@article{MTMT:36095611,
	title = {Mapping the temporal transcriptomic signature of a viral pathogen through CAGE and nanopore sequencing},
	url = {https://m2.mtmt.hu/api/publication/36095611},
	author = {Tombácz, Dóra and Kakuk, Balázs and Torma, Gábor and Fülöp, Ádám and Dörmő, Ákos and Gulyás, Gábor and Csabai, Zsolt and Boldogkői, Zsolt},
	doi = {10.1371/journal.pone.0320439},
	journal-iso = {PLOS ONE},
	journal = {PLOS ONE},
	volume = {20},
	unique-id = {36095611},
	year = {2025},
	eissn = {1932-6203},
	orcid-numbers = {Tombácz, Dóra/0000-0001-5520-2978; Kakuk, Balázs/0000-0002-4314-5707; Torma, Gábor/0000-0003-3241-0955; Csabai, Zsolt/0000-0003-0031-0116; Boldogkői, Zsolt/0000-0003-1184-7293}
}

@article{MTMT:35730680,
	title = {Temporal transcriptional profiling of host cells infected by a veterinary alphaherpesvirus using nanopore sequencing},
	url = {https://m2.mtmt.hu/api/publication/35730680},
	author = {Tombácz, Dóra and Maróti, Zoltán and Oláh, Péter and Dörmő, Ákos and Gulyás, Gábor and Kalmár, Tibor and Csabai, Zsolt and Boldogkői, Zsolt},
	doi = {10.1038/s41598-025-87536-0},
	journal-iso = {SCI REP},
	journal = {SCIENTIFIC REPORTS},
	volume = {15},
	unique-id = {35730680},
	abstract = {In our research, we performed temporal transcriptomic profiling of host cells infected with Equid alphaherpesvirus 1 (EHV-1) by utilizing direct cDNA sequencing based on nanopore MinION technology. The sequencing reads were harnessed for transcript quantification at various time points. Viral infection-induced differential gene expression was identified through the edgeR package. The identified genes were segmented into six groups based on their kinetic characteristics. The initial three clusters encompass immediate-early response genes, typically transcription factors and elements of antiviral signaling pathways. These genes were either upregulated (cluster 1) or downregulated (clusters 2 and 3) during the early infection phase. The remaining three clusters include late response genes. In these categories, it is challenging to determine whether changes in gene expression are directly connected to the viral infection or merely side effects of the infection. A study of gene associations using the STRINGDB software revealed several gene networks that might be directly impacted by the virus. We also explored whether gene co-expression could be a result of their collective regulation by upstream transcription factors using the Gene Regulatory Network database. Finally, our differential transcript usage (DTU) analysis identified a number of genes that exhibited altered proportions of transcript isoforms in comparison to non-infected cells. Thus, our analysis revealed that EHV-1 infection not only alters host gene expression but also leads to differential use of transcript isoforms, particularly splice variants.},
	year = {2025},
	eissn = {2045-2322},
	orcid-numbers = {Tombácz, Dóra/0000-0001-5520-2978; Maróti, Zoltán/0000-0002-0515-117X; Kalmár, Tibor/0000-0002-0419-2009; Csabai, Zsolt/0000-0003-0031-0116; Boldogkői, Zsolt/0000-0003-1184-7293}
}

@article{MTMT:35526514,
	title = {Cross-comparison of gut metagenomic profiling strategies},
	url = {https://m2.mtmt.hu/api/publication/35526514},
	author = {Gulyás, Gábor and Kakuk, Balázs and Dörmő, Ákos and Járay, Tamás Flórián and Prazsák, István and Csabai, Zsolt and Henkrich, Miksa Máté and Boldogkői, Zsolt and Tombácz, Dóra},
	doi = {10.1038/s42003-024-07158-6},
	journal-iso = {COMMUN BIOL},
	journal = {COMMUNICATIONS BIOLOGY},
	volume = {7},
	unique-id = {35526514},
	year = {2024},
	eissn = {2399-3642},
	orcid-numbers = {Kakuk, Balázs/0000-0002-4314-5707; Csabai, Zsolt/0000-0003-0031-0116; Boldogkői, Zsolt/0000-0003-1184-7293; Tombácz, Dóra/0000-0001-5520-2978}
}

