Design and analysis of algorithms for biologists College of Medicine Grades: Midterm exam 50%. Final exam 50%. SHU-CHUN TENG Friday 789 PTMP8012 3

In the first semester: ?? Learn the background knowledge of information retrieval. ?? Learn the knowledge about Naive Bayes classification. ?? Be able to extract blog entries; identify opinion words and sentences. ?? Prepare training instances for the recommendation engine. ?? In the second semester: ?? Develop the recommendation engine. ?? Develop a fancy web interface. College of Management LING-CHIEH KUNG IM4001 2

1. INTRODUCTION 2. PROMISES OF STEM CELL RESEARCH 3. DEVELOPMENTAL CELL BIOLOGY 4. EMBRYONIC STEM CELLS 5. THERAPEUTIC CLONING 6. PLASTICITY OF STEM CELLS 7. STEM CELL HOMING AND ENGRAFTMENT 8. STEM CELL FATE: INTRINSIC AND EXTRINSIC FACTORS 9. STEM CELLS AND CANCERS 10. HEMATOPOIETIC STEM CELLS 11. MESENCHYMAL STEM CELLS 12. NEURONAL STEM CELLS 13. LIVER STEM CELLS 14. CORNEAL STEM CELLS College of Bio-Resources & Agriculture Thursday 678 Biot8002 3 The upper limit of the number of non-majors: 20.

This is a class integrates the concepts of structural biology and bioinformatics. The basic principle of amino acids and structre will be explained first, then the modern methods to resolve atomic resolution of protein structures. The relation of protein structure and function will be emphasized in the third part of this class. Bioinformatic principles, methods and modern developments will be followed. 1. Understand amino acids and protein structures. 2. Modern approaches to resolve protein structure. 3. Protein structure and function. 4. Software-based analysis of protein sequence. 5. Bioinformatic theories 6. Current developments of bioinformatics methods. College of Bio-Resources & Agriculture This class will be taught in English. CHII-SHEN YANG Friday 678 Biot8003 3 The upper limit of the number of non-majors: 15.

IT IS NOW CLEAR THAT LOTS OF NON-CODING RNAS IN THE GENOME ARE FUNCTIONAL AND VERY POWERFUL IN REGULATING GENE ACTIVITIES AND DEVELOPMENTAL PROCESS. DEPENDS ON THE BACKGROUND OF THE STUDENTS, AROUND 1/3 OF THE LECTURES WILL BE GIVEN BY THE INSTRUCTOR FOR INTRODUCING BASIC CONCEPTS IN NON-CODING RNA REGULATED GENE SILENCING, INCLUDING THE POST-TRANSCRIPTIONAL REGULATION BY SIRNA, MICRORNA AND REPRODUCTIVE ORGAN SPECIFIC PIRNAS. THESE WILL COVER THE PHYSIOLOGICAL PROCESS INCLUDING GENOMIC IMPRINTING, SEX CHROMOSOME COMPENSATION, SILENCING OF ENDOGENOUS RETROTRANSPOSONS AND STEM CELL BIOLOGY. IN ADDITION, THE INVOLVEMENT OF NON-CODING RNA RELATED REGULATORY MECHANISMS IN CARCINOGENESIS WILL BE DISCUSSED. FOR THE REST OF THE CLASSES, STUDENTS WILL BE ASSIGNED THE MOST UPDATED ORIGINAL RESEARCH PAPERS AND CONFERENCE ARTICLES AS WELL AS THE MILESTONE PUBLICATIONS. THEY WILL BE RANDOMLY DIVIDED INTO 2 GROUPS FOR EACH ASSIGNMENT. ONE GROUP WILL BE PRESENTING THE ARTICLES AND STUDENTS IN THE OTHER GROUP ARE EXPECTED TO CHALLENGE THE PAPERS FROM THE EXPERIMENTAL DESIGN, THE METHODOLOGY TO THE INTERPRETATION OF THE DATA. STUDENTS IN THE 1ST GROUP SHOULD DEFEND FOR THE PAPERS AS IF IT’S THEIR MANUSCRIPT. STUDENTS FROM THE 2ND GROUP SHOULD ALSO PROVIDE CONSTRUCTIVE ADVICE AS HOW TO IMPROVE THE MANUSCRIPT SO THAT IT CAN BE PUBLISHED IN A HIGHER IMPACT JOURNAL. College of Bio-Resources & Agriculture PREFERABLY HAVING STUDIED ONE OF THE FOLLOWING SUBJECTS: (INTRODUCTORY) EPIGENETICS, SPECIAL TOPICS IN REPROGRAMMING, GENETICS AND EPIGENETICS IN GERM AND STEM CELLS Friday 34 Biot8014 2

