TrưỜng đẠi học khoa học tự nhiên chưƠng trình đÀo tạo trình đỘ ĐẠi học ngàNH: sinh họC ĐẠt chuẩn quốc tế Mà SỐ: 52420101 Hà Nội, 2012

Baxevanis A. D., Ouellette B. F. F. Bioinformatics (A Practical Guide to the Analysis of Genes and Proteins). John Wiley & Sons, 2005

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Baxevanis A. D., Ouellette B. F. F. Bioinformatics (A Practical Guide to the Analysis of Genes and Proteins). John Wiley & Sons, 2005.

  • Lesk A. M. Introduction to Bioinformatics. 3rd ed. Oxford University Press, 2008.

  • Mount D. W. Bioinformatics: Sequence and Genome Analysis (Genome Analysis). Cold Spring Harbor Laboratory Press, 2001.

    1. Course overview:

    Introduction to Bioinformatics, nucleotide and protein sequence databases, genomic mapping databases, information retrieval from biological databases, genomic databases. Predictive methods using DNA sequences, sequence polymorphisms, predictive methods using protein sequences, protein structure analysis, intermolecular interactions and biological pathways. Assessing pairwise sequence similarity, creation and analysis of protein multiple sequence alignments. Phylogenetic analysis. Primer design.

    1. Detailed course description:

    Chapter 1. Biological databases

    1.1. Sequence databases

    1.1.1. Primary and secondary databases

    1.1.2. Nucleotide sequence databases

    1.1.3. Protein sequence databases

    1.2. Mapping databases

    1.2.1. Genomic map elements

    1.2.2. Types of maps

    1.2.3. Genomic mapping resources

    1.2.4. Comparative maps

    1.2.5. Practical uses of mapping resources

    1.3. Information retrieval from biological databases

    1.3.1. Integrated information retrieval: The entrez system

    1.3.2. Gene-centric information retrieval: LocusLink

    1.3.3. Medical databases

    1.4. Genomic databases

    1.4.1. UCSC

    1.4.2. NCBI

    1.4.3. Ensembl

    Chapter 2. Analysis of DNA sequences

    2.1. Predictive methods using DNA sequences

    2.1.1. Gene prediction methods

    2.1.2. Gene prediction programs

    2.1.3. Promoter analysis: Characterization and prediction

    2.2. Sequence polymorphisms

    2.2.1. Overview of evolution and origins of polymorphisms

    2.2.2. Types of polymorphisms

    2.2.3. SNP discovery methods

    2.2.4. Public databases and browsers

    2.2.5. Genotyping

    2.2.6. The international haplotype map project

    Chapter 3. Analysis of protein sequences and structure

    3.1. Predictive methods using protein sequences

    3.1.1. Predicting features of individual residues

    3.1.2. Predicting function

    3.2. Protein structure analysis

    3.2.1. Protein structure databases

    3.2.2. Three-demensional visualization

    3.2.3. Protein structure comparison

    3.3. Intermolecular interactions and biological pathways

    3.3.1. Pathway and molecular interaction databases

    3.3.2. Prediction algorithms for pathways and interactions

    3.3.3. Resources for interaction prediction

    3.3.4. Network and pathway visualization tools

    Chapter 4. Assessing pairwise sequence similarity

    4.1. Global versus local sequence alignments

    4.2. Dotplots alignment

    4.3. Scoring matrices:

    4.3.1. Position independent matrices

    4.3.2. Position specific score matrices (PSSMs)

    4.4. Local sequence alignment: BLAST

    4.5. Global sequence alignment: Needleman-Wunsch

    4.6. Other programs for pairwise sequence alignment

    Chapter 5. Creation and analysis of protein multiple sequence alignments

    5.1. Introduction to multiple alignment

    5.2. Scoring functions

    5.3. Multiple alignment construction

    5.3.1. Traditional approaches: optimal, progressive

    5.3.2. Aligment parameters: Similarity matrices, gap penalties

    5.3.3. Iterative and co-operative approaches

    5.4. Multiple alignment analysis

    5.4.1. Quality analysis/error detection

    5.4.2. Conserved/ homologous regions

    5.5. Multiple alignment applications

    5.6. Programs for the multiple alignments

    5.6.1. ClustalW

    5.6.2. T-Coffee

    5.6.3. MAFFT


    5.6.5. ProbCons

    5.6.6. Other programs

    Chapter 6. Phylogenetic analysis

    6.1. Fundanental elements of phylogenetic models

    6.2. Phylogenetic data analysis

    6.3. Alignment: Building the data model and extraction of a phylogenetic data set

    6.4. Determining the substitution model

    6.4.1. Models of substitution rates between bases

    6.4.2. Models of substitution rates between amino acids

    6.5. Tree-building methods

    6.5.1. Distance-based methods

    6.5.2. Character-based methods

    6.6. Tree evaluation

    6.7. Phylogenetic analysis softwares

    Chapter 7. Primer design

    7.1. Introduction to PCR and primer design

    7.2. Parameters for primer design

    7.2.1. Parameters for each primer design

    7.2.2. Parameters for primer pair design

    7.3. Programs available for primer design

    7.3.1. Primer design for PCR

    7.3.2. Primer design for quantitative PCR

    80. Proteomics and Structural Biology

    1. Course number: BIO3435

    2. Credit: 3

    3. Prerequisites: Biochemistry and Molecular Biology, Biophysics

    4. Teaching language: Vietnamese, English

    5. Instructors: Trinh Hong Thai, PhD, Associate Professor, Department of Biology, College of Science, Vietnam National University.

    6. Course objectives:

    • Knowledge: To understand the main concepts of Proteomics and Structural Biology. To understand and analyse the data of mass spectrum and protein structure.

    • Skills: Practical doing in analysis of mass spectrum and protein structure.

    • Attitude: To work in group, confidence, activity and flexibility .

    1. Assignment and testing:

    Grading on the basis of student performance in problem sets, projects/presentations, class participation and written examination.

    1. Required textbooks:

    • Liebler D.C. Introduction to proteomics: tools for the new biology. Humana Press, 2002.

    • Veenstra T.D., Yates J.R. Proteomics for Biological Discovery. John Wiley & Sons, 2006.

    • Hoffmann E.D., Stroobant V.. Mass Spectrometry: Principles and Applications. John Wiley & Sons, 2001.

    • Petsko G.A., Ringe D. Protein Stucture and Function. Sinauer Associates, 2003.

    1. Course overview:

    Introduction to proteomics. Protein fractionation methods for proteomics. Mass spectrometry for protein and pepetide analysis. Protein identification by peptide mass fingerprinting and tandem mass spectrometry data. Peptide sequence analysis by tandem mass spectrometry. Applications of proteomics in mining proteomes, protein expresion profiling, identifying protein-protein interaction and protein complexes, and mapping protein modifications. Novel approaches in Proteomics. Introduction to structural biology. Levels of protein structure. Predictive methods and analysis of protein structure.

