Search

Your search keyword '"Koonin, Eugene V."' showing total 3,713 results
Start Over Author "Koonin, Eugene V."
3,713 results on '"Koonin, Eugene V."'

4. Addendum: Cellular differentiation into hyphae and spores in halophilic archaea

Author

Tang, Shu-Kun, Zhi, Xiao-Yang, Zhang, Yao, Makarova, Kira S., Liu, Bing-Bing, Zheng, Guo-Song, Zhang, Zhen-Peng, Zheng, Hua-Jun, Wolf, Yuri I., Zhao, Yu-Rong, Jiang, Song-Hao, Chen, Xi-Ming, Li, En-Yuan, Zhang, Tao, Chen, Pei-Ru, Feng, Yu-Zhou, Xiang, Ming-Xian, Lin, Zhi-Qian, Shi, Jia-Hui, Chang, Cheng, Zhang, Xue, Li, Rui, Lou, Kai, Wang, Yun, Chang, Lei, Yin, Min, Yang, Ling-Ling, Gao, Hui-Ying, Zhang, Zhong-Kai, Tao, Tian-Shen, Guan, Tong-Wei, He, Fu-Chu, Lu, Yin-Hua, Cui, Heng-Lin, Koonin, Eugene V., Zhao, Guo-Ping, and Xu, Ping

Published
2024
Full Text
View/download PDF

7. Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs

Author

Lee, Benjamin D, Neri, Uri, Roux, Simon, Wolf, Yuri I, Camargo, Antonio Pedro, Krupovic, Mart, Consortium, RNA Virus Discovery, Simmonds, Peter, Kyrpides, Nikos, Gophna, Uri, Dolja, Valerian V, and Koonin, Eugene V

Subjects
Biological Sciences, RNA, Circular, Viroids, RNA, Catalytic, RNA, Viral, Ecosystem, Plant Diseases, RNA Virus Discovery Consortium, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

Viroids and viroid-like covalently closed circular (ccc) RNAs are minimal replicators that typically encode no proteins and hijack cellular enzymes for replication. The extent and diversity of viroid-like agents are poorly understood. We developed a computational pipeline to identify viroid-like cccRNAs and applied it to 5,131 metatranscriptomes and 1,344 plant transcriptomes. The search yielded 11,378 viroid-like cccRNAs spanning 4,409 species-level clusters, a 5-fold increase compared to the previously identified viroid-like elements. Within this diverse collection, we discovered numerous putative viroids, satellite RNAs, retrozymes, and ribozy-like viruses. Diverse ribozyme combinations and unusual ribozymes within the cccRNAs were identified. Self-cleaving ribozymes were identified in ambiviruses, some mito-like viruses and capsid-encoding satellite virus-like cccRNAs. The broad presence of viroid-like cccRNAs in diverse transcriptomes and ecosystems implies that their host range is far broader than currently known, and matches to CRISPR spacers suggest that some cccRNAs replicate in prokaryotes.

Published
2023

8. Four principles to establish a universal virus taxonomy

Author

Simmonds, Peter, Adriaenssens, Evelien M, Zerbini, F Murilo, Abrescia, Nicola GA, Aiewsakun, Pakorn, Alfenas-Zerbini, Poliane, Bao, Yiming, Barylski, Jakub, Drosten, Christian, Duffy, Siobain, Duprex, W Paul, Dutilh, Bas E, Elena, Santiago F, García, Maria Laura, Junglen, Sandra, Katzourakis, Aris, Koonin, Eugene V, Krupovic, Mart, Kuhn, Jens H, Lambert, Amy J, Lefkowitz, Elliot J, Łobocka, Małgorzata, Lood, Cédric, Mahony, Jennifer, Meier-Kolthoff, Jan P, Mushegian, Arcady R, Oksanen, Hanna M, Poranen, Minna M, Reyes-Muñoz, Alejandro, Robertson, David L, Roux, Simon, Rubino, Luisa, Sabanadzovic, Sead, Siddell, Stuart, Skern, Tim, Smith, Donald B, Sullivan, Matthew B, Suzuki, Nobuhiro, Turner, Dann, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, and Vasilakis, Nikos

Subjects
Infectious Diseases, Infection, Humans, Bacteriophages, Metagenomics, Phylogeny, Viruses, Biological Sciences, Agricultural and Veterinary Sciences, Medical and Health Sciences, Developmental Biology
Abstract

A universal taxonomy of viruses is essential for a comprehensive view of the virus world and for communicating the complicated evolutionary relationships among viruses. However, there are major differences in the conceptualisation and approaches to virus classification and nomenclature among virologists, clinicians, agronomists, and other interested parties. Here, we provide recommendations to guide the construction of a coherent and comprehensive virus taxonomy, based on expert scientific consensus. Firstly, assignments of viruses should be congruent with the best attainable reconstruction of their evolutionary histories, i.e., taxa should be monophyletic. This fundamental principle for classification of viruses is currently included in the International Committee on Taxonomy of Viruses (ICTV) code only for the rank of species. Secondly, phenotypic and ecological properties of viruses may inform, but not override, evolutionary relatedness in the placement of ranks. Thirdly, alternative classifications that consider phenotypic attributes, such as being vector-borne (e.g., "arboviruses"), infecting a certain type of host (e.g., "mycoviruses," "bacteriophages") or displaying specific pathogenicity (e.g., "human immunodeficiency viruses"), may serve important clinical and regulatory purposes but often create polyphyletic categories that do not reflect evolutionary relationships. Nevertheless, such classifications ought to be maintained if they serve the needs of specific communities or play a practical clinical or regulatory role. However, they should not be considered or called taxonomies. Finally, while an evolution-based framework enables viruses discovered by metagenomics to be incorporated into the ICTV taxonomy, there are essential requirements for quality control of the sequence data used for these assignments. Combined, these four principles will enable future development and expansion of virus taxonomy as the true evolutionary diversity of viruses becomes apparent.

Published
2023

10. Thermodynamics of Evolution and the Origin of Life

Author

Vanchurin, Vitaly, Wolf, Yuri I., Koonin, Eugene V., and Katsnelson, Mikhail I.

