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Alexey Sergushichev
Researcher at Saint Petersburg State University of Information Technologies, Mechanics and Optics
Publications - 60
Citations - 8168
Alexey Sergushichev is an academic researcher from Saint Petersburg State University of Information Technologies, Mechanics and Optics. The author has contributed to research in topics: Medicine & Biology. The author has an hindex of 18, co-authored 48 publications receiving 5529 citations. Previous affiliations of Alexey Sergushichev include JetBrains & Saint Petersburg State University.
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Fast gene set enrichment analysis
TL;DR: FGSEA method is presented, able to estimate arbitrarily low GSEA P-values with a higher accuracy and much faster compared to other implementations, and a polynomial algorithm is presented to calculate GSEAP-values exactly.
Journal ArticleDOI
Network integration of parallel metabolic and transcriptional data reveals metabolic modules that regulate macrophage polarization.
Abhishek K. Jha,Stanley Ching-Cheng Huang,Alexey Sergushichev,Alexey Sergushichev,Vicky Lampropoulou,Yulia Ivanova,Ekaterina Loginicheva,Karina Chmielewski,Kelly M. Stewart,Juliet Ashall,Bart Everts,Edward J. Pearce,Edward M. Driggers,Maxim N. Artyomov +13 more
TL;DR: An integrated high-throughput transcriptional-metabolic profiling and analysis pipeline provides a highly integrated picture of the physiological modules supporting macrophage polarization, identifying potential pharmacologic control points for both macrophages.
Posted ContentDOI
An algorithm for fast preranked gene set enrichment analysis using cumulative statistic calculation
TL;DR: It is shown that it is possible to make hundreds of thousands permutations in a few minutes, which leads to very accurate p-values, which allows applying standard FDR correction procedures, which are more accurate than the ones currently used.
Journal ArticleDOI
Itaconate Links Inhibition of Succinate Dehydrogenase with Macrophage Metabolic Remodeling and Regulation of Inflammation
Vicky Lampropoulou,Alexey Sergushichev,Monika Bambouskova,Sharmila Nair,Emma E. Vincent,Ekaterina Loginicheva,Luisa Cervantes-Barragan,Xiucui Ma,Stanley Ching-Cheng Huang,Takla Griss,Carla J. Weinheimer,Shabaana A. Khader,Gwendalyn J. Randolph,Edward J. Pearce,Russell G. Jones,Abhinav Diwan,Michael S. Diamond,Maxim N. Artyomov +17 more
TL;DR: It is shown that itaconate modulates macrophage metabolism and effector functions by inhibiting succinate dehydrogenase-mediated oxidation of succinate, and this action exerts anti-inflammatory effects when administered in vitro and in vivo during Macrophage activation and ischemia-reperfusion injury.
Journal ArticleDOI
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
Keith Bradnam,Joseph Fass,Anton Alexandrov,Paul Baranay,Michael Bechner,Inanc Birol,Sébastien Boisvert,Jarrod Chapman,Guillaume Chapuis,Guillaume Chapuis,Rayan Chikhi,Rayan Chikhi,Hamidreza Chitsaz,Wen-Chi Chou,Jacques Corbeil,Cristian Del Fabbro,T. Roderick Docking,Richard Durbin,Dent Earl,Scott J. Emrich,Pavel Fedotov,Nuno A. Fonseca,Ganeshkumar Ganapathy,Richard A. Gibbs,Sante Gnerre,Elenie Godzaridis,Steve Goldstein,Matthias Haimel,Giles Hall,David Haussler,Joseph B. Hiatt,Isaac Ho,Jason T. Howard,Martin Hunt,Shaun D. Jackman,David B. Jaffe,Erich D. Jarvis,Huaiyang Jiang,Sergey Kazakov,Paul J. Kersey,Jacob O. Kitzman,James R. Knight,Sergey Koren,Tak-Wah Lam,Dominique Lavenier,Dominique Lavenier,François Laviolette,Yingrui Li,Zhenyu Li,Binghang Liu,Yue Liu,Ruibang Luo,Iain MacCallum,Matthew D. MacManes,Nicolas Maillet,Sergey Melnikov,Bruno Vieira,Delphine Naquin,Zemin Ning,Thomas D. Otto,Benedict Paten,Octávio S. Paulo,Adam M. Phillippy,Francisco Pina-Martins,Michael Place,Dariusz Przybylski,Xiang Qin,Carson Qu,Filipe J. Ribeiro,Stephen Richards,Daniel S. Rokhsar,Daniel S. Rokhsar,J. Graham Ruby,J. Graham Ruby,Simone Scalabrin,Michael C. Schatz,David C. Schwartz,Alexey Sergushichev,Ted Sharpe,Timothy I. Shaw,Jay Shendure,Yujian Shi,Jared T. Simpson,Henry Song,Fedor Tsarev,Francesco Vezzi,Riccardo Vicedomini,Jun Wang,Kim C. Worley,Shuangye Yin,Siu-Ming Yiu,Jianying Yuan,Guojie Zhang,Hao Zhang,Shiguo Zhou,Ian F Korf +95 more
TL;DR: The Assemblathon 2 as mentioned in this paper presented a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and a snake) from 21 participating teams.