    1. Detailed course description:

    Chapter 1. Proteomics and proteome

    1.1. Proteomics

    1.1.1. Introduction to proteomics

    1.1.2. Tools of proteomics

    1.1.3. Applications of proteomics

    1.2. The proteome

    1.2.1. The proteome and genome

    1.2.2. Proteins as modular structure

    1.2.3. Functional protein families

    1.2.4. Deducing the proteome from the genome

    1.2.5. Gene expression and protein levels

    Chapter 2. Protein fractionation methods

    2.1. Subcellular fractionation

    2.2. Fractionation of protein complexes

    2.3. Fractionation of individual proteins

    2.3.1. The problem of protein solubility

    2.3.2. Chromatographic techniques

    2.3.3. Electrophoresis techniques

    2.4. Present and future trends in protein fractionation in proteomics

    2.5. Protein digestion techniques

    2.5.1. Overview of proteases

    2.5.2. In-gel digestions

    Chapter 3. Mass spectrometry

    3.1. Introduction

    3.2. Ionization methods

    3.2.1. Electrospray Ionization

    3.2.2. Matrix-assisted laser desorption ionization

    3.2.3. Desorption electrospray ionization

    3.3. Mass analyzers

    3.3.1. Ion-trap mass spectrometer

    3.3.2. Time-of-flight mass spectrometer

    3.3.3. Triple quadrupole mass spectrometer

    3.3.4. Quadrupole time-of-flight mass spectrometer

    3.3.5. Fourier transform ion cyclotron resonance mass spectrometry

    Chapter 4. Protein identification

    4.1. Peptide mass fingerprinting (PMF)

    4.1.1. Introduction to PMF

    4.1.2. Analytical approach using PMF

    4.1.3. Software tools for PMF

    4.2. Tandem mass spectrometry ESI

    4.2.1. Applying ESI tandem MS to protein identification

    4.2.2. Software tools for identifying proteins from ESI tendem MS data

    Chapter 5. Peptide sequence analysis

    5.1. Peptid sequence

    5.2. Peptide ion fragmentation in MS-MS

    5.3. The MS-MS spectrum

    5.4. PSI spectrum

    Chapter 6. Application of proteomics

    6.1. Proteome analysis

    6.1.1. Proteomic analysis by two- dimensional polyacrylamide gel electrophoresis and MALDI-TOF.

    6.1.2. Proteomic analysis by online two-dimensional peptide chromatography and LC tandem MS/MS.

    6.1.3. Proteomic analysis by offline two-dimensional peptide chromatography and LC MALDI-TOF/TOF.

    6.2. Protein expression profiling

    6.2.1. Quantitative proteomics using 2-D gels and 2-D DIGE

    6.2.2. Quantitative proteomics using LC-MS and isotope labeling: ICAT, iTRAQ, NBS

    6.3. Identifying protein-protein interations and protein complexes

    6.3.1. Identifying protein-protein interations

    6.3.2. Characterization of functional protein complexes

    6.4. Characterization of post-translational modifications

    6.4.1. Identification of phosphorylated proteins

    6.4.2. Identification of glycosylated proteins

    6.4.3. Other post-translational modifications

    Chapter 7. Structural biology

    7.1. Introduction to structural biology

    7.2. Amino acids: the building blocks of protein

    7.3. The three-dimensinal structure of proteins

    7.3.1. Overview of protein structure

    7.3.2. Protein conformation

    7.3.3. Levels of protein structure

    7.3.4. The structural classification of proteins (SCOP)

    7.3.5. Protein folding

