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UNIVERSITY OF BRITISH COLUMBIA Faculty of Graduate Studies Proposal Graduate Program in Bioinformatics 2005
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Page 1: Bioinformatics Program

UNIVERSITY OF BRITISH COLUMBIA

Faculty of Graduate Studies

ProposalGraduate Program in Bioinformatics

2005

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PROPOSED PROGRAM IN BIOINFORMATICS

Table of Contents

I. GENERAL INFORMATIONa. Title of degree program ………………………………………………………………..4b. Faculty, School, or Department planning to offer the program ………………….4c. Implementation date……………………………………………………………………4

II. RATIONALE FOR THE PROGRAMa. Background…………………………………………………………………………….4b. Objectives of the program……………………………………………………………...5c. Student Interest………………………………………………………………………...6d. Program Design …………………….………………………………………………...7e. Enrollment…..……………………………………………………………………….…7

III. PROGRAM ORGANIZATION AND SPECIFICATIONSa. Bioinformatics Governance………..…………………………………………………...8b. Program overview……..………………………………………………………………10c. Doctor of Philosophy.…………………………………….…………………………...11d. Master of Science…………………………..…………………………………………11e. Student Supervisory Committees...……………………………………………………12f. Examinations……………………………………………………………………...…...12g. Outline of program for typical student…………………………..……………………12

IV. EXISTING COURSES DIRECTLY IDENTIFIED WITH THE PROGRAM AND NEW COURSES IMPLEMENTED BY THE PROGRAMa. Existing Courses……………….………………………………………………………13b. New Courses…..………………………………………………………………………14

V. LABORATORY RESEARCH ROTATIONS………………………..……………14

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

VII. PRESENT AND PROJECTED RESOURCESa. Qualified faculty………………………………………………………………………16b. Research facilities and ongoing research programs………………………….………16c. External research funding available and faculty research awards……………………17d. Library resources………………………………………………………………….….17e. Administrative support staff……………………………………………………..……17f. Budgetary impact and anticipated sources of external financial support……………..17

VIII. PARTNERSHIPS, COLLABORATIONS AND INSTITUTIONAL SUPPORT …......................................................................................................................................17

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

I. PROGRAM DIRECTOR AND ADVISORY BOARDII. LIST OF PROGRAM FACULTYIII. LIST OF PROGRAM ASSOCIATED FACULTYIV. LIST OF PROGRAM ADJUCT FACULTYV. LIST OF INDUSTRY PARTNERSVI. LIST OF RESEARCH ROTATIONS

VII. LIST OF UBC PROGRAM GRADUATES

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GRADUATE PROGRAM IN BIOINFORMATICS

I. GENERAL INFORMATIONa) Title of degree program

Bioinformatics Graduate Program. This would be a new post-graduate degree designation, with students graduating with a degree in Bioinformatics.

b) Faculty, School, or Department offering the programThe Faculty of Graduate Studies would be the host faculty. Dr. Steven Jones, Director of Bioinformatics at the Genome Sciences Centre, BC Cancer Agency (BCCA) and Associate Professor, Medical Genetics, will serve as the program director.

c) Implementation date We would like the new program to begin by September 2006.

II. RATIONALE FOR THE PROGRAMa) Background The CIHR/MSFHR Bioinformatics Training Program has been in existence since

September 2002, with students registered 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. Supervisors in the program feel that the time is right to establish an independent graduate program offering degrees in Bioinformatics.

The explosion of biological information in genomics, proteomics and health-care has created an enormous demand for highly skilled scientists trained in both computational and biological research: bioinformaticians. The importance of bioinformatics is increasingly acknowledged. The December 12, 2002 issue of The Economist notes that “once 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 efficiency through mathematical modeling. 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 biological information, such as macromolecular 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 advertisements 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 first 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 health research, Canada needs scientists trained in bioinformatics.

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In September 2002, a CIHR/MSFHR grant-funded Bioinformatics Training Program was initiated. This innovative program broke new ground by offering a novel, trans-disciplinary training program designed 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 masters or doctorates in bioinformatics.

Since the program’s September 2002 inception, 29 students out of over 500 applicants have been enrolled. These students come from diverse backgrounds and originate from different Universities across Canada, from Turkey, Singapore, the USA and the UK.

