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UNIVERSITY OF BRITISH COLUMBIA


Faculty of Graduate Studies










Proposal

Graduate
Program in Bioinformatics






2005


2

P
ROPOSED PROGRAM IN BIOINFORMATICS


Table of Contents


I.

GENERAL INFORMATION

a.

Title of degree program …………………………………………………
…………
…..4

b.

Fac
ulty, School, or Department
plannin
g to offer the program ………………….4

c.

Implementation

date……………………………………………………………………4


II.

RATIONALE

FOR THE PROGRAM

a.

Background
…………………………………………………………………………….4

b.

Objectives of the program……………………………………………………
……
…...5

c.


Student Interes
t………………………………………………………………………...6

d
.

Program Design …………………….
……………………………
…………………...7

e
.

Enrollment…..……………………………………………………………………
….
…7


III
.

PROGRAM

ORGANIZATION

AND SPECIFICATIONS

a.

Bioinformatics Governance………..
……………………………………

………….
..
8

b
. Program overview……..
………………………………………………………………10

c
. Doctor of Philosophy.…
………………………………….…………………………
...
11

d. Master of Scien
ce…………………………..…………………………………………11

e
. Student Supervisory Committees
...……………………………………………………12

f
.

Examinations
………………………………………………………………
……...…...12

g
.

Outline of program for typical student………
…………………..……………………12


I
V.

EXISTING COURSES DIRECTLY IDENTIFIED WITH THE PROGRAM

AND NEW

COURSES

IMPLEMENT
ED BY

THE
PROGR
AM

a.

Existing Cou
rs
es……………….………………………………………………………13

b.

New Courses…..…………………………
……………………………………………
1
4


V
.

LABORATORY
RESEAR
CH ROTATIONS
…………………
……..
……………
14


VI. CALENDAR STATEMENT
………………………………………………………
16


VI
I
.

PRESENT AND PROJECTED RESOURCES

a.

Qualified facu
lty………………………………………………………………………16

b.

Research facilities and ongoing r
esearch progr
ams………………………….………16

c.

External research funding available and f
aculty research awards……………………
1
7

d.

Library resources……………………………
…………………………………….….1
7

e.

Administrative support

staff……………………………………………………..……17

f.

Budgetary impact and anticipated sources of ex
ternal financial support……………
..
1
7


VI
I
I
. PARTNERSHIPS, COLLABORATIONS AND INSTITUTIONAL SUPPORT


…....
.............................................................................................................................
.....
1
7




3

APPENDICES
…………………
.
..
……………………………
.
………………………
.18


I.

PROGRAM DIRECTOR AND ADVISORY BOARD

II.

LIST OF PROGRAM FACULTY

III.

LIST OF PROGRAM ASSOCIATED FACULTY

IV.

LIST OF PROGRAM ADJUCT FACULTY

V.

LIST OF INDUSTRY PARTNERS

VI.

LIST OF RESEARCH ROTATIONS


VI
I
.
LIST OF

UBC
PROGRAM GRADUATES



4

GR
ADUATE PROGRAM IN BIOINFORMATICS


I.

GENERAL INFORMATION

a)

Title of degree program

Bioinformatics Graduate

Program.

This would be a new
p
ost
-
graduate
degree

designation, with students graduating with a degree in Bioinformatics.


b)

Faculty, School,
or
Depa
rtment

offering

the program

The
Faculty of Graduate Studies would

be the host fa
culty.

Dr. Steven Jones, Director
of Bioinformatics at the Genome Sciences Centre,
BC Cancer Agency (BCCA) and
Associate

Professor, Medical Genetics, will serve as the prog
ram director.


c)

Implementation date


We would like the
new
program
to be
gin

by

September 2006
.


II.
RATIONALE

FOR THE PROGRAM

a)

Background


The

CIHR/MSFHR Bioinformatics Training Program has been in existence since
September 2002
,

with students regi
stered in either the Genetics Graduate Program or
the Statistics Department. The program has graduated

six

Master’s students,
with
an
additional eleven

students
pursuing
their Master’s
degrees and another eleven

students
entering doctoral

programs in the
laboratories of participating members. S
upervisors
in the program fee
l that the time is right to establish an independent graduate program
offering degrees in Bioinformatics.



The

explosion of biological information
in genomics, proteomics and healt
h
-
care
has
created a
n enormous

demand for
highly skilled scientists trained in both

computational
and

biological research:

bioinformaticians
.

The impor
tance of bioinformatics is

increasingly acknowledged.

T
he December 12, 2002 issue

of

The Economist

notes
that


o
nce an obscure part of computer science, bioinformatics has become a linchpin of
biotechnology's progress. In the struggle for speed and agility, bioinformatics offers
unparalleled effici
ency through mathematical model
ing. In the quest for new drugs
, it
promises new ways to look at biology through data mining. And it is the only practical
way of making sense of the ensuing deluge of data
.


Bioinformatics uses computational methods to organize, mine, and analyze bi
ological
information, such as

macromo
lecular sequence data (proteins, DNA, RNA)

or

data
obtained through transcriptional profiling, proteomics, metabolomics, etc
.

At present,
there is a serious shortage of individuals capable of working in bioinformatics.

This is
evident in the number of adve
rtisements for these positions in the classified sections of
scientific journals.

As an indication of the demand for newly trained bioinformaticians,
a White Paper on Bioinformatics in Canada (2002) reported the need for an estimated
215 positions in the f
irst two years (2001/2002) for Genome Canada projects alone
(
http://bioinformatics.ca/docs/whitepaper.pdf
).
To fully exploit the data that has been
gathered, and to accelerate the pace of healt
h research, Canada needs scientists trained
in bioinformatics
.


5

In September 2002, a CIHR/MSFHR grant
-
funded Bioinformatics
Training
Program
was init
iated. This innovative program
broke

new ground by offering a

novel
,

trans
-
disciplinary

training program des
igned and taught in a cooperative effort by leading
researchers and their institutions in British Columbia
.

Faculty

from

UBC

collaborate

with
research scientists from

the BC Cancer Agency

(BCCA)
, SFU

and other
institutions in BC
to prepare

students for mas
ters or doctorates in
b
ioinformatics
.


Since the program’s Sep
tember
2002 inception
, 29

students out of over
5
00 a
pplicants
have been enrolled.
These students come from diverse backgrounds and originate from
different Universities across Canada, from Turke
y
,
Singapore, the USA
and the UK
.




The program introduce
s

students to a broad range of approaches relevant to health
research
,

including computational genomic
s, proteomics, epidemiology, and

statistical
genetics, as well as aspects of structural biology
and bio
-
molecular modeling.

