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001-es BibID:	BIBFORM117877
035-os BibID:	(cikkazonosító)45 (Scopus)85181689003 (WOS)001138932000001
Első szerző:	Rádai Zoltán (biológus)
Cím:	An overlooked phenomenon : complex interactions of potential error sources on the quality of bacterial de novo genome assemblies / Zoltán Rádai, Alex Váradi, Péter Takács, Nikoletta Andrea Nagy, Nicholas Schmitt, Eszter Prépost, Gábor Kardos, Levente Laczkó
Dátum:	2024
ISSN:	1471-2164
Megjegyzések:	Background: Parameters adversely affecting the contiguity and accuracy of the assemblies from Illumina next-generation sequencing (NGS) are well described. However, past studies generally focused on their additive effects, overlooking their potential interactions possibly exacerbating one another's effects in a multiplicative manner. To investigate whether or not they act interactively on de novo genome assembly quality, we simulated sequencing data for 13 bacterial reference genomes, with varying levels of error rate, sequencing depth, PCR and optical duplicate ratios. Results: We assessed the quality of assemblies from the simulated sequencing data with a number of contiguity and accuracy metrics, which we used to quantify both additive and multiplicative effects of the four parameters. We found that the tested parameters are engaged in complex interactions, exerting multiplicative, rather than additive, effects on assembly quality. Also, the ratio of non-repeated regions and GC% of the original genomes can shape how the four parameters affect assembly quality. Conclusions: We provide a framework for consideration in future studies using de novo genome assembly of bacterial genomes, e.g. in choosing the optimal sequencing depth, balancing between its positive effect on contiguity and negative effect on accuracy due to its interaction with error rate. Furthermore, the properties of the genomes to be sequenced also should be taken into account, as they might influence the effects of error sources themselves.
Tárgyszavak:	Orvostudományok Egészségtudományok idegen nyelvű folyóiratközlemény külföldi lapban folyóiratcikk Bacterial genomes Optical duplicates PCR duplicates Sequencing depth Sequencing error
Megjelenés:	BMC Genomics. - 25 : 1 (2024), p. 1-8. -
További szerzők:	Váradi Alex (1991-) (biológus) Takács Péter (1966-) (informatikus) Nagy Nikoletta Andrea (1990-) (biológus) Schmitt, Nicholas Prépost Eszter Kardos Gábor (1974-) (szakorvos, klinikai mikrobiológus) Laczkó Levente (1992-) (biológus)
Internet cím:	Szerző által megadott URL DOI Intézményi repozitóriumban (DEA) tárolt változat
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001-es BibID:	BIBFORM104502
035-os BibID:	(cikkazonosító)150 (WoS)000876298200001 (Scopus)85140850635
Első szerző:	Rádai Zoltán (biológus)
Cím:	State and physiology behind personality in arthropods: a review / Zoltán Rádai, Johanna Kiss, Nikoletta A. Nagy, Anna Ágnes Somogyi, Attila Fülöp, Zsófia Tóth, Melinda Alexáné Babits, Zoltán Németh
Dátum:	2022
ISSN:	0340-5443
Megjegyzések:	In the endeavour to understand the causes and consequences of the variation in animal personality, a wide range of studies were carried out, utilising various aspects to make sense of this biological phenomenon. One such aspect integrated the study of physiological traits, investigating hypothesised physiological correlates of personality. Although many of such studies were carried out on vertebrates (predominantly on birds and mammals), studies using arthropods (mainly insects) as model organisms were also at the forefront of this area of research. In order to review the current state of knowledge on the relationship between personality and the most frequently studied physiological parameters in arthropods, we searched for scientific articles that investigated this relationship. In our review, we only included papers utilising a repeated-measures methodology to be conceptually and formally concordant with the study of animal personality. Based on our literature survey, metabolic rate, thermal physiology, immunophysiology, and endocrine regulation, as well as exogenous agents (such as toxins) were often identified as significant affectors shaping animal personality in arthropods. We found only weak support for state-dependence of personality when the state is approximated by singular elements (or effectors) of condition. We conclude that a more comprehensive integration of physiological parameters with condition may be required for a better understanding of state's importance in animal personality. Also, a notable knowledge gap persists in arthropods regarding the association between metabolic rate and hormonal regulation, and their combined effects on personality. We discuss the findings published on the physiological correlates of animal personality in arthropods with the aim to summarise current knowledge, putting it into the context of current theory on the origin of animal personality.
Tárgyszavak:	Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban folyóiratcikk Consistent behaviour Repeatability Physiology State-dependent Condition Metabolic rate Hormonal regulation
Megjelenés:	Behavioral Ecology and Sociobiology. - 76 (2022), p. 1-20. -
További szerzők:	Kiss Johanna (1989-) (zoológus) Nagy Nikoletta Andrea (1990-) (biológus) Somogyi Anna Ágnes (1988-) (biológus) Fülöp Attila (1987-) (biológus) Tóth Zsófia (1991-) (biológus) Alexáné Babits Melinda Németh Zoltán (1976-) (biológus)
Internet cím:	Szerző által megadott URL DOI Intézményi repozitóriumban (DEA) tárolt változat
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001-es BibID:	BIBFORM096409
035-os BibID:	(cikkazonosító)17924 (WOS)000695272000092 (Scopus)85114664567
Első szerző:	Rádai Zoltán (biológus)
Cím:	Taxonomic bias in AMP prediction of invertebrate peptides / Rádai Zoltán, Kiss Johanna, Nagy Nikoletta A.
Dátum:	2021
ISSN:	2045-2322
Tárgyszavak:	Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban folyóiratcikk
Megjelenés:	Scientific Reports. - 11 (2021), p. 1-10. -
További szerzők:	Kiss Johanna (1989-) (zoológus) Nagy Nikoletta Andrea (1990-) (biológus)
Internet cím:	Szerző által megadott URL DOI Intézményi repozitóriumban (DEA) tárolt változat
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