    7.4. Predicting protein structure

    7.4.1. Visualizing protein structure

    7.4.2. Predicting secondary structure of protein

    7.4.3. Protein structure evaluation

    7.4.4. Protein modeling

    7.5. Predicting protein function

    7.5.1. Structural and functional motifs

    7.5.2. Function prediction from protein structure

    7.6. Predicting RNA structure

    7.6.1. Introduction to RNA structure

    7.6.2. RNA secondary structure thermodynamics

    7.6.3. Programs available for RNA secondary structure prediction

    7.6.4. Predicting RNA tertiary structure

    7.7. Physical methods of determining the three-dimensional structure of proteins

    7.7.1. X-ray crystallography

    7.7.2. Nuclear magnetic resonance (NMR)

    82. Tropical Ecology and Conservation

    1. Course number: BIO4047

    2. Credit: 3

    3. Prerequisites: Basic Ecology (BIO3406).

    4. Teaching language: Vietnamese

    5. Instructors: (Full name, academic title and degree, academic units and faculties)

    - Department of Invertebrate Zoology: Assoc.Prof. Dr. Nguyễn Văn Vịnh, Assoc.Prof. Dr. Nguyễn Xuân Quýnh, Assoc.Prof. Dr. Nguyễn Văn Quảng, Dr. Trần Anh Đức, Dr.. Nguyễn Quang Huy, BSc. Nguyễn Thanh Sơn, BSc. Ngô Thị Minh Thu

    - Department of Vertebrate Zoology: Assoc.Prof. Dr. Nguyễn Xuân Huấn, Dr. Lê Thu Hà, BSc. Vũ Ngọc Thành, MSc. Nguyễn Thị Lan Anh, MSc. Hoàng Trung Thành, MSc. Thạch Mai Hoàng, MSc. Nguyễn Thành Nam, MSc. Nguyễn Huy Hoàng

    - Department of Botany: Assoc.Prof. Dr. Nguyễn Trung Thành, Dr. Nguyễn Thùy Liên, MSc. Nguyễn Anh Đức, MSc. Nguyễn Thị Kim Thanh, BSc. Hồ Thị Tuyết Sương

    - Laboratory of Ecology and Environmental Biology: Dr. Lê Thu Hà, Dr. Đoàn Hương Mai, MSc. Trương Ngọc Kiểm, MSc. Bùi Thị Hoa

    1. Course objectives: (knowledge, skills, attitude)

    6.1. Knowledge:

    - To broaden the knowledge on biodiversity already acquired in previous course on Invertebrate Zoology, Vertebrate Zoology, Botany, Ecology, in the context of Vietnamese tropical ecosystems. To synthesize the knowledge above during fieldwork.

    - To be able to understand better, to compare and differentiate the relationships between organisms and their living environment.

    - To learn, to explore and understand basic knowledge on biogeography and conservation biology.

    6.2. Personal skills and professional attitude

    - To understand and be able to apply field study methods: observation, recording and obtaining data methods, collecting and preserving methods.

    - To be able to analyze and synthesize data obtained from field surveys.

    - To strengthen critical thinking ability, careness, honesty in scientific activities.

    - To strengthen the ability to overcome difficulties, cooperative skills, discipline in work.

    6.3 Social skills and attitude

    - To build and enhance the love for nature, environmental awareness.

    - To enhance the ambitions and career awareness.

    6.4. Ability to apply knowledge in real life

    - To be able to apply basic biology knowledge in real situations.

    - To be able to apply information technology in biological research.

    1. Assignment and testing

    - Continuous assessment based on fieldwork performance.

    - Final exam grade based on practical reports after fieldwork.

