Alexey Sergushichev, PhD

Division

• Immunobiology

Additional Titles

• Adjunct Professor, ITMO University, St. Petersburg, Russia

Social Media

• Twitter/X

Education

• BSc in Computer Science (with honors), ITMO University, Saint Petersburg, Russia (2011)
• MSc in Computer Science (with honors), ITMO University, Saint Petersburg, Russia (2013)
• PhD in Bioinformatics, ITMO University, Saint Petersburg, Russia (2016)

Professional Recognition

• Skoltech Systems Biology Fellowship (2017-2019)

Research Statement

My general research interest lies in developing computational approaches for analysis of high-throughput data to help uncover novel biology. More specifically, there are three major directions my lab focuses on. 

1. Pathway analysis: we maintain and improve the FGSEA package (https://bioconductor.org/packages/fgsea) for pathway analysis, with recent developments targeted towards working with single-cell and spatial data.
2. Network analysis: our lab works on a set of network analysis approaches with a focus on applications in the immunometabolism field (https://artyomovlab.wustl.edu/shiny/gatom/). 
3. Public data mining: we facilitate access to public transcriptomics data with gene expression analysis web-tools like Phantasus (https://alserglab.wustl.edu/phantasus).

Publications

D Mogilenko, A Sergushichev, MN Artyomov. Systems Immunology Approaches to Metabolism. Annual Review of Immunology, doi:10.1146/annurev-immunol-101220-031513.

A Gainullina, …, A Sergushichev, MN Artyomov, ImmGen Consortium. Network analysis of large-scale ImmGen and Tabula Muris datasets highlights metabolic diversity of tissue mononuclear phagocytes. Cell Reports, doi:10.1016/j.celrep.2023.112046.

M Kleverov, D Zenkova, V Kamenev, M Sablina, MN Artyomov, A Sergushichev. (2024) Phantasus, a web application for visual and interactive gene expression analysis. eLife 13:e85722. https://doi.org/10.7554/eLife.85722

G Korotkevich, V Sukhov, N Budin, B Shpak, MN Artyomov, A Sergushichev. Fast gene set enrichment analysis. bioRxiv, doi:10.1101/060012.

N Alexeev, J Isomurodov, V Sukhov, G Korotkevich, A Sergushichev. Markov chain Monte Carlo for active module identification problem. BMC Bioinformatics, doi:10.1186/s12859-020-03572-9.

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.

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.

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Assistant
Elizabeth Moore
melizabeth@wustl.edu
314-362-9103