IMB - 2016 Winter School in Mathematical & Computational Biology - Program
←
→
Page content transcription
If your browser does not render page correctly, please read the page content below
2016 Winter School
in
Mathematical & Computational Biology
4-8 July 2016
Auditorium
Queensland Bioscience Precinct
The University of Queensland
Brisbane, Australia
Program
Hosted by:
IMB
2016
Winter
School
in
Mathematical
and
Computational
Biology
4-‐8
July
2016
http://bioinformatics.org.au/ws16
Queensland
Bioscience
Precinct
(Building
#80)
The
University
of
Queensland
Brisbane,
Australia
MONDAY
4
JULY
2016
08:00
Registration
desk
open
NEXT
GENERATION
SEQUENCING
&
BIOINFORMATICS
09:00
–
09:05
Welcome
and
introduction
Dr
Nicholas
Hamilton
Research
Computing
Centre
and
Institute
for
Molecular
Bioscience
The
University
of
Queensland
09:05
–
09:45
Next-‐generation
sequencing
overview
(Game
of
Thrones
Edition)
Dr
Ken
McGrath
Australian
Genome
Research
Facility
Ltd,
Brisbane
09:45
–
10:30
NGS
mapping,
errors
and
quality
control
Dr
Felicity
Newell
Queensland
University
of
Technology,
Brisbane
10:30
–
11:00
Morning
Tea
11:00
–
11:45
Mutation
detection
in
whole-‐genome
sequencing
Dr
Ann-‐Marie
Patch
QIMR
Berghofer
Medical
Research
Institute,
Brisbane
11:45
–
12:30
De
novo
genome
assembly
A/Professor
Torsten
Seemann
Victorian
Life
Sciences
Computation
Initiative,
The
University
of
Melbourne
12:30
–
13:30
Lunch
13:30
–
14:30
Long-‐read
sequencing:
an
overview
of
technologies
and
applications
Dr
Mathieu
Bourgey
Montréal
Node,
McGill
University
and
Genome
Québec
Innovation
Centre,
Canada
14:30
–
15:15
Genomics
resources
-‐
feeding
your
inner
bioinformatician
A/Professor
Mik
Black
University
of
Otago,
Dunedin,
New
Zealand
15:15
–
15:45
Afternoon
Tea
15:45
–
16:30
Defensive
NGS
informatics
-‐
what
can
go
wrong
and
how
do
you
know
when
to
throw
in
the
towel?
Mr
John
Pearson
QIMR
Berghofer
Medical
Research
Institute,
Brisbane
16:30
–
17:15
The
current
and
upcoming
challenges
and
opportunities
in
bioinformatics
Dr
Annette
McGrath
DATA61
|
CSIRO,
Canberra
17:15
–
17:30
Resource
talk:
what
the
Australian
Bioinformatics
and
Computational
Biology
Society
can
do
for
you
Professor
David
Lovell,
Queensland
University
of
Technology,
Brisbane
17:45
Social
BBQ
Venue:
Auditorium
foyer
i
TUESDAY
5
JULY
2016
NEXT
GENERATION
SEQUENCING
&
BIOINFORMATICS
09:00
–
09:45
Analysing
RNA-‐seq
data:
differential
expression
and
beyond
Dr
Alicia
Oshlack
Murdoch
Childrens
Research
Institute,
Melbourne
09:45
–
10:30
MicroRNAs
-‐
sequencing,
analysis
...
and
then
what?
