trigram

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

trigram	frequency
the author funder	1027
version posted february	1027
is the author	1027
the copyright holder	1027
copyright holder for	1027
certified by peer	1020
by peer review	1020
not certified by	1020
biorxiv preprint https	981
which was not	962
was not certified	962
holder for this	890
org licenses by	871
to display the	861
license to display	860
granted biorxiv a	860
biorxiv a license	860
a license to	860
it is made	860
display the preprint	860
has granted biorxiv	860
the preprint in	860
who has granted	860
for this preprintthis	818
preprintthis version posted	818
this preprintthis version	818
preprint in perpetuity	723
licenseavailable under a	651
international licenseavailable under	651
is made the	651
made the copyright	651
the number of	261
com b rqvmzs	226
com b tes	217
b tes g	217
is made available	210
available under a	145
made available under	145
in the copyright	137
thisthis version posted	137
for thisthis version	137
holder for thisthis	137
preprint in the	137
under a preprint	137
based on the	129
io view corchea	128
vtwe pe https	127
in order to	105
as well as	101
com b kjin	94
no reuse allowed	93
allowed without permission	93
reuse allowed without	93
all rights reserved	93
it is not	92
com document d	90
hkqd b gmabgnhrduyigpd	89
document d hkqd	89
a set of	89
jhxsou edit smartreference	89
d hkqd b	89
ue ofupuwd jhxsou	89
ofupuwd jhxsou edit	89
nucleic acids res	86
each of the	76
made available for	75
a cc license	74
is also made	74
and is also	74
copyright under usc	74
this article is	74
also made available	74
is not subject	74
a us government	74
is a us	74
for use under	74
subject to copyright	74
use under a	74
article is a	74
us government work	74
available for use	74
not subject to	74
under a cc	74
to copyright under	74
usc the copyright	74
under usc the	74
for this preprint	72
one of the	66
licenseunder a not	65
a not certified	65
international licenseunder a	65
which wasthis version	65
due to the	65
available the copyright	65
made available the	65
wasthis version posted	65
in terms of	62
can be used	60
c tes g	59
we used the	59
com c tes	59
com c kjin	58
ar m on	52
h ar m	52
m on y	52
mutations in the	49
targeted gene profiling	49
com c rqvmzs	47
in this study	47
followed by harmony	47
be used to	46
m m d	46
the distribution of	45
for each of	45
no no no	45
proceedings of the	44
compared to the	44
we found that	43
gene expression data	43
the performance of	43
whole genome sequencing	42
of the data	42
of cancer mutations	40
the era of	40
era of high	39
in the era	39
the effect of	39
at least one	39
for quality control	39
the polar set	38
the set of	38
quality control of	38
a fully automated	38
shown in figure	37
automated approach for	37
resolution whole genome	37
that can be	37
cancer mutations in	37
control of cancer	37
fully automated approach	37
the size of	37
approach for quality	37
arxiv preprint arxiv	37
the presence of	36
achieved by the	36
total number of	35
distribution of the	35
version of the	35
size of the	35
according to the	35
househam et al	35
genes selected by	34
with respect to	34
in the first	33
the development of	33
in addition to	33
axis denotes the	32
bi tio n	32
drc in presence	32
international conference on	32
in presence of	32
was used to	32
on the other	32
hi bi tio	32
m m m	32
in hi bi	32
h h h	31
biorxiv preprint http	31
differential expression analysis	31
the use of	31
the proportion of	31
cell rna sequencing	31
well as the	30
driver and passenger	30
a subset of	30
is used to	30
the identification of	30
is based on	30
universal hitting sets	29
in this work	29
the analysis of	29
between the two	29
the total number	29
p c a	29
the training set	29
of the same	29
of the top	29
such as the	29
associated with the	29
cells in the	28
in this case	28
we calculated the	28
the fact that	28
part of the	28
the other hand	28
there is a	28
is defined as	28
genes in the	28
in the context	28
the expression of	28
in the same	28
the quality of	28
from the same	27
a total of	27
for a given	27
in the range	27
the results of	27
tangherloni et al	27
based on a	26
are used to	26
of the national	26
by the best	26
a variety of	26
academy of sciences	26
the majority of	26
layered polar sets	26
of the tested	26
as shown in	26
most of the	25
of the genes	25
likely to be	25
the best ae	25
in the reference	25
head and neck	25
value of the	25
can be found	25
ae for each	24
en ge ne	24
nucleic acids research	24
of the most	24
e ig en	24
best ae for	24
ig en ge	24
at the same	24
for the sample	24
of the three	24
some of the	24
supplementary figure s	24
the effects of	24
remdesivir drc in	24
included in the	24
structure of the	24
is shown in	24
the reference sequence	24
the probability that	24
to estimate the	23
genes based on	23
was supported by	23
the context of	23
set of genes	23
any of the	23
the tested dimension	23
it can be	23
and passenger mutations	23
associated with ad	23
supported by the	23
in the dataset	23
similar to the	23
journal and volume	22
the human genome	22
overview of the	22
g m m	22
we show that	22
as a result	22
we observed that	22
number of genes	22
we use the	22
the gene expression	22
and volume and	22
the list of	22
for each gene	22
in the data	22
of the original	21
a and b	21
parental genome sequences	21
in the original	21
the length of	21
large number of	21
obtained from the	21
of the human	21
related to the	21
more than one	21
scc and pcc	21
pca followed by	21
are shown in	21
available at https	21
in which the	21
representation of the	21
as part of	20
a plot of	20
have been developed	20
may not be	20
of the cell	20
of gene expression	20
chr chr chr	20
the svm model	20
of the two	20
depending on the	20
wide association studies	20
the latent space	20
present in the	20
in supplementary materials	20
