Materials of the summer school on bioinformatics
This summer, the first summer bioinformatics school was held in Moscow. It was attended by more than 100 people who came from different parts of Russia and the CIS and were divided into two streams: "computer science" and "biologists". The event was organized by the Institute of Bioinformatics in collaboration with SPbAU RAS, Moscow State University, IITP RAS and the GameChangers program.
About how was the school itself, our students have already written on Habré. Now everyone who has not had the opportunity to participate in the school can familiarize himself with the reports he is interested in: we have posted all the videos of lectures and all the slides of the presentations online.
If you hear about bioinformatics for the first time, then I advise you first of all to look at the introductory lecture by Alla Lapidus, who will put everything in its place. Now Alla occupies a leading position in the Center for Genomic Bioinformatics at St. Petersburg State University and in the Laboratory of Algorithmic Biology at SPbAU RAS, and earlier for a long time she led genome projects at the DOE Joint Genome Institute (California).
')
Under the cat 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 a huge thank you to Kirill Grigoriev, who filmed and processed all videos from school free of charge, Yaroslav Baranov and Pavel Yakovlev, who helped in the shooting, as well as yasha_somov for help with the equipment.
The first day of school was spent on the biological faculty of Moscow State University and consisted of quite complex lectures, in which leading scientists told about the latest trends in bioinformatics:
1. Bioinformatics approaches to the study of microevolution
The winner of the megagrant program, the head of the Evolutionary Genomics Laboratory at the Moscow State University, Alexey 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. The following topics were considered: population variability, mutation process, drift, negative, positive and balancing selection, reproduction, geographical structure of populations. [slides]
2. Genetic reprogramming of somatic cells: what bioinformatics gives us
In the second lecture, the enormous potential of stem cells and, in particular, induced pluripotent stem cells (IPSC) for the development of new methods of cell therapy, the creation of model systems to study the mechanisms of diseases and the development of drugs were discussed. The lecture discussed the properties and functional markers of the reprogramming of iPSCs, and also described how, using changes in DNA methylation, modification and transcription of histones in combination with bioinformatic methods, create specific markers that distinguish stem cells and determine their fate. [slides]
3. Reading the human genome as a tool for improving some anthropological and historical hypotheses
Further, 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, such an unexpected and interesting topic as the comparison of genetic and linguistic data was touched upon. [slides]
4. Molecular features of the evolution of the human brain
Philip told about the phenotype, genotype and the process of transition from phenotype to genotype; the development of the human brain: the transcript of the brain, the specific expression of genes of various species and its differences, features and mechanisms in the human body; gene expression studies of people with autism; comparison of Neanderthals and modern people. [slides]
Starting from the second day, the school was held in the suburbs. Lectures began with the most simple to understand, with a gradual increase in complexity by the end of the school:
5. Bioinformatics and its applications
The history of the discipline and various interpretations of the concept of “bioinformatics” were told, as well as about the main areas of application of bioinformatics, including the use of bioinformatics in medicine. [slides]
6. Molecular biology for informatics
In several lectures, an introduction to molecular biology was given to non-biological students, including such topics 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]
7. Development of scientific software: best practices and approaches
It was told about the recommended methods and ways of developing scientific software. Many of these methods have long been known and successfully used in software development, but they require adaptation to the “scientific environment”. Special attention is given in the lecture to technologies for optimizing the performance of software systems. [slides]
8. Simple ways to analyze complex data.
In the second lecture, Philip spoke in more detail about the field of his scientific work, including the study of human-specific RNA compared to other mammals, such as chimpanzees and mice; brain aging processes; long non-coding RNA. [slides]
9. Analysis of NGS data
It was told about the history of sequencing, gave an overview of popular and emerging technologies today, described their features and applications. The lecture discusses in detail the process and the existing programs for assembling the genome, and also gives an answer to the question whether there is a single best assembler. [slides]
Posts of Andrew andrewprzh on this topic on Habré: Bioinformatics: a look from the inside and again about bioinformatics: the assembly of bacterial genomes .