The program introduces students to a broad range of approaches relevant to health research, including computational genomics, proteomics, epidemiology, and statistical genetics, as well as aspects of structural biology and bio-molecular modeling. It allows students with backgrounds in biology, computer science or statistics to gain the necessary skills in each field to work together to learn how to critically assess and solve bioinformatics problems.

The program adopts an interdisciplinary learning approach for students to promote the all-important development of a common language between the computational and biological components of the bioinformatics discipline. The training program produces 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-disciplinary nature of the program encourages 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 bioinformatics programs are being established 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 program 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 training 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 specific program objectives are to apply innovative trans-disciplinary approaches to train graduates to:

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

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Articulate research questions and experimental designs from different perspectives

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

Approach health research in an innovative and creative manner with the combined background knowledge of biology, computer science and statistics.

Apply these approaches to other basic biological research questions to unlock the secrets of biological functions in bacterial, animal and plant genomes.

The strategic objectives of the proposed program are: 1) to build on BC’s growing reputation and excellence as a leader in bioinformatics, genomics and population-based approaches to health care and 2) to integrate bioinformatics with basic biology to further the current research excellence in other life science sectors in the province. The program will integrate academic centres in computer science, statistics, molecular biology, and biotechnology, with translational research groups at hospitals and at the clinical interface. Members of the UBC Bioinformatics Centre, the Genetics Graduate program, the department of Statistics, the Bioinformatics, Empirical & Theoretical Algorithmics Laboratory in Computer Science, the Genome Sequence Centre at the BC Cancer Agency, and the Michael Smith Laboratories have been instrumental 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 support bioinformatics research in the life sciences.

b) Student Interest The training grant program 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 twelve 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 enquiries 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 highly qualified 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.

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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 independent research skills. The program trains bioinformaticians at both the MSc and PhD level, with exposure to original research at all stages. 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 such 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 disease, controlling insects, and developments for crop hardiness and enhancement will advance agricultural and plant research.

e) EnrollmentThe program anticipates an enrollment of approximately 10 students per year initially. In the future, as more students 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.

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Currently, students are recruited from top universities in North America, Asia and Europe. The program typically has a mix of Canadian students, landed immigrants and foreign students.

III. PROGRAM ORGANIZATION AND SPECIFICATIONSThe program brings together a trans-disciplinary team from several departments at UBC.

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 reviewing 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 Facilitator

Bioinformatics Faculty

Associate Faculty

Advisory Board

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strong individual bioinformatics expertise that have diverse perspectives across a broad range of techniques and disciplines that are essential to acquire comprehensive bioinformatics research training. These specialists will be selected for their dedication and drive to see a bioinformatics graduate program in British Columbia. Membership will be reviewed every three years, with at least two new faculty members appointed every new term beginning July 1. The program directorship and associate directorship will be reviewed every five years.

Bioinformatics Graduate Program Faculty/ MentorsFaculty members 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 outside 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 supervisory 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 their 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 one each of these committees.

A. Steering CommitteeThis 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 other issues. It will also sets admission and degree requirements in compliance with the requirements of the Faculty of Graduate Studies.

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In addition to deciding policy matters of the graduate program, members of this committee serve on all thesis supervisory 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 CommitteeThis 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 Studies regarding their acceptability to the program.

C. Student Issues CommitteeThis committee addresses student issues and disciplinary matters, regarding student’s conduct. A representative from the Bioinformatics Student Caucus will be an integral member of this committee.

Associate FacultyAcademics who have a strong 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 supervisory committees.

Adjunct FacultyAcademics and researchers with a strong expertise in bioinformatics, who are from institutions outside of UBC and who have existing collaborations with UBC Bioinformatics faculty or are capable of initiating a collaborative 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 Director, Associate Director and other program faculty, will be the point of contact for applicants, faculty and students. The coordinator will assist the advisory board with all aspects of the program’s administration. As well as coordinating the program, this position will 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 that 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 satisfy the general regulations of the Faculty of Graduate Studies and must be acceptable to the Bioinformatics Graduate program admissions committee.