gwas summary statistics	20
s ti or	20
in the future	20
a number of	20
of the gene	20
the university of	20
de bruijn graph	20
the user can	20
rna sequencing data	20
bdca g s	19
to account for	19
in this paper	19
national academy of	19
throughput sequencing data	19
booeshaghi and pachter	19
that are not	19
precision and recall	19
is the number	19
function of the	19
age and sex	19
in proceedings of	19
analysis of the	19
the national academy	19
a random minimizer	19
of the input	19
performance of the	19
found that the	18
corresponding to the	18
all of the	18
to the same	18
the genes selected	18
bound on the	18
the most common	18
the link energy	18
small number of	18
be found in	18
used in the	18
to evaluate the	18
by using the	18
a polar set	18
for each method	18
an overview of	18
institutes of health	18
and can be	18
the ability to	18
compared with the	18
in the input	18
to be a	18
the ssnp totalsnp	18
which is a	18
which can be	18
the best results	18
the case of	18
note that the	18
s ssu rrna	18
the glm egs	18
yes no no	18
in the graph	18
of the model	17
the probability of	17
lower bound on	17
to identify the	17
the difference between	17
we used a	17
seq data analysis	17
in this section	17
the mutation rate	17
the rest of	17
the parental genome	17
more likely to	17
a wide range	17
of single cells	17
a small number	17
by the different	17
informative gene selection	17
by particlechromo d	17
for all the	17
were able to	17
in this manuscript	17
of all the	17
the distance between	17
of computer science	17
found to be	17
fortin et al	17
genes that are	17
different types of	17
wide range of	17
abide data set	16
gene selection methods	16
to obtain the	16
summary statistics datasets	16
the end of	16
of raloxifene log	16
the problem of	16
structural variant method	16
in the case	16
defined as the	16
we do not	16
journal of the	16
a random sequence	16
glm egs method	16
national institutes of	16
be used for	16
presence of raloxifene	16
the user to	16
the different strategies	16
as described in	16
value is better	16
the application of	16
in the supplementary	16
analysis of single	16
raloxifene log c	16
cancer genome atlas	16
of the reference	16
the weight matrix	16
gene profiling data	16
of the protein	16
genes and the	16
to compute the	16
a list of	16
area under the	16
kia et al	16
a combination of	16
to determine the	16
quality of the	16
false discovery rate	16
there is no	16
of the dataset	16
are provided in	16
in the following	16
cell library sizes	15
to measure the	15
the turnover rate	15
the importance of	15
volume and issue	15
is available at	15
it is possible	15
with the same	15
this is a	15
nanopore methylation detection	15
can also be	15
results show that	15
zhang et al	15
no no yes	15
derived from the	15
show that the	15
based on their	15
the accuracy of	15
variation in the	15
that do not	15
types of cancer	15
used in this	15
comparison of the	15
d structure of	15
auroc and auprc	15
the mean of	15
and cell type	15
of the disease	15
length of the	15
of the graph	15
a mean ari	15
the significant structural	15
described in the	15
is associated with	15
a comparison of	15
mb and kb	15
of a gene	15
we showed that	15
found in the	15
results for the	15
number of mutations	15
out of the	15
significant structural variant	15
particle swarm optimization	14
association with ad	14
have to be	14
we observe that	14
ssu and lsu	14
were used to	14
be used as	14
of atorvastatin and	14
in the sample	14
depends on the	14
the authors declare	14
no yes no	14
the sum of	14
of cell types	14
the data set	14
the d structure	14
learning sparse log	14
the hierarchical bayesian	14
the raw data	14
yes yes yes	14
are associated with	14
and analysis of	14
of a drug	14
ssnp totalsnp ratio	14
tumor cells and	14
is provided in	14
the same gene	14
at the end	14
by the user	14
the same time	14
of the expression	14
which is the	14
in the field	14
the association of	14
the swarm size	14
the downstream analysis	14
we were able	14
it has been	14
need to be	14
gmmmd followed by	14
to ensure that	14
s n e	14
adjusted rand index	14
relative to the	14
v a e	14
cell gene expression	14
nitrogen content of	14
to each other	14
supplementary table s	14
other types of	14
values of the	14
rest of the	14
associated genes and	14
d structure reconstruction	14
de bruijn graphs	14
provided by the	13
wide association study	13
m a p	13
in other words	13
different cell types	13
the value of	13
respect to the	13
of the results	13
in contrast to	13
use of the	13
ranked genes were	13
principal component analysis	13
genes with ad	13
length isoform quantification	13
adversarial clustering explanation	13
results of the	13
gene set gs	13
using the same	13
and read counts	13
been developed to	13
in fig a	13
the absence of	13
the cancer genome	13
malekian et al	13
of the an	13
total link energy	13
followed by bbknn	13
the order of	13
in the human	13
ratios for high	13
in a given	13
gyra and parc	13
selected by triku	13
in the model	13
corresponds to the	13
along with the	13
the role of	13
randomly selected genes	13
was able to	13
changes in the	13
the abide data	13
the last k	13
on the same	13
issue or issue	13
difference between the	13
we use a	13
is similar to	13
number of cells	13
in the current	13
each of these	13
a pair of	13
observed that the	13
gene expression matrix	13
cortical thickness measures	13
omeprazole and clopidogrel	13
generalized linear model	13
presented in the	13
of genes that	13
to generate the	13
in the second	13
umap u m	13
of which are	13
have the same	13
t s n	13
the sliding window	13
to capture the	13
cohort target set	13
the refined bert	13
u m a	13
analysis of rna	13
set of k	13
downloaded from the	13
to calculate the	13
at the gene	12
for both the	12
machine learning models	12
the percentage of	12
consistent with the	12
