Courses

BIOINFO COMP BIO
Data structures; file input and output; sequential statements; if statements; loop; arithmetic operations; shell scripts; basic Linux operating system commands.

SEM COMP BIO I
Presentation and discussion of topics related to computational biology of current interest.

SEM COMP BIO II
Presentation and discussion of topics related to computational biology of current interest and presentation of students’ research progress.

SPEC PROJ COMP BIO
Special project in interesting computational biology problems with advisor’s supervision.

STAT METH COMP BIO
Probability and statistical theory; random variables; probability distribution; multiple random variables; parameter estimation; maximum likelihood estimation; hypothesis testing; covariance and correlation; nonparametric testing; Markov chain and model; regression analysis and linear model; multiple linear regression.

ALGOR ASP COMP BIO
Asymptotic analysis; exhaustive search; dynamic programming algorithms; greedy algorithms; divide-and-conquer algorithms; graph algorithm; combinatorial pattern matching; clustering methods; trees.

INDIVIDUAL STUDY
Independent study on topics of student’s choice under the supervision of an instructor; analysis and interpretation of data and material; report writing of the INDIVIDUAL STUDY.

DISSERTATION

DISSERTATION

DISSERTATION

DIS DISS SEM
Presentation and discussion of topics related to computational biology of current interest and presentation of students’ research progress.

QUALIFYING EXAM

APP BAYESIAN INF
Baysian approaches to statistical inference; biomedical concepts and applications Bayes inference for large samples from likelihoods, non-functional information and conjugate priors; empirical Bayes; Bayesian approaches to linear and nonlinear regression, model selection; Bayesian hypothesis testing; numerical computing methods.

STAT INFO THEO
Data compression; data transmission; information theory; fundamentally statistical problems in estimation, prediction and model selection; new concepts of random selection of information.

SC SUP ANAL
Introduction to decision analysis; elements of decision problems; structuring decision; making choices; sensitivity analysis probability basic; subjective probability; value of information; risk attitudes; utility axioms; paradoxes and implications. conflicting objectives.

DATA MINING/APP
Preq 2301286 or C.F.
Structured and unstructured data mining; association rules; meta data; forecast models; knowledge discovery metamodel; K-means algorithm; data clustering; dimensionality reduction.

ART NEURAL NETWORK
PRER: 2301653 or C.F.
Elementary principles of neurophysiology, artificial neuron models, single and multiple layer networks, cascade correlation, recurrent networks, self-organizing maps, bidirectional associative memory, counterpropagation networks, adaptive resonance theory, spatiotemporal sequences, hardware realization of neuron networks, fault tolerant design aspects.

DATABASE SYSTEMS
Advanced data modeling, deductive databases, object-oriented databases, distributed and multi- databased systems, emerging database technology.

BIOMOL MODEL
Introduction: structures, properties and interactions of biomolecules; modeling and dynamics simulation of biomelecules; computer-aided drug design; applications.

MOL PHYLOGEN
PRER 2303403 or C.F.
Principles and methodologies in molecular phylogenetics; evolution at the molecular level; evolutionary changes of DNA and protein sequences; phylogenetic trees; phylogenetic tree inferences; statistical tests of phylogenetic trees; molecular clocks; evolution from genetic polymorphism; population tree from genetic markers.

POPULATION ECOL
PRER: 2303221, 2303222 or C.F.
Abundance and distribution of animals and plants in relation to physical and biological environments, techniques and methods forestimating population size, mathematical models of population dynamics and application, laboratory works and field study.

MOL BIO
Analysis of structure and function of genetic material in living organism, gene cloning techniques, gene isolation and gene expression, various modes of gene transfer to prokaryotic and eukaryotic cells, mechanism of gene inactivation and reactivation, applications of molecular biology in agriculture, medical science and industry, trends in molecular biology.

MOL ECOL
PRER: 2303221 and 2303562 or C.F.
The application of molecular biology techniques in a wide range of ecological studies including molecular identification, behavioural ecology, population ecology, phylogeography and conservation ecology.

MOL BIO LAB
PRER 2303562 2303101 and 2310301 or C.F.
Demonstrations and laboratory practices on experimental design, recording, reading and analysis of result in molecular biology research, general knowledge of molecular biology techniques, equipment and materials used in these techniques, concepts of research presentation.

PLANT MOL BIOL
PRER: 2310301,2305261 or C.F.
Plant gene structure and expression with emphasis on growth and development; plant gene responses to physical and biological factors; plant signal transduction; applications and current topics in plant molecular biology.

COMP PL MOL ANAL
PRER 230526 or C.F.
Computing techniques in plant molecular biology analysis with emphasis on data searching, data retrieval, formatting, objective oriented programs accession, data analysis and interpretation, and the effective application of software packages.

BIOCHEMICAL GENE
The study of gene expression and its regulation. Subjects cover the synthesis, regulation and activity of enzyme hemoglobin, immunoglobulin, hormone, pigmentation and etc. Inherited diseases or some defects caused by specific biochemical disorders, multifactorial genetic diseases and immunogenetics are demonstrated.

