Introduction
Academia Sinica has established the Taiwan International Graduate Program (TIGP) in collaboration with a consortium of key national research universities in Taiwan. The purpose of the program is to develop the research manpower pool in those modern multidisciplinary fields that are important in the future economical and social development of Taiwan and to enhance the innovative potential and academic standards of research in these and related fields.

TIGP will offer Ph.D. programs in only selected disciplines to be agreed upon between Academia Sinica and its national research universities partners. It is the intent of the Program to offer Ph.D. degree programs only in inter-disciplinary areas in the physical sciences, applied sciences, engineering, biological and agricultural sciences, health and medical sciences, and humanities and social sciences.

Academia Sinica will assume principal oversight of the academic options of the Program. It will provide the intellectual leadership, the research resources, and the research and physical facilities. Qualified and interested faculty members of the participating national research universities are invited to join the various programs as affiliated faculty of the Program, and participate in the teaching of courses, supervision of research, and mentoring of the international graduate students.

The Taiwan International Graduate Program has been established to attract highly qualified young researchers both from home and abroad in order to help jump-start the development of several frontier areas that are crucial to the future development in science and technology. Specific graduate programs have been developed to enhance the innovative potential and academic standards of research on these and related fields. Within this context, the graduate program on “Bioinformatics” is designed to offer specific training and research opportunities to Ph.D. students interested in working on this particular area.

The TIGP Program on Bioinformatics (BP) is a joint-degree program sponsored by Academia Sinica (Institute of Information Science, Institute of Statistical Science, and Institute of Biomedical Sciences), National Tsing Hua University, National Chiao Tung University and National Yang Ming University. Additional teaching support will be available from other major research universities in Taiwan. Unlike most Bioinformatics programs offered in other universities that adopt existing courses in various departments, our courses are specifically designed for BP students and taught by active and experienced researchers in bioinformatics. The program provides interdisciplinary training and research opportunities that seamlessly integrate the related areas so that students can be well-prepared for independent research in this new, fascinating areas of bioinformatics. We will focus on genetics and proteomics study and emphasize data transfer, data analysis, biological information and biological feature extraction, knowledge management using advanced computation methodologies and computer science technology.

Course Programs
There are three types of courses:

1. Required courses: courses to be taken by all students
2. Core courses: basic courses in molecular biology and computing methods. Students with sufficient prior background can waive some of these courses (if approved by the program committee)
3. Elective courses. A total of 24 credit units are required for graduation.

1. Required courses: Directed Reading (1 credit unit, 1.5 hours/week for two semesters) Seminar (1 credit unit per semester, a total of 4 credit units)

2. Core courses: B1. Basic molecular biology for bioinformatics (3 credit units) Functions of the molecules and organelles in the cell Basic strategies of biochemistry-assay and cell fraction Enzyme kinetics and mechanisms Major pathways and principles in biology Introduction to genetics Introduction to genes and gene structures Gene expression & regulation DNA replication & other perpetuations Genetic engineering Introduction to protein structures Forces that determine protein structures Protein structure determination Protein structure prediction B2. Basic molecular biology for bioinformatics II (3 credit units) Genome sequence acquisition & analysis The human genome project Genomic variations Genomics Databases & Bioinformatics Applications (I) Genomics Databases & Bioinformatics Applications (II) Introduction to statistical genetics Introduction to evolutionary genomics DNA Microarrays: principles and applications (I) DNA Microarrays: principles and applications (II) Transcriptome - related bioinformatics databases & applications Protein informatics Structural proteomics & drug design Protein-protein interaction network and databases Databases of biochemical pathways C1. Biological computing I：Design and analysis of algorithms for biologists (3 credit units) Introduction to data structure Growth of functions & Asymptotic notation Recurrence relations Sorting - insertion sort, quicksort, mergesort, heapsort, radix sort The greedy method The divide-and-conquer strategy Tree searching strategies Dynamic programming Graph algorithms - Representations, BFS, DFS Graph algorithms – MST Data mining NP-completeness Approximation algorithms Case studies of computational biology problem specification and modeling solutions C2. Biological computing II (3 credit units) Dynamic programming – applications (alignment, structure prediction ) BLAST and its variations Stochastic processes and probability theory Hidden Markov Models Basic statistics: random variables, distributions, estimation, testing hypothesis, randomization Regression Experimental design and ANOVA Sampling and resampling Statistical graphics Analysis of microarray data: data pre-processing, missing data imputation, permutation test Association rules: categorical and continuous random variables, relationship among multiple variables Multivariate analysis: clustering, PCA, canonical correlation, classification, etc Statistical genetics

