Research Square (Research Square),
Journal Year:
2023,
Volume and Issue:
unknown
Published: May 8, 2023
Abstract
Objectives
The
goal
of
this
study
was
to
use
a
new
machine-learning
framework
based
on
max-linear
competing
risk
factor
models
identify
parsimonious
set
differentially
expressed
genes
(DEGs)
that
play
pivotal
role
in
the
development
colorectal
cancer
(CRC).
Methods
Transcriptome
data
from
six
public
datasets
were
analyzed,
and
Chinese
cohort
collected
validate
findings.
Results
discovered
four
critical
DEGs
-
CXCL8,
PSMC2,
APP,
SLC20A1
exhibit
high
accuracy
detecting
CRC
diverse
populations
ethnicities.
Notably,
PSMC2
CXCL8
appear
central
CRC,
alone
could
potentially
serve
as
an
early-stage
marker
for
CRC.
Conclusions
This
work
represents
pioneering
effort
applying
model
human
malignancies,
reproducibility
results
across
suggests
identified
can
provide
comprehensive
description
transcriptomic
features
practical
implications
research
include
potential
personalized
assessment
tailored
treatment
plans
patients.
npj Precision Oncology,
Journal Year:
2024,
Volume and Issue:
8(1)
Published: Jan. 20, 2024
Abstract
The
goal
of
this
study
was
to
use
a
new
interpretable
machine-learning
framework
based
on
max-logistic
competing
risk
factor
models
identify
parsimonious
set
differentially
expressed
genes
(DEGs)
that
play
pivotal
role
in
the
development
colorectal
cancer
(CRC).
Transcriptome
data
from
nine
public
datasets
were
analyzed,
and
Chinese
cohort
collected
validate
findings.
discovered
four
critical
DEGs
-
CXCL8,
PSMC2,
APP,
SLC20A1
exhibit
highest
accuracy
detecting
CRC
diverse
populations
ethnicities.
Notably,
PSMC2
CXCL8
appear
central
CRC,
alone
could
potentially
serve
as
an
early-stage
marker
for
CRC.
This
work
represents
pioneering
effort
applying
model
human
malignancies,
interpretability
reproducibility
results
across
suggests
identified
can
provide
comprehensive
description
transcriptomic
features
practical
implications
research
include
potential
personalized
assessment
precision
diagnosis
tailored
treatment
plans
patients.
Cancer Informatics,
Journal Year:
2023,
Volume and Issue:
22
Published: Jan. 1, 2023
Hepatocellular
carcinoma
(HCC)
is
one
of
the
most
fatal
cancers
in
world.
There
an
urgent
need
to
understand
molecular
background
HCC
facilitate
identification
biomarkers
and
discover
effective
therapeutic
targets.
Published
transcriptomic
studies
have
reported
a
large
number
genes
that
are
individually
significant
for
HCC.
However,
reliable
remain
be
determined.
In
this
study,
built
on
max-linear
competing
risk
factor
models,
we
developed
machine
learning
analytical
framework
analyze
data
identify
miniature
set
differentially
expressed
(DEGs).
By
analyzing
9
public
whole-transcriptome
datasets
(containing
1184
samples
672
nontumor
controls),
identified
5
critical
(DEGs)
(ie,
CCDC107,
CXCL12,
GIGYF1,
GMNN,
IFFO1)
between
control
samples.
The
classifiers
these
DEGs
reached
nearly
perfect
performance
was
further
validated
US
Caucasian
cohort
collected
17
with
paired
tissue).
conceptual
advance
our
work
lies
modeling
gene-gene
interactions
correcting
batch
effect
analytic
framework.
demonstrated
clear
signature
patterns
results
interpretable,
robust,
reproducible
across
diverse
cohorts/populations
various
disease
etiologies,
indicating
intrinsic
variables
can
describe
overall
features
at
genomic
level.
applied
study
may
pave
new
way
improving
transcriptome
profiling
analysis
human
cancers.
Vaccines,
Journal Year:
2022,
Volume and Issue:
10(5), P. 761 - 761
Published: May 11, 2022
Hoping
to
find
genomic
clues
linked
COVID-19
and
end
the
pandemic
has
driven
scientists'
tremendous
efforts
try
all
kinds
of
research.
Signs
progress
have
been
achieved
but
are
still
limited.
