Master's and PhD studies in bioinformatics

• Krzysztof Kotlarz was recruited to the UPWr Doctoral School without having completed his Master's degree. It's possible.
• What can a student do at the most important scientific conference in their field?
• Modern biology "happens" in a computer – this knowledge is given to students not only in the scientific community

When asked what is so interesting about bioinformatics, Krzysztof Kotlarz enthusiastically says: – Everything! The most interesting is working with various bits of data describing living organisms. Discovering and analysing this amount of data and looking for all the relationships is what keeps me going. I could do so non-stop, especially that only now do we have equipment that allows us to make such calculations and analyses. 

No special treatment

His passion for bioinformatics started during his undergraduate studies, where he participated in a project carried out by Prof. Joanna Szyda. She asked him if he would like to be recruited to the Doctoral School of the Wrocław University of Environmental and Life Sciences.

– But I did not have a Master's degree, so I had to find out if it was at all possible – says Krzysztof Kotlarz, adding that during the recruitment not only documents and interviews were important, but also points awarded, among others, for international cooperation and scientific publication. Most importantly, however, he did not receive any special treatment.

– I was admitted to the school during my Master's studies, so as it turns out it is possible – smiles Krzysztof, who is currently in the second year of his Master's degree in bioinformatics and his Doctoral thesis concerns the application of Artificial Intelligence methods for the analysis of large-scale data in the context of the genetic analysis of cattle.

The first part of the project involves the use of Deep Learning methods to create a classifier of correctly and incorrectly identified polymorphisms based on data on the entire DNA sequences of the genome. The second part of the analysis concerns the classification of cows as susceptible and resistant to mastitis based on the genotypes of polymorphisms also obtained from the sequence of whole genomes. The final stage of the work is the creation of a cattle breed classifier - also based on genomic DNA sequence data and a model for imputing a full set of genome-wide SNP genotypes.

Bioinformatics – a hot topic

– Bioinformatics is an interdisciplinary subject. It is often difficult for computer scientists to understand the complex biological aspect of bioinformatics analysis, but we are bridging this gap because biological knowledge is crucial for writing a programme to analyse collected data on, for example, polymorphisms in cows. Analysis is only a part of the work, and biological knowledge is essential to understand what is being analysed and what the obtained result means - explains Krzysztof, stressing that an additional aspect covered in the research he conducts in collaboration with the Biostatistics Laboratory of the Department of Genetics at the UPWr is high-performance and parallel computing, the result of which is a project using a classical biostatistics tool - linear mixed models to calculate the effects of metabolic sequences.

- A unique aspect of the project is the combination of classic statistics with the possibilities offered by high-performance calculations performed on supercomputers using large-scale biological data. The project uses the results of single mutations, which we convert into functional units expressed by metabolic pathways. And its aim is to estimate the impact of metabolic pathways on growth in dairy cattle breeds – explains the doctoral student of Prof. Szyda, who was among just a handful of scholars from around the world honoured with an invitation to the most important conference for livestock genetic improvement scientists. The World Congress on Genetics Applied to Livestock Production takes place every four years - in 2014 the conference took place in Vancouver, in 2018 in Auckland, and this year it will take place in Rotterdam.

Ideas for students science clubs

– It's a great distinction for me, and another step in my scientific journey. I will present a project concerning the estimation of the influence of metabolic pathways on growth in dairy cattle breeds using linear mixed models on the basis of single mutation effects - says Krzysztof, who has been lecturing students since this academic year and is the leader of the Bioinformatics Students' Society, the activity of which is mainly based on the analysis of data from next-generation sequencing (NGS).

– I want to popularise bioinformatics through the Students' Society and show that studies in this field are relevant, as every modern approach to biology is nowadays necessary for progress in science. Not everything can be tested on a scale. Modern biology is studied on computers. And I appreciate the interest of the students who often ask about the projects. I am also planning meetings with representatives of biotechnological companies to interest them not only in the scientific aspect, but also in the commercial aspect of bioinformatics – emphasises Krzysztof Kotlarz, who is not only a student, but also works as a bioinformatician in a Polish biotechnological company in the field of drug development and commercialisation, where he deals with searching for targets with therapeutic potential in oncology.