It allows
students with backgrounds in biology, computer s
cience or

statistics to gain the
ne
cessary skills in each field

t
o

work together to learn how to critically assess and
solve bioinformatics problems.



The program adopts

an interdisciplinar
y learning approach for students

to promote the
all
-
important development of a common language between the computational and
biological components of the bioinformatics discipl
ine.

The training program
produce
s

team players: biologists
who can define computational problems and complete
programming tasks, and computer scientists, statisticians and mathematicians who
understand the fundamental questions in biology/genetics sufficiently to develop
computational tools and resources to answer

them.

The trans
-
discipl
inary nature of the
program

encourage
s

students to think in ways that are

both

innovative and
also
specific to the problems encountered in bioinformatics.


The demand for this type of training is apparent as more and more bioinform
at
ics
programs are being establishe
d at different institutions throughout the world
, with
Harvard, Yale and Stanford among the top institutions developing programs

(
www.iscb.org/univ.shtml
).
This
CIHR/MSFHR
-
funded
p
rogram has proved to be a
very successful model upon which to build
a graduate program. We now have
the

ability to operate as an
independent program
within
the Faculty of Graduate Studies at
UBC
.


b)

Objectives of the program


The goal of the graduate

trai
ning
program

is to create computationally sophisticated
biologists and biologically sophisticated computational scientists able to interact
synergistically to address

a variety of
research questions and
,

over time
,

to develop a
“common language”.

The speci
fic
program
objectives are to apply innovative trans
-
disciplinar
y approaches to train graduate
s to:




Know how and when to apply critical computational methods to answer
biological questions


6



Articulate research questions and experimental designs from diffe
rent
perspectives



Be able to design computer
-
based experiments
, conduct these experiments
and to analyze and interpret
the
results



A
pproach health research in an innovat
ive and creative manner with the

combined background
knowledge
of biology, computer sci
ence and statistics.



App
ly these approaches to other basic biological research questions

to unlock
the secret
s

of biological function
s

in bacterial, animal and plant genomes.


The strategic objective
s

of the
proposed
program
are: 1)

to build on BC’s growin
g
reputation and excellence as a leader in bioinformatics, genomics and population
-
based approaches to health care and 2)

to
inte
grate

bioinformatics with basic biology

to further the current research excellence in other life science sectors in the provinc
e.
The program will
integrate
academic centres in
computer science, statistics,

molecular
biology, and biotechnology, with translational research groups at hospital
s and at the
clinical interface. Members of the
UBC

Bioinformatics Centre, the
Genetics Grad
uate
p
rogram
, the
d
epartment of Statistics, the
Bioinformatics, Empirical & Theoretical
Algorithm
ics

L
ab
oratory in Computer Science,

t
he Genome Sequence Cen
tre at the
BC Cancer Agency
, and the Michael Smith Laboratories
have been
i
nstrumental in
developing

the current

program
.

As the program moves forward,
the priority will

be to
integrate other
departments

at UBC

in the faculties of Medicine, Science, Forestry, and
Land and Food Systems

that
broadly
supp
ort bioinformatics research in

the life
sciences.



b
)
Student Interest


The
training grant p
rogram

created an enormous amount of interest from its inception
,
with applicants applying
from all parts of the world
.

In the first year, it received over
four hundred enquires and ninety applicants, from which t
welve students were selected
and seven accepted.

These enquires came from India, Asia and Europe, as well as from
students in the

top schools in North America.

In the

second year, the program received
a similar number of both
e
nquiries and applicants.

From

these, six students were
enrolled.

In 2004, from over two hundred applicants, seven students were selected.

In
addition, the program administrator fields three to five enquiries per week.

As it begins

its fourth year, the program has accepted ten hig
hly q
ualified students from out of

seventy
-
five applicants. The number of applicants
to the program
has dropped
only
because there are now
more institutions in North America, Europe and Asia offering
bioinformatics training

(
www.iscb.org/univ.shtml
)
as they see the world
-
wide demand
for bioinformaticians increasing
.
However, our program remains competitive with
these other institutions due to its highly regarded scientists and
its
comprehensive
training.








7

d
)

Program

Design



The program
is
student
-
centered, with a focus on structured courses in the first
year.

As students progress in

the program, there is

increased flexibility to encourage the
development of creative, analytical and independen
t research skills.

The program
train
s

bioinformaticians at
both
the
MSc and

PhD level, with exposure to original
research

at all stage
s
.
Students currently

receive a two
-
year stipend

funded
from a
CIHR/MSFHR scholarship
.

However,

support from NSERC, SSHRC,

Killam, UGF
and other University departmental sources
are

anticipated

and encouraged
.


The graduates of this program will become leaders in the field of bioinformatics,
applying their expertise in the world of commercial biotechnology research in areas
su
ch as targeted drug design, or they will enter health research and specialize in areas
such as cancer or infectious disease genomics, population and medical genetics.

Other
applications, such as developing models for combating
destructive animal and crop
d
isease, controlling
insects,

and developments for

crop hardiness and enhancement
will
advance

agricultural
and plant
research.


e
)
Enrollment

The program

anticipates an
enrollment
of approximately
10 students per year

initially
.

In the future,
as
more stud
ents
in other life sciences programs
become aware of
bioinformatics as a
relevant
field of study

and
new undergraduate training programs
produce a greater number of
suitable
candidates for the program

(
http://bioinformatics.ca/bioinformatics_resources/courses_and_programs/programs/
),
we anticipate

increased enrollment.



8

Currently, s
tudents are recruited from top u
niversities in North America, Asia and
Europe. T
he program typically

has a mix of Canadian

students, landed immigrants and
foreign students.



III
. PROGRAM

ORGANIZATION

AND SPECIFICATIONS

The program brings together a tra
ns
-
disciplinary team

from
several
departments
at
UB
C.




a)
Bioinformatics
Governance


Advisory Board and Program Director

The Advisory

Board (Appendix I), will consist

of the Program Director
, Associate
Director and other appointed

board members
, who will be responsible for overseeing
policy and revie
wing the program curriculum in compliance with the policies of the
Faculty of Graduate Studies
.
It will be composed of

a core group of individuals with

Steering



Committee

Student Issues

Committee



Adjunct Faculty

Admissions


Committee

Program Coordinator

and Grants Fa
cilitator



Bioinformatics Faculty






Associate Faculty

Advisory
Board


9

strong individual bioinformatics expertise that have diverse perspectives across a
broad range of techn
iques and disciplines that are essential to acquire comprehensive
bioinformatics research t
raining. These specialists will be

selected for their
dedication and drive to see a

bioinformatics graduate

program in British Columbia.
M
embers
hip will be

reviewed

every
three year
s, with at least

two

new

faculty
members appointed every new term

beginning
July 1. The program director
ship and
associate directorship

will be

reviewed every five years.



