Published in Current Protocols, 2023
Recommended citation: McLean, C., Sorokin, A., Armstrong, J. D., & Sorokina, O. (2023). Computational pipeline for analysis of biomedical networks with BioNAR. Current Protocols, 3, e940. doi: 10.1002/cpz1.940 https://doi.org/10.1002/cpz1.940
Published in Bioinformatics Advances, 2023
Recommended citation: Colin McLean, Anatoly Sorokin, Thomas Ian Simpson, James Douglas Armstrong, Oksana Sorokina, BioNAR: an integrated biological network analysis package in bioconductor, Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad137 https://www.mdpi.com/2184026
Published in Biomolecules, 2023
Recommended citation: Anatoly Sorokin, Igor Goryanin, "FBA-PRCC. Partial Rank Correlation Coefficient (PRCC) Global Sensitivity Analysis (GSA) in Application to Constraint-Based Models." Biomolecules 2023, 13(3), 500 https://www.mdpi.com/2184026
Published in Data, 2022
Recommended citation: Sorokin, Anatoly A., Denis S. Bormotov, Denis S. Zavorotnyuk, Vasily A. Eliferov, Konstantin V. Bocharov, Stanislav I. Pekov, Evgeny N. Nikolaev, and Igor A. Popov. 2023. "Aggregation of Multimodal ICE-MS Data into Joint Classifier Increases Quality of Brain Cancer Tissue Classification" Data 8, no. 1: 8. https://doi.org/10.3390/data8010008 https://www.mdpi.com/2306-5729/8/1/8
Published in Bioinformatics Advances, 2022
Recommended citation: Oksana Sorokina, Anatoly Sorokin, J Douglas Armstrong, "Synaptome.db: A Bioconductor package for synaptic proteomics data", Bioinformatics Advances, 2022, vbac086 https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbac086/6825339
Published in Anim. Open Access J. MDPI, 2021
Recommended citation: Sergei Sokolov, Ksenia Fursova, Irina Shulcheva, Daria Nikanova, Olga Artyemieva, Evgenia Kolodina, Anatoly Sorokin, Timur Dzhelyadin, Margarita Shchannikova, Anna Shepelyakovskaya, Natalia Zinovieva, Fedor Brovko, "Comparative Analysis of Milk Microbiomes and Their Association with Bovine Mastitis in Two Farms in Central Russia.." Anim. Open Access J. MDPI, 2021. https://www.mdpi.com/2076-2615/11/5/1401/htm
Published in Anal. Chem., 2021
Recommended citation: Evgeny Zhvansky, Daniil Ivanov, Anatoly Sorokin, Anna Bugrova, Evgeny Nikolaev, Igor Popov, "Interactive Estimation of Heterogeneity from Mass Spectrometry Imaging.." Anal. Chem., 2021. https://pubs.acs.org/doi/abs/10.1021/acs.analchem.1c00437
Published in Dokl. Biochem. Biophys., 2021
Recommended citation: K Fursova, S Sokolov, M Shchannikova, D Nikanova, O Artem'eva, E Kolodina, A Sorokin, T Dzhelyadin, I Shulcheva, A Shepelyakovskaya, N Zinovieva, F Brovko, "Changes in the Microbiome of Milk in Cows with Mastitis.." Dokl. Biochem. Biophys., 2021. https://link.springer.com/article/10.1134/S1607672921020046
Published in Mass Spectrom. Tokyo Jpn., 2021
Recommended citation: Evgeny Zhvansky, Anatoly Sorokin, Vsevolod Shurkhay, Denis Zavorotnyuk, Denis Bormotov, Stanislav Pekov, Alexander Potapov, Evgeny Nikolaev, Igor Popov, "Comparison of Dimensionality Reduction Methods in Mass Spectra of Astrocytoma and Glioblastoma Tissues.." Mass Spectrom. Tokyo Jpn., 2021. https://www.jstage.jst.go.jp/article/massspectrometry/10/1/10_A0094/_article
Published in J. Mass Spectrom., 2020
Recommended citation: Evgeny Zhvansky, Vasiliy Eliferov, Anatoly Sorokin, Vsevolod Shurkhay, Stanislav Pekov, Denis Bormotov, Daniil Ivanov, Denis Zavorotnyuk, Konstantin Bocharov, Iliyas Khaliullin, Maksim Belenikin, Aleksandr Potapov, Evgeny Nikolaev, Igor Popov, "Assessment of Variation of Inline Cartridge Extraction Mass Spectra.." J. Mass Spectrom., 2020. http://doi.wiley.com/10.1002/jms.4640
