Doctoral Studies

Genomics and Proteomics - Field

Brief description of field

The field of Genomics and Proteomics focuses on the study of the relationships between genetic information of an organism and the complex proteins that the genome encodes. It also focuses on the function of non-coding sequences of the genome, such as regulatory functions. Students should gain knowledge from various fields of genomics and proteomics.
Functional genomics studies the relationship between the sequence and structure of genes and their function in the organism. It also seeks to shed light on the so-called non-coding sequences that make up the larger part of the genome. Evolutionary genomics seeks to explain the causes and consequences of changes in the genomes during evolution. It allows, based on genomic data, the construction phylogenetic trees. Comparative genomics compares the genome on a large scale in order to understand the biological essence and reveal general principles valid for all kinds of genomes. It is expected that many biological sequences, structures and functions are shared among organisms. The combination of genomes in analyses may then lead to more accurate results. It also deals with comparing a very long sequences, it uses the comparative approaches for finding genes, assigning their functions, and identifying key regulatory areas. Applied Genomics has and will continue to have a lot of utilization in various fields of human activity. For example in medicine and pharmacology microbial and viral genomics are of significance as they enable the development of new drugs against specific pathogens. It will also enable us to discover the causes of genetic diseases and to improve and streamline the methods of genetic testing and diagnosis - use of DNA chips.
Proteomics is a field that deals with the global evaluation of the expression of genetic information at the level of proteins (proteome), but also examines the structure and interactions of proteins. The main aims of proteomics, according to the Human Proteome Organization (HUPO) from 2001, are to identify all the proteins encoded by the human genome (or genomes of other organisms especially “model” organisms), followed by determining a) their expression in different cells of the given organism - expression proteomics, b) their subcellular localization in various organelles, c) the post-translational modifications, d) their interactions (b-d are aims of structural proteomics) and e) the relationship between structure and function (functional proteomics).

This field of study has an interdisciplinary character and uses the approaches of analytical chemistry, biochemistry, molecular biology and genetics, statistics, computer science, and computer modeling.

Students who plan to apply for admission to the Genomics and Proteomics doctoral programme, therefore need to possess the knowledge and skills (in the context of the chosen topic) at a master's level in one of these disciplines: molecular biology, cell biology, biochemistry, analytical chemistry, and genetics, and also know the basics of the other disciplines including mathematical methods in biology.

Profile of a typical graduate

The graduate student of Genomics and Proteomics will acquire extensive and in-depth knowledge about the structure and function of the genome at all basic levels of living systems ( i.e., the viral genome, the genome of bacteria, protozoa, fungi and yeasts, algae, higher plants, animals and human genome in more detail). Students deepen their knowledge and skills in basic biological disciplines (especially genetics, molecular biology, microbiology, immunology, biostatistics, physiology of organisms), in biochemistry and chemistry (general biochemistry, enzymology, biochemical methods) and in biophysics (biophysical methods).
In addition to the theoretical principles of the discipline, students are also closely acquainted with performing basic and advanced methods used in various disciplines. Graduates of this field of study will find jobs in various fields: particularly in research focused on the analysis of genomes(basic research as well as applied research), in bioinformatics (including evolutionary aspects), in the field of molecular medicine (cancer, familial and hereditary diseases, gene therapy), in genetic engineering of microorganisms, plants, and animals, in the development of new biotechnologies, in pharmacogenomics, and in analyzing the proteome of individual groups of organisms, including humans.

Requirements for applicants

The basic requirement is completion of a master's degree in the field of biology, biochemistry, biophysics, or analytical chemistry. Optimally the student should choose a thesis related to his or her field of interest and expertise. During the admission the candidate’s general overview will be examined along with his/her motivation and knowledge in the field of the chosen thesis. The candidates ability to communicate in English is usually verified by the candidate briefly presenting his previous professional experience (e.g., in the framework of his/her master’s thesis).