Bioinformatics Graduate Program Faculty/ Mentors

F
aculty memb
ers from UBC

(Appendix II)

will
teach and supervise graduate students

in the program. As a group, these mentors

have an outstanding record of research
supervision and training. In addition, they have strong existing collaborations within
the group and outs
ide it, and each has shown the ability to speak the common
language of bioinformatics.



Responsibilities
required of all Program Faculty
include:



Participation as mentor/supervisor of an incoming Bioinformatics student.



Participation on one or more superv
isory committees of a Bioinformatics student.



Mentoring and evaluation of assigned students.



Submission of research proposals for student research laboratory rotations
(expectation is that one is submitted each rotation, although it may not be selected
by
students).



Attendance at student research rotation presentations


3 per year.



Participation on one of the following faculty committees: steering committee,
admissions committee or student issues committee.



Teaching responsibilities within the program, as

negotiated with their home
departments.


A core faculty group currently exists, but
is anticipated to grow, as new
bioinformatics faculty are being recruited at UBC, though UBiC
. A formal process of
reviewing new candidates will be undertaken to ensure th
eir suitability for the
program.


Supervisory
Committees
:

Each of the student committees
will be comprised of an equal balance of faculty with
computer science backgrounds and biological backgrounds.
At least one member
from the Advisory board will sit on
e each of these committees.


A.

Steering Committee

This committee will be

responsible for
integrating
new
developments in
bioinformatics into the program. It will oversee
the curriculum, budget plans
,
team
-
taught courses, rotations, student assessments
and
o
ther issues.
It
will
also
s
ets admission and degree requirements

in compliance with the requirements of
the Faculty of Graduate Studies
.



10

In addition to deciding policy m
atters of the graduate program,
members
of this
committee serve on all thesis supervis
ory and examination committees, and

are
available at any time to provide advice and support to the students when needed.
They will help students choose their rotations and advise them on the membership
of
their
supervisory committee
.

B.

Admissions Committee

This committee

will be

responsible for evaluation of all applications for
admission to the Bioinformatics Graduate Program, and
will make
recommendations to the Faculty of Graduate Stud
ies regarding their acceptability
to

the program.



C.

Student Issues Committee

This committee a
ddresses student issues

and disciplinary matters, regarding
student’s conduct. A represen
tative from the Bioinformatics Student C
aucus will
be an integral member
of this committee.



Associate Faculty

Academics who

have a str
ong interest in bioinformatics, but whose specialty is in
another field
will be
encouraged to
participate
in the research rotation component of
the program

and may serve on student supervi
sory committees.



Adjunct Faculty

Academics

and researchers

with
a
strong expertise in bioinformatics
,

who

are
f
rom
institutions outside of UBC

and who

have
existing
collaborations
with UBC
Bioinformatics faculty or are capable of initiating a collab
orative project
,

may
participate in the research rotation
component of the
program

as a co
-
supervisor and
may serve on student thesis committees
.




Program Coordinator
/Grants Facilitator

The
program coordinator
, in liaison with the Dir
ector, Associ
ate Director

and other
pr
ogram faculty
,
will be the
point of contact for

applicants
, faculty and students.
The
c
oordinator
will
assist the advisory

board with all aspects of the program’s
administration.

As well as coordinating the program, this position w
ill also be
responsible for
assistance and support for faculty members in applying for research
funding.
Funding for this position will not depend on UBC resources.



b
)

Program Overview

The Bioinformatics Graduate Program is a trans
-
disciplinary program t
hat combines
computational and biological disciplines for

students pursing an MSc or PhD

This
program is intended to accommodate the diverse background of students and the broad
nature of bioinformatics research. Students, who apply for entrance, must sati
sfy the
general regulations of the Faculty of Graduate Studies and must be acceptable to the
Bioinformatics Graduate program admissions committee.


11

c)

Doctor of Philosophy


A.
Admission Requirements

Students admitted to the PhD

degree program normally p
oss
ess an MSc

degree in
Bioinformatics or a related area, with clear evidence of research ability or potential.
Tr
ansfer from the MSc to the PhD

program is permitted under regulations set by the
Faculty of Graduate Studies.



B.
Program Requirements

T
here are no specific course requirements for the PhD degree program apart from
the
thesis;

however, the student’s PhD committee has the prerogative to impose
course requirements where course deficiencies are perceived.
Students proceeding
towards a PhD mus
t pass an oral qualifying examination within the first 24 months
of study. All students are required to present a Bioinformatics Graduate program
seminar upon completion of their program, and before their thesis defense.

A student’s committee for the doct
orate will consist of the thesis supervisor and
three others. The supervisor and at least one other member must be

members of the
Bioinformatics g
raduate program.

d)
Master of Science


A.
Admission Requirements

Successful applicants require a BSc or e
quivalent, majoring in a biological
discipline (such as biology, genetics, microbiology, molecular biology, medicine) or
in a quantitative science (such as computer science, mathematics, statistics, physics,
e
ngineering).
If the applicant has a degree in a

biological science, they should also
have significant experience in a quantitative science or vice versa.

Students
must
also meet current Faculty of Graduate Studies admission requirements, with the
expectation that most successful applicants will signifi
cantly exceed these minimum
requirements.



B.
Program Requirements

The required courses for the program are: i) CPSC 545 (Algorithms for
B
ioinformatics)


3 credits, ii) MEDG 548C (Problem
-
based Learning in
Bioinformatics)
-

3 credits and iii) GENE 501

(Special Topics in Bioinformatics)
-

3 credits. Students are also required to complete three elective courses from
computer science, statistics, medical genetics and other related faculties for a total
of nine credits.
Required program credits equal a tot
al of 18 course credits and a 12
credit thesis.



As well, three non
-
credit four
-
month research rotations will be required to be
completed in bioinformatics
-
affiliated laboratories.


Students entering the program with either a Bach
elors degree or a Master
s degree
will be expected to complete the same required course work and electives. Course
equivalencies will be considered, and the student may replace required program
courses with electives, upon the approval of their mentor and supervisory

12

committee. Th
e program must be started in the September term in order to
complete the required courses and research rotations as outlined.


The student’s graduate program will be decided by the student, and their assigned
mentor and committee members. The mentor and co
mmittee members will ensure
that the student takes courses that remedy any deficiencies in the student’s
undergraduate preparation. All students must complete 18 credits of graduate
course work in their first year, three four
-
month laboratory research rota
tions
under the supervision of bioinformatics
-
affiliated faculty, and meet the formal
requirements of the Faculty of Graduate Studies. At the beginning of their second
year, upon the recommendation of their thesis supervisor and committee, students
continu
e their MSc in bioinformatics or transfer to a PhD program in
bioinformatics or related discipline.

