Bioinformatics course

General description

The main goal of the "Bioinformatics" course is to prepare students and postgraduates to work with large data sets related to DNA analysis or mass spectroscopy. It will be especially useful for students who plan to change higher education institutions when entering a master's or postgraduate program.

The bioinformatics course was organized by the Explogen LLC company and with the participation of experts from the Ivan Franko National University of Lviv. Therefore, there will be an opportunity to communicate with people who are making money with their knowledge and skills in genome sequencing and analysis.

The course is designed for undergraduate, master’s, and postgraduate students of biological specialties (regardless of the course of study and institution of higher education). The maximum number of participants is 30. If there are more interested people, we will offer free participation in the lectures (without awarding a certificate).

The duration of the course is 6 weeks (from 20.09.2022 to 01.11.2022), 30 hours (1 ECTS credit). Classes (lectures and practical/seminars) will be held online at times that do not overlap with students' main studies at universities.

Credits for the course can be credited to the main place of study. To date, confirmation letters on the approval of course credits for undergraduate students of biological specialties have been received from five universities: Kherson State University, Odesa Mechnikov National University, Vasyl Stefanyk Precarpathian National University, Oles Honchar Dnipro National University, and Karazin Kharkiv National University.

Registration: until 15.09.2022 (closed)

If there are more applications than the grant program (maximum 30), then in the official registration, priority will be given to students and postgraduates of partner universities and students who have suffered greatly due to the war and have not yet completed the relevant courses. For another 30 participants, we will offer free participation in lectures (without awarding a certificate).

Scholarship: 30 scholarships of 200 euros. If there are more applicants for the scholarship, priority will be given to students who lived in areas close to hostilities and who had to move to another region of Ukraine. It is also important whether students have taken part in the offered courses. Successful completion of the exam is assumed after completion of the course.

After sending the completed registration form, everyone who sent the application will receive a letter to the e-mail box with a notification about the registration/rejection and the possible receipt/non-receipt of the scholarship.


The course was given from 20 September to November 1, 2022. About 300 participants from 36 Ukrainian universities applied to participate in the course. 34 students were selected for the course and 30 of them received a scholarship in the amount of 200 Eur. 31 student successfully passed the final exam and received certificates of completion (1 ECTS credit). Additionally, due to high interest to the course, 152 students were given the opportunity to attend the lecture part of the course.

Details of the curriculum

Download of lectures and other teaching material

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Introduction to Bioinformatics.

The emergence of the term and the modern definition of bioinformatics. Pioneering works of Prof. Margaret Oakley Dayhoff. From gene to trait. Relationships between bioinformatics, computing and systems biology. Modern bioinformatics problems.

Databases. Pairwise sequence alignment.

Bioinformatic databases - model of the National Center for Biotechnology Information (NCBI): PubMed; Taxonomy; GenBank; Genome; Gene Expression Omnibus (GEO) datasets.  Specialized databases - on the example of PATRIC. The concept of a pairwise alignment, basic terms (coincidences, discrepancies, gaps). Homology of sequences. Methods for evaluation of pairwise alignments. Algorithms - dynamic programming (ACS) and heuristic (BLAST). Demonstration of the BLAST web service interface. Karlin-Altschul statistics and the Expectation number (E).

Multiple sequence alignment (MSA).

Progressive methods of multiple sequence alignment. New tools of multiple sequence alignment (T-COFFEE, MUSCLE, MSAProbs). Models based on a multiple sequence alignment – consensus sequence, position-specific score matrices (PSSM), Weblogo, Hidden Markov model (HMM). Main web services based on HMM (TMHMM, GeneMark, Pfam, HHPred).

DNA sequencing.

The principles. DNA sequencing by Sanger. Genome sequencing approaches before NGS. Next generation DNA sequencing. Illumina and 454 GS20. Oxford Nanopore and PacBio.

Principles of DNA sequence assembly.

Type of assemblers (de-bruijn-graph DBG and overlap–layout–consensus OLC). Pros and cons of de novo vs mapping to reference. NGS assemblers - PHRAP/Consed, Newbler, Velvet, Spades. 3-rd generation assemblers. CANU, Flye, Shasta. Genome annotation tools.

Biology and evolution.

Origin of genetic variation and basic concepts of evolutionary biology and molecular evolution. Evolutionary forces, fate of alleles in the population.

Neutral evolution, mutation/drift equilibrium.

Wondering in the space of genotypes.

Methods of phylogenetic reconstruction.

Phylogenetic trees: nomenclature, tree-thinking, editing and format conversion. Three main approaches to the evolutionary history reconstruction. Distance based methods, Likelihood methods and Bayesian inference phylogenetic reconstructions. Substitution models. Multilocus analysis of phylogenies, coalescent methods.

Application of phylogenetics. Phylogenomics.

