Ph.D. Molecular Biology and Bioinformatics

Doctor of Science Programme in Molecular Biology and

Bioinformatics

Degree Designation Ph.D. (Molecular Biology and Bioinformatics)

Curriculum Structure

Plan

1.1

Plan 2.1 Plan 1.2 Plan 2.2

Required Courses

Elective Courses not less than

Thesis

-

-

48

Total 48

8

4

36

48

-

-

72

72

8

16

48

72

Courses Description

Plan 1.1 and Plan 2.2

Thesis

319-694 Thesis

Ph.D. candidate prepares thesis project proposal, research strategies, conduct experiments, discusses and publishes the work under supervision of a thesis committee

Plan 1.2

Credit

48(0-

144-0)

Thesis

319-695 Thesis

Ph.D. candidate prepares thesis project proposal, research strategies, conduct experiments, discusses and publishes the work under supervision of a thesis committee

Plan 2.1

Credit

72(0-

216-0)

Thesis

319-693 Thesis

Ph.D. candidate prepares thesis project proposal, research strategies, conduct experiments, discusses

Credit

36(0-

108-0) and publishes the work under supervision of a thesis committee

Required Courses

Credit

318-501 Molecular Biology for Biological Science*

Study of living systems at the molecular level, structure of genes and chromosomes, regulation of gene expression at the level of DNA, RNA and protein synthesis, signal transduction pathways and gene regulation, the cell cycle, abnormal regulatory processes

318-502 Molecular Biology for Engineers and Computer

2(2-0-

4)

Scientists**

This course is designed for who lack the biological prerequisites, essential aspects of cell biology and molecular biology, macromolecules and organization of the cell, cell cycle and signal transduction, DNA structure and organization, the genetic code, and gene expression and its regulation, polymerase chain reaction and genome sequencing

318-503 Bioinformatics 1

DNA sequence analysis, multiple sequence alignment, phylogenetic tree construction, computational genomics, gene expression and protein structure analyses

* For graduate from Biological Science

** For graduate from Engineering and Computer Science

318-504 Bioinformatics 2

Algorithmic and probabilistic methods for analysis of

DNA and protein, data mining analysis, write computer programs for data analysis

318-671 Seminar in Molecular Biology and Bioinformatics 1

2(2-0-

4)

2(1-2-

3)

2(1-2-

3) molecular biology,

1)

presentation and interpretation of research findings, understand the code of conduct for researchers


Seminar in advanced topics in molecular biology and

1(0-2-

1) bioinformatics, emphasize the rationale for research projects and the presentation and interpretation of research findings

Elective Courses Credit

Course is divided into two majors, (Molecular biology and

Bioinformatics Agriculture and Environment, Molecular biology and Bioinformatics Medicine each major select 4 credits not less than or 16 credits

Molecular biology and Bioinformatics Agriculture and

Environment

318-505 Yeast Genetic Engineering

Genetic engineering of yeast Saccharomyces cerevisiae and other speices, yeast as a heterogeneous host for production of recombinant protein, yeast as a model organism for functional

Genomics studies

2(2-0-

4)

318-506 Plant Genetic Engineering

The scientific and technical advances which underlie the production of genetically modified crops, plant genome organization and gene expression, plant tissue culture and genetic transformation, genetic manipulation to confer the improvement of crop yield and quality

318-507 Intellectual Properties

Surveys intellectual property laws, including patents, copyrights, trademarks, design protection, how to apply for a patent, look for technology that is available for licensing

318-508 Functional Genomics

Acquisition of DNA expression data, identify highyield candidate genes/ ESTs for further biological investigation, the basics of the various bioinformatics methodologies available to analyze

RNA expression data sets

318-509 Metabolic Network Reconstruction

To reconstruct a metabolic network. The interplay between the many different intracellular reactions, how the fluxes through the different pathways are regulated. Analysis of the interaction between

2(2-0-

4)

1(1-0-

2)

2(2-0-

4)

2(2-0-

4)

different cellular reactions


Discussion of up-to-date research and development findings with guest speakers and visiting scientists











1(0-2-

1)

1(0-2-

1)

1(0-2-

1)

1(0-2-

1)

1(0-2-

1)

1(0-2-

1)

318-681 Special Topics in Molecular Biology and

Bioinformatics 1

Independent study on interesting issues in progress or new findings in molecular biology and bioinformatics


Bioinformatics 2


319-501 Techniques in Genomics and Proteomics

Current and emerging technologies and approaches for genome sequencing, analyzing protein structure and function, protein:protein interactions and microarrays

1(1-0-

2)

1(1-0-

2)

2(1-3-

2)

