Anatoly Sorokin

Anatoly Sorokin

Still alive

Sitemap

A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.

Pages

Posts

The new Bioconductor release

2 minute read

Published:

The new version (1.4) of the BioNAR package is released. In this version we add the number of important features:

New package version in Bioconductor

less than 1 minute read

Published:

We’ve got the new version of the package BioNAR accepted for the Bioconductor release 3.17. The package is designed for step by step analysis biological networks with sophisticated metrics such as Perturbation Entropy or Disease-Disease separation. Package contains number of real networks as datasets: presynaptic PPI network and Barabasi’s bipartite Diseasome network Goh.t al. 2007.

New package in Bioconductor

less than 1 minute read

Published:

We’ve got the new package BioNAR accepted for the Bioconductor release 3.16. The package is designed for step by step analysis biological networks with sophisticated metrics such as Perturbation Entropy or Disease-Disease separation. Package contains number of real networks as datasets: presynaptic PPI network and Barabasi’s bipartite Diseasome network Goh.t al. 2007.

portfolio

publications

Automated Analysis of Interatomic Contacts in Proteins.

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

The Edinburgh human metabolic network reconstruction and its functional analysis.

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

The systems biology graphical notation.

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

Systems biology reveals new strategies for personalizing cancer medicine and confirms the role of PTEN in resistance to trastuzumab.

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

A Community-Driven Global Reconstruction of Human Metabolism

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

Electrostatic Map of T7 DNA: Comparative Analysis of Functional and Electrostatic Properties of T7 RNA Polymerase-Specific Promoters.

Published in J. Biomol. Struct. Dyn., 2014

Access paper here

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

Dynamics of Elongation Factor 2 Kinase Regulation in Cortical Neurons in Response to Synaptic Activity.

Published in J. Neurosci. Off. J. Soc. Neurosci., 2015

Access paper here

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

Comparative Metagenomic Analysis of Electrogenic Microbial Communities in Differentially Inoculated Swine Wastewater-Fed Microbial Fuel Cells

Published in Scientifica, 2017

Access paper here

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/

Feature Selection Algorithm for Spray-from-Tissue Mass Spectrometry

Published in Eur J Mass Spectrom Chichester, 2017

Access paper here

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

High-Resolution Mass Spectra Processing for the Identification of Different Pathological Tissue Types of Brain Tumors

Published in Eur J Mass Spectrom Chichester, 2017

Access paper here

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

Bacterial Promoter Prediction: Selection of Dynamic and Static Physical Properties of DNA for Reliable Sequence Classification.

Published in J. Bioinform. Comput. Biol., 2018

Access paper here

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

Evolutionary Dynamics of Microbial Communities in Bioelectrochemical Systems

Published in J. Comput. Sci. Syst. Biol., 2020

Access paper here

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

Assessment of Variation of Inline Cartridge Extraction Mass Spectra.

Published in J. Mass Spectrom., 2020

Access paper here

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

Comparison of Dimensionality Reduction Methods in Mass Spectra of Astrocytoma and Glioblastoma Tissues.

Published in Mass Spectrom. Tokyo Jpn., 2021

Access paper here

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

Comparative Analysis of Milk Microbiomes and Their Association with Bovine Mastitis in Two Farms in Central Russia.

Published in Anim. Open Access J. MDPI, 2021

Access paper here

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

Aggregation of Multimodal ICE-MS Data into Joint Classifier Increases Quality of Brain Cancer Tissue Classification.

Published in Data, 2022

Access paper here

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

talks

Modelling of bacterial metabolism and metabolic interspecies interactions in reach media

Published:

Since 1999 when the first GEnome-scale Metabolic model (GEM) was published 1, GEMs have provided an invaluable tool for analysis of the physiological capabilities of living organisms. Initially, it was single-cell organisms mainly bacteria, but more complex were added later. Development of the human metabolic reconstruction (2, 3) and reorganisation it with tissue-specific submodels into an integrated whole-body model (4) open the avenue for a better understanding of pathological processes such as cancer development. Apart from human GEM, several large collections of models were created by manual curation (5), semi-automated reconstruction (6), or fully-automated reconstruction (see in 7) techniques.

teaching

Teaching experience 1

Undergraduate course, University 1, Department, 2014

This is a description of a teaching experience. You can use markdown like any other post.

Teaching experience 2

Workshop, University 1, Department, 2015

This is a description of a teaching experience. You can use markdown like any other post.