htseq and featurecounts	12
shown in fig	12
p rin t	12
a higher scc	12
b b k	12
this work was	12
is the first	12
taking into account	12
for differential expression	12
re p rin	12
tes g p	12
ccf and read	12
that the top	12
is the total	12
have been used	12
the training data	12
map of the	12
wolfers et al	12
in some cases	12
b k n	12
in the figure	12
in the tumor	12
the test set	12
the precision and	12
american journal of	12
for which the	12
fixed interval sampling	12
were used for	12
number of reads	12
k n n	12
to deal with	12
peak memory usage	12
of polar sets	12
close to the	12
the amount of	12
the scc and	12
to compare the	12
transcriptional regulatory network	12
number of isoforms	12
cell types and	12
the output of	12
as an example	12
to find the	12
soda for sparc	12
the simulated data	12
tes g x	12
data for the	12
and the g	12
single cell rna	12
be associated with	12
in the previous	12
in the training	12
a large number	12
as a function	12
e n s	12
gene expression and	12
tcga breast cancer	12
read counts distribution	12
using the following	12
negative matrix factorization	12
of the inter	12
each of which	12
selected by the	12
the aid of	12
multiple sequence alignment	12
a lu e	12
a range of	12
v a lu	12
the range of	12
the field of	12
imaging and clinical	12
quinn et al	12
allows us to	12
are needed to	12
this can be	12
figure shows the	12
that there is	12
by comparing the	12
hierarchical bayesian models	12
the annotation matrix	12
national center for	12
so that the	12
braak and cdr	12
mers in a	12
we plan to	12
the active site	12
wide cna segments	12
a mean value	12
a function of	12
understanding of the	12
then used to	12
p re p	12
regressing out site	12
marquand et al	12
that were not	11
levothyroxine and eptifibatide	11
for nanopore methylation	11
addition to the	11
itr og en	11
in this way	11
we show the	11
ha lia na	11
the data are	11
materials and methods	11
nb loss function	11
generated by particlechromo	11
by the national	11
used to build	11
value of k	11
machine learning model	11
n itr og	11
ie m e	11
the niagads genomicsdb	11
the relationship between	11
data in the	11
is the same	11
gm cell hi	11
original research articles	11
rather than the	11
full set of	11
are more likely	11
for all methods	11
represented as a	11
og en a	11
of cells in	11
p ra te	11
s ti not	11
m e n	11
shown to be	11
peripheral blood mononuclear	11
s ie m	11
neural information processing	11
the gene set	11
that it is	11
information processing systems	11
used to identify	11
were downloaded from	11
te ns e	11
is the only	11
as compared to	11
to have a	11
a to m	11
the reliability ratios	11
as input to	11
of a single	11
ur ea a	11
differences in the	11
en a to	11
in neural information	11
ra te ns	11
it is important	11
to derive the	11
the leiden algorithm	11
available in the	11
the tumor microenvironment	11
mean ari of	11
rqvmzs p yv	11
a hierarchical bayesian	11
no yes yes	11
the particlechromo d	11
for patient set	11
of drug repurposing	11
versions of the	11
the confidence interval	11
advances in neural	11
of the covid	11
in international conference	11
best results for	11
the concept of	11
used to generate	11
ssnp totalsnp ratios	11
for each sample	11
of the proposed	11
l o g	11
to m s	11
denotes the scc	11
be explained by	11
of the cells	11
the ground truth	11
the sparc data	11
of the first	11
no competing interests	11
of thousands of	11
could not be	11
orders of magnitude	11
human reference genome	11
a ur ea	11
into a single	11
resulted in a	11
we developed a	11
pinto et al	11
training and test	11
we compare the	11
link energy of	11
blood mononuclear cells	11
absent from the	11
due to their	11
to the other	11
rqvmzs j j	11
to provide a	11
provided in the	11
distance between the	11
a threshold of	11
not s ti	11
rqvmzs ic y	11
k k k	11
targeted capture sequencing	11
the correlation between	11
site effects in	11
information about the	11
mutation rate and	11
to the number	11
the original annotation	11
different from the	11
mutations from the	11
seq data with	11
the first layer	11
mmdae followed by	11
the model is	11
the curation team	11
we computed the	11
mean of the	11
with deep learning	11
it does not	11
ccf computation for	11
in complex with	11
the full set	11
biorxiv preprint mailto	11
work was supported	11
species and tissue	11
in figure b	11
are in the	11
are based on	11
t ha lia	11
have shown that	11
used as a	11
null distribution of	11
that have been	11
lia na t	11
of the training	11
showed that the	11
is able to	11
shown in the	10
score in the	10
we want to	10
across the different	10
calculated using the	10
tumor cells killed	10
and ccf computation	10
were associated with	10
each fs method	10
residual permutation approach	10
of the number	10
gyra s l	10
peak analysis and	10
simulated and real	10
the need for	10
by the authors	10
poisson loss function	10
of the american	10
journal and issue	10
of a given	10
the result of	10
issue and volume	10
journal of physiology	10
yes no yes	10
region of the	10
at local confidence	10
in the polar	10
the variation in	10
is not a	10
this is the	10
ranked genes and	10
of the annotation	10
link energy is	10
global confidence at	10
m d a	10
the nb loss	10
to represent the	10
the supplementary material	10
the nitrogen content	10
from the ncbi	10
using only the	10
and lsu rrna	10
the error rate	10
of each gene	10
conflict of interest	10
activation value of	10
the tcga breast	10
correlated with the	10
applied to the	10
of the polar	10
has been used	10
compositional data analysis	10
the scope of	10
a lower bound	10
a gene is	10
of the selected	10
none of the	10
is available on	10
an excel file	10
part of a	10
structures generated by	10
for the gene	10
probability that the	10
the same as	10
a tool for	10
d a e	10
from each other	10
universal hitting set	10
validation of the	10