10. Introduction to RNA reading
It was told about transcriptome sequencing technologies and data analysis techniques specific for this type of experiment, including methods for leveling short reads with regard to splicing, assembly of transcripts, methods of isoform reconstruction, comparative analysis of gene expression, and methods for searching for deformations in the genome and fusion genes (fusion genes). [slides]
11. De Bruyn graphs and assembly algorithms
It was told about the formulation of the genome assembly problem and the use of the De Bruyn graphs for its solution. The lecture also discusses various problems associated with sequencing errors or lack of resources. [slides]
12. Bioinformatics in the laboratory: understanding the next-generation sequencing data
It was told about various computer programs that allow analyzing the Next Generation Sequencing (NGS) data, and about the principles that allow them to be effectively combined and used. [slides]
13. Applications and sequencing databases
In her second lecture, Alla told about the history of the development of sequencing technologies and the diversity of existing biological databases, which is dictated by the diversity of the challenges and the growing application of these technologies at present (for example, in personalized medicine). [slides]
14. Investments in biotech: obvious and non-obvious stories
This lecture was about several biotech projects through the eyes of innovators and investors, and also presented the personal experience of the speaker, who is the founder of the bioinformatics startup iBinom, on interaction with venture funds and development institutions. [slides]
15. Assembly and annotation of large genomes.
It was told about libraries for sequencing and resequencing, chromosome assembly, the use of reference genomes of closely related species and various aspects of gene annotation. [slides]
16. Medical bioinformatics: present and trends
It was told about the main applications of bioinformatics in medicine and promising directions of its development; on genomic medicine, objectives 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 for the clinical interpretation of bioinformatic data (basic methods for building analysis pipelines, modular organization, existing frameworks and services specific to biomedical software, design features). [slides]
The mini-conference was held in the format of presentations of the participants of the summer school, which was moderated by Mikhail Raiko (SPSU, SPbAU RAS). At the competitive selection stage there was an opportunity to submit abstracts, and the selected 13 people spoke about their research in fifteen-minute reports. Detailed topics and slides of the speakers can be found on the website .
18. Analysis of NGS data
In the framework of this seminar for informatics, it is detailed about efficient algorithms and methods for analyzing NGS data. In the second part of the seminar, Anton Korobeinikov, also from the algorithmic biology laboratory of the St. Petersburg University of the Russian Academy of Sciences, joined Andrei Przhibelsky.
19. Review of biotechnology
It was told about modern directions of research in the field of monoclonal antibodies, described their types, properties and range of applications, as well as analyzed in detail the development process with consideration of its stages and methods used (for example, biotechnological company BIOCAD). [slides]
20. Bioinformatics of DNA-protein interaction and gene regulation
It was told about the difference between DNA sequences of different species, why similar genes work in different ways and why specific genes work at a specific point in time (in a particular tissue). Issues such as RNA synthesis and subsequent stages, tissue-specific expression, regulation and transcription regulators are covered, as well as an overview of various methods and technologies for studying DNA-protein interaction and gene regulation and comparing existing programs. [slides]
21. E-value in BLAST
In two lectures, filled with mathematics, they talked about statistical principles and results, allowing to evaluate the significance of matches between strings and to distinguish truly non-random coincidences from random ones (for bioinformatics BLAST is a standard tool for searching for similarity between protein and nucleotide sequences, the most cited scientific article 90 s) It is assumed that the listener of the lecture is familiar with the basic concepts of statistics and probability theory (distribution, random variable, mean, estimation, statistical hypothesis).
