Briefings in Bioinformatics,
Journal Year:
2023,
Volume and Issue:
24(1)
Published: Jan. 1, 2023
DNA
and
RNA
sequencing
technologies
have
revolutionized
biology
biomedical
sciences,
full
genomes
transcriptomes
at
very
high
speeds
reasonably
low
costs.
(RNA-Seq)
enables
transcript
identification
quantification,
but
once
has
concluded
researchers
can
be
easily
overwhelmed
with
questions
such
as
how
to
go
from
raw
data
differential
expression
(DE),
pathway
analysis
interpretation.
Several
pipelines
procedures
been
developed
this
effect.
Even
though
there
is
no
unique
way
perform
RNA-Seq
analysis,
it
usually
follows
these
steps:
1)
reads
quality
check,
2)
alignment
of
a
reference
genome,
3)
aligned
reads'
summarization
according
an
annotation
file,
4)
DE
5)
gene
set
and/or
functional
enrichment
analysis.
Each
step
requires
make
decisions,
the
wide
variety
options
resulting
large
volumes
often
lead
interpretation
challenges.
There
also
seems
insufficient
guidance
on
best
obtain
relevant
information
derive
actionable
knowledge
transcription
experiments.
In
paper,
we
explain
steps
in
detail
outline
differences
similarities
different
popular
options,
well
advantages
disadvantages.
We
discuss
non-coding
multi-omics,
meta-transcriptomics
use
artificial
intelligence
methods
complementing
arsenal
tools
available
researchers.
Lastly,
complete
visually
illustrating
results
are
not
absolute
truths
algorithmic
decisions
greatly
impact
Annual Review of Cell and Developmental Biology,
Journal Year:
2022,
Volume and Issue:
38(1), P. 263 - 289
Published: May 25, 2022
Covalently
closed,
single-stranded
circular
RNAs
can
be
produced
from
viral
RNA
genomes
as
well
the
processing
of
cellular
housekeeping
noncoding
and
precursor
messenger
RNAs.
Recent
transcriptomic
studies
have
surprisingly
uncovered
that
many
protein-coding
genes
subjected
to
backsplicing,
leading
widespread
expression
a
specific
type
(circRNAs)
in
eukaryotic
cells.
Here,
we
discuss
experimental
strategies
used
discover
characterize
diverse
circRNAs
at
both
genome
individual
gene
scales.
We
further
highlight
current
understanding
how
are
generated
mature
transcripts
function.
Some
act
impact
regulation
by
serving
decoys
or
competitors
for
microRNAs
proteins.
Others
form
extensive
networks
ribonucleoprotein
complexes
encode
functional
peptides
translated
response
certain
stresses.
Overall,
emerged
an
important
class
RNAmolecules
physiological
processes,
including
early
development,
immune
responses,
neurogenesis,
tumorigenesis.
Journal of Hematology & Oncology,
Journal Year:
2021,
Volume and Issue:
14(1)
Published: Aug. 30, 2021
Abstract
Background
Hepatocellular
carcinoma
(HCC)
is
one
of
the
most
common
malignancies
globally.
Despite
aggressive
and
multimodal
treatment
regimens,
overall
survival
HCC
patients
remains
poor.
Main
Circular
RNAs
(circRNAs)
are
noncoding
(ncRNAs)
with
covalently
closed
structures
tissue-
or
organ-specific
expression
patterns
in
eukaryotes.
They
highly
stable
have
important
biological
functions,
including
acting
as
microRNA
sponges,
protein
scaffolds,
transcription
regulators,
translation
templates
interacting
RNA-binding
protein.
Recent
advances
indicated
that
circRNAs
present
abnormal
tissues
their
dysregulation
contributes
to
initiation
progression.
Furthermore,
researchers
revealed
some
might
serve
diagnostic
biomarkers
drug
targets
clinical
settings.
In
this
review,
we
systematically
evaluate
characteristics,
biogenesis,
mechanisms
functions
further
discuss
current
shortcomings
potential
directions
prospective
studies
on
liver
cancer-related
circRNAs.
Conclusion
CircRNAs
a
novel
class
ncRNAs
play
significant
role
progression,
but
internal
applications
need
investigation.
International Journal of Oral Science,
Journal Year:
2022,
Volume and Issue:
14(1)
Published: Aug. 5, 2022
Osteoarthritis
(OA)
is
a
prevalent
degenerative
joint
disease
characterized
by
cartilage
loss
and
accounts
for
major
source
of
pain
disability
worldwide.
However,
effective
strategies
repair
are
lacking,
patients
with
advanced
OA
usually
need
replacement.
Better
comprehending
pathogenesis
may
lead
to
transformative
therapeutics.
Recently
studies
have
reported
that
exosomes
act
as
new
means
cell-to-cell
communication
delivering
multiple
bioactive
molecules
create
particular
microenvironment
tunes
behavior.
Specifically,
exosome
cargos,
such
noncoding
RNAs
(ncRNAs)
proteins,
play
crucial
role
in
progression
regulating
the
proliferation,
apoptosis,
autophagy,
inflammatory
response
cells,
rendering
them
promising
candidates
monitoring
treatment.
This
review
systematically
summarizes
current
insight
regarding
biogenesis
function
their
potential
therapeutic
tools
targeting
OA,
suggesting
realms
improve
management.
Micromachines,
Journal Year:
2023,
Volume and Issue:
14(2), P. 459 - 459
Published: Feb. 16, 2023
There
has
been
significant
progress
made
in
the
field
of
nanopore
biosensor
development
and
sequencing
applications,
which
address
previous
limitations
that
restricted
widespread
use.
These
innovations,
paired
with
large-scale
commercialization
biological
by
Oxford
Nanopore
Technologies,
are
making
platforms
a
mainstay
contemporary
research
laboratories.
Equipped
ability
to
provide
long-
short
read
information,
quick
turn-around
times
simple
sample
preparation,
sequencers
rapidly
improving
our
understanding
unsolved
genetic,
transcriptomic,
epigenetic
problems.
However,
there
remain
some
key
obstacles
have
yet
be
improved.
In
this
review,
we
general
introduction
principles,
discussing
solid-state
developments,
single-base
detection,
library
preparation
considerations.
We
present
examples
important
clinical
applications
give
perspective
on
potential
future
molecular
diagnostics.
