Study plan

SPECIALIZATION COMPUTATIONAL BIOLOGY, BIOINFORMATICS AND MODELING prepares prepares excellent researchers and experts with good orientation in the broader programme (interactions between chemicals, environment and health, risk assessment) and have deep and detailed knowledge within their specialization – i.e. innovative assessment of individual, population and environmental factors affecting human and ecosystem health and methodological developments of models and bioinformatic tools for big data analyses.


STATE DOCTORAL EXAMINATION (SDE)

Students are advised to register for the SDE after completion of four semesters. Students should demonstrate broad orientation as well as detailed knowledge in their own field. Requirements are set for three basic parts of the SDE: (i) proficiency in the fundamentals of the broader scientific discipline - research of interaction between environment and health, (ii) deep understanding to the particular scientific field of specialization, and (iii) detailed knowledge within to the topic(s) of the doctoral research project including context.

As a compulsory part of preparation for the SDE students need to successfully complete four specialized classes (full semester). Students are advised to choose courses taught in English to increase their practical experience with foreign language. Upon consultation with advisor and within their specialization students could choose from the courses offered by Faculty of Science, within MU, or other universities.

SDE is typically held separately and precedes the dissertation thesis defence and students are required to submit short-thesis for SDE. This short-thesis consists of the literature search and introduction to the research project, its aims and methods and could also include actual state of project and actual results. The short thesis should be 10-20 pages long and submitted at least three days before SDE to the head of examination committee.

DISSERTATION THESIS AND THE DEFENCE

In accordance with international standards the preferred form of dissertation thesis is a commented collection of original published works – research papers. The thesis text should also include comprehensive theoretical introduction into the topic (ca 10-20 pages without references) and integrating comment (ca 10-20 pages without references) covering and interconnecting all performed studies in a logical way within the current state of the art. The text should also demonstrate student’s deep understanding of the field within a context broader than topics of individual papers or projects.

The submitted thesis should fulfill the following criteria Should be based on at least three original works. At least one should be published or accepted in impacted journal above the median within the filed (according to ISI WOS) and student should be the first author. At least one other published or accepted paper in a journal with IF (ISI WOS) with students at minimum as a co-author. If submitted thesis just fulfills these minimal criteria the committee evaluates the thesis critically with emphasis on the overall quality of results. In exceptional case lower amount of original papers can be accepted, if student independently worked in extensive research and/or published results as a first author of a paper in some of best multidisciplinary journals, such as Nature, Science, PNAS etc.

The dissertation thesis is recommended to be submitted in English and the defence should also be organized in English language with at least one reviewer or committee member from a reputable foreign institution.

Mandatory duties are defined within the individual study plan (ISP). The overal study load should correspond to ca. 60 ECTS credit points (each ECTS credit point represents ca. 25 hours of work, i.e. 1500 hours of study, work and related duties per year) per year.

The reference values below are suggestions and concrete values should be described in details in each ISP upon agreement between student and advisor and approved by the programme board.

Students are obliged to advance research and study competences (activities 1-9) in five areas. The biggest share should be covered by area A – research and development (ca. 70%) and area B – theoretical preparation (ca. 20%). The shares of areas C to E are variable and complementary contribute to the student’s complex profile.

The requirements within the specialization are defined by the dissertation topic and attended specialized courses (competence – area B).

ACTIVITIES OF THE ISP

(A) research and development activities (ca. 70 % of workload)

1. Research, dissertation project, literature search of the actual state of the topic, planning and the scientific activities itself (50%).
2. Publications (at least three papers need to be demonstrated before thesis defence and could be in different stages of publication process), thesis writing, knowledge synthesis, critical assessment of novelty and results interpretation (15%)
3. Presentation of results on scientific seminars, symposia, conferences etc., including preparation of talks and/or poster presentations (5%)

(B) Attending specialized courses and theoretical preparation (20%). Students should attend courses to deep professional knowledge in own specialization. State-of-the-art development should gain at seminars.

4. Theoretical professional preparation (15%) – students should attend and successfully complete at least four specialized courses (full-semester) covering broader field of research and own specialization.

C2003 Environmental Chemistry
Bi2003 Ecotoxicology
E4200 Modelling and Interpretation of Environmetal Data
Bi5444 Analysis of sequencing data
Bi7491 Regression modelling
Bi8601 Advanced statistical methods
Bi7527 Data analysis in R
Bi7528 Analysis of genomic and proteomic data
Bi7490 Advanced nonparametric methods

5. Doctoral seminars (5%) - E0401 - Advances in Environmental Health Sciences (2 h /week).

(C) International experience and competitiveness

6. Further improving of language competences – with emphasis on specialized courses, seminar participation, results presentation and preparation of publications, all in English.
7. Stay or internship abroad, mandatory participation in international cooperation. The minimal requirement is 1 month of a foreign stay, but longer stays (3+ months) are preferred with regard to the particular student’s topic.

(D) Pedagogical competences

8. Students should gain pedagogical competencies by active participation in contact classroom work and/or instructing classes (typically seminars and lab. courses) or by advising bachelor or master SP students. The overall demand is about 100 hours through the entire doctoral studies.

(E) Other transferrable skills.

9. Students should gain practical experience with preparation and management of projects (e.g. FRMU, mobility grants and awards) and participate in other soft-skills courses based on the availability.

Bioinformatics assessment of omics mass spectrometry data to comprehensively evaluate exposure factors
Innovative data analysis and modeling techniques to evaluate human exposure to chemical pollutants
Quantitative proteomics to characterize human intestinal microbiota
Development of image-based phenotypic screening for toxicology
In silico modelling of biophysical properties of biotechnologically interesting proteins
Bioinformatics applications in studies of Haloalkane Dehalogenase
Microfluidics and lab on a chip in environmental research
Characterization and analyses of lipid biomarker data of Alzheimer's disease