22. Biotechnology for biologists
In his second lecture, Alexander spoke on the example of the company BIOCAD about the structure and organization 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]
23. My first 100 projects on IonTorrent: bioinformatics story
It was told about practical experience and results of using IonTorrent equipment for various purposes: reading and assembling genome, resolution, libraries of paired reads, metagenomics, 16S analysis and others. [slides]
24. Writing for Scientists
It was told about the rules and methods of writing scientific articles in English, proper use of vocabulary, punctuation, structure of the text and common mistakes. [slides]
25. Dynamics of synthetic networks of gene regulation
This lecture dealt with the construction of artificial regulatory networks with a given behavior, such as 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, a number of open topical problems. [slides]
26. Dynamics of synthetic networks of gene regulation
In the next lecture, Alexey, a colleague of Michael, continued the topic of building artificial regulatory networks with complex dynamics. [slides]
27. Bioinformatics assessment of human stem cell perfection
In this research report, Maria, an employee of the laboratory of Sergey Kiselyov (who gave a lecture on the genetic reprogramming of somatic cells on the first day), spoke about the comparison of embryonic stem cells (ESCs) and induced pluripotent stem cells (IPSCs), which have a different genetic nature and solve evidence problems their identities. The lecture dealt with the creation of an isogenic system that allows for comparisons of expression (Illumina HT12) and CpG methylation (Illumina 450k) of ESCs, differentiated cells and iPSCs. The story highlights the molecular and bioinformatics methods used in the analysis, as well as the preliminary results of this study. [slides]
28. The use of maps in the assembly of genomes
Despite the fact that the last lecture of the school was held at 10 am on Saturday (after Friday's farewell evening), almost all school participants were able to visit it, and Alexey talked about different ways of mapping genomes - from using BAC clones to radiation hybrids and assembling with the use of closely related reference genomes, including the determination of the order of scaffolds, which is an important step for assembling and finishing genomes. [slides]
Given the great interest in the school and the positive feedback from participants, we decided to hold it annually. In the summer of 2014 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 on Coursera ( course post ).
I would also like to thank the team of the school’s organizers, Katya Chaikina 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 company JetBrains, for the stable support of the Institute of Bioinformatics over the past three years. And also: Russian Venture Company, Dynasty funds and RFBR; BIOCAD, Diam and Life Technologies.
A beautiful report on the school’s results can be found here (carefully, PDF of 6.5 MB) .
Institute of Bioinformatics: website , twitter , VKontakte , summer school on bioinformatics 2014 .
About how was the school itself, our students have already written on Habré. Now everyone who has not had the opportunity to participate in the school can familiarize himself with the reports he is interested in: we have posted all the videos of lectures and all the slides of the presentations online.
If you hear about bioinformatics for the first time, then I advise you first of all to look at the introductory lecture by Alla Lapidus, who will put everything in its place. Now Alla occupies a leading position in the Center for Genomic Bioinformatics at St. Petersburg State University and in the Laboratory of Algorithmic Biology at SPbAU RAS, and earlier for a long time she led genome projects at the DOE Joint Genome Institute (California).
')
Under the cat 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 a huge thank you to Kirill Grigoriev, who filmed and processed all videos from school free of charge, Yaroslav Baranov and Pavel Yakovlev, who helped in the shooting, as well as yasha_somov for help with the equipment.
The first day of school was spent on the biological faculty of Moscow State University and consisted of quite complex lectures, in which leading scientists told about the latest trends in bioinformatics:
1. Bioinformatics approaches to the study of microevolution
Alexey Kondrashov (University of Michigan, MSU)
The winner of the megagrant program, the head of the Evolutionary Genomics Laboratory at the Moscow State University, Alexey 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. The following topics were considered: population variability, mutation process, drift, negative, positive and balancing selection, reproduction, geographical structure of populations. [slides]
Video
2. Genetic reprogramming of somatic cells: what bioinformatics gives us
Sergey Kiselev (IOGEN RAS)
In the second lecture, the enormous potential of stem cells and, in particular, induced pluripotent stem cells (IPSC) for the development of new methods of cell therapy, the creation of model systems to study the mechanisms of diseases and the development of drugs were discussed. The lecture discussed the properties and functional markers of the reprogramming of iPSCs, and also described how, using changes in DNA methylation, modification and transcription of histones in combination with bioinformatic methods, create specific markers that distinguish stem cells and determine their fate. [slides]
Video
3. Reading the human genome as a tool for improving some anthropological and historical hypotheses
Egor Prokhorchuk (Center "Bioengineering" RAS)
Further, 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, such an unexpected and interesting topic as the comparison of genetic and linguistic data was touched upon. [slides]
Video
4. Molecular features of the evolution of the human brain
Philip Haytovich (Shanghai Institutes for Biological Sciences)
Philip told about the phenotype, genotype and the process of transition from phenotype to genotype; the development of the human brain: the transcript of the brain, the specific expression of genes of various species and its differences, features and mechanisms in the human body; gene expression studies of people with autism; comparison of Neanderthals and modern people. [slides]
Video
Starting from the second day, the school was held in the suburbs. Lectures began with the most simple to understand, with a gradual increase in complexity by the end of the 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” were told, as well as about the main areas of application of bioinformatics, including the use of bioinformatics in medicine. [slides]
Video
6. Molecular biology for informatics
Natalia Volodina (SPbAU RAS)
In several lectures, an introduction to molecular biology was given to non-biological students, including such topics 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]
Video
7. Development of scientific software: best practices and approaches
Konstantin Okonechnikov (Max Planck Institute for Infection Biology, Berlin)
It was told about the recommended methods and ways of developing scientific software. Many of these methods have long been known and successfully used in software development, but they require adaptation to the “scientific environment”. Special attention is given in the lecture to technologies for optimizing the performance of software systems. [slides]
