Interdisciplinary doctoral programme in BIOMEDICINE
Curriculum and schedules

The structure of the programme is designed to emphasise organised study in the first year and the beginning of the second year, while later, the emphasis is on research and the preparation of the doctoral dissertation.
 

In the first year of study, doctoral candidates, within the framework of core courses obtain fundamental theoretical knowledge and expertise of scientific work. 20 ECTS have to be from the core course of scientific field they are enrolled into. In agreement with the mentor or co-ordinator, 10 ECTS can be chosen from other core courses.

In the second year of study, students fulfil their obligations arising from the elective course (15 ECTS). The selected courses according to student`s research work must be approved by the mentor. 
 

Registration of topic

Students should register the topic of the doctoral dissertation no later then in beginning of the second semester of the second year of studies.

Registration of topic of doctoral dissertation as well as evaluation of each doctoral dissertation are in the domain of the faculty senate responsible for a given scientific field. The Senate of the University of Ljubljana has to consent to the doctoral dissertation topic and the proposed mentor.

The core of the third year is research work, and preparation of the doctoral dissertation. 

In the fourth year, the focus is on individual research work, publication of the scientific article and preparation of the doctoral dissertation. Students also present the results of their research work and defend their doctoral dissertation publicly.

Mobility

Students are allowed to select 10 ECTS from elective courses from other doctoral programmes at the University of Ljubljana and comparable programmes of foreign universities. The selected courses must be approved by the mentor and the coordinator of the specific scientific field. Elective credits can be selected also from the university pool of the generic skills courses, listed at the web site of the University of Ljubljana.

The programme is composed of three types of courses:

• core courses
• elective theoretical courses
• elective individual research courses 

The published list is for academic year 2019/2020.

The doctoral candidates, together with their mentors and the field coordinators, design individual study programmes by selecting courses from core and both types of elective course pools. The core courses are modular. For each scientific field a choice of at least 20 credits is needed from the core modules proposed by the respective scientific fields, while the remaining 10 credits can be chosen from modules of other core courses. Remaining credits can be obtained from the selection of various elective courses. Elective credits can also be selected from the university pool of generic skills courses, listed at the web page of the University of Ljubljana.

Core courses

Core courses are designed for each specific scientific field. The content of courses is chosen on the basis of the research work of the professors.

Each scientific field proposed at least one core course, which is as a rule constructed from modules. The selection of modules is made in agreement with the mentor and the field coordinator.

Core courses

Code: J-1-400
Course title: Medical Cell Biology

Contents:
The course Medical Cell Biology enables in depth study of cell structures and functions, their alterations during pathological processes at molecular level, and upgrading of that knowledge in some important areas of medicine. The course consists of the obligatory module Fundamentals of medical cell biology and four elective modules: Cell biology in human reproduction, Biology of malignant cells and translational oncology, Cell biology in clinical genetics and System medicine of multifactorial disorders such as human reproductive biology, Oncology, genetics and multifactorial disorders. The course is composed of a core module (Module 1) and four elective modules.

Module 1: Fundamentals of medical cell biology
The basic module focuses on cell and molecular mechanisms of normal and abnormal cell cycle, cell death, the role of cell junctions in development, differentiation and diseases, the role of cell compartments of biosynthetic and endocytotic pathway in normal and transformed cells, the role of peroxisomes and mitochondria and on the structure and function of cytoskeleton during cell differentiation and their role in various diseases.

Module 2: Reproductive biology in vivo and in vitro
The module deals with the development of gonads, oogenesis, folliculogenesis, spermatogenesis, fertilization, embryogenesis. Students get knowledge on assisted reproduction and stem cells.

Module 3: Biology of malignant cells and translational oncology
Students acquire knowledge on fundamentals of cancer biology, carcinogenesis, principles and targets for cancer treatment, new treatment approaches and advances in translational oncology.

Module 4: Cell biology in clinical genetics
The module covers genetic defects in different areas of the cell function and their impact on the disease development. Such knowledge is crucial for adequate treatment decisions, follow-up of the patients and prognosis, as well as for genetic counselling.

Module 5: System medicine of multifactorial disorders
The module 5 consists of work on the project, which is based on the most recent scientific discoveries and research interests of the study group. The study focuses on the systems approaches of the post-genome era, the computation with large datasets, statistics, data modelling and on the role of global genome studies for the predictive personalized medicine.