319-502 Computer in Molecular Biology

New technologies and tools for understand the major issues concerning representation and analysis of genomes, sequences and proteins

2(1-2-3)

319-503 Science Communication 2(1-2-3)

To make scientific activity more understandable

319-504 Biosafety 1(1-0-

Introduces the safety and quality control issues related to product development in the biotechnology industry, issues related to government regulations,

Cartagena protocol on biosafety, the basics of risk assessment, safety, storage and disposal of hazardous materials, the information pertains to a laboratory for Biosafety Level 1-4 (BSL1-4) facilities,

Biosafety guidelines

Elective in other courses

322-552 Combinatorial Design

Selected topics from design theory, latin squares, finite geometries, finite fields, error correcting codes, other related topics

344-563 Database Management System

Database system architecture, Relational database and normalization process, Database models and database design, Relational database languages : relational algebra and relational calculus languages,

Database security and integrity, Transactions and concurrency control

344-564 Information Retrieval

Information retrieval models, Retrieval evaluation,

Query language and operations, Text and

2)

Credit

3(3-0-

6)

3(3-0-

6)

3(3-0-

6)

multimedia operations, Indexed and searching,

Parallel and distributed information retrieval,

Libraries and bibliographical systems, Digital libraries

344-571 Artificial Intelligence

Concepts and theories of intelligent systems,

Searching techniques, Heuristic search,

Propositional logic, Predicate logic, Production systems, Logic reasoning systems, Deductive and inductive inference systems, Uncertainty,

Knowledge representation such as frame, conceptual graph, recursive transition network,

Introduction to Prolog programming, Overview on expert system, machine learning, neural network, robotics, computer vision and natural language processing

344-572 Expert Systems

Knowledge acquisition, Interviewing for content and classification, Conceptualizing the domain expert,

Rule-based reasoning, Logics and automated reasoning, Inferencing, Knowledge representation,

Explanations, Uncertainty management,

Probabilistic Uncertainty, Belief theory and fuzzy set theory, Expert system life cycle, Building expert system using expert system shells, Validation and integration

3(3-0-

6)

3(3-0-

6)

344-573 Neural Networks (Prerequisite : 344-571)

Biological neural networks, Brain central and modulation systems, Pattern recognition, Pattern classification, Neural network modeling, Artificial neural network, Unsupervised learning, Matching and self-organized networks, Supervised learning,

Back propagation neural network, Adaptive resonance theory, Neural networks based on competition, Fuzzy reasoning, Applications of neural networks algorithms and learning models

344-662 Data Warehouse and Data Mining

Architecture and infrastructures of data warehouse,

Design and implementation of data warehouses,

Techniques in data mining, Knowledge representations, Use of data mining software

346-521 Analysis of Advanced Statistical Models

(Prerequisite : 346-502)

Definition of a statistical model, generalized linear models, likelihood function and parameter estimation, models for continuous data, model for binomial data, model for Poisson data, models for negative binomial data, models for zero-inflated

Poisson data, computer software applications

3(3-0-

6)

3(3-0-

6)

3(2-2-

5)

346-531 Applied Multivariate Analysis (Prerequisite : 346-

502)

Aspects of multivariate analysis, the multivariate normal distribution, comparisons of several multivariate means, multivariate regression, discrimination and classification, path analysis, cluster analysis, principal component analysis, factor analysis, canonical correlation analysis, computer software applications

346-532 Experimental Designs (Prerequisite : 346-502)

Introduction; design and analysis of single-factor experiments, single-factor experiments having repeated measures on the same elements, design and analysis of factorial experiments, factorial experiments in which some of the interactions are confounded, Latin Squares and related designs, analysis of covariance, repeated measurement, computer software applications

346-534 Statistical Decision Theory (Prerequisite : 346-501)

Review of probability, basic concepts of decision analysis, elementary decision problems, continuousvariable decision problems, sufficient statistics and

3(2-2-

5)

3(2-2-

5)

3(3-0-

6)

conjugate distributions, multivariate normal process, sequential decision problems

346-542 Simulation Techniques (Prerequisite : 346-541)

Principle and concept of simulation; concepts in discrete-event; random number generator; random events; monte-carlo simulation; simulation examples; verification and validation of simulation; output analysis; comparison and evaluation of alternative system; computer software applications

347-531 Biological Statistics and Research Methodology

Science research methodology, inferential statistics, sampling survey techniques, experimental designs, simple correlation and simple linear regression analysis, multiple linear regression, computer software applications

347-532 Applied Statistics for Research

Introduction to data analysis, normal distribution, sampling distributions, estimation and hypothesis testing, one way analysis of variance, correlation and simple linear regression analysis, multiple linear regression, Chi-square test, strategies for selecting appropriate statistical methods, computer software applications

