trigram

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trigram	frequency
version posted january	1337
the copyright holder	1337
holder for this	1337
copyright holder for	1337
is the author	1337
the author funder	1337
certified by peer	1328
by peer review	1328
biorxiv preprint https	1291
which was not	1260
was not certified	1259
not certified by	1259
preprintthis version posted	1250
for this preprintthis	1250
this preprintthis version	1250
com b m	988
b m kdl	887
org licenses by	879
granted biorxiv a	877
the preprint in	877
license to display	877
who has granted	877
has granted biorxiv	877
to display the	877
preprint in perpetuity	877
display the preprint	877
a license to	877
biorxiv a license	877
it is made	523
all rights reserved	449
reuse allowed without	448
no reuse allowed	448
allowed without permission	448
made the copyright	435
licenseavailable under a	435
is made the	435
international licenseavailable under	435
available under a	364
it is the	363
is the copyright	355
international licensemade available	355
licensemade available under	355
the number of	307
com b bnwyax	293
com b h	265
b h ctd	265
based on the	119
m kdl qaa	107
kdl qaa http	106
b m zzqk	101
i i i	94
m kdl gtt	92
m o i	92
kdl gtt http	91
m kdl jg	89
as well as	89
kdl jg a	89
made available under	87
is made available	87
for this preprint	87
jg a http	84
which was notthis	78
was notthis version	78
international licensea certified	78
available under the	78
licensea certified by	78
under the copyright	78
notthis version posted	78
kdl lmi h	75
c h ctd	75
com c h	75
m kdl lmi	75
lmi h http	74
m kdl bijvc	71
kdl bijvc http	70
ps ta t	69
m kdl vecw	68
we found that	68
kdl vecw http	67
m kdl ahwg	66
can be used	65
kdl ahwg http	64
in this study	63
each of the	62
according to the	61
we used the	61
one of the	61
the performance of	59
m kdl udus	58
m kdl wfrst	58
kdl udus http	57
see methods section	57
due to the	57
kdl xp y	56
m kdl xp	56
nucleic acids res	56
kdl wfrst http	56
com c bnwyax	56
kdl sj we	54
m kdl sj	54
be used to	54
extended data fig	53
sj we http	52
the distribution of	52
xp y http	52
in order to	51
mammalian methylation array	51
m kdl isag	50
the proportion of	49
in terms of	49
kdl isag http	49
com c m	48
was used to	48
the set of	48
m oc k	47
number of mismatches	47
a set of	47
compared to the	46
the mammalian methylation	46
t re l	45
ta t re	45
expression levels of	45
total number of	44
at least one	43
a total of	43
stat and stat	43
of cell lines	42
h h h	42
the majority of	42
nucleic acids research	42
the accuracy of	41
the scalar curvature	40
the edited cytidine	40
m enrich seq	39
hbv integration sequences	39
with respect to	38
was obtained from	38
are shown in	38
that can be	37
part of the	37
see figure s	36
hbv integration sites	36
dimer bound to	36
for m enrich	35
data was obtained	35
cancer cell lines	35
the sum of	35
genes that are	34
with hbv integration	34
on the other	34
the use of	34
used in the	34
of the cell	34
the total number	33
of gene expression	33
present in the	33
to assess the	33
m kdl vjim	32
in the same	32
kdl vjim http	32
o i ifnl	32
as shown in	32
the other hand	31
the analysis of	31
shown in figure	31
polya selection gse	31
the context of	31
c h o	30
from the same	30
h homo sapiens	30
of the model	30
of the same	30
valid read pairs	30
the fraction of	30
were obtained from	29
were used to	29
which can be	29
for each of	29
in addition to	28
single cell rna	28
structure of the	28
the presence of	28
is used to	28
min ps ta	27
the single cell	27
to evaluate the	27
time min ps	27
the r package	26
single cell data	26
a b c	26
in the human	26
of cell types	26
genes in the	26
the cell type	26
in the context	26
it is not	26
included in the	26
supported by the	26
two technical replicates	26
of the two	26
u rna editing	25
the size of	25
o i m	25
for each cell	25
with each two	25
infected with sars	25
average mutual information	25
with editing frequency	25
can also be	25
analysis of the	25
each two technical	25
c m zzqk	25
the gene expression	24
obtained from the	24
found in the	24
per unit increments	24
precision and recall	24
after stimulation with	24
of the data	24
size of the	24
a list of	23
thiamine c h	23
the case of	23
of the top	23
defined as the	23
we used a	23
to determine the	23
as described in	23
available at https	23
response to chemotherapy	23
c m kdl	23
edwards et al	22
on the same	22
of stat and	22
the expression of	22
the mammalian array	22
the percentage of	22
wide range of	22
the results of	22
at the same	22
was used for	22
gene expression data	22
u mrna editing	22
the image patches	22
i m o	22
mismatches in regulatory	22
in the case	22
galiez et al	22
deephbv with hbv	22
a subset of	22
changes in the	22
performance of the	22
respect to the	22
of the edited	22
was supported by	22
associated with the	22
each cell type	22
b and c	22
tcga pan cancer	22
three biological replicates	21
well as the	21
phage and host	21
m kdl xpakk	21
maximal atu clusters	21
electronic health care	21
of downstream sequence	21
found that the	21
based on a	21
in contrast to	21
health care records	21
the importance of	21
such as the	21
with at least	21
out of the	21
five cancer types	20
an r package	20
r ef s	20
ef s eq	20
m fi time	20
is the number	20
were classified as	20
journal of statistical	20
human and mouse	20
more than one	20
figure s a	20
found to be	20
a wide range	20
consistent with the	20
the development of	20
large number of	20
b c d	20
of a single	20
c l c	20
the fact that	20
kdl xpakk http	19
accuracy of the	19
to be the	19
to estimate the	19
we compared the	19
and can be	19
of statistical software	19
downstream sequence to	19
the impact of	19
of the gene	19
length of the	19
cell lines and	19
supplementary figure s	19
ta t r	19
we show that	19
most of the	19
a and b	19
used in this	19
the quality of	19