to address the	10
the null distribution	10
to generate a	10
the form of	10
adverse drug reactions	10
the r package	10
data from the	10
the higher the	10
the genome of	10
analysis and ccf	10
accuracy of the	10
sum of squared	10
lecture notes in	10
known to be	10
available on github	10
number of selected	10
from the training	10
subsets of the	10
attention feed forwad	10
k if m	10
new data projection	10
and neck cancer	10
into account the	10
page of table	10
using the default	10
chromosome conformation capture	10
by global confidence	10
refined bert model	10
the average of	10
stan development team	10
variants of concern	10
and ligand type	10
should be addressed	10
to remove the	10
and issue and	10
we compared the	10
can be downloaded	10
the specific density	10
be used in	10
confidence at local	10
two types of	10
kirchoff et al	10
be able to	10
embryonic stem cells	10
number of samples	10
brain imaging data	10
of data and	10
in the low	10
a database of	10
the de bruijn	10
the cells in	10
subunit ribosomal rna	10
to this end	10
to build a	10
content of the	10
the first two	10
computation for the	10
of the sparc	10
of both the	10
for further analysis	10
proportion of subjects	10
would like to	10
of genes and	10
supplementary section s	10
of the log	9
we would like	9
global confidence values	9
of the tumor	9
gov pubmed https	9
of the mutation	9
filter not plastid	9
the peak memory	9
to quantify the	9
of the sequences	9
dimensional embeddings of	9
for the same	9
gene expression in	9
identification of the	9
tes g h	9
of tumor cells	9
deepsea and basset	9
the compiled ad	9
listed in table	9
pbmc k v	9
feed forwad attention	9
of the genome	9
human embryonic stem	9
on machine learning	9
w bases away	9
larger than the	9
to use the	9
from the truth	9
of the image	9
are given in	9
as in the	9
of cyp c	9
to the sparc	9
antisense rna hgnc	9
the results for	9
the genes with	9
in the paper	9
this study was	9
t t t	9
the sparc curation	9
in gene expression	9
is difficult to	9
under the null	9
deep neural networks	9
for each cluster	9
local confidence values	9
for each cell	9
upper bound on	9
department of computer	9
lead to a	9
site as a	9
in line with	9
a method for	9
we did not	9
represented by a	9
better than the	9
in real data	9
scaespy can be	9
in which we	9
the cost of	9
com pachterlab bp	9
are available at	9
x x x	9
allele frequency method	9
mean value of	9
for the top	9
of the corresponding	9
expression of the	9
d en si	9
for predicting ad	9
many of the	9
dr af t	9
the variation graph	9
are likely to	9
receptive field size	9
subset of the	9
the realistic data	9
of levothyroxine and	9
region sample set	9
we sought to	9
it should be	9
the data and	9
are highlighted in	9
the machine learning	9
for individual i	9
competing interests the	9
interests the authors	9
a series of	9
mapped to the	9
one or more	9
see methods for	9
gene set enrichment	9
and the other	9
ssu rrna sequences	9
and rrna sensor	9
cell types in	9
the total link	9
excel file detailing	9
filter not mrna	9
a negative binomial	9
to predict the	9
expression analysis of	9
markov chain monte	9
of breast cancer	9
for the dimensions	9
weight matrix of	9
at swarm size	9
referred to as	9
position in the	9
bulk genome sequences	9
chain monte carlo	9
can be obtained	9
of somatic mutations	9
defined in the	9
the reference genome	9
sequences of the	9
number of false	9
there are two	9
the need to	9
is composed of	9
of particlechromo d	9
the expressions of	9
of interest in	9
of informative genes	9
to a single	9
tools such as	9
quantile empirical p	9
because of the	9
used to derive	9
number of sequences	9
cells that are	9
the input of	9
than that of	9
are the most	9
genes that have	9
is possible that	9
independent test set	9
international journal of	9
average cortical thickness	9
an array of	9
generalized linear models	9
of the sequence	9
were found to	9
drug repurposing screening	9
associated genes in	9
mmdvae followed by	9
plot of the	9
data used in	9
to the best	9
the human and	9
high weight genes	9
mutation effect prediction	9
we evaluated the	9
for the analysis	9
gene expression omnibus	9
given by the	9
usa department of	9
as the reference	9
of rrna sequences	9
the dimension of	9
and quantification of	9
sequences that pass	9
the drug repurposing	9
the simulated dataset	9
on simulated data	9
of the overall	9
set for patient	9
the original paper	9
in the sequence	9
boxplot showing the	9
due to its	9
the allele frequency	9
assigned to the	9
they do not	9
been used to	9
chromosome and genome	9
is one of	9
effects in the	9
w bases apart	9
sample set for	9
tsne t s	9
we have developed	9
en si ty	9
a lot of	9
the pearson correlation	9
of intervention time	9
the bulk genome	9
true and predicted	9
we assume that	9
school of medicine	9
yes yes no	9
used to calculate	9
in any of	9
lsu rrna sequences	9
li et al	9
the ratio of	9
mer in a	9
take into account	9
is known to	9
a b c	9
of the features	9
can be easily	9
niagads gwas summary	9
the degree of	9
of the subject	9
distribution of p	9
can be applied	9
the null hypothesis	9
the gene level	9
used as the	9
it is the	8
it is worth	8
selected in the	8
of squared errors	8
is clear that	8
the model was	8
support vector machine	8
at the strain	8
prokaryotic ssu rrna	8
gene and cell	8
on a single	8
confidence interval of	8
sparc curation team	8
mutations in cancer	8
deviation of the	8
braak e ig	8
position of the	8
of driver and	8
do not have	8
was used for	8
thioguanosine log c	8
the total energy	8
the creation of	8
and the number	8
full list of	8
rqvmzs df v	8
allows users to	8
the assumption that	8
amyloid lowering intervention	8
instead of the	8
we applied the	8
number of unique	8
the ability of	8
for each transcript	8
to the gene	8
achieved the best	8
can be considered	8
g is ix	8
provided in supplementary	8
the gm datasets	8
