
barr virus	16
high levels	16
hspa motif	16
cd tr	16
interfering rnas	16
rna complex	15
synonymous site	15
rdrp activity	15
data structures	15
premature termination	15
murine leukemia	15
national center	15
time points	15
dna binding	15
pathway iii	15
kinetic model	15
conserved regions	15
frameshifted ribosomes	15
chaperone activity	15
duchenne muscular	15
binding affinity	15
solution structure	15
melting curve	15
cirv genome	15
template tunnel	15
loop i	15
nuclease domains	15
archaeal exosome	15
site trnas	15
coronavirus replication	15
mobility shift	15
quantified using	15
reticulocyte lysate	15
translational bypassing	15
interfering rna	15
cell viability	15
reporter system	15
nuclease domain	15
degfact values	15
synonymous sites	15
coding regions	15
closely related	15
translational recoding	15
genetic code	15
see also	15
host protein	15
acid residues	15
dna samples	15
recent advances	15
data suggest	15
analysis revealed	15
tertiary structure	15
well plates	15
contains two	15
exon inclusion	15
real mutations	15
binding motif	15
polymerase i	14
subgenomic mrna	14
mis assays	14
cleavage sites	14
clef zinc	14
structural features	14
genes encoding	14
terminal domains	14
splicing pattern	14
clinical samples	14
prf stimulation	14
release factor	14
positive fraction	14
two types	14
rna strands	14
type dnag	14
bp hairpin	14
transfer rna	14
cell cycle	14
protein binding	14
cognate trna	14
gene silencing	14
induce frameshifting	14
calculated using	14
large subunit	14
cells transfected	14
results suggest	14
rna oligonucleotides	14
poliovirus rna	14
gene copy	14
lys mcm	14
pol i	14
functional analysis	14
coding sequence	14
query sequence	14
lna dna	14
three different	14
reference genomes	14
tagged madp	14
pseudoknot structure	14
exogenous expression	14
trna lys	14
nuclear extracts	14
structure prediction	14
structural element	14
csfv ns	14
dynamic range	14
tl sl	14
hydrogen bonds	14
nt downstream	14
elp mutant	14
pol gene	14
rate constant	14
specific binding	14
type i	14
cdi systems	14
state abundance	14
based assays	14
target gene	14
access publication	14
translation elongation	14
novo initiation	13
long terminal	13
ribosome frameshifting	13
amplification products	13
fhv rna	13
phylogenetic analysis	13
termination codons	13
sequence comparison	13
recoding signals	13
mm imidazole	13
final intensity	13
quantitative pcr	13
molecular weight	13
structural studies	13
dna viruses	13
frameshift inducing	13
significant differences	13
true positives	13
independent experiments	13
zika virus	13
predicted stem	13
purified using	13
translocational ribosome	13
target cells	13
reporter plasmid	13
may play	13
deep sequencing	13
dimer formation	13
biotechnology information	13
lung cancer	13
new england	13
complete genome	13
human cd	13
analyzed using	13
mrna secondary	13
rna template	13
trna leu	13
capture probe	13
relaxation dispersion	13
target sequence	13
simplex virus	13
pathway ii	13
proteins encoded	13
attenuation structure	13
target cell	13
publication charges	13
total number	13
type pk	13
reaction mixture	13
site codon	13
mm tcep	13
herpes simplex	13
high affinity	13
antisense activity	13
luciferase expression	13
binding proteins	13
panhandle structure	13
santa cruz	13
mhc class	13
quadruplex structure	13
ese site	12
decoding center	12
binding scores	12
genome annotation	12
yeast saccharomyces	12
ifn production	12
thank dr	12
pred balb	12
also used	12
dna amplification	12
cut site	12
uniformly labeled	12
life technologies	12
pcr reaction	12
primers used	12
theophylline aptamer	12
host cells	12
mrna pseudoknot	12
final assay	12
refseq records	12
virus genomes	12
phenol chloroform	12
sliding window	12
acting rna	12
full length	12
associated proteins	12
frameshifting rna	12
trigger ifn	12
supplementary tables	12
highly similar	12
inhibitory activity	12
terminal repeat	12
nsp nsp	12
specific conjugate	12
fidelity modulation	12
template switching	12
control sequence	12
class ii	12
wobble position	12
rna metabolism	12
protein expression	12
ribosomes stalled	12
gfp minigenome	12
terminal residues	12
protein complexes	12
protein family	12
rna sample	12
nmr studies	12
viral infections	12
ribosomal subunit	12
compare lanes	12
elongation cycle	12
type levels	12
viral species	12
binding buffer	12
prf occurs	12
sox targeting	12
rna genomes	12
cpv vp	12
terminal edge	12
nuclear antigen	12
frameshift efficiencies	12
treated cells	12
cell leukemia	12
also supplementary	12
degradometer software	12
plant viruses	12
induced frameshifting	12
untranslated regions	12
sl sl	12
slippery codon	12
naturally occurring	12
rate constants	12
site conservation	12
virus infection	12
reporter assay	12
rna stem	12
viral protein	12
trna movement	11
site rna	11