t r el	19
a number of	18
storage browser brain	18
scalar curvature of	18
with the highest	18
for a given	18
and the number	18
a range of	18
the structure of	18
to have a	18
shown in the	18
be associated with	18
to the number	18
data from the	18
com storage browser	18
stimulation with il	18
cell type clustering	18
the difference in	18
normalized to maximal	18
the predicted atus	18
drug prescriptions in	18
it can be	18
materials and methods	18
there is a	18
in the first	18
bronchial epithelial cells	18
to account for	18
university of california	18
of cell division	18
depending on the	18
x x x	18
associated with a	17
the cancer type	17
to identify the	17
be found in	17
prescriptions in electronic	17
m fi ps	17
are associated with	17
due to its	17
in electronic health	17
splice altering variants	17
natl acad sci	17
it is possible	17
biorxiv preprint http	17
were downloaded from	17
can be seen	17
fraction of samples	17
there is no	17
we calculated the	17
overlapping cell lines	17
cd t cells	17
number of cells	17
bl et s	17
we note that	17
the scalar curvatures	17
on the mammalian	17
fi ps ta	17
r package for	17
to the same	17
this work was	17
the cell types	17
correspond to the	17
are used to	17
ta bl et	17
com work bibliography	17
s ta t	17
in the final	17
between the two	17
different cell types	17
the utility of	17
resulted in a	17
derived from the	17
fi time min	16
the ensembl annotation	16
of the predicted	16
is available at	16
the human genome	16
used as a	16
the basis of	16
area under the	16
is consistent with	16
bivariate wavelet analysis	16
scalar curvatures computed	16
is given by	16
h ctd n	16
patients with a	16
p a tie	16
that of the	16
two molecules of	16
and rienrich seq	16
image patch dataset	16
induced by il	16
regulatory sequence motif	16
relative to the	16
severe acute respiratory	16
terms of the	16
a large number	16
the role of	16
proceedings of the	16
m g ta	16
then used to	16
is associated with	16
work bibliography http	16
c d e	16
number of reads	16
is shown in	16
so that the	16
of cell type	16
can be found	16
each cell line	16
downloaded from the	16
the length of	16
g ta bl	16
a tie n	16
using the same	16
we did not	16
the expression levels	15
in patients with	15
is based on	15
enrich seq rienrich	15
that are not	15
relationship between the	15
h e a	15
a deep learning	15
backus and smith	15
of editing frequency	15
be due to	15
corresponding to the	15
analysing drug prescriptions	15
is one of	15
by deepmm and	15
c x c	15
splice variant window	15
selection gse sars	15
for the same	15
was performed using	15
use of the	15
a lth y	15
cells infected with	15
a variety of	15
the effect of	15
a stop codon	15
work was supported	15
cancer genome atlas	15
in the other	15
shown in fig	15
in the data	15
the choice of	15
heterotypic and homotypic	15
of the sequence	15
a klein bottle	15
sci u s	15
for which the	15
seq rienrich seq	15
j biol chem	15
deep learning model	15
which is the	15
number of species	15
e a lth	15
acute respiratory syndrome	15
is not a	15
the ability of	15
sum of the	15
and secondary structure	15
number of cell	15
was applied to	15
as a result	15
the debar package	15
school of medicine	15
expression profiles of	15
figure shows the	15
of editing sites	15
latex r e	15
of the most	15
for each sample	15
ensembl and refseq	15
in at least	15
in supplementary table	15
of the human	15
the similarity of	15
u s a	15
acad sci u	15
common essential genes	15
to this end	15
to quantify the	15
overview of the	14
to be associated	14
nsclc cell lines	14
were used for	14
which is a	14
of mismatches for	14
may not be	14
to the most	14
the output of	14
one or more	14
the test set	14
were found to	14
the relationship between	14
cell types in	14
the user can	14
apolipoprotein b mrna	14
for each gene	14
human bronchial epithelial	14
and galiez et	14
of the national	14
r package version	14
vero e cells	14
bound to two	14
the bias rate	14
chen et al	14
different types of	14
the second fundamental	14
in this paper	14
second fundamental form	14
the absence of	14
applied to the	14
similar to the	14
extent to which	14
and triplex motifs	14
differences in the	14
the mooring sequence	14
proc natl acad	14
likely to be	14
shows that the	14
in the training	14
on the basis	14
to two molecules	14
tie n t	14
the decision threshold	14
is defined as	14
the true value	14
and found that	14
a mixture of	14
end of the	14
the training data	14
each pair of	14
indicate that the	14
the most frequently	14
of the variant	13
ra and gp	13
of hbv integration	13
with each other	13
of these genes	13
in the reference	13
gene expression and	13
that have been	13
sample sample sample	13
as ranked by	13
each of these	13
principal component analysis	13
of the number	13
u and v	13
a function of	13
enrich seq and	13
gene expression profile	13
shading corresponds to	13
involved in the	13
version of the	13
the correlation between	13
p r s	13
m kdl m	13
visualization of the	13
as part of	13
the ambient space	13
is set to	13
obtained from three	13
to calculate the	13
corresponds to the	13
so as to	13
genes of the	13
shown to be	13
i ifnl sars	13
to measure the	13
of the four	13
mock mock h	13
replicates with each	13
the end of	13
showed that the	13
respiratory syndrome coronavirus	13
and is also	13
univariate wavelet analysis	13
innate immune responses	13
distribution of the	13
to the rpgg	13
the value of	13
combat qn pc	13
we developed a	13
the ability to	13
biological replicates with	13
columns represent cancer	13
the mathematical models	13
expression level of	13
available for use	13
to predict the	13
l c x	13
h ctd k	13
the two cytokines	13
location of the	13
i i preprint	13
tumor suppressor gene	13
general ccn score	13
that do not	13
ve ro e	13
positive and negative	13
within a given	13
is also made	13
allowed us to	13
tm p r	13
the ground truth	13