All students are required to present a
Bioinformatics Graduate program seminar upon completion of their program, and
before their thesis defense.


A studen
t’s committee for the Master of Science will consist of the
thesis
supervisor and two other members
. The supervisor and at least one other member
must be

members of the Bioinformatics g
raduate program.



e
)

Student Supervisory Committee
s


The first
student supervisory c
ommittee
will consist

of a program mentor/faculty in
the area of the student’s interest, as stated on their ap
plication. Two other members
will be

selected from the Bioinformatics Faculty or Associate Faculty.
The

student
supervisory c
ommittee
will monitor

the

student's progress r
egularly during his/her
course work and research r
otations. A committee meeting will be

held within the first
six weeks of the student entering the program.




Once the student has completed their research
rotations, they
will
select

a thesis
supervisor, based on a mutual agreement between the student and the faculty member.
A
thesis
supervisory committee
will be
selected at this time, consisting of at least two
other faculty or associate faculty members, on
e of whom should be from an area that
is outside the supervisor’s immediate area of expertise.
C
ommittee meeti
ngs will be

held at least yearly, with

the first meeting

held
prior to October 15
th
, when the student
must decide on their career path, either to
continue as a Masters or a Doctoral student.


f
)


Examinations

Masters students must pass an oral thesis defense and are required to write a formal
thesis. Students who wish to transfer to a PhD, without finishing a Masters degree
must write a formal rese
arch proposal and pass
the comprehensive exam
.


A

written
thesis and oral examination
are required to obtain a PhD.


g
)


Outline of program for typical students

Upon acceptance by the Faculty of Graduate Studies
, students
will be

assigned a
mentor (in the
area of research they are interested in) and two commit
tee members.

The committee

advise
s them on what electives best complete their deficiencies and

13

meet their
interest
s
, and
help
s

to
map out a program to best meet the student’s
research and career goals.



Students
begin their first
four
-
month research
rotation in the

first

term

of the program
,

while they are attending classes.

The second research rotation is completed in the
second term, along with course work as well. It is highly recommended that stude
nts
weight their course load equally
over
the first and second ter
ms. Students

enter their
final rotation lab

over the summer term
.

This final lab rotation is usually the lab that
they complete their thesis work in, but this is not a requirement. However,
i
t is
assumed that the student will choose one of the three labs

where

they have spent a
research rotation
. Again, this is not a requirement.

A
n October 15 dead
line

in the
second year of study

has been imposed, at which time the

student
s must
choose their
research path, either to finish their MSc degree or
to
transfer to a PhD.

At this time, a
thesis supervisor and
two or three

committee members are
chosen

who may
or may
not be the same as
the original committee assigned when the student entered the
p
rogram
.

This thesis commit
tee will make recommendations regarding

the student’s
selected career
path and give final approval, pursuant
on the student meeting current
Faculty of Graduate Studies criteria.



I
V.
EXISTING COURSES DIRECTLY IDENTIFIED WITH THE PROGRA
M

AND NEW COURSES IMPLEMENT
ED BY

THE PROGRAM


a)

Existing courses

The
following mandatory courses must

to be completed by MSc

students

for a total
of nine credits:


1)

CPSC 545

(Computer Science Dept)


Algorithms for Bioinformatics




The course comprises th
e
study
of
algorithms for the acquisition and analysis of



information from DNATopics Sequence similarity; Sequence

alignment

and




multiple sequence alignment; String alignment and algorithms for optimal



alignment; Proteins and folding; Ph
ysical Mapping;

P
hylogenies.




2)

MEDG 548C

(Medical Genetics Dept)



Problem
-
based Learning in

Bioinformatics


This

pr
oblem
-
based learning course

develop
s

a
students' ability to exchange ideas

in small groups focused on real but simplified

problem
s
in bioinformatics.
Problems are
carefully selected to cover all aspects of bioinformatics research.


3)

GENE 501

(Genetics Graduate Program)



Special Topics in Bioinformatics



This discussion
-
based
bioinformatics course

expose
s

students to the lates
t



developments in b
ioinformatics analysis and algorithms.

It
runs
in conjunction


w
ith the VanBug Seminar Se
ries, in which the students

have the opportunity


to meet and discuss their work with guest speakers, both local and internationa
l


scientists.





14

Th
e following are current UBC

course electives

available to program participants:


Three electiv
es are required for a total of nine

credits.



Students choose from a number of elective course options to promote advanced study

in are
as
relevant

to
bioinformatics
applications in he
alth care. Students are

guided

by

their mentors to ensure that they have the required pre
-
requisites.

We anticipate that
this list will expand as students in non
-
health related biological disciplines enroll
in the
program.


Computer Science

CPSC 304


Introduction to Relational Databases

CPSC 445


Algorithms in Bioinformatics


CPSC 504


Database Design

CPSC 506


Complexity of Computation

CPSC 564


Data Mining


Health Care and Epidemiology

HCEP 511


Cance
r Epidemiology




Math


MATH

561


Mathematical Biology

II


MATH

612D


Topics in Mathematical Biology


Medical Genetics

MEDG 505
-

Genomic Analysis

MEDG 521/PATH 531


Molecular and Cell Biology of Cancer


Statistics


STAT 527


Topics in Bio
statistics

STAT 540


Statistical Methods for High Dimensional Biology


b)

New courses


1)
BIOF 599
-

Master of Science (in Bioinformatics)

thesis course



12 credits



Pass/Fail

format





2)

BIOF 699
-

PhD
(
in Bioinformatics
)

thesis cours
e



0 credits


Pass/Fail

format




V
.

LABORATORY RESEARCH ROTATIONS

The program is designed

to maximize the exposure of

students to a broad range of
research topics that require expertise in bioinformatics.
The opportunity to complete
signif
icant practical work on real bioinformatics problems is one of the
distinguishing features of
this program.




15

The
re are three

research rotations
;

one in the first term of study, one in the second
term of study and the final
extending over the summer term.

Each is

four
month
s in

duration. The program coordinator contacts

the program’s

faculty and
associated
faculty, including industrial partners and collaborators, and encourages them to
propose student research projects.
Adjunct faculty may propose collabora
tive
projects with bioinformatics faculty.
Students are also encouraged to research and
propose projects for their rotations.
During the

selection process
, an advisor assists
the student in choosing from a diverse set of rotation projects. Students are
enc
ouraged to sample from both biological and computer
-
related project labs.

The
participation of a significant number of associate
faculties
, based in research
institutes, universities and private companies in BC, ensures that good matches are
made for resea
rch rotations.


