In the summer of 2018, an annual summer school on bioinformatics was held near St. Petersburg, where 100 undergraduate and graduate students came to study bioinformatics and learn about its use in various fields of biology and medicine.
The main focus of this school was on cancer research, but there were lectures in other areas of bioinformatics, ranging from evolution to the analysis of single-cell sequencing data. During the week, the guys learned how to work with next-generation sequencing data, programmed in Python and R, used standard bioinformatics tools and frameworks, got acquainted with the methods of systems biology, population genetics and drug modeling in the study of tumors, and much more.
Below you will find a video of 18 lectures given at the school, with a brief description and slides. Those marked with an asterisk "*" are quite basic, they can be watched without prior preparation.
1*. Oncogenomics and personalized oncology | Mikhail Pyatnitsky, Research Institute of Biomedical Chemistry
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Mikhail briefly spoke about the genomics of tumors and how understanding the evolution of cancer cells allows us to solve practical problems of oncology. The lecturer paid special attention to explaining the difference between oncogenes and oncosuppressors, methods of searching for "cancer genes" and identifying molecular subtypes of tumors. In conclusion, Mikhail paid attention to the future of oncogenomics and the problems that may arise.
2*. Genetic diagnostics of hereditary tumor syndromes | Andrey Afanasiev, yRisk
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Andrei spoke about hereditary tumor syndromes and analyzed their biology, epidemiology and clinical manifestations. Part of the lecture is devoted to the issue of genetic testing - who needs to undergo it, what is being done for this, what difficulties arise in processing data and interpreting the results, and, finally, what benefits it brings to patients and their relatives.
3*. The Pan-Cancer Atlas | German Demidov, BIST/UPF
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Despite decades of research in the field of genomics and epigenomics of cancer, the answer to the question "how, where and why do tumor syndromes occur" is still not complete. One of the reasons for this is the need for a standardized acquisition and processing of huge amounts of data in order to detect effects of small magnitude, which are difficult to detect in a limited data set (and this is the size that is typical for a study within one or more laboratories), but which collectively play a role. a huge role in such a complex and multifactorial disease as cancer.
In the past few years, many of the strongest research groups in the world, realizing this problem, began to join their efforts in an attempt to detect and describe all these effects. Herman spoke about one of these initiatives (The PanCancer Atlas) and the results obtained as part of the work of this consortium of laboratories and published in a special issue of Cell in this lecture.
4. ChIP-Seq in the study of epigenetic mechanisms | Oleg Shpynov, JetBrains Research
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Gene expression is regulated in a variety of ways. At his lecture, Oleg spoke about epigenetic regulation by modifying histones, studying these processes using the ChIP-seq method, and methods for analyzing the results.
5. Multiomics in cancer research | Konstantin Okonechnikov, German Cancer Research Center
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The development of experimental technologies in molecular biology has made it possible to combine the study of a wide range of functional processes in cells, organs, or even the whole organism. To establish links between the components of biological processes, it is necessary to use multiomics, which combines massive experimental data from genomics, transcriptomics, epigenomics, and proteomics. Konstantin gave illustrative examples of the use of multiomics in the field of cancer research with a focus on pediatric oncology.
6. Versatility and limitations of single cell analysis | Konstantin Okonechnikov
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A more detailed lecture on single cell RNA sequencing and methods for analyzing this data, as well as ways to overcome obvious and hidden problems in their study.
7. Analysis of single-cell RNA-seq data | Konstantin Zaitsev, Washington University in St. Louis
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Introductory lecture on single cell sequencing. Konstantin discusses sequencing methods, challenges in the lab and bioinformatics stages, and ways to overcome them.
8. Diagnosis of muscular dystrophy using nanoscale sequencing | Pavel Avdeev, George Washington University
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Sequencing using Oxford Nanopore technology has advantages that can be used to identify the genetic causes of diseases such as muscular dystrophy. In his lecture, Pavel spoke about the development of a pipeline for diagnosing this disease.
9*. Graph representation of the genome | Ilya Minkin, Pennsylvania State University
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Graph models allow a compact representation of a large number of similar sequences and are often used in genomics. Ilya spoke in detail about how graphs are used to restore genomic sequences, how and why the de Bruyn graph is used, how much such a βgraphβ approach increases the accuracy of mutation search, and what unresolved problems with the use of graphs still remain.
