Alexey Stupnikov

Bioinformatics of direct chemical reprogramming.
Introducing computational methods to identify chemical agents, potentially assisting cell state alteration in direct chemical reprogramming problem.

Hobotnica: exploring molecular sig natures and biomarkers quality.
Introducing and applying rank statistics based approach to evaluate molecular signatures quality for data stratification.

1. Stupnikov A, McInerney CE, Savage KI, McIntosh SA, Emmert-Streib F, Kennedy R, Salto-Tellez M, Prise KM, McArt DG. Robustness of differential gene expression analysis of RNA-seq. Comput Struct Biotechnol J. 2021 May 26;19:3470-3481. doi: 10.1016/j.csbj.2021.05.040. PMID: 34188784; PMCID: PMC8214188.
2. Imada EL, Sanchez DF, Collado-Torres L, Wilks C, Matam T, Dinalankara W, Stupnikov A, Lobo-Pereira F, Yip CW, Yasuzawa K, Kondo N, Itoh M, Suzuki H, Kasukawa T, Hon CC, de Hoon MJL, Shin JW, Carninci P, Jaffe AE, Leek JT, Favorov A, Franco GR, Langmead B, Marchionni L. Recounting the FANTOM CAGE-Associated Transcriptome. Genome Res. 2020 Jul;30(7):1073-1081. doi: 10.1101/gr.254656.119. Epub 2020 Feb 20. PMID: 32079618; PMCID: PMC7397872.
3. Stupnikov A, O'Reilly PG, McInerney CE, Roddy AC, Dunne PD, Gilmore A, Ellis HP, Flannery T, Healy E, McIntosh SA, Savage K, Kurian KM, Emmert-Streib F, Prise KM, Salto-Tellez M, McArt DG. Impact of Variable RNA-Sequencing Depth on Gene Expression Signatures and Target Compound Robustness: Case Study Examining Brain Tumor (Glioma) Disease Progression. JCO Precis Oncol. 2018 Sep 13;2:PO.18.00014. doi: 10.1200/PO.18.00014. PMID: 30324181; PMCID: PMC6186166.
4. Ellis HP, McInerney CE, Schrimpf D, Sahm F, Stupnikov A, Wadsley M, Wragg C, White P, Prise KM, McArt DG, Kurian KM. Clinically Actionable Insights into Initial and Matched Recurrent Glioblastomas to Inform Novel Treatment Approaches. J Oncol. 2019 Dec 31;2019:4878547. doi: 10.1155/2019/4878547. PMID: 32082376; PMCID: PMC7012245.
5. Smolander J, Stupnikov A, Glazko G, Dehmer M, Emmert-Streib F. Comparing biological information contained in mRNA and non-coding RNAs for classification of lung cancer patients. BMC Cancer. 2019 Dec 3;19(1):1176. doi: 10.1186/s12885-019-6338-1. PMID: 31796020; PMCID: PMC6892207.
6. Mazin PV, Shagimardanova E, Kozlova O, Cherkasov A, Sutormin R, Stepanova VV, Stupnikov A, Logacheva M, Penin A, Sogame Y, Cornette R, Tokumoto S, Miyata Y, Kikawada T, Gelfand MS, Gusev O. Cooption of heat shock regulatory system for anhydrobiosis in the sleeping chironomid Polypedilum vanderplanki. Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):E2477-E2486. doi: 10.1073/pnas.1719493115. Epub 2018 Feb 20. PMID: 29463761; PMCID: PMC5877948.
7. Stupnikov A, Tripathi S, de Matos Simoes R, McArt D, Salto-Tellez M, Glazko G, Dehmer M, Emmert-Streib F. samExploreR: exploring reproducibility and robustness of RNA-seq results based on SAM files. Bioinformatics. 2016 Nov 1;32(21):3345-3347. doi: 10.1093/bioinformatics/btw475. Epub 2016 Jul 10. PMID: 27402900.