stimulatory structure	11
polymerase iii	11
viral rdrp	11
sequence records	11
compressed sensing	11
rich sequences	11
high sensitivity	11
amplification using	11
frame control	11
vitro translation	11
structured rna	11
allowed us	11
normalized chi	11
highly efficient	11
cpv capsid	11
comparative analysis	11
dna fragment	11
downstream structure	11
trna gly	11
mechanical stability	11
lna modifications	11
positive rate	11
hcv replication	11
stimulatory element	11
aa mutant	11
antiviral therapy	11
ibv pseudoknot	11
will also	11
infectious diseases	11
superfamily genes	11
programmed frameshifting	11
extension activity	11
rna substrate	11
flow cytometry	11
dependent manner	11
structure may	11
regulatory elements	11
genome sequencing	11
least three	11
vero cells	11
site closure	11
translational termination	11
mouse hepatitis	11
antiviral sirnas	11
rna modification	11
nonstructural protein	11
results show	11
cell growth	11
observations suggest	11
located within	11
trna accommodation	11
terminal part	11
trna species	11
rdrp interface	11
life sciences	11
recent years	11
complementary sequences	11
protein interaction	11
domain proteins	11
sarcoma virus	11
two separate	11
mcm side	11
coronavirus infectious	11
dna molecules	11
uga stop	11
viral rnas	11
nonspecific amplification	11
partially double	11
wobble uridine	11
molecular interactions	11
analysis using	11
three independent	11
switch hairpin	11
prf efficiency	11
activate ifn	11
england biolabs	10
target sequences	10
viral sequence	10
direct rna	10
recent study	10
ribosomal rnas	10
trna phe	10
increasing amounts	10
positive events	10
recoded genes	10
quadruplex formation	10
limited number	10
rna element	10
reporter mrna	10
structural protein	10
hairpin rna	10
pseudoknot structures	10
conserved among	10
neuronal cell	10
sequence motif	10
complete genomes	10
perkin elmer	10
much higher	10
technical errors	10
antiviral mirnas	10
rna sequencing	10
mechanical explanation	10
loaded onto	10
biological replicates	10
type pseudoknot	10
loop region	10
cell surface	10
cultured cells	10
frameshift sequence	10
fold increase	10
end labeled	10
digital pcr	10
unmodified sirna	10
transcription elongation	10
reaction conditions	10
measured using	10
mouse model	10
containing trna	10
genome analysis	10
gene products	10
type cells	10
helix destabilization	10
chop genes	10
loop structures	10
reporter plasmids	10
also shown	10
rna helices	10
relative copy	10
proteins involved	10
data show	10
cancer cells	10
using either	10
internal loop	10
less efficient	10
input set	10
critical role	10
regulatory sequences	10
determined using	10
dna structures	10
relative expression	10
snp genotyping	10
thermo scientific	10
sodium dodecyl	10
ribosome aligning	10
rna profiles	10
moloney murine	10
error bars	10
efficient frameshifting	10
rna structural	10
capture probes	10
mrna destabilizing	10
chemical shift	10
public health	10
rdrp core	10
rrna transcript	10
conventional primers	10
pseudoknot stem	10
translation reactions	10
morpholino oligomers	10
viral processes	10
denaturation temperature	10
nucleotide polymorphisms	10
nmr experiments	10
labeled samples	10
two rna	10
drug discovery	10
exosome containing	10
pcr analysis	10
tertiary structures	10
endonucleolytic cleavage	10
annotation pipeline	10
control sample	10
acid sequences	10
bicistronic reporter	10
inhibitor cocktail	10
rna sequences	10
growth factor	10
translation termination	10
hhge per	10
polyacrylamide gels	10
pseudoknot function	10
dna oligonucleotides	10
rt efficiency	10
bacterial lineages	10
range rna	10
loop sequence	10
magnetic particles	10
phylogenetic tree	10
bulk reactions	10
coronavirus hku	10
dna mix	10
first base	10
high level	10
rna targets	10
modification deficiency	10
experimental data	10
studies using	10
mrna pseudoknots	10
structurally aligned	10
mature peptide	10
reaction buffer	10
cell proliferation	10
distance rna	10
distantly related	10
new insights	10
melting temperature	10
sequence retrieval	10
reticulum stress	10
trna binding	10
sequence composition	9
large rnas	9
structure similarity	9
replication protein	9
rabbit reticulocyte	9
target molecules	9
short hairpin	9
rrna decay	9
different levels	9
subunit genes	9
decoding rules	9
upstream regions	9
cognate codons	9
protein structure	9
bars represent	9
innate immune	9
silencing activity	9
hairpin structure	9
reverse genetics	9
drug resistance	9
oxford nanopore	9
target engagement	9
expressing cells	9
frame codons	9
codon context	9
like structures	9
vivo studies	9
ucc uga	9
may lead	9
ethidium bromide	9
rna duplex	9
sequence databases	9
dna sample	9
proteolytic processing	9
acid binding	9
host factors	9
flock house	9
dex xxy	9
comparative genomics	9
mirna constructs	9