Subjects
Quantitative Biology - Populations and Evolution, Condensed Matter - Disordered Systems and Neural Networks, Condensed Matter - Statistical Mechanics, Computer Science - Machine Learning
Abstract

We outline a phenomenological theory of evolution and origin of life by combining the formalism of classical thermodynamics with a statistical description of learning. The maximum entropy principle constrained by the requirement for minimization of the loss function is employed to derive a canonical ensemble of organisms (population), the corresponding partition function (macroscopic counterpart of fitness) and free energy (macroscopic counterpart of additive fitness). We further define the biological counterparts of temperature (biological temperature) as the measure of stochasticity of the evolutionary process and of chemical potential (evolutionary potential) as the amount of evolutionary work required to add a new trainable variable (such as an additional gene) to the evolving system. We then develop a phenomenological approach to the description of evolution, which involves modeling the grand potential as a function of the biological temperature and evolutionary potential. We demonstrate how this phenomenological approach can be used to study the "ideal mutation" model of evolution and its generalizations. Finally, we show that, within this thermodynamics framework, major transitions in evolution, such as the transition from an ensemble of molecules to an ensemble of organisms, that is, the origin of life, can be modeled as a special case of bona fide physical phase transitions that are associated with the emergence of a new type of grand canonical ensemble and the corresponding new level of description, Comment: 23 pages

Published
2021
Full Text
View/download PDF

11. Towards a Theory of Evolution as Multilevel Learning

Author

Vanchurin, Vitaly, Wolf, Yuri I., Katsnelson, Mikhail I., and Koonin, Eugene V.

Subjects
Quantitative Biology - Populations and Evolution, Condensed Matter - Disordered Systems and Neural Networks, Computer Science - Machine Learning
Abstract

We apply the theory of learning to physically renormalizable systems in an attempt to develop a theory of biological evolution, including the origin of life, as multilevel learning. We formulate seven fundamental principles of evolution that appear to be necessary and sufficient to render a universe observable and show that they entail the major features of biological evolution, including replication and natural selection. These principles also follow naturally from the theory of learning. We formulate the theory of evolution using the mathematical framework of neural networks, which provides for detailed analysis of evolutionary phenomena. To demonstrate the potential of the proposed theoretical framework, we derive a generalized version of the Central Dogma of molecular biology by analyzing the flow of information during learning (back-propagation) and predicting (forward-propagation) the environment by evolving organisms. The more complex evolutionary phenomena, such as major transitions in evolution, in particular, the origin of life, have to be analyzed in the thermodynamic limit, which is described in detail in the accompanying paper., Comment: 29 pages, 3 figures

Published
2021
Full Text
View/download PDF

13. Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer

Author

McBride, Dillon S., Garushyants, Sofya K., Franks, John, Magee, Andrew F., Overend, Steven H., Huey, Devra, Williams, Amanda M., Faith, Seth A., Kandeil, Ahmed, Trifkovic, Sanja, Miller, Lance, Jeevan, Trushar, Patel, Anami, Nolting, Jacqueline M., Tonkovich, Michael J., Genders, J. Tyler, Montoney, Andrew J., Kasnyik, Kevin, Linder, Timothy J., Bevins, Sarah N., Lenoch, Julianna B., Chandler, Jeffrey C., DeLiberto, Thomas J., Koonin, Eugene V., Suchard, Marc A., Lemey, Philippe, Webby, Richard J., Nelson, Martha I., and Bowman, Andrew S.

Published
2023
Full Text
View/download PDF

14. Cellular differentiation into hyphae and spores in halophilic archaea

Author

Tang, Shu-Kun, Zhi, Xiao-Yang, Zhang, Yao, Makarova, Kira S., Liu, Bing-Bing, Zheng, Guo-Song, Zhang, Zhen-Peng, Zheng, Hua-Jun, Wolf, Yuri I., Zhao, Yu-Rong, Jiang, Song-Hao, Chen, Xi-Ming, Li, En-Yuan, Zhang, Tao, Chen, Pei-Ru, Feng, Yu-Zhou, Xiang, Ming-Xian, Lin, Zhi-Qian, Shi, Jia-Hui, Chang, Cheng, Zhang, Xue, Li, Rui, Lou, Kai, Wang, Yun, Chang, Lei, Yin, Min, Yang, Ling-Ling, Gao, Hui-Ying, Zhang, Zhong-Kai, Tao, Tian-Shen, Guan, Tong-Wei, He, Fu-Chu, Lu, Yin-Hua, Cui, Heng-Lin, Koonin, Eugene V., Zhao, Guo-Ping, and Xu, Ping

Published
2023
Full Text
View/download PDF

15. Alternating active-dormitive strategy enables overtaking by disadvantaged prey through Parrondo's paradox

Author

Wen, Tao, Koonin, Eugene V., and Cheong, Kang Hao

Subjects
Quantitative Biology - Populations and Evolution, Nonlinear Sciences - Chaotic Dynamics
Abstract

Dormancy is a costly adaptive strategy that is widespread among living organisms inhabiting diverse environments. We explore mathematical models of predator-prey systems, in order to assess the impact of prey dormancy on the competition between two types of prey, a perennially active (PA) and capable of entering dormancy (dormitive). Both the active form and the dormant form of the dormitive prey are individually at a disadvantage compared to the PA prey and would go extinct due to their low growth rate, energy waste on the production of dormant prey, and inability of the latter to grow autonomously. However, the dormitive prey can paradoxically outcompete the PA prey with superior traits and even cause its extinction by alternating between the two losing strategies. This outcome recapitulates the game-theoretic Parrondo's paradox, where two losing strategies combine to achieve a winning outcome. We observed higher fitness of the dormitive prey in rich environments because a large predator population in a rich environment cannot be supported by the prey without adopting an evasive strategy, that is, dormancy. In such environments, populations experience large-scale fluctuations, which can be survived by dormitive but not by PA prey. Dormancy of the prey appears to be a natural evolutionary response to self-destructive over-predation that stabilizes evolving predator-prey systems through Parrondo's paradox.

