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, construction of 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 applications in various fields of human activity. For example in medicine and pharmacology, the 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.

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, structural biology, genetics, statistics, computer science, and computer modelling.

Students, who plan to apply for admission to the Genomics and Proteomics doctoral program, 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/or 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, structural 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 topic 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 topic. The candidate’s 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). The applicant have to obtain 180 out of the 300 points:

  1. field of expertise             60 points/100     
  2. language skills                60 points/100     
  3. formal criteria                 60 points/100

Formal criteria will include assessment of previous education and practice (based on master diploma and reference letter). Electronic application (https://is.muni.cz/prihlaska) must include:

  • curriculum vitae (special form)
  • diploma copy (BSc., MSc.) and its appendices/transcripts (Czech or English)
  • reference letter (e.g. from master thesis supervisor)
  • admission fee

Study requirements and completion of studies

Student must provide and follow individual study plan (ISP) and report about his research achievements every semester. Student shall collect 240 credit points during his/her 4-years studies. Successful study must be concluded with the State Doctoral Examination and doctoral thesis defence. The subject of the State Doctoral 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 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 the field of expertise.

The dissertation thesis must contain the results published or accepted for publication in the journal listed in Web of Science (WoS) with impact factor above the field median. Student must be the first author on such a publication. In co-authored publications, student must specify his contribution. If student co-authored at least 3 papers, then the preferred format of doctoral thesis is a set of publications or manuscripts accompanied by a comprehensive introduction and commentary (article 31 of the MU Study and Examination Regulations). If the student publishes less than 3 publications, the format of the dissertation thesis must be a monography with experimental results.

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/her 3-year average number of publications in journals with IF above the median of the relevant WoS category. The same theses can not 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 take new PhD students.

The annual evaluation of doctoral students

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. Student must prepare individual study plan (ISP) for whole studies (within the first year) and then detail it for every semester (before 20.9. and 20.2.). The ISP must be approved by the supervisor for every semester (before 30.9. a 28.2.). Student must provide progress report for every semester (before 31.1. a 31.8.). All students shall provide description of research activities, a summary of the results obtained, the full citations of publications and conference papers in a given period, report of the internship, if it took place, and other activities, (e.g. work with youth, popularization of science etc.). Then, supervisor approves and comments the report (before 15.2. a 15.9.). If the student does not meet targets, supervisor can initiate process leading to stipend reduction (unsatisfactory results) or study termination (e.g. student does not fulfil study criteria). In such cases, supervisor must inform Doctoral Board and faculty department administrating PhD studies. 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 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 at least once a year. When appropriate, further communication with the student and the supervisor might 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 8, paragraph 3 is from one-half to two -thirds of the minimum credit value of study. The specific value will be determined by Doctoral Board based on the contents of the 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 student’s knowledge in the field beyond the Master's degree level (recommended and other courses – see below),

b) courses deepening specialized knowledge (compulsory elective courses),

c) specialized FGP seminar (C9950) ,

d) assistance in teaching undergraduate and master's programs.

If decided by the Doctoral Board, the study may include the preparation of theses for one’s doctoral dissertation.

 

Recommended individual student plan for Genomics and proteomics field

Year 1

Code

Course Name

Credits

Extent and Intensity

Type of Completion

Teacher(s)

