Abstract
The
most
dynamic
and
repetitive
regions
of
great
ape
genomes
have
traditionally
been
excluded
from
comparative
studies
1–3
.
Consequently,
our
understanding
the
evolution
species
is
incomplete.
Here
we
present
haplotype-resolved
reference
analyses
six
species:
chimpanzee,
bonobo,
gorilla,
Bornean
orangutan,
Sumatran
orangutan
siamang.
We
achieve
chromosome-level
contiguity
with
substantial
sequence
accuracy
(<1
error
in
2.7
megabases)
completely
215
gapless
chromosomes
telomere-to-telomere.
resolve
challenging
regions,
such
as
major
histocompatibility
complex
immunoglobulin
loci,
to
provide
in-depth
evolutionary
insights.
Comparative
enabled
investigations
diversity
previously
uncharacterized
or
incompletely
studied
without
bias
mapping
human
genome.
Such
include
newly
minted
gene
families
lineage-specific
segmental
duplications,
centromeric
DNA,
acrocentric
subterminal
heterochromatin.
This
resource
serves
a
comprehensive
baseline
for
future
humans
closest
living
relatives.
Nucleic Acids Research,
Год журнала:
2024,
Номер
53(D1), С. D1243 - D1249
Опубликована: Окт. 26, 2024
The
UCSC
Genome
Browser
(https://genome.ucsc.edu)
is
a
widely
utilized
web-based
tool
for
visualization
and
analysis
of
genomic
data,
encompassing
over
4000
assemblies
from
diverse
organisms.
Since
its
release
in
2001,
it
has
become
an
essential
resource
genomics
bioinformatics
research.
Annotation
data
available
on
includes
both
internally
created
maintained
tracks
as
well
custom
track
hubs
provided
by
the
research
community.
This
last
year's
updates
include
25
new
annotation
such
gnomAD
4.1
human
GRCh38/hg38
assembly,
addition
three
public
hubs,
significant
expansions
to
Archive[GenArk)
system
interacting
with
enormous
variety
assemblies.
We
have
also
made
improvements
our
interface,
including
browser
graphic
page,
popup
dialog
feature
that
now
displays
item
details
without
requiring
navigation
away
main
page.
GenePred
been
upgraded
right-click
options
zooming
precise
navigation,
along
enhanced
mouseOver
functions.
Additional
grouping
hub
description
info
links.
A
tutorial
focusing
Clinical
Genetics
added
Browser.
Molecular & Cellular Proteomics,
Год журнала:
2023,
Номер
22(9), С. 100631 - 100631
Опубликована: Авг. 11, 2023
Ribosome
profiling
(Ribo-Seq)
has
proven
transformative
for
our
understanding
of
the
human
genome
and
proteome
by
illuminating
thousands
noncanonical
sites
ribosome
translation
outside
currently
annotated
coding
sequences
(CDSs).
A
conservative
estimate
suggests
that
at
least
7000
ORFs
are
translated,
which,
first
glance,
potential
to
expand
number
protein
CDSs
30%,
from
∼19,500
over
26,000
CDSs.
Yet,
additional
scrutiny
these
raised
numerous
questions
about
what
fraction
them
truly
produce
a
product
those
can
be
understood
as
proteins
according
conventional
term.
Adding
further
complication
is
fact
published
estimates
vary
widely
around
30-fold,
several
thousand
hundred
thousand.
The
summation
this
research
left
genomics
proteomics
communities
both
excited
prospect
new
regions
in
but
searching
guidance
on
how
proceed.
Here,
we
discuss
current
state
ORF
research,
databases,
interpretation,
focusing
assess
whether
given
said
"protein
coding."
Cell,
Год журнала:
2024,
Номер
187(5), С. 1255 - 1277.e27
Опубликована: Фев. 1, 2024
Despite
the
successes
of
immunotherapy
in
cancer
treatment
over
recent
decades,
less
than
<10%–20%
cases
have
demonstrated
durable
responses
from
immune
checkpoint
blockade.