Study requirements and completion of studies

The subject of the Final State Examination is the examination of one’s professional knowledge in the field of genomics and proteomics and other related disciplines, particularly in molecular and cell biology, structural biology, bioinformatics, and in the experimental approaches used in the field. The student should especially be able to prove sufficient general knowledge in the field studied and in-depth knowledge in areas related to his/her Ph.D. thesis, including being familiar with recent major publications in their field of expertise.

The dissertation must contain the results published or accepted for publication. The preferred form is a set of publications or manuscripts accepted for publication dealing with the subject of dissertation, accompanied by a comprehensive introduction and commentary (article 31 of the MU Study and Examination Regulations). In at least one of the publications the student must be the first author. At least three publications in peer-reviewed journals with impact factor are required; when the combined impact factor exceeds 4, the number of publications may be lower than three.

The role of the supervisor of the doctoral dissertation may only be carried out by a worker who conducts scientific research in the field of genomics and proteomics or related fields and publishes original scientific articles in international journals of high quality. In one year, the supervisor may take up as many PhD students as is his 3 year average of publications in journals with IF above the median of the relevant WoS category. The same theses cannot be listed under more than one field of study. The supervisor must, on request of the committees, be able to demonstrate that he has the infrastructure and sufficient financial resources necessary to fund the topic of the thesis. The latest from the 3rd year of the study, the supervisor must submit to a student clear publication strategy, which is set to meet the minimum publication conditions for graduation by the end of the 4th year. Supervisors whose students do not meet the publication conditions repeatedly, will be suspended to adopt new PhD students.

The annual evaluation of doctoral students

The Doctoral Board for the doctoral study program in Biochemistry decided, on 17 February 2016, that the annual evaluation of doctoral students according to article 27, paragraph 6, letter h of the MU Study and Examination Regulations will be carried out through the University Information System.
Every year, before the end of May, all students have to provide a progress report covering the past academic year. In the IS agenda "Doctoral Students Evaluation" they fill in the fields "Doctoral thesis status" (description of research activities, a summary of the results obtained, the full citations of publications and conference papers in a given period), "Internships, stays for the purpose of work and study as well as other activities" (report of the internship, if it took place, and other activities, eg. work with youth, popularization of science etc.), and "Overall comment" (fulfilment of the individual study plan) .
If the supervisor agrees with the student’s report, he/she accepts the texts for permanent storage by choosing "Pre-fill all the texts prepared by the student," and adds his/her commentaries. In the case of the disagreement he/she may ask the student for amendments, or instead give only his/her own opinion. Supervisor alone fills in the field "Performance of the student's duties" visible for the student. A hidden field "Private Note" is also available for the supervisor. If the student is ending the third year of the full-time study and has not yet a first-author publication, the supervisor should establish, in the "Performance of the student's duties" field, a plan and a time-line for the student on how to meet publication requirements by the end of the fourth year.
The Doctoral Board will conduct a final evaluation in the "Commentary by the Board for Doctoral Studies". When appropriate, further communication with the student and the supervisor may be initiated.