Published
2021

18. Punctuated equilibrium as the default mode of evolution of large populations on fitness landscapes dominated by saddle points in the weak-mutation limit

Author

Bakhtin, Yuri, Katsnelson, Mikhail I., Wolf, Yuri I., and Koonin, Eugene V.

Subjects
Quantitative Biology - Populations and Evolution, Condensed Matter - Statistical Mechanics, Nonlinear Sciences - Adaptation and Self-Organizing Systems
Abstract

Punctuated equilibrium is a mode of evolution in which phenetic change occurs in rapid bursts that are separated by much longer intervals of stasis during which mutations accumulate but no major phenotypic change occurs. Punctuated equilibrium has been originally proposed within the framework of paleobiology, to explain the lack of transitional forms that is typical of the fossil record. Theoretically, punctuated equilibrium has been linked to self-organized criticality (SOC), a model in which the size of avalanches in an evolving system is power-law distributed, resulting in increasing rarity of major events. We show here that, under the weak-mutation limit, a large population would spend most of the time in stasis in the vicinity of saddle points in the fitness landscape. The periods of stasis are punctuated by fast transitions, in lnNe time (Ne, effective population size), when a new beneficial mutation is fixed in the evolving population, which moves to a different saddle, or on much rarer occasions, from a saddle to a local peak. Thus, punctuated equilibrium is the default mode of evolution under a simple model that does not involve SOC or other special conditions., Comment: 25 pages, 2 figures

Published
2020

20. Evolution of regulatory signatures in primate cortical neurons at cell-type resolution.

Author

Kozlenkov, Alexey, Vermunt, Marit W, Apontes, Pasha, Li, Junhao, Hao, Ke, Sherwood, Chet C, Hof, Patrick R, Ely, John J, Wegner, Michael, Mukamel, Eran A, Creyghton, Menno P, Koonin, Eugene V, and Dracheva, Stella

Subjects
GABAergic neurons, H3K27ac histone modification, glutamatergic neurons, primate evolution, regulatory elements
Abstract

The human cerebral cortex contains many cell types that likely underwent independent functional changes during evolution. However, cell-type-specific regulatory landscapes in the cortex remain largely unexplored. Here we report epigenomic and transcriptomic analyses of the two main cortical neuronal subtypes, glutamatergic projection neurons and GABAergic interneurons, in human, chimpanzee, and rhesus macaque. Using genome-wide profiling of the H3K27ac histone modification, we identify neuron-subtype-specific regulatory elements that previously went undetected in bulk brain tissue samples. Human-specific regulatory changes are uncovered in multiple genes, including those associated with language, autism spectrum disorder, and drug addiction. We observe preferential evolutionary divergence in neuron subtype-specific regulatory elements and show that a substantial fraction of pan-neuronal regulatory elements undergoes subtype-specific evolutionary changes. This study sheds light on the interplay between regulatory evolution and cell-type-dependent gene-expression programs, and provides a resource for further exploration of human brain evolution and function.

Published
2020

21. 2022 taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Author

Kuhn, Jens H., Adkins, Scott, Alkhovsky, Sergey V., Avšič-Županc, Tatjana, Ayllón, María A., Bahl, Justin, Balkema-Buschmann, Anne, Ballinger, Matthew J., Bandte, Martina, Beer, Martin, Bejerman, Nicolas, Bergeron, Éric, Biedenkopf, Nadine, Bigarré, Laurent, Blair, Carol D., Blasdell, Kim R., Bradfute, Steven B., Briese, Thomas, Brown, Paul A., Bruggmann, Rémy, Buchholz, Ursula J., Buchmeier, Michael J., Bukreyev, Alexander, Burt, Felicity, Büttner, Carmen, Calisher, Charles H., Candresse, Thierry, Carson, Jeremy, Casas, Inmaculada, Chandran, Kartik, Charrel, Rémi N., Chiaki, Yuya, Crane, Anya, Crane, Mark, Dacheux, Laurent, Bó, Elena Dal, de la Torre, Juan Carlos, de Lamballerie, Xavier, de Souza, William M., de Swart, Rik L., Dheilly, Nolwenn M., Di Paola, Nicholas, Di Serio, Francesco, Dietzgen, Ralf G., Digiaro, Michele, Drexler, J. Felix, Duprex, W. Paul, Dürrwald, Ralf, Easton, Andrew J., Elbeaino, Toufic, Ergünay, Koray, Feng, Guozhong, Feuvrier, Claudette, Firth, Andrew E., Fooks, Anthony R., Formenty, Pierre B. H., Freitas-Astúa, Juliana, Gago-Zachert, Selma, García, María Laura, García-Sastre, Adolfo, Garrison, Aura R., Godwin, Scott E., Gonzalez, Jean-Paul J., de Bellocq, Joëlle Goüy, Griffiths, Anthony, Groschup, Martin H., Günther, Stephan, Hammond, John, Hepojoki, Jussi, Hierweger, Melanie M., Hongō, Seiji, Horie, Masayuki, Horikawa, Hidenori, Hughes, Holly R., Hume, Adam J., Hyndman, Timothy H., Jiāng, Dàohóng, Jonson, Gilda B., Junglen, Sandra, Kadono, Fujio, Karlin, David G., Klempa, Boris, Klingström, Jonas, Koch, Michel C., Kondō, Hideki, Koonin, Eugene V., Krásová, Jarmila, Krupovic, Mart, Kubota, Kenji, Kuzmin, Ivan V., Laenen, Lies, Lambert, Amy J., Lǐ, Jiànróng, Li, Jun-Min, Lieffrig, François, Lukashevich, Igor S., Luo, Dongsheng, Maes, Piet, Marklewitz, Marco, Marshall, Sergio H., Marzano, Shin-Yi L., McCauley, John W., Mirazimi, Ali, Mohr, Peter G., Moody, Nick J. G., Morita, Yasuaki, Morrison, Richard N., Mühlberger, Elke, Naidu, Rayapati, Natsuaki, Tomohide, Navarro, José A., Neriya, Yutaro, Netesov, Sergey V., Neumann, Gabriele, Nowotny, Norbert, Ochoa-Corona, Francisco M., Palacios, Gustavo, Pallandre, Laurane, Pallás, Vicente, Papa, Anna, Paraskevopoulou, Sofia, Parrish, Colin R., Pauvolid-Corrêa, Alex, Pawęska, Janusz T., Pérez, Daniel R., Pfaff, Florian, Plemper, Richard K., Postler, Thomas S., Pozet, Françoise, Radoshitzky, Sheli R., Ramos-González, Pedro L., Rehanek, Marius, Resende, Renato O., Reyes, Carina A., Romanowski, Víctor, Rubbenstroth, Dennis, Rubino, Luisa, Rumbou, Artemis, Runstadler, Jonathan A., Rupp, Melanie, Sabanadzovic, Sead, Sasaya, Takahide, Schmidt-Posthaus, Heike, Schwemmle, Martin, Seuberlich, Torsten, Sharpe, Stephen R., Shi, Mang, Sironi, Manuela, Smither, Sophie, Song, Jin-Won, Spann, Kirsten M., Spengler, Jessica R., Stenglein, Mark D., Takada, Ayato, Tesh, Robert B., Těšíková, Jana, Thornburg, Natalie J., Tischler, Nicole D., Tomitaka, Yasuhiro, Tomonaga, Keizō, Tordo, Noël, Tsunekawa, Kenta, Turina, Massimo, Tzanetakis, Ioannis E., Vaira, Anna Maria, van den Hoogen, Bernadette, Vanmechelen, Bert, Vasilakis, Nikos, Verbeek, Martin, von Bargen, Susanne, Wada, Jiro, Wahl, Victoria, Walker, Peter J., Whitfield, Anna E., Williams, John V., Wolf, Yuri I., Yamasaki, Junki, Yanagisawa, Hironobu, Ye, Gongyin, Zhang, Yong-Zhen, and Økland, Arnfinn Lodden