Published in J. Comput. Sci. Syst. Biol., 2020
Recommended citation: Lukasz Szydlowski, Anatoly Sorokin, Olga Vasieva, Susan Boerner, Veyacheslav Feodorovich, Igor Goryanin, "Evolutionary Dynamics of Microbial Communities in Bioelectrochemical Systems." J. Comput. Sci. Syst. Biol., 2020. https://www.hilarispublisher.com/open-access/evolutionary-dynamics-of-microbial-communities-in-bioelectrochemical-systems.pdf
Published in Sci. Rep., 2019
Recommended citation: Stanislav Pekov, Vasily Eliferov, Anatoly Sorokin, Vsevolod Shurkhay, Evgeny Zhvansky, Alexander Vorobyev, Alexander Potapov, Eugene Nikolaev, Igor Popov, "Inline Cartridge Extraction for Rapid Brain Tumor Tissue Identification by Molecular Profiling.." Sci. Rep., 2019. https://www.nature.com/articles/s41598-019-55597-7
Published in Bioinformatics (Oxford, England), 2018
Recommended citation: Askarbek Orakov, Nazgul Sakenova, Anatoly Sorokin, Igor Goryanin, "ASAR: Visual Analysis of Metagenomes in R.." Bioinformatics (Oxford, England), 2018. http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=29211828&retmode=ref&cmd=prlinks
Published in J. Bioinform. Comput. Biol., 2018
Recommended citation: Artem Ryasik, Mikhail Orlov, Evgenia Zykova, Timofei Ermak, Anatoly Sorokin, "Bacterial Promoter Prediction: Selection of Dynamic and Static Physical Properties of DNA for Reliable Sequence Classification.." J. Bioinform. Comput. Biol., 2018. http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=29382253&retmode=ref&cmd=prlinks
Published in Front. Genet., 2018
Recommended citation: Mikhail Orlov, Irina Garanina, Gleb Fisunov, Anatoly Sorokin, "Comparative Analysis of Mycoplasma Gallisepticum vlhA Promoters.." Front. Genet., 2018. https://www.frontiersin.org/article/10.3389/fgene.2018.00569/full
Published in Eur J Mass Spectrom Chichester, 2017
Recommended citation: Evgeny Zhvansky, Anatoly Sorokin, Igor Popov, Vsevolod Shurkhay, Alexander Potapov, Eugene Nikolaev, "High-Resolution Mass Spectra Processing for the Identification of Different Pathological Tissue Types of Brain Tumors." Eur J Mass Spectrom Chichester, 2017. http://journals.sagepub.com/doi/abs/10.1177/1469066717721484
Published in Eur J Mass Spectrom Chichester, 2017
Recommended citation: Anatoly Sorokin, Evgeny Zhvansky, Vsevolod Shurkhay, Konstantin Bocharov, Igor Popov, Nikita Levin, Dmitry Zubtsov, Denis Bormotov, Yury Kostyukevich, Alexander Potapov, Eugene Nikolaev, "Feature Selection Algorithm for Spray-from-Tissue Mass Spectrometry." Eur J Mass Spectrom Chichester, 2017. http://journals.sagepub.com/doi/abs/10.1177/1469066717721843
Published in Scientifica, 2017
Recommended citation: Irina Khilyas, Anatoly Sorokin, Larisa Kiseleva, David Simpson, V Fedorovich, Margarita Sharipova, Mami Kainuma, Michael Cohen, Igor Goryanin, "Comparative Metagenomic Analysis of Electrogenic Microbial Communities in Differentially Inoculated Swine Wastewater-Fed Microbial Fuel Cells." Scientifica, 2017. https://www.hindawi.com/journals/scientifica/2017/7616359/
Published in FEBS J., 2016
Recommended citation: A Ryasik, Mikhail Orlov, E Temlyakova, Anatoly Sorokin, "Classification of E. Coli Promoters with DNA Open States Dynamic Characteristics." FEBS J., 2016. http://doi.wiley.com/10.1111/febs.13808
