Alexander Kurilshikov, PhD

MSc in Biology Dept of Cytology and Genetics, Novosibirsk State University, Russian Federation

PhD thesis: Biodiversity of bacterial agents associated with Ixodidae ticks. 2016, ICBFM SB RAS, Novosibirsk, Russian Federation

Keywords: bioinformatics, genomics, metagenomics, computational biology, statistical genetics, systems biology, machine learning

Email

See all my papers in Google scholar

About me

I am a postdoc working on microbiome research with Sasha Zhernakova and Jingyuan Fu. Our team aims to explore the interactions between the human microbiome and other kind of human ‘omics’ data to investigate the possible impact of the microbiota on human health.

Using data from the LifeLines-DEEP population cohort, we showed how the gut microbiome is shaped by external and intrinsic factors such as diet, medication and diseases (Zhernakova et al, Science, 2016). Now I’m focusing on further analysis of the microbiome’s role in shaping human serum metabolism, which is the key element in many metabolic disorders and cardiovascular disease events.

Selected papers

• Host Genetics and Gut Microbiome: Challenges and Perspectives. Kurilshikov A, Wijmenga C, Fu J, Zhernakova A. Trends Immunol. 2017;38(9):633-647.
• Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, … Imhann F, Brandsma E, Jankipersadsing SA, Joossens M, Cenit MC, Deelen P, Swertz MA; LifeLines cohort study, Weersma RK, Feskens EJ, Netea MG, Gevers D, Jonkers D, Franke L, Aulchenko YS, Huttenhower C, Raes J, Hofker MH, Xavier RJ, Wijmenga C, Fu J. Science. 2016;352(6285):565-9.
• Population-level analysis of gut microbiome variation. Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y, Faust K, Kurilshikov A, Bonder MJ, … Tigchelaar EF, Eeckhaudt L, Fu J, Henckaerts L, Zhernakova A, Wijmenga C, Raes J. Science. 2016;352(6285):560-4.
• Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity. Schirmer M et al. Cell. 2016;167(4):1125-1136.e8.
• Lytic bacteriophage PM16 specific for Proteus mirabilis: a novel member of the genus Phikmvvirus. Morozova V, Kozlova Y, Shedko E, Kurilshikov A, … Tikunova N. Arch Virol. 2016.
• Comparative Metagenomic Profiling of Symbiotic Bacterial Communities Associated with Ixodes persulcatus, Ixodes pavlovskyi and Dermacentor reticulatus Ticks. Kurilshikov A, Livanova NN, …Tikunova NV. PLoS One. 2015 Jul 8;10(7):e0131413. doi: 10.1371/journal.pone.0131413.
• Evolutionary time-scale of primate bocaviruses. Babkin IV, Tyumentsev AI, Tikunov AY, Kurilshikov AM, …Tikunova NV. Infect Genet Evol. 2013;14:265-74.
• MicroRNA drop in the bloodstream and microRNA boost in the tumour caused by treatment with ribonuclease A leads to an attenuation of tumour malignancy. Mironova N, Patutina O, Brenner E, Kurilshikov A, Vlassov V, Zenkova M. PLoS One. 2013;8(12):e83482.
• Unbiased approach to profile the variety of small non-coding RNA of human blood plasma with massively parallel sequencing technology. Semenov DV, Baryakin DN, Brenner EV, Kurilshikov AM, … Richter VA. Expert Opin Biol Ther. 2012;12 Suppl 1:S43-51.
• A comparative study of cell-free apoptotic and genomic DNA using FISH and massive parallel sequencing. Morozkin ES, Loseva EM, Morozov IV, Kurilshikov AM, ... Laktionov PP. Expert Opin Biol Ther. 2012;12 Suppl 1:S11-7.

Teaching experience

• Research Summer School in Statistical Omics 2016 (Split, Croatia, 2016, tutor on the practical workshop)
• R practical course for UMCG students, Groningen, 2016
• Systems Biology and Bioinformatics Summer School 2015 (Novosibirsk, Russia, 2015, leading the metagenomics course with theoretical and practical lessons)
• Research Summer School in Statistical Omics 2015 (Split, Croatia, 2015, tutor on the practical workshop)