Published
2022
Full Text
View/download PDF

23. The sounds of science: a symphony for many instruments and voices

Author

Alexander, Gerianne, Allen, Roland E., Atala, Anthony, Bowen, Warwick P., Coley, Alan A., Goodenough, John, Katsnelson, Mikhail, Koonin, Eugene V., Krenn, Mario, Madsen, Lars S., Mansson, Martin, Mauranyapin, Nicolas P., Rasel, Ernst, Reich, Linda E., Yampolskiy, Roman, Yasskin, Philip B., Zeilinger, Anton, and Lidstrom, Suzy

Subjects
Physics - Popular Physics, General Relativity and Quantum Cosmology
Abstract

This paper is a celebration of the frontiers of science. Goodenough, the maestro who transformed energy usage and technology through the invention of the lithium ion battery, opens the programme, reflecting on the ultimate limits of battery technology. This applied theme continues through the subsequent pieces on energy related topics (the sodium ion battery and artificial fuels, by Mansson) and the ultimate challenge for 3 dimensional printing the eventual production of life, by Atala. A passage by Alexander follows, reflecting on a related issue: How might an artificially produced human being behave? Next comes a consideration of consiousness and free will by Allen and Lidstrom. Further voices and new instruments enter as Bowen, Mauranyapin and Madsen discuss whether dynamical processes of single molecules might be observed in their native state. The exploitation of chaos in science and technology, applications of Bose Einstein condensates and a consideration of the significance of entropy follow in pieces by Reichl, Rasel and Allen, respectively. Katsnelson and Koonin then discuss the potential generalisation of thermodynamic concepts in the context of biological evolution. Entering with the music of the cosmos, Yasskin discusses whether we might be able to observe torsion in the geometry of the universe. The crescendo comes with the crisis of singularities, their nature and whether they can be resolved through quantum effects, in the composition of Coley. The climax is Krenn, Melvin and Zeilinger consideration of how computer code can be autonomously surprising and creative. In a harmonious counterpoint, Yampolskiy concludes that such code is not yet able to take responsibility for coauthoring a paper., Comment: Please send comments and questions to Suzy Lidstrom

Published
2019
Full Text
View/download PDF

33. On the feasibility of saltational evolution

Author

Katsnelson, Mikhail I., Wolf, Yuri I., and Koonin, Eugene V.

Subjects
Quantitative Biology - Populations and Evolution
Abstract

Is evolution always gradual or can it make leaps? We examine a mathematical model of an evolutionary process on a fitness landscape and obtain analytic solutions for the probability of multi-mutation leaps, that is, several mutations occurring simultaneously, within a single generation in one genome, and being fixed all together in the evolving population. The results indicate that, for typical, empirically observed combinations of the parameters of the evolutionary process, namely, effective population size, mutation rate, and distribution of selection coefficients of mutations, the probability of a multi-mutation leap is low, and accordingly, the contribution of such leaps is minor at best. However, we show that, taking sign epistasis into account, leaps could become an important factor of evolution in cases of substantially elevated mutation rates, such as stress-induced mutagenesis in microbes. We hypothesize that stress-induced mutagenesis is an evolvable adaptive strategy., Comment: Extended version, in particular, the section is added on non-equilibrium model of stress-induced mutagenesis

Published
2018
Full Text
View/download PDF

34. Physical foundations of biological complexity

Author

Wolf, Yuri I., Katsnelson, Mikhail I., and Koonin, Eugene V.