COURSE DESCRIPTION: THIS HALF-YEAR GRADUATE COURSE AIMS TO INTRODUCE BASIC GENE SILENCING CONCEPTS AND RESEARCH TECHNIQUES AVAILABLE TO ADDRESS GENE SILENCING QUESTIONS IN PLANT AS WELL AS OTHER ORGANISMS. STUDENTS ARE EXPECTED TO DEVELOP THE ABILITY TO CRITICALLY EVALUATE AND INTERPRET PUBLISHED RESEARCH ARTICLES. THEY WILL ALSO LEARN TO EXTRACT INFORMATION FROM INTERNATIONAL CONFERENCES BY LISTENING TO EXPERTS OF EACH FIELD INTRODUCING THEIR RESEARCH. OUTLINE: 1. INTRODUCTION – OVERVIEW 2. SENSE CO-SUPPRESSION IN PLANT 3. TRANSGENE CO-SUPPRESSION IN ANIMALS 4. PLANT VIRUS RESISTANCE VS. CO-SUPPRESSION 5. TRANSCRIPTIONAL GENE SILENCING (TGS) 6. POST-TRANSCRIPTIONAL GENE SILENCING (PTGS) 7. VIRUS-INDUCE GENE SILENCING (VIGS) 8. SILENCING SIGNAL TRANSPORTATION 9. SMALL RNA 10. SIRNA PATHWAY 11. MIRNA PATHWAY 12. FUNCTION OF DICER 13. FUNCTION OF RNA-INDUCE SILENCING COMPLEX (RISC) 14. FUNCTIONS OF DICER-LIKE PROTEINS (DCLS) IN PLANT 15. DCL1 VS. MIRNA BIOGENESIS 16. FUNCTION OF DCL2 AND NAT-SIRNA 17. FUNCTION OF DCL3 AND DNA METHYLATION 18. FUNCTION OF DCL4 AND TRANS-SIRNA 19. ARGONATURE FAMILY 20. SUPPRESSION OF GENE SILENCING 21. RNAI TECHNOLOGY 22. MIRNA TECHNOLOGY College of Bio-Resources & Agriculture Monday 234 Biot8016 3

THE ANIMAL BIOTECHNOLOGY PART WILL PROVIDE STUDENTS A STATE-OF-THE-ART OF RESEARCH AND TECHNOLOGY, AS WELL AS ITS APPLICATIONS, INCLUDING DEVELOPMENTAL BIOLOGY, CELLULAR BIOLOGY AND SIGNAL TRANSDUCTION, STEM CELL BIOLOGY, APPLIED ANIMAL BIOTECHNOLOGY, REGENERATIVE MEDICINE, AND CANCER BIOLOGY ETC. GUEST SPEAKERS WILL PLAN TO BE INVITED FOR THE LECTURES AS NECESSARY. THE PLANT BIOTECHNOLOGY PART WILL PROVIDE STUDENTS MORE KNOWLEDGE IN PLANT MOLECULAR BIOLOGY, PLANT PHYSIOLOGY, PLANT PATHOLOGY, AND PLANT BIOTECHNOLOGY ETC. 動物組教師包括本所李宣書、林劭品老師及宋麗英老師，亦將邀請合聘張俊哲老師、丁詩同老師、_信志老師、楊寧_老師、楊淑美老師、楊文欽老師及蕭培文老師，或動物科技領域之校_外相關教師如李士傑老師與_益群老師等。 植物組教師包括本所林詩舜及陳仁治老師，亦將邀請合聘_鵬林、葉國禎、邱子珍、洪傳揚、常怡雍等老師進行授課。 COURSE TOPICS IN ANIMAL PART INCLUDING: 1. DEVELOPMENTAL BIOLOGY 2. NUCLEAR REPROGRAMMING 3. CELLULAR BIOLOGY 4. SIGNAL TRANSDUCTION 5. APPLIED ANIMAL BIOTECHNOLOGY 6. STEM CELL BIOLOGY 7. CANCER BIOLOGY 8. REGENERATIVE MEDICINE COURSE TOPICS IN PLANT PART INCLUDING: 1. PLANT GENE TRANSFORMATION 2. PLANT MOLECULAR BIOLOGY RESEARCH RESOURCES 3. PHOTOSYNTHESIS & PHOTO-SIGNALING 4. PLANT NUTRITION 5. PLANT HORMONE 6. PLANT DEVELOPMENT 7. BIOTIC STRESS 8. ABIOTIC STRESS College of Bio-Resources & Agriculture FUNDAMENTAL KNOWLEDGE OF MICROBIOLOGY AND BIOCHEMISTRY Tuesday 234 Biot8019 3

