We are talking about the people of the future who decipher the organic big date. Over the past two decades, the amount of biological data that can be analyzed has grown many times over due to the deciphering of the human genome. Until then, we could not have imagined that, from the information stored literally in our blood, it would be possible to determine our origin, check how the body would respond to certain drugs, and even change our biological heredity.
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The attributes of the average bioinformatician are the same as those of a programmer - red eyes, stooped posture and coffee cup marks on the desktop. However, this table is not working on abstract algorithms and commands, but on the code of nature itself, which can tell us a lot about us and the world around us.
Specialists in this field deal with huge amounts of data (for example, the results of sequencing the genome of one person occupy about 100 gigabytes). Therefore, the processing of such an array of information requires the approaches and tools of Data Science. It is logical that a successful bioinformatician should understand not only biology and chemistry, but also data analysis methods, statistics and mathematics - this makes his profession quite rare and in demand. Such specialists are especially needed in the areas of innovative medicine and drug development. Tech giants like IBM and Intel , dedicated to the study of bioinformatics.
What does it take to become a bioinformatician?
- Biology and Chemistry (university level);
- Matstat, linear algebra, probability theory;
- Programming languages ββ(Python and R, often also using C++);
- For structural bioinformatics: understanding of mathematical analysis and the theory of differential equations.
You can enter the field of bioinformatics with both a biological background and knowledge of programming and mathematics. For the former, working with ready-made bioinformatics programs is suitable, for the latter, a more algorithmic profile of the specialty.
What do bioinformaticians do?
Modern bioinformatics is divided into two main branches - structural bioinformatics and sequence bioinformatics. In the first case, we see a person who sits in front of a computer and runs programs that help to study biological objects (for example, DNA or proteins) in 3D visualizations. They build computer models that make it possible to predict how a drug molecule will interact with a protein, what the spatial structure of a protein looks like in a cell, what properties of a molecule explain its interactions with cellular structures, etc.
Structural bioinformatics methods are actively used both in academic science and in industry: it is difficult to imagine a pharmaceutical company that can do without such specialists. In recent years, computer methods have greatly simplified the process of searching for potential drugs, making pharmaceutical development a much faster and cheaper process.
SARS-CoV-2 RNA-dependent RNA polymerase (left) and its association with the RNA duplex.
What is a genome?
The genome is all the information about the structure of the heredity of an organism. In almost all living beings, the carrier of the genome is DNA, but there are organisms that transmit their hereditary information in the form of RNA. The genome is passed from parents to children, and during this process of transmission, errors can occur - mutations.
Interaction of the drug remdesivir with the RNA-dependent RNA polymerase of the SARS-CoV-2 virus.
Sequence bioinformatics works with a higher level of organization of living matter - from individual nucleotides, DNA and genes, to whole genomes and their comparisons with each other.
Imagine a person who sees a set of letters of the alphabet (but not simple, but genetic or amino acid) in front of him and looks for patterns in them, explaining and confirming them statistically, using computer methods. Sequence bioinformatics explains which mutation is associated with a disease or why harmful substances accumulate in a patient's blood. In addition to medical data, sequence bioinformatics studies patterns of distribution of organisms across the earth, population differences between groups of animals, and the roles and functions of specific genes. Thanks to this science, it is possible to test the effectiveness of drugs and study the biological mechanisms that explain their action.
For example, thanks to bioinformatics analysis, mutations leading to the development of cystic fibrosis, a monogenic disease caused by a breakdown of the gene of one of the chloride channels, were found and described. And now we know much better who is the closest biological relative of man and how our ancestors settled around the planet. Moreover, every person, by reading his genome, can find out where his family comes from and what ethnic group he belongs to. Many foreign (, ) and Russian (, ) services allow you to get this service for a relatively low price (about 20 thousand rubles).
DNA test results for lineage and population from MyHeritage.
The results of the analysis of the DNA test for population affiliation from the company 23andMe.
How is the genome read?