in optimal solutions	8
not wgs filter	8
optimal polar set	8
ranked genes are	8
to select the	8
jain et al	8
of anisomycin log	8
of the existing	8
with ddis involving	8
detailing the full	8
gene selection and	8
differentially weighted edges	8
squamous cell carcinoma	8
manifold approximation and	8
time and memory	8
the position of	8
that it can	8
pca and aes	8
w w w	8
in supplementary table	8
different fs methods	8
to the truth	8
edit smartreference ruyzz	8
ns e n	8
across a wide	8
with cell library	8
as we have	8
of machine learning	8
file detailing the	8
the prediction of	8
the values of	8
lice n se	8
were used as	8
in the study	8
the evolution of	8
estimate of the	8
was used as	8
for statistical computing	8
correlation between the	8
and the x	8
the pbmc datasets	8
not refseq filter	8
com dcgerard ldsep	8
parc s i	8
is used for	8
ribosomal rna ti	8
majority of the	8
and the resulting	8
of integration sites	8
anisomycin log c	8
identified by the	8
are known to	8
our previous work	8
on the cell	8
in the active	8
with the following	8
genomic distributions of	8
number of k	8
not mrna filter	8
information in the	8
were obtained using	8
been shown to	8
genes in each	8
the level of	8
administration of atorvastatin	8
of selected k	8
the layered polar	8
of layered polar	8
associated with ddis	8
as it is	8
d e r	8
io r xiv	8
contribute to the	8
obtained by comparing	8
the genes in	8
k v human	8
sequences that are	8
back to the	8
for the gm	8
informative genes selected	8
comparing the particlechromo	8
s pe r	8
presence of thioguanosine	8
university of michigan	8
d o i	8
for the development	8
cerad e ig	8
start and end	8
are required to	8
that there are	8
gyra d n	8
maximum activation value	8
we demonstrate that	8
using the svm	8
briefings in bioinformatics	8
the other two	8
the back pocket	8
than the other	8
bayesian linear model	8
is a set	8
the primary data	8
of synonymous motifs	8
swarm size values	8
compatible with u	8
greater than the	8
a deep learning	8
from the reference	8
for each individual	8
of the other	8
we find that	8
the sequence of	8
a drug pair	8
stored in a	8
single administrations of	8
of the mean	8
cancer data set	8
the sparc consortium	8
in the latent	8
tes g is	8
is less than	8
correspondence should be	8
the design of	8
of the total	8
we performed a	8
from the database	8
the sequence is	8
an r package	8
for targeted gene	8
the mean abundance	8
nelfinavir drc in	8
the treatment of	8
in the form	8
the integration sites	8
more difficult to	8
the advantage of	8
structure with the	8
it is clear	8
associated with a	8
can be accessed	8
to determine if	8
in the realistic	8
of nitrogen atoms	8
results from the	8
m and m	8
nine data sets	8
of genes in	8
could be used	8
and supplementary fig	8
the tet profile	8
of cortical thickness	8
a ms a	8
separation of the	8
h p a	8
cd t cells	8
er s http	8
the purpose of	8
step of the	8
the running time	8
mer in the	8
on a random	8
se rv ed	8
methods on the	8
label label label	8
the fs methods	8
ranked genes based	8
description of the	8
the most recent	8
strainflair and kraken	8
can be seen	8
using a threshold	8
than of the	8
density of a	8
has to be	8
the landscape of	8
serve as a	8
two or more	8
m s pe	8
used for the	8
only the bulk	8
zheng et al	8
the expected vaf	8
dimension of the	8
upon removal of	8
per cell division	8
ti not s	8
new england journal	8
tet profile of	8
able to identify	8
o b se	8
it is a	8
selected weight matrix	8
polar set condition	8
disease neuroimaging initiative	8
of the datasets	8
b rqvmzs j	8
to build the	8
to each of	8
results suggest that	8
the selection of	8
in the analysis	8
to study the	8
rqvmzs ix r	8
aligned to the	8
the types of	8
kernel density estimation	8
the ncbi taxonomy	8
subjects and samples	8
we have shown	8
to reduce the	8
effect on the	8
number of cell	8
deep learning models	8
increase in the	8
probability that a	8
equal to the	8
values in the	8
is important to	8
the national institute	8
b se rv	8
journal of medicine	8
from the true	8
be considered as	8
the consensus sequence	8
smartreference ruyzz p	8
england journal of	8
not tls ti	8
mers in the	8
atp binding region	8
an upper bound	8
presence of anisomycin	8
the previous layer	8
be applied to	8
integration of single	8
cdr e ig	8
the sample size	8
regions of the	8
e n itr	8
ruyzz p https	8
between driver and	8
machine learning algorithms	8
nr i and	8
in relation to	8
minimizer compatible with	8
the relevance of	8
individual target set	8
of more than	8
with the trait	8
of the parental	8
were obtained by	8
the predicted genes	8
n d e	8
of the peak	8
is greater than	8
snps in the	8
there are no	8
of thioguanosine log	8
in all the	8
b io r	8
each pair of	8
based on our	8
the tumor cells	8
their association with	8
information presented in	8
in our previous	8
were calculated using	8
the latent variables	8
is due to	8
as measured by	8
list of all	8
methods have been	8
not included in	8
available at the	8
used to determine	8
followed by a	8
with at least	8
the first and	8
set of information	8
of information presented	8
the structures generated	7
the poisson loss	7
original annotation matrix	7
reference variation graph	7
lead to the	7
the mixture of	7
under a the	7
liu et al	7
tes g gkvg	7
was applied to	7
is present in	7
to address this	7
b rqvmzs glz	7
specific density of	7
and out of	7
performed on the	7
was found to	7
sparc data structure	7
the yarza set	7
based on these	7
seq data in	7
s t im	7
of hpv integration	7
with ad traits	7
the cell surface	7
to make the	7
rqvmzs a vg	7
the basic bert	7
single nucleotide polymorphisms	7
the differences in	7
rqvmzs er s	7
subjects per arm	7
data can be	7
adult gbm sample	7
b rqvmzs ji	7
in this figure	7
genome sequences of	7
simple bayesian linear	7
b rqvmzs chqb	7
chemical structures of	7
and the top	7
needs to be	7