Autumn semester

Compulsory Courses

XD100

Ph.D. Thesis

10

0/0

z

supervisor

C9950

FGP seminar

2

0/2

z

Fajkus, Hejátko, Zdráhal …

Compulsory Elective Courses

CG920

Genomics - a basic course

2

2/0/0

zk

Hejátko

C7301

Genomics - practice

3

0/0/3

z

Hejátko, Konečná …

Bi5000

Bioinformatics

2+2

2/0

zk

Pantůček

Bi9061

Bioinformatics - practice

1

0/1

z

Damborský

Recommended Courses

Bi7090

Molecular biology of eukaryotes

2+2

2/0

zk

Šmarda

Bi7312

Practical course of molecular biology of eukaryotes

2

0/2

z

Šmarda, Beneš

C7942

Bioanalytics I - Biomacromolecules

2+2

2/0

zk

Havliš

Other Courses

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

XD100

Ph.D. Thesis

10

0/0

z

supervisor

C9950

FGP seminar

2

02//0

z

Fajkus, Hejátko, Zdráhal …

Compulsory Elective Courses

C8202

Proteomics - a basic course

1+2

1/0

zk

Zdráhal, Konečná, Janda

C8302

Proteomics - practice

3

0/3

z

Hejátko, Zdráhal, Konečná

C9041

Structure and function of eukaryotic chromosomes

2+2

2/0

zk

Fajkus, Fojtová, Fajkusová

C9042

Analysis of chromatin structure - practical training

2

0/2

z

Fajkus, Schrumpfová, Sýkorová

Recommended Courses

Bi6400

Methods of molecular biology

3+2

3/0

zk

Šmarda, Beneš, Pantůček

Bi6405

Methods of molecular biology - practice

3

0/3

z

Šmarda, Beneš

Bi8090

Gene engineering

2+2

2/0

zk

Doškař

Other Courses

Bi6120

Plant Cell, Tissue, and Organ Culture

2+2

2/0

zk

Cempírková

Bi6120c

Plant Cell, Tissue and Organ Culture - practical course

2

0/2

z

 Cempírková

S2011

Hormones in plant development

2

0/2

Zk

Boisivon Robert

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

XD100

Ph.D. Thesis

15

0/0

z

supervisor

XD102

Teaching assistance

2

2/0

z

supervisor

C9950

FGP seminar

2

0/2

 

Fajkus, Hejátko, Zdráhal …

Compulsory Elective Courses

C7350

Protein characterisation using mass spectrometry

1+2

1/0

zk

Zdráhal, Konečná, Pospíšilová

C7230

Advanced methods of biophysics in experimental biology

2+2

2/0

zk

Hofr

C7235

Advanced methods of biophysics in experimental biology - practice

2

0/2

z

Hofr

Recommended Courses

C9045

Biology of yeasts

2+2

2/0

zk

Paleček, Svoboda

C9140

Biology of yeasts - practice

2

0/2

z

Paleček,Svoboda

C8857

Protein Preparation and Characterization III - Protein-Mediated Interaction

1+2

1/0

zk

Krejčí

Other Courses

IV105

Bionformatics seminar

1

0/1/0

k

Lexa

IV108

Bionformatics II

2

1/1/0

zk

Lexa

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

XD100

Ph.D. Thesis

15

0/0

z

supervisor

XD102

Teaching assistance

2

2/0

z

supervisor

C9950

FGP seminar

2

0/2

 

Fajkus, Hejátko, Zdráhal …

Compulsory Elective Courses

S2008

Developmental and cellular biology of plants

2+2

2/0

k

Nodzynski, Zwiewka

CG030

Structure and function of protein complexes

2+2

2/0

Zk

Paleček

Recommended Courses

Bi8350

Evolutionary genomics

2+2

2/0

zk

Kejnovský, Hobza

C7943

Bioanalytics II - Analytical methods in clinical praxis

2+2

2/0

zk

Havliš

F8310

The molecular interactions in biology and chemistry

3+1

2/0

k

Šponer

CG031

Modelling of protein complexes - practice

2

0/1

Z

Paleček

Other Courses

Bi9910

Molecular Biology of the Tumor

2+2

2/0

zk

Šmardová

IV106

Bionformatics seminar

1

0/1

k

Lexa

C3900

Molecular mechanisms of  cellular agging

1

1/0

Zk

Procházková Schrumpfová

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

XD100

Ph.D. Thesis

20

0/0

z

supervisor

XD102

Teaching assistance

1

1/0

z

supervisor

C9950

FGP seminar

2

0/2

 

Fajkus, Hejátko, Zdráhal …

Compulsory Elective Courses

 

 

 

 

 

 

C9530

Structure of biomacromolecules

2+2

2/0

zk

Žídek, Fadrná, Damborský

C9531

Structure of biomacromolecules - practice

1

0/1

z

Žídek

 