This
paper
intends
prove
existence
at
least
three
signature
patterns
seven
subtypes
by
five
critical
genes
(the
smallest
subset
genes)
using
blood-sampled
datasets.
These
signatures
provide
crucial
information
in
diagnosis
(including
ICU
patients),
research
focuses,
treatment
methods.
Unlike
existing
approaches
focused
on
gene
fold-changes
pathways,
gene-gene
nonlinear
competing
interactions
driving
forces
finding
subtypes.
Furthermore,
method
leads
high
accuracy
with
hospitalized
patients,
showing
biological
mathematical
equivalences
between
status
a
methodological
advantage
over
other
methods
that
cannot
lead
accuracy.
As
result,
as
new
biomarkers,
findings
can
be
much
more
informative
than
for
interpreting
mechanisms,
developing
second
(third)
generation
vaccines,
antiviral
drugs,
methods,
eventually
bringing
hopes
an
pandemic.
Biology,
Journal Year:
2024,
Volume and Issue:
13(4), P. 245 - 245
Published: April 7, 2024
Earlier
research
has
established
the
existence
of
reliable
interactive
genomic
biomarkers.
However,
DNA
methylation
biomarkers,
not
to
mention
interactivity,
have
yet
be
identified
at
epigenetic
level.
This
study,
drawing
from
865,859
sites,
discovered
two
miniature
sets
Infinium
MethylationEPIC
each
having
eight
CpG
sites
(genes)
interact
with
other
and
disease
subtypes.
They
led
nearly
perfect
(96.87–100%
accuracy)
prediction
COVID-19
patients
diseases
or
healthy
controls.
These
can
jointly
explain
some
post-COVID-19-related
conditions.
optimally
performing
biomarkers
reported
in
literature
become
potential
druggable
targets.
Among
these
cg16785077
(gene
MX1),
cg25932713
PARP9),
cg22930808
PARP9)
levels
indicate
that
initial
SARS-CoV-2
virus
may
better
treated
as
a
transcribed
viral
into
RNA
virus,
i.e.,
an
concerned
scientists
field.
Such
discovery
significantly
change
scientific
thinking
knowledge
viruses.
Vaccines,
Journal Year:
2022,
Volume and Issue:
10(10), P. 1657 - 1657
Published: Oct. 2, 2022
Genes
functionally
associated
with
SARS-CoV-2
infection
and
genes
related
to
the
COVID-19
disease
can
be
different,
whose
distinction
will
become
first
essential
step
for
successfully
fighting
against
pandemic.
Unfortunately,
this
has
not
been
completed
in
all
biological
medical
research.
Using
a
newly
developed
max-competing
logistic
classifier,
two
genes,
ATP6V1B2
IFI27,
stand
out
critical
transcriptional
response
differential
expressions
derived
from
NP/OP
swab
PCR.
This
finding
is
evidenced
by
combining
these
another
gene
predicting
status
achieve
better-indicating
accuracy
than
existing
classifiers
same
number
of
genes.
In
addition,
three
other
form
five-gene
classifier
outperforms
ten
or
more
These
pandemic
as
new
focus
direction
their
exceptional
accuracy.
Comparing
functional
effects
100%
identified
tested
blood
samples
our
earlier
work,
on
infection,
signature
patterns
antibodies,
are
significantly
different.
We
use
total
fourteen
cohort
studies
(including
breakthrough
infections
omicron
variants)
1481
justify
results.
Such
significant
findings
help
explore
causal
pathological
links
between
disease,
fight
targeted
vaccines,
antiviral
drugs,
therapies.
Vaccines,
Journal Year:
2022,
Volume and Issue:
10(11), P. 1774 - 1774
Published: Oct. 22, 2022
COVID-19
vaccines
can
be
the
tugboats
for
preventing
SARS-CoV-2
infections
when
they
are
practical
and,
more
importantly,
without
adverse
effects.
However,
reality
is
that
may
result
in
short-term
or
long-term
impacts
on
COVID-19-related
diseases
and
even
trigger
formation
of
new
variants
SARS-CoV-2.
Using
published
data,
we
use
a
set
optimized-performance
genomic
biomarkers
(MND1,
CDC6,
ZNF282)
to
study
benefits
effects
BNT162b2
vaccine.
We
found
vaccine
lowered
expression
values
genes
MND1
CDC6
while
heightening
ZNF282
individuals
who
naïve,
which
expected
satisfies
biological
equivalence
between
disease
signature
patterns
established
literature.
also
COVID-19-convalescent
octogenarians
responded
reversely.