true positive	9
restriction sites	9
chemical probe	9
dna repair	9
protein coding	9
creb atf	9
stimulatory rnas	9
ii transcription	9
signal peptide	9
clef fold	9
pcr using	9
cellular stress	9
protein complex	9
sk snrnp	9
gel filtration	9
stimulatory signal	9
immediately downstream	9
bip promoter	9
transcription factors	9
melting curves	9
gov genome	9
mcf cells	9
frameshift event	9
terminal transferase	9
rna molecules	9
transcriptional regulation	9
medium containing	9
frame aa	9
search interface	9
house virus	9
sirna sequences	9
lna substitutions	9
ebov minigenome	9
pestivirus ns	9
rna folding	9
phosphate group	9
rna sequence	9
pol frameshift	9
sense end	9
recombination junction	9
transcriptional slippage	9
viral dna	9
low abundance	9
myotonic dystrophy	9
coli strain	9
nidovirus helicase	9
cleavage products	9
mm theophylline	9
ternary complex	9
dna substrate	9
coronavirus nsp	9
sequence identity	9
residues within	9
rous sarcoma	9
dna motifs	9
strand annealing	9
uuu uua	9
immunity protein	9
mouth disease	9
rna fragments	9
biologically active	9
time dlamp	9
like module	9
frame stop	9
rna motifs	9
standard deviations	9
data analysis	9
nonstructural proteins	9
sulfolobus solfataricus	9
insertion sequence	9
ornithine decarboxylase	9
rna cleavage	9
previously published	9
computational analysis	9
theophylline treatment	9
ribosome biogenesis	9
frameshifting ribosomal	9
nuclear ribonucleoprotein	9
reference gene	9
molecular mechanisms	9
increased frameshifting	9
entry tunnel	9
gene pages	9
recombinant protein	9
metabolic pathways	9
broad range	9
type ii	9
ebov trailer	9
subgenomic rna	9
dnax gene	9
promoter region	9
standard deviation	9
hel domains	9
correct stoichiometric	9
recoding site	9
first nucleotide	9
virus ns	9
shift assay	9
probing analysis	9
frameshifting efficiencies	9
ntp entry	9
rna helicase	9
fetal bovine	9
metadata terms	9
trna selection	9
extended duplex	8
number variation	8
based detection	8
mm nh	8
dna oligonucleotide	8
mrna abundance	8
rs interaction	8
programmed frameshift	8
response element	8
data support	8
using two	8
associated coronavirus	8
total rnas	8
protease inhibitors	8
imino proton	8
previous observations	8
well conserved	8
typhoon fla	8
structural analysis	8
hash function	8
sequence elements	8
minor groove	8
tar rna	8
retrieved sequences	8
web server	8
diarrhea virus	8
highly variable	8
uaa stop	8
oxygen species	8
may affect	8
multivalent ligands	8
nef coding	8
disulfide bond	8
human telomerase	8
prf signals	8
shows little	8
helix substrate	8
denaturing polyacrylamide	8
stoichiometric ratios	8
steady state	8
degradation products	8
genbank accession	8
disease virus	8
minigene construct	8
associated herpesvirus	8
kcl mm	8
sample preparation	8
investigate whether	8
cuug pk	8
previously shown	8
polynucleotide kinase	8
input sequences	8
potential therapeutic	8
computational binding	8
closing base	8
myc promoter	8
fold change	8
living cells	8
coat protein	8
deacylated trna	8
binding specificity	8
human diseases	8
isolation source	8
receptor subunit	8
respiratory syncytial	8
alanine substitution	8
fluorescence intensity	8
two copies	8
error rates	8
sequence read	8
viral refseq	8
previously observed	8
plasmid dna	8
template sequence	8
quantitative chip	8
mm sodium	8
frameshifted product	8
much lower	8
capsid protein	8
mechanical unfolding	8
high throughput	8
fluorescent protein	8
min sketch	8
splicing regulatory	8
solfataricus dnag	8
given sequence	8
transferase activity	8
molecular dynamics	8
potential role	8
examine whether	8
cdna library	8
spacer region	8
essential role	8
close proximity	8
hek cells	8
esterified methyl	8
hj secondary	8
protein families	8
ebna mrna	8
frameshift sites	8
physicochemical properties	8
mediated mrna	8
structural information	8
sequence classification	8
biologically relevant	8
messenger rnas	8
point mutation	8
plant virus	8
exonuclease activity	8
viral particles	8
two independent	8
telomerase inhibition	8
present study	8
heterogeneous nuclear	8
uridine modifications	8
higher level	8
translation products	8
standard error	8
amersham biosciences	8
polymerase structure	8
genome browser	8
third stem	8
triplex structures	8
oligonucleotide primers	8
viral infectivity	8
telomeric dna	8
high concentrations	8
inner capsids	8
sox cleavage	8
also provides	8
transcriptional activation	8
regulate gene	8
minimal ibv	8
ethanol precipitation	8
syncytial virus	8
hash values	8
terminal amino	8
modification deficient	8
dsrna viruses	8
sindbis virus	8
transposable elements	8
nonsense suppression	8
using standard	8
dependent transcription	8
mrna splicing	8
probabilistic data	8
data collection	8
reporter gene	8
second pmo	8
parp catalytic	8
immune evasion	8
conformational changes	8
recently developed	8