Subjects
Condensed Matter - Statistical Mechanics, Condensed Matter - Disordered Systems and Neural Networks, Quantitative Biology - Populations and Evolution
Abstract

Biological systems reach hierarchical complexity that has no counterpart outside the realm of biology. Undoubtedly, biological entities obey the fundamental physical laws. Can today's physics provide an explanatory framework for understanding the evolution of biological complexity? We argue here that the physical foundation for understanding the origin and evolution of complexity can be envisaged at the interface between the theory of frustrated states resulting in pattern formation in glass-like media and the theory of self-organized criticality (SOC). On the one hand, SOC has been shown to emerge in spin glass systems of high dimensionality. On the other hand, SOC is often viewed as the most appropriate physical description of evolutionary transitions in biology. We unify these two faces of SOC by showing that emergence of complex features in biological evolution typically if not always is triggered by frustration that is caused by competing interactions at different organizational levels. Competing interactions and frustrated states permeate biology at all organizational levels and are tightly linked to the ubiquitous competition for limiting resources. This perspective extends from the comparatively simple phenomena occurring in glasses to large-scale events of biological evolution, such as major evolutionary transitions. We therefore submit that frustration caused by competing interactions in multidimensional systems is the general driving force behind the emergence of complexity, within and beyond the domain of biology., Comment: 27 pages, 2 figures

Published
2018
Full Text
View/download PDF

35. Minimum Information about an Uncultivated Virus Genome (MIUViG)

Author

Roux, Simon, Adriaenssens, Evelien M, Dutilh, Bas E, Koonin, Eugene V, Kropinski, Andrew M, Krupovic, Mart, Kuhn, Jens H, Lavigne, Rob, Brister, J Rodney, Varsani, Arvind, Amid, Clara, Aziz, Ramy K, Bordenstein, Seth R, Bork, Peer, Breitbart, Mya, Cochrane, Guy R, Daly, Rebecca A, Desnues, Christelle, Duhaime, Melissa B, Emerson, Joanne B, Enault, François, Fuhrman, Jed A, Hingamp, Pascal, Hugenholtz, Philip, Hurwitz, Bonnie L, Ivanova, Natalia N, Labonté, Jessica M, Lee, Kyung-Bum, Malmstrom, Rex R, Martinez-Garcia, Manuel, Mizrachi, Ilene Karsch, Ogata, Hiroyuki, Páez-Espino, David, Petit, Marie-Agnès, Putonti, Catherine, Rattei, Thomas, Reyes, Alejandro, Rodriguez-Valera, Francisco, Rosario, Karyna, Schriml, Lynn, Schulz, Frederik, Steward, Grieg F, Sullivan, Matthew B, Sunagawa, Shinichi, Suttle, Curtis A, Temperton, Ben, Tringe, Susannah G, Thurber, Rebecca Vega, Webster, Nicole S, Whiteson, Katrine L, Wilhelm, Steven W, Wommack, K Eric, Woyke, Tanja, Wrighton, Kelly C, Yilmaz, Pelin, Yoshida, Takashi, Young, Mark J, Yutin, Natalya, Allen, Lisa Zeigler, Kyrpides, Nikos C, and Eloe-Fadrosh, Emiley A

Subjects
Microbiology, Biological Sciences, Genetics, Human Genome, Databases, Genetic, Genome, Viral, Genomics, Virus Cultivation, Viruses
Abstract

We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere.

Published
2019

42. Towards physical principles of biological evolution

Author

Katsnelson, Mikhail I., Wolf, Yuri I., and Koonin, Eugene V.

Subjects
Quantitative Biology - Other Quantitative Biology, Condensed Matter - Statistical Mechanics, Quantitative Biology - Populations and Evolution
Abstract

Biological systems reach organizational complexity that far exceeds the complexity of any known inanimate objects. Biological entities undoubtedly obey the laws of quantum physics and statistical mechanics. However, is modern physics sufficient to adequately describe, model and explain the evolution of biological complexity? Detailed parallels have been drawn between statistical thermodynamics and the population-genetic theory of biological evolution. Based on these parallels, we outline new perspectives on biological innovation and major transitions in evolution, and introduce a biological equivalent of thermodynamic potential that reflects the innovation propensity of an evolving population. Deep analogies have been suggested to also exist between the properties of biological entities and processes, and those of frustrated states in physics, such as glasses. We extend such analogies by examining frustration-type phenomena, such as conflicts between different levels of selection, in biological evolution. We further address evolution in multidimensional fitness landscapes from the point of view of percolation theory and suggest that percolation at level above the critical threshold dictates the tree-like evolution of complex organisms. Taken together, these multiple connections between fundamental processes in physics and biology imply that construction of a meaningful physical theory of biological evolution might not be a futile effort., Comment: Invited article, Focus Issue on 21th Century Frontiers, final version