10*. Entertaining proteomics | Pavel Sinitsyn, Max Planck Institute of Biochemistry (2 parts)
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Proteins are responsible for most of the biochemical processes in a living organism, and so far proteomics is the only method of global analysis of the state of thousands of proteins simultaneously. The range of tasks to be solved is impressive - from identifying antibodies and antigens to determining the localization of several thousand proteins. In his lectures, Pavel talked about these and other applications of proteomics, its current development and pitfalls in data analysis.
eleven*. Basic principles of molecular simulations | Pavel Yakovlev, BIOCAD
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An introductory theoretical lecture on molecular dynamics: why is it needed, what does it do and how is it used in relation to drug development. Pavel paid attention to the methods of molecular dynamics, the explanation of molecular forces, the description of relationships, the concepts of "force field" and "integration", limitations in modeling, and much more.
12*. Molecular biology and genetics | Yuri Barbitov, Institute of Bioinformatics
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A three-part introduction to molecular biology and genetics for undergraduate and graduate students of engineering. The first lecture discusses the concepts of modern biology, questions of the structure of the genome and the occurrence of mutations. The second covers in detail the issues of gene functioning, the processes of transcription and translation, the third covers the regulation of gene expression and basic molecular biological methods.
13*. Principles of NGS Data Analysis | Yuri Barbitov, Institute of Bioinformatics
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The lecture talks about second generation sequencing (NGS) methods, their types and characteristics. The lecturer explains in detail how the output data from the sequencer is structured, how it is converted for analysis, and what are the ways to work with it.
14*. Using the command line, practice | Gennady Zakharov, EPAM
A practical overview of useful Linux command line commands, options, and the basics of their use. The examples are directed to the analysis of sequenced DNA sequences. In addition to standard Linux operations (for example, cat, grep, sed, awk), utilities for working with sequences (samtools, bedtools) are considered.
15*. Data visualization for the little ones | Nikita Alekseev, ITMO University
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Everyone happened to illustrate the results of their scientific projects or understand other people's diagrams, graphs and pictures. Nikita told how to correctly interpret graphs and diagrams, highlighting the main thing from them; how to draw clear pictures. The lecturer also emphasized what to look for when reading an article or watching a commercial.
16*. Careers in bioinformatics | Victoria Korzhova, Max Planck Institute of Biochemistry
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Victoria spoke about the structure of academic science abroad and what you need to pay attention to in order to build a career in science or industry as an undergraduate, graduate or postgraduate student.
17*. How to write a CV for a scientist | Victoria Korzhova, Max Planck Institute of Biochemistry
What to leave in the CV and what to remove? What facts will be of interest to a potential head of the lab, and which ones are better not to mention? How to arrange information so that your resume attracts attention? The lecture will provide answers to these and other questions.
18*. How the bioinformatics market works | Andrey Afanasiev, yRisk
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How does the market work and where does bioinformatics work? The answer to this question is detailed, with examples and advice, in Andrey's lecture.
the end
As you may have noticed, the lectures at the school are quite broad in terms of topics - from molecular modeling and the use of graphs to assemble the genome, to the analysis of single cells and building a scientific career. We at the Institute of Bioinformatics try to include a variety of topics in the school program in order to cover as many bioinformatics disciplines as possible, and so that each participant learns something new and useful for himself.
The next bioinformatics school will be held from July 29 to August 3, 2019 near Moscow. . This year's theme will be bioinformatics in developmental biology and aging research.
For those who want to study bioinformatics in depth, we continue to accept applications for our in St. Petersburg. Or follow our news about the opening of the program in Moscow this autumn.
For those who are not in St. Petersburg or Moscow, but really want to become a bioinformatician, we have prepared on algorithms, programming, genetics and biology.
We also have dozens which you can start going through right now.
In 2018, the Bioinformatics Summer School was held with the support of our long-term partners - JetBrains, BIOCAD and EPAM, for which many thanks to them.
All bioinformatics!
PS If it seemed to you a little, ΠΈ .
Source: habr.com