signal intensity	8
specific rna	8
identical sequences	8
significant decrease	8
tris ph	8
real time	8
authors thank	8
dataset containing	8
rna helicases	8
hairpin rnas	8
fold higher	8
genome viruses	8
defective genomes	8
multiple alignments	8
openarray tm	8
cov rna	8
blast search	8
enzymatic mutation	8
single stranded	8
rna interaction	8
japanese encephalitis	8
genetic diversity	8
hcv ns	8
noesy walk	8
target dna	8
transcription termination	8
predicted structure	8
two mutants	8
reactive oxygen	8
vitro transcribed	8
rules enriches	8
budding yeast	8
destabilizing elements	8
dpo system	8
molar ratio	8
previous work	8
much larger	8
wobble nucleoside	8
two major	8
illumina results	8
coronavirus rna	8
sample set	8
helix substrates	8
promote efficient	8
specific target	8
complementary oligonucleotides	8
kissing interactions	8
frameshifting frequency	8
frameshifting activity	8
sequence comparisons	8
cov pseudoknot	8
capillary electrophoresis	8
stem loop	8
results obtained	8
bioinformatics resource	8
genome segments	8
structural rearrangements	8
plasmodium falciparum	8
rdrp palm	8
duplex dna	8
two trnas	8
single copy	8
cell epitopes	8
metagenomic data	8
rotavirus nsp	8
cancer cell	8
antiviral agents	8
two genes	8
new data	8
home page	8
genomic sequences	8
antiviral mirna	8
peak heights	8
little correlation	8
primer pairs	8
also tested	8
culture supernatant	8
coronavirus genomes	8
primer set	8
time course	8
sirna duplex	8
beet western	8
high error	8
data types	8
recombination event	8
stem length	8
simian retrovirus	8
specific conjugates	7
integrated dna	7
stimulatory signals	7
luciferase reporters	7
batch sequence	7
rich sequence	7
rt codon	7
solution containing	7
programmed cell	7
gibbs free	7
labeled poly	7
highly associated	7
ncbi taxonomy	7
quadruplex nucleic	7
mammalian riboswitch	7
viral diarrhea	7
imagequant software	7
exclusion chromatography	7
enzymatic activities	7
heptameric patterns	7
chloroform extraction	7
randomized nrmegs	7
refseq genome	7
significant difference	7
reading phase	7
analysis tools	7
induce ifn	7
arg codon	7
ensure synthesis	7
may occur	7
first time	7
hydrogen peroxide	7
using rna	7
yeast ribosomal	7
small number	7
eukaryotic ribosome	7
heat shock	7
replicase gene	7
target specificity	7
previously identified	7
events occurring	7
nucleotide substitutions	7
elongation complex	7
gene regulation	7
two sets	7
hairpin stem	7
selenocysteine insertion	7
medicinal chemistry	7
large rna	7
er stress	7
aptamer stem	7
modified peptides	7
luciferase assays	7
cdna synthesis	7
nucleotide position	7
middle east	7
binding domains	7
mcm ucu	7
gene sequences	7
functional role	7
new segment	7
mrna degradation	7
forming sequence	7
trna gln	7
histocompatibility complex	7
rna bands	7
frameshift assay	7
potential target	7
data mining	7
host shutoff	7
likely due	7
frameshift assays	7
superfamily neighborhoods	7
rna hairpin	7
min incubation	7
dna sequence	7
sequence profile	7
different strains	7
sequence datasets	7
among different	7
hyperosmotic shock	7
ncl binding	7
taxonomic classification	7
frameshifting site	7
expression vectors	7
similar results	7
protein database	7
mrna structure	7
shrna expression	7
coding genes	7
agarose gels	7
freely available	7
reporter assays	7
minion sequencing	7
rt site	7
mdx mouse	7
virus genomic	7
translation system	7
human breast	7
sequencing efforts	7
predicted free	7
chemical shifts	7
results indicated	7
luciferase genes	7
genome neighbor	7
alternative reading	7
phase ii	7
vast majority	7
pcr reactions	7
human genes	7
efficient coronavirus	7
structure maps	7
detection capture	7
rna domain	7
see materials	7
primary screening	7
experimentally validated	7
immune system	7
highly divergent	7
ribosylate phosphorylated	7
detection method	7
comparative sequence	7
accession number	7
frameshifter rna	7
accession numbers	7
human disease	7
independent manner	7
expressing wild	7
frameshift stimulation	7
expression level	7
control construct	7
stranded nucleic	7
unpublished data	7
higher affinity	7
sample buffer	7
downstream stimulatory	7
seed length	7
target rna	7
fever virus	7
stem formation	7
linear relationship	7
scientific community	7
grown overnight	7
cellular toxicity	7
eukaryotic mrna	7
widely used	7
pseudoknot required	7
dna templates	7
different positions	7
growth inhibition	7
mutant sirt	7
coli dnax	7
known binding	7
search page	7
primer design	7
kinase activity	7
uag stop	7
enriches gene	7
rt stop	7
binding assays	7
nuclear magnetic	7
specific amplicons	7
results demonstrate	7
nucleotide polymorphism	7
similar pattern	7
conjugates containing	7
sequence diversity	7
terminal residue	7
rna oligonucleotide	7
containing archaea	7
restriction enzyme	7
start codon	7
methyl group	7