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c) Doctor of Philosophy

A. Admission RequirementsStudents admitted to the PhD 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.

B. Program RequirementsThere 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 must 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 doctorate will consist of the thesis supervisor and three others. The supervisor and at least one other member must be members of the Bioinformatics graduate program.

d) Master of Science

A. Admission RequirementsSuccessful applicants require a BSc or equivalent, 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, engineering). 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 significantly exceed these minimum requirements.

B. Program RequirementsThe required courses for the program are: i) CPSC 545 (Algorithms for Bioinformatics) – 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 total 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 Bachelors degree or a Masters 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

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committee. The 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 committee 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 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 thesis supervisor and committee, students continue 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 student’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 graduate program.

e) Student Supervisory Committees The first student supervisory committee will consist of a program mentor/faculty in

the area of the student’s interest, as stated on their application. Two other members will be selected from the Bioinformatics Faculty or Associate Faculty. The student supervisory committee will monitor the student's progress regularly during his/her course work and research rotations. 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, one of whom should be from an area that is outside the supervisor’s immediate area of expertise. Committee meetings 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) ExaminationsMasters 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 research proposal and pass the comprehensive exam. A written thesis and oral examination are required to obtain a PhD.

g) Outline of program for typical studentsUpon acceptance by the Faculty of Graduate Studies, students will be assigned a mentor (in the area of research they are interested in) and two committee members. The committee advises them on what electives best complete their deficiencies and

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meet their interests, and helps 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 students weight their course load equally over the first and second terms. 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, it 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. An October 15 deadline in the second year of study has been imposed, at which time the students 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 program. This thesis committee 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.

IV. EXISTING COURSES DIRECTLY IDENTIFIED WITH THE PROGRAMAND NEW COURSES IMPLEMENTED BY THE PROGRAM

a) Existing coursesThe 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 the 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; Physical Mapping; Phylogenies. 2) MEDG 548C (Medical Genetics Dept) – Problem-based Learning in Bioinformatics This problem-based learning course develops a students' ability to exchange ideas

in small groups focused on real but simplified problems 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 exposes students to the latest developments in bioinformatics analysis and algorithms. It runs in conjunction with the VanBug Seminar Series, in which the students have the opportunity to meet and discuss their work with guest speakers, both local and international scientists.

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The following are current UBC course electives available to program participants:

Three electives are required for a total of nine credits.

Students choose from a number of elective course options to promote advanced studyin areas relevant to bioinformatics applications in health 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 ScienceCPSC 304 – Introduction to Relational DatabasesCPSC 445 – Algorithms in Bioinformatics CPSC 504 – Database DesignCPSC 506 – Complexity of ComputationCPSC 564 – Data Mining

Health Care and EpidemiologyHCEP 511 – Cancer Epidemiology

Math MATH 561 – Mathematical Biology II MATH 612D – Topics in Mathematical Biology

Medical GeneticsMEDG 505- Genomic Analysis MEDG 521/PATH 531 – Molecular and Cell Biology of Cancer

Statistics STAT 527 – Topics in BiostatisticsSTAT 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 course – 0 credits Pass/Fail format

V. LABORATORY RESEARCH ROTATIONSThe 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 significant practical work on real bioinformatics problems is one of the distinguishing features of this program.

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There 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 months 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 collaborative 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 encouraged 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 research rotations.

An important aspect of the program is the research experience it provides in industrial labs. A list of companies that have participated in the program thus far can be found in Appendix V. The program has also received funding from the Western Economic Diversification Fund to develop more industrial participation. To maintain academic integrity for each industrial placement, students are assigned a supervisor who is university-appointed.

In addition, the program also has an international component in which students work with biotechnology companies and renowned scientists across Canada and throughout the world. Program participants have completed research rotations at the International Rice Research Institute in the Philippines, the European Bioinformatics Institute in Cambridge, UK, and at Merck-Frosst in Montreal.

Students are required to make a formal presentation on their rotation research to the program’s faculty, associated faculty, and their fellow students. As well, research work 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 and supervisors can be found in Appendix VI.

Prior to making their third rotation selection, 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 that student during the remainder of their thesis research.

Once a proposal has been selected, the student enters the lab of their chosen supervisor and additional committee members are chosen to form their 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.