Code: B-1-100
Course title: Selected advanced topics in Biochemistry and Molecular biology

Contents:
Core course entitled »Selected advanced topics in Biochemistry and Molecular biology« is devided into three independent modules,each equivalent to 10 ECTS:

Module 1: Selected biochemical processes with regulatory mechanisms
Included are topics on metabolism of xenobiotics and ROS, mitochondrial biogenesis, growth, ontogenetic development in mammals, struture and functional assimetry of biological membranes, membrane microdomains, protein interaction with lipid membranes, and mechanisms of signal transduction in regulating cellular processes.

Module 2: Structure and function of biological molecules and designed biological systems
Included are topics in molecular immunology and proteolysis.Techniques of protein engineering and molecular modelling of proteins for prediction of their function will be presented.

Module 3: Functional genomics and proteomics
Included are topics on genome structure, organization and regulation, comparative genomics and principles of global genome analysis. Theoretial principles and experimental approaches of transgenesis, transcriptomics, proteomics, metabolomics, interactomics and bioinformatics will be presented.

Students can sign in all three modules (30 ECTS) or at least two of them while the remaining 10 credits can be selected from modules offered in other core courses.

Code: L-1-300
Course title: Algorithms of clinical biochemical diagnostics

Contents:
Course is organized into three modules consisting of eight independent blocks (each 5 ECTS). Student can select any combination of blocks Each block is independently evaluated by separate score. For this research field each student have to elect 4 to 6 blocks.

Module 1: Laboratory biomedicine consists of two blocks.
Block 1: Scientific approaches in laboratory medicine, where students will learn the inductive and deductive approaches to problem solving in laboratory medicine. Using model cases, the students will critically evaluate their hypotheses, the credibility of the obtained results and the methodology used.

Block 2: Stepwise approach to clinical and biochemical diagnostics with interpretation will introduce students to the use of various mental pathways and stepwise approach in the laboratory diagnostics of common disorders. Based on this knowledge the student will be able to make evidence-based proposals for guidelines patients management.

Module 2: Molecular markers of diseases consists of three blocks.
Block 1: Common genetic diseases. Students will learn the screening (prenatal and postnatal diagnosis, family and population studies) and confirmatory tests of accumulating or missing metabolites and the correlation of laboratory results with the clinical symptoms of model diseases.

Block 2: Immune diseases. Students will learn the laboratory approaches to the diagnosis of immune-mediated diseases and hypersensitivity states using the analytes and tests in primary and targeted search for immune system disorders.

Block 3: Malignant disorders. Students will learn the use of biological molecules in the screening tests, tumor markers, extracellular tumor DNA, use of DNA / RNA tests, immunological tests, biosensors and microarrays, preparation of monoclonal antibodies, aptamers, siRNA, RNA / DNA probes and recombinant proteins in the diagnosis of malignancy.

Module 3: Translational Biomedicine consists of three blocks.
Block 1: Pharmacogenomic diagnostics. Students will learn the approaches to pharmacogenomic diagnostics and individualized therapy, pharmacogenomics of metabolic enzymes, receptors, transporters, miRNA and the direct and reverse pharmacogenomics in drug design, target identification and in preclinical and clinical studies.

Block 2. Cellular and Tissue Engineering. Students will understand different approaches in the preparation of complex cell and tissue cultures intended for advanced treatments or as system for testing artificial substances and materials in vitro.

Block 3: “Omic” Technologies and Tools (advanced technologies and tools in translational biomedicine. Students will learn about the advanced technologies in the areas of genomics, transcriptomics, proteomics and metabolomics and their implementation to laboratory practice and biomedicine.

Code: K-1-500
Course title: Research in clinical medicine

The subject is divided in three consecutive modules (each brings 10 ECTS). Module 3 is divided into several thematic blocks, which take place simultaneously. The student chooses two of three thematic blocks.

Module 1: Fundamentals in medical research
This module deals with ethics in research work, presentation of research and performance, evidence-based medicine, project preparation, intellectual property protection, research funding, writing and analysis of articles, characteristics of clinical research, cell and animal models.

