Lectures from school on bioinformatics from A to Z

In the summer of 2019, the summer school on bioinformatics was held for the seventh time - a weekly educational intensive for a hundred students and recent graduates from different cities and countries taking their first steps in this field.

Biologists, physicians, programmers, mathematicians, physicists, chemists - the most common specialties of school participants - conditionally divided into two streams of "biologists" and "computer scientists." Lectures and practices were devoted to various bioinformatics methods and their application in medicine and biology: from evolution to analysis of single-cell sequencing data and aging.

Below we share the overview, videos and slides of 15 past lectures. Marked with an asterisk "*" can be viewed without preparation or with basic knowledge.

Enjoy watching!



1. * Introduction to NGS Technologies | Barbitov Yuri, Institute of Bioinformatics

Video | Slides

Yuri talked about the basic methods of next generation sequencing (NGS) and the mechanisms that underlie data acquisition. The story explains the mechanism of action of the polymerase chain reaction (PCR), Senger sequencing, the difference between different second and third generation sequencing technologies. Separately, experimental approaches are given that allow one to obtain different types of data.



2. * Bioinformatics tricks for the analysis of ancient DNA | Tatyana Tatarinova, University of La Verne

Video | Slides

Ancient DNA attracts the attention of scientists as a source of data on species and organisms that are no longer alive at the present time. However, due to the poor preservation of DNA, the method of bioinformatic data processing is different and requires a large number of tricks. Tatyana talks about such approaches using the example of ancient DNA from the remains of the Khazar people.



3. Sequencing and analysis of cancer genomes | Sergey Aganezov, Johns Hopkins University

Video | Slides

Somatic mutations during the development of cancer can greatly change the karyotype of the genome in the cells and give them a population advantage, which leads to an uncontrolled proliferation of the malignant tumor. The analysis of structural genetic changes in the cells of such tumors plays an important role in studying the causes and understanding of the development of cancer.

The lecture shows how methods and knowledge from the fields of graph theory, combinatorics, and linear programming can be used to obtain a more accurate and informative picture of structural changes in the genome of cancer cells.

Sergey talked about algorithmic approaches for the restoration of rearranged genomic karyotypes in groups of cancer cells in sequenced heterogeneous malignant tumors. He also examined the difficulties that non-haploid genomes of healthy and cancer cells make, and described models for working with sequencing of heterogeneous cancers.



4. * "Non-ethereal" efforts of the mind: why mathematics and programming are in demand in biomed | Pyotr Vlasov, Institute of Science and Technology

Video | Slides

In modern biology, medicine and pharmacology, research and applied tasks are increasingly being created that require in-depth knowledge of the Physics and Mathematics and IT-technologies.

Why has the sharp increase in the volume of experimental and theoretical data brought the bio / medical field closer to the field of mathematics and IT? How exactly is the synergy of mathematical / programmatic approaches and a deep understanding of biology "projected" onto the modern development of drugs and personalized biomedicine? In recent years, we managed to understand what's new in the key genotype-phenotype relationship for biomedics, including in the context of a wide variety of diseases? How does this understanding reveal new “targets” for therapy? And why is it in such studies that good knowledge of mathematics and programming is in demand?

In his lecture, Peter discussed these and other issues using specific resources and tools for analyzing biomedical data, as well as some fundamental research problems.



5. * Editing the human genome at the embryo level | Denis Rebrikov, Russian National Research Medical University named after Pirogov

Video | Slides

The CRISPR genome editing system allows targeted changes to the nucleotide sequence of DNA. The lecturer talked about how using this technique you can make potential editing of human embryos at the zygote stage, what are the dangers and risks, and how do you evaluate the safety of the approach. Denis also gave an overview of the cloning technologies and scientific approaches that underlie these processes.



6. Why are B cells so different? | Ilaria Tarasova, Walter and Eliza Hall Institute of Medical Research

Video | Slides

How to transcribe activated lymphocytes with a transcript to understand the expression of which genes depends on time and which on the number of divisions? What are the differences between B cells and why so many functional types in the body? The answers to these and other questions are given by Ilaria in his lecture.



7. * Cutting and sewing courses: how designer proteins are used in medicine and biotechnology | Anton Chugunov, IBCh RAS, Biomolecule

Video | Slides

Anton told what approaches exist for directed modification and even design “from scratch” of proteins with the desired properties. But these are new drugs, and molecules for biotechnology, and even new opportunities in the energy sector.