Video
8. Simple ways to analyze complex data.
Philip Haytovich (Shanghai Institutes for Biological Sciences)
In the second lecture, Philip spoke in more detail about the field of his scientific work, including the study of human-specific RNA compared to other mammals, such as chimpanzees and mice; brain aging processes; long non-coding RNA. [slides]
Video
9. Analysis of NGS data
Andrey Przibelsky (SPbAU RAS)
It was told about the history of sequencing, gave an overview of popular and emerging technologies today, described their features and applications. The lecture discusses in detail the process and the existing programs for assembling the genome, and also gives an answer to the question whether there is a single best assembler. [slides]
Posts of Andrew andrewprzh on this topic on Habré: Bioinformatics: a look from the inside and again about bioinformatics: the assembly of bacterial genomes .
Video
10. Introduction to RNA reading
Konstantin Okonechnikov (Max Planck Institute for Infection Biology, Berlin)
It was told about transcriptome sequencing technologies and data analysis techniques specific for this type of experiment, including methods for leveling short reads with regard to splicing, assembly of transcripts, methods of isoform reconstruction, comparative analysis of gene expression, and methods for searching for deformations in the genome and fusion genes (fusion genes). [slides]
Video
11. De Bruyn graphs and assembly algorithms
Sergey Nurk (SPbAU RAS)
It was told about the formulation of the genome assembly problem and the use of the De Bruyn graphs for its solution. The lecture also discusses various problems associated with sequencing errors or lack of resources. [slides]
Video
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 analyzing the Next Generation Sequencing (NGS) data, and about the principles that allow them to be effectively combined and used. [slides]
Video
13. Applications and sequencing databases
Alla Lapidus (Center for Genomic Bioinformatics, St. Petersburg State University, SPbAU RAS)
In her second lecture, Alla told about the history of the development of sequencing technologies and the diversity of existing biological databases, which is dictated by the diversity of the challenges and the growing application of these technologies at present (for example, in personalized medicine). [slides]
Video
14. Investments in biotech: obvious and non-obvious stories
Andrey Afanasyev (iBinom, MSU)
This lecture was about several biotech projects through the eyes of innovators and investors, and also presented the personal experience of the speaker, who is the founder of the bioinformatics startup iBinom, on interaction 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)
It was told about libraries for sequencing and resequencing, chromosome assembly, the use of reference genomes of closely related species and various aspects of gene annotation. [slides]
Video
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; on genomic medicine, objectives 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 for the clinical interpretation of bioinformatic data (basic methods for building analysis pipelines, modular organization, existing frameworks and services specific to biomedical software, design features). [slides]
Video
17. Mini-conference (student presentations)
The mini-conference was held in the format of presentations of the participants of the summer school, which was moderated by Mikhail Raiko (SPSU, SPbAU RAS). At the competitive selection stage there was an opportunity to submit abstracts, and the selected 13 people spoke about their research in fifteen-minute reports. Detailed topics and slides of the speakers can be found on the website .
18. Analysis of NGS data
Andrey Przibelsky (SPbAU RAS)
In the framework of this seminar for informatics, it is detailed about efficient algorithms and methods for analyzing NGS data. In the second part of the seminar, Anton Korobeinikov, also from the algorithmic biology laboratory of the St. Petersburg University of the Russian Academy of Sciences, joined Andrei Przhibelsky.
