SPbU’s Center for Algoritnmic Biotechnology No 1: Pavel Pevzner
July 25, International Society for Computational Biology (ISCB) recognizes Pavel Pevzner, who leads the Centre for Algorithmic Biotechnology, Institute of Translational Medicine, SPbU, with the Accomplishment by a Senior Scientist Award for significant contributions he or she has made to the field. Each year the ISCB selects an outstanding biologist and gives the award to honour scientists who have contributed to the advancement of computational biology.
Pavel Pevzner is Candidate of Physics and Mathematics (MFTI, 1998), Professor of the University of California (2000), and the father of the laboratories of bioinformatics in the USA and Russia.
Author of more than 200 articles in the world’s leading journals and taught over 20 young scientists who work in the universities worldwide, including Harvard and Princeton. H-index is 80.
The Center for Algoritnmic Biotechnology (CAB), Institute of Translational Medicine, SPbU, was founded in 2014 under the Megagrant of the Government of the Russian Federation and SPbU to focus on computational biomedicine.
“ISCB’s Senior Scientist Award is not for me, it is the award to honour my teachers and students who I have spent the last 25 years with”, — said Pavel Pevzner.
– What is the focus of your students in St Petersburg?
– The CAB is a team No 1 in the genome assembly in the world, that is software to assemble large genomes from high coverage short read data. “To assemble a genome is a hard nut to crack, it is like to collect a jigsaw puzzle with millions of pieces, rather than thousands. Young people from the CAB in their early twenties managed to create an algorithm to assemple a genome. We called it SPAdes — Sankt-Peterburg Assembler. Over 5 years, scientists all over the world have been using the SPAdes, which was initially created in Russia, in St Petersburg. The article which describes the assembler have been cited 2,000 time during 5 years and got the most cited one in Russia.
– Most likely, it was you who had done the most as you are respected professor, experienced in the field...
– The case is that it was a team work: I just gave a momentum, then we need a bulk of energy and ideas from everybody to create the algorithm which honours St Petersburg University in genomics and personalized medicine, especially in microbiome studies (study of thousands of bacteria in our body). The assembler is at the forefront in the field. Another fact that the University is recognized globally is that the experts worldwide will come to St Petersburg to take part in the conference held in SPbU. This is definitely tribute to the University.
– You have a long way to go, you cannot be satisfied with what you have already achieved.
– Definitely. Bioinformatics is gaining momentum, and we are in a race. If you don’t want to lose, you should be always on guard. The case was that when we had finished our first assembler and analyzed how it could work, we encountered lots of other problems: how to assemble viruses and microbiomes, how to use new technologies, whether we can use existing technologies... Our assembler is of particular importance in antibiotics studies. It is an extremely urgent task, as the Director of the Center of the Disease Control, USA, put it, we have reached the bottom: we die from bacteria resistant to antibiotics, and if we don’t come up with new antibiotics, we will be heading towards death loop ...
– How can bioinformatics help?
– The perfect place to find new antibiotics is ocean. My colleagues, who I am jealous a bit, travel to the most exotic places and collect biological samples in the ocean to perform experiments. To interpret the experimental results and understand which antibiotics are hidden in the samples, bioinformatics can help, as you have to process big data. CAB’s workers Alla Mikheenko and Aleksei Gurevich are developing new technologies to find antibiotics, in particular they published an article in Nature Chemical Biology in 2017. It describes the first algorithm to find antibiotics across large database of mass-specters collected in the hundreds of laboratories worldwide. So, the Center for Algoritnmic Biotechnology of the Institute of Translational Biomedicine, SPbU, is at the forefront of science globally.
– Another problem in medicine which many sciences focus on is our immune system. Does bioinformatics create new technologies in this field as well?
– The CAB is actively involved in the field, and today is just right time to delve into the subject. It was too early 6 years ago, when I started to work in St Petersburg, as my colleagues had just started to study our immune system, its anti-bodies and how it works. Now the situation is different: we have a clear view of the computational tasks that we have to solve. I suppose that we will have joint projects with the Auto-Immune Mosaic Laboratory at SPbU, led by Yehuda Shoenfeld.
– The CAB takes part in another global project — a so-called “walking laboratory” Larry Smarr, Professor of the University of California, has created out of him after he had known that he had had Crohn's disease.
– Yes, we supply bioinformatics support: for the last 12 years Larry Smarr has been studying his own microbiome and analyzing what has been happening in his body as the disease has been progressing, which is a serious auto-immune condition when your body destroys its cells. Among many world’s centres St Petersburg Centre was chosen: Dmitrii Meleshko and Sergei Nurku have one million hours to work on the super-computer in the University of California to analyse Smarr’s microbiome, while Aleksei Gurevich, Anton Korobeinikov and Aleksandr Shlemov analyse his metabolome (a complete set of small-molecule chemicals found within a biological sample) by using their VarQuest algorithm. I hope that it will benefit SPbU globally and bring new publications in the world’s leading journals.
– What will the CAB focus on in 3 years?
– I wish I could know. We would delve into it…