AS
Alexey Sergushichev
SoftwareTranscriptomeEnergy MetabolismGene Expression ProfilingimmunologyagingAlgorithmsbioinformaticscardiomyopathycomputational biology
On Valency
published · living versionsW_26xzgw86·v1 · currentpublished
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
with Keith R. Bradnam, Joseph N. Fass, Anton Alexandrov, Paul Baranay +86
1 version
Preprints & journals
64 papers in the corpus · 2013–2026Clonal CD8 T cells link peripheral and intrathecal immunity in ALS4 progression: a multiomics reference for ALS.42818511 · Terekhova, Marina, Melhem, Rima, Zeng, Carisa et al.2026 · 0 citationsResearch square. 2026
GAMclust: identification of regulated metabolic modules in bulk, single cell and spatial gene expression data.42633560 · Gainullina, Anastasiia, Chikina, Evgeniia, Artyomov, Maxim N et al.2026 · 1 citationBioinformatics (Oxford, England). 2026;42(9)
Transcriptome signatures for the identification of bevacizumab responders in ovarian cancer.42576234 · Zolotareva, Olga, Legler, Karen, Tsoy, Olga et al.2026 · 1 citationGenome medicine. 2026;18(1)
Hash-augmented adaptive multilevel splitting Monte Carlo algorithm for accurate estimation of two-sample permutation test p-values2607.12853v1 · Nikita Golikov, Vladimir Sukhov, Gennady Korotkevich et al.2026 · 0 citationsarXiv
Immune Checkpoint Therapy Drives Maturation of a Cellular Neighborhood Nucleated by T Cell-APC Triads Enabling Spatially Compartmentalized Tumor Immunity.41993481 · Medrano, Ruan F V, Sukhov, Vladimir, Hoffer-Hawlik, Kevin et al.2026 · 1 citationbioRxiv : the preprint server for biology. 2026
O-GlcNAcylation and low glycolysis underpin Th2 polarization by dendritic cells10.64898/2026.02.03.703465v1 · Pelgrom, L. R., Quik, M., Fernandez, J. J. et al.2026 · 0 citationsbioRxiv
Digital Modeling of Spatial Pathway Activity from Histology Reveals Tumor Microenvironment Heterogeneity2512.09003v2 · Ling Liao, Changhuei Yang, Maxim Artyomov et al.2025 · 0 citationsarXiv
CORESH: a gene signature-based search engine for public gene expression datasets.40322919 · Sukhov, Vladimir, Nugmanova, Aigul, Vorontsov, Yury et al.2025 · 3 citationsNucleic acids research. 2025;53(W1):W187-W192
Transcriptome signature for the identification of bevacizumab responders in ovarian cancer2501.04869v1 · Olga Zolotareva, Karen Legler, Olga Tsoy et al.2025 · 2 citationsarXiv
Analysis of Variants Induced by Combined Ex Vivo Irradiation and In Vivo Tumorigenesis Suggests a Role for the ZNF831 p.R1393Q Variant in Cutaneous Melanoma Development.39675662 · Usoltsev, Dmitrii, Njauw, Ching-Ni, Ji, Zhenyu et al.2025 · 2 citationsThe Journal of investigative dermatology. 2025;145(7):1728-1739.e7
Complex trait susceptibilities and population diversity in a sample of 4,145 Russians.39043636 · Usoltsev, Dmitrii, Kolosov, Nikita, Rotar, Oxana et al.2024 · 14 citationsNature communications. 2024;15(1):6212
Oxylipins and metabolites from pyroptotic cells act as promoters of tissue repair.38926576 · Mehrotra, Parul, Maschalidi, Sophia, Boeckaerts, Laura et al.2024 · 113 citationsNature. 2024;631(8019):207-215
Phantasus, a web application for visual and interactive gene expression analysis.38742735 · Kleverov, Maksim, Zenkova, Daria, Kamenev, Vladislav et al.2024 · 113 citationseLife. 2024;13
Molecular effects of cardiac contractility modulation in patients with heart failure of ischemic aetiology uncovered by transcriptome analysis.38361583 · Lyasnikova, E, Sukhareva, K, Vander, M et al.2024 · 8 citationsFrontiers in cardiovascular medicine. 2024;11:1321005
CR1 variants contribute to FSGS susceptibility across multiple populations.38076851 · Skitchenko, Rostislav, Modrusan, Zora, Loboda, Alexander et al.2025 · 4 citationsmedRxiv : the preprint server for health sciences. 2023
Gene, cell type, and drug prioritization analysis suggest genetic basis for the utility of diuretics in treating Alzheimer disease.37250495 · Pinakhina, Daria, Loboda, Alexander, Sergushichev, Alexey et al.2023 · 3 citationsHGG advances. 2023;4(3):100203
