Materials of the summer school on bioinformatics

  • Tutorial
This summer, the first bioinformatics summer school was held in Moscow. It was attended by over 100 people who came from different parts of Russia and the CIS and were divided into two streams: “computer scientists” and “biologists”. The event was organized by the Institute of Bioinformatics in cooperation with SPbAU RAS, Moscow State University, IPPI RAS and GameChangers program.

About how the school itself went, our students already wrote on the hub . Now everyone, who did not have the opportunity to participate in the school, can get acquainted with the reports that interest him: we have posted all the videos of the lectures and all the slides of the presentations online.

If this is your first time hearing about bioinformatics, I advise you first to watch the introductory lectureAlla Lapidus, who will put everything in its place. Now Alla occupies a leading position in the center of genomic bioinformatics of St. Petersburg State University and in the laboratory of algorithmic biology at St. Petersburg University of Economics, and previously, for a long time, she led genome projects at DOE Joint Genome Institute (California).



Under the cutscene, you can see a list of all past lectures, including their brief descriptions that will help you navigate, as well as full videos in Russian.

And at the very beginning of this list, I want to say thank you very much to Kirill Grigoryev, who shot and processed all the videos from the school, Yaroslav Baranov and Pavel Yakovlev, who helped in the shooting, and also yasha_somov for help with the equipment.

The first day of the school was held at the biology faculty of Moscow State University and consisted of rather complicated lectures in which leading scientists talked about the latest trends in bioinformatics:

1. Bioinformatic approaches to the study of microevolution
Alexei Kondrashov (University of Michigan, Moscow State University)


The winner of the megagrant program, the head of the Laboratory for Evolutionary Genomics, FBB Moscow State University, Alexei Kondrashov, spoke about what microevolution and population are, what characteristics they have, what tasks are in the study of microevolution and the role of bioinformatics in this process. Such topics as variability of populations, mutational process, drift, negative, positive and balancing selection, reproduction, geographical structure of populations were considered. [slides]

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2. Genetic reprogramming of somatic cells: what bioinformatics gives us
Sergey Kiselev (IOGEN RAS)


The second lecture talked about the huge potential of stem cells and, in particular, induced pluripotent stem cells (iPSCs) for the development of the latest methods of cell therapy, the creation of model systems to study the mechanisms of diseases and the development of drugs. The lecture discussed the properties and functional markers of iPSC reprogramming, as well as how to create specific markers that distinguish stem cells and determine their fate using changes in DNA methylation, modification and transcription of histones in combination with bioinformatics methods. [slides]

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3. Reading the human genome as an instrument for improving some anthropological and historical hypotheses
Egor Prokhorchuk (Center for Bioengineering RAS)


Then it was told about the application of bioinformatics methods in anthropology, as well as the problem of ethics in the field of genetic research. In addition, an unexpected and interesting topic was touched on, such as a comparison of genetic and linguistic data. [slides]

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4. Molecular Features of the Evolution of the Human Brain
Philip Khaitovich (Shanghai Institutes for Biological Sciences)


Philip talked about the phenotype, genotype and the process of transition from phenotype to genotype; human brain development: brain transcript, specific expression of genes of various species and its differences, features and mechanisms in the human body; study of gene expression of people with autism; comparison of Neanderthals and modern people. [slides]

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Starting from the second day, the school was held in the suburbs. Lectures began with the simplest to understand, with a gradual increase in complexity by the end of school:

5. Bioinformatics and its applications
Alla Lapidus (Center for Genomic Bioinformatics, St. Petersburg State University, SPbAU RAS)


The history of the discipline and various interpretations of the concept of “bioinformatics”, as well as about the main areas of application of bioinformatics, including the use of bioinformatics in medicine, were told. [slides]

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6. Molecular biology for computer scientists
Natalya Volodina (SPbAU RAS)


Several lectures gave an introduction to molecular biology for students of non-biological specialties, including topics such as the structure and functions of DNA and RNA, the central dogma of molecular biology (DNA → RNA → protein), the structure of proteins and their functions, the main components of the cell and their functions. [slides 1] + [slides 2]

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7. Development of scientific software: best practices and approaches
Konstantin Okonechnikov (Max Planck Institute for Infection Biology, Berlin)


It was told about the recommended techniques and methods for developing scientific software. Many of these methods have long been known and successfully applied in the field of software development, but require adaptation to the "scientific environment". Special attention in the lecture is given to technologies for optimizing the performance of software systems. [slides]