3(2-2-

5)

4(3-2-

7)

3(3-0-

6)

326-512 Microbial Physiology

Structures and functions of microbial cells, microbial growth, microbial control, transportation of substances, energy production of heterotrophs and

3(2-3-

4) autotrophs, metabolism of carbohydrate, lipid, nitrogen and control of metabolisms

326-641 Advanced Bacteriology

Presentation and group discussion of current

3(3-0-6) knowledge from published articles on bacteriology

326-681 Advanced Virology

Presentation and group discussion of current knowledge from published articles on virology

330-602 Advance Cell Biology

Light microscopes and electron microscopes; ultrastructures of cells and organelles;

3(3-0-

6)

4(3-3-

6) differentiation, specialization and cell aging and death, cancer cell; methods for cytological and cytochemical analysis and cell/tissue culture

Molecular biology and Bioinformatics Medicine

Elective Courses

318-505 Yeast Genetic Engineering

Credit

2(2-0-

Genetic engineering of yeast Saccharomyces cerevisiae and other speices, yeast as a heterogeneous host for production of recombinant protein, yeast as a model organism for functional

Genomics studies

318-507 Intellectual Properties

Surveys intellectual property laws, including patents, copyrights, trademarks, design protection, how to apply for a patent, look for technology that is available for licensing

318-508 Functional Genomics

Acquisition of DNA expression data, identify highyield candidate genes/ ESTs for further biological investigation, the basics of the various bioinformatics methodologies available to analyze

RNA expression data sets

318-509 Metabolic Network Reconstruction

To reconstruct a metabolic network. The interplay between the many different intracellular reactions, how the fluxes through the different pathways are regulated. Analysis of the interaction between different cellular reactions

318-510 Protein Technology and Engineering

4)

1(1-0-

2)

2(2-0-

4)

2(2-0-

4)

Study on interaction among chemical structure of proteins, physical structure of proteins, properties of enzymes, kinetics of enzymes, biochemical techniques of protein purification, modeling of protein structure and its modification by genetic engineering and protein structure analysis

318-511 Genetic Engineering

Definition and application of genetic engineering, structure and function of DNA, flow of genetic information, recombinant DNA technology, cloning, site directed mutagenesis, sequencing, gene expression, the impacts of genetic engineering in medicine, environmental science and agriculture, biosafety control







2(2-0-

4)

3(2-3-

4)

1(0-2-

1)

1(0-2-

1)

1(0-2-

1)








Bioinformatics 1


1(0-2-

1)

1(0-2-

1)

1(0-2-

1)

1(1-0-

2)


Bioinformatics 2


1(1-0-

2)

319-502 Computer in Molecular Biology

New technologies and tools for understand the

2(1-2-3)

major issues concerning representation and analysis of genomes, sequences and proteins

319-503 Science Communication 2(1-2-3)

To make scientific activity more understandable

319-504 Biosafety

Introduces the safety and quality control issues related to product development in the biotechnology industry, issues related to government regulations,

Cartagena protocol on biosafety, the basics of risk assessment, safety, storage and disposal of hazardous materials, the information pertains to a laboratory for Biosafety Level 1-4 (BSL1-4) facilities,

1(1-0-

2)

Biosafety guidelines

Elective in other courses

322-552 Combinatorial Design

Selected topics from design theory, latin squares, finite geometries, finite fields, error correcting codes, other related topics

344-563 Database Management System

Database system architecture, Relational database and normalization process, Database models and database design, Relational database languages :

Credit

3(3-0-

6)

3(3-0-

6)

relational algebra and relational calculus languages,

Database security and integrity, Transactions and concurrency control

344-564 Information Retrieval

Information retrieval models, Retrieval evaluation,

Query language and operations, Text and multimedia operations, Indexed and searching,

Parallel and distributed information retrieval,

Libraries and bibliographical systems, Digital libraries

344-571 Artificial Intelligence

Concepts and theories of intelligent systems,

Searching techniques, Heuristic search,

Propositional logic, Predicate logic, Production systems, Logic reasoning systems, Deductive and inductive inference systems, Uncertainty,

Knowledge representation such as frame, conceptual graph, recursive transition network,

Introduction to Prolog programming, Overview on expert system, machine learning, neural network, robotics, computer vision and natural language processing

3(3-0-

6)

3(3-0-

6)

344-572 Expert Systems

Knowledge acquisition, Interviewing for content and classification, Conceptualizing the domain expert,

Rule-based reasoning, Logics and automated reasoning, Inferencing, Knowledge representation,