Systems Immunology Approaches to Metabolism.37126419 · Mogilenko, Denis A, Sergushichev, Alexey, Artyomov, Maxim N2023 · 39 citationsAnnual review of immunology. 2023;41:317-342
Understanding Complex Trait Susceptibilities and Ethnical Diversity in a Sample of 4,145 Russians Through Analysis of Clinical and Genetic Data10.1101/2023.03.23.534000v1 · Usoltsev, D., Kolosov, N., Rotar, O. et al.2023 · 5 citationsbioRxiv
Tumor-associated macrophages respond to chemotherapy by detrimental transcriptional reprogramming and suppressing stabilin-1 mediated clearance of EGF.36960065 · Larionova, Irina, Kiselev, Artem, Kazakova, Elena et al.2023 · 14 citationsFrontiers in immunology. 2023;14:1000497
Network analysis of large-scale ImmGen and Tabula Muris datasets highlights metabolic diversity of tissue mononuclear phagocytes.36708514 · Gainullina, Anastasiia, Mogilenko, Denis A, Huang, Li-Hao et al.2023 · 39 citationsCell reports. 2023;42(2):112046
GWAS of depression in 4,520 individuals from the Russian population highlights the role of MAGI2 (S-SCAM) in the gut-brain axis.36685848 · Pinakhina, Daria, Yermakovich, Danat, Vergasova, Ekaterina et al.2023 · 13 citationsFrontiers in genetics. 2022;13:972196
Integrated multi-omics analysis of adverse cardiac remodeling and metabolic inflexibility upon ErbB2 and ERRα deficiency.36097051 · Dufour, Catherine R, Xia, Hui, B'chir, Wafa et al.2022 · 7 citationsCommunications biology. 2022;5(1):955
GCDPipe: risk gene, cell type, and drug ranking for complex traits10.1101/2022.07.27.501775v1 · Pinakhina, D., Loboda, A., Sergushichev, A. et al.2022 · 0 citationsbioRxiv
Shiny GATOM: omics-based identification of regulated metabolic modules in atom transition networks.35639928 · Emelianova, Mariia, Gainullina, Anastasiia, Poperechnyi, Nikolay et al.2023 · 13 citationsNucleic acids research. 2022;50(W1):W690-W696
Genotype imputation and polygenic score estimation in northwestern Russian population.35763490 · Kolosov, Nikita, Rezapova, Valeriia, Rotar, Oxana et al.2022 · 7 citationsPloS one. 2022;17(6):e0269434
Case Report: Supernormal Vascular Aging in Leningrad Siege Survivors.35677697 · Rotar, Oxana, Boyarinova, Maria, Moguchaya, Ekaterina et al.2022 · 2 citationsFrontiers in cardiovascular medicine. 2022;9:843439
Non-canonical glutamine transamination sustains efferocytosis by coupling redox buffering to oxidative phosphorylation.34650273 · Merlin, Johanna, Ivanov, Stoyan, Dumont, Adélie et al.2021 · 100 citationsNature metabolism. 2021;3(10):1313-1326
Loss of Mir146b with aging contributes to inflammation and mitochondrial dysfunction in thioglycollate-elicited peritoneal macrophages.34423778 · Santeford, Andrea, Lee, Aaron Y, Sene, Abdoulaye et al.2021 · 13 citationseLife. 2021;10
A non-canonical role for glutamate decarboxylase 1 in cancer cell amino acid homeostasis, independent of the GABA shunt.10.1101/2021.02.17.431489v1 · Samborska, B., Griss, T., Ma, E. H. et al.2021 · 2 citationsbioRxiv
A 300-kb microduplication of 7q36.3 in a patient with triphalangeal thumb-polysyndactyly syndrome combined with congenital heart disease and optic disc coloboma: a case report.33218365 · Zlotina, Anna, Melnik, Olesia, Fomicheva, Yulia et al.2021 · 7 citationsBMC medical genomics. 2020;13(1):175
Markov chain Monte Carlo for active module identification problem.33203350 · Alexeev, Nikita, Isomurodov, Javlon, Sukhov, Vladimir et al.2021 · 8 citationsBMC bioinformatics. 2020;21(Suppl 6):261
LMNA Mutations G232E and R482L Cause Dysregulation of Skeletal Muscle Differentiation, Bioenergetics, and Metabolic Gene Expression Profile.32906763 · Ignatieva, Elena V, Ivanova, Oksana A, Komarova, Margarita Y et al.2021 · 18 citationsGenes. 2020;11(9)
Tonic TCR Signaling Inversely Regulates the Basal Metabolism of CD4+ T Cells.32769180 · Milam, Ashley A Viehmann, Bartleson, Juliet M, Buck, Michael D et al.2021 · 21 citationsImmunoHorizons. 2020;4(8):485-497
Generation of two iPSC lines (FAMRCi007-A and FAMRCi007-B) from patient with Emery-Dreifuss muscular dystrophy and heart rhythm abnormalities carrying genetic variant LMNA p.Arg249Gln.32659731 · Perepelina, Kseniya, Kostina, Aleksandra, Klauzen, Polina et al.2025 · 7 citationsStem cell research. 2020;47:101895