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VI. CALENDAR STATEMENTThe Bioinformatics Graduate program is a trans-disciplinary program that 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 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 students must complete 18 credits of graduate course work in their first year, 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 thesis supervisor and committee, students continue their MSc in bioinformatics or transfer to a PhD program in bioinformatics or related discipline. Students admitted to the PhD 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 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 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 Graduate program. A student’s committee for the doctorate will consist of the thesis supervisor and three other members. The supervisor and at least one other member must be members of the Bioinformatics Graduate program.

VII. PRESENT AND PROJECTED RESOURCESa) Qualified faculty

Approximately 80 faculty, associated and adjunct faculty members participate in the program. Faculty from related departments with bioinformatics-related research programs 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. Acceptance will be based on research funding and publication records.

b) Research facilities and ongoing research programsOutstanding 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 environment for bioinformatics graduate research education, and already provides an excellent milieu for graduate students. Industrial partners, and local and international collaborators also provide diverse and challenging venues.

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c) External research funding available and faculty research awardsThe program is currently funded by a CIHR/MSFHR grant until March 2008. This provides a two-year stipend for all of the program’s MSc students. However, due to the high standard of qualifications of the program’s current students and previous applicants, we anticipate applicants eligible for NSERC, SSHRC, UGF and Killam awards will apply. For students not eligible for scholarship funding, only those faculties that have ongoing research support would participate in the program. 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 resourcesNo new library resources are required.

e) Administrative support staffThe program is administered by a Bioinformatics Program Coordinator/Grants Facilitator, presently funded by the CIHR/MSFHR grant. We are requesting 50% of this position 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 supportThe budgetary impact should be minimal as existing resources 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 their first year, all students are required to apply for scholarship support. Additional external financial support will be sought to provide necessary student and administrative funding.

VIII. PARTNERSHIPS, COLLABORATIONS AND INSTITUTIONAL SUPPORTThe Training Grant program 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 Computer Science Department has assisted in the development of computer science modules and the admission of students into the program to undergraduate courses, as needed. In addition to financial support from CIHR for a five-year term, the Michael Smith Foundation for Health Research has matched funding and we 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.

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APPENDIX I.

PROGRAM DIRECTOR AND ADVISORY BOARD

The current Advisory board consists of twelve scientists:

Steven Jones , Program Director of Bioinformatics Graduate Program; Director of Bioinformatics, Genome 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, Canadian Bioinformatics Workshops at UBC Bioinformatics Centre; Assistant Professor, MBB, SFU; MSFHR Scholar

Jennifer Bryan, Assistant Professor, Michael Smith Laboratories and Statistics, UBC; Adjunct Faculty, UBC Bioinformatics Centre

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, Director of the Michael Smith Laboratories; Professor, Medical Genetics, 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 Sciences Centre, BCCA; Adjunct Professor, MBB, SFU; Core Faculty, and Scientific Coordinator of the Canadian Bioinformatics 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

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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 Professor, Michael Smith Laboratories and Statistics, UBC; Adjunct Faculty, UBC Bioinformatics Centre

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

Anne Condon, Assistant Professor, Computer Science, UBC; NSERC Chair for Women 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 Sciences Centre, BCCA; Core Faculty, and Scientific Coordinator of the Canadian Bioinformatics Workshops (CBW).

Paul Pavlidis, UBC Bioinformatics Centre; Assistant Professor, Psychiatry, UBC

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

Mark Wilkinson, Medical Genetics, UBC

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APPENDIX III

LIST OF PROGRAM ASSOCIATED FACULTY

The programs associated faculty is comprised of scientists affiliated with UBC departments, lower mainland hospitals and research institutions.

