Current Opinion in Structural Biology,
Journal Year:
2024,
Volume and Issue:
86, P. 102824 - 102824
Published: May 8, 2024
Determining
how
chromatin
is
structured
in
the
nucleus
critical
to
studying
its
role
gene
regulation.
Recent
advances
analysis
of
single-cell
architecture
have
considerably
improved
our
understanding
cell-type-specific
chromosome
conformation
and
nuclear
architecture.
In
this
review,
we
discuss
methods
used
for
3D
conformation,
including
sequencing-based
methods,
imaging-based
techniques,
computational
approaches.
We
further
review
application
these
study
topology
neural
development
disorders.
Science Advances,
Journal Year:
2025,
Volume and Issue:
11(9)
Published: Feb. 26, 2025
3D
organization
of
the
genome
plays
a
critical
role
in
regulating
gene
expression.
How
3D-genome
differs
among
different
cell
types
and
relates
to
type–dependent
transcriptional
regulation
remains
unclear.
Here,
we
used
genome-scale
DNA
RNA
imaging
investigate
transcriptionally
distinct
mouse
cerebral
cortex.
We
uncovered
wide
spectrum
differences
nuclear
architecture
types,
ranging
from
size
nucleus
higher-order
chromosome
structures
radial
positioning
chromatin
loci
within
nucleus.
These
variations
exhibit
strong
correlations
with
both
total
activity
type–specific
marker
genes.
Moreover,
found
that
methylated
binding
protein
MeCP2
promotes
active-inactive
segregation
regulates
transcription
position–dependent
manner
is
highly
correlated
its
function
modulating
compartmentalization.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2025,
Volume and Issue:
unknown
Published: Jan. 8, 2025
Modeling
long-range
DNA
dependencies
is
crucial
for
understanding
genome
structure
and
function
across
a
wide
range
of
biological
contexts.
However,
effectively
capturing
these
extensive
dependencies,
which
may
span
millions
base
pairs
in
tasks
such
as
three-dimensional
(3D)
chromatin
folding
prediction,
remains
significant
challenge.
Furthermore,
comprehensive
benchmark
suite
evaluating
that
rely
on
notably
absent.
To
address
this
gap,
we
introduce
DNAL
ong
B
ench
,
dataset
encompassing
five
important
genomics
consider
up
to
1
million
pairs:
enhancer-target
gene
interaction,
expression
quantitative
trait
loci,
3D
organization,
regulatory
sequence
activity,
transcription
initiation
signals.
comprehensively
assess
evaluate
the
performance
methods:
task-specific
expert
model,
convolutional
neural
network
(CNN)-based
three
fine-tuned
foundation
models
-
HyenaDNA,
Caduceus-Ph,
Caduceus-PS.
We
envision
standardized
resource
with
potential
facilitate
comparisons
rigorous
evaluations
emerging
sequence-based
deep
learning
account
dependencies.
BioData Mining,
Journal Year:
2025,
Volume and Issue:
18(1)
Published: March 28, 2025
The
integration
of
multi-omics
data
from
diverse
high-throughput
technologies
has
revolutionized
drug
discovery.
While
various
network-based
methods
have
been
developed
to
integrate
data,
systematic
evaluation
and
comparison
these
remain
challenging.
This
review
aims
analyze
approaches
for
evaluate
their
applications
in
We
conducted
a
comprehensive
literature
(2015-2024)
on
discovery,
categorized
into
four
primary
types:
network
propagation/diffusion,
similarity-based
approaches,
graph
neural
networks,
inference
models.
also
discussed
the
three
scenario
including
target
identification,
response
prediction,
repurposing,
finally
evaluated
performance
by
highlighting
advantages
limitations
specific
applications.
shown
promise
challenges
computational
scalability,
integration,
biological
interpretation.
Future
developments
should
focus
incorporating
temporal
spatial
dynamics,
improving
model
interpretability,
establishing
standardized
frameworks.
International Journal of Surgery,
Journal Year:
2024,
Volume and Issue:
110(10), P. 6748 - 6762
Published: June 21, 2024
The
advent
of
personalized
bone
prosthesis
materials
and
their
integration
into
orthopedic
surgery
has
made
a
profound
impact,
primarily
as
result
the
incorporation
three-dimensional
(3D)
printing
technology.
By
leveraging
digital
models
additive
manufacturing
techniques,
3D
enables
creation
customized,
high-precision
implants
tailored
to
address
complex
anatomical
variabilities
challenging
defects.
In
this
review,
we
highlight
significant
progress
in
utilizing
printed
prostheses
across
wide
range
procedures,
including
pelvis,
hip,
knee,
foot,
ankle,
spine
surgeries,
tumor
resections.
preoperative
planning,
surgical
navigation,
postoperative
rehabilitation
not
only
enhances
treatment
outcomes
but
also
reduces
risks,
accelerates
recovery,
optimizes
cost-effectiveness.
Emphasizing
potential
for
care
improved
patient
outcomes,
review
underscores
pivotal
role
advancing
practice
towards
precision,
efficiency,
patient-centric
solutions.
evolving
landscape
holds
promise
revolutionizing
approaches,
enhancing
ultimately
improving
quality
patients.
Journal of Experimental Botany,
Journal Year:
2024,
Volume and Issue:
75(17), P. 5357 - 5365
Published: March 2, 2024
The
invention
of
chromosome
conformation
capture
(3C)
techniques,
in
particular
the
key
method
Hi-C
providing
genome-wide
information
about
chromatin
contacts,
revolutionized
way
we
study
three-dimensional
organization
nuclear
genome
and
how
it
affects
transcription,
replication,
DNA
repair.
Because
frequency
contacts
between
pairs
genomic
segments
predictably
relates
to
distance
linear
genome,
obtained
by
has
also
proved
useful
for
scaffolding
sequences.
Here,
review
recent
improvements
experimental
procedures
its
various
derivatives,
such
as
Micro-C,
HiChIP,
Capture
Hi-C.
We
assess
advantages
limitations
present
examples
their
use
plant
studies.
report
on
progress
development
computational
tools
used
assembling