Published
2017
Full Text
View/download PDF

43. 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Author

Kuhn, Jens H., Adkins, Scott, Agwanda, Bernard R., Al Kubrusli, Rim, Alkhovsky, Sergey V., Amarasinghe, Gaya K., Avšič-Županc, Tatjana, Ayllón, María A., Bahl, Justin, Balkema-Buschmann, Anne, Ballinger, Matthew J., Basler, Christopher F., Bavari, Sina, Beer, Martin, Bejerman, Nicolas, Bennett, Andrew J., Bente, Dennis A., Bergeron, Éric, Bird, Brian H., Blair, Carol D., Blasdell, Kim R., Blystad, Dag-Ragnar, Bojko, Jamie, Borth, Wayne B., Bradfute, Steven, Breyta, Rachel, Briese, Thomas, Brown, Paul A., Brown, Judith K., Buchholz, Ursula J., Buchmeier, Michael J., Bukreyev, Alexander, Burt, Felicity, Büttner, Carmen, Calisher, Charles H., Cao, Mengji, Casas, Inmaculada, Chandran, Kartik, Charrel, Rémi N., Cheng, Qi, Chiaki, Yuya, Chiapello, Marco, Choi, Il-Ryong, Ciuffo, Marina, Clegg, J. Christopher S., Crozier, Ian, Dal Bó, Elena, de la Torre, Juan Carlos, de Lamballerie, Xavier, de Swart, Rik L., Debat, Humberto, Dheilly, Nolwenn M., Di Cicco, Emiliano, Di Paola, Nicholas, Di Serio, Francesco, Dietzgen, Ralf G., Digiaro, Michele, Dolnik, Olga, Drebot, Michael A., Drexler, J. Felix, Dundon, William G., Duprex, W. Paul, Dürrwald, Ralf, Dye, John M., Easton, Andrew J., Ebihara, Hideki, Elbeaino, Toufic, Ergünay, Koray, Ferguson, Hugh W., Fooks, Anthony R., Forgia, Marco, Formenty, Pierre B. H., Fránová, Jana, Freitas-Astúa, Juliana, Fu, Jingjing, Fürl, Stephanie, Gago-Zachert, Selma, Gāo, George Fú, García, María Laura, García-Sastre, Adolfo, Garrison, Aura R., Gaskin, Thomas, Gonzalez, Jean-Paul J., Griffiths, Anthony, Goldberg, Tony L., Groschup, Martin H., Günther, Stephan, Hall, Roy A., Hammond, John, Han, Tong, Hepojoki, Jussi, Hewson, Roger, Hong, Jiang, Hong, Ni, Hongo, Seiji, Horie, Masayuki, Hu, John S., Hu, Tao, Hughes, Holly R., Hüttner, Florian, Hyndman, Timothy H., Ilyas, M., Jalkanen, Risto, Jiāng, Dàohóng, Jonson, Gilda B., Junglen, Sandra, Kadono, Fujio, Kaukinen, Karia H., Kawate, Michael, Klempa, Boris, Klingström, Jonas, Kobinger, Gary, Koloniuk, Igor, Kondō, Hideki, Koonin, Eugene V., Krupovic, Mart, Kubota, Kenji, Kurath, Gael, Laenen, Lies, Lambert, Amy J., Langevin, Stanley L., Lee, Benhur, Lefkowitz, Elliot J., Leroy, Eric M., Li, Shaorong, Li, Longhui, Lǐ, Jiànróng, Liu, Huazhen, Lukashevich, Igor S., Maes, Piet, de Souza, William Marciel, Marklewitz, Marco, Marshall, Sergio H., Marzano, Shin-Yi L., Massart, Sebastien, McCauley, John W., Melzer, Michael, Mielke-Ehret, Nicole, Miller, Kristina M., Ming, Tobi J., Mirazimi, Ali, Mordecai, Gideon J., Mühlbach, Hans-Peter, Mühlberger, Elke, Naidu, Rayapati, Natsuaki, Tomohide, Navarro, José A., Netesov, Sergey V., Neumann, Gabriele, Nowotny, Norbert, Nunes, Márcio R. T., Olmedo-Velarde, Alejandro, Palacios, Gustavo, Pallás, Vicente, Pályi, Bernadett, Papa, Anna, Paraskevopoulou, Sofia, Park, Adam C., Parrish, Colin R., Patterson, David A., Pauvolid-Corrêa, Alex, Pawęska, Janusz T., Payne, Susan, Peracchio, Carlotta, Pérez, Daniel R., Postler, Thomas S., Qi, Liying, Radoshitzky, Sheli R., Resende, Renato O., Reyes, Carina A., Rima, Bertus K., Luna, Gabriel Robles, Romanowski, Víctor, Rota, Paul, Rubbenstroth, Dennis, Rubino, Luisa, Runstadler, Jonathan A., Sabanadzovic, Sead, Sall, Amadou Alpha, Salvato, Maria S., Sang, Rosemary, Sasaya, Takahide, Schulze, Angela D., Schwemmle, Martin, Shi, Mang, Shí, Xiǎohóng, Shí, Zhènglì, Shimomoto, Yoshifumi, Shirako, Yukio, Siddell, Stuart G., Simmonds, Peter, Sironi, Manuela, Smagghe, Guy, Smither, Sophie, Song, Jin-Won, Spann, Kirsten, Spengler, Jessica R., Stenglein, Mark D., Stone, David M., Sugano, Jari, Suttle, Curtis A., Tabata, Amy, Takada, Ayato, Takeuchi, Shigeharu, Tchouassi, David P., Teffer, Amy, Tesh, Robert B., Thornburg, Natalie J., Tomitaka, Yasuhiro, Tomonaga, Keizō, Tordo, Noël, Torto, Baldwyn, Towner, Jonathan S., Tsuda, Shinya, Tu, Changchun, Turina, Massimo, Tzanetakis, Ioannis E., Uchida, Janice, Usugi, Tomio, Vaira, Anna Maria, Vallino, Marta, van den Hoogen, Bernadette, Varsani, Arvind, Vasilakis, Nikos, Verbeek, Martin, von Bargen, Susanne, Wada, Jiro, Wahl, Victoria, Walker, Peter J., Wang, Lin-Fa, Wang, Guoping, Wang, Yanxiang, Wang, Yaqin, Waqas, Muhammad, Wèi, Tàiyún, Wen, Shaohua, Whitfield, Anna E., Williams, John V., Wolf, Yuri I., Wu, Jiangxiang, Xu, Lei, Yanagisawa, Hironobu, Yang, Caixia, Yang, Zuokun, Zerbini, F. Murilo, Zhai, Lifeng, Zhang, Yong-Zhen, Zhang, Song, Zhang, Jinguo, Zhang, Zhe, and Zhou, Xueping