Dr. Chris Bajdik, Health Care and Epidemiology, Cancer Control Research, BCCRC.Dr. Hugh Brock, Zoology, UBCDr. Angela Brooks-Wilson, Medical Genetics, Genome Sciences Centre, BCCADr. Allan Eaves, Medicine, Terry Fox Laboratory, BCCRCDr. Connie Eaves, Medical Genetics, Terry Fox Laboratory, BCCRCDr. Joanne Emerman, Anatomy, UBCDr. Brett Finlay, Michael Smith Laboratories, UBC Dr. Rick Gallagher, Health Care and Epidemiology, Cancer Control Research, BCCRCDr. Raphael Gottardo, Statistics, UBCDr. Steven Hallam, Microbiology and Immunology, UBCDr. Robert Hancock, Microbiology and Immunology, UBCDr. Michael Hayden, Centre for Molecular Medicine and Therapeutics, UBCDr. Charles Haynes, Michael Smith Laboratories, UBCDr. Rob Holt, Psychiatry, UBCDr. Pam Hoodless, Medical Genetics, Terry Fox Laboratory, BCCRCDr. Keith Humphries, Medicine, Terry Fox Laboratory, BCCRCDr. Rob Kay, Medical Genetics, Terry Fox Laboratory, BCCRCDr. Patrick Keeling, Botany, UBCDr. Leah Keshet, Math, UBCDr. Michael Kobor, Medical Genetics, UBCDr. Jim Kronstad, Michael Smith Laboratories, UBCDr. Gerry Krystal, Pathology & Laboratory Medicine, Terry Fox Laboratory, BCCRCDr. Wan Lam, Pathology & Laboratory Medicine, Cancer Genetics, BCCRCDr. Peter Lansdorp, Pathology & Laboratory Medicine, Terry Fox Laboratory, BCCRCDr. Nhu Le, Statistics, Cancer Control Research, BCCRCDr. Victor Ling, Pathology & Laboratory Medicine, Cancer Genetics, BCCRCDr. Calum MacAulay, Pathology & Laboratory Medicine, Cancer Imaging, BCCRCDr. Dixie Mager, Medical Genetics, Terry Fox Laboratory, BCCRCDr. Don Moerman, Zoology, UBCDr. Ed Moore, Physiology, UBCDr. Colleen Nelson, Surgery, UBCDr. Raymond Ng, Computer Science, UBCDr. James Piret, Michael Smith Laboratories, UBCDr. Anne Rose, Medical Genetics, UBCDr. Miriam Rosin, Pathology & Laboratory Medicine, Cancer Control Research, BCCRCDr. Elizabeth M. Simpson, Medical Genetics, UBCDr. John Spinelli, Health Care and Epidemiology, Cancer Control Research, BCCRCDr. Fumio Takei, Pathology & Laboratory Medicine, Terry Fox Laboratory, BCCRCDr. Z. Jane Wang, Electrical and Computer Engineering, UBC

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APPENDIX IV.

LIST OF PROGRAM ADJUNCT FACULTY

The programs adjunct faculty is comprised of scientists affiliated with the BCCA, SFU and UVic.

Dr. Andrew Beckenbach, Biological Sciences, SFUDr. Christopher Beh, Molecular Biology and Biochemistry, SFUDr. Bruce Brandhorst, Molecular Biology and Biochemistry, SFUDr. Felix Breden, Biological Sciences, SFUDr. Fiona Brinkman, Molecular Biology and Biochemistry, SFUDr. Andrew Coldman, Cancer Control Strategy, BCCADr. Veronica Dahl, Computing Science, SFUDr. William Davidson, Molecular Biology and Biochemistry, SFUDr. Charmaine Dean, Statistical and Actuarial Science, SFUDr. Eldon Emberly, Physics, SFUDr. Martin Ester, Computing Science, SFUDr. Jinko Graham, Statistical and Actuarial Science, SFUDr. Qianping Gu, Computing Science, SFUDr. Arvind Gupta, Computing Science, SFUDr. Jiawei Han, Computing Science, SFUDr. Nicholas Harden, Molecular Biology and Biochemistry, SFUDr. Nancy Hawkins, Molecular Biology and Biochemistry, SFUDr. Barry Honda, Molecular Biology and Biochemistry, SFUDr. Keith Kirkpatrick, Computing Science, SFUDr. Ben Koop, Biology, UVicDr. Michael Leroux, Molecular Biology and Biochemistry, SFUDr. Brad McNeney, Statistical and Actuarial Science, SFUDr. Gregg Morin, Genome Sciences Centre, BCCADr. Robert Olafson, Biochemistry and Microbiology, UVicDr. Mark Paetzel, Molecular Biology and Biochemistry, SFUDr. Frederic Pio, Molecular Biology and Biochemistry, SFUDr. Cenk Sahinalp, Computing Science, SFUDr. Carl Schwarz, Statistical and Actuarial Science, SFUDr. Jamie Scott, Molecular Biology and Biochemistry, SFUDr. Dipankar Sen, Molecular Biology and Biochemistry, SFUDr. Michael J. Smith, Molecular Biology and Biochemistry, SFUDr. Peter Unrau, Molecular Biology and Biochemistry, SFUDr. Chris Upton, Biochemistry and Microbiology, UVicDr. Esther Verheyen, Molecular Biology and Biochemistry, SFUDr. Ke Wang, Computing Science, SFUDr. Kay Wiese, IT, SFU

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APPENDIX V.

