scATAC-seq preprocessing and imputation evaluation system for visualization, clustering and digital footprinting.

Autor: Akhtyamov P; Department of Biomedical Physics, Moscow Institute of Physics and Technology (National Research University), 9 Institutskiy per., 141701, Moscow Region, Russian Federation.; The National Medical Research Center for Endocrinology, Dm. Ulyanova, 11, 117036, Moscow, Russian Federation., Shaheen L; Department of Biomedical Physics, Moscow Institute of Physics and Technology (National Research University), 9 Institutskiy per., 141701, Moscow Region, Russian Federation.; The National Medical Research Center for Endocrinology, Dm. Ulyanova, 11, 117036, Moscow, Russian Federation., Raevskiy M; Department, École Polytechnique Fédérale de Lausanne, Rte Cantonale, 1015, Lausanne, Vaud, Switzerland., Stupnikov A; Department of Biomedical Physics, Moscow Institute of Physics and Technology (National Research University), 9 Institutskiy per., 141701, Moscow Region, Russian Federation.; The National Medical Research Center for Endocrinology, Dm. Ulyanova, 11, 117036, Moscow, Russian Federation.; Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Science, Leninsky prospect, 33, build. 2, 119071, Moscow, Russian Federation., Medvedeva YA; Department of Biomedical Physics, Moscow Institute of Physics and Technology (National Research University), 9 Institutskiy per., 141701, Moscow Region, Russian Federation.; The National Medical Research Center for Endocrinology, Dm. Ulyanova, 11, 117036, Moscow, Russian Federation.; Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Science, Leninsky prospect, 33, build. 2, 119071, Moscow, Russian Federation.

Publikováno v: Briefings in bioinformatics [Brief Bioinform] 2023 Nov 22; Vol. 25 (1).

Approaches for sRNA Analysis of Human RNA-Seq Data: Comparison, Benchmarking.

Autor: Bezuglov V; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia.; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia., Stupnikov A; Department of Biomedical Physics, Moscow Institute of Physics and Technology, 141701 Moscow, Russia.; National Medical Research Center for Endocrinology, 115478 Moscow, Russia., Skakov I; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia., Shtratnikova V; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia., Pilsner JR; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48201, USA., Suvorov A; Department of Environmental Health Sciences, University of Massachusetts, Amherst, MA 01003, USA., Sergeyev O; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia.

Publikováno v: International journal of molecular sciences [Int J Mol Sci] 2023 Feb 20; Vol. 24 (4). Date of Electronic Publication: 2023 Feb 20.

ITAS: Integrated Transcript Annotation for Small RNA.

Autor: Stupnikov A; Moscow Institute of Physics and Technology, 141701 Moscow, Russia.; National Medical Research Center for Endocrinology, 115478 Moscow, Russia., Bezuglov V; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia.; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia., Skakov I; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia., Shtratnikova V; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia., Pilsner JR; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48201, USA., Suvorov A; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia.; Department of Environmental Health Sciences, University of Massachusetts, Amherst, MA 01003, USA., Sergeyev O; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia.

Publikováno v: Non-coding RNA [Noncoding RNA] 2022 May 02; Vol. 8 (3). Date of Electronic Publication: 2022 May 02.

Comparing biological information contained in mRNA and non-coding RNAs for classification of lung cancer patients.

Autor: Smolander J; Predictive Society and Data Analytics Lab, Faculty of Information Technology and Communication Sciences, Tampere University, Tampere, Finland.; Turku Centre for Biotechnology, University of Turku, Turku, Finland., Stupnikov A; Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, USA., Glazko G; Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, USA., Dehmer M; Institute for Intelligent Production, Faculty for Management, University of Applied Sciences Upper Austria, Steyr, Austria.; Department of Mechatronics and Biomedical Computer Science, UMIT, Hall in Tyrol, Austria.; College of Artificial Intelligence, Nankai University, China, Tianjin, China., Emmert-Streib F; Predictive Society and Data Analytics Lab, Faculty of Information Technology and Communication Sciences, Tampere University, Tampere, Finland. v@bio-complexity.com.; Institute of Biosciences and Medical Technology, Tampere, Finland. v@bio-complexity.com.

Publikováno v: BMC cancer [BMC Cancer] 2019 Dec 03; Vol. 19 (1), pp. 1176. Date of Electronic Publication: 2019 Dec 03.

Impact of Variable RNA-Sequencing Depth on Gene Expression Signatures and Target Compound Robustness: Case Study Examining Brain Tumor (Glioma) Disease Progression.

Autor: Stupnikov A; Queen's University Belfast; Johns Hopkins University, Baltimore, MD., O'Reilly PG; Queen's University Belfast., McInerney CE; Queen's University Belfast., Roddy AC; Queen's University Belfast., Dunne PD; Queen's University Belfast., Gilmore A; Queen's University Belfast., Ellis HP; Brain Tumour Research Centre, University of Bristol, Bristol, United Kingdom., Flannery T; Belfast Health and Social Care Trust, Belfast, United Kingdom., Healy E; Belfast Health and Social Care Trust, Belfast, United Kingdom., McIntosh SA; Queen's University Belfast., Savage K; Queen's University Belfast., Kurian KM; Brain Tumour Research Centre, University of Bristol, Bristol, United Kingdom., Emmert-Streib F; Tampere University of Technology, Tampere, Finland., Prise KM; Queen's University Belfast., Salto-Tellez M; Queen's University Belfast; Belfast Health and Social Care Trust, Belfast, United Kingdom., McArt DG; Queen's University Belfast.

Publikováno v: JCO precision oncology [JCO Precis Oncol] 2018 Sep 13; Vol. 2.