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Alexey Stupnikov
Alexey Stupnikov
Moscow Institute of Physics and Technology
Verifisert e-postadresse på phystech.edu
Tittel
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Robustness of differential gene expression analysis of RNA-seq
A Stupnikov, CE McInerney, KI Savage, SA McIntosh, F Emmert-Streib, ...
Computational and structural biotechnology journal 19, 3470-3481, 2021
762021
Cooption of heat shock regulatory system for anhydrobiosis in the sleeping chironomid Polypedilum vanderplanki
PV Mazin, E Shagimardanova, O Kozlova, A Cherkasov, R Sutormin, ...
Proceedings of the National Academy of Sciences 115 (10), E2477-E2486, 2018
402018
Comparing biological information contained in mRNA and non-coding RNAs for classification of lung cancer patients
J Smolander, A Stupnikov, G Glazko, M Dehmer, F Emmert-Streib
BMC cancer 19, 1-15, 2019
262019
Recounting the FANTOM CAGE-Associated Transcriptome
EL Imada, DF Sanchez, L Collado-Torres, C Wilks, T Matam, ...
Genome research 30 (7), 1073-1081, 2020
252020
samExploreR: Exploring reproducibility and robustness of RNA-seq results based on SAM files
A Stupnikov, S Tripathi, R de Matos Simoes, D McArt, M Salto-Tellez, ...
Bioinformatics 32 (21), 3345-3347, 2016
132016
Approaches for sRNA Analysis of Human RNA-Seq Data: Comparison, Benchmarking
V Bezuglov, A Stupnikov, I Skakov, V Shtratnikova, JR Pilsner, A Suvorov, ...
International Journal of Molecular Sciences 24 (4), 4195, 2023
72023
Hobotnica: exploring molecular signature quality
A Stupnikov, A Sizykh, A Favorov, B Afsari, S Wheelan, L Marchionni, ...
F1000Research 10 (1260), 1260, 2022
72022
Effects of subsampling on characteristics of RNA-seq data from triple-negative breast cancer patients
A Stupnikov, GV Glazko, F Emmert-Streib
Chinese Journal of Cancer 34, 1-12, 2015
72015
In Silico Drug Repurposing in Multiple Sclerosis Using scRNA-Seq Data
A Shevtsov, M Raevskiy, A Stupnikov, Y Medvedeva
International Journal of Molecular Sciences 24 (2), 985, 2023
62023
Clinically actionable insights into initial and matched recurrent glioblastomas to inform novel treatment approaches
HP Ellis, CE McInerney, D Schrimpf, F Sahm, A Stupnikov, M Wadsley, ...
Journal of Oncology 2019 (1), 4878547, 2019
62019
scATAC-seq preprocessing and imputation evaluation system for visualization, clustering and digital footprinting
P Akhtyamov, L Shaheen, M Raevskiy, A Stupnikov, YA Medvedeva
Briefings in Bioinformatics 25 (1), bbad447, 2024
52024
ITAS: Integrated Transcript Annotation for Small RNA
A Stupnikov, V Bezuglov, I Skakov, V Shtratnikova, JR Pilsner, A Suvorov, ...
Non-Coding RNA 8 (3), 30, 2022
52022
Impact of variable rna-sequencing depth on gene expression signatures and target compound robustness: case study examining brain tumor (Glioma) disease progression
A Stupnikov, PG O’Reilly, CE McInerney, AC Roddy, PD Dunne, ...
JCO precision oncology 2, 1-17, 2018
52018
NUQA: estimating cancer spatial and temporal heterogeneity and evolution through alignment-free methods
AC Roddy, A Jurek-Loughrey, J Souza, A Gilmore, PG O’Reilly, ...
Molecular biology and evolution 36 (12), 2883-2889, 2019
32019
Assessing the Differential Methylation Analysis Quality for Microarray and NGS Platforms
A Budkina, YA Medvedeva, A Stupnikov
International Journal of Molecular Sciences 24 (10), 8591, 2023
22023
CFM: a database of experimentally validated protocols for chemical compound-based direct reprogramming and transdifferentiation
A Sizykh, K Murtazalieva, Y Vyshkvorkina, A Stupnikov, YA Medvedeva
F1000Research 10, 295, 2021
22021
Mutational landscape of primary and recurrent glioblastoma reveals potentially actionable SNVs including WNT pathway variation
MH Ellis, F Sahm, D Schrimpf, A Stupnikov, M Wadsley, C Wragg, D McArt, ...
Neuro-oncology 20 (Suppl 1), i16, 2018
12018
GPU-accelerated Kendall distance computation for large or sparse data
P Akhtyamov, A Nabi, V Gafurov, A Sizykh, A Favorov, Y Medvedeva, ...
GigaScience 13, giae088, 2024
2024
Comprehensive analysis of alternative polyadenylation across cancer phenotypes
EL Imada, DF Sanchez, T Matam, L Collado-Torres, C Wilks, ...
Cancer Research 79 (13_Supplement), 908-908, 2019
2019
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Artikler 1–19