Dr
Pamela
Mukhopadhyay
QIMR
Berghofer
Medical
Research
Institute,
Brisbane
10:30
–
11:00
Morning
Tea
TUESDAY
5
JULY
2016
BIOINFORMATICS
METHODS,
MODELS
AND
APPLICATIONS
TO
DISEASE
11:00
–
11:45
Evolution
teaches
protein
prediction
Professor
Burkhard
Rost
Technische
Universität
München
(TUM),
Munich,
Germany
11:45
–
12:45
Lunch
12:45
–
13:30
Personalised
health:
harnessing
the
power
of
diversity
Professor
Burkhard
Rost
Technische
Universität
München
(TUM),
Munich,
Germany
13:30
-‐
14:15
The
predictive
power
of
machine
learning
techniques
in
data-‐driven
biomedical
knowledge
discovery
Dr
Jiangning
Song,
Monash
University
14:15
–
15:00
Personalised
medicine:
discriminating
disease-‐causing
from
neutral
genetic
variations
Professor
Yaoqi
Zhou
Griffith
University,
Brisbane
15:00
–
15:30
Afternoon
Tea
15:30
–
16:15
Processing,
integrating
and
analysing
chromatin
immunoprecipitation
followed
by
sequencing
(ChIP-‐seq)
data
Ms
Alexandra
Essebier,
The
University
of
Queensland
16:15
–
17:00
VariantSpark:
applying
Spark-‐based
machine
learning
methods
to
genomic
information
Dr
Denis
Bauer
CSIRO
Health
Program,
Sydney
17:00
–
17:15
Resource
talk:
how
QCIF
enables
research
Ms
Belinda
Weaver
e-‐Research
Analyst
Team
Manager,
Queensland
Cyber
Infrastructure
Foundation,
Brisbane
ii
WEDNESDAY
6
JULY
2016
BIOINFORMATICS
METHODS,
MODELS
AND
APPLICATIONS
TO
DISEASE
09:00
–
09:45
The
role
of
common
genetic
variations
in
complex
diseases
and
pharmacogenomics
studies
Dr
Siew-‐Kee
Amanda
Low
The
University
of
Sydney
09:45
–
10:30
I've
got
my
list
of
differentially
expressed
genes,
now
what?
Dr
Mirana
Ramialison
Australian
Regenerative
Medicine
Institute,
Monash
University,
Melbourne
10:30
–
11:00
Morning
Tea
11:00
–
12:00
Bioinformatics
software
testing
and
quality
assurance
Dr
Joshua
W.K.
Ho
Victor
Chang
Cardiac
Research
Institute,
Sydney
12:00
–
12:30
Panel
discussion
Chair:
Professor
Mark
Ragan
Institute
for
Molecular
Bioscience,
The
University
of
Queensland
***
FREE
WEDNESDAY
AFTERNOON
***
SPECIAL
ACTIVITIES
IN
THE
AFTERNOON
12:30
–
13:00
IMB
tour
(1)
–
Limited
to
50
attendees
only
Meeting
point:
Auditorium
foyer
13:00
–
13:30
IMB
tour
(2)
-‐
If
more
requests
are
received
and
is
also
limited
to
50
attendees
only
Meeting
point:
Auditorium
foyer
14:00
–
17:00
Special
Wednesday
Afternoon
Workshop
An
introduction
to
Galaxy
with
the
NeCTAR
Genomics
Virtual
Laboratory
Dr
Igor
Makunin
Research
Computing
Centre,
The
University
of
Queensland
Venue:
Multi
Media
Room
(Room
3.141,
access
through
the
auditorium
foyer)
(This
workshop
is
limited
to
36
attendees
only
and
is
intended
for
bench
scientists,
and
no
previous
informatics
experience
is
needed.)
What
is
required
before
attending
the
workshop?
Remember
to
download
Galaxy
Workshop
Information
Sheet
from
the
2016
Winter
School
web
site.