An important aspect of the program is the research experience it provides in
industrial labs.

A list of companies that have parti
cipated in the program thus far

can
be found in A
ppendix

V
.
The program has
also
received funding from the W
estern
E
conomic
Diversification

Fund t
o

develop more industrial participation
.

To
maintain academic integrity

f
or

each
industrial
placement, students are
assigned
a
supervisor who is university
-
appointed.



In addition, t
he program also has an internation
al component

in which students work
with
biotechnology companies and renowned scientists across Canada and
throughout the world
.


P
rogram participants
have
completed research rotations
at
the
International
Rice
Research
Institute in
the Philippines
,
the Eu
ropean Bioinformatics
Institute
in
Cambridge,
UK, and
at
Merck
-
Frosst in Montreal.



Students are

required to make a formal presentation on their rotation r
esearch to the
program’s faculty
, associated faculty,

and their fellow students.

As well, research
w
ork
is
documented and archived in the individual laboratories

where the rotation is
carried out
.

A complete listing of all research rotations and the affiliated laboratory
a
nd supervisor
s

can be found in A
ppen
dix

V
I
.


Prior to making

their third rotation s
election, students are asked to carefully consider
all research proposals in regards to continuing their thesis research. Faculty who
submit proposals must realize students may choose their lab as their thesis lab and
therefore must commit to supporting th
at student during the remainder of their thesis
research.


Once a proposal has been selected, the studen
t enters the lab of their

chosen
supervisor and additional committee members are chosen to form the
ir

thesis
committee.

Upon the recommendation of
their

supervisor
and committee members,
students who meet the Faculty of Graduate Studies criteria may be permitted to
transfer to the PhD stream instead of completing their MSc.





16

VI.

CALENDAR STATEMENT

The Bioinformatics

Graduate p
rogram

is a trans
-
discipli
nary program that combines
computational and biological disciplines for students pursing a
n

MSc or PhD.

This
program is intended to accommodate the diverse background of students and the
broad nature of bioinformatics research.
Students,

who apply for entr
ance
,

must
satisfy the general regulations of the Faculty of Graduate Studies

and must

be
acceptable to the Bioinformatics Graduate program

admissions committee.


The student’s graduate program will be decided by the student, and their assigned
mentor and

committee members.
The mentor and committee members will ensure
that the student takes courses that remedy any deficiencies in the student’s
undergraduate preparation.
All
Masters
s
tudents
must
complete 18

credits

of
graduate
course work in their

first y
e
ar,

three four
-
month laboratory research
rotations under the supervision of bioinformatics
-
affiliated faculty
, and meet the
formal requirements of the Faculty of Graduate Studies
.

At the beginning of their
second year,
upon the recommendation of their
thes
is
supervisor and committee,
s
tudents continue the
ir

MSc in bioin
formatics or
transfer to a PhD program in
bioinformatics

or related discipline.

Students admitted to the Ph
D degree

program
normally possess an MSc

degree in Bioinformatics or a related area,

with clear
evidence of research ability or

potential. Transfer from the MSc to the PhD

program
is permitted under regulations set by the Faculty of Graduate Studies.

Students
proceeding towards a PhD must pass an oral qualifying examination within the fi
rst
24 months of study. All students are required to present a Bioinformatics Graduate
program seminar upon completion of their program, and before the
ir

thesis defense.


A student’s committee for the Master of Science will consist of the
thesis superviso
r
and two other members
. The supervisor and at least one other member must be
members of the Bioinformatics Graduate program. A student’s committee for the
doctorate will consist of the th
esis supervisor and three other members
. The
supervisor and at lea
st one other member must be members of the Bioinformatics
Graduate program.


VI
I
.
PRESENT AND PROJECTED RESOURCES

a)

Qualified faculty

Approximately 80

facu
lty,

associated
and adjunct
faculty members

participate in the
pro
gram. Faculty from related departm
ents

with bioinformatics
-
related research
p
rograms

or researchers who wish to initiate a collaboration with a faculty member
may apply to the
steering

committee for supervision
of
a
proposed research
rotation
project. A
cceptance will be based on research f
unding and publication records.


b)

Research facilities and ongoing research programs

Outstanding research by UBC

faculty is being carried out at various sites across
Vancouver

and the lower mainland
.

The Genome Sciences Centre, BCCA,
is a rich
environmen
t for
bioinformatics
graduate research education, and already provide
s

an
excellent milieu for graduate students.

Industrial partners
,

and
local and
international
collaborators
also
provide diverse and challenging venues.


17

c)

External research funding avail
able and faculty research awards

The program is
currently
f
unded by a CIHR/MSFHR grant until

March 2008
. This
provides a
two
-
year
stipend for
all of
the program’s
MSc
students.

However, d
ue to
the high standard of qualifications of the program’s current st
udents and previous
applicants, we anticipate applicants eligible for NSERC, SSHRC, UGF and Killam
awards will apply.
For students not eligible for scholarship funding,
o
nly
those
faculties that

have

ongoing research support would
participate
in the progra
m.

Additional support for recruitment of students and program advertising has been
garnered from the Alfred P. Sloan Foundation
. The Western Economic Diversification
Fund has also provided funds for recruitment of industrial participants for the research
rotations
.


d) Library resources

No new library resources are required.


e) Administrative support staff

The program is administered by a Bioinformatics Pro
gram Coordinator
/Grants
Facilitator
,
presently
funded by the

CIHR/MSFHR grant.

W
e

are requesting

50
%

of
this posi
tion

be

supported by UBC funds, but the success of the program does not
depend upon this funding.


f)
Budgetary impact and anticipated sources of external financial support

The budgetary impact should be minimal as existing resourc
es
are
used.

Students
entering the program will need to have either scholarship support or a Training Grant
stipend for the first two years, and participating faculty will guarantee support for the
duration
of

a
PhD program
.

Upon admission or during th
eir first year,
all
students are

required to apply for scholarship support.

Additional e
xternal financial support
will be
sought to prov
ide necessary student
and administrative
funding.


VI
II
. PARTNERSHIPS, COLLABORATIONS AND INSTITUTIONAL SUPPORT

The Training G
rant

prog
r
am has received support from

the participating institutions.

The BCCA provides

both administrative support and student resources for the
program.

As well, they

have recruited researchers qualified

to become
program
faculty
.

The Michael Smith

labs provide

space and infrastructure to support the
program at UBC.

The Bioinformatics Centre

has provided Bioinformatics Workshop
training, student resources, and is recruiting faculty that will be an integral part of the
program.
The Co
mputer Science Department

has
assisted

in the development of
computer science modules and the admission of students in
to

the pro
gram to
undergraduate courses, as

needed.