node and edge	13
mock mock mock	13
be used as	13
any of the	13
represent cancer types	13
induced by hypil	13
x c l	13
an average of	13
the debar pipeline	13
in figure s	13
gse mock mock	13
bnwyax e ooj	13
to test the	13
r s s	13
of each cell	13
data for the	13
the extent to	13
loci with reads	13
c al u	13
most frequently recurring	13
presence absence data	13
computed scalar curvatures	13
frequently recurring genes	13
cell lines with	13
kdl m hq	13
y stat p	13
when applied to	13
spatial transcriptomics data	13
variation in the	13
to generate a	13
in response to	13
rows correspond to	13
in which the	13
left to right	13
mapped to the	13
t p m	13
and columns represent	13
representation of the	13
directional changes in	12
classification general ccn	12
usc the copyright	12
a vector of	12
cell types and	12
the integrated datasets	12
used to identify	12
in the analysis	12
located in the	12
see figures s	12
on the array	12
the numbers of	12
members of the	12
related to the	12
org content early	12
seq data of	12
bnwyax uh g	12
in the second	12
m fi pstat	12
b a lf	12
the amino acid	12
in the rna	12
made available for	12
also made available	12
mrna editing sites	12
oligonucleotide compositions of	12
is not subject	12
gene expression in	12
the epic array	12
of amino acids	12
used for the	12
s stat p	12
of the sars	12
copyright under usc	12
on perfect matching	12
the formation of	12
mismatches in mooring	12
the capsule network	12
for use under	12
different cancer types	12
general classification general	12
and the other	12
the calculation of	12
global network optimization	12
to copyright under	12
not subject to	12
to investigate the	12
all of the	12
for the original	12
amino acid sequence	12
h t h	12
which could be	12
of the enzyme	12
pearson correlation coefficient	12
favorable interactions with	12
calculated for each	12
available in the	12
of new infections	12
shown as a	12
generated by the	12
half of the	12
a us government	12
activation by il	12
that it is	12
data can be	12
y s stat	12
considered to be	12
use under a	12
we find that	12
is a us	12
the change in	12
a combination of	12
for the analysis	12
bnwyax g buj	12
genes in each	12
have the same	12
base content of	12
cell type proportions	12
cancer cell line	12
attention intensive regions	12
cell lines that	12
kinetics of stat	12
validated by experimental	12
points in the	12
of the sequences	12
read pairs per	12
us government work	12
article is a	12
a series of	12
the human population	12
this article is	12
than that of	12
the rate of	12
and analysis of	12
a cc license	12
under usc the	12
we reasoned that	12
under a cc	12
in multiple sclerosis	12
have been proposed	12
ecology and evolution	12
mock h homo	12
of the integrated	12
the cell lines	12
identified by regtools	12
host prediction accuracy	12
m r c	12
based on perfect	12
in the number	12
to understand the	12
be used for	12
on the right	12
uniformly sampled from	12
academy of sciences	12
uniform read distribution	12
of resistant biomolecules	12
cell rna sequencing	12
subject to copyright	12
in this work	12
in figure b	12
general ccn scores	12
it has been	12
could not be	12
on the human	11
isotropic gaussian noise	11
association of editing	11
male and female	11
log p v	11
the identification of	11
cancer type specific	11
log nm ps	11
as described above	11
curvatures computed for	11
wrote the manuscript	11
cpgs on the	11
dependent changes in	11
used as the	11
have shown that	11
the fractional error	11
for the pbmc	11
m hq http	11
to the human	11
global length scale	11
in the model	11
random forest classifier	11
spike and ace	11
the same time	11
the list of	11
that were not	11
and south korea	11
noise in the	11
with and without	11
end genes of	11
the contribution of	11
the expression level	11
university school of	11
shown in blue	11
focused on the	11
comparison of the	11
a measure of	11
p v al	11
depends on the	11
of the three	11
in this case	11
were able to	11
the training set	11
cells in the	11
editing frequency with	11
of stat phosphorylation	11
is expected to	11
in the future	11
and amino acid	11
standard deviation of	11
the detection of	11
we also found	11
to compute the	11
would like to	11
selection gse mock	11
closer to the	11
in the population	11
h ctd q	11
we observed a	11
used to evaluate	11
the integrated dataset	11
may be due	11
of the models	11
computed for the	11
as a function	11
the pqa score	11
defined by the	11
usa department of	11
of the main	11
nm ps ta	11
sensitivity and specificity	11
be explained by	11
and host sequences	11
rna editing targets	11
we observed that	11
in regulatory motif	11
are expected to	11
the other two	11
described in the	11
some of the	11
of predicted atus	11
shown in table	11
al u e	11
of the ligand	11
of the manifold	11
maximal atu cluster	11
for the first	11
fold change of	11
the mathematical model	11
for the top	11
points on k	11
using the default	11
v al u	11
the two communities	11
of the samples	11
within the same	11
r e https	11
the human epic	11
amino acid continuous	11
ai c index	11
refers to the	11
value of the	11
values of the	11
stat activation by	11
the experimental data	11
of regulatory sequence	11
human pancreatic islets	10
included in this	10
to reduce the	10
and homotypic multiplets	10
can lead to	10
na na na	10
for min at	10
the ratio of	10
to this work	10
downstream of the	10
in rpe cells	10
of three biological	10
conflict of interest	10
average power plot	10
de bruijn graph	10
function in the	10
probes on the	10
to ensure the	10
blanc et al	10
of the american	10
broad and sanger	10
of the virus	10
to those of	10
was carried out	10
sequences tcga pan	10
calculated using the	10
su br ea	10
the result of	10
the original dataset	10
the global length	10
molecules of stat	10
known to be	10
authors contributed equally	10
gene expression profiles	10