To
enhance
efficacy
immunotherapies,
combination
therapies
suppressing
multiple
evasion
mechanisms
are
increasingly
contemplated.
better
understand
cell
surveillance
and
diverse
tumor
tissues,
we
comprehensively
characterized
landscape
more
1,000
tumors
across
ten
different
cancers
using
CPTAC
pan-cancer
proteogenomic
data.
We
identified
seven
distinct
subtypes
based
on
integrative
learning
type
compositions
pathway
activities.
then
thoroughly
categorized
unique
genomic,
epigenetic,
transcriptomic,
proteomic
changes
associated
with
each
subtype.
Further
leveraging
deep
phosphoproteomic
data,
studied
kinase
activities
subtypes,
which
revealed
potential
subtype-specific
therapeutic
targets.
Insights
this
work
will
facilitate
development
future
strategies
precision
targeting
existing
agents.
Nucleic Acids Research,
Год журнала:
2024,
Номер
53(D1), С. D948 - D957
Опубликована: Дек. 4, 2024
Ensembl
(www.ensembl.org)
is
an
open
platform
integrating
publicly
available
genomics
data
across
the
tree
of
life
with
a
focus
on
eukaryotic
species
related
to
human
health,
agriculture
and
biodiversity.
This
year
has
seen
continued
expansion
in
number
represented,
>4800
>31
300
prokaryotic
genomes
available.
The
new
site,
currently
beta,
develop,
holding
>2700
genome
assemblies.
site
provides
genome,
gene,
transcript,
homology
variation
views,
will
replace
current
Rapid
Release
site;
this
represents
key
step
towards
provision
single
integrated
site.
Additional
activities
have
included
developing
improved
regulatory
annotation
for
human,
mouse
agricultural
species,
expanding
Variant
Effect
Predictor
tool.
To
learn
more
about
Ensembl,
help
documentation
are
along
extensive
training
program
that
can
be
accessed
via
our
pages.
Trends in Genetics,
Год журнала:
2025,
Номер
unknown
Опубликована: Янв. 1, 2025
MicroRNAs
(miRNAs)
are
key
regulators
of
gene
expression
and
control
cellular
functions
in
physiological
pathophysiological
states.
miRNAs
play
important
roles
disease,
stress,
development,
now
being
investigated
for
therapeutic
approaches.
Alternative
processing
during
biogenesis
results
the
generation
miRNA
isoforms
(isomiRs)
which
further
diversify
regulation.
Single-cell
RNA-sequencing
(scsRNA-seq)
technologies,
together
with
computational
strategies,
enable
exploration
miRNAs,
isomiRs,
interacting
RNAs
at
level.
By
integration
other
miRNA-associated
single-cell
modalities,
can
be
resolved
different
stages
In
this
review
we
discuss
(i)
experimental
assays
that
measure
isomiR
abundances,
(ii)
methods
their
analysis
to
investigate
mechanisms
post-transcriptional
The
pathogenesis
of
complex
diseases
is
intricately
linked
to
various
genes
and
network
medicine
has
enhanced
understanding
diseases.
However,
most
network-based
approaches
ignore
interactions
mediated
by
noncoding
RNAs
(ncRNAs)
databases
only
focus
on
the
association
between
Based
mentioned
questions,
we
have
developed
DisGeNet,
a
database
focuses
not
disease-associated
but
also
among
genes.
Here,
associations
genes,
as
well
these
are
integrated
into
disease-centric
network.
As
result,
there
total
502
688
interactions/associations
involving
6697
diseases,
5780
lncRNAs
(long
RNAs),
16
135
protein-coding
2610
microRNAs
stored
in
DisGeNet.
These
can
be
categorized
protein-protein,
lncRNA-disease,
microRNA-gene,
microRNA-disease,
gene-disease,
microRNA-lncRNA.
Furthermore,
users
input
name/ID
diseases/genes
for
search,
about
search
content
browsed
list
or
viewed
local
network-view.
Database
URL:
https://disgenet.cn/.