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8. Simple methods for analyzing complex data
Philipp Haitovich (Shanghai Institutes for Biological Sciences)


In the second lecture, Philip spoke in more detail about the scope of his scientific activities, including the study of human-specific RNA in comparison with other mammals, such as chimpanzees and mice; brain aging processes; long non-coding RNA. [slides]

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9. Analysis of NGS data
Andrey Przhibelsky (SPbAU RAS)


They told about the history of sequencing, gave an overview of popular and developing technologies today, described their features and applications. The lecture discusses in detail the process and existing programs for assembling the genome, and also answers the question of whether there is a single best assembler. [slides]

Posts by Andrei andrewprzh on this subject on the hub: Bioinformatics: an inside look and Again on bioinformatics: assembling bacterial genomes .

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10. Introduction to RNA reading
Konstantin Okonechnikov (Max Planck Institute for Infection Biology, Berlin)


The transcriptome sequencing technologies and data analysis techniques specific to this type of experiment were described, including methods for aligning short reads taking into account splicing, transcript assembly, isoform reconstruction methods, comparative analysis of gene expression, as well as methods for searching for strains in the genome and fusion genes (fusion genes). [slides]

Video


11. Graphs de Bruyne and assembly algorithms
Sergey Nurk (SPbAU RAS)


It was told about the statement of the problem of genome assembly and the use of graphs de Bruyne to solve it. The lecture also discusses various issues related to sequencing errors or lack of resources. [slides]

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12. Bioinformatics in the laboratory: understanding the next generation sequencing data
Konstantin Okonechnikov (Max Planck Institute for Infection Biology, Berlin)


It was told about various computer programs that allow the analysis of Next Generation Sequencing (NGS) data, and about the principles that allow them to be combined and used effectively. [slides]

Video


13. Applications and sequencing databases
Alla Lapidus (Center for Genomic Bioinformatics, St. Petersburg State University, St. Petersburg Academy of Sciences)


In her second lecture, Alla talked about the history of the development of sequencing technologies and the diversity of existing biological databases, which is dictated by the variety of challenges and the growing application of these technologies at present (for example, in personalized medicine). [slides]

Video


14. Investing in biotechnology: obvious and non-obvious stories
Andrei Afanasyev (iBinom, Moscow State University)


This lecture talked about several biotechnological projects through the eyes of innovators and investors, and also presented in detail the personal experience of the speaker, who is the founder of the bioinformatic startup iBinom, in interacting with venture funds and development institutions. [slides]

Video


15. Assembly and annotation of large genomes
Pavel Dobrynin (Center for Genomic Bioinformatics, St. Petersburg State University)


Libraries for sequencing and sequencing, chromosome assembly, the use of reference genomes of closely related species, and various aspects of gene annotation were discussed. [slides]

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16. Medical bioinformatics: present and trends
Alexander Pavlov, Anton Bragin (Sequoia Genetics)


It was told about the main applications of bioinformatics in medicine and promising directions of its development; about genomic medicine, tasks and requirements for the quality of clinical data, approaches to their production and translation. The second part of the lecture is devoted to the technical aspects of creating software designed for the clinical interpretation of bioinformatics data (basic methods for constructing analysis pipelines, modular organization, existing frameworks and services specific to biomedical software, design features). [slides]

Video


17. Miniconference (student presentations)


The mini-conference was held in the format of presentations by participants of the summer school, moderated by Mikhail Raiko (SPbSU, SPbAU RAS). At the stage of competitive selection, it was possible to submit abstracts, and the selected 13 people spoke about their research in the format of fifteen-minute reports. Detailed topics and slides of speakers can be found on the website .

18. Analysis of NGS data
Andrey Przhibelsky (SPbAU RAS)


In the framework of this seminar for computer scientists, detailed information was provided about effective algorithms and methods for analyzing NGS data. In the second part of the seminar, Anton Korobeinikov joined Andrey Przhibelsky, also from the Laboratory of Algorithmic Biology, St. Petersburg University of Economics.