structural elements	7
protein kinase	7
ortholog group	7
bacterial toxin	7
two complementary	7
ebov genome	7
reporter genes	7
rna aptamer	7
hela cells	7
human coronavirus	7
specific detection	7
final extension	7
antimicrobial peptides	7
dna microarrays	7
sars pseudoknot	7
ctd phosphorylation	7
conformational change	7
coronaviruses ensure	7
cellular gene	7
stimulating pseudoknot	7
universal hash	7
murine cytomegalovirus	7
dna polymerases	7
rrna processing	7
type rna	7
culture cells	7
dna complex	7
exonic splicing	7
apoptotic stimuli	7
estimated using	7
structure analysis	7
cellular protein	7
group coronaviruses	7
aligned sequences	7
significant amount	7
mrna sequences	7
positively charged	7
page gel	7
crick base	7
sensing matrix	7
toxin proteins	7
unwinding activity	7
based multiplex	7
frameshift protein	7
tagged proteins	7
dna aptamers	7
respiratory viruses	7
type rpl	7
mcm group	7
cancer samples	7
pluc cells	7
sequences based	7
like structure	7
magnetic resonance	7
luc vector	7
read archive	7
final volume	7
translational control	7
spectral crowding	7
read segment	7
sequence motifs	7
metal ions	7
sequence containment	7
skipping activity	7
gtp hydrolysis	7
gag gag	7
bacterial genomes	7
occupancy status	7
fluorescence reporter	7
direct sequencing	7
circular dichroism	7
different groups	7
dystrophin expression	7
conserved motif	7
replication initiation	7
therapeutic applications	7
noesy spectra	7
unique domain	7
recent studies	7
ebna synthesis	7
dnase i	7
rho cells	7
upper panel	7
sepharose beads	7
bovine viral	7
immediately upstream	7
least two	7
time point	7
acuucc pk	7
transcription initiation	7
site selection	7
rin system	7
efficient frameshift	7
hydroxyl acylation	7
arg mcm	7
lesser extent	7
animal models	7
using primers	7
promoter regions	7
yeast gene	7
remaining nucleotides	7
database search	7
quantitative analysis	7
potentially form	7
viral communities	7
translating ribosomes	7
nanopore sequencing	7
lower aptamer	7
manually curated	7
base pairings	7
cognate trnas	7
better understand	7
golden mean	7
rna extraction	7
dnag proteins	7
possible role	7
supt cells	7
using lipofectamine	7
green fluorescent	7
expression system	7
increased expression	7
reversible adp	7
loading buffer	7
final sirna	7
containing exosome	7
yeast apoptosis	7
may provide	7
rna stability	7
sox protein	7
well annotated	7
specific recognition	7
dependent polymerases	7
dpo primer	7
wt ltr	7
eukaryotic systems	7
different types	7
expression profiling	7
among rna	7
fold lower	7
healthcare life	7
rna fragmentation	7
east respiratory	7
complete loss	7
core region	7
competent cells	7
rna pull	7
ethanol precipitated	7
phosphorylated ssrna	7
sequence using	6
guide strand	6
gene page	6
expression analysis	6
novel rna	6
frameshifting signals	6
dependent activation	6
dendritic cells	6
length protein	6
organism category	6
annealed aon	6
predictive value	6
frameshifting programmed	6
ncbi viral	6
heptanucleotide sequence	6
master mix	6
frameshift motif	6
sirnas targeting	6
lung tissue	6
data bank	6
rna probe	6
deletion mutant	6
ectopic expression	6
mb ccc	6
kindly provided	6
technical assistance	6
mobile genes	6
readthrough protein	6
ncbi reference	6
regulatory roles	6
chemical probing	6
sequence homology	6
virus life	6
structural changes	6
constructed using	6
pol expression	6
translational accuracy	6
ring finger	6
well plate	6
chlamydia trachomatis	6
sense primer	6
associated factor	6
nucleotide resolution	6
ribosomal movement	6
may form	6
cd expression	6
diploid copy	6
cells grown	6
rb repeats	6
amplification event	6
initiation site	6
structures may	6
oxidative agents	6
base triples	6
enzymatic activity	6
genetic decoding	6
processed using	6
obtained using	6
analysis software	6
dpo primers	6
digital arrays	6
breast cancers	6
minion nanopore	6
codon recognition	6
long reads	6
using hrm	6
also noted	6
allele allele	6
heteropolymeric tail	6
variable mode	6
fold less	6
short interfering	6
conserved structure	6
chemical exchange	6
nar gkm	6
nar gkq	6
specific probe	6
cell nucleus	6
reference databases	6
click chemistry	6
first strand	6
duplex unwinding	6
complete set	6
sufu superfamily	6
query time	6
multiplex detection	6
cov genome	6
increased affinity	6
catalytically inactive	6
rdrp fidelity	6
nascent peptide	6
targeting hiv	6
cdk activity	6
mature mirna	6
genomic rnas	6
rna tertiary	6
genbank records	6
quality metrics	6
assays using	6
rtsl ld	6
expression plasmid	6
located upstream	6
data obtained	6
quality assessment	6
parp fl	6
antigen presentation	6
analysis resource	6
western yellows	6
may contribute	6
hairpin constructs	6
annealing temperature	6
binding channel	6
yeast trna	6
calf serum	6
hairpin construct	6
luciferase activities	6
using imagequant	6
