@article{MTMT:32080152,
	title = {Time-course transcriptome analysis of host cell response to poxvirus infection using a dual long-read sequencing approach},
	url = {https://m2.mtmt.hu/api/publication/32080152},
	author = {Maróti, Zoltán and Tombácz, Dóra and Prazsák, István and Moldován, Norbert and Csabai, Zsolt and Torma, Gábor and Balázs, Zsolt and Kalmár, Tibor and Dénes, Béla and Snyder, Michael and Boldogkői, Zsolt},
	doi = {10.1186/s13104-021-05657-x},
	journal-iso = {BMC RES NOTES},
	journal = {BMC RESEARCH NOTES},
	volume = {14},
	unique-id = {32080152},
	issn = {1756-0500},
	year = {2021},
	eissn = {1756-0500},
	orcid-numbers = {Maróti, Zoltán/0000-0002-0515-117X; Tombácz, Dóra/0000-0001-5520-2978; Moldován, Norbert/0000-0003-4138-586X; Csabai, Zsolt/0000-0003-0031-0116; Torma, Gábor/0000-0003-3241-0955; Balázs, Zsolt/0000-0003-3537-7441; Kalmár, Tibor/0000-0002-0419-2009; Dénes, Béla/0000-0002-9889-529X; Boldogkői, Zsolt/0000-0003-1184-7293}
}

@article{MTMT:32109464,
	title = {Time-Course Transcriptome Profiling of a Poxvirus Using Long-Read Full-Length Assay},
	url = {https://m2.mtmt.hu/api/publication/32109464},
	author = {Tombácz, Dóra and Prazsák, István and Torma, Gábor and Csabai, Zsolt and Balázs, Zsolt and Moldován, Norbert and Dénes, Béla and Snyder, Michael and Boldogkői, Zsolt},
	doi = {10.3390/pathogens10080919},
	journal-iso = {PATHOGENS},
	journal = {PATHOGENS},
	volume = {10},
	unique-id = {32109464},
	year = {2021},
	eissn = {2076-0817},
	orcid-numbers = {Tombácz, Dóra/0000-0001-5520-2978; Torma, Gábor/0000-0003-3241-0955; Csabai, Zsolt/0000-0003-0031-0116; Balázs, Zsolt/0000-0003-3537-7441; Moldován, Norbert/0000-0003-4138-586X; Dénes, Béla/0000-0002-9889-529X; Boldogkői, Zsolt/0000-0003-1184-7293}
}

@article{MTMT:31406099,
	title = {Long-read assays shed new light on the transcriptome complexity of a viral pathogen.},
	url = {https://m2.mtmt.hu/api/publication/31406099},
	author = {Tombácz, Dóra and Prazsák, István and Csabai, Zsolt and Moldován, Norbert and Dénes, Béla and Snyder, Michael and Boldogkői, Zsolt},
	doi = {10.1038/s41598-020-70794-5},
	journal-iso = {SCI REP},
	journal = {SCIENTIFIC REPORTS},
	volume = {10},
	unique-id = {31406099},
	abstract = {Characterization of global transcriptomes using conventional short-read sequencing is challenging due to the insensitivity of these platforms to transcripts isoforms, multigenic RNA molecules, and transcriptional overlaps. Long-read sequencing (LRS) can overcome these limitations by reading full-length transcripts. Employment of these technologies has led to the redefinition of transcriptional complexities in reported organisms. In this study, we applied LRS platforms from Pacific Biosciences and Oxford Nanopore Technologies to profile the vaccinia virus (VACV) transcriptome. We performed cDNA and direct RNA sequencing analyses and revealed an extremely complex transcriptional landscape of this virus. In particular, VACV genes produce large numbers of transcript isoforms that vary in their start and termination sites. A significant fraction of VACV transcripts start or end within coding regions of neighbouring genes. This study provides new insights into the transcriptomic profile of this viral pathogen.},
	year = {2020},
	eissn = {2045-2322},
	orcid-numbers = {Tombácz, Dóra/0000-0001-5520-2978; Csabai, Zsolt/0000-0003-0031-0116; Moldován, Norbert/0000-0003-4138-586X; Dénes, Béla/0000-0002-9889-529X; Boldogkői, Zsolt/0000-0003-1184-7293}
}

@article{MTMT:30330053,
	title = {Dynamic Transcriptome Profiling Dataset of Vaccinia Virus Obtained from Long-read Sequencing Techniques},
	url = {https://m2.mtmt.hu/api/publication/30330053},
	author = {Tombácz, Dóra and Prazsák, István and Szűcs, Attila and Dénes, Béla and Snyder, Michael and Boldogkői, Zsolt},
	doi = {10.1093/gigascience/giy139},
	journal-iso = {GIGASCIENCE},
	journal = {GIGASCIENCE},
	volume = {7},
	unique-id = {30330053},
	issn = {2047-217X},
	abstract = {Poxviruses are large DNA viruses infecting humans and animals. Vaccinia virus (VACV) has been applied as a live vaccine for immunization against smallpox, which was eradicated by 1980 as a result of worldwide vaccination. VACV is the prototype of poxviruses in the investigation of the molecular pathogenesis of the virus. Short-read sequencing methods have revolutionized transcriptomics; but, they are not efficient in distinguishing between the RNA isoforms and transcript overlaps. Long-read sequencing (LRS) is much better suited to solve these problems, and also allow direct RNA sequencing. Despite the scientific relevance of VACV, no LRS data have been generated for the viral transcriptome so far.For the deep characterization of the VACV RNA profile, various LRS platforms and library preparation approaches were applied. The raw reads were mapped to the VACV reference genome and also to the host (Chlorocebus sabaeus) genome. In this study, we applied the Pacific Biosciences RSII and Sequel platforms, which altogether resulted in 937,531 mapped reads of inserts (1.42 Gb), while we obtained 2,160,348 aligned reads (1.75 Gb) from the different library preparation methods, using the MinION device from Oxford Nanopore Technologies.By applying cutting-edge technologies, we were able to generate a large dataset that can serve as a valuable resource for the investigation of the dynamic VACV transcriptome, the virus-host interactions and RNA base modifications. These data can provide useful information for novel gene annotations in the VACV genome. Our dataset can also be applied for analyzing the currently available LRS platforms, library preparation methods and bioinformatics pipelines.},
	keywords = {VACCINIA VIRUS; Long-read sequencing; Poxvirus; Oxford Nanopore Technologies; full-length transcriptome; Pacific Biosciences; RS II system; Sequel system; MinION system; direct RNA sequencing},
	year = {2018},
	eissn = {2047-217X},
	orcid-numbers = {Tombácz, Dóra/0000-0001-5520-2978; Szűcs, Attila/0000-0003-2803-7123; Dénes, Béla/0000-0002-9889-529X; Boldogkői, Zsolt/0000-0003-1184-7293}
}