 

 

 

 

 

Recommended Courses

C9025

Evolutionary and comparative plant cytogenetics

2+2

2/0

zk

Lysák

C9035

Evolutionary and comparative plant cytogenetics - practice

3+1

2/0

k

Lysák, Mandáková

Other Courses

C8858

Biocatalysis

1+2

2

zk

Prokop

S1001

Chemical properties, structure and interactions of nucleic acids

3+2

3

Zk

Fojta, Vorlíčková

CB070

Protein crystallography

1+2

1/0

zk

Marek

CB080

Protein crystallography - practice

1

0/1

z

Marek

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

X100

Ph.D. Thesis

20

0/0

z

supervisor

XD102

Teaching assitance

1

1/0

z

supervisor

C9950

FGP seminar

2

0/2

 

Fajkus, Hejátko, Zdráhal …

Compulsory Elective Courses

Recommended Courses

Bi7921

Current trends in biological data analysis

2+2

2/0

zk

Brabec, Pekár

Other Courses

C9085

Protein-RNA interactions

1+2

1/0

zk

Štefl

DSMBz01

Molecular biology and genetics

5

0/0

k

Dvořák, Slaninová …

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

XD100

Ph.D. Thesis

30

0/0

z

supervisor

C9950

FGP seminar

2

0/2

 

Fajkus, Hejátko, Zdráhal …

Spring Semester

Compulsory Courses

XD100

Ph.D. Thesis

30

0/0

z

supervisor

C9950

FGP seminar

2

0/2

 

Fajkus, Hejátko, Zdráhal …

Courses available during the whole course of study

Code

Course Name

Credits

Extent and Intensity

Type of Completion

Teacher(s)

Autumn Semester

Compulsory Courses

XD105

Scientific publication writing

5

 

z

supervisor

XD106

Lecture in the foreign language

5

 

z

supervisor

Recommended Courses

JA003

English for Scientists

3

0/2/0

z

Burianová

S2009

Mendel Centre Seminars in the Bio-omics

2

0/2

Z

Říha

S5005

Field seminar – The Bio-omics

4

0/2

Z

Havliš

Other Courses

Bi0580

Developmetal genetics

2+2

2/0

zk

Vyskot

Bi5000

Introduction to Practical Bioinformatics

2+2

1/1

zk

Pantůček

Bi7120

Molecular biology of prokaryotes

2+2

2/0

zk

Doškař

Bi7140

Molecular biology of viruses

2+2

2/0

zk

Růžičková

Bi7240

Applied Genetics and Plant Breeding

2+2

2/0

zk

Řepková

Bi7430

Molecular biotechnology

2+2

2/0

zk

Prokop, Dvořák

Bi9325

Human molecular genetics

2+2

2/0

zk

Veselská, Doškař

C5920

Good laboratory practice

1+2

1/0

zk

Bláha

 

Spring Semester

Compulsory Courses

XD105

Scientific publication writing

5

 

z

supervisor

XD106

Lecture in the foreign language

5

 

z

supervisor

Recommended Courses

S5005

Field seminar – The Bio-omics

4

0/2

Z

Havliš

S2009

Mendel Centre Seminars in the Bio-omics

2

0/2

Z

Říha

Other Courses

C9141

Journal Club

1

1/0

k

Peška

Bi7490

Introduction to Stochastic Modeling

2+2

2/0

zk

Dušek, Jarkovský

Bi8110

Genotoxicity and cancerogenesis

2+2

2/0

zk

Hofmanová, Kozubík

Bi8240

Plant genetics

2+2

2/0

zk

Řepková

Bi8290

Evolutionary Developmental Biology of Plants

2+2

2/0

zk

Mgr. Žlůvová Jitka, Ph.D.

Bi8313

Genetic Engineering - Laboratory Course

2

0/2

z

Pantůček

Bi8600

Multivariate Methods

2+2

2/0

zk

Dušek, Jarkovský, Némethová

C6210

Biotechnology

2+2

2/0

zk

Mandl

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 enrol 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 enrol 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


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