Transcriptomic profiling of experimental arterial injury reveals new mechanisms and temporal dynamics in vascular healing response.34617037 · Röhl, Samuel, Rykaczewska, Urszula, Seime, Till et al.2022 · 23 citationsJVS-vascular science. 2020;1:13-27
Generation of two iPSC lines (FAMRCi006-A and FAMRCi006-B) from patient with dilated cardiomyopathy and Emery-Dreifuss muscular dystrophy associated with genetic variant LMNAp.Arg527Pro.32059175 · Perepelina, Kseniya, Klauzen, Polina, Khudiakov, Aleksandr et al.2021 · 7 citationsStem cell research. 2020;43:101714
Clinical Response to Personalized Exercise Therapy in Heart Failure Patients with Reduced Ejection Fraction is Accompanied by Skeletal Muscle Histological Alterations.31694310 · Lelyavina, Tatiana A, Galenko, Victoria L, Ivanova, Oksana A et al.2020 · 5 citationsInternational journal of molecular sciences. 2019;20(21)
Truncating Variant in Myof Gene Is Associated With Limb-Girdle Type Muscular Dystrophy and Cardiomyopathy.31297131 · Kiselev, Artem, Vaz, Raquel, Knyazeva, Anastasia et al.2020 · 15 citationsFrontiers in genetics. 2019;10:608
LKB1 expressed in dendritic cells governs the development and expansion of thymus-derived regulatory T cells.30940876 · Pelgrom, Leonard R, Patente, Thiago A, Sergushichev, Alexey et al.2020 · 47 citationsCell research. 2019;29(5):406-419
Skeletal Muscle Resident Progenitor Cells Coexpress Mesenchymal and Myogenic Markers and Are Not Affected by Chronic Heart Failure-Induced Dysregulations.30719048 · Dmitrieva, R I, Lelyavina, T A, Komarova, M Y et al.2022 · 18 citationsStem cells international. 2019;2019:5690345
Publisher Correction: Mycobacterium tuberculosis carrying a rifampicin drug resistance mutation reprograms macrophage metabolism through cell wall lipid changes.30327492 · Howard, Nicole C, Marin, Nancy D, Ahmed, Mushtaq et al.2021 · 7 citationsNature microbiology. 2018;3(11):1327
Mycobacterium tuberculosis carrying a rifampicin drug resistance mutation reprograms macrophage metabolism through cell wall lipid changes.30224802 · Howard, Nicole C, Marin, Nancy D, Ahmed, Mushtaq et al.2019 · 109 citationsNature microbiology. 2018;3(10):1099-1108
The Soft Vertex Classification for Active Module Identification Problem10.1101/407460v1 · Alexeev, N., Isomurodov, J., Korotkevich, G. et al.2018 · 0 citationsbioRxiv
De novo mutations in FLNC leading to early-onset restrictive cardiomyopathy and congenital myopathy.29858533 · Kiselev, Artem, Vaz, Raquel, Knyazeva, Anastasia et al.2019 · 67 citationsHuman mutation. 2018;39(9):1161-1172
Rare Case of Ulnar-Mammary-Like Syndrome With Left Ventricular Tachycardia and Lack of TBX3 Mutation.29963074 · Zlotina, Anna, Kiselev, Artem, Sergushichev, Alexey et al.2024 · 6 citationsFrontiers in genetics. 2018;9:209
Electrophilic properties of itaconate and derivatives regulate the IκBζ-ATF3 inflammatory axis.29670287 · Bambouskova, Monika, Gorvel, Laurent, Lampropoulou, Vicky et al.2018 · 712 citationsNature. 2018;556(7702):501-504
Draft Genome Sequence of Coxiella burnetii Historical Strain Leningrad-2, Isolated from Blood of a Patient with Acute Q Fever in Saint Petersburg, Russia.29348343 · Freylikhman, Olga, Kiselev, Artem, Kazakov, Sergey et al.2020 · 4 citationsGenome announcements. 2018;6(3)
Generation of iPSC line from desmin-related cardiomyopathy patient carrying splice site mutation of DES gene.29034897 · Khudiakov, Aleksandr, Kostina, Daria, Zlotina, Anna et al.2018 · 10 citationsStem cell research. 2017;24:77-80
Generation of iPSC line from patient with arrhythmogenic right ventricular cardiomyopathy carrying mutations in PKP2 gene.29034900 · Khudiakov, Aleksandr, Kostina, Daria, Zlotina, Anna et al.2018 · 16 citationsStem cell research. 2017;24:85-88
TREM2 Maintains Microglial Metabolic Fitness in Alzheimer's Disease.28802038 · Ulland, Tyler K, Song, Wilbur M, Huang, Stanley Ching-Cheng et al.2017 · 1,253 citationsCell. 2017;170(4):649-663.e13
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