both the parents	7
with the number	7
to be associated	7
proc natl acad	7
compared to other	7
supplementary information for	7
in section s	7
to match the	7
node of the	7
that they have	7
end of the	7
of the fs	7
the default parameter	7
used in our	7
of driver mutations	7
tes g ap	7
b rqvmzs er	7
of genes to	7
rqvmzs ueke http	7
agbm sample cgy	7
we tested the	7
r core team	7
here we present	7
if there is	7
information from the	7
wgs filter not	7
swarm optimization algorithm	7
b rqvmzs ydma	7
b rqvmzs mwfz	7
it is also	7
the parents and	7
values of all	7
of drug pairs	7
the mb and	7
in the selected	7
ug x http	7
is equivalent to	7
ssu rrna mito	7
authors declare that	7
rqvmzs glz http	7
explained by the	7
obtained by the	7
and predicted values	7
genetic evidence for	7
fig a and	7
to investigate the	7
b rqvmzs up	7
regions of interest	7
the genes that	7
in figure a	7
proportion of detected	7
caravagna et al	7
ssu rrna and	7
that particlechromo d	7
the standard deviation	7
have been proposed	7
the brain fgn	7
estimation of the	7
scpnmf step ii	7
as the number	7
on the raw	7
review of the	7
like to thank	7
terms of the	7
rqvmzs tcb http	7
rqvmzs ug x	7
shows that the	7
among the top	7
the integration of	7
of escherichia coli	7
im t r	7
national cancer institute	7
batch effects in	7
science and technology	7
rate and the	7
by the number	7
selected based on	7
sequenced cancer genomes	7
activation values of	7
plos comput biol	7
effects of the	7
b rqvmzs ug	7
a the copyright	7
of these two	7
an increase in	7
and has been	7
that did not	7
of the latent	7
the relative abundances	7
the amino acid	7
of cells that	7
nature reviews genetics	7
b rqvmzs fjzp	7
expected hitting time	7
the site frequency	7
the data sets	7
are listed in	7
the interpretation of	7
b rqvmzs wpg	7
site frequency spectrum	7
of chromosome p	7
gene expression matrices	7
the gene ontology	7
on the number	7
lead to an	7
this is not	7
that in the	7
all pairs of	7
and biomarker identification	7
the same size	7
rqvmzs tqet http	7
turnover rate t	7
o c gp	7
rqvmzs mqr http	7
to the fact	7
differential utr usage	7
embeddings of the	7
button on the	7
g ap gd	7
at the time	7
to be used	7
can be run	7
shown in table	7
presence or absence	7
of the entire	7
the raw dataset	7
in the top	7
c and agatha	7
be in the	7
multiple mapped reads	7
raw nucleotide sequences	7
first principal component	7
to readers with	7
we hypothesized that	7
the siamese embedding	7
identified in the	7
when using the	7
kjin cdsll https	7
t im t	7
b rqvmzs ncpj	7
the remaining genes	7
relative position representation	7
to our knowledge	7
a mixture of	7
to facilitate the	7
regardless of the	7
teleporting random walk	7
in the number	7
cell journal and	7
l and l	7
of the gwas	7
loss function and	7
the query string	7
detection and quantification	7
specific minimizers on	7
selected by each	7
the human reference	7
uniform manifold approximation	7
that they are	7
on the top	7
in the table	7
two versions of	7
small sample sizes	7
number of patients	7
associated with drug	7
the journal of	7
xist regulator hgnc	7
rqvmzs wpg http	7
the first k	7
that could be	7
the reference graph	7
in at least	7
chinese academy of	7
b rqvmzs cimd	7
and only if	7
rl f http	7
the numbers of	7
we present the	7
rqvmzs cimd http	7
tes g ovhrz	7
are able to	7
of the sds	7
annotated in the	7
activate the an	7
the ari values	7
susin et al	7
real and simulated	7
number of copies	7
b rqvmzs p	7
the data from	7
that of the	7
of the alevin	7
our understanding of	7
be involved in	7
authors declare no	7
model for predicting	7
as described below	7
ti m e	7
cell type prediction	7
the progression of	7
important to note	7
to note that	7
g yrf j	7
of the underlying	7
were identified by	7
generated from the	7
and test sets	7
features are selected	7
the choice of	7
a normative model	7
and pcc value	7
and used to	7
allowed us to	7
of genes selected	7
number of shared	7
ensg ense ftx	7
transcription factor binding	7
short article title	7
enriched go terms	7
in the presence	7
weight genes in	7
are the same	7
of these genes	7
between true and	7
than in the	7
we note that	7
the hidden layer	7
of omeprazole and	7
and it is	7
rqvmzs chqb http	7
to test whether	7
for a particular	7
are included in	7
the other methods	7
rqvmzs mwfz http	7
absence of a	7
distribution in the	7
forwad attention feed	7
coverage of the	7
for the dataset	7
university of pennsylvania	7
gsea bar full	7
for each dataset	7
are used as	7
hpv integration sites	7
functional gene networks	7
k v mouse	7
also be used	7
university of california	7
study that measures	7
of color blindness	7
many of these	7
sequencing error rate	7
at least two	7
we conclude that	7
for particlechromo d	7
the second stage	7
calculated the precision	7
of booeshaghi and	7
the density of	7
bind to the	7
the expected hitting	7
additive and multiplicative	7
center for biotechnology	7
not srcdb pdb	7
tens of thousands	7
pcc value is	7
the scientific community	7
between age and	7
approximation and projection	7
the activation loop	7
breast cancer cells	7
which may be	7
false positive rate	7
is designed to	7
zakeri et al	7
the maximum activation	7
and normal cells	7
rqvmzs ji a	7
pred and succ	7
those in the	7
that should be	7
focus on the	7
the entropy of	7
rqvmzs pf t	7
effect of the	7
in the expression	7
for single cell	7
and rob patro	7
from the plot	7
b rqvmzs tqet	7
the imputed data	7
a gaussian process	7
assessment of the	7
t r io	7
mitochondrial and ribosomal	7
to improve the	7
in the main	7
number of nitrogen	7
they are not	7
the prr of	7
j j http	7
b rqvmzs mqr	7
because they are	7
expected number of	7
if and only	7
related to ad	7
default parameter settings	7
reached a mean	7
except for the	7
genes that were	7
using the posterior	7
is that the	7
rqvmzs bd o	7
ribosomal and mitochondrial	7