Published
2021
Full Text
View/download PDF

44. Correction to: 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Author

Kuhn, Jens H., Adkins, Scott, Agwanda, Bernard R., Al Kubrusli, Rim, Alkhovsky, Sergey V., Amarasinghe, Gaya K., Avšič-Županc, Tatjana, Ayllón, María A., Bahl, Justin, Balkema-Buschmann, Anne, Ballinger, Matthew J., Basler, Christopher F., Bavari, Sina, Beer, Martin, Bejerman, Nicolas, Bennett, Andrew J., Bente, Dennis A., Bergeron, Éric, Bird, Brian H., Blair, Carol D., Blasdell, Kim R., Blystad, Dag-Ragnar, Bojko, Jamie, Borth, Wayne B., Bradfute, Steven, Breyta, Rachel, Briese, Thomas, Brown, Paul A., Brown, Judith K., Buchholz, Ursula J., Buchmeier, Michael J., Bukreyev, Alexander, Burt, Felicity, Büttner, Carmen, Calisher, Charles H., Cao, Mengji, Casas, Inmaculada, Chandran, Kartik, Charrel, Rémi N., Cheng, Qi, Chiaki, Yuya, Chiapello, Marco, Choi, Il-Ryong, Ciuffo, Marina, Clegg, J. Christopher S., Crozier, Ian, Dal Bó, Elena, de la Torre, Juan Carlos, de Lamballerie, Xavier, de Swart, Rik L., Debat, Humberto, Dheilly, Nolwenn M., Di Cicco, Emiliano, Di Paola, Nicholas, Di Serio, Francesco, Dietzgen, Ralf G., Digiaro, Michele, Dolnik, Olga, Drebot, Michael A., Drexler, J. Felix, Dundon, William G., Duprex, W. Paul, Dürrwald, Ralf, Dye, John M., Easton, Andrew J., Ebihara, Hideki, Elbeaino, Toufic, Ergünay, Koray, Ferguson, Hugh W., Fooks, Anthony R., Forgia, Marco, Formenty, Pierre B. H., Fránová, Jana, Freitas-Astúa, Juliana, Fu, Jingjing, Fürl, Stephanie, Gago-Zachert, Selma, Gāo, George Fú, García, María Laura, García-Sastre, Adolfo, Garrison, Aura R., Gaskin, Thomas, Gonzalez, Jean-Paul J., Griffiths, Anthony, Goldberg, Tony L., Groschup, Martin H., Günther, Stephan, Hall, Roy A., Hammond, John, Han, Tong, Hepojoki, Jussi, Hewson, Roger, Hong, Jiang, Hong, Ni, Hongo, Seiji, Horie, Masayuki, Hu, John S., Hu, Tao, Hughes, Holly R., Hüttner, Florian, Hyndman, Timothy H., Ilyas, M., Jalkanen, Risto, Jiāng, Dàohóng, Jonson, Gilda B., Junglen, Sandra, Kadono, Fujio, Kaukinen, Karia H., Kawate, Michael, Klempa, Boris, Klingström, Jonas, Kobinger, Gary, Koloniuk, Igor, Kondō, Hideki, Koonin, Eugene V., Krupovic, Mart, Kubota, Kenji, Kurath, Gael, Laenen, Lies, Lambert, Amy J., Langevin, Stanley L., Lee, Benhur, Lefkowitz, Elliot J., Leroy, Eric M., Li, Shaorong, Li, Longhui, Lǐ, Jiànróng, Liu, Huazhen, Lukashevich, Igor S., Maes, Piet, de Souza, William Marciel, Marklewitz, Marco, Marshall, Sergio H., Marzano, Shin-Yi L., Massart, Sebastien, McCauley, John W., Melzer, Michael, Mielke-Ehret, Nicole, Miller, Kristina M., Ming, Tobi J., Mirazimi, Ali, Mordecai, Gideon J., Mühlbach, Hans-Peter, Mühlberger, Elke, Naidu, Rayapati, Natsuaki, Tomohide, Navarro, José A., Netesov, Sergey V., Neumann, Gabriele, Nowotny, Norbert, Nunes, Márcio R. T., Olmedo-Velarde, Alejandro, Palacios, Gustavo, Pallás, Vicente, Pályi, Bernadett, Papa, Anna, Paraskevopoulou, Sofia, Park, Adam C., Parrish, Colin R., Patterson, David A., Pauvolid-Corrêa, Alex, Pawęska, Janusz T., Payne, Susan, Peracchio, Carlotta, Pérez, Daniel R., Postler, Thomas S., Qi, Liying, Radoshitzky, Sheli R., Resende, Renato O., Reyes, Carina A., Rima, Bertus K., Luna, Gabriel Robles, Romanowski, Víctor, Rota, Paul, Rubbenstroth, Dennis, Rubino, Luisa, Runstadler, Jonathan A., Sabanadzovic, Sead, Sall, Amadou Alpha, Salvato, Maria S., Sang, Rosemary, Sasaya, Takahide, Schulze, Angela D., Schwemmle, Martin, Shi, Mang, Shí, Xiǎohóng, Shí, Zhènglì, Shimomoto, Yoshifumi, Shirako, Yukio, Siddell, Stuart G., Simmonds, Peter, Sironi, Manuela, Smagghe, Guy, Smither, Sophie, Song, Jin-Won, Spann, Kirsten, Spengler, Jessica R., Stenglein, Mark D., Stone, David M., Sugano, Jari, Suttle, Curtis A., Tabata, Amy, Takada, Ayato, Takeuchi, Shigeharu, Tchouassi, David P., Teffer, Amy, Tesh, Robert B., Thornburg, Natalie J., Tomitaka, Yasuhiro, Tomonaga, Keizō, Tordo, Noël, Torto, Baldwyn, Towner, Jonathan S., Tsuda, Shinya, Tu, Changchun, Turina, Massimo, Tzanetakis, Ioannis E., Uchida, Janice, Usugi, Tomio, Vaira, Anna Maria, Vallino, Marta, van den Hoogen, Bernadette, Varsani, Arvind, Vasilakis, Nikos, Verbeek, Martin, von Bargen, Susanne, Wada, Jiro, Wahl, Victoria, Walker, Peter J., Wang, Lin-Fa, Wang, Guoping, Wang, Yanxiang, Wang, Yaqin, Waqas, Muhammad, Wèi, Tàiyún, Wen, Shaohua, Whitfield, Anna E., Williams, John V., Wolf, Yuri I., Wu, Jiangxiang, Xu, Lei, Yanagisawa, Hironobu, Yang, Caixia, Yang, Zuokun, Zerbini, F. Murilo, Zhai, Lifeng, Zhang, Yong-Zhen, Zhang, Song, Zhang, Jinguo, Zhang, Zhe, and Zhou, Xueping

Published
2021
Full Text
View/download PDF

45. A unique role for DNA (hydroxy)methylation in epigenetic regulation of human inhibitory neurons.

Author

Kozlenkov, Alexey, Li, Junhao, Apontes, Pasha, Hurd, Yasmin L, Byne, William M, Koonin, Eugene V, Wegner, Michael, Mukamel, Eran A, and Dracheva, Stella

