@article{MTMT:32618973,
	title = {Dual isoform sequencing reveals complex transcriptomic and epitranscriptomic landscapes of a prototype baculovirus},
	url = {https://m2.mtmt.hu/api/publication/32618973},
	author = {Torma, Gábor and Tombácz, Dóra and Moldován, Norbert and Fülöp, Ádám and Prazsák, István and Csabai, Zsolt and Michael, Snyder and Boldogkői, Zsolt},
	doi = {10.1038/s41598-022-05457-8},
	journal-iso = {SCI REP},
	journal = {SCIENTIFIC REPORTS},
	volume = {12},
	unique-id = {32618973},
	issn = {2045-2322},
	year = {2022},
	eissn = {2045-2322},
	orcid-numbers = {Torma, Gábor/0000-0003-3241-0955; Tombácz, Dóra/0000-0001-5520-2978; Moldován, Norbert/0000-0003-4138-586X; Csabai, Zsolt/0000-0003-0031-0116; Boldogkői, Zsolt/0000-0003-1184-7293}
}

@article{MTMT:32581214,
	title = {Integrative profiling of Epstein–Barr virus transcriptome using a multiplatform approach},
	url = {https://m2.mtmt.hu/api/publication/32581214},
	author = {Fülöp, Ádám and Torma, Gábor and Moldován, Norbert and Szenthe, Kálmán and Bánáti, Ferenc and Almsarrhad, Islam and Csabai, Zsolt and Tombácz, Dóra and Minárovits, János and Boldogkői, Zsolt},
	doi = {10.1186/s12985-021-01734-6},
	journal-iso = {VIROL J},
	journal = {VIROLOGY JOURNAL},
	volume = {19},
	unique-id = {32581214},
	issn = {1743-422X},
	abstract = {Background Epstein-Barr virus (EBV) is an important human pathogenic gammaherpesvirus with carcinogenic potential. The EBV transcriptome has previously been analyzed using both Illumina-based short read-sequencing and Pacific Biosciences RS II-based long-read sequencing technologies. Since the various sequencing methods have distinct strengths and limitations, the use of multiplatform approaches have proven to be valuable. The aim of this study is to provide a more complete picture on the transcriptomic architecture of EBV. Methods In this work, we apply the Oxford Nanopore Technologies MinION (long-read sequencing) platform for the generation of novel transcriptomic data, and integrate these with other's data generated by another LRS approach, Pacific BioSciences RSII sequencing and Illumina CAGE-Seq and Poly(A)-Seq approaches. Both amplified and non-amplified cDNA sequencings were applied for the generation of sequencing reads, including both oligo-d(T) and random oligonucleotide-primed reverse transcription. EBV transcripts are identified and annotated using the LoRTIA software suite developed in our laboratory. Results This study detected novel genes embedded into longer host genes containing 5 '-truncated in-frame open reading frames, which potentially encode N-terminally truncated proteins. We also detected a number of novel non-coding RNAs and transcript length isoforms encoded by the same genes but differing in their start and/or end sites. This study also reports the discovery of novel splice isoforms, many of which may represent altered coding potential, and of novel replication-origin-associated transcripts. Additionally, novel mono- and multigenic transcripts were identified. An intricate meshwork of transcriptional overlaps was revealed. Conclusions An integrative approach applying multi-technique sequencing technologies is suitable for reliable identification of complex transcriptomes because each techniques has different advantages and limitations, and the they can be used for the validation of the results obtained by a particular approach.},
	keywords = {EPSTEIN-BARR VIRUS; Transcriptome; SPLICE VARIANT; Herpesvirus; transcription start site; Long-read sequencing; nanopore sequencing; PacBio sequencing; transcript isoform; Transcription end site},
	year = {2022},
	eissn = {1743-422X},
	orcid-numbers = {Torma, Gábor/0000-0003-3241-0955; Moldován, Norbert/0000-0003-4138-586X; Bánáti, Ferenc/0000-0002-8999-523X; Csabai, Zsolt/0000-0003-0031-0116; Tombácz, Dóra/0000-0001-5520-2978; 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:32109459,
	title = {Combined nanopore and single-molecule real-time sequencing survey of human betaherpesvirus 5 transcriptome},
	url = {https://m2.mtmt.hu/api/publication/32109459},
	author = {Kakuk, Balázs and Tombácz, Dóra and Balázs, Zsolt and Moldován, Norbert and Csabai, Zsolt and Torma, Gábor and Megyeri, Klára and Snyder, Michael and Boldogkői, Zsolt},
	doi = {10.1038/s41598-021-93593-y},
	journal-iso = {SCI REP},
	journal = {SCIENTIFIC REPORTS},
	volume = {11},
	unique-id = {32109459},
	issn = {2045-2322},
	year = {2021},
	eissn = {2045-2322},
	orcid-numbers = {Kakuk, Balázs/0000-0002-4314-5707; Tombácz, Dóra/0000-0001-5520-2978; Balázs, Zsolt/0000-0003-3537-7441; Moldován, Norbert/0000-0003-4138-586X; Csabai, Zsolt/0000-0003-0031-0116; Torma, Gábor/0000-0003-3241-0955; Boldogkői, Zsolt/0000-0003-1184-7293}
}