http://bioinformatics.org.au/ws16/program/
iii
THURSDAY
7
JULY
2016
ADVANCED
BIO-‐DATA
VISUALISATION
09:00
–
10:30
Data
visualisation
in
bioinformatics:
exploring
the
‘dark’
proteome
Dr
Seán
O’Donoghue
CSIRO,
Sydney
10:30
–
11:00
Morning
Tea
11:00
–
12:00
Experimentation
at
the
interface
of
art
and
science:
narrative,
cognitive
embodiment
and
alternative
visual
language
Dr
Kate
Patterson,
Garvan
Institute
of
Medical
Research,
Sydney
12:00
–
13:00
Lunch
13:00
–
14:00
Network
and
data
visualisation
and
analysis
in
Cytoscape
Dr
Melissa
Davis
Walter
and
Eliza
Hall
Institute
for
Medical
Research,
Melbourne
14:00
–
15:00
Big
data
visual
analytics
Professor
Seok-‐Hee
Hong
University
of
Sydney
15:00
–
15:30
Afternoon
Tea
15:30
–
17:00
Creating
data
visualisations
that
won’t
be
forgotten
using
the
R
programming
language
Dr
Chris
Brown
Australian
Rivers
Institute,
Griffith
University,
Brisbane
17:00
–
17:15
Resource
talk:
what
the
COMBINE
network
does
for
ECRs
in
bioinformatics
and
computational
biology
Ms
Leah
Roberts
Vice
President,
COMBINE
(Computational
Biology
and
Bioinformatics
Student
Group)
School
of
Chemistry
and
Molecular
Biosciences,
The
University
of
Queensland
iv
FRIDAY
8
JULY
2016
ECOGENOMICS
09:00
–
09:05
Welcome
&
introduction
Professor
Gene
Tyson
Australian
Centre
for
Ecogenomics,
The
University
of
Queensland
09:05
–
09:45
The
extraordinary
evolution
of
the
great
ape
microbiome
Professor
Howard
Ochman
University
of
Texas,
Austin,
USA
09:45
–
10:30
Tools
and
methods
for
microbial
ecological
genomics
Dr
David
Wood
Australian
Centre
for
Ecogenomics,
The
University
of
Queensland
10:30
–
11:00
Morning
Tea
11:00
–
11:45
Illuminating
microbial
dark
matter
via
single-‐cell
genomics
Dr
Christian
Rinke
Australian
Centre
for
Ecogenomics,
The
University
of
Queensland
12:00
–
13:00
IMB
Friday
Noon
Seminar
in
conjunction
with
Winter
School
Towards
4
dimensional
(eco)
systems
biology
in
the
sea
Professor
Edward
F.
DeLong
University
of
Hawaii,
Honolulu,
USA
13:00
–
13:45
Lunch
13:45
–
14:30
Genomes
from
metagenomes:
recovery
and
analysis
of
population
genomes
Dr
Kate
Ormerod
Australian
Centre
for
Ecogenomics,
The
University
of
Queensland
14:30
–
15:15
Community
diversity
in
metagenomes:
one,
many
and
thousands
Dr
Ben
Woodcroft
Australian
Centre
for
Ecogenomics,
The
University
of
Queensland
15:15
–
16:00
Comparing
the
variome
and
pan-‐genome
of
bacterial
isolates
A/Professor
Torsten
Seemann
Victorian
Life
Sciences
Computation
Initiative,
The
University
of
Melbourne
16:00
Winter
School
wrap-‐up
and
refreshment
with
IMB/ECRs
~*~*~*~*~
v
BIOGRAPHY
AND
ABSTRACT
Dr
Ken
McGrath
Brisbane
Node
Manager
Australian
Genome
Research
Facility
Ltd
(AGRF)
Brisbane
Biography:
Ken
McGrath
is
the
node
manager
of
the
Brisbane
Lab
of
the
Australian
Genome
Research
Facility,
based
at
the
UQ
St
Lucia
campus.
Ken
has
worked
with
plant
and
microbial
genetics
and
transcriptomics,
and
completed
his
PhD
in
biochemistry
and
molecular
pathology
at
UQ
in
2005.
Following
this,
his
postdoctoral
research
involved
examining
the
transcriptomes
of
mixed
microbial
communities
in
industrial
and
agricultural
settings.
In
2009,
Ken
joined
the
AGRF,
and
currently
manages
a
range
of
lab
processes
and
sequencing
projects
including
next-‐generation
sequencing
platforms.
Ken
is
also
a
founding
member
of
the
“eXtreme
Microbiome
Project”
-‐
an
international
collaboration
studying
microbial
communities
of
the
extreme
environments
around
our
planet.
Date:
Monday
4
July
2016
Presentation
title:
Next-‐generation
sequencing
overview
(Game
of
Thrones
Edition)
Abstract:
The
“Next-‐Generation
Sequencing”
landscape
is
one
of
constant
change,
with
new
and
emerging
technologies
always
competing
with
established
platforms
-‐
much
like
the
different
characters
and
families
from
the
“Game
of
Thrones”
universe.
Using
this
analogy,
Ken
talks
about
the
sequencing
technologies
that
have
had
their
day
on
the
throne,
and
looks
in
detail
at
the
current
rulers
–
and
who
is
best
positioned
to
usurp
them.
In
doing
so,
Ken
will
explain
how
the
sequencing
technologies
work
and
give
examples
of
projects
that
can
be
run
on
them,
as
well
as
hint
at
what’s
“next”
in
Next-‐Gen.