Module 2: Methods in clinical research
Data collection, bias, representativeness, qualitative methods, conducting surveys, modern statistical methods, information methods.

Module 3: Achievements in clinical research
AThe module consists of individual thematic blocks (5 ECTS each), a Doctoral candidate chooses two of the blocks, or instead one module (10 credits) from the scientific fields of medicine - basic orientation,  biochemistry, microbiology or neuroscience.
Thematic blocks are: Imaging methods, Genetic methods, Immunology and allergology, Physiology of the cardiovascular system, Physiology of respiration, Physiology and biomechanics of the locomotor system, Basic and clinical pharmacology, Cardiovascular medical sciences, Emergency and intensive medicine, Hematology and oncology, Medical sciences of operative disciplines, Hyperbaric medicine. 

Code: G-1-600
Course title : Genetics

Contents:
The »Genetics« core course is intended to provide students with solid foundations in transmission (Mendelian), microbial, molecular genetics, cytogenetics, population, quantitative, evolutionary genetics, epigenetics, genomics, and in use of bioinformatics tools in genetic analyses. Students in the Genetics PhD programme are required to complete modules 1 and 2, whereas the third module can be from module 3 (Bioinformatics tools) or any module offered in other obligatory core PhD courses. Students from other PhD programmes may enrol any of the three GENETICS modules though enrolling module 2 requires prerequisite knowledge in basic genetics covered in module 1.

Module 1: Genetic concepts I covers various basic genetic concepts and fields of biological systems from microbes to mammals.

Module 2: Genetic concepts II provides an advanced course on theoretical and applied genetics as well as contemporary genomics. Emphasis is on analyses of genome structure or variation and applications in biomedicine and biotechnology.

Module 3: Bioinformatics tools is aimed at teaching students how to efficiently use some of the main bioinformatics tools and databases for genetic, genomic and protein analyses. Emphasis of the module is on practical problem-based projects. In summary, contents covered in the three modules of the genetics core course should provide students with the necessary skills and knowledge of contemporary concepts and scientific approaches used in classical and genomic analyses. Students should be able to apply this knowledge and expertise to tackle their projects on model organisms, microbes, domestic animals, plants, wildlife or humans. 
 

Code: M-1-410
Course title: Selected Topics in Microbiology

Contents:
The subject »Selected Topics in Microbiology« deals with complex relationships between microorganisms, between microorganisms and their hosts, and between microorganisms and their natural environment using selected cases and examples.

The subject is divided into three modules each evaluated with 10 credits (ECTS). The students inscribe the subject (30 ECTS) as a combination of three or selection of at least two modules.

Module 1: Basic medical microbiology
The structure and function of microorganisms in physiological and pathological circumstances and the mechanisms that underlay the development of human microbial diseases will be presented.

Module 2: Clinical microbiology
Diagnostic algorithms in clinical microbiology, critical interpretation of the results of microbiological testing, most frequent errors made when ordering microbiological tests and their medical and economic consequences and problems with communication between the laboratory and clinicians will be presented.

Module 3: Microbial identification, diversity, and evolution
Traditional, molecular and polyphasic taxonomy, microbial diversity (bacterial and archaeal diversity as well as the diversity of eukaryotic microorganisms i.e. algal, fungal and diversity of protists) along with topics from molecular evolution will be presented.

Code: N-1-540
Course title: Neuroscience

Contents:
The course entitled "Neuroscience" reviews updated knowledge and research in neurobiology at molecular, cellular and systemic levels, anatomy and histology of central and peripheral nervous systems, development and plasticity of the nervous system in physiological and pathological conditions, function of sensory and motor systems, regulation of physiological functions, neuropharmacology, behavioural and cognitive neuroscience, neurological, neurosurgical and psychiatric diseases including ethical considerations.
The course is divided into two independent modules, each equivalent to 10 ECTS. Students can sign in both modules (20 ECTS).

Module 1: Basic neuroscience

Module 2: Clinical neuroscience

Code: F-1-200
Course title: Pharmaceutical sciences

Contents:
The core course ''Pharmaceutical sciences'' deals with scientific principles of medicinal chemistry, pharmaceutical biology, pharmaceutical technological operations, delivery systems and pharmaceutical nanotechnology, molecular biopharmacy and health economics, social pharmacy, pharmacoeconomics and pharmacoepidemiology.

