Dr. Sergey Naumenko, Research Associate
Sergey received B.Sc and M.Sc in Computer Science from Kharkiv National University of Radio and Electronics (Kharkiv, Ukraine). Then he joined the sector of nonlinear dynamics in Keldysh Institute of Applied Mathematics (Moscow, Russia), where he studied self-reproducing cellular automata, DNA computing, models of the evolution of early life and the origin of genetic code. In KIAM Sergey also taught a course on Biology Inspired Computing.
Sergey worked on PhD project and defended PhD thesis in the joint laboratory of Evolutionary Genomics (Moscow State University, Russia) and Molecular Evolution (Institute for Information Transmission problems of Russian Academy of Sciences, Moscow, Russa) lead by Alexey Kondrashov and Georgii Bazykin http://evolgenomicsen.fbb.msu.ru/. He studied patterns of molecular evolution of protein-coding genes in mammals and insects (epistasis, homoplasy in phylogenetic trees), and inferred the phylogeny of lake Baikal Gammarid species flock using de-novo assembled transcriptomes. Also Sergey was involved in system administration of HPC for NGS data processing in the lab.
During several years Sergey taught Linux Administration and Parallel programming courses in D.Mendeleyev University of Chemical Technology of Russia (Moscow, Russia), and co-organized ACM-style programming contests for students.
At CCM Sergey is helping clinical researches to investigate molecular causes of rare diseases using WES, WGS, and RNA-seq data analyses: he produces annotated small variant reports for genome and exome analysts in Care4Rare project using WES and WGS data; calls and annotates structural variants using WGS data; performs expression outlier, aberrant splicing, small variant analyses using RNA-seq data. Sergey is specializing in using bcbio (https://bcbio-nextgen.readthedocs.io/en/latest/) sequencing analysis toolkit.
Publications: https://scholar.google.ca/citations?user=SeL177gAAAAJ&hl=en, github:https://github.com/naumenko-sa, twitter: https://twitter.com/SergeyNaumenko6