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19. Overview of Biotechnology
Alexander Karabelsky (BIOCAD)


It was told about the modern directions of research in the field of monoclonal antibodies, their types, properties and spectrum of application are described, and the development process is examined in detail with a review of its stages and methods used (for example, the biotechnological company BIOCAD). [slides]

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20. Bioinformatics of DNA-protein interaction and regulation of genes
Vsevolod Makeev (IOGEN RAS, MIPT)


It was told how the DNA sequences of different species differ, why similar genes work differently, and why specific genes work at a particular point in time (in a particular tissue). Issues such as RNA synthesis and subsequent stages, tissue-specific expression, regulation and transcriptional regulators are covered, as well as an overview of various methods and technologies for studying DNA-protein interaction and gene regulation and a comparison of existing programs. [slides]

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21. E-value at BLAST
Anton Korobeinikov (SPbAU RAS, SPbSU)


Two lectures filled with mathematics talked about statistical principles and results that allow us to evaluate the significance of coincidences between strings and to distinguish truly nonrandom coincidences from random ones (for bioinformatics BLAST is a standard tool for finding similarity between sequences of proteins and nucleotides, the most cited scientific article 90 years). It is assumed that the student is familiar with the basic concepts of statistics and probability theory (distribution, random variable, average, estimate, statistical hypothesis).

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22. Biotechnology for biologists
Alexander Karabelsky (BIOCAD)


In his second lecture, Alexander spoke on the example of BIOCAD about the structure and organization of work of modern pharmaceutical companies, the types and properties of drugs for the treatment of cancer and autoimmune diseases, immunoglobulins and the reasons for their diversity, the use of antibodies and their properties in therapy, as well as other related topics. [slides]

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23. My first 100 projects on IonTorrent: the story of bioinformatics
Dmitry Alekseev (Research Institute of FHM)


Practical experience and the results of using IonTorrent equipment for various purposes were described: reading and assembling the genome, reservations, paired read library, metagenomics, 16S analysis and others. [slides]

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24. Writing for Scientists
Natalya Kuznetsova (IBCh RAS)


They talked about the rules and techniques for writing scientific articles in English, the correct use of vocabulary, punctuation, text structure and common mistakes. [slides]

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25. Dynamics of synthetic networks of gene regulation
Mikhail Ivanchenko (UNN)


This lecture talked about the construction of artificial regulatory networks with predetermined behavior, for example, fluorescently oscillating colonies of bacteria, as well as the necessary mathematical models and methods for their study, the most important theoretical and experimental results obtained in this area, and a number of open topical problems. [slides]

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26. Dynamics of synthetic networks of gene regulation
Alexey Zaikin (University College London)


In the next lecture, Alexei, Mikhail’s colleague, continued the topic of building artificial regulatory networks with complex dynamics. [slides]

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27. Bioinformational assessment of the perfection of human stem cells
Maria Shutova (IOGEN RAS)


In this scientific report, Maria, an employee of the laboratory of Sergey Kiselyov (who gave a lecture on genetic reprogramming of somatic cells on the first day), spoke about comparing embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) of different genetic nature and solving the problem of proof their identity. The lecture talked about creating an isogenic system that allows comparisons of expression (Illumina HT12) and CpG methylation (Illumina 450k) of hESCs, differentiated cells and iPSCs. The story covers the molecular and bioinformation methods used in the analysis, as well as the preliminary results of this study are announced. [slides]

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28. Using maps in the assembly of genomes
Alexey Makunin (Center for Genomic Bioinformatics, St. Petersburg State University)


Despite the fact that the last lecture of the school took place at 10 a.m. on Saturday (after Friday's farewell evening), almost all school participants were able to attend it, and Alexey spoke about various methods of mapping genomes - from using BAC clones to the method of radiation hybrids and assembling with the use of closely related reference genomes, including determining the order of scaffolds, which is an important step for assembling and finishing genomes. [slides]

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Finally


Given the great interest in the school and the positive feedback from the participants, we decided to conduct it annually. In the summer of 2014, the school will be held in St. Petersburg. In addition, if you are interested in the topic, then sign up for the beginning online course on algorithms in bioinformatics at Coursera (the hub of the course ).

I would also like to thank the team of school organizers - Katya Chaykina and Anya Chernysh - without whom the school would not have taken place, as well as all the friends and volunteers who helped us. And, of course, our good sponsors, especially the well-known JetBrains company for the stable support of the Institute of Bioinformatics over the past three years. And also: Russian venture capital company, Dynasty funds and the Russian Federal Property Fund; BIOCAD, Diaem and Life Technologies.

A beautiful report on the results of the school can be read here (carefully, PDF 6.5 MB) .

Institute of Bioinformatics: website , twitter , Vkontakte , summer school on bioinformatics 2014 .

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