The
heightened
CDC6.
In
addition,
it
ZNF282.
Such
raise
outstanding
concerns
about
whether
not
should
take
current
it.
These
findings
at
level
provide
insights
into
developing
next-generation
vaccines,
antiviral
drugs,
pandemic
management
guidance.
Advances in Biomarker Sciences and Technology,
Journal Year:
2023,
Volume and Issue:
5, P. 105 - 123
Published: Jan. 1, 2023
Omicron
and
its
subvariants
have
become
the
predominant
SARS-CoV-2
variants
worldwide.
The
Omicron's
basic
reproduction
number
(R0)
has
been
close
to
20
or
higher.
However,
it
is
not
known
what
caused
such
an
extremely
high
R0
whether
intrinsic
gene-gene
interactions
are
different
from
earlier
variants.
Find
explanation
for
infection.
Max-linear
competing
logistic
regression
classifier.
We
found
that
jumped
away
which
can
be
fully
described
by
a
miniature
set
of
genes
reported
in
our
work.
gene
PTAFR
(Platelet
Activating
Factor
Receptor)
highly
correlated
with
variants,
so
CCNI
(Cyclin
I),
conserved
chimpanzee,
Rhesus
monkey,
dog,
cow,
mouse,
rat,
chicken,
zebrafish,
frog.
combination
lead
100%
accuracy
differentiating
COVID-19
infection
negative.
hypothesize
were
potentially
COVID-19-infected
animals
back
humans.
In
addition,
there
also
several
other
two-gene
interactions,
besides
CCNI,
accuracy.
Such
observations
explain
Omicron"s
fast-spread
capability
as
either
those
infection,
i.e.,
multiplication
R0s
leads
much
higher
R0.
At
genomic
level,
PTAFR,
identified
this
work
rise
druggable
targets
antiviral
drugs
existing
drugs.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2022,
Volume and Issue:
unknown
Published: Jan. 25, 2022
Abstract
Hoping
to
find
genomic
clues
linked
COVID-19
and
end
the
pandemic
has
driven
scientists’
tremendous
efforts
try
all
kinds
of
research.
Signs
progress
have
been
achieved
but
are
still
limited.
This
paper
intends
prove
existence
at
least
three
signature
patterns
seven
subtypes
by
five
critical
genes
(the
smallest
subset
genes).
These
signatures
provide
crucial
information
in
diagnosis
(including
ICU
patients),
research
focuses,
treatment
methods.
Unlike
existing
approaches
focused
on
gene
fold-changes
pathways,
gene-gene
nonlinear
competing
interactions
driving
forces
finding
subtypes.
Furthermore,
method
leads
100%
accuracy,
which
shows
biological
mathematical
equivalences
between
status
a
methodological
advantage
over
other
methods
that
cannot
lead
accuracy.
As
result,
as
new
biomarkers,
findings
can
be
much
more
informative
than
for
interpreting
mechanisms,
developing
second
(third)
generation
vaccines,
antiviral
drugs,
methods,
eventually
bringing
hopes
an
pandemic.
Research Square (Research Square),
Journal Year:
2022,
Volume and Issue:
unknown
Published: Aug. 15, 2022
Abstract
COVID-19
vaccines
can
be
the
tugboats
of
preventing
SARS-CoV-2
infections
when
they
are
practical
and,
more
importantly,
without
adverse
effects.
However,
reality
is
that
may
result
in
short-term
or
long-term
impacts
on
COVID-19-related
diseases
and
even
trigger
formation
new
variants
SARS-CoV-2.
Using
published
data,
we
use
a
set
high-performance
genomic
biomarkers
(MND1,
CDC6,
ZNF282)
to
study
benefits
effects
BNT162b2
vaccine.
We
found
vaccine
lowered
expression
values
genes
MND1
CDC6
while
heightening
ZNF282
individuals
with
SARS-CoV-2-naive,
which
expected
satisfies
biological
equivalence
between
disease
signature
patterns
established
literature.
also
adversely
affected
convalescent
octogenarians.
It
heightened
CDC6.
In
addition,
it
ZNF282.
Such
raise
outstanding
concerns
about
whether
not
should
take
current
it.
These
findings
at
level
provide
insights
into
developing
next-generation
vaccines,
antiviral
drugs,
pandemic
management
guidance.