In addition to financial support from CIHR for a
five
-
year term, the Michael Smith Foundation for

Health Research ha
s matched
funding and w
e anticipate that this funding will be renewed.
As well,
the program has
partnered with MITACS (Mathematics of Information Technology and Complex
Systems) to train students in the rotation component of the program. They will
provide

student resources, in addition to stipend support for
six four
-
month rotations
.
The program has also
received funding from
the Alfred

P. Sloan Foundation
and the

Western Economic Diversification Fund
.


18

A
PPENDIX I.


PRO
GRAM DIRECTOR
AND ADVISORY BOARD


The

current
Advisory
board consists

of twelve

scientists:


Steven Jones , Program Director of Bioinformatics

Graduate Program
;

Director of
Bioinformatics,
Genom
e Sciences Centre, BCCA; Assistant

Professor, Medical
Genetics, UBC;
Adjunct Faculty and Associate
Director, UBC Bioinformatics
Centre;
Adjunct Professor, Molecular Biology

& Biochemistry (MBB), SFU


David Baillie,
Honorary Faculty
, Medical Genetics, UBC;
Adjunct Faculty, UBC
Bioinformatics Centre;
Canadian Research Chair in Genomics at MBB, SFU


Fiona
Brinkman
,
Core

Faculty,
C
anadian Bioinformatics Workshops

at UBC
Bioinformatics Centre
;
Assistant Professor, MBB, SFU;
MSFHR Scholar


Jennifer Bryan, Assist
ant Professor, Michael Smith Laboratories

and Statistics, UBC
;
Adjunct Faculty, UBC Bioinformatics C
entre


Artem Cherkasov, Assistant Professor, Faculty of Medicine, Infectious Diseases, UBC


Arvind Gupta,
Scientific Director of the Mathematics of Information Technology and
Complex Systems (MITACS), NCE
; Professor, Computer Science, SFU


Phil Hieter,
Di
rector of the Michael Smith Laboratories
; Professor, Medical Genetics,
UBC


Marco Marra, Scientific Director of Genom
e Sciences Centre, BCCA; Associate


Professor, Medical Genetics, UBC; Adjunct Professor, MBB, SFU


Francis
Ouellette,
A
ssociate Director of

Bioinformatics

Graduate

Program; Director of
the
UBC Bioinformatics Centre
; Associate Professor, Medical Genetics, UBC;
Associate Member, Genome Sciences Centre, BCCA; Adjunct Professo
r, MBB,
SFU; Core Faculty, and Scientific C
oordinator of the Canadian
B
ioinformatics
Workshops


Frederic Pio, Assistant Professor, MBB, SFU; ASI Provincial Research Fellow


S. Cenk Sahinalp, Canada Research Chair in Computational Genomics;

Associate
Professor of Computing Science, SFU


Wyeth Wasserman, Centre for Molecular
Medicine & Therapeutics; Associate Professor,
Medical Genetics, UBC
; Adjunct Faculty, UBC Bioinformatics Centre


19

APPENDIX II.


LIST OF
PROGRAM
FACULTY
/MENTORS


Steven Jones, Program Director of Bioinformatics Graduate Program
;

Assistant
Professor, Medical
Genetics, UBC
;

Adjunct

Faculty and Associate Director, UBC
Bioinformatics Centre


David Baillie,
Honorary Faculty
, Medical Genetics, UBC
; Adjunct Faculty,
UBC
Bioinformatics Centre


Ryan Brinkman, Medical Genetics, UBC


Jennifer Bryan, Assistant Professo
r, Michael Smith Laboratories and Statistics, UBC
;
Adjunct Faculty,
UBC
Bioinformat
ics Centre


Artem Cherkasov, Assistant Professor, Faculty of Medicine, Infectious Diseases, UBC


Ann
e

Condon, Assistant Professor, Computer Science, UBC; NSERC Chair for Wom
en
in Science and Engineering


Phil Hieter, Director of the Michael Smith Laboratories; Professor, Medical Genetics,
UBC


Holger Hoos, Associate Professor, Computer Science, UBC


Marco Marra, Scientific Director of Genome Sciences Centre, BCCA; Associate

Professor, Medical Genetics, UBC; Adjunct Professor, MBB, SFU


Francis Ouellette, Associate Director of Bioinformatics Graduate Program; Director of

the UBC Bioinformatics Centre;
Associate Professor, Medical Genetics, UBC;
Associate Member, Genome Science
s Centre, BCCA;
Core Faculty, and Scientific
C
oordinator of the Canadian Bioinformatics Workshops (CBW).


Paul Pavlidis,
UBC Bioinformatics Centre; Assistant Professor, Psych
iatry, UBC


Wyeth Wasserman, Centre for Molecular Medicine & Therapeutics; Associa
te Professor,
Medical Genetics, UBC
; Adjunct Faculty, UBC Bioinformatics Centre


Mark Wilkinson, Medical Genetics, UBC








20

APPENDIX III


LIST OF
PROGRAM
ASSOCIATED FACULTY


The programs associated
faculty is

comprised of scientists
affiliated with

UBC

d
epartments,

lower mainland
hospitals

and research institutions
.


Dr. Chris

Bajdik, Health Care and Epidemiology, Cancer Control Research, BCCRC.

Dr. Hugh Brock, Zoology, UBC

Dr. Angela Brooks
-
Wilson, Medical Genetics, Genome Sciences Centre, BCC
A

Dr. Allan

Eaves, Medicine, Terry Fox Laboratory, BCCRC

Dr. Connie Eaves, Medical Genetics, Terry Fox Laboratory, BCCRC

Dr. Joanne Emerman, Anatomy, UBC

Dr. Bre
tt Finlay, Michael Smith Laboratories
, UBC


Dr. Rick Gallagher, Health Care and Epidemiology, Cancer Contr
ol Research, BCCRC

Dr. Raphael Gottardo, Statistics, UBC

Dr. Steven Hallam, Microbiology and Immunology, UBC

Dr. Robert Hancock, Microbiology and Immunology, UBC

Dr. Michael Hayden, Centre for Molecular Medicine and Therapeutics, UBC

D
r. Charles Haynes, Mi
chael Smith

Labor
atories
, UBC

Dr. Rob Holt, Psychiatry, UBC

Dr. Pam Hoodless, Medical Genetics, Terry Fox Laboratory, BCCRC

Dr. Keith Humphries, Medicine, Terry Fox Laboratory, BCCRC

Dr. Rob Kay, Medical Genetics, Terry Fox Laboratory, BCCRC

Dr. Patrick Ke
eling, Botany, UBC

Dr. Leah Keshet, Math, UBC

Dr. Michael Kobor, Medical Genetics, UBC

Dr. Jim Kronstad, Michael Smith Laboratories
, UBC

Dr. Gerry Krystal,
Pathology & Laboratory
Medicine, Terry Fox Laboratory, BCCRC

Dr. Wan Lam,
Pathology & Laboratory
Med
icine, Cancer Genetics, BCCRC

Dr. Peter Lansdorp,
Pathology & Laboratory Medicine
, Terry Fox Laboratory, BCCRC