and test set	7
ti not srcdb	7
b rqvmzs ueke	7
srcdb pdb prop	7
the species and	7
memory usage of	7
of computational biology	7
of the methods	7
for site effects	7
the decoupled motifs	7
the activation value	7
breast cancer data	7
weight matrix ws	7
the parameters of	7
obtained the best	7
run of the	7
model for the	7
common form of	7
and does not	7
a variation graph	7
see supplementary fig	7
role in the	7
the aim of	7
in a hierarchical	7
a universal hitting	7
data to the	7
the structure of	7
gs for subject	7
functions of the	7
drug repurposing screenings	7
natl acad sci	7
half of the	7
most common form	7
we present a	7
very similar to	7
interstitial lung disease	7
set gs for	7
can lead to	7
in the last	7
statistic value of	7
is applied to	7
only sequences that	7
with quinolone resistance	7
the advent of	7
similar to those	7
breast cancer cell	7
the informative genes	7
as described previously	7
states of america	7
ji a http	7
the addition of	7
predicted genes with	7
conformation of the	7
cell data using	7
funding this work	7
higher scc and	7
of the observed	7
which is not	7
we refer to	7
rqvmzs ydma http	7
this type of	7
to check the	7
p yv http	7
small human cohorts	7
no more than	7
a test set	7
three cell types	7
microscope images show	7
used as input	7
by the sparc	7
refseq filter not	7
particlechromo d algorithm	7
n s t	7
in the development	7
and pca followed	7
as long as	7
such that the	7
are designed to	7
was obtained from	7
presence of a	7
with the sparc	7
of the predicted	7
rqvmzs rl f	7
in single cell	7
of the previous	7
not certified bythis	7
access to the	7
b rqvmzs tcb	7
each gene and	7
number of times	7
to someone with	7
the rate of	7
and the corresponding	7
will be selected	7
united states of	7
is the size	7
data sets and	7
extracted from the	7
generated using the	7
edit smartreference s	7
rqvmzs fjzp http	7
were aligned to	7
involved in the	7
in the database	7
bythis version posted	7
b rqvmzs rl	7
to show the	7
ssu rrna mitochondria	7
polar set a	7
can be computed	7
fast and accurate	7
in patients with	7
layered polar set	7
evaluation of the	7
for an an	7
rqvmzs ncpj http	7
rqvmzs up http	7
in the legend	7
tes g yrf	7
for d structure	7
with the simulated	7
certified bythis version	7
the pic datasets	7
the area under	7
from the original	7
and ribosomal genes	7
considered as a	7
to a specific	7
of the major	7
can be done	7
on chromosome was	7
to select a	7
fail sequences that	7
to simulate the	7
cid and cid	7
to obtain a	7
is a new	6
peak on chromosome	6
by using a	6
of amyloid lowering	6
the comparison of	6
each node of	6
model inference speed	6
tes g ksjuz	6
the type of	6
values of k	6
can then be	6
with the co	6
are accessible to	6
tes g f	6
selected with the	6
number of features	6
and gene expression	6
high degree of	6
observe that the	6
to optimize the	6
identified as the	6
s g i	6
of normative models	6
case of a	6
ip rk ts	6
or cell related	6
a measure of	6
optimal solutions for	6
downstream analysis of	6
tes g egnuo	6
c kjin cdsll	6
using normative models	6
declare that they	6
computer science and	6
ability to predict	6
range of input	6
between very small	6
and end positions	6
the advantages of	6
showing the ari	6
small subunit ribosomal	6
of the tcga	6
the center position	6
we set the	6
expected proportion of	6
the particle swarm	6
the combination of	6
the idealized data	6
b kallisto alevin	6
mrna filter not	6
the input data	6
m d v	6
structure produced using	6
of gene set	6
this data set	6
tes g qaj	6
the structure produced	6
the same way	6
properties of the	6
cancer cell lines	6
b rqvmzs df	6
to that of	6
effect removal tools	6
cs achieved by	6
evolution of the	6
if there are	6
genes such as	6
of at least	6
on the rna	6
from the data	6
g x omi	6
with site effects	6
performance of our	6
selection of genes	6
differences between the	6
we calculate the	6
com alexmascension triku	6
gb of memory	6
selected small rna	6
the average prr	6
ptn ip rk	6
refers to the	6
types of data	6
in the genome	6
the supplementary materials	6
the time of	6
from bulk sequencing	6
published in april	6
for subject k	6
johnson et al	6
and in the	6
used to infer	6
tes g iigur	6
for each layer	6
associated with each	6
for this field	6
analysis scripts code	6
hs achieved by	6
effect prediction algorithms	6
to minimize the	6
without the aid	6
d chromosome and	6
mackay et al	6
phe side chain	6
is used as	6
and turnover rates	6
to serve as	6
to assess the	6
of each method	6
we apply the	6
and for the	6
is a significant	6
of real data	6
used the following	6
totalsnp ratio and	6
the estimated turnover	6
mer from a	6
in the cancer	6
tes g kwodd	6
m em or	6
is the most	6
analysis showed that	6
illustration of the	6
our results show	6
when applied to	6
window lists all	6
the de analysis	6
rqvmzs uxwc http	6
n is the	6
there are many	6
max activation value	6
gp o c	6
tes g xjiz	6
of the mixture	6
of a random	6
user can also	6
of human genetics	6
s rrna gene	6
supplementary figures s	6
is the probability	6
to the expected	6
computed by strainflair	6
the definition lines	6
different combinations of	6
average number of	6
is not clear	6
in the two	6
g f wh	6
difficult to interpret	6
the kernel density	6
implemented in python	6
reconstruction from hi	6
n n p	6
prr changes for	6
the availability of	6
created based on	6
the percentile plots	6
sequences from silva	6
of marburg virus	6
adult gbm samples	6
em or y	6
plot shows the	6
is uploaded to	6
to specify that	6
reported in the	6
cell related information	6
the jaccard distance	6
g p kbb	6
cutevariant is a	6
not present in	6
bases away from	6
of the p	6
in figure c	6
layer of the	6
c a p	6
cancer mutation census	6
si ty fa	6
kb gm cell	6
c om b	6
domain specific language	6
by the model	6
the goal of	6
described in methods	6
median js distance	6
resulting in a	6
