Alexey A. Sergushichev, PhD

Currently

I am a bioinformatics group leader at joint ITMO University & JetBrains Research laboratory. I graduated from ITMO University in 2013 and received Master degree with honors in Computer Science. In 2016 I defended my PhD thesis under supervision of Maxim Artyomov. I’m working on computational algorithms and methods for gene expression analysis with a specific focus on metabolic networks.

Employment

2010- ITMO University Researcher at Computer Technologies Laboratory

2013— Washington University in St. Louis Visiting researcher at Maxim Artyomov’s laboratory

Education

2013-16 ITMO University Bioinformatics PhD (supervisors: Maxim Artyomov and Anatoly Shalyto)

2011-13 ITMO University MSc with honors in Computer Science

2007-11 ITMO University BSc with honors in Computer Science

Main publications

2017

TK Ulland, WM Song, SCC Huang, JD Ulrich, A Sergushichev et al. TREM2 Maintains Microglial Metabolic Fitness in Alzheimer’s Disease. Cell, doi:10.1016/j.cell.2017.07.023.

JE Isomurodov, AA Loboda, AA Sergushichev. Ranking Vertices for Active Module Recovery Problem. Algorithms for Computational Biology 2017, doi:10.1007/978-3-319-58163-7_5.

2016

MN Artyomov, A Sergushichev, JD Schilling. Integrating immunometabolism and macrophage diversity. Seminars in Immunology, doi:10.1016/j.smim.2016.10.004

V Lampropoulou, A Sergushichev et al. Itaconate Links Inhibition of Succinate Dehydrogenase with Macrophage Metabolic Remodeling and Regulation of Inflammation. Cell Metabolism, doi:10.1016/j.cmet.2016.06.004

A Sergushichev. An algorithm for fast preranked gene set enrichment analysis using cumulative statistic calculation. Preprint, doi:10.1101/060012.

AA Loboda, MN Artyomov, AA Sergushichev. Solving generalized maximum-weight connected subgraph problem for network enrichment analysis. Workshop on Algorithms in Bioinformatics 2016, doi:10.1007/978-3-319-43681-4_17.

AA Sergushichev et al. GAM: a web-service for integrated transcriptional and metabolic network analysis. Nucleic Acids Research, doi:10.1093/nar/gkw266

2015 EE Vincent, A Sergushichev et al. Mitochondrial Phosphoenolpyruvate Carboxykinase Regulates Metabolic Adaptation and Enables Glucose-Independent Tumor Growth. Molecular cell, doi:10.1016/j.molcel.2015.08.013

AK Jha, SCC Huang, A Sergushichev et al. Network integration of parallel metabolic and transcriptional data reveals metabolic modules that regulate macrophage polarization. Immunity, doi:10.1016/j.immuni.2015.02.005

2013

AV Aleksandrov, SV Kazakov, AA Sergushichev, FN Tsarev, AA Shalyto The use of evolutionary programming based on training examples for the generation of finite state machines for controlling objects with complex behavior. Journal of Computer and Systems Sciences International, doi:10.1134/S1064230713020020

2011 A Alexandrov, A Sergushichev, S Kazakov, F Tsarev. Genetic algorithm for induction of finite automata with continuous and discrete output actions. Proceedings of the 13th annual conference companion on Genetic and evolutionary computation, doi:10.1145/2001858.2002089