rna decay	6
novo synthesis	6
asf expression	6
hairpin structures	6
bacterial species	6
primary determinant	6
possible explanation	6
molar excess	6
like activity	6
gkm sha	6
structure downstream	6
dna helicase	6
major histocompatibility	6
analysis indicated	6
salt buffer	6
reporter mrnas	6
modified wobble	6
relatively small	6
metagenomic sequence	6
also includes	6
molecular replacement	6
buffer mm	6
redundant sequence	6
transcribed using	6
rdrp intra	6
much smaller	6
mature peptides	6
terminal end	6
wt sequence	6
rna signals	6
restriction site	6
vol vol	6
cytoplasmic polyhedrosis	6
gkq sha	6
dsrna replication	6
triple helix	6
following conditions	6
relative abundance	6
positive bacteria	6
human cov	6
recoding event	6
arg ccu	6
proviral genome	6
two cis	6
provide new	6
signaling pathway	6
polycistronic transcript	6
wide variety	6
coronavirus sequences	6
mer product	6
lna modification	6
certain cases	6
movement impeded	6
standard decoding	6
leader panhandle	6
washed twice	6
ie heptameric	6
aaa aag	6
cognate aminoacyl	6
helical domain	6
complementary rna	6
ii occupancy	6
rna dna	6
gaaa tetraloop	6
recently reported	6
drug development	6
background dna	6
pcr assays	6
bd biosciences	6
edta ph	6
mrna synthesis	6
unless otherwise	6
bp stem	6
minigenome assay	6
metabolic pathway	6
well characterized	6
viral macrodomains	6
glu mcm	6
standardized metadata	6
see table	6
human embryonic	6
genome rna	6
mutation detection	6
mirna polycistron	6
structural insights	6
protein data	6
studying recoding	6
profile comparisons	6
bacterial insertion	6
drosophila melanogaster	6
containing reporter	6
peptides binding	6
sirna expression	6
superfamily gene	6
hairpin formation	6
metagenomic sequencing	6
mutant sequences	6
stimulate frameshifting	6
led us	6
quadruplex ligand	6
reporter constructs	6
kcal mole	6
snrnp complex	6
important target	6
may represent	6
binding properties	6
incubated overnight	6
regulatory protein	6
sg mrnas	6
alkaline hydrolysis	6
positions along	6
radiolabeled rna	6
illumina sequencing	6
biotinylated rna	6
pk mutant	6
triple residue	6
mbp alone	6
sequence inversion	6
targeting rna	6
hnh domains	6
frameshift stimulators	6
ncm group	6
gold nanoparticles	6
magnetic particle	6
sequencing errors	6
pseudoknots promote	6
human tissues	6
profile searches	6
also performed	6
mm pmsf	6
coding gap	6
less archaea	6
patterns clusters	6
based approach	6
predicted rna	6
family reoviridae	6
gene neighborhoods	6
fhv genome	6
comparative study	6
sequences containing	6
cellular rna	6
relatively high	6
protein annotation	6
sigma aldrich	6
hash table	6
coronavirus infection	6
rna strand	6
evolutionarily conserved	6
rna transcripts	6
selective amplification	6
gly mcm	6
tumor growth	6
available online	6
applied science	6
sequence variation	6
ibv infection	6
native polyacrylamide	6
structural similarity	6
viral life	6
polyamine levels	6
media containing	6
coding rnas	6
lys codon	6
mammalian antizyme	6
sequence search	6
higher concentrations	6
trna glu	6
parp cat	6
whether vp	6
frameshifting characterization	6
virus polymerase	6
containing mg	6
rna modifications	6
cell lysate	6
per cell	6
accessed march	6
red lines	6
hnh fold	6
dystrophin restoration	6
specific primers	6
also present	6
site specificity	6
frameshift errors	6
systematic analysis	6
direct evidence	6
cellular proteins	6
sequences within	6
function relationships	6
containing complex	6
functional genomic	6
negatively charged	6
efficient programmed	6
isotopically labeled	6
nt upstream	6
chromatin condensation	6
two distinct	6
virus gag	6
increase efficiency	6
search results	6
molecules targeting	6
dodecyl sulfate	6
acid chaperone	6
chip assays	6
functional importance	6
pcr step	6
cdi toxins	6
max rate	6
encoded rna	6
roche applied	6
expressing flag	6
semliki forest	6
stability assays	6
nuclear protein	6
differential melting	6
modification systems	6
complex containing	6
structural data	6
codon redefinition	6
purified ncl	6
hiv infection	6
test codons	6
also show	6
site predictions	6
antisense primer	6
xxz zzn	6
atp utp	6
stimulating rna	6
genome structural	6
kinetic pathways	6
dystrophy type	6
cellular components	6
raw data	6
roc curves	6
genomic sequence	6
like protease	6
rnp complex	6
data type	6
pyrimidine nucleotides	6
serum albumin	6
randomly chosen	6
spacing distances	6
hydrogen bonding	6
culture medium	6
pseudoknot enhance	6
mrna entrance	6
functional genomics	6
dna synthesis	6
fold wild	6
truncated form	6
ml reaction	6
rease fold	6
type samples	6
enhance mechanical	6
represent means	6
metagenomic samples	6
human herpesvirus	6
ray diffraction	6
read sequencing	6
electrophoretic mobility	6
mm mn	6
see http	6
signal processing	6
ssrna cy	6
gene encoding	6
serial passage	6