8. Epigenetic regulation and aging | Oleg Shpinov, JetBrains Research

Video| Slides

Aging is the complex process that living organisms are subject to. In the lecture, Oleg examined the basic principles of epigenetic regulation, experimental and computational methods for data processing, including a comprehensive ChIP-Seq data analysis solution - JBR Genome Browser and SPAN Semisupervised Peak ANalyzer .

The lecture also mentions methylation hours, a method for predicting biological age by the level of chemical modifications of a DNA molecule. The audience concludes with a story about the study of the human epigenome in development and aging, which is conducted by Washington University in St. Louis and the JetBrains Research laboratory.



9. * Introduction to machine learning | Grigory Sapunov, Intento

Video| Slides

Machine Learning as a Field of Artificial Intelligence continues to attract the attention of researchers. We can say that this is an alternative to programming, which can help reveal patterns in data that are not visible to the ordinary eye. The lecturer tells in detail about each stage of model training and the importance of the quality of the data supplied to the input.



10. RNA-seq data analysis | Alexey Sergushichev, ITMO University

Video | Slides

RNA sequencing data (RNA-seq) allows you to evaluate the change in gene pool expression in tissues or entire organisms. Alexey spoke about protocols and RNA sequencing in general, quantification and approaches to the analysis of differential gene expression.



11. * Algorithms for assembling the genome | Andrey Przhibelsky, SPbSU TsAB

Video | Slides

Genome assembly is a complex algorithmic computational process. Andrei spoke about assembly algorithms based on graph de Bruyne and metrics, which are important to pay attention to during assembly.



12. Search for rare pathogenic alleles with great effect in the Finnish population | Vasily Ramensky, Federal State Budgetary Institution National Medical Research Center for Preventive Medicine of the Ministry of Health of Russia

Video | Slides

It is believed that rare genomic variants strongly affect the risks of developing common diseases and the significance of quantitative phenotypic traits. Despite the development of technology, modern research still lacks a sufficient number of samples to reliably identify such options.

In isolated populations that have gone through a stage of strong population decline, for example, in Finnish, harmful alleles can be observed with much higher frequencies than in ordinary populations. Sequencing of 78 genes in 6,000 Finns showed the importance of having large and well-described cohorts for the successful search for rare variants.

Sequencing of exoms of 20,000 inhabitants of northern and eastern Finland revealed 43 new associations of harmful variants with 25 characters. Most of the detected new harmful alleles are found in Finns with frequencies 10-100 times greater than in other European populations. To identify such options in other European populations would require samples of hundreds of thousands or even millions of individuals.

Vasily spoke about the fundamental possibility of detecting rare clinically significant variants by sequencing sufficiently large cohorts and the effectiveness of using isolated populations to solve such a problem.



13. * Search for biomarkers from proteomes and other expression data using machine learning methods | Elena Chuklina, ETH Zürich

Video |Slides

Elena spoke about the concept of biomarkers and how and how well machine learning works for their search. The lecture mentions different types of machine learning and provides a step-by-step implementation algorithm - Elena shows with examples how this can be used in medicine on real proteomic data and the results of the analysis of differential gene expression.



14. * In the world of proteomics | Pavel Sinitsyn, Max Planck Institute Of Biochemistry

Video | Slides

Pavel talks about various principles and approaches to obtaining data in proteomics. The lecturer explains in detail each step of data acquisition, peptide selection features and shows the difference in the approaches of bottom-up and top-down methods.



15. The study of brain development at the level of single cells | Konstantin Okonechnikov, German Cancer Research Center

Video | Slides

Konstantin in his lecture gives a detailed overview of single-cell sequencing technologies and shows how single-cell data can be used in brain research. Separately, the lecturer discusses approaches to the processing of single cell data.

In the end

Summer schools have been held annually since 2013, and many videos of different years have accumulated on the YouTube channel in the public domain with a wide coverage of topics.

And until May 1, applications for the summer school 2020 will be open , which will be held in St. Petersburg from July 27 to August 1. For those who want deeper knowledge - until February 22, you can catch a retraining program in bioinformatics in St. Petersburg and Moscow or at an on- site seminar on systems biology .

School 2019 was held thanks to the support of JetBrains , BIOCAD and EPAM , for which they are very grateful.

Bioinformatics to all and see you soon!

PS - Previous posts on Habré with an overview of lectures on bioinformatics: 2018 , 2017 , 2016 .