BIOINFO MED RES
Introduction; NCBI and Ensemble database for human disease genes detection; Bioedit and ClustalX program; promoter prediction; SNP database for human disease gene analysis; linkage analysis for human disease gene mapping; linkage analysis program; analysis of virus sequence; microarray; bioinformatics for recombinant DNA construction to transfect into human cell line; PLINK and StatCalC program for statistical analysis in population genetics; case study and research topic.

MET PL MOL BIOL
Techniques employed in plant molecular biology studies including construction of recombinant DNA vectors for plant gene transfer, and detection of plant gene expression at the nucleic acid and protein levels.

MET PL MOL BIOL LAB
Demonstration and practice of plant molecular biology techniques including construction for recombinant DNA vectors for plant gene transfer, and detection of plant gene expression at the nucleic acid and protein levels.

MUTATION
PRER 2305261 or C.F.
Types of chromosomal and gene mutations, consequent effects of mutation; various theories of spontaneous and induced mutations; mutagens and methods of induction of mutation used in animals, plants and microorganisms; applications of mutation researches for development of the country.

ADV MOL GEN
Advanced molecular genetics; genome, gene and gene expression; molecular mechanisms conceming growth differentiation and development; application on forensic science and archaeogenetics; introduction to laboratory and comparison of nucleic acid and genetic materials among organisms; sample preparation and comparative study of DNA and RNA among species; DNA replication; protein synthesis and gene regulation; genetic engineering, bioinformatics and molecular genetics applications.

BIOINFORMATICS I
Introduction to bioinformatics, using the internet and operating systems for working with databases, databases for biological research, retrieval of information and submitting sequences to the databases, sequence analysis including nucleotide and amino acid sequence alignments, database searching, phylogenetic analysis, predictive methods for gene structures and protein sequences, analysis and design of protein tertiary structure and nucleic acids, analysis of genome and gene expression in genomic scale.

MOL BIOL GENE
Organization of genome and chromosome in eukaryotes; gene and gene evolution; mutation and DNA repair; signals and gene control; genes in development and programmed cell death; oncogenes; applications of gene technology; functional genomics.

GENE ENG
Integration of basic and modern principles of molecular genetics and biochemistry; principle of genetic engineering and its application to biological sciences.

GENE ENG LAB
COREQ: 2310454 or 231055 or, C.F.
Recombinant DNA technology; extraction, cutting and joining of DNA, transformation; screening of genes of interested genes.

GENO SYST BIO
Principles of genomics, experimental and computational methods for genomic studies; high-throughput experiments, large-scale information and data analysis; analysis of genome, transcriptome, and proteome; functional and structural genomics; genome variations and polymorphisms; comparative genomics; principles of system biology; analysis of biological systems: network motifs and dynamics; statistical modeling, dynamic system modeling; system engineering and synthetic biology; tools and resources for genomics and system biology studies; additional current topics, trends, new technologies and future advancements in the fields.

BIO INTRA MICROBES
PRER 2312302 or 2312351 or C.F.
Biology of host cells; genome characteristics and evolution of intracellular microbes and their niches; types of interaction between intracellular microbes and their hosts; endocytosis and phagosome maturation; methods to study intracellular microbes; intracellular symbionts; intracellular pathogenic parasites and fungi; intracellular pathogenic bacteria; host immune responses to intracellular pathogens; strategies for drug and vaccine development.

YEAST GENETICS
PRER 2312361 or C.F.
Classical yeast genetics; mechanisms of gene expression and regulation; cell division cycle; mating type; genome and extrachromosomal DNA; genetic manipulation.

ADV MICRO GENE
Presentation and discussion of the papers that published recently in the international journals in the field of bacterial, viral, fungal and yeast genetics with industrial applications.

BIO ASP COMP BIO
Basic molecular biology: gene expression, gene and transcript regulation, protein structure and function, basic evolution, and phylogenetic principles; algorithms and data analysis approaches in computational biology; probabilistic approaches and machine learning including their applications for studies in computational biology such as sequence alignment, sequence motif analysis, gene expression analysis, pathway and regulatory network analysis, SNP analysis, biological modeling and simulation, structural prediction, comparative genomics and biological image analysis; analysis of large-scale biological datasets.

FUND BIOINF MED
Principles of basic Bioinformatics and its applications in data analysis and comparative analysis of nucleotide sequences, amino acid sequences, analysis of mutations, phylogenetics and design of oligonucleotides to be used in several molecular biological techniques.

CELL MOLECULAR BIO
Technical principles of cells and molecular biology, structure and functions of genes, proteins, and cells.

HMG
Level material on DNA, chromosomes and pedigree patterns, general principles, application of cloning and molecular by hybridization, structure, function, evolution genome mapping and mutational instability of the human genome and human genes; human genetic diseases, dissecting and manipulating genes.