mutagenesis kit	6
mrna tension	6
standard rna	6
gene family	6
overall thermodynamic	6
central role	6
starting template	6
site may	6
family members	6
test construct	6
degradation assays	6
reaction containing	6
free water	6
type ribosomes	6
recognition motif	6
illumina miseq	6
stable rna	6
mrna fragments	6
sequence divergence	6
coli cells	6
viral lifecycle	6
embedded within	6
mcm ucc	6
pol ratio	6
one nucleotide	6
induce ribosomal	6
cell cultures	6
mer peptides	6
endogenous xbp	6
structural variation	6
sequenced genomes	6
throughput sequencing	6
marburg virus	6
consensus sequence	6
ascorbic acid	6
high accuracy	6
cypb expression	6
hill coefficient	6
large ribosomal	6
acting signals	6
conditions tested	6
human telomeric	6
signal peptides	6
significantly reduced	6
structurally similar	6
rna recognition	6
stralsv algorithm	6
nt fragment	6
rnase inhibitor	6
detected using	6
replication complex	6
ribosomal subunits	6
capsid proteins	6
immune responses	6
primary sequence	6
direct role	6
rrm domain	6
using real	6
yet another	6
translational fidelity	6
hiv inhibiting	6
oligonucleotide probes	6
mrna channel	6
spaced seeds	6
stimulatory effect	6
done using	6
hnh endovii	6
transfected ft	6
several viruses	6
signal transduction	6
parp family	6
flavivirus ns	6
recombination junctions	6
abi prism	6
growth kinetics	6
missense errors	6
structural probing	6
polyhedrosis virus	6
regulatory role	6
high efficiency	6
mrna structures	6
surface proteins	6
extraction kit	5
nmd pathway	5
highly structured	5
yeast strains	5
default parameters	5
human genomic	5
mutually exclusive	5
hel domain	5
trna anticodon	5
optimal fidelity	5
sars virus	5
assay time	5
dna ends	5
noncoding rna	5
amplification reactions	5
annealing temperatures	5
cellular processes	5
structural polyprotein	5
like protein	5
bulk reaction	5
previously characterized	5
menu bar	5
leader interaction	5
control samples	5
rdrp attenuation	5
canonical base	5
ifn response	5
three samples	5
bip promoters	5
also showed	5
located downstream	5
polynucleotide phosphorylase	5
genotyping pcr	5
free ld	5
ribosylate rna	5
mediated antiviral	5
yellow dwarf	5
quantitative proteomics	5
specific amplificaiton	5
frameshift motifs	5
global architecture	5
different species	5
genome records	5
environmental conditions	5
long read	5
reactions containing	5
theophylline binding	5
vector using	5
mean fluorescence	5
ntd deletion	5
known examples	5
type sample	5
wt rtsl	5
codon ccc	5
probe sets	5
loop mutants	5
current study	5
comprehensive database	5
cells infected	5
either wild	5
flow cytometer	5
mutation screening	5
activates transcription	5
reactivity data	5
intrinsically disordered	5
analysis showed	5
sequences upstream	5
rt efficiencies	5
leu uag	5
loop rna	5
model system	5
targeting sirna	5
filter parameter	5
relatively low	5
viral escape	5
maximum number	5
fusion proteins	5
replicase proteins	5
per chip	5
ty assay	5
identify novel	5
enhanced conservation	5
purified human	5
specific reactions	5
interacting proteins	5
uga codons	5
conformation change	5
stop product	5
na hpo	5
erbb amplification	5
noise ratio	5
misincorporation assays	5
quadruplex ligands	5
protein partners	5
ribosomal helicase	5
frameshifting pseudoknots	5
rich rna	5
i molecules	5
zinc ions	5
well represented	5
mediates rna	5
gene function	5
chemically synthesized	5
good agreement	5
tagged sirt	5
nacl concentration	5
resolution structures	5
plasma cell	5
gkr sha	5
foster city	5
phosphorylated rna	5
using dna	5
database issue	5
hidden markov	5
inducing frameshifting	5
time melting	5
chemical cross	5
pseudoknots involved	5
synthesized viral	5
ms analysis	5
yeast promoters	5
pulse sequences	5
mrna destabilization	5
classical swine	5
enzymatic synthesis	5
degradation factor	5
new twist	5
yeast cell	5
translational reading	5
infectious disease	5
rna probes	5
viral discovery	5
primer sets	5
high conservation	5
family proteins	5
gel mobility	5
mm iptg	5
conserved rna	5
highly expressed	5
oncogene promoters	5
supplementary material	5
ibv pk	5
slippage model	5
drug design	5
neu oncogene	5
wash buffer	5
based design	5
scalar couplings	5
high resolution	5
trna pyl	5
future studies	5
gamma subunit	5
neural network	5
regions within	5
viral growth	5
dmem supplemented	5
conventional primer	5
gks sha	5
sense rna	5
microarray analysis	5
different lengths	5
assay development	5
protein levels	5
mrna target	5
th percentile	5
peptide sequence	5
wt ns	5
labeled rnas	5
active mechanisms	5
type sars	5
based system	5
transactivation domain	5
fluorescent signal	5
expected number	5
interaction involving	5
different mechanisms	5
similarity search	5
myostatin pathway	5
expressing rpl	5
lower case	5
subcellular localization	5
primers listed	5
