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Discovering New Orthologous Groups with P-COGs
Biochemical Genetics, Springer Science+Business Media, LLC, part of Springer Nature, United States. 2026. Article 1573-4927.
Deciphering the evolutionary history of genes is foundational for biomedical research, enabling the identification of compensatory mutations in disease-associated genes and the selection of evolutionarily relevant model organisms. However, challenges of multi-isoform handling, the presence of incomplete genomes/proteomes initial datasets, and problems of evolutionary history representation are still present. To address these issues, we introduce a novel framework based on the Clusters of Orthologous Groups (COG) method, primarily designed for improving phylogenetic tree clustering in studying evolutionary history of eukaryotes, P-COGs (Pavlov's COGs). It encourages the use of a single sequence dataset for both constructing phylogenetic trees and inferring COGs. We demonstrate the tool's utility through an evolutionary study of the voltage-dependent chloride channel genes family (CLCN). Moreover, P-COGs allowed us to observe multiple clusters of orthologous genes in CLCN that were not identified by other COG-based tools. Additionally, we resolved the evolutionary history of hundreds of cancer-associated genes with P-COGs to support accurate evolution-based variant effect prediction. The resulting COG graphs are accessible via our interactive web application ( https://epicenter.1spbgmu.ru/shiny/pavlovscogs/ ). P-COGs is openly available at https://github.com/bugds/Pavlovs_COGs.
David J. L., Leonid Grinin, Korotayev A., , in: Complexity in Universal Evolution. A Big History Perspective.: Springer, 2026. Ch. 22 P. 585–608.
This collective monograph explores focus on complexity aspects in Big History against the background of complexity growth in the Universe, on our planet, and in biological, social, and cultural systems. Complexity growth is regarded as the connecting thread of evolutionary development and as a leading trend of Big History. The cosmic development chapters examine symmetries ...
Added: August 10, 2026
Gabdrahmanov R., Tsoy T., Martinez-Garcia E. et al., , in: Proceedings of the 21st International Conference on Informatics in Control, Automation and Robotics - (Volume 1) ICINCO 2024.: SciTePress, 2024. P. 511–518.
Computer simulations are growing in popularity in robotics research due to their near-zero cost of error and lower labor intensity. One of necessary components of a simulation, in addition to a robot model, is a model of a world in which the robot operates. While it is always possible to construct a world model manually, ...
Added: March 17, 2026
Anna Volodkevich, Ivanova V., Vasilev A. et al., , in: Advances in Information Retrieval: 47th European Conference on Information Retrieval, ECIR 2025, Lucca, Italy, April 6–10, 2025, Proceedings, Part IV.: Springer, 2025. P. 425–430.
Simulators for recommender systems are widely used for recommender systems performance evaluation and feedback loop effects analysis. Existing simulators often propose inflexible pipelines, are focused on narrow research tasks, or are not adapted to work with industrial large data volumes. To address these challenges, we developed the Sim4Rec simulation framework. The Sim4Rec models key aspects ...
Added: April 10, 2025
Shamarina E., В кн.: Революция и эволюция: модели развития в науке, культуре, социуме: Труды IV Международной научной конференции.: М.: Русское общество истории и философии науки, 2023. С. 524–528.
Friedman's notion of a constitutive a priori principle points to his conception of scientific development. In general, the theory of meaning is based on the idea that natural language has rules, and the "meaning" of a word is due to the function of the rule that governs its use. These rules determine which statements are ...
Added: January 10, 2024
Temereva E., Neuroscience and Behavioral Physiology 2022 Vol. 52 P. 77–85
The development and structure of the nervous system are traditionally used for phylogenetic analysis and reconstruction of evolutionary events. Phoronids are an unusual group of protostome animals whose organizational and developmental characteristics are similar to those of deuterostomes. This article presents a brief description of the development and structure of the nervous system in phoronids ...
Added: January 1, 2023
Chirkov S., Tsygankova S., Rastorguev S. et al., Plant Disease 2021 Vol. 105 No. 8 P. 2260
Fig mosaic virus (FMV) (genus Emaravirus in the family Fimoviridae) is considered the etiological agent of fig mosaic disease (FMD), which is recorded in most of the fig-growing areas with an average global infection rate of 33%. The multipartite FMV genome is composed of six negative monocistronic ssRNAs, each of which is separately encapsidated (Preising et al. 2021). Although ...
Added: October 20, 2021
Savelieva A., Temereva E., Invertebrate Biology 2020 Vol. 139 No. 2 Article e12286
The organization of the body cavities is an important morphological trait that can be used for establishing the phylogenetic relationships between different groups of animals. In the present study, the hemocoel and coelomic system of 10-h-old juvenile and adult hermaphroditic oikopleurids, Oikopleura gracilis, are examined using light and transmission electron microscopy. The trunk hemocoel in ...
Added: November 8, 2020
Stoianova Olga, T.A.Lezina, Ivanova V. V., Вестник Санкт-Петербургского университета. Серия 5. Экономика 2020 Vol. 36 No. 2 P. 243–265
At present, the focus of discussions on digital transformation has shifted from issues of its necessity to problems of assessing a company’s readiness for digital transformation. The specificity of digital transformation in Russia requires new criteria of readiness and prioritization of existing criteria. This study explores a combination of factors (prerequisites) that determine the readiness ...