1
BIOGRAPHY
AND
ABSTRACT
Dr
Felicity
Newell
Research
Fellow
in
Computational
Biology
Queensland
University
of
Technology
Brisbane
Biography:
Felicity
Newell
originally
trained
in
the
fields
of
molecular
and
cellular
biology,
and
received
her
PhD
from
The
University
of
Queensland
in
2007.
Following
this,
she
completed
a
Master
of
Information
Technology
at
the
Queensland
University
of
Technology.
She
has
worked
as
a
bioinformatics
programmer,
developing
biological
web
applications
at
QFAB
and
software
for
the
analysis
of
cancer
sequencing
data
at
the
Queensland
Centre
for
Medical
Genomics
at
UQ.
Since
then,
she
has
conducted
postdoctoral
research
at
The
University
of
Queensland
Diamantina
Institute,
and
this
year
she
joined
QUT
as
a
Research
Fellow
in
Computational
Biology.
Her
current
interests
involve
using
next-‐generation
sequencing
data
to
investigate
the
genetics
of
autoimmune
diseases
and
cancer.
Date:
Monday
4
July
2016
Presentation
title:
NGS
mapping,
errors
and
quality
control
Abstract:
The
first
step
that
is
often
required
to
analyse
next
generation
sequencing
data
is
to
align
the
reads
that
are
generated
to
a
reference
genome.
Current
sequencing
platforms
can
generate
high
volumes
of
raw
read
data.
Such
reads
are
usually
short
in
length
and
may
contain
sequencing
errors.
Therefore
tools
that
perform
mapping
need
to
be
able
to
efficiently
identify
the
location
of
a
read
within
the
reference
genome
while
accounting
for
real
sequence
variations
as
well
as
technical
artefacts.
In
this
presentation
I
will
describe
some
of
the
approaches
to
sequence
alignment,
highlighting
some
of
the
popular
tools
that
are
in
use.
A
good
understanding
of
the
common
errors
and
biases
that
can
occur
with
mapping
is
necessary
in
order
to
obtain
high
quality
data
from
downstream
analyses
such
as
variant
detection.
I
will
also
discuss
some
of
these
errors
and
outline
some
quality
controls
steps
that
can
be
performed.
2
BIOGRAPHY
AND
ABSTRACT
Dr
Ann-‐Marie
Patch
Senior
Research
Officer
Medical
Genomics
Group
QIMR
Berghofer
Medical
Research
Institute
Brisbane
Biography:
Ann-‐Marie
is
currently
a
Senior
Research
Officer
within
the
Medical
Genomics
group
led
by
Dr
Nicola
Waddell,
at
the
QIMR
Berghofer
Medical
Research
Institute.
Her
current
research
focuses
on
cancer
genomics
working
with
large
collaborative
groups
to
identify
the
molecular
basis
of
melanoma
and
mesothelioma.
The
detection
and
advancement
in
the
understanding
of
the
consequences
of
structural
variants
in
cancer,
linking
to
understanding
the
mechanisms
of
DNA
repair
are
of
particular
interest
to
her.
With
a
PhD,
gained
in
2006
from
the
University
of
Exeter
UK,
that
combined
bioinformatics
and
laboratory
approaches
to
study
fission
and
budding
yeast
genetics
she
joined
the
intertwined
research
and
diagnostic
teams
of
Prof.
Andrew
Hattersley
and
Prof.
Sian
Ellard
at
the
Peninsula
College
of
Medicine
&
Dentistry
and
Royal
Devon
and
Exeter
Molecular
Genetics
Laboratory
using
next-‐generation
sequencing
to
identify
monogenic
causes
of
neonatal
diabetes
and
causal
mutations
for
a
broad
spectrum
of
genetic
disorders.
Cancer
genomics
has
been
her
focus
for
the
last
five
years
leading
the
analysis
of
the
ovarian
cancer
data
as
part
of
the
Australian
ICGC
team
led
by
Prof.
Sean
Grimmond
that
she
continues
in
her
current
role.