Individual study plan

The recommended study plan is based on the Study and Examination Regulations MU, especially Art . 30, Special enactment for the course of study:
(1) The students will conduct their studies according to the Individual Study Plan approved by the doctoral board, which is based on the proposal of the student and is presented by the supervisor . The Individual Study Plan is superior to the academic year schedule.
(2) ) The credit value for the “Ph.D. thesis” course under Article 30 , paragraph 5 is one-half to two -thirds of the minimum credit value of study . The specific value will be determined by departmental council based on the contents of programme. Meeting the requirements of this course will be evaluated by the supervisor by a colloquium in each semester in which the student has enrolled for the course.
(3) During the course of study, the student is required to demonstrate proficiency in academic and professional English or another foreign language usual for the program or discipline. This competence is verified by one of the following ways:
a) by completing two adequate semestral courses
b) obtaining a credit for publishing a foreign-language scientific paper for a journal or proceedings and a credit for giving a talk in a foreign language in front of an academic audience at an international conference or similar event; credits are awarded by the supervisor, or evaluator appointed by the doctoral board.
(4) The other important constituents of a doctoral degree programme, apart from the preparation of a dissertation (Article 30 , paragraph 5), are especially:
a) courses expanding and deepening the students knowledge in the field beyond the Master's degree level ,
b) courses deepening specialized knowledge,
c) specialized seminars ,
d) assistance in teaching undergraduate and master's programs.
If decided by the doctoral board, the study may include the preparation of theses for ones doctoral dissertation.
Year 1
Code
Course Name
Credits
Extent and Intensity
Type of Completion
Teacher(s)
Autumn semester
Compulsory Courses
Ph.D. Thesis
6
0/0
z
Teaching assistance
1
1/0
z
Compulsory Elective Courses
Genomics - a basic course
1+2
1/0
zk
Genomics - practice
3
0/3
z
Bioinformatics
2+2
2/0
zk
Bioinformatics - practice
1
0/1
z
Recommended Courses
Molecular biology of eukaryotes
2+2
2/0
zk
Practical course of molecular biology of eukaryotes
2
0/2
z
Bioanalytics I - Biomacromolecules
2+2
2/0
zk
Other Courses
Experiment planning and optimisation
2
1/2
zk
Students may also, according to the specialization of their thesis, choose from the complete range of courses, optimally worth a total of 10 credits.
Spring semester
Compulsory Courses
Ph.D. Thesis
8
0/0
z
Teaching assistance
1
1/0
z
Compulsory Elective Courses
Proteomics - a basic course
1+2
1/0
zk
Proteomics - practice
3
0/3
z
Structure and function of eukaryotic chromosomes
2+2
2/0
zk
Analysis of chromatin structure - practical training
2
0/2
z
Recommended Courses
Methods of molecular biology
3+2
3/0
zk
Methods of molecular biology - practice
3
0/3
z
Gene engineering
2+2
2/0
zk
Other Courses
Plant Cell, Tissue, and Organ Culture
2+2
2/0
zk
Plant Cell, Tissue and Organ Culture - practical course
2
0/2
z
Students may also, according to the specialization of their thesis, choose from the complete range of courses, optimally worth a total of 10 credits.
Year 2
Code
Course Name
Credits
Extent and Intensity
Type of Completion
Teacher(s)
Autumn semester
Compulsory Courses
Ph.D. Thesis
15
0/0
z
Teaching assistance
2
2/0
z
Compulsory Elective Courses
Protein characterisation using mass spectrometry
1+2
1/0
zk
Advanced methods of biophysics in experimental biology
2+2
2/0
zk
Advanced methods of biophysics in experimental biology - practice
2
0/2
z
Recommended Courses
Biology of yeasts
2+2
2/0
zk
Biology of yeasts - practice
2
0/2
z
Study of interactions between proteins and DNA
1+2
1/0
zk
Other Courses
Bionformatics seminar
1
0/1/0
k
Bionformatics seminar
2
1/1/0
zk
Students may also, according to the specialization of their thesis, choose from the complete range of courses, optimally worth a total of 4 credits.
Spring semester
Compulsory Courses
Ph.D. Thesis
15
0/0
z
Teaching assistance
2
2/0
z
Compulsory Elective Courses
Developmental and cellular biology of plants