Subjects
Brain, Neurons, Cell Nucleus, Humans, Brain Diseases, Cadaver, DNA Methylation, Epigenesis, Genetic, Neural Inhibition, Polymorphism, Single Nucleotide, Adult, Male, Epigenesis, Genetic, Polymorphism, Single Nucleotide, Brain Disorders, Genetics, Human Genome, Biotechnology, Mental Health, Neurosciences, 1.1 Normal biological development and functioning, Neurological
Abstract

Brain function depends on interaction of diverse cell types whose gene expression and identity are defined, in part, by epigenetic mechanisms. Neuronal DNA contains two major epigenetic modifications, methylcytosine (mC) and hydroxymethylcytosine (hmC), yet their cell type-specific landscapes and relationship with gene expression are poorly understood. We report high-resolution (h)mC analyses, together with transcriptome and histone modification profiling, in three major cell types in human prefrontal cortex: glutamatergic excitatory neurons, medial ganglionic eminence-derived γ-aminobutyric acid (GABA)ergic inhibitory neurons, and oligodendrocytes. We detected a unique association between hmC and gene expression in inhibitory neurons that differed significantly from the pattern in excitatory neurons and oligodendrocytes. We also found that risk loci associated with neuropsychiatric diseases were enriched near regions of reduced hmC in excitatory neurons and reduced mC in inhibitory neurons. Our findings indicate differential roles for mC and hmC in regulation of gene expression in different brain cell types, with implications for the etiology of human brain diseases.

Published
2018

46. Gearing up to handle the mosaic nature of life in the quest for orthologs

Author

Forslund, Kristoffer, Pereira, Cecile, Capella-Gutierrez, Salvador, da Silva, Alan Sousa, Altenhoff, Adrian, Huerta-Cepas, Jaime, Muffato, Matthieu, Patricio, Mateus, Vandepoele, Klaas, Ebersberger, Ingo, Blake, Judith, Breis, Jesualdo Tomás Fernández, Boeckmann, Brigitte, Gabaldón, Toni, Sonnhammer, Erik, Dessimoz, Christophe, Lewis, Suzanna, Bello, Carla, Briois, Sébastien, Chalstrey, Edward, Chiba, Hirokazu, Conchillo-Solé, Oscar, Daubin, Vincent, DeLuca, Todd, Dufayard, Jean-Francois, Durand, Dannie, Fernández-Breis, Jesualdo Tomás, Glover, Natasha, Hauser, Alexander, Heller, Davide, Kaduk, Mateusz, Koch, Jan, Koonin, Eugene V, Kriventseva, Evgenia, Kuraku, Shigehiro, Lecompte, Odile, Lespinet, Olivier, Levy, Jeremy, Liebeskind, Benjamin, Linard, Benjamin, Marcet-Houben, Marina, Martin, Maria, McWhite, Claire, Mekhedov, Sergei, Moretti, Sebastien, Müller, Steven, Nadia, El-Mabrouk, Notredame, Cédric, Penel, Simon, Pereira, Cécile, Pilizota, Ivana, Redestig, Henning, Robinson-Rechavi, Marc, Schreiber, Fabian, Sjölander, Kimmen, Škunca, Nives, Steinegger, Martin, Szklarczyk, Damian, Thomas, Paul, Thuer, Ernst, Train, Clément, Uchiyama, Ikuo, Wittwer, Lucas, Xenarios, Ioannis, Yates, Bethan, Zdobnov, Evgeny, and Waterhouse, Robert M

Subjects
Biological Sciences, Human Genome, Genetics, Biotechnology, Quest for Orthologs Consortium, Quest for Orthologs Consortium, Mathematical Sciences, Information and Computing Sciences, Bioinformatics, Biological sciences, Information and computing sciences, Mathematical sciences
Abstract

The Quest for Orthologs (QfO) is an open collaboration framework for experts in comparative phylogenomics and related research areas who have an interest in highly accurate orthology predictions and their applications. We here report highlights and discussion points from the QfO meeting 2015 held in Barcelona. Achievements in recent years have established a basis to support developments for improved orthology prediction and to explore new approaches. Central to the QfO effort is proper benchmarking of methods and services, as well as design of standardized datasets and standardized formats to allow sharing and comparison of results. Simultaneously, analysis pipelines have been improved, evaluated and adapted to handle large datasets. All this would not have occurred without the long-term collaboration of Consortium members. Meeting regularly to review and coordinate complementary activities from a broad spectrum of innovative researchers clearly benefits the community. Highlights of the meeting include addressing sources of and legitimacy of disagreements between orthology calls, the context dependency of orthology definitions, special challenges encountered when analyzing very anciently rooted orthologies, orthology in the light of whole-genome duplications, and the concept of orthologous versus paralogous relationships at different levels, including domain-level orthology. Furthermore, particular needs for different applications (e.g. plant genomics, ancient gene families and others) and the infrastructure for making orthology inferences available (e.g. interfaces with model organism databases) were discussed, with several ongoing efforts that are expected to be reported on during the upcoming 2017 QfO meeting.

Published
2018

48. Diversity, origin, and evolution of the ESCRT systems

Author

Makarova, Kira S., primary, Tobiasson, Victor, additional, Wolf, Yuri I., additional, Lu, Zhongyi, additional, Liu, Yang, additional, Zhang, Siyu, additional, Krupovic, Mart, additional, Li, Meng, additional, and Koonin, Eugene V., additional

Published
2024
Full Text
View/download PDF

49. ICTV Virus Taxonomy Profile: Kolmioviridae 2024

Author

Kuhn, Jens H., primary, Babaian, Artem, additional, Bergner, Laura M., additional, Dény, Paul, additional, Glebe, Dieter, additional, Horie, Masayuki, additional, Koonin, Eugene V., additional, Krupovic, Mart, additional, Paraskevopoulou, Sofia, additional, de la Peña, Marcos, additional, Smura, Teemu, additional, and Hepojoki, Jussi, additional

Published
2024
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results