squamous cell carcinoma	10
and machine learning	10
fraction of the	10
to maximal il	10
a web server	10
in figure a	10
n ai ve	10
of the first	10
ucsc genome browser	10
test set of	10
of the genome	10
bronchoalveolar lavage fluid	10
to be a	10
zero scalar curvature	10
the most common	10
measured m z	10
were removed from	10
the same cell	10
the process of	10
m zzqk xjeg	10
it is important	10
the range of	10
two refseq annotations	10
e ns em	10
bound to stat	10
the manifold dimension	10
whole genome sequencing	10
we use the	10
seq data and	10
data and the	10
of the total	10
from the reference	10
to compare the	10
cell type specificity	10
function of the	10
cancer type of	10
shah et al	10
those of the	10
mass spectrometry phenomena	10
public research allele	10
the magnitude of	10
understanding of the	10
the triplex package	10
receiver operating characteristic	10
br ea d	10
ai ve c	10
gene expression levels	10
coefficient of variation	10
and oligonucleotide compositions	10
in methods section	10
scalar curvatures were	10
cell type k	10
in the network	10
the first and	10
t h t	10
differentially expressed genes	10
it is a	10
the overlapping cell	10
contributed equally to	10
c b i	10
levels of ifns	10
we found a	10
extracted from the	10
latex s https	10
side of the	10
was used as	10
to the reference	10
of the cleft	10
limited number of	10
is possible to	10
components of the	10
wavelet power levels	10
of the protein	10
the two refseq	10
k valid read	10
cell type clusters	10
scalar curvatures for	10
in health and	10
ve c d	10
hu and sun	10
resulting in a	10
cancer dependency map	10
c ac o	10
in each subtype	10
in each annotation	10
are provided in	10
research allele frequency	10
of the tumor	10
was set to	10
number of classifications	10
with default parameters	10
au content of	10
results suggest that	10
most variable genes	10
h ctd rpd	10
provided by the	10
the start of	10
in the field	10
from three biological	10
values for the	10
in the two	10
the spike ace	10
ns em bl	10
the need for	10
single gene mrna	10
klein bottle embedding	10
which have been	10
response to il	10
the evaluation of	10
persson et al	10
true value of	10
the negative class	10
for at least	10
of the corresponding	10
change of three	10
levels of the	10
c j i	10
number of genes	10
the cell line	10
the theory of	10
ncbi and refseq	10
the basis for	10
the authors declare	10
set of n	10
for all three	10
zhang et al	10
indicates that the	10
cell types from	9
of the five	9
are present in	9
annotated by chasmplus	9
the course of	9
blood mononuclear cells	9
according to their	9
bnwyax q esm	9
yang et al	9
excluded from the	9
atus by seqatu	9
a the copyright	9
of all the	9
subpopulations of cells	9
the effects of	9
genes were found	9
that the gene	9
bnwyax z a	9
the human reference	9
are able to	9
cells indicate that	9
all eur amr	9
note that the	9
is that the	9
a group of	9
h b e	9
based on their	9
c and d	9
for each node	9
the study of	9
driver within a	9
is calculated by	9
to increase the	9
this suggests that	9
in supp tab	9
bnwyax odthp http	9
for each variant	9
for genes that	9
the three annotations	9
rna sequencing data	9
the expression value	9
the spike protein	9
predicted atus by	9
interactions with the	9
the type of	9
is calculated as	9
the distance between	9
with environmental distance	9
be seen from	9
p m ifnl	9
the inclusion of	9
marks within cells	9
the th percentile	9
we focused on	9
scatter plot showing	9
points uniformly sampled	9
the difference between	9
belonging to the	9
conflicts of interest	9
data in the	9
ii gene pairs	9
theory of resistant	9
number of items	9
of each sample	9
to find the	9
b bnwyax odthp	9
by the number	9
amino acid type	9
effective gene lengths	9
of the single	9
difference in the	9
integration sequences tcga	9
on the left	9
journal of vegetation	9
we were able	9
of valid read	9
are the most	9
u n g	9
peripheral blood mononuclear	9
the spread of	9
m zzqk meu	9
triplex motifs in	9
of the graph	9
addition to the	9
vs r ef	9
need to be	9
number of valid	9
in agreement with	9
fo ld c	9
the nature of	9
in a given	9
editing sites with	9
information about the	9
sequence to per	9
s s s	9
is shown for	9
in the main	9
been shown to	9
higher proportion of	9
it is also	9
homotypic and heterotypic	9
natural language processing	9
provided in supplementary	9
closest point on	9
greater than the	9
cd t cell	9
edited cytidine in	9
we selected the	9
of the species	9
found to have	9
added to the	9
of the vp	9
compared the performance	9
for pbmc and	9
show that the	9
primary human bronchial	9
in the refseq	9
biorxiv preprint mailto	9
peerthis version posted	9
b a l	9
from the abc	9
a driver within	9
quality of the	9
of vegetation science	9
eur amr sas	9
nugent et al	9
of points in	9
compositions of sars	9
the amount of	9
small cell lung	9
for each pcr	9
phosphorylation kinetics of	9
to address this	9
to the gene	9
rna editing in	9
seq data with	9
copy number alterations	9
bnwyax wm a	9
scalar curvature is	9
indicated by the	9
with the same	9
can then be	9
consortium et al	9
we analyzed the	9
samples of covid	9
as a driver	9
of the input	9
in the vp	9
cov and sars	9
levels of stat	9
obtained from two	9
national academy of	9
nodes u and	9
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classification profiles of	9
run run run	9
in new infections	9
each cancer type	9
for predicting response	9
to per unit	9
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prediction accuracy of	9
n points uniformly	9
international conference on	9
genes associated with	9
a ci containing	9
in secondary structure	9
p b m	9
proportional to the	9
number of samples	9
flagged by coil	9
given tcga cohort	9
apob rna editing	9
along with the	9
of the debar	9
the posterior distributions	9
b m c	9
model input features	9
none of the	9
r at io	9
of the genes	9
n points from	9