The core course comprises 15 independent modules, each equivalent to 15 ECTS. The students can select a combination of modules (10 ECTS each) depending on their research topic.

Modules:
Module 1.1.: Drug structure and their properties
Module 1.2.: Drug targets and interactions
Module 1.3.: Drug design methodologies
Module 2.1.: Biomolecules as targets for diagnosis and therapy
Module 2.2.: Biological and gene medical products
Module 2.3.: Herbal medicines
Module 3.1.: Pharmacokinetics and its role in drug discovery and development
Module 3.2.: Biopharmaceutical analysis of LADME processes
Module 3.3.: Pharmacokinetic-pharmacodynamic analysis.
Module 4.1.: Pharmaceutical manufacturing proceses
Module 4.2.: Drug delivery systems
Module 4.3.: Pharmaceutical nanotechnology and nanomedicines
Module 5.1.: Social pharmacy
Module 5.2.: Health economics
Module 5.3.: Pharmacoepidemiology

Short presentations of modules of the core course »Pharmaceutical sciences«.

Code: S-1-420
Course title: Research aspects of public health

Contents:
The course consists of two modules, 10 ECTS each.

Module 1: Determinants of health and disease
Biological background of health problems, determinants of health (lifestyle, work environment), selected health problems (mainly cancer and mental health), groups at risk, research methodology.

Module 2: Methodology of public health interventions
Health systems and health policy, quality of care, health promotion, prevention (vaccination, screening, epidemiological monitoring), primary care, rehabilitation, research methodology.

Code: T-1-340
Course title: Toxicology

Contents:
Understanding the mechanisms how chemicals disrupt biological targets is increasingly important in deciding on the safe use of chemical in the workplace and in everyday life.

The course attempts to introduce on the selected cases: mechanisms of transport of compounds across the cell membrane and toxic effects of compounds on it; the role of metabolism in the formation of reactive metabolites that covalently interact with macromolecules of cells; the role of radicals and substances capable of redox reactions to generate oxidative stress in cells; mechanisms of necrotic and apoptotic cell death induced by compounds; specific/nonspecific activation of enzymes and receptors caused by xenobiotics; toxic effects of compounds on mitochondria and peroxisomes, and energy state of cells; specific and nonspecific interactions (covalent /noncovalent) of substances with macromolecules in relation to the toxic effects of compounds (genotoxicity, immunotoxicity, etc.); mechanisms of toxic action of various groups of xenobiotics, which occur in the environment in different groups of organisms (bacteria, animals, plants, fungi); the application of biosensors and biomarkers for evaluation of the toxicity of compounds in conjunction with the corrupting effects on individual organisms, populations, community and ecosystem.

The course is divided into three independent modules, each equivalent to 10 ECTS. Students can sign in all three modules (30 ECTS) or at least two of them while the remaining 10 credits can be selected from modules offered in other core courses.

Module 1: Relationship between structure and toxicity
Covalent and noncovalent interactions of xenobiotics with macromolecules in living cells will be presented and formation of reactive oxygen compounds will be discussed in relation with genotoxic and immunotoxic effects of the compounds. Biotransformation reactions of the substance (functionalisation and conjugation) will be explained, and the consequences of the presence of their products in different tissues will be discussed. The role of radicals in the cell will be presented and the groups of substances that allow their formation will be discussed. We will also present some of the xenobiotics that non-specifically or specifically interact with cell macromolecules. Basic understanding of toxicological tests, including the quantum mechanic methods and bimolecular simulations that allow toxicity prediction of substances will be presented.

Module 2: Influence of toxic compounds on processes within cell
The effects of substances on the transport across membranes will be discussed, and the mechanisms of necrotic and apoptotic cell death induced by xenobiotics will be explained. The toxicity of a substance caused by the activation / suppression of cytokine and nuclear receptors will be described. The examples of xenobiotics that interfere with the processes of energy and interact with mitochondria and peroxisomes, immune system and genetic material will be presented.