    1. Required textbooks (authors, textbook name, publisher, year of publication)

    Trần Đình Nghĩa (chủ biên), Phan Huy Dục, Hà Đình Đức, Bùi Công Hiển, Nguyễn Xuân Huấn, Nguyễn Văn Quảng, Nguyễn Xuân Quýnh, Đặng Thị Sy, Nguyễn Nghĩa Thìn. Sổ tay Thực tập thiên nhiên. Nhà xuất bản Đại học Quốc gia Hà Nội, 2005.

    1. Course overview (approximately 120 words)

    This is a field work course. The main content are knowledges of biodiversity,ecosystems, ecology, biogeography, and conservation biology in the context of Vietnamese tropical ecosytems. Students will work in groups and study three research themes, namely botanical biodiversity, biodiversity of invertebrates and biodiversity of vertebrates in selected habitats.

    Students will learn a variety of methods in field work such as observing, collecting specimens, identification and preservation of specimens. After field work, students will summarize studying results and write a scientific report. This course also provides essential skills, professional manner in biological fieldstudies, and nutures interest in protection of nature and environment.

    1. Detailed course description (discribed in chapters, main topics, subtopics, topics)

    Chapter 1: The importance of course and student responsibility

      1. Objectives.

      2. Requirements for students.

      3. Scientific skills and manners.

    Chapter 2: Natural conditions and Habitats of the Field Area

      1. Location.

      2. Terrance.

      3. Climate and hydrological conditions.

      4. Habitats.

    Chapter 3: Terrestrial Insects

      1. Requirements.

      2. Content.

      3. Identification keys to common families

    Chaper 4: Aquatic invertebrates.

      1. Research methods and techniques.

      2. Description of freshwater common macro-invertebrates.

    Chapter 5: Pisces, Amphibia and Reptilia

      1. Pisces

      2. Amphibia.

      3. Reptilia.

    Chapter 6: Aves and Mammalia

      1. Studies on fauna of Aves and Mammalia.

      2. Methods for Aves study.

      3. Methods for Mammalia study.

    Chapter 7: Tracheophyta

      1. Requirements.

      2. Types of valuation.

      3. Detailed content.

    Chapter 8: Fungi and Algae

      1. Fungi.

      2. Algae.

    83. Graduation Thesis (An example syllabus of genetic department)

    1. Course code: BIO4075

    2. Number of credits: 10

    3. Prerequisite courses: mandatory courses, elective courses and experiments

    4. Language of lecture: English or Vietnamese

    5. Lecturer: The staff of Department of Genetics

    - Assoc.Prof.Dr. Dinh Doan Long

    Tel: 0912150799


    - Dr. Nguyễn Thị Hồng Vân

    Tel: 0912627679


    - MSc. Nguyễn Vãn Sáng

    Tel: 04.38584748


    • PhD. student Trần Ðức Long

    Tel: 04.38584748


    • Time and place of working: Administrative time, from Monday to Friday, Department of Genetics, Faculty of Biology, VNU University of Science.

    • Address: Department of Genetics, Faculty of Biology, VNU University of Science, 334 Nguyen Trai, Thanh Xuan, Hanoi.

    6. Course objectives:

    6.1. Knowledge:

    After this course, students have the knowledge and skills to develop their ability in scientific research as follows:

    • To recognize the research problem and to form the scientific hypothesis in genetics and relevant fields.

    • To have the skills at design experiments to confirm the supposition.

    • To be able to apply the principles of genetics and modern biology and use the equipments for research to implement the designed experiments.

    • To have the skills at data collection and analysis

    • To have the ability to present, discuss the research results fluently, to argue and explain the results.

    6.2. Personal and professional skills and attitudes

    • To have a passion for biology; to be trained to have the creation, patience, precision, objectiveness and to work in plan.

    • To form the ablity to report in public about scientific project, to work independently or to work in group.

    6.3. Interpersonal skills

    • To understand how to apply the concepts, theoritical principles into practice.

    • To have logical and scientific thinking, contribute their ability to develop the country.

    6.4. Ability to apply the knowledge into practice

    • To be able to apply the knowledge and research skills to resolve the real problems in genetics or relevant fields.

    • To employ the thought of scientist in different activities of life (management, production or business...).

    7. Assessment and grading:

    To assess via the defence the graduation thesis of student to Committee of thesis assessment.

    8. Textbook: none

    9. Course descriptions:

    Graduation thesis is conducted by students as a small research project in the fields of genetics or related ones under the supervision of lecturer(s) with a defined scientific topic. The student could rise up the research idea by themselves or/and by the advice of their supervisor(s). The research project for the thesis should be performed in at least 6 months. The thesis must be presented in both forms of writing and oral presentaton those will be evaluated by a Faculty‘s examiner committee according to (but not limited to) the following criteria: i) experimental design skills, ii) practical skills, iii) data presentation skills and iv) validation and interpretation of research data.

    10. Content in detail

    The content of the course is prescribed by the instructor to every student.

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