3. Elective courses: 　At least one of the following two courses C3 and C4: C3. Advanced algorithms in computational biology (3 credit units) String matching - KMP, Boyer-Moore Sequence analysis algorithms Multiple sequence alignment Restriction mapping - Double digest problem Map assembly - Interval graphs SVM Gene-prediction algorithms Genome rearrangements Phylogenetic trees construction Structure prediction Protein classification Computational proteomics Selected topics C4. Advanced statistical methods (3 credit units) Introduction to microarray experiments: principles and experimental design Biomedical image analysis (2D gel, DNA and protein chips) Advanced analysis of microarray data Markov Chain Monte Carlo Exploratory data analysis and visualization Cluster analysis: hierarchical clustering, k-means, self-organizing maps, gene shaving, plaid models, dimension reduction, principal component analysis, singular value decomposition, correspondence analysis, multi-dimensional scaling Supervised learning: discriminant analysis, neural networks, error-rate concepts, support vector machines, tree-based methods, bagging, boosting Bayesian networks: graphical probabilistic models and related computation algorithms, applications to genetic networks Comparative genomics Genetic modeling Current research topics of interest L1. Lab work (1 credit unit, spend 6 hours/week working in a lab of student's choice for one semester) This courses can be taken more than once, but not with the same lab.

TA and Chinese Language
TA experience is an essential part of our program. Thus, all students from TIGP must serve as TA for at least one semester. Additionally, in order to help their daily lives' communication with the local people, international students are required to take a required one year course of Mandarin Chinese.

Academic System
The program emphasizes research training and developing one's capability and self-confidence for independent research. Once entering this program, students can choose mentors and thesis advisors for their study according to their research interests. Students are required to advance to doctoral candidacy by the end of the third year or the beginning of the fourth year. A student may petition for probation; but he or she still needs to complete this requirement by the end of the fourth year in the program.

In this program, we invite faculty from various disciplines to participate. This program adopts a team-teaching system, where each faculty member teaches a subject according to his or her expertise. In keeping up with the international trend, all courses are offered in English.

Advance to Candidacy
Requirements for advancing to candidacy include:

1. Satisfactory completion of coursework: core courses and 24 credit units.
2. Satisfactory performance in a written qualifying exam (must finish before the end of the third year), which will be offered once every year after the winter break. The exam will cover C1, C2, B1, B2 and at least one of C3 or C4.
3. A TOEFL score of 100(IBT) or 250(CBT) is required for non-native speakers.
4. Research Plan approved by director of research group.
5. Successful defense of the above research plan.

Degree Requirements

1. At least two (full) papers presented at leading international conferences (such as RECOMB, ISMB and PSB) and journals in the field as approved by the exam committee.
2. Ph.D. thesis.
3. Successful defense of the thesis, in which the candidate must show that she/he has made original and substantial scientific contribution.

Admission to the Ph.D. Program
The Program admits students to the fall semester only. The following materials and qualification are required for application:

1. Master's or Bachelor's degree in biology, computer science, statistics or other related areas.
2. Fluency in English: TOEFL score of 550 (213 on computer-based) or higher. However, this can be waived for those who have obtained bachelor or master degrees from English speaking countries (not including India). The TOEFL score could be submitted later, but must be before 8/31.
3. GRE score from the general exam. For the Bioinformatics Program, an applicant may submit one of the following material in place of a GRE general test score:
   • Any evidence of research ability such as papers published in international conferences or journals.
   • Satisfactory performance in any course or project work related to the design of algorithms or probability such as discrete mathematics, algorithms, computational complexity, data structure, probability, computer architecture, compiler, and computer programming.
4. (Required) Basic programming skills
5. A Statement of Purpose that includes a research plan
6. Official transcripts from academic institutions attended after senior high school
7. Three letters of recommendation
8. GRE score from related subject exam (highly recommended, but not mandatory)

Applicants in Taiwan can take the General English Proficiency Test (GEPT) administered by the Language Training and Testing Center.
Applicants are required to submit their high-intermediate level certificate when applying for admission.