and cell type	9
certified by peerthis	9
health and disease	9
does not have	9
triplex motifs and	9
for a total	9
ricotta et al	9
balf samples of	9
calculated by the	9
fold induction log	9
in the genome	9
differential motif usage	9
for each dataset	9
s and s	9
by peerthis version	9
was annotated by	9
the first prescription	9
mismatches in the	9
bnwyax o i	9
studies have shown	9
stimulated with il	9
sas afr eas	9
and motion estimation	9
expression profiles from	9
correlation with environmental	9
gemms and tumoroids	9
used to train	9
using the r	9
computed using the	9
by using the	9
the diversity of	9
the virus genome	9
cell division events	9
small number of	9
in more than	9
measured by the	9
the tumor transcriptome	9
the national academy	9
in our study	9
by chasmplus as	9
of gene induction	9
the riemannian curvature	9
bnwyax hbt j	9
regardless of the	9
in the viral	9
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for the image	9
we performed a	9
and of the	9
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i gene pairs	9
an open source	9
of the disease	9
a l f	9
within cells indicate	9
of the rna	9
used to generate	9
making use of	9
the loss function	9
ranked by fraction	9
gene was annotated	9
from the cancer	9
l u n	9
the kinetics of	9
a given tcga	9
n h b	9
to create a	9
cell lung cancer	9
the five cancer	9
chasmplus as a	9
the frequency of	9
under a the	9
by fraction of	9
two types of	9
of triplex motifs	9
this study are	9
of mismatches in	9
the pbmc dataset	9
number of genomes	9
seq and rienrich	9
c index https	9
the same number	9
in this analysis	9
in all the	9
red marks within	9
c c l	8
the reference transcriptome	8
a comparison of	8
high levels of	8
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o i ifnb	8
observed in the	8
on the x	8
ccn classification scores	8
secondary structure of	8
partial shapley values	8
percentage of the	8
a random forest	8
was downloaded from	8
the most important	8
the gene pairs	8
wm a http	8
before and after	8
seq data is	8
kgp cohort dv	8
a result of	8
in the dataset	8
that could be	8
gordon k smyth	8
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of response to	8
correlation between the	8
number of patients	8
by the national	8
deep neural networks	8
hbt j http	8
the host prediction	8
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bnwyax ax xh	8
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in the following	8
the maximum number	8
compared with reshuffled	8
bnwyax f tt	8
in the cell	8
performance of sclapa	8
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dist and ge	8
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both homotypic and	8
this dataset we	8
zzqk q l	8
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the similarity between	8
the concentration of	8
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bnwyax thhr http	8
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by experimental tsss	8
b bnwyax e	8
hebert et al	8
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are listed in	8
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bnwyax dctjj http	8
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numbers of new	8
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data and materials	8
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for rienrich seq	8
at least two	8
number of clusters	8
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at each point	8
unknown general classification	8
we tested the	8
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revealed that the	8
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b bnwyax dctjj	8
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bnwyax ezh http	8
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the location of	8
b bnwyax o	8
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with reshuffled controls	8
q esm http	8
the main text	8
bnwyax ayqe http	8
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public research cohort	8
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increase in the	8
the probability of	8
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extrinsic differential geometry	8
glnexus opt v	8
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the united states	8
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presence of a	8
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em density map	8
along mrna transcripts	8
aligned to the	8
residues in the	8
data was normalized	8
ranked by binomial	8
by flow cytometry	8
h m r	8
the nuclear norm	8
in the spike	8
the true proportions	8
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h ctd jlne	8
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n c b	8
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b bnwyax wm	8
b bnwyax hbt	8
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exon skipping event	8
lakshmanan et al	8
and transcriptomic data	8
this is not	8
m a p	8
ctd ndo a	8
bnwyax eqqvf http	8
we considered the	8
barcode and metabarcode	8
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for curvature estimation	8
not present in	8
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the broad and	8
c n h	8
under the curve	8
the levels of	8
used to detect	8
were converted to	8
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sampled from the	8
a limited number	8
pstat and pstat	8
hidden subpopulations of	8
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view of the	8
the atus in	8
bnwyax assl http	8
sequence of the	8
m zzqk ld	8
b bnwyax ezh	8
site of the	8
c log nm	8
nature reviews genetics	8
single cell reference	8
science and technology	8
to be more	8
all three annotations	8
profiling of gene	8
institutes of health	8
h ctd ndo	8
at the end	8
ro e lo	8
ancestral and subclonal	8
e c ac	8