Today, genome sequencing is a routine procedure that will cost anyone about thousand rubles (including in Russia). To read your genome, you just need to donate blood from a vein in a special laboratory: in two weeks you will receive a ready-made result with a detailed description of your genetic characteristics. In addition to your genome, you can analyze the genomes of the intestinal microbiota: you will learn the characteristics of the bacteria that inhabit your digestive system, as well as get advice from a professional nutritionist.
The genome can be read by various methods, one of the main ones now is the so-called "next generation sequencing". To carry out this procedure, you must first obtain biological samples. In every cell of the body, the genome is the same, so most often blood is taken to read the genome (this is the easiest). The cells then break down and separate the DNA from everything else. Then, the resulting DNA is crushed into many small pieces and "sewn" to each of them with special adapters - artificially synthesized known nucleotide sequences. Then the DNA chains are separated, and single-stranded chains are attached to a special plate with the help of adapters, on which sequencing is carried out. During sequencing, complementary fluorescently labeled nucleotides are added to the DNA sequence. Each labeled nucleotide, when attached, emits a beam of light of a certain wavelength, which is recorded on a computer. So the computer reads short sequences of the original DNA, which are then assembled into the original genome using special algorithms.
An example of the data that sequence bioinformaticians work with is the alignment of amino acid sequences.
Where do bioinformaticians work and how much do they earn?
The path of bioinformatics is traditionally divided into two main areas - industry and science. A career as a bioinformatics scientist usually begins with a postgraduate position at one of the major institutions. Initially, bioinformaticians receive a base rate based on their institution, the number of grants they participate in, and their number of affiliationsβthe places they are formally employed. Over time, the number of grants and affiliations grows, and after about a couple of years of work in the academic environment, a bioinformatician without problems receives an average salary (70-80 thousand rubles), but much depends on diligence and diligence. The most experienced bioinformaticians end up running their own labs in their areas of expertise.
Where do you study bioinformatics?
- Moscow State University - Faculty of Bioengineering and Bioinformatics
- HSE - Data Analysis in Biology and Medicine (Master's Program)
- MIPT - Department of Bioinformatics
- Institute of Bioinformatics (NPO)
Unlike an academy, no one in the industry will spend their time teaching an employee the necessary skills, so getting there is usually more difficult. The career path of a bioinformatician in industry varies greatly depending on their specialization and location. On average, salaries in this field fluctuate thousand rubles, depending on experience and specialization.
Famous bioinformaticians
The history of bioinformatics should be traced back to Frederick Sanger, an English scientist who received the Nobel Prize in Chemistry in 1980 for discovering a way to read a DNA sequence. Since then, every year the methods of reading sequences have been improved, but the method of "Sanger sequencing" has served as the basis for all further research in this area.
By the way, many programs created specifically by Russian scientists are now widely used all over the world - for example, a genomic assembler , β St. Petersburg genome assembler, created at the St. Petersburg Institute, helps scientists around the world assemble short DNA sequences into large sequences in order to reconstruct the original genomes of organisms.
Discoveries and achievements of bioinformatics
Nowadays, bioinformaticians make many useful discoveries. It would be impossible to imagine the development of drugs for coronavirus without deciphering its genome and complex bioinformatics analysis of the processes that occur during the course of the disease. International scientists using comparative genomics and machine learning to understand what coronaviruses have in common with other pathogens.
It turned out that one of these features is the evolutionary enhancement of nuclear localization signals (NLS) of pathogenic viruses. This research could help to study strains of viruses that may be potentially harmful to humans in the future, and possibly start preventive drug development.
In addition, bioinformaticians have played a key role in the development of new genome editing techniques, in particular the CRISPR/Cas9 system (a technology based on the immune system). ). Thanks to the bioinformatic analysis of the structure of these proteins and their evolutionary development, the accuracy and efficiency of this system has increased significantly in recent years, which has made it possible to purposefully edit the genomes of many organisms (including humans).
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Source: habr.com