Video
19. Review of biotechnology
Alexander Karabelsky (BIOCAD)
It was told about modern directions of research in the field of monoclonal antibodies, described their types, properties and range of applications, as well as analyzed in detail the development process with consideration of its stages and methods used (for example, biotechnological company BIOCAD). [slides]
Video
20. Bioinformatics of DNA-protein interaction and gene regulation
Vsevolod Makeev (IOGEN RAS, MIPT)
It was told about the difference between DNA sequences of different species, why similar genes work in different ways and why specific genes work at a specific point in time (in a particular tissue). Issues such as RNA synthesis and subsequent stages, tissue-specific expression, regulation and transcription regulators are covered, as well as an overview of various methods and technologies for studying DNA-protein interaction and gene regulation and comparing existing programs. [slides]
Video
21. E-value in BLAST
Anton Korobeinikov (SPbAU RAS, SPSU)
In two lectures, filled with mathematics, they talked about statistical principles and results, allowing to evaluate the significance of matches between strings and to distinguish truly non-random coincidences from random ones (for bioinformatics BLAST is a standard tool for searching for similarity between protein and nucleotide sequences, the most cited scientific article 90 s) It is assumed that the listener of the lecture is familiar with the basic concepts of statistics and probability theory (distribution, random variable, mean, estimation, statistical hypothesis).
Video
Video
22. Biotechnology for biologists
Alexander Karabelsky (BIOCAD)
In his second lecture, Alexander spoke on the example of the company BIOCAD about the structure and organization 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]
Video
23. My first 100 projects on IonTorrent: bioinformatics story
Dmitry Alekseev (SRI FHM)
It was told about practical experience and results of using IonTorrent equipment for various purposes: reading and assembling genome, resolution, libraries of paired reads, metagenomics, 16S analysis and others. [slides]
Video
24. Writing for Scientists
Natalya Kuznetsova (IBCh RAS)
It was told about the rules and methods of writing scientific articles in English, proper use of vocabulary, punctuation, structure of the text and common mistakes. [slides]
Video
25. Dynamics of synthetic networks of gene regulation
Mikhail Ivanchenko (UNN)
This lecture dealt with the construction of artificial regulatory networks with a given behavior, such as 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, a number of open topical problems. [slides]
Video
26. Dynamics of synthetic networks of gene regulation
Alexey Zaikin (University College London)
In the next lecture, Alexey, a colleague of Michael, continued the topic of building artificial regulatory networks with complex dynamics. [slides]
Video
27. Bioinformatics assessment of human stem cell perfection
Maria Shutova (IOGEN RAS)
In this research report, Maria, an employee of the laboratory of Sergey Kiselyov (who gave a lecture on the genetic reprogramming of somatic cells on the first day), spoke about the comparison of embryonic stem cells (ESCs) and induced pluripotent stem cells (IPSCs), which have a different genetic nature and solve evidence problems their identities. The lecture dealt with the creation of an isogenic system that allows for comparisons of expression (Illumina HT12) and CpG methylation (Illumina 450k) of ESCs, differentiated cells and iPSCs. The story highlights the molecular and bioinformatics methods used in the analysis, as well as the preliminary results of this study. [slides]
Video
28. The use of 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 was held at 10 am on Saturday (after Friday's farewell evening), almost all school participants were able to visit it, and Alexey talked about different ways of mapping genomes - from using BAC clones to radiation hybrids and assembling with the use of closely related reference genomes, including the determination of the order of scaffolds, which is an important step for assembling and finishing genomes. [slides]
Video
Finally
Given the great interest in the school and the positive feedback from participants, we decided to hold it annually. In the summer of 2014 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 on Coursera ( course post ).
I would also like to thank the team of the school’s organizers, Katya Chaikina 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 company JetBrains, for the stable support of the Institute of Bioinformatics over the past three years. And also: Russian Venture Company, Dynasty funds and RFBR; BIOCAD, Diam and Life Technologies.
A beautiful report on the school’s results can be found here (carefully, PDF of 6.5 MB) .
Institute of Bioinformatics: website , twitter , VKontakte , summer school on bioinformatics 2014 .
Source: https://habr.com/ru/post/198784/
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