LIST OF INDUSTRY PARTNERS

BioCad, Vancouver, British Columbia

Inimex Pharmaceuticals Inc., Vancouver, British Columbia

Merck-Frosst, Montreal, Quebec

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APPENDIX VI.

LIST OF RESEARCH ROTATIONS

January, 2003

• Keith Boroevich: Primate retroelement differences database (PRED_DB): Identification of indel patterns in the primate lineage (with Dixie Mager, BCCA)

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

• Shannan Ho Sui: Identification and characterization of alternative promoters in the human genome (with Wyeth Wasserman, UBC)

• Byron Kuo: Data mining to identify groups of genetically-related cancers (with Chris Bajdik, BCCA)

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

• Perseus Missirlis: Identification of conserved cis-regulatory elements in double-stranded 1break repair genes (with Angela Brooks-Wilson, BCCA)

• Fred Peng: Genecomber analysis (with Francis Ouellette, UBC)• Chris Walsh: Comparative physical mapping of the genomes of 3 varities of

Cryptococcus neoformans (with Jim Kronstad, UBC)

May, 2003

• 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 BioCAD)

• Shannan Ho Sui: Constructing protein interaction maps for Chlamydia genomes (with Bob Brunham and Art Cherkasov, UBC)

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

• Drew Lett: A Bayesian approach 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: Gene locations and functions in eukaryotes (with David Baillie, SFU)• Chris Walsh: Conserved transcription factor binding site detection in co-

expressed genes (with Wyeth Wasserman, UBC)

September, 2003

• Keith Boroevich: Gene expression aided phylogenetic foot printing in Caenorhabditis elegans (with David Baillie, SFU)

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• 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 co-regulated genes in biomedically-linked pathways and processes (with Brian Kennedy and Francis Ouellette, UBC)

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

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

• Perseus Missirlis: Identification of regulatory mutations in the SNAP-25 gene in schizophrenia (with Robert Holt, BCCA)

• Fred Peng: Transcriptional regulatory networks in apoptotic cascade (with Frederic Pio, SFU)

• Chris Walsh: PSORT-B+: Improving protein subcellular localization prediction 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: Inverse protein folding (with Arvind Gupta, SFU)• 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 Wasserman, 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 drug targets (with Artem Cherkasov, UBC)• Carri-Lyn Mead: GeMS (with Francis Ouellette, UBC)• Alison Meynert: Bioinformatics analyses (with Ewan Birney at the European

Bioinformatics Institute, Cambridge, UK)

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September, 2004

• Debra Fulton: Improving orthologous gene detection for a large 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 institutional 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 Meynert: 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 and 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)

• Wynne 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 cis-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 drug 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 common evidence network for neurodegenerative disorders hypothesis (with Francis Ouellette and Anne Condon, UBC)

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APPENDIX VII.

LIST OF UBC PROGRAM GRADUATES

Byron KuoB.Sc., Computer Science, University of British Columbia, 2002B.Sc., Cell Biology and 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 ColumbiaCo-supervisor: Dr. Wyeth Wasserman - Centre for Molecular Medicine & Therapeutics, UBC

September 1, 2005

 

Michael HsingB.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 MissirlisB.Sc. Honors, Life Sciences, Queens University, 2002

"CIS-FEATURES MEDIATING CAG/CTG REPEAT INSTABILITY, THE SATELLOG DATABASE, AND CANDIDATE REPEAT PRIORITIZATION IN SCHIZOPHRENIA"

M.Sc. Supervisor: Dr. Robert Holt - Genome Sciences Centre, BCCA

August 13, 2004

 

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