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ir f ir	8
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was performed by	8
the availability of	8
in sle patients	8
the gene was	8
there are several	8
the maximal atu	8
the image patch	8
h ctd gs	8
r c n	8
for which we	8
the random forest	8
the differences in	8
bnwyax kxhhl http	8
r tl r	8
the integration of	8
of cells that	8
a part of	8
can be applied	8
seq data were	8
to differences in	8
not depend on	8
triplex motifs are	8
at io n	8
the top most	8
dv glnexus opt	8
the mean of	8
islet and islet	8
the extent of	8
and it is	8
b bnwyax iqbee	8
of machine learning	8
of a gene	8
similarity network fusion	8
ac e c	8
average number of	8
t t t	8
bnwyax bifqg http	8
b bnwyax z	8
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tl r tl	8
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were found in	8
figure s b	8
l l in	8
the environmental gradient	8
two cell types	8
higher than the	8
to develop a	8
the complexity of	8
dna barcode data	8
together with the	8
the final model	8
other cell types	8
the mean and	8
bnwyax shsw http	8
obtained from one	8
regions of the	8
suggests that the	8
with the most	8
for each locus	8
was normalized to	8
and supplementary table	8
b bnwyax karn	8
we also used	8
b bnwyax bifqg	8
riemannian curvature tensor	8
we do not	8
seq data from	8
of the novel	8
gene in the	8
b bnwyax uh	8
cell type annotations	8
two principal components	8
genomic and transcriptomic	8
triplex motifs were	8
cells stimulated with	8
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deepmm and phenix	8
o i http	8
more likely to	8
m zzqk qisc	8
b bnwyax q	8
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bnwyax iqbee http	8
research cohort kgp	8
the predicted main	8
for evidence of	8
and the proportion	8
number of sequences	8
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b e ve	8
glia and endothelial	8
by binomial p	8
grade serous ovarian	8
c el l	8
four out of	8
b bnwyax ayqe	8
al u h	8
rate of stat	8
f ir f	8
as training data	8
we measured the	8
results are shown	8
is the same	8
as the reference	8
two or more	8
and standard deviation	8
genomes that occur	8
expression value of	8
by fitting a	7
supplemental files and	7
have been used	7
arbab et al	7
time min time	7
zzqk at m	7
c ha ng	7
the input of	7
cl on al	7
been used to	7
zero scalar curvatures	7
s ub cl	7
b bnwyax ymsj	7
batch correction methods	7
ax xh http	7
could be used	7
com elakatos liquidcna	7
from the data	7
min time min	7
suggesting that the	7
johns hopkins university	7
no competing interests	7
low percent of	7
in human cells	7
li et al	7
than or equal	7
the correlation with	7
we refer to	7
accuracy of phirbo	7
the landscape of	7
for recurrently disrupted	7
of disease modules	7
in each of	7
the department of	7
from the figure	7
was found in	7
difference between the	7
com acnash rdrugtrajectory	7
with an exon	7
frequency pretrained model	7
data represents the	7
in the r	7
patient derived xenografts	7
phosphorylated stat and	7
this study was	7
pacific biosciences sequel	7
of a novel	7
the innate immune	7
we also calculated	7
as a measure	7
stably expressing wt	7
which they are	7
triplex and g	7
breast invasive carcinoma	7
ctd crk v	7
as opposed to	7
of cytokine signaling	7
our results to	7
we downloaded the	7
we evaluated the	7
g en e	7
h ctd s	7
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in cell type	7
h ctd yrlys	7
frequency in the	7
we examined the	7
of type i	7
to each other	7
the denoising pipeline	7
more sustained stat	7
cell and tissue	7
expected to have	7
significant differences in	7
activation of stat	7
outside the country	7
ctd eix e	7
an important role	7
profile hidden markov	7
in method s	7
results from the	7
approach can be	7
times greater than	7
with or without	7
all the genes	7
a table containing	7
b bnwyax fenjn	7
with ccn scores	7
in the form	7
represented by a	7
sensitivity of the	7
results in a	7
in return plots	7
bnwyax jkgi http	7
generated from the	7
is the total	7
first prescription event	7
the evolution of	7
iv e ge	7
outside of the	7
were assigned to	7
overall secondary structure	7
bias rate of	7
the whole genome	7
the evaluation data	7
e st im	7
h ctd eix	7
of the clusters	7
of single cell	7
recurrently disrupted genes	7
the order of	7
department of automation	7
mathematical models and	7
curvature of image	7
m zzqk srq	7
the major arc	7
pep slc a	7
genes recurrently disrupted	7
are required to	7
away from the	7
to the model	7
to the virus	7
cell type in	7
ccn scores from	7
was calculated using	7
the phase difference	7
the same as	7
are consistent with	7
nature of the	7
these authors contributed	7
with the number	7
highlighted in red	7
ifns and isgs	7
from left to	7
in the protein	7
expected number of	7
in recent years	7
the selection of	7
the pearson correlation	7
mapping rates to	7
methods based on	7
also be used	7
of the mooring	7
point on k	7
were calculated for	7
of which have	7
figure s d	7
n o p	7
the quantification of	7
m zzqk uwiz	7
ub cl on	7
distribution of gof	7
are plotted against	7
in the presence	7
mathematical models of	7
distribution along mrna	7
predicting response to	7
s s tm	7
national institutes of	7
of the image	7
web server for	7
we noticed that	7
is an open	7
in this way	7
type of interest	7
bias rate function	7
the intergenic region	7
that there are	7
the enrichment of	7
be applied to	7
general tumor types	7
expression in the	7
and pearson correlation	7
prescription event on	7
way and greene	7
the ace spike	7
roadmap epigenomics consortium	7
of the expression	7
b bnwyax htdux	7
across cancer types	7
circulating tumor dna	7
to obtain a	7
similar to those	7
with the variant	7
they do not	7
which has been	7
represents the mean	7
chain probability map	7
was calculated by	7
please place fig	7
in a cell	7
than the decision	7
genes that were	7