Published in J. Neurosci. Off. J. Soc. Neurosci., 2015
Recommended citation: Justin Kenney, Oksana Sorokina, Maja Genheden, Anatoly Sorokin, J Armstrong, Christopher Proud, "Dynamics of Elongation Factor 2 Kinase Regulation in Cortical Neurons in Response to Synaptic Activity.." J. Neurosci. Off. J. Soc. Neurosci., 2015. http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=25698741&retmode=ref&cmd=prlinks
Published in J. Biomol. Struct. Dyn., 2014
Recommended citation: S Kamzolova, P Beskaravainy, A Osypov, T Dzhelyadin, E Temlyakova, Anatoly Sorokin, "Electrostatic Map of T7 DNA: Comparative Analysis of Functional and Electrostatic Properties of T7 RNA Polymerase-Specific Promoters.." J. Biomol. Struct. Dyn., 2014. http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=23895582&retmode=ref&cmd=prlinks
Published in Bioinformatics (Oxford, England), 2013
Recommended citation: Oksana Sorokina, Anatoly Sorokin, J Douglas, Vincent Danos, "A Simulator for Spatially Extended Kappa Models.." Bioinformatics (Oxford, England), 2013. http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=24021382&retmode=ref&cmd=prlinks
Published in Nat. Biotechnol., 2013
Here we describe Recon 2, a community-driven, consensus "metabolic reconstruction", which is the most comprehensive representation of human metabolism that is applicable to computational modeling.
Recommended citation: Ines Thiele, Neil Swainston, Ronan Fleming, Andreas Hoppe, Swagatika Sahoo, Maike Aurich, Hulda Haraldsdottir, Monica Mo, Ottar Rolfsson, Miranda Stobbe, Stefan Thorleifsson, Rasmus Agren, Christian B{\"o}lling, Sergio Bordel, Arvind Chavali, Paul Dobson, Warwick Dunn, Lukas Endler, David Hala, Michael Hucka, Duncan Hull, Daniel Jameson, Neema Jamshidi, Jon Jonsson, Nick Juty, Sarah Keating, Intawat Nookaew, Nicolas Le, Naglis Malys, Alexander Mazein, Jason Papin, Nathan Price, Evgeni Selkov, Martin Sigurdsson, Evangelos Simeonidis, Nikolaus Sonnenschein, Kieran Smallbone, Anatoly Sorokin, Johannes {\noopsort{beek}}{van Beek}, Dieter Weichart, Igor Goryanin, Jens Nielsen, Hans Westerhoff, Douglas Kell, Pedro Mendes, Bernhard Palsson, "A Community-Driven Global Reconstruction of Human Metabolism." Nat. Biotechnol., 2013. https://www.nature.com/articles/nbt.2488
Published in Eur. J. Pharm. Sci., 2012
Recommended citation: Anatoly Sorokin, Gene Selkov, Igor Goryanin, "A User-Defined Data Type for the Storage of Time Series Data Allowing Efficient Similarity Screening." Eur. J. Pharm. Sci., 2012. http://linkinghub.elsevier.com/retrieve/pii/S0928098711004404
Published in J. Biomol. Struct. Dyn., 2011
Recommended citation: S Kamzolova, P Beskaravainy, Anatoly Sorokin, "Electrostatic Properties of Bacteriophage T7 Early Promoters Recognized by E. Coli RNA Polymerase." J. Biomol. Struct. Dyn., 2011. http://www.csa.com/partners/viewrecord.php?requester=gs&collection=ENV&recid=14806445
Published in In the proceedings of Biomarkers and Human Biomonitoring, 2011
Recommended citation: A FUCIC, A Sorokin, "Chapter 13. Biomarkers of Exposure and Effect: Ionizing Radiation." In the proceedings of Biomarkers and Human Biomonitoring, 2011. http://pubs.rsc.org/en/content/chapter/bk9781849732420-00199/978-1-84973-242-0/unauth
Published in Cancer Res, 2009
In this study, we aimed to develop a new kinetic model that could be interrogated to predict resistance to receptor tyrosine kinase (RTK) inhibitor therapies and directly test predictions in vitro and in clinical samples.
