Current Opinion in Biotechnology,
Journal Year:
2024,
Volume and Issue:
86, P. 103078 - 103078
Published: Feb. 15, 2024
Single-cell
technologies
have
been
widely
used
in
biological
studies
and
generated
a
plethora
of
single-cell
data
to
be
interpreted.
Due
the
inclusion
priori
metabolic
network
knowledge
as
well
gene-protein-reaction
associations,
genome-scale
models
(GEMs)
powerful
tool
integrate
thereby
interpret
various
omics
mostly
from
bulk
samples.
Here,
we
first
review
two
common
ways
leverage
with
GEMs
then
discuss
advances
on
integrative
analysis
GEMs.
We
end
by
presenting
our
views
current
challenges
perspectives
this
field.
Nature,
Journal Year:
2023,
Volume and Issue:
614(7949), P. 742 - 751
Published: Feb. 8, 2023
Abstract
Cell
identity
is
governed
by
the
complex
regulation
of
gene
expression,
represented
as
gene-regulatory
networks
1
.
Here
we
use
inferred
from
single-cell
multi-omics
data
to
perform
in
silico
transcription
factor
perturbations,
simulating
consequent
changes
cell
using
only
unperturbed
wild-type
data.
We
apply
this
machine-learning-based
approach,
CellOracle,
well-established
paradigms—mouse
and
human
haematopoiesis,
zebrafish
embryogenesis—and
correctly
model
reported
phenotype
that
occur
a
result
perturbation.
Through
systematic
perturbation
developing
zebrafish,
simulate
experimentally
validate
previously
unreported
results
loss
noto
,
an
established
notochord
regulator.
Furthermore,
identify
axial
mesoderm
regulator,
lhx1a
Together,
these
show
CellOracle
can
be
used
analyse
factors,
provide
mechanistic
insights
into
development
differentiation.
Nature Reviews Drug Discovery,
Journal Year:
2023,
Volume and Issue:
22(6), P. 496 - 520
Published: April 28, 2023
Single-cell
technologies,
particularly
single-cell
RNA
sequencing
(scRNA-seq)
methods,
together
with
associated
computational
tools
and
the
growing
availability
of
public
data
resources,
are
transforming
drug
discovery
development.
New
opportunities
emerging
in
target
identification
owing
to
improved
disease
understanding
through
cell
subtyping,
highly
multiplexed
functional
genomics
screens
incorporating
scRNA-seq
enhancing
credentialling
prioritization.
ScRNA-seq
is
also
aiding
selection
relevant
preclinical
models
providing
new
insights
into
mechanisms
action.
In
clinical
development,
can
inform
decision-making
via
biomarker
for
patient
stratification
more
precise
monitoring
response
progression.
Here,
we
illustrate
how
methods
being
applied
key
steps
discuss
ongoing
challenges
their
implementation
pharmaceutical
industry.
There
have
been
significant
recent
advances
development
remarkable
Ferran
colleagues
primarily
pipeline,
from
decision-making.
Ongoing
potential
future
directions
discussed.
Cell,
Journal Year:
2024,
Volume and Issue:
187(10), P. 2343 - 2358
Published: May 1, 2024
As
the
number
of
single-cell
datasets
continues
to
grow
rapidly,
workflows
that
map
new
data
well-curated
reference
atlases
offer
enormous
promise
for
biological
community.
In
this
perspective,
we
discuss
key
computational
challenges
and
opportunities
reference-mapping
algorithms.
We
how
mapping
algorithms
will
enable
integration
diverse
across
disease
states,
molecular
modalities,
genetic
perturbations,
species
eventually
replace
manual
laborious
unsupervised
clustering
pipelines.