@article{MTMT:32109423,
	title = {Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing},
	url = {https://m2.mtmt.hu/api/publication/32109423},
	author = {Maróti, Zoltán and Tombácz, Dóra and Moldován, Norbert and Torma, Gábor and Jefferson, Victoria A. and Csabai, Zsolt and Gulyás, Gábor and Dörmő, Ákos and Boldogkői, Miklós and Kalmár, Tibor and Meyer, Florencia and Boldogkői, Zsolt},
	doi = {10.1038/s41598-021-93142-7},
	journal-iso = {SCI REP},
	journal = {SCIENTIFIC REPORTS},
	volume = {11},
	unique-id = {32109423},
	issn = {2045-2322},
	year = {2021},
	eissn = {2045-2322},
	orcid-numbers = {Maróti, Zoltán/0000-0002-0515-117X; Tombácz, Dóra/0000-0001-5520-2978; Moldován, Norbert/0000-0003-4138-586X; Torma, Gábor/0000-0003-3241-0955; Csabai, Zsolt/0000-0003-0031-0116; Kalmár, Tibor/0000-0002-0419-2009; Boldogkői, Zsolt/0000-0003-1184-7293}
}

@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},
	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:31989778,
	title = {Dynamic Transcriptome Sequencing of Bovine Alphaherpesvirus Type 1 and Host Cells Carried Out by a Multi-Technique Approach},
	url = {https://m2.mtmt.hu/api/publication/31989778},
	author = {Tombácz, Dóra and Moldován, Norbert and Torma, Gábor and Nagy, Tibor and Hornyák, Ákos and Csabai, Zsolt and Gulyás, Gábor and Boldogkői, Miklós and Jefferson, Victoria A. and Zádori, Zoltán and Meyer, Florencia and Boldogkői, Zsolt},
	doi = {10.3389/fgene.2021.619056},
	journal-iso = {FRONT GENET},
	journal = {FRONTIERS IN GENETICS},
	volume = {12},
	unique-id = {31989778},
	year = {2021},
	eissn = {1664-8021},
	orcid-numbers = {Tombácz, Dóra/0000-0001-5520-2978; Moldován, Norbert/0000-0003-4138-586X; Torma, Gábor/0000-0003-3241-0955; Nagy, Tibor/0000-0002-4451-0796; Csabai, Zsolt/0000-0003-0031-0116; Boldogkői, Zsolt/0000-0003-1184-7293}
}

@article{MTMT:31940598,
	title = {Combined Short and Long-Read Sequencing Reveals a Complex Transcriptomic Architecture of African Swine Fever Virus},
	url = {https://m2.mtmt.hu/api/publication/31940598},
	author = {Torma, Gábor and Tombácz, Dóra and Csabai, Zsolt and Moldován, Norbert and Mészáros, István and Zádori, Zoltán and Boldogkői, Zsolt},
	doi = {10.3390/v13040579},
	journal-iso = {VIRUSES-BASEL},
	journal = {VIRUSES},
	volume = {13},
	unique-id = {31940598},
	year = {2021},
	eissn = {1999-4915},
	orcid-numbers = {Torma, Gábor/0000-0003-3241-0955; Tombácz, Dóra/0000-0001-5520-2978; Csabai, Zsolt/0000-0003-0031-0116; Moldován, Norbert/0000-0003-4138-586X; Boldogkői, Zsolt/0000-0003-1184-7293}
}

@article{MTMT:31672953,
	title = {Time-course profiling of bovine alphaherpesvirus 1.1 transcriptome using multiplatform sequencing},
	url = {https://m2.mtmt.hu/api/publication/31672953},
	author = {Moldován, Norbert and Torma, Gábor and Gulyás, Gábor and Hornyák, Ákos and Zádori, Zoltán and Jefferson, Victoria A. and Csabai, Zsolt and Boldogkői, Miklós and Tombácz, Dóra and Meyer, Florencia and Boldogkői, Zsolt},
	doi = {10.1038/s41598-020-77520-1},
	journal-iso = {SCI REP},
	journal = {SCIENTIFIC REPORTS},
	volume = {10},
	unique-id = {31672953},
	issn = {2045-2322},
	year = {2020},
	eissn = {2045-2322},
	orcid-numbers = {Moldován, Norbert/0000-0003-4138-586X; Torma, Gábor/0000-0003-3241-0955; Csabai, Zsolt/0000-0003-0031-0116; Tombácz, Dóra/0000-0001-5520-2978; 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},
	issn = {2045-2322},
	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}
}