Explanations, Uncertainty management,

Probabilistic Uncertainty, Belief theory and fuzzy set theory, Expert system life cycle, Building expert system using expert system shells, Validation and integration

344-573 Neural Networks (Prerequisite : 344-571)

Biological neural networks, Brain central and modulation systems, Pattern recognition, Pattern classification, Neural network modeling, Artificial neural network, Unsupervised learning, Matching and self-organized networks, Supervised learning,

Back propagation neural network, Adaptive resonance theory, Neural networks based on competition, Fuzzy reasoning, Applications of neural networks algorithms and learning models

344-662 Data Warehouse and Data Mining

Architecture and infrastructures of data warehouse,

Design and implementation of data warehouses,

Techniques in data mining, Knowledge

3(3-0-

6)

3(3-0-

6)

3(3-0-

6)

representations, Use of data mining software

346-521 Analysis of Advanced Statistical Models

(Prerequisite : 346-502)

Definition of a statistical model, generalized linear models, likelihood function and parameter estimation, models for continuous data, model for binomial data, model for Poisson data, models for negative binomial data, models for zero-inflated

Poisson data, computer software applications

346-531 Applied Multivariate Analysis (Prerequisite : 346-

502)

Aspects of multivariate analysis, the multivariate normal distribution, comparisons of several multivariate means, multivariate regression, discrimination and classification, path analysis, cluster analysis, principal component analysis, factor analysis, canonical correlation analysis, computer software applications

346-532 Experimental Designs (Prerequisite : 346-502)

Introduction; design and analysis of single-factor experiments, single-factor experiments having repeated measures on the same elements, design and analysis of factorial experiments, factorial

3(2-2-

5)

3(2-2-

5)

3(2-2-

5)

experiments in which some of the interactions are confounded, Latin Squares and related designs, analysis of covariance, repeated measurement, computer software applications

346-534 Statistical Decision Theory (Prerequisite : 346-501)

Review of probability, basic concepts of decision analysis, elementary decision problems, continuousvariable decision problems, sufficient statistics and conjugate distributions, multivariate normal process, sequential decision problems

346-542 Simulation Techniques (Prerequisite : 346-541)

Principle and concept of simulation; concepts in discrete-event; random number generator; random events; monte-carlo simulation; simulation examples; verification and validation of simulation; output analysis; comparison and evaluation of alternative system; computer software applications

347-531 Biological Statistics and Research Methodology

Science research methodology, inferential statistics, sampling survey techniques, experimental designs, simple correlation and simple linear regression analysis, multiple linear regression, computer software applications

3(3-0-

6)

3(2-2-

5)

4(3-2-

7)

347-532 Applied Statistics for Research

Introduction to data analysis, normal distribution, sampling distributions, estimation and hypothesis testing, one way analysis of variance, correlation and simple linear regression analysis, multiple linear regression, Chi-square test, strategies for selecting appropriate statistical methods, computer software applications

326-651 Advanced Immunology

Presentation and group discussion of current knowledge from published articles on immunology

364-511 Human Genetics

Basic knowledge in human genetics and common genetic disorders, technique of history taking, interviewing patients and their families and the construction of genetic pedigree, studies on population genetics, cytogenetics, molecular genetics, biochemical genetics, immunogenetics, genetics of cancer, and other genetic applications

373-570 Biomedical Laboratory Techniques

Theory, principle and laboratory techniques used in biomedical science research, research ethics, basic techniques in biochemistry, pharmacology, molecular biology, immunology and cell culture

3(3-0-

6)

3(3-0-

6)

2(2-0-

4)

2(0-4-

2)

373-590 Biomedical Topic Discussion

Reviewed study of medical/ biomedical articles and literatures relevant to the subject of dissertation with critical appraisal and presentation to advisors and colleagues, open discussion and exchange of knowledge among speakers and audiences to enhance the learning process

660-711 Philosophy and Methodology of Dental Research

Definition and types of research, how to acquire knowledge, reliability of bioinformatics, analysis of problems, research desing, ethics, and how to read and criticize paper

660-713 Advanced Oral Science

Molecular biology of craniofacial development, cleft lip and palate, current concepts of tooth eruption, molecular mechanisms of oral cancer, wound healing, tissue engineering, basic science of the prevention of dental caries and periodontal diseases, application of molecular biology in dental research

2(2-0-

4)

2(2-0-

4)

3(3-0-

6)

660-791 Animal Cell Culture in Medical Research

Study of theory and laboratory technique in cell and tissue culture, particularly mammalian cells for experimental research such as toxicity test for dental materials, mitogenic factors, and cell communication

2(1-3-

2)

Ph.D. Molecular Biology and Bioinformatics

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