The aim of this course is provide students a state of the art of the knowledge in early embryo development and pluripotent stem cells (i.e. embryonic stem cells and induced pluripotent stem cells) research and its applications. Students will be asked to present in particular topic they were assign. College of Bio-Resources & Agriculture 碩士班及博士班修習過生殖生理學、胚胎生物學、人數限制 3 人 Thursday 34 Biot8022 2

Contents Microbiological System Microbial cultivation Microbial engineering Microbial molecular biology Microbial biotechnology 　Current status of bio-industry College of Bio-Resources & Agriculture 需先修過 應用微生物與生物技術 或 微生物_酵工程 CHENG, KUAN-CHEN Friday 678 Biot8023 3

This course will consist of two hours of lecture and one hour of writing exercises. Students will be assigned writing assignments, and at the end of the term. They should have been able to finish a draft of their research on a general topic, making use of the moves and techniques that they have learned from the course. In addition, they shall be required to give a 10-minute oral presentation of their paper. This course will train students to learn how to write an academic journal research paper. The course will consist of an introduction to academic English and to the framework of each part of an academic paper. Students will also be trained how to make an oral presentation of their research. College of Bio-Resources & Agriculture 1.Students are required to attend all classes. No more than three excused absences are permitted.

2.Active participation in class discussions is required.

3.Writing assignments are carefully scheduled as stages toward the fulfillment of the course’s objectives. Late assignments will not be accepted.
Friday 234 Biot7020 3

1．緒論 2．廢棄物的特性指標及分析方法 3．廢棄物的特性 4．廢棄物處理方法 5．池塘 6．好氣處理 7．厭_處理 8．堆肥化處理 9．養殖廢水與廢棄物處理 10．_染源控制 11．實驗 本課程主要針對生物_業廢棄物的種類及其對生態環境之影響,廢棄物的特性及分析方法,現行之處理方法,_染源之控制及管理,以及廢棄物之回收及利用等作整體性的介紹，希望學生在修習本課程之後對農業廢棄物的現況能有通盤的了解。 College of Bio-Resources & Agriculture CHU-YANG CHOU Tuesday 789 BME5703 3

This course introduces the state-of-the-art energy technology and development. Subjects include energy generation, storage and conversion technology and related applications will be covered. For example: hydrogen economy, nuclear energy, wind power and solar cells, batteries, green buildings etc. I aim to prepare students with abilities of active learning and creative thinking. Innovative pedagogical methods such as fishbowl discussion, brainstorming, mock conference, and debate etc. will be practiced in this class. College of Bio-Resources & Agriculture Students are required to study the assigned contents each week, and exchange ideas and thoughts in class. 50% of the final grade is based on in-class discussions, while the other 50% is based on the final report. The topics of final projects, which focus on energy issues facing Taiwan, will be developed over the course of the classes by each student. HSUN-YI CHEN Tuesday 6 Friday 34 BME5920 3