The above submitted application materials will not be returned to applicants under any circumstances.
The complete application materials must reach TIGP before March 31, 2006 .
Please send them to:
Admission Office
Taiwan International Graduate Program
128, Sec. 2, Academia Road
Nankang, Taipei 115
Taiwan.

For administrative reasons, students will need to officially register at our partner institutions, i.e. National Tsing Hua University , National Chiao Tung University or National Yang Ming University , depending on their research interests. Upon completion of our program, students will receive a diploma of Ph.D. degree from the designated partner institution and a certificate jointly signed by the President of Academia Sinica and the President of the partner institution.

The payment of tuition fees (about US$ 1,500 per year) are due upon registration.

Fellowship and Stipends
The TIGP will provide full fellowship support for all graduate students for 3 years. The stipend levels are about NT$ 32,000 (about US$ 980) per month. In subsequent years, the financial support may be provided by the student's thesis advisor.

Medical Insurance
Four months after they receive their student I.D., the students will qualify for Taiwan's National Health Insurance Program. The students pay the same premium (about US$ 210 per year) as all the Taiwan citizens and will be entitled to the same medical coverage.

Living and Housing Costs
On campus self-catering student dormitory providing single study bedrooms is available to TIGP students at reasonable costs (for details please visit our website at http://www.sinica.edu.tw/~tigp/dorm.html).

　

Off-campus private housing is generally more expensive. Rents for off-campus apartments range from NT$ 5,000 - 15,000 per month.

Meals are also available at the Activity Center Cafeteria/Dining Hall, the Cafe, the Chinese restaurant, and the Western restaurant on the Academia Sinica campus at modest costs.

Ms. Nancy Yang

Administrative Assistant
Taiwan International Graduate Program 128, Section 2, Academia Road Nankang, Taipei 115, Taiwan
E-mail: nancyy@gate.sinica.edu.tw
Tel.: 886-2-2789-8050
Fax: 886-2-2789-8045

Dr. Wen-Lian Hsu
Institute of Information Science Academia Sinica 128, Section 2, Academia Road Nankang, Taipei, Taiwan115
E-mail: hsu@iis.sinica.edu.tw
Tel: 886-2-2788-3799 ext 1804
Fax: 886-2-2782-4814

Dr. Ting-Yi Sung
Institute of Information Science Academia Sinica 128, Section 2, Academia Road Nankang, Taipei, Taiwan 115
E-mail: tsung@iis.sinica.edu.tw
Tel: 886-2-2788-3799 ext 1711
Fax: 886-2-2782-4814

Ms. Elsa Pan
Assistant to Bioinformatics Program
Institute of Information Science Academia Sinica 128, Section 2, Academia Road Nankang, Taipei, Taiwan 115
E-mail: elsapan@iis.sinica.edu.tw
Tel: 886-2-2788-3799 ext 2213
Fax: 886-2-2782-4814

Websites Information
Taiwan International Graduate Program, Academia Sinica:

http://www.tigp.sinica.edu.tw

http://www.iis.sinica.edu.tw

http://www.nthu.edu.tw

http://www.nctu.edu.tw

http://www.ym.edu.tw

This program is sponsored by
Institute of Information Science, Academia Sinica
in cooperation with
Department of Life Sciences and Department of Computer Sciences,
National Tsing Hua University
&
Department and Institute of Biological Science and Technology,
National Chiao Tung University
&
Department of Bioinformatics
National Yang Ming University