common feature	5
different regions	5
genomes project	5
chronological ageing	5
hyperosmotic stress	5
gel purified	5
agarose beads	5
ibv frameshift	5
endpoint detection	5
american type	5
two positions	5
different functions	5
several bacteria	5
sco kpta	5
time quantitative	5
vrna replication	5
poorly understood	5
random projection	5
sequence context	5
wt construct	5
opposite effect	5
synthesis using	5
functional significance	5
agilent technologies	5
protein production	5
genomes using	5
mammalian gene	5
structurally conserved	5
directly adjacent	5
plasmids containing	5
immunoprecipitated complexes	5
hash value	5
viral gene	5
genomes resource	5
low level	5
independent translation	5
latter case	5
transduced cells	5
kshv sox	5
atf family	5
open conformation	5
conserved gene	5
equal volume	5
approach using	5
rna tails	5
morpholino oligomer	5
diffraction data	5
simultaneous detection	5
computational approaches	5
past decade	5
frameshifting motif	5
enrichment analyses	5
antiviral effect	5
expression plasmids	5
solid red	5
catalytic efficiency	5
sparse recovery	5
tomato bushy	5
biotinylated beads	5
bacillus subtilis	5
min time	5
vivo applications	5
antiviral effects	5
bond formation	5
cardinality estimation	5
superfamily helicase	5
virus module	5
protein factors	5
mrna translation	5
elongating ribosome	5
fidelity level	5
rtsl binding	5
ribosome function	5
forming oligonucleotides	5
complete viral	5
small fraction	5
respiratory tract	5
cascading bloom	5
stunt virus	5
check boxes	5
ribosylation mediated	5
mrna steady	5
different protein	5
using molecular	5
sirt mediates	5
sf helicases	5
virema will	5
positive chambers	5
ribosome moves	5
sequence bloom	5
storage buffer	5
model predicts	5
unique sequences	5
length nsp	5
virus nuclear	5
may explain	5
different human	5
muscle growth	5
cpv dsrna	5
cell membranes	5
critical reading	5
arterivirus helicase	5
fold increases	5
protein samples	5
anticodon interactions	5
one codon	5
containing reads	5
conserved protein	5
significantly higher	5
dna sequences	5
sequence variability	5
eukaryotic pathogen	5
clinically relevant	5
type culture	5
tumor cells	5
synthesis activities	5
previous study	5
low levels	5
lower panel	5
assay performance	5
imino protons	5
single molecule	5
frameshift events	5
based alignment	5
ec numbers	5
maximal frameshifting	5
complete medium	5
genome capture	5
control sequences	5
downstream mrna	5
specific background	5
transcriptional regulatory	5
eukaryotic rna	5
first identified	5
multiple copies	5
loop size	5
pfam database	5
phosphorylated ends	5
kda polypeptide	5
strongly suggests	5
asymmetric unit	5
form stable	5
well defined	5
restriction endonuclease	5
intact rna	5
different time	5
sequences may	5
first position	5
analyses revealed	5
nearest neighbor	5
gkl sha	5
target recognition	5
total frameshift	5
nuca family	5
transfection reagent	5
binding activities	5
strongly suggest	5
capsid shell	5
somatic mutations	5
translocation step	5
functional sirnas	5
viruses including	5
mutants defective	5
rna targeting	5
conformational switch	5
nuclear extract	5
spacer lengths	5
nar gku	5
probes will	5
cell pellets	5
negative controls	5
pairwise sequence	5
phylogenetically conserved	5
nmr methods	5
regeneration system	5
bvdv ns	5
terminal sequence	5
viral structural	5
days post	5
virus strain	5
nmr relaxation	5
specific priming	5
mrna sequence	5
two species	5
box binding	5
pathogen detection	5
entrance channel	5
efficient rt	5
rna ends	5
genomic data	5
sequencing datasets	5
elution fraction	5
one base	5
continue translation	5
novel coronavirus	5
experimental studies	5
bacterial genes	5
newly developed	5
vitro experiments	5
two active	5
caenorhabditis elegans	5
acylation analyzed	5
important roles	5
skeletal muscle	5
virus identification	5
evidence suggests	5
complementary nucleic	5
experimentally tested	5
gku sha	5
residue mutant	5
murine coronavirus	5
swine fever	5
result showed	5
nt antiviral	5
cel i	5
uses two	5
kda nsp	5
cleavage efficiency	5
i transcription	5
small rnas	5
key role	5
mediated rna	5
specific product	5
vienna rna	5
specific manner	5
roc curve	5
mode ttp	5
avian infectious	5
sc complete	5
rna oligo	5
computational tools	5
square statistic	5
expressed genes	5
long conventional	5
also shows	5
rational design	5
mediated regulation	5
primary structure	5
modified nucleosides	5
ribosome pausing	5
cleared lysate	5
human nucleolin	5
quantity one	5
palm domain	5
dodecyl sulphate	5
upstream stop	5
stimulatory elements	5
dna technologies	5
type madp	5
lentiviral transduction	5
increased rates	5
frame codon	5
conserved residue	5
spin systems	5
human cell	5
local thermodynamic	5
heptameric slippery	5
rna biology	5
amplified using	5
terminal nuclease	5
public databases	5