in regulatory sequence	7
the possibility of	7
for each species	7
summary of the	7
to the sars	7
reported to be	7
data obtained from	7
of ace in	7
followed by the	7
of the population	7
account for the	7
com calculate https	7
cell line dpgs	7
mean and standard	7
regulation of rna	7
expected by chance	7
klein bottle embeddings	7
m zzqk n	7
the atom difference	7
the mbrave platform	7
performed using the	7
y stat a	7
cells that are	7
of severe illness	7
the regulation of	7
d e f	7
or infected with	7
the similarity relation	7
and balf samples	7
bnwyax karn http	7
of effective gene	7
content of the	7
that there is	7
m zzqk iwwe	7
for each probe	7
the model performance	7
splice junction region	7
experiments with each	7
a t g	7
should be addressed	7
y stat b	7
le ng th	7
from the true	7
of cancer cell	7
h ctd crk	7
in the absence	7
our deepmm method	7
as a proxy	7
to a quadratic	7
the robustness of	7
genetically engineered mouse	7
allows us to	7
the computed scalar	7
to minimize the	7
as lx http	7
as it is	7
figure s c	7
stat phosphorylation by	7
used by blast	7
stat phosphorylation kinetics	7
disrupted genes in	7
a single cell	7
of the embryo	7
by variants which	7
of cancer models	7
an exon skipping	7
distance between the	7
probability of severe	7
which resulted in	7
this is a	7
the user to	7
l c c	7
results showed that	7
washington university school	7
bnwyax as lx	7
posterior distributions for	7
mouse and rat	7
interests the authors	7
to provide a	7
is the set	7
to remove the	7
the residues that	7
bnwyax ymsj http	7
competing interests the	7
of the reference	7
features in the	7
of developmental time	7
ct iv e	7
end genes and	7
the enzymatic cleft	7
cell types were	7
motifs and mls	7
em density maps	7
of a klein	7
for statistical computing	7
ge ne le	7
atlas research network	7
b bnwyax as	7
can be described	7
em maps at	7
of the variants	7
the figure that	7
h ctd jmtrf	7
an mrna transcript	7
evaluation of the	7
protein data bank	7
important role in	7
b bnwyax ax	7
of stop codons	7
genome atlas research	7
correlation with mls	7
cardiac motion estimation	7
the most frequent	7
bnwyax dwirj http	7
start of the	7
o i tp	7
in the single	7
h ctd jel	7
of the experimental	7
doubletdetector and archr	7
can be set	7
nucleotides upstream and	7
the average mutual	7
that the use	7
by the two	7
fi c log	7
fc lo g	7
a cell type	7
expected to work	7
results of analysis	7
region of the	7
in relation to	7
journal of the	7
either of the	7
reveals genes recurrently	7
research interests are	7
ne le ng	7
recurrently disrupted by	7
i tp m	7
demonstrate the utility	7
with the human	7
ctd k rob	7
to address the	7
in a more	7
cell type specific	7
has also been	7
of gof p	7
did not observe	7
are in supp	7
s tm p	7
h ctd pj	7
ct io n	7
of the n	7
the first two	7
of samples and	7
were included in	7
association with editing	7
epithelial cells and	7
bnwyax xh a	7
of fdissim indices	7
in mooring sequence	7
briefings in bioinformatics	7
have at least	7
m fi c	7
material and methods	7
for cell type	7
of vntr length	7
ctd pj xm	7
matching for m	7
more than cell	7
used to compute	7
to a given	7
ld c ha	7
results of the	7
major cell type	7
alpha and beta	7
is essential for	7
to allow for	7
depend on the	7
h ctd gyl	7
this resulted in	7
alveolar epithelial cells	7
q l http	7
of a given	7
is supported by	7
after the first	7
annotated by the	7
classification heatmap of	7
cov and mers	7
of the cancer	7
of ifns and	7
m m m	7
the copy number	7
nucleotides downstream of	7
models of the	7
m zzqk at	7
less than or	7
it is necessary	7
the hbv integration	7
and is a	7
a single variant	7
b bnwyax jkgi	7
the scope of	7
shown in red	7
due to their	7
in the original	7
the top scored	7
the changes in	7
epithelial sodium channels	7
gene i in	7
the same date	7
bnwyax htdux http	7
the eas population	7
analysis for recurrently	7
cell line mixtures	7
of the major	7
ctd s lm	7
of analysis for	7
many of the	7
cell lines using	7
lowly expressed genes	7
we assume that	7
gene regulatory network	7
of computer science	7
position in the	7
the reference genome	7
in the sequence	7
top scored models	7
we applied the	7
ctd jlne http	7
in bacterial genomes	7
zzqk xjeg http	7
s c o	7
a length of	7
to filter out	7
we also observed	7
to that of	7
female cell lines	7
cell lines from	7
regulatory t cells	7
differential expression analysis	7
compared to other	7
h ctd jzyin	7
stop codon when	7
a database of	7
allele frequency pretrained	7
and scnn g	7
machine learning research	7
were compared to	7
on gene expression	7
to be used	7
more essential in	7
b bnwyax dwirj	7
the other dataset	7
h ctd haw	7
by blast and	7
were annotated by	7
were used as	7
the edwards et	7
there was no	7
the two datasets	7
convolutional neural networks	7
read distribution along	7
c to u	7
the royal society	7
were extracted from	7
and in the	7
both types of	7
publicly available data	7
zzqk n pa	7
of the royal	7
were based on	7
pair of annotations	7
across the two	7
each image patch	7
built by deepmm	7
detected by atac	7
the ensembl genes	7
are shown for	7
the subset of	7
e ge ne	7
disrupted by variants	7
h ctd akii	7
ha ng e	7
by the same	7
amino acid and	7
for node u	7
identified by the	7
plotted against the	7
there is an	7
h ctd jzbjy	7
batch correction pipelines	7
for of the	7
false discovery rate	7
for each cancer	7
h ctd me	7
of a stop	7
for all the	7
funding this work	7
stat a p	7
quadruplex and triplex	7
mol cell biol	7
was found using	7
is represented by	7
differentially essential genes	7
details of the	7
the abundance of	7
the most relevant	7
c o re	7
in table s	7
host prediction performance	7
convolutional neural network	7
to identify genes	7
of patients with	7
are the same	7
the efficacy of	7
b shows the	7
to the true	7
the standard deviation	7
ta t m	6
h ctd jqzsb	6
p re gu	6
as for the	6
ctd pgh u	6