Date:
Monday
4
July
2016
Presentation
title:
Mutation
detection
in
whole-‐genome
sequencing
Abstract:
Through
landmark
studies
carried
out
as
part
of
the
Australian
International
Cancer
Genome
Consortium
projects
studying
the
molecular
basis
of
pancreatic,
ovarian
and
now
melanoma
tumours
the
development
of
robust
mutation
detection
methods
has
been
key.
Initially
at
the
Queensland
Centre
for
Medical
Genomics,
at
IMB
and
now
at
the
QIMR
Berghofer
Medical
Research
Institute
an
expert
team
of
researchers
and
informatics
specialists
have
set
up
a
high
performing
framework
to
enable
the
analysis
of
whole
human
genomes
for
the
presence
of
DNA,
RNA
and
epigenetic
variants
that
are
associated
with
the
hallmarks
of
cancer.
This
talk
will
describe
and
discuss
the
principles
and
challenges
of
identifying
the
full
range
of
mutation
types
including
single
nucleotide
variants,
indels
up
to
large
structural
variants
(SVs)
using
whole
genome
sequencing.
I
will
present
the
bases
of
mutation
detection
for
ICGC
projects
with
examples
of
how
mechanisms
driving
tumorigenesis
may
be
identified.
3
BIOGRAPHY
AND
ABSTRACT
A/Professor
Torsten
Seemann
Lead
Bioinformatician
Victorian
Life
Sciences
Computation
Initiative
and
Microbiological
Diagnostics
Unit
Public
Health
Laboratory
The
University
of
Melbourne
Biography:
A/Prof.
Torsten
Seemann
is
lead
bioinformatician
at
the
Victorian
Life
Sciences
Computation
Initiative
and
the
Microbiological
Diagnostics
Unit
Public
Health
Laboratory,
both
at
the
University
of
Melbourne.
His
work
uses
bioinformatics
and
genomics
to
better
understand
the
spread
and
evolution
of
bacterial
pathogens
and
antimicrobial
resistance.
He
is
best
known
for
his
software
tools
which
are
used
internationally,
and
he
is
a
strong
supporter
of
open
science.
Date:
Monday
4
July
2016
Presentation
title:
De
novo
genome
assembly
Abstract:
How
do
we
generate
the
genome
sequence
of
our
favourite
organism?
In
this
talk
I
will
introduce
the
problem
of
de
novo
genome
assembly;
describe
the
strategies
and
caveats
of
the
way
the
problem
is
tackled;
and
outline
ways
to
assess
the
results.
The
related
problems
of
transcriptome
and
metagenome
assembly,
and
how
the
latest
technologies
are
transforming
de
novo
assembly,
will
also
be
touched
upon.
4
BIOGRAPHY
AND
ABSTRACT
Dr
Mathieu
Bourgey
Bioinformatics
Manager
Canadian
Centre
for
Computational
Genomics
(C3G)
Montréal
Node,
McGill
University
and
Genome
Québec
Innovation
Centre
Montréal,
Canada
Biography:
Mathieu
Bourgey
is
the
manager
of
the
Research
and
Development
team
at
the
Montréal
node
of
the
Canadian
Centre
for
Computational
Genomics.
He
completed
his
Master
degree
with
honours
in
2003
at
the
Université
Pierre
et
Marie
Curie
-‐
Paris
VI
(France)
working
on
developing
evolution
model
of
genomics
large
repeats.
He
transitioned
to
Université
Paris-‐Sud
XI
(France)
for
his
PhD
work
on
modeling
risk
of
developing
the
coeliac
disease
based
on
genetic
and
familial
information.
Following
this,
his
postdoctoral
research
at
Université
de
Montréal
focused
on
modeling
gene-‐gene
interactions
and
foeto-‐maternal
interactions
in
the
susceptibility
to
childhood
leukemia.
After
completing
his
postdoctoral
studies
in
2010,
he
participated
at
the
development
of
the
bioinformatics
side
of
a
large
next
generation
sequencing
project
of
Acute
Lymphoblastic
Leukemia
samples.
In
2011,
Mathieu
joined
the
bioinformatics
platform
of
the
McGill
University
and
Genome
Québec
Innovation
Centre
(MUGQIC)
as
senior
analyst
where
he
was
involved
in
the
analysis
of
a
wide
range
of
genomics
projects
from
bacteria
to
humans
using
all
the
various
type
of
sequencing
technology
available
(Illumina,
454,
Life
Technology
and
PacBio).