Added: October 3, 2020
Temereva E., Zoology 2020 Vol. 143 P. 1–14
The structure of the lophophore nervous system may help clarify the status of the clade Lophophorata, whose monophyly is debated. In the current study, antibody labeling and confocal laser scanning microscopy revealed previously undescribed main nerve elements in the lophophore in adult phoronids: Phoronis australis and Phoronopsis harmeri. In both species, the nervous system includes ...
Added: September 30, 2020
Sergeyev V., Sergeev I., Логистика и управление цепями поставок 2020 № 1 С. 3–12
The problems of digital transformation of supply chains are considered. A framework for the digital transformation of the supply chain is proposed, which consists of four basic elements: digitalization of customer experience, digitalization of products and services, digitalization of operations / processes, digital transformation of the company / supply chain. The content (functional) structure ...
Added: August 27, 2020
Temereva E., Kosevich I., Frontiers in Zoology 2018 Vol. 15 No. 1 P. 1–15
Introduction: Among bryozoans, cyclostome anatomy is the least studied by modern methods. New data on the
nervous system fill the gap in our knowledge and make morphological analysis much more fruitful to resolve some
questions of bryozoan evolution and phylogeny.
Results: The nervous system of cyclostome Crisia eburnea was studied by transmission electron microscopy and
confocal laser scanning microscopy. ...
Added: October 18, 2019
Temereva E., Invertebrate Zoology 2018 Vol. 15 No. 4 P. 366–372
The phylogeny of bryozoans is ambiguous and apparently cannot be resolved
by molecular methods alone. Morphological data from previously unstudied species may
help establishing relationships between the main groups of the Bryozoa and may help to
clarify bryozoan phylogeny. The Cyclostomata is the least studied group of bryozoans. The
nervous system of cyclostomes has not been described utilising modern ...
Added: October 18, 2019
Temereva E., Scientific Reports 2017 Vol. 7 No. 1 P. 1–16
The validity of the Lophophorata as a monophyletic group remains controversial. New data on the
innervation of the lophophore, which is a unique feature of the lophophorates, may help clarify the
status of the Lophophorata and provide new information on the early evolution of the group. In this
paper, the organization of the nervous system of the lophophore ...
Added: October 18, 2019
Temereva E., Invertebrate Zoology 2017 Vol. 14 No. 1 P. 85–91
The status of the Lophophorates is one of the central problems of current zoology. There is a contradiction between the molecular results, which mainly indicate the polyphyly of the lophophorates, and morphological results, which indicate the monophyly of the lophophorates. An understanding of lophophore innervation can help answer question about the status of the lophophorates. ...
Added: October 18, 2019
Temereva E., Evolution and Development 2017 Vol. 19 No. 4-5 P. 171–189
Nervous system organization differs greatly in larvae and adults of many species, but
has nevertheless been traditionally used for phylogenetic studies. In phoronids, the
organization of the larval nervous system depends on the type of development. With
the goal of understanding the ground plan of the nervous system in phoronid larvae, the
development and organization of the larval nervous ...
Added: October 18, 2019
Temereva E., BMC Evolutionary Biology 2017 Vol. 17 No. 1 P. 1–19
Background: The nervous system in brachiopods has seldom been studied with modern methods. An
understanding of lophophore innervation in adult brachiopods is useful for comparing the innervation of the same
lophophore type among different brachiopods and can also help answer questions about the monophyly of the
lophophorates. Although some brachiopods are studied with modern methods, rhynchonelliform brachiopods still
require ...
Added: October 18, 2019
Vukovic D., Petrovic M., Demirovic D. et al., Journal of the Geographical Institute "Jovan Cvijić" 2017 Vol. 67 No. 1 P. 37–52
The paper deals with conceptual guidelines, basic aspects and spatial frameworks of the development of agritourism. The holistic approach, in this regard, includes the integrated and the comprehensive aspects of tourist stays in the countryside. The authors define the impact of agritourism on rural surroundings and analyze the influence of spending leisure time outside urban ...
Added: December 23, 2017
Grünthal R., Nichols J., Lingua Posnaniensis 2017 Vol. 58 No. 2 P. 11–31
The transitivizing/detransitivizing typology of Nichols et al. 2004 also proves useful to historical linguistics. We focus on language families of northern Eurasia, chiefly the three oldest families (Indo-European, Uralic, Nakh-Daghestanian), some of their daughter branches aged about 2000-3000 years, and one younger family for which we have data on enough daughters to support a family ...
Added: November 14, 2017
Cella K., Carmona L., Ekimova I. et al., Plos One 2016
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Added: November 29, 2016
Grinin L. E., Ilyin I., Andreev A., Social Evolution & History 2016 Vol. 15 No. 1 P. 58–84
The present article analyzes the world order in the past, present and future as well as the main factors, foundations and ideas underlying the maintaining and change of the international and global order. The first two sections investigate the evolution of the world order starting from the ancient times up to the late twentieth century. ...
Added: June 14, 2016
Shershakov S., В кн.: Proceedings of the 9th Central & Eastern European Software Engineering Conference in Russia.: NY: ACM, 2013.
Process-aware information systems (PAIS) enable developing models for interaction of processes, monitoring accuracy of their execution and checking if they interact with each other properly. PAIS can generate large data logs that contain the information about the interaction of processes in time. Studying PAIS logs with the purpose of data mining and modeling lies within ...
Added: December 21, 2013