evaluated using the	6
copy number values	6
associated with editing	6
in the host	6
we focus on	6
genetic and intergenic	6
that in the	6
based prediction of	6
of apolipoprotein b	6
from a healthy	6
evolution of the	6
high number of	6
of gene i	6
of the module	6
assessment of the	6
correlation with the	6
cell types with	6
the existence of	6
and the gene	6
m enrich and	6
calculated for the	6
zzqk c cd	6
a computational tool	6
of the best	6
the expected number	6
is necessary to	6
formula difference of	6
mean of the	6
d iff er	6
on relaxed matching	6
h ctd cq	6
re gu la	6
and h cells	6
b bnwyax xh	6
by means of	6
result in a	6
the sample size	6
cytoplasmic phosphorylated stat	6
chem inf model	6
by using a	6
ty s c	6
dorsal root ganglion	6
were derived from	6
in cell lines	6
transcriptomic and methylomic	6
h ctd wqpb	6
we also tested	6
s lm http	6
ctd lyx d	6
h ctd xd	6
h ctd qaf	6
deviation of the	6
small membrane protein	6
n pa http	6
and for the	6
model to predict	6
live cell microscopy	6
uniform distribution of	6
an alignment file	6
pan cancer peaks	6
ri ty s	6
like to thank	6
the genome of	6
the poisson distribution	6
the true scalar	6
of this work	6
of publicly available	6
re interaction non	6
of the tumour	6
of the phage	6
of less than	6
to study the	6
an aupr of	6
the reliability of	6
of data and	6
free or bound	6
fic ie nt	6
have been developed	6
we calculate the	6
carried out using	6
is annotated as	6
all cell types	6
were generated by	6
in the respective	6
can be easily	6
ngsc di pbmc	6
the design of	6
result was found	6
pbmc and islet	6
the human blood	6
another type of	6
an auroc of	6
number of days	6
engineered mouse models	6
this can be	6
we found the	6
predicted to be	6
wavelet coherence plot	6
normalized by the	6
and may be	6
to assess whether	6
l o g	6
are available at	6
even when the	6
of alternative polyadenylation	6
du ct io	6
originally reported scalar	6
from the training	6
r su br	6
availability of data	6
of deletion bps	6
al e c	6
on the digraph	6
overlapped with the	6
variance of the	6
c or re	6
of image patch	6
scalar curvature estimate	6
score in the	6
are ranked by	6
of more than	6
broad range of	6
have developed a	6
higher than those	6
of the il	6
showed favorable interactions	6
from one representative	6
se nt ia	6
labelled cancer category	6
fe ct iv	6
lg unchanged regulated	6
n kax http	6
h n o	6
dissimilarity and environmental	6
the reference panel	6
ef fic ie	6
the removal of	6
the cancer genome	6
ctd cq b	6
on the gene	6
ctd r by	6
number of times	6
does not depend	6
of thousands of	6
we investigated the	6
and in silico	6
to the phmm	6
u p re	6
pathway enrichment analysis	6
those in the	6
expression of ace	6
can be obtained	6
with less than	6
the deep learning	6
scnn g in	6
sequences flagged by	6
chromatin state annotations	6
pearson correlation of	6
a single nucleotide	6
order of the	6
lung cancer cell	6
where is the	6
different values of	6
and bayesian inference	6
last month of	6
in the initial	6
map of the	6
machine learning and	6
reads of support	6
to compute scalar	6
the elapsed month	6
of the results	6
blast and phirbo	6
of the original	6
a more sustained	6
of maximal atu	6
to the average	6
such that the	6
the positive class	6
from a single	6
for d d	6
number of errors	6
annotations after filtering	6
the furin site	6
a gene is	6
shows the number	6
type i and	6
as indicated by	6
for n points	6
and thiamine c	6
essential genes and	6
expressing wt il	6
from a given	6
data for all	6
gp and il	6
o re interaction	6
the klein bottle	6
in xiamen university	6
the target sequence	6
automation in xiamen	6
the compositions of	6
insights into the	6
the purpose of	6
is a linear	6
phase difference image	6
gender ami gender	6
in the united	6
the application of	6
we constructed a	6
variants associated with	6
of the time	6
for islet and	6
from the analysis	6
the raw fastq	6
science article pii	6
has the highest	6
multiplets detected by	6
ctd gyl http	6
m zzqk nhfw	6
containing the scalar	6
from the two	6
this result was	6
weighted sum of	6
h ctd cclhp	6
zzqk ld http	6
the splice junction	6
as the number	6
the national institutes	6
analyzed in this	6
are available from	6
co ef fic	6
a cell line	6
control sirna irf	6
cell marker gene	6
is most likely	6
proportion of the	6
acid and secondary	6
ami gender ami	6
were mapped to	6
m s d	6
of five cancer	6
been proposed to	6
s im ila	6
use of refseq	6
comparison to the	6
em bl vs	6
cd t and	6
or re la	6
n co ef	6
ccn scores in	6
the probe sequence	6
zzqk uwiz http	6
s lrrfip p	6
needs to be	6
a reduction in	6
there are no	6
corresponds to a	6
to a new	6
base composition and	6
in figure d	6
s spen p	6
only a small	6
hidden markov models	6
the novel junction	6
polymerase chain reaction	6
resource for the	6
of the mammalian	6
scalar curvature for	6
the possibility that	6
is not the	6
cis containing the	6
bnwyax t woi	6
journal of machine	6
our results show	6
applied by debar	6
by dividing the	6
a handful of	6
are found in	6
b bnwyax rxwn	6
scores of the	6
e c el	6
of the heart	6
the rest of	6
for the other	6
lead to a	6
of each gene	6
of biological chemistry	6
the variance of	6
that does not	6
and compared to	6
that cell line	6
these results demonstrate	6
mg tablet oral	6
human epic array	6
impact on the	6
to one of	6
have not been	6
of a manifold	6
that the two	6
a capsule network	6
be required to	6
that the atus	6
expression combination of	6
the generation of	6
box counting dimension	6
in figures and	6
number of deletion	6
training data and	6
we developed an	6
bps associated with	6
overlap between the	6
r core team	6
may lead to	6
dependent on the	6
multivariable linear regression	6
used to determine	6
the power spectrum	6
la tio n	6
of automation in	6
bnwyax fenjn http	6
gene essentiality in	6
cumulative distribution function	6
at any time	6
to address these	6