Recommended citation: Dana Faratian, Alexey Goltsov, Galina Lebedeva, Anatoly Sorokin, Stuart Moodie, Peter Mullen, Charlene Kay, In Hwa Um, Simon Langdon, Igor I Goryanin, and David J Harrison. (2009). "Systems biology reveals new strategies for personalizing cancer medicine and confirms the role of PTEN in resistance to trastuzumab." Cancer Res, vol. 69 (16) pp. 6713-6720. https://doi.org/10.1158/0008-5472.CAN-09-0777
Published in Nat Biotechnol, 2009
We present the Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists.
Recommended citation: Nicolas Le Novère, Michael Hucka, Huaiyu Mi, Stuart Moodie, Falk Schreiber, Anatoly Sorokin, et al. (2009). "The systems biology graphical notation." Nat Biotechnol, vol. 27 (8) pp. 735-741. https://doi.org/10.1038/nbt.1558
Published in BMC Syst. Biol., 2009
Recommended citation: Gavin Thomas, Jeremy Zucker, Sandy Macdonald, Anatoly Sorokin, Igor Goryanin, Angela Douglas, "A Fragile Metabolic Network Adapted for Cooperation in the Symbiotic Bacterium Buchnera Aphidicola." BMC Syst. Biol., 2009. http://www.biomedcentral.com/1752-0509/3/24
Published in In the proceedings of BGRS 2004, 2008
Recommended citation: S Kamzolova, Anatoly Sorokin, T Dzhelyadin, P Beskaravainy, A Osypov, "ELECTROSTATIC PROPERTIES OF E. COLI GENOME DNA." In the proceedings of BGRS 2004, 2008. http://www.bionet.nsc.ru/meeting/bgrs_proceedings/papers/2004/BGRS_2004_V1_018.pdf
Published in Mol Syst Biol, 2007
In this paper, we present a high-quality human metabolic network manually reconstructed by integrating genome annotation information from different databases and metabolic reaction information from literature.
Recommended citation: Hongwu Ma, Anatoly Sorokin, Alexander Mazein, Alex Selkov, Evgeni Selkov, Oleg Demin, and Igor I Goryanin. (2007). "The Edinburgh human metabolic network reconstruction and its functional analysis." Mol Syst Biol, vol. 3 p. 135. https://doi.org/10.1038/msb4100177
Published in J. Bioinform. Comput. Biol., 2006
Recommended citation: Anatoly Sorokin, Alexandr Osypov, Timur Dzhelyadin, Petr Beskaravainy, Svetlana Kamzolova, "Electrostatic Properties of Promoter Recognized by E. Coli RNA Polymerase Esigma70.." J. Bioinform. Comput. Biol., 2006. http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=16819795&retmode=ref&cmd=prlinks
Published in J. Biomol. Struct. Dyn., 2005
Recommended citation: S Kamzolova, Anatoly Sorokin, T Dzhelyadin, P Beskaravainy, A Osypov, "Electrostatic Potentials of E.Coli Genome DNA." J. Biomol. Struct. Dyn., 2005. http://www.jbsdonline.com/c3021/c4189/Electrostatic-Potentials-of-iEcoli-i-Genome-DNA-p-341-346-p13159.html
Published in J. Biomol. Struct. Dyn., 1999
Recommended citation: R Polozov, T Dzhelyadin, Anatoly Sorokin, N Ivanova, V Sivozhelezov, S Kamzolova, "Electrostatic Potentials of DNA. Comparative Analysis of Promoter and Nonpromoter Nucleotide Sequences.." J. Biomol. Struct. Dyn., 1999. http://www.tandfonline.com/doi/abs/10.1080/07391102.1999.10508322
Published in Bioinformatics (Oxford, England), 1999
Tools are described for the analysis of ligand-protein contacts (LPC software) and contacts of structural units (CSU software) such as helices, sheets, strands and residues.
Recommended citation: V Sobolev, A Sorokine, J Prilusky, E Abola, M Edelman, "Automated Analysis of Interatomic Contacts in Proteins.." Bioinformatics (Oxford, England), 1999. https://academic.oup.com/bioinformatics/article/15/4/327/238299