Mammalian Genome,
Journal Year:
2023,
Volume and Issue:
34(3), P. 364 - 378
Published: April 19, 2023
Abstract
Existing
phenotype
ontologies
were
originally
developed
to
represent
phenotypes
that
manifest
as
a
character
state
in
relation
wild-type
or
other
reference.
However,
these
do
not
include
the
phenotypic
trait
attribute
categories
required
for
annotation
of
genome-wide
association
studies
(GWAS),
Quantitative
Trait
Loci
(QTL)
mappings
any
population-focussed
measurable
data.
The
integration
and
biological
information
with
an
ever
increasing
body
chemical,
environmental
data
greatly
facilitates
computational
analyses
it
is
also
highly
relevant
biomedical
clinical
applications.
Ontology
Biological
Attributes
(OBA)
formalised,
species-independent
collection
interoperable
intended
fulfil
role.
OBA
standardised
representational
framework
observable
attributes
are
characteristics
entities,
organisms,
parts
organisms.
has
modular
design
which
provides
several
benefits
users
integrators,
including
automated
meaningful
classification
terms
computed
on
basis
logical
inferences
drawn
from
domain-specific
cells,
anatomical
entities.
axioms
provide
previously
missing
bridge
can
computationally
link
Mendelian
GWAS
quantitative
traits.
term
components
semantic
links
enable
knowledge
across
specialised
research
community
boundaries,
thereby
breaking
silos.
Nucleic Acids Research,
Journal Year:
2024,
Volume and Issue:
52(W1), P. W83 - W94
Published: May 20, 2024
Abstract
Galaxy
(https://galaxyproject.org)
is
deployed
globally,
predominantly
through
free-to-use
services,
supporting
user-driven
research
that
broadens
in
scope
each
year.
Users
are
attracted
to
public
services
by
platform
stability,
tool
and
reference
dataset
diversity,
training,
support
integration,
which
enables
complex,
reproducible,
shareable
data
analysis.
Applying
the
principles
of
user
experience
design
(UXD),
has
driven
improvements
accessibility,
discoverability
Labs/subdomains,
a
redesigned
ToolShed.
capabilities
progressing
two
strategic
directions:
integrating
general
purpose
graphical
processing
units
(GPGPU)
access
for
cutting-edge
methods,
licensed
support.
Engagement
with
global
consortia
being
increased
developing
more
workflows
resourcing
run
them.
The
Training
Network
(GTN)
portfolio
grown
both
size,
learning
paths
direct
integration
tools
feature
training
courses.
Code
development
continues
line
Project
roadmap,
job
scheduling
interface.
Environmental
impact
assessment
also
helping
engage
users
developers,
reminding
them
their
role
sustainability,
displaying
estimated
CO2
emissions
generated
job.
Data Science,
Journal Year:
2022,
Volume and Issue:
5(2), P. 97 - 138
Published: Jan. 4, 2022
An
increasing
number
of
researchers
support
reproducibility
by
including
pointers
to
and
descriptions
datasets,
software
methods
in
their
publications.
However,
scientific
articles
may
be
ambiguous,
incomplete
difficult
process
automated
systems.
In
this
paper
we
introduce
RO-Crate,
an
open,
community-driven,
lightweight
approach
packaging
research
artefacts
along
with
metadata
a
machine
readable
manner.
RO-Crate
is
based
on
Schema$.$org
annotations
JSON-LD,
aiming
establish
best
practices
formally
describe
accessible
practical
way
for
use
wide
variety
situations.
structured
archive
all
the
items
that
contributed
outcome,
identifiers,
provenance,
relations
annotations.
As
general
purpose
data
metadata,
used
across
multiple
areas,
bioinformatics,
digital
humanities
regulatory
sciences.
By
applying
"just
enough"
Linked
Data
standards,
simplifies
making
outputs
FAIR
while
also
enhancing
reproducibility.
article
available
at
https://w3id.org/ro/doi/10.5281/zenodo.5146227
Science,
Journal Year:
2024,
Volume and Issue:
386(6723)
Published: Nov. 14, 2024
The
genome
is
a
sequence
that
encodes
the
DNA,
RNA,
and
proteins
orchestrate
an
organism’s
function.
We
present
Evo,
long-context
genomic
foundation
model
with
frontier
architecture
trained
on
millions
of
prokaryotic
phage
genomes,
report
scaling
laws
DNA
to
complement
observations
in
language
vision.