Phylogeny as a backbone and null model of evolutionary biology. Population history, demography and selection. Method of phylogenetics contrasts. Test for selection. Fst outliers. Challenges and limitations of whole genome based phylogenetic reconstruction.  Genotyping by sequencing and artificial data downscaling. DdRAD sequencing.

Sources of biomedical data. Monogenic human disorders.

Comparative description of scientific and clinical studies. Principles of EBM (evidence-based medicine). Types of clinical trials.  What are Clinical Practice Guidelines, how to find and use them. The main sources of clinical data: NCBI Clinical Trials, Database, Medscape, Cochrane Library.  Alternative open access Big Data sources. Pattern of inheritance. Linkage analysis. Working with OMIM (An Online Catalog of Human Genes and Genetic Disorders). Molecular and gene therapy of monogenic.

NGS (Next Generation Sequencing) in clinical practice.

NGS workflow. Bioinformatics analysis of NGS data. Commonly used tools for NGS data analysis. Modern nomenclature of NGS results. Criteria for NGS interpretation, prediction algorithms and necessarily databases. Clinical application of NGS. Clinical cases presentation.

Complex human traits.

GWAS analysis. Genetics and environmental factors measurement. Genome-Wide Association Study (GWAS) - method description. GWAS catalog. Interpretation of genomic study; definition of absolute risk, relative risk, odds ratio. Examples of GWAS success (diabetes, hypertension, schizophrenia, cancer). Genome study value in clinical practice.

BLAST search and results interpretation.
Introduction to genome browsers.
Algorithm of phylogenetic analysis.
Biomedical databases. The basic principles of search and evaluation of clinical data.
Undergraduate students, master students, PhD students
12 lectures
Practical classes
3 lesson
6 weeks
1 ECTS credit
Date Time Lecturer Subject
20 September, Tue 18:00 Bohdan Ostash Lecture 1. Introduction to Bioinformatics.
22 September, Thu 18:00 Bohdan Ostash Lecture 2. Databases. Pairwise sequence alignment.
25 September, Set 10:00 Bohdan Ostash Seminar, group 1: BLAST search and results interpretation.
25 September, Sun 12:00 Bohdan Ostash Seminar, group 2: BLAST search and results interpretation.
27 September, Tue 18:00 Bohdan Ostash Lecture 3. Multiple sequence alignment (MSA).
29 September, Thu 18:00 Markiyan Samborskyy Lecture 4. DNA sequencing.
2 October, Sun 10:00 Yuriy Rebets Practical class 1: Introduction to genome browsers.
4 October, Tue 18:00 Markiyan Samborskyy Lecture 5. Principles of DNA sequence assembly.
6 October, Thu 18:00 Oleksandr Zinenko Lecture 6. Biology and evolution.
9 October, Sun 10:00 Yuriy Rebets Practical class 2: Introduction to genome browsers.
9 October, Sun 12:00 Yuriy Rebets Practical class 3: Introduction to genome browsers.
11 October, Tue 18:00 Oleksandr Zinenko Lecture 7. Neutral evolution, mutation/drift equilibrium.
13 October, Thu 18:00 Oleksandr Zinenko Lecture 8. Methods of phylogenetic reconstruction.
16 October, Sun 10:00 Oleksandr Zinenko Seminar, group 1: Algorithm of phylogenetic analysis.
16 October, Sun 12:00 Oleksandr Zinenko Seminar, group 2: Algorithm of phylogenetic analysis.
18 October, Tue 18:00 Oleksandr Zinenko Lecture 9. Application of phylogenetics. Phylogenomics.
20 October, Thu 18:00 Nataliya Matiytsiv Lecture 10. Sources of biomedical data. Monogenic human disorders.
25 October, Tue 18:00 Nataliya Matiytsiv Lecture 11. NGS (Next Generation Sequencing) in clinical practice.
27 October, Thu 18:00 Nataliya Matiytsiv Lecture 12. Complex human traits.
30 October, Sun 10:00 Nataliya Matiytsiv Seminar, group 1: Biomedical databases. The basic principles of search and evaluation of clinical data.
30 October, Sun 12:00 Nataliya Matiytsiv Seminar, group 2: Biomedical databases. The basic principles of search and evaluation of clinical data.
1 November, Tue 18:00  



Professor at the Department of Genetics and Biotechnology, Ivan Franko National University of Lviv.

Chief Bioinformatics Scientist, Cofounder Explogen LLC: Lviv, UA

Associate Professor at the Department of Genetics and Biotechnology, Ivan Franko National University of Lviv.

Candidate of science (PhD) The Museum of Nature at V. N. Karazin Kharkiv National University, Kharkiv

Chief Research Officer at Explogen LLC, Lviv.

I graduated from the Department of Genetics and Biotechnology of Ivan Franko Lviv National University in 2001 and received PhD in molecular genetics in 2005.

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