Dr. Nhu Le, Statistics, Cancer Control Research, BCCRC

Dr. Victor Ling,
Pathology & Laboratory
Medicine, Cancer Genetics, BCCRC

Dr. Calum MacAul
a
y,
Pathology & Laboratory
Medicine, Cancer Imaging, BCCRC

Dr. Dixie Mager, Medical Genetics, Terry Fox Laboratory, BCCRC

Dr. Don Moerman, Zoology, UBC

Dr. Ed Moore, Physiology, UBC

Dr. Colleen Nelson
, Surgery, UBC

Dr. Raymond Ng, Computer Science, UBC

Dr.
James Piret,
Michael Smith Laboratories
, UBC

Dr. Anne Rose, Medical Genetics, UBC

Dr. Miriam Rosin,
Pathology & Laboratory
Medicine, Cancer Control Research, BCCRC

Dr. Elizabeth M. Simpson,
Medical Genetics
, UBC

Dr. John Spinelli, Health Care and Epidemiol
ogy, Cancer Control Research, BCCRC

Dr. Fumio Takei,
Pathology & Laboratory
Medicine, Terry Fox Laboratory, BCCRC

Dr. Z. Ja
ne W
ang, Electrical and Computer Engineering, UBC


21

APPENDIX IV
.


LIST OF PROGRAM
ADJUNCT FACULTY


The programs adjunct faculty is com
prised of scientists affiliated with
the BCCA, SFU
and
U
Vic.


Dr. Andrew Beckenbach, Biological Sciences, SFU

Dr. Christopher Beh, Molecular Biology and Biochemistry, SFU

Dr. Bruce Brandhorst, Molecular Biology and Biochemistry, SFU

Dr. Felix Breden, Biolo
gical Sciences, SFU

Dr. Fiona Brinkman, Molecular Biology and Biochemistry, SFU

Dr. Andrew Coldman, Cancer Control Strategy, BCC
A

Dr. Veronica Dahl, Computing Science, SFU

Dr. William Davidson, Molecular Biology and Biochemistry, SFU

Dr. Charmaine Dean, St
atistical and Actuarial Science, SFU

Dr. Eldon Emberly, Physics, SFU

Dr. Martin Ester, Computing Science, SFU

Dr. Jinko Graham, Statistical and Actuarial Science, SFU

Dr. Qianping Gu, Computing Science, SFU

Dr. Arvind Gupta, Computing Science, SFU

Dr. Jiaw
ei Han, Computing Science, SFU

Dr. Nicholas Harden, Molecular Biology and Biochemistry, SFU

Dr. Nancy Hawkins, Molecular Biology and Biochemistry, SFU

Dr. Barry Honda, Molecular Biology and Biochemistry, SFU

Dr. Keith Kirkpatrick, Computing Science, SFU

Dr
. Ben Koop, Biology, UVic

Dr. Michael Leroux, Molecular Biology and Biochemistry, SFU

Dr. Brad McNeney, Statistical and Actuarial Science, SFU

Dr. Gregg Morin, Genome Sciences Centre, BCCA

Dr. Robert Olafson, Biochemistry and Microbiology, UVic

Dr. Mark Pa
etzel, Molecular Biology and Biochemistry, SFU

Dr. Frederic Pio, Molecular Biology and Biochemistry, SFU

Dr. Cenk Sahinalp, Computing Science, SFU

Dr. Carl Schwarz, Statistical and Actuarial Science, SFU

Dr. Jamie Scott, Molecular Biology and Biochemistry,

SFU

Dr. Dipankar Sen, Molecular Biology and Biochemistry, SFU

Dr. Michael J. Smith, Molecular Biology and Biochemistry, SFU

Dr. Peter Unrau, Molecular Biology and Biochemistry, SFU

Dr. Chris Upton, Biochemistry and Microbiology, UVic

Dr. Esther Verheyen,
Molecular Biology and Biochemistry, SFU

Dr. Ke Wang, Computing Science, SFU

Dr. Kay Wiese, IT, SFU





22

APPENDIX V.


LIST OF INDUSTRY PARTNERS


BioCad
, Vancouver, British Columbia


Inimex Pharmaceuticals Inc.
, Vancouver, British Columbia


Merck
-
Frosst, Montr
eal, Quebec


23

APPENDIX
V
I
.



LIST OF RESEARCH ROTATIONS



January, 2003




Keith Boroevich: Primate retroelement differences datab
ase (PRED
_DB):
I
dentification of indel patterns in the primate lineage (with Dixie Mage
r, BCCA
)



Michael Hsing: The assessment of
gene function through synthetic genetic array
analysis (with Phil Hieter and Wyeth Wasserman
, UBC)



Shan
nan Ho Sui: Identification and characterization of alternative promoters in
the h
um
an g
enome (with Wyeth Wasserman
, UBC
)



Byron Kuo: Data m
ining to
identi
fy groups of genetically
-
related c
ancers (with
Chris Bajdik
, BCCA
)



Drew Lett: Interaction
-
based protein classification: the death domain superfamily
(with Frederic Pio, SFU)



Perseu
s Missirlis: Identification of conserved cis
-
regulatory elements in double
-
s
tranded 1break repair g
enes (with Angela Brooks
-
Wilson
, BCCA
)



Fred Peng: Genecomber a
nalysis (with Francis Ouellett
e, UBC
)



Chris Walsh:
Comparative physical mapping of the genomes of 3 varit
ies of
Cryptococcus neoformans (with Jim Kronstad, UBC)


May, 200
3




Keith Boroevich: Investigation of nuclear membrane structure in longevity of
Caenorhabditis elegans (with Steve Jones
, BCCA
)



Michael Hsing: Modeling and simulating cell signaling systems by semantic
networks (with Allen Delaney and Conor Shankey at BioC
AD)



Shannan Ho Sui: Constructing protein interaction m
aps for
Chlamydia

g
enomes
(with Bob Brunham and Art Cherkasov
, UBC
)



Byron Kuo: Gene expression profiling of innate i
mmunity (with Marc
-
Etienne
Rousseau at Inimex
, Vancouver
)



Drew Lett: A Bayesian appro
ach to cDNA microarray image analysis (with
Jenny Bryan, UBC)



Perseus Missirlis: Correlation of GeMS flanking sequences with GeMS sequence
mutability (with Francis Ouellette
, UBC
)