Evo
generalizes
across
proteins,
enabling
zero-shot
function
prediction
competitive
domain-specific
models
generation
functional
CRISPR-Cas
transposon
systems,
representing
first
examples
protein-RNA
protein-DNA
codesign
model.
also
learns
how
small
mutations
affect
whole-organism
fitness
generates
megabase-scale
sequences
plausible
architecture.
These
capabilities
span
molecular
scales
complexity,
advancing
our
understanding
control
biology.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: Feb. 27, 2024
The
genome
is
a
sequence
that
completely
encodes
the
DNA,
RNA,
and
proteins
orchestrate
function
of
whole
organism.
Advances
in
machine
learning
combined
with
massive
datasets
genomes
could
enable
biological
foundation
model
accelerates
mechanistic
understanding
generative
design
complex
molecular
interactions.
We
report
Evo,
genomic
enables
prediction
generation
tasks
from
to
scale.
Using
an
architecture
based
on
advances
deep
signal
processing,
we
scale
Evo
7
billion
parameters
context
length
131
kilobases
(kb)
at
single-nucleotide,
byte
resolution.
Trained
prokaryotic
genomes,
can
generalize
across
three
fundamental
modalities
central
dogma
biology
perform
zero-shot
competitive
with,
or
outperforms,
leading
domain-specific
language
models.
also
excels
multi-element
tasks,
which
demonstrate
by
generating
synthetic
CRISPR-Cas
complexes
entire
transposable
systems
for
first
time.
information
learned
over
predict
gene
essentiality
nucleotide
resolution
generate
coding-rich
sequences
up
650
kb
length,
orders
magnitude
longer
than
previous
methods.
multi-modal
multi-scale
provides
promising
path
toward
improving
our
control
multiple
levels
complexity.
International Medical Science Research Journal,
Journal Year:
2024,
Volume and Issue:
4(4), P. 509 - 520
Published: April 20, 2024
This
review
delves
into
Information
Technology's
(IT)
transformative
impact
on
precision
medicine
and
genomics,
spotlighting
the
pivotal
role
of
bioinformatics,
data
mining,
machine
learning,
blockchain
technologies
in
advancing
personalized
healthcare.
A
comprehensive
analysis
outlines
how
these
IT-enabled
approaches
facilitate
analysis,
interpretation,
application
vast
genomic
sets,
thereby
enhancing
disease
prediction,
diagnosis,
treatment
an
individual
level.
Despite
promising
advancements,
also
addresses
significant
challenges,
including
complexity,
interoperability,
ethical
considerations,
digital
divide,
underscoring
necessity
for
multidisciplinary
collaboration
innovation
to
overcome
hurdles.
The
paper
concludes
by
emphasizing
potential
emerging
patient-centred
care
realizing
vision
medicine,
which
promises
improved
healthcare
outcomes
through
strategies.
Keywords:
Precision
Medicine,
Genomics,
Bioinformatics,
Machine
Learning,
Data
Security.
Genome biology,
Journal Year:
2024,
Volume and Issue:
25(1)
Published: Jan. 8, 2024
Abstract
Background
Transcription
factors
bind
DNA
in
specific
sequence
contexts.
In
addition
to
distinguishing
one
nucleobase
from
another,
some
transcription
can
distinguish
between
unmodified
and
modified
bases.
Current
models
of
factor
binding
tend
not
take
modifications
into
account,
while
the
recent
few
that
do
often
have
limitations.
This
makes
a
comprehensive
accurate
profiling
affinities
difficult.
Results
Here,
we
develop
methods
identify
sites
DNA.
Our
expand
standard
///
alphabet
include
cytosine
modifications.
We
Cytomod
create
genomic
sequences
also
enhance
MEME
Suite,
adding
capacity
handle
custom
alphabets.
adapt
well-established
position
weight
matrix
(PWM)
model
affinity
this
expanded
alphabet.
Using
these
methods,
modification-sensitive
motifs.
confirm
established
preferences,
such
as
preference
ZFP57
C/EBPβ
for
methylated
motifs
c-Myc
unmethylated
E-box
Conclusions
known
preferences
tune
parameters,
discover
novel
wide
array
factors.
Finally,
validate
our
predictions
OCT4
using
cleavage
under
targets
release
nuclease
(CUT&RUN)
experiments
across
conventional,
methylation-,
hydroxymethylation-enriched
sequences.
approach
readily
extends
other
As
more
genome-wide
single-base
resolution
modification
data
becomes
available,
expect
method
will
yield
insights
altered
many
different