Module 3: Influence of toxic compounds on environment and ecosystems
This module presents: effects of xenobiotic on suborganism, organism, population and ecosystem level; extrapolation of toxicological data from molecular and physiological levels to higher levels of biological organization; bioavailability of xenobiotics and other harmful substances in soil and water; biotransformation way of some important groups of xenobiotics and other harmful substances in soil and water; path intake of residues of drugs and their metabolites in the environment, their behavior (adsorption/desorption, distribution, decomposition) and their toxic effects in the environment; the possibility of bio-accumulation and toxic effects of residues of substances in aquatic and terrestrial organisms in the environment.

Code: V-1-700
Course title: Regulation processes in healthy and diseased animals

Contents:

Module 1: Regulation of basic processes in animals
Module 1 deals with morphological and functional characteristics of animal cell, cell as hereditary carrier, transfer of hereditary information on offspring, regulation of gene expression and cell signaling. It also covers biochemical and physiological processes and their neuroendocrine regulation crucial for maintenance of homeostasis and responsiveness of the organism to various environmental influences. It also enables students to expand their knowledge of progenesis, fertilization and early embryonic development in domestic animals, and to become acquainted with modern research methods.

Module 2: Disruption of homeostasis and disease processes
Module 2 deals in depth with main causes for disturbances and basic pathophysiological processes in organisms, important in developing and understanding of the mechanisms of disease and establishing clinical diagnosis and disease therapy. It enables recognition of organism dysfunction through morphological alterations in organs, tissues and cells and contribute to better understanding of organism response to the impact of harmful factors in disease processes. It also deals with the interconnection between changes in the biochemical parameters and the function of organ systems, mineral and electrolyte metabolism disturbances and the assessment of acid-bases balance and changes associated with the alimentary intoxications.

Module 3: Food safety
In module 3, students gain knowledge and understanding of positive and negative effect of interaction between human and animals, with an emphasis on consuming products of animal origin, using epidemiological and statistical tools to estimate the risk, gain new knowledge in the technology of meat and dairy processing industries, as well as fish processing industry, clams, crabs, frogs, eggs, honey and products from these commodities.
 

Elective courses

The various scientific fields offer a great variety of elective courses. The candidate can choose between elective theorethical courses and elective individual research courses evaluated with 5 credits. The courses are offered by professors who are also leading scientists in their respective scientific fields. Elective individual research courses are offered by researchers who can accept doctoral candidates in their laboratories, where they can aquire up-to-date scientific technologies and approaches to experimental work. A total of

10 elective credits can be selected from the university pool of generic skills courses, listed at the web page of University of Ljubljana (http://bit.ly/doktorski_studij).

Elective theoretical courses

Elective individual research courses

The core course schedules are published here in early September each year. Schedules for elective courses are designed individually.

The courses are coded with a capital letter and two numbers. The capital letter indicates the scientific field or a combination of fields. The first number indicates the type of the course and the second one consists of three digits, the first indicating the location and the last two the consecutive number of the course. 

Scientific fields:
G - Genetics
B - Biochemistry and Molecular Biology
F - Pharmacy
L - Clinical Biochemistry and Laboratory Biomedicine
J - Basic Medical Science
K - Clinical Medicine
M - Microbiology
N - Neuroscience
V - Veterinary Medicine
S – Public Health
T - Toxicology 

Types of courses:
1 – core courses
2 – elective theoretical courses
3 – elective individual research courses 

Course locations:

1 – Faculty of Medicine - Biochemistry and Molecular Biology
2 – Faculty of Pharmacy – Pharmacy
3 – Faculty of Pharmacy - Clinical Biochemistry and Laboratory Biomedicine, Toxicology
4 – Faculty of Medicine – Basic Medical Science, Public Health, Microbiology
5 – Faculty of Medicine, University Medical Centre Ljubljana, Institut of Oncology Ljubljana, University Psyhiatric Hospital Ljubljana – Clinical Medicine, Neuroscience
6 – Biotechnical Faculty - Microbiology, Genetics
7 – Veterinary Faculty – Veterinary Medicine
8 – Faculty of Chemistry and Chemical Technology
9 – research institutes: Josef Stefan Institute, Chemical Institute, National Institute of Biology

Hence, the course bearing the code B-2-940 belongs in the area of biochemistry and molecular biology (B), is an elective theoretical course (2) and is carried out at a research institute (9).