implementation of the	6
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ty fa ct	6
the three models	6
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method for the	6
and real data	6
individual i at	6
density factor of	6
the validation set	6
date month year	6
are mapped to	6
we will refer	6
the receptive field	6
rqvmzs cxxa http	6
be found at	6
a collection of	6
be related to	6
less than of	6
b rqvmzs yagn	6
mir a mirna	6
the silhouette coefficient	6
plger diffutr paper	6
codon usage bias	6
to identify and	6
linear combination of	6
is at most	6
implemented in the	6
in conjunction with	6
c rqvmzs cxxa	6
the content of	6
have been implicated	6
the results obtained	6
in our case	6
oluwadarelab particlechromo d	6
results on the	6
we see that	6
of genes with	6
account for the	6
data analysis using	6
of the four	6
or internal ti	6
f a c	6
b rqvmzs tmou	6
the ingroup analysis	6
atorvastatin and a	6
the plot it	6
vecscreen plus taxonomy	6
and kb resolution	6
with a higher	6
and neurons for	6
hierarchical bayesian approach	6
the independent test	6
not chloroplast filter	6
b rqvmzs vqgd	6
a given cell	6
of the functional	6
cell type identification	6
of fs methods	6
compatible with a	6
ribotyper and rrna	6
liquid phase separation	6
in human cancer	6
of subjects with	6
on the independent	6
and may be	6
gene or cell	6
to impute dropout	6
of the rowdiff	6
modal imaging and	6
of the non	6
resolution for the	6
belonging to the	6
the fraction of	6
ti or s	6
overall accuracy of	6
of the study	6
and the imputed	6
hypothesis generation systems	6
types of images	6
g xbz p	6
b rqvmzs ix	6
the same cell	6
dataset with the	6
of the single	6
with and without	6
tes g qcquj	6
to avoid the	6
all the structures	6
trait of interest	6
g td vb	6
in an adult	6
cell biology papers	6
e m in	6
hierarchical bayesian model	6
prediction of protein	6
differential gene expression	6
window size of	6
amii achieved by	6
the other is	6
the false discovery	6
outside of the	6
from sequenced cancer	6
availability of data	6
with age and	6
of each of	6
highly variable genes	6
cell lineage tree	6
cell surface receptors	6
g p pxd	6
evidence for ad	6
the objective function	6
or s ti	6
amino acid sequence	6
three or more	6
tes g zgbvl	6
b rqvmzs bd	6
like small molecules	6
and the rest	6
cell type annotation	6
of scpnmf is	6
is possible to	6
cell linage tree	6
can only be	6
approximately half of	6
of human papillomavirus	6
data has been	6
y g b	6
transcriptional profiling of	6
to interpret the	6
of a fragment	6
a cohort of	6
a group of	6
c rqvmzs ic	6
the discovery of	6
rqvmzs tmou http	6
neurons for the	6
mc and ma	6
df v http	6
represents the structure	6
goal is to	6
has not been	6
are available in	6
ligand type labels	6
com shobistassen via	6
that we can	6
m e m	6
sequence of the	6
bulk sequencing data	6
the driver and	6
for biotechnology information	6
are composed of	6
b rqvmzs a	6
across a range	6
the features are	6
and the identification	6
values achieved by	6
more than of	6
relevance of the	6
the max activation	6
the same scale	6
relevant gene identification	6
rqvmzs yagn http	6
protein interaction networks	6
of mutations from	6
subject k in	6
has been developed	6
whom correspondence should	6
tes g sc	6
methods do not	6
support vector machines	6
with the aim	6
tes g cxcxs	6
see supplementary table	6
in two ways	6
ix r http	6
in the individual	6
features selected by	6
which leads to	6
a p c	6
expressions of all	6
genome sequence and	6
university of cambridge	6
software package for	6
out site effects	6
ti or internal	6
calculated from the	6
that the number	6
tool for the	6
department of biomedical	6
database can be	6
by selecting the	6
is ix http	6
has been reported	6
not mitochondrial ti	6
ding et al	6
in the tfbs	6
impute dropout events	6
tend to have	6
to understand the	6
to the next	6
kjin kb e	6
ratio of the	6
state of the	6
with the help	6
they have no	6
in the genomicsdb	6
r package for	6
associated genes from	6
distribution is the	6
datasets can be	6
using the r	6
corresponding to a	6
to call cnvs	6
value for the	6
annotation matrix a	6
modified combat model	6
from the polar	6
type annotation on	6
the reference variation	6
the most important	6
vast majority of	6
the siamese network	6
read alignment with	6
bacterial and archaeal	6
allows for the	6
of the th	6
physiology journal and	6
across the entire	6
in figure panel	6
for prediction of	6
vm achieved by	6
b rqvmzs zohm	6
the ribovore documentation	6
on each dataset	6
data sets that	6
likely associated with	6
on the order	6
by combining the	6
s ribosomal rna	6
the national institutes	6
obtained with the	6
srr v mouse	6
the atp binding	6
the utility of	6
ddis involving atorvastatin	6
of single cell	6
hgmm k v	6
or y g	6
fms achieved by	6
the absolute value	6
umap visualisation of	6
is supported by	6
of the average	6
aid of the	6
obtained on the	6
the source code	6
the upper bound	6
for a specific	6
of biomedical engineering	6
sequences in the	6
their ability to	6
association of the	6
can be a	6
v a ls	6
ari values achieved	6
and neck squamous	6
with a random	6
but it is	6
with or without	6
the significance of	6
available through the	6
the protein sequence	6
protein kinase structures	6
mutation and turnover	6
on date month	6
drug pair and	6
related pathways and	6
the genome sequences	6
has been shown	6
sequence compression complexity	6
years before conversion	6
chloroplast filter not	6
a c om	6
with the aid	6
turnover rate and	6
parameters of the	6
the calculated metrics	6
in the optimal	6
ratio and the	6
is at least	6
that aims to	6
bulked segregant analysis	6
we used two	6
journal of machine	6
d v a	6
the basset model	6
shown in this	6
yuen et al	6
the history of	6
b rqvmzs sxxl	6
of the sample	6
the abundance of	6
the residual permutation	6
ieee transactions on	6
the birth rate	6