2+1
2/0
k
Genetic codes
1
1/0
k
Recommended Courses
Evolutionary genomics
2+2
2/0
zk
Bioanalytics II - Analytical methods in clinical praxis
2+2
2/0
zk
The molecular interactions in biology and chemistry
3+1
2/0
k
Other Courses
Molecular Biology of the Tumor
2+2
2/0
zk
Bionformatics seminar
1
0/1
k
Students may also, according to the specialization of their thesis, choose from the complete range of courses, optimally worth a total of 4 credits.
Year 3
Code
Course Name
Credits
Extent and Intensity
Type of Completion
Teacher(s)
AutumnSemester
Compulsory Courses
Ph.D. Thesis
20
0/0
z
Compulsory Elective Courses
Protein crystallography
1+2
1/0
zk
Protein crystallography - practice
1
0/1
z
Recommended Courses
Evolutionary and comparative plant cytogenetics
2+2
2/0
zk
Evolutionary and comparative plant cytogenetics
3+1
2/0
k
Other Courses
Biocatalysis
1+2
2
zk
Structure of biomacromolecules
2+2
2/0
zk
Structure of biomacromolecules - practice
1
0/1
z
Students may also, according to the specialization of their thesis, choose from the complete range of courses, optimally worth a total of 2 credits.
Spring Semester
Compulsory Courses
Ph.D. Thesis
20
0/0
z
Compulsory Elective Courses
Early Molecular Evolution
1
1/0
k
Recommended Courses
Current trends in biological data analysis
2+2
2/0
zk
Other Courses
Protein-RNA interactions
1+2
1/0
zk
Molecular biology and genetics
5
0/0
k
Students may also, according to the specialization of their thesis, choose from the complete range of courses, optimally worth a total of 2 credits.
Year 4
Code
Course Name
Credits
Extent and Intensity
Type of Completion
Teacher(s)
Autumn Semester
Compulsory Courses
Ph.D. Thesis
30
0/0
z
Spring Semester
Compulsory Courses
Ph.D. Thesis
30
0/0
z
Courses available during the whole course of study
Code
Course Name
Credits
Extent and Intensity
Type of Completion
Teacher(s)
Autumn Semester
Compulsory Courses
Scientific publication writing
5
z
Lecture in the foreign language
5
z
Recommended Courses
Professional English for molecular biologists
2
0/2
z
Advances in molecular biology and genetics I.
3
2/0
z
Seminar
2
0/2
z
Seminar of the Dept. Functional genomics and Proteomics
2
0/2
z
Other Courses
Developmetal genetics
2+2
2/0
zk
Introduction to Practical Bioinformatics
2+2
1/1
zk
Molecular biology of prokaryotes
2+2
2/0
zk
Molecular biology of viruses
2+2
2/0
zk
Applied Genetics and Plant Breeding
2+2
2/0
zk
Molecular biotechnology
2+2
2/0
zk
Human molecular genetics
2+2
2/0
zk
Human molecular genetics
1+2
1/0
zk
Spring Semester
Compulsory Courses
Scientific publication writing
5
z
Lecture in the foreign language
5
z
Recommended Courses
Advances in molecular biology and genetics II.
3
2/0
z
Seminar MBG
2
0/2
z
Seminar of the Dept. Functional genomics and Proteomics
2
0/2
z
Other Courses
Journal Club
1
1/0
k
Introduction to Stochastic Modeling
2+2
2/0
zk
Genotoxicity and cancerogenesis
2+2
2/0
zk
Plant genetics
2+2
2/0
zk
Evolutionary Developmental Biology of Plants
2+2
2/0
zk
Genetic Engineering - Laboratory Course
2
0/2
z
Multivariate Methods
2+2
2/0
zk
Biotechnology
2+2
2/0
zk
A possible alternative for any semester: Internship related to dissertation: 1 week = 5 credits, 1 month = 10 credits, 1 semester = 30 credits.
The students will enroll in seminar courses according to the department they are under (department, laboratory).
The courses listed above are just an example of what courses doctoral students can enroll in.
In addition to the compulsory and compulsory elective courses, students may choose other courses, special lectures, seminars, etc. from the complete range of courses available at that time; even from other colleges / universities.
The specific individual study plan is set up by the supervisor and student so that it meets the requirements of the doctoral state examination and the needs of a given doctoral dissertation thesis.

List of members of doctoral committee

List of supervisors

Commission for state doctoral exams and defenses

List of current doctoral topics


login
© 2011 Přírodovědecká fakulta Masarykovy univerzity. tel: +420 549 49 1111, e-mail:
Všechna práva vyhrazena.
Webmaster: Alan Kuběna,
Grafický design: © 2011 Mgr. Pavel Brabec,
Obsahová struktura: © 2011 Mgr. Zuzana Kobíková
Počet přístupů: 780538 od 2.8.2011