CORE COURSES:

B-1-100   Selected advanced topics in Biochemistry and Molecular biology
B-1-101     1  Selected metabolic processes with regulatory mechnisms
B-1-102     2 Strucure and function of biological molecules
B-1-103     3  Functional genomics and proteomics                 

F-1-200      Pharmaceutical sciences
F-1-211      1. 1 Drug structure and their properties
F-1-212      1. 2 Drug targets and interactions
F-1-213      1. 3 Drug design methodologies
F-1-221      2. 1 Biomolecules as targets for diagnosis and therapy
F-1-222      2. 2 Biological and gene medical products
F-1-223      2. 3 Herbal medicines
F-1-231      3. 1 Pharmacokinetics and its role in drug discovery and development
F-1-232      3. 2 Biopharmaceutical analysis of LADME processes
F-1-233      3. 3 Pharmacokinetic-pharmacodynamic analysis
F-1-241      4. 1 Pharmaceutical manufacturing proceses
F-1-242      4. 2 Drug delivery systems
F-1-243      4. 3 Pharmaceutical nanotechnology and nanomedicines
F-1-251      5. 1 Social  pharmacy
F-1-252      5. 2 Health economics
F-1-253      5. 3 Pharmacoepidemiology                

L-1-300      Algorithms of clinical biochemical diagnostics
L-1-310      1. Laboratory biomedicine
L-1-311            1. 1 Scientific approaches in laboratory medicine
L-1-312            1. 2 Stepwise approach to clinical and biochemical diagnostics with      interpretation
L-1-320      2. Molecular markers of diseases
L-1-321            2. 1 Common genetic diseases
L-1-322            2. 2 Immune diseases
L-1-323            2. 3 Malignant disorders 
L-1-330      3. Translational Biomedicine
L-1-331            3. 1 Pharmacogenomic diagnostics
L-1-332            3. 2 Cellular and Tissue Engineering
L-1-333            3. 3 Omic” Technologies and Tools (advanced technologies and tools in    translational biomedicine                

T-1-340      Toxicology
T-1-341     1. Relationship between structure and toxicity
T-1-342     2. Influence of toxic compounds on processes within cell
T-1-343     3. Influence of toxic compounds on environment and ecosystems                

J-1-400      Medical Cell Biology
J-1-401     1. Fundamentals of medical cell biology
J-1-402     2. Reproductive biology in vivo and in vitro
J-1-403     3. Biology of Malignant Cells and Translational Oncology
J-1-404     4. Cell biology in clinical genetics
J-1-405     5. Systems medicine of multifactorial disorders                

M-1-410     Selected Topics in Microbiology
M-1-411    1. Basic medical microbiology
M-1-412    2. Clinical microbiology
M-1-615    3. Microbial identification, diversity, and evolution                

S-1-420      Research aspects of public health
S-1-421      Determinants of health and disease
S-1-422      Methodology of public health interventions                 

K-1-500      Research in clinical medicine
K-1-510      1. Methods in medical research
K-1-520      2. Basic science in medical research
K-1-530      3. Achievements in clinical research
K-1-531           3. 1 Cardiovascular medical sciences
K-1-532           3. 2 Medical sciences of surgical disciplines
K-1-533           3. 3 Emergency and intensive medicine
K-1-534           3. 4 Hematology and oncology
K-1-535           3. 5 Hyperbaric medicine
K-1-536           3. 6 Immunology and allergology
K-1-537           3. 7 Imaging methods
K-1-538           3. 8 Genetic methods
K-1-539           3. 9 Physiology of the cardiovascular system
K-1-531           3. 10 Physiology of respiration
K-1-531           3. 11 Physiology and biomechanics of the locomotor system
K-1-531           3. 12 Basic and clinical pharmacology and drug development

N-1-540      Neuroscience

N-1-541      2. Basic neuroscience
N-1-542      3. 1 Clinical Neuroscience – Neurology
N-1-543      3. 2 Clinical Neuroscience – Psychiatry
N-1-544      3. 3 Clinical Neuroscience - Psychology                

G-1-600     Genetics
G-1-601     Genetic concepts I
G-1-602     Genetic concepts II
G-1-603     Bioinformatics tools                

V-1-700      Regulation processes in healthy and diseased animals
V-1-701     1. Regulation of basic processes in animals
V-1-702     2. Disruption of homeostasis and disease processes
V-1-703     3. Food safety