In
2014,
he
became
team
leader
of
the
data
production
and
service
at
the
MUGQIC
bioinformatics
platform
and
in
2015
he
started
managing
the
bioinformatics
research
and
development
group.
He
manages
software
and
analysis
pipeline
development
on
a
wide
range
of
next-‐
generation
sequencing
platforms
technology
and
takes
part
in
national
and
international
projects
studying
cancer
genomics,
genome
assembly
and
transcriptomics.
He
is
also
involved
in
the
organisation
of
international
genomics
workshops.
Date:
Monday
4
July
2016
Presentation
title:
Long-‐read
sequencing:
an
overview
of
technologies
and
applications
Abstract:
Next-‐generation
sequencing
technologies
offer
vast
improvements
over
traditional
Sanger
sequencing.
However,
these
major
sequencing
technologies
suffer
from
a
main
limitation,
the
short
lengths
of
their
reads.
Short
reads
are
poorly
suited
to
study
complex
genomic
regions
or
for
nonreference-‐based
analysis.
Long
reads
offer
an
alternative
approach
to
overcome
many
of
these
limitations.
With
longer
reads
we
can
sequence
through
extended
repetitive
regions,
detect
base
modifications,
identify
gene
isoforms
and
assemble
finished
genomes.
Pacific
BioSciences,
Oxford
Nanopore
and
Illumina
are
the
three
major
competitors
which
developed
different
long
reads
sequencing
technologies.
Each
of
their
technologies
has
specific
limitations
that
need
to
be
taken
into
consideration
while
designing
a
long
read
sequencing
project.
5
BIOGRAPHY
AND
ABSTRACT
Associate
Professor
Mik
Black
Department
of
Biochemistry
University
of
Otago
Dunedin,
New
Zealand
Biography:
Mik
received
a
BSc
(Hons)
in
statistics
from
the
University
of
Canterbury,
and
an
MSc
(mathematical
statistics)
and
PhD
(statistics)
from
Purdue
University.
After
completing
his
PhD
in
2002,
Mik
returned
to
New
Zealand
to
work
as
a
lecturer
in
the
Department
of
Statistics
at
the
University
of
Auckland.
An
ongoing
involvement
in
a
number
of
Dunedin-‐based
collaborative
genomics
projects
resulted
in
a
move
to
the
University
of
Otago
in
2006.
Mik's
research
focuses
on
the
development
and
application
of
statistical
methods
for
the
analysis
of
data
from
genomics
experiments,
with
a
particular
emphasis
on
human
disease.
Mik
is
also
heavily
involved
in
two
major
initiatives
designed
to
put
in
place
sustainable
national
research
infrastructure
for
NZ:
NZGL
(New
Zealand
Genomics
Ltd)
for
genomics
(where
he
was
the
interim
Bioinformatics
Team
Leader
during
2012-‐
2013),
and
NeSI
(New
Zealand
eScience
Infrastructure)
for
computing/eResearch.
Date:
Monday
4
July
2016
Presentation
title:
Genomics
resources
-‐
feeding
your
inner
bioinformatician
Abstract:
In
the
current
research
environment,
the
ability
to
manage,
analyse
and
interpret
data
produced
by
high-‐
throughput
sequencing
platforms
has
become
an
essential
skill
for
both
wet-‐
and
dry-‐lab
researchers.
While
a
number
of
options
exist
for
outsourcing
these
tasks,
the
reality
is
that
researchers
still
need
(and
desire)
a
level
of
analytic
skill
that
allows
them
to
perform
basic
exploratory
analysis
of
their
data,
without
having
to
rely
on
external
assistance.
In
this
talk,
I
will
discuss
some
of
the
initiatives
that
have
been
undertaken
in
New
Zealand
and
Australia
to
provide
both
genomics
and
bioinformatics
support
for
researchers,
as
well
as
highlighting
some
of
the
tools
and
skills
that
help
to
ensure
the
robustness
and
reproducibility
of
the
analyses
being
carried
out.