Fred Peng: Gen
e locations and functions in e
ukaryotes (with David Baillie
, S
FU
)



Chris Walsh:
Conserved transcription factor binding site de
tection in co
-
expressed genes (with Wyeth Wasserman, UBC)


September, 2003




Keith Boroevich:

Gene expression aided phylogenetic f
oot printing in
Caenorhabditis elegans

(with David Baillie
, SFU
)


24



Michael Hsing: Computational analysis and simulation of phosphatidylinositol 3
-
kinase mediated pathways and their roles in the process of bacterial invasions
(with Artem Cherkasov
, UBC
)



Shannan Ho Sui: Analysis of c
o
-
regulated genes in biomedically
-
linke
d pathways
and processes (with Brian Kennedy and Francis Ouellette
, UBC
)



Byron Kuo: A gene discovery tool for SAGE a
nalysis (with Elizabeth Simpson
,
UBC
)



Drew Lett: Vertebrate gene structure analysis quality index (with Francis
Ouellette, UBC)



Perseus Mis
sirlis: Identification of regulatory mutations in the SNAP
-
2
5 gene in
schizophrenia (with
Robert Holt
, BCCA
)



Fred Peng: Transcriptional regulatory networks in apoptotic c
ascade (with
Frederic Pio
, SFU
)



Chris Walsh:
PSORT
-
B+: Improving protein subcellular
localization predict
ion
for Gram
-
positive bacteria (with Fiona Brinkman, SFU)


January, 2004




Dan Baluta: Comparative vertebrate analysis of non
-
coding regions of human chr
21q22:11

(with Francis Ouellette
, UBC
)



Debra Fulton
:
Expression of clustering in
C.

elegans

(with Steven Jones, BCCA
)



Ben Good
:
Detection of genomic rearrangements involving endogenous
retroviruses
(with

Dixie Mager, BCCA
)



Jessica Lee
:
Bioinformatics (with Ryan Brinkman, BCCA
)



Carri
-
Lyn Mead
: I
nverse protein folding

(with

Arvind Gupta, S
FU
)



Alison Meynert
:
Computationally predicting cell
-
surface exposed proteins
(with

Fiona Brinkman, SFU
)



May, 2004




Dan Baluta
:

In silico

search for
Salmonella typhimurium

effectors

(with Brett
Finlay, UBC
)



Debra Fulton
:
Bioinformatics
(with
Wyeth Wasserm
an, UBC and James
Mortimer at Merck
-
Frosst
)



Ben Good: Bioinformatics (with Richard Bruskiewich at the International Rice
Research Institute, Philippines)



Jessica Lee
: Structural
differences confer from indels as novel d
rug


t
argets (with A
rtem Cherka
sov, UBC
)



Carri
-
Lyn Mead
:
GeMS (with Francis Ouellette, UBC)



Alison Meynert
:
Bioinformatics analyses (with Ewan Birney at the European
Bioinformatics Institute, Cambridge, UK)






25

September, 2004




Debra Fulton
:
Improving orthologous gene detection for a la
rge comparative
analysis of chicken, bovine and human gene responses to infection
(with
Fiona
Brinkman, SFU)



Ben Good: Strategy for semantic web service
-
based retrieval, storage and
browsing of confocal image data and annotation in a multi
-
user instituti
onal
environment (with Mark Wilkinson, UBC)



Jessica Lee
:
Regulation of innate immunity in human cells (with Robert Hancock,
UBC)



Carri
-
Lyn Mead
:
Testing a novel strategy to identify critical genes and regulatory
domains (with Dixie Mager, BCCA)



Alison Me
ynert
:
Mutations in transcriptional
-
related processes causing
neurodegenerative disorders (with Anne Condon and Francis Ouellette, UBC)



January, 2005




Han Hao: Building an antibody database for cancer research (Wam Lam, BCCA)



Morgan Langille: Syntax an
d semantics applied to guided integration of
biological data
(with
Mark Wilkinson, UBC)



Yvonne Li: Improving orthologous gene detection for a large comparative
analysis of chicken, bovine and human gene responses to infection (with Fiona
Brinkman, SFU)



W
ynne Lock: The role of transposable elements in mammalian gene regulation
(with Dixie Mager, BCCA)



Kelvin Zhang: Detection of mutations pattern in mitochondrial DNA in prostate
cancer (with Ke Wang, SFU)



May, 2005




Han Hao: Computational prediction of c
is
-
regulatory elements in Cryptococcus
neoformans (with Steven Jones, BCCA and Jim
Kronstad
, UBC)



Morgan Langille: Comparative analysis of genomic islands
(with
Fiona
Brinkman, SFU)



Yvonne Li: In silico development and cheminformatics study of novel dru
g leads
for the human cortisol binding globulin (CGB) (with Artem Cherkasov, UBC)



Wynne Lock: Selection of regulatory cassettes for targeted transcription in the
mouse brain (with Wyeth Wasserman and Elizabeth
Simpson, UBC
)



Kelvin Zhang: Constructing a co
mmon evidence network for neurodegenerative
disorders hypothesis (with Francis Ouellette

and Anne Condon, UBC)







26

APPENDIX V
I
I
.


LIS
T OF

UBC
PROGRAM GRADUATES


Byron Kuo

B.Sc., Computer Science, University of British Columbia, 2002

B.Sc., Cell Biology an
d Genetics, University of British Columbia, 1999


SAGE2SPLICE: UNMAPPED SAGE TAGS

REVEAL NOVEL SPLICE
JUNCTIONS”

M.Sc. Supervisor: Dr. Elizabeth M. Simpson
-

Centre for Molecular Medicine &
Therapeutics, University of British Columbia

Co
-
supervisor: Dr. Wy
eth Wasserman
-

Centre for Molecular Medicine & Therapeutics,
UBC


September 1, 2005



Michael Hsing

B.Sc. Honors, Molecular Biology & Biochemistry, Simon Fraser University, 2002

"MODELING OF CELL SIGNALING PATHWAYS IN MACROPHAGES BY
SEMANTIC NETWORKS"

M.
Sc. Supervisor: Dr. Artem Cherkasov
-

Medicine, Department of Infectious Diseases,
UBC


February 23, 2005



Perseus Missirlis

B.Sc. Honors, Life Sciences, Queens University, 2002

"C
IS
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FEATURES MEDIATING CAG/CTG REPEAT INSTABILITY, THE
SATELLOG DATABASE, AN
D CANDIDATE REPEAT PRIORITIZATION IN
SCHIZOPHRENIA"

M.Sc. Supervisor: Dr. Robert Holt
-

Genome Sciences Centre, BCCA

August 13, 2004