6
BIOGRAPHY
AND
ABSTRACT
Mr
John
Pearson
Team
Leader
Genome
Informatics
QIMR
Berghofer
Medical
Research
Institute
Brisbane
Biography:
John
Pearson
has
spent
25
years
as
a
bioinformatician
creating
software
for
medical
researchers
and
has
worked
at
NIH,
UQ,
QIMR
Berghofer
and
was
a
founding
Faculty
member
at
the
Translational
Genomics
Research
Institute
(TGen)
in
Phoenix,
Arizona.
John
has
held
software
development
grants
from
Microsoft,
the
American
Cancer
Society,
and
the
National
Institutes
of
Health
and
has
participated
in
the
1000
Genomes
Project
and
the
International
Cancer
Genome
Consortium.
Date:
Monday
4
July
2016
Title:
Defensive
NGS
informatics
-‐
what
can
go
wrong
and
how
do
you
know
when
to
throw
in
the
towel?
Abstract:
Next-‐generation
sequencing
has
radically
changed
medical
research
by
allowing
deep
interrogation
of
the
DNA
and
RNA
of
pathogenic
organisms,
families
with
inherited
disorders
and
the
de-‐novo
mutations
responsible
for
tumourigenesis.
As
with
any
new
technology,
a
"gold
rush"
mentality
can
arise
where
being
first
to
the
a nswer
can
push
rigour
and
methodological
soundness
into
the
background.
In
this
seminar,
I'll
talk
from
QCMG
experience
about
some
of
the
ways
sequencing
can
go
wrong,
how
the
problems
became
apparent,
what
we
did
about
them,
and
tools
we
developed
to
try
to
catch
the
same
problems
in
future.
7
BIOGRAPHY
AND
ABSTRACT
Dr
Annette
McGrath
Principal
Research
Scientist
and
Team
Leader
in
Life
Science
Informatics
DATA61
|
CSIRO
Canberra
Annette
McGrath
graduated
from
the
National
University
of
Ireland
with
a
PhD
in
molecular
biology
and
from
The
University
of
Queensland
with
a
graduate
diploma
in
statistics.
Following
postdoctoral
work
in
bioinformatics
on
multiple
sequence
alignment,
she
worked
for
three
years
as
a
staff
scientist
and
team
leader
in
a
biotech
company
in
Auckland,
New
Zealand.
She
then
spent
eight
years
as
Head
of
Bioinformatics
at
the
Australian
Genome
Research
Facility,
followed
by
Head
of
Bioinformatics
at
Queensland
Facility
for
Advanced
Bioinformatics
in
2010.
In
2011
she
was
recruited
to
establish
and
lead
the
CSIRO
Bioinformatics
Core,
dedicated
to
enhancing
capability
in
bioinformatics
across
CSIRO.
She
is
a
Principal
Research
Scientist
and
Team
Leader
in
life
science
informatics
in
CSIRO
Data61
with
interests
in
the
application
of
‘omics
technologies
and
big
data
and
with
a
passion
for
bioinformatics
education
and
training.
Date:
Monday
4
July
2016
Presentation
title:
The
current
and
upcoming
challenges
and
opportunities
in
bioinformatics
Abstract:
Molecular
biology
has
become
a
data
science,
driven
by
advances
in
measurement
and
data
acquisition
technologies
that
allow
very
substantial
amounts
of
data
to
be
readily
produced
and
aided
by
spectacular
drops
in
the
price
of
this
data.
The
impact
of
this
shift
to
a
data-‐driven
science
can
be
seen
across
a
broad
range
of
applications
–
from
human
health,
advanced
manufacturing,
agriculture
and
ecosystems.
As
molecular
techniques
improve,
many
practical
and
methodological
challenges
are
presented
by
increased
in
data
volumes,
complexity
and
dimensionality
of
the
data.
Bioinformatics
is
facing
challenges
in
managing,
storing,
processing,
analysing
and
integrating
different
types
of
molecular
biological
information.
Nonetheless,
there
is
a
wealth
of
research
opportunities
emerging
for
bioinformaticians
as
effective
analysis
and
interpretation
of
molecular
bioscience
data
offers
new
ways
to
uncover
hidden
patterns
in
data
and
to
build
better
predictive
models.
This
talk
will
present
an
overview
of
where
genomics
and
bioinformatics
are
currently
having
an
impact
and
will
also
take
a
look
at
some
of
the
challenges
and
opportunities
likely
in
coming
years
in
the
field
of
bioinformatics.
8
You can also read