@article{MTMT:35201514,
	title = {Exploring the transcriptomic profile of human monkeypox virus via CAGE and native RNA sequencing approaches},
	url = {https://m2.mtmt.hu/api/publication/35201514},
	author = {Nagy, Gergely Ármin and Tombácz, Dóra and Prazsák, István and Csabai, Zsolt and Dörmő, Ákos and Gulyás, Gábor and Kemenesi, Gábor and Tóth, Gábor Endre and Holoubek, Jiří and Růžek, Daniel and Kakuk, Balázs and Boldogkői, Zsolt},
	doi = {10.1128/msphere.00356-24},
	journal-iso = {MSPHERE},
	journal = {MSPHERE},
	volume = {9},
	unique-id = {35201514},
	issn = {2379-5042},
	year = {2024},
	eissn = {2379-5042},
	orcid-numbers = {Tombácz, Dóra/0000-0001-5520-2978; Csabai, Zsolt/0000-0003-0031-0116; Kemenesi, Gábor/0000-0001-9775-3065; Tóth, Gábor Endre/0000-0002-7201-9646; Kakuk, Balázs/0000-0002-4314-5707; Boldogkői, Zsolt/0000-0003-1184-7293}
}

@misc{MTMT:34848307,
	title = {Exploring the Transcriptomic Profile of Human Monkeypox Virus via CAGE and Native RNA Sequencing Approaches},
	url = {https://m2.mtmt.hu/api/publication/34848307},
	author = {Nagy, Gergely Ármin and Tombácz, Dóra and Prazsák, István and Csabai, Zsolt and Dörmő, Ákos and Gulyás, Gábor and Kemenesi, Gábor and Tóth, Gábor E. and Holoubek, Jiří and Růžek, Daniel and Kakuk, Balázs and Boldogkői, Zsolt},
	unique-id = {34848307},
	year = {2024},
	orcid-numbers = {Tombácz, Dóra/0000-0001-5520-2978; Csabai, Zsolt/0000-0003-0031-0116; Kemenesi, Gábor/0000-0001-9775-3065; Kakuk, Balázs/0000-0002-4314-5707; Boldogkői, Zsolt/0000-0003-1184-7293}
}

@misc{MTMT:34670012,
	title = {Cross-Comparison of Gut Metagenomic Profiling Strategies},
	url = {https://m2.mtmt.hu/api/publication/34670012},
	author = {Gulyás, Gábor and Kakuk, Balázs and Dörmő, Ákos and Járay, Tamás Flórián and Prazsák, István and Csabai, Zsolt and Miksa, Máté Henkrich and Boldogkői, Zsolt and Tombácz, Dóra},
	unique-id = {34670012},
	year = {2024},
	orcid-numbers = {Kakuk, Balázs/0000-0002-4314-5707; Csabai, Zsolt/0000-0003-0031-0116; Boldogkői, Zsolt/0000-0003-1184-7293; Tombácz, Dóra/0000-0001-5520-2978}
}

@misc{MTMT:34186518,
	title = {Novel Herpesvirus Transcripts with Putative Regulatory Roles in DNA Replication and Global Transcription},
	url = {https://m2.mtmt.hu/api/publication/34186518},
	author = {Torma, Gábor and Tombácz, Dóra and Almsarrhad, Islam and Csabai, Zsolt and Nagy, Gergely Ármin and Kakuk, Balázs and Gulyás, Gábor and Lauren, McKenzie Spires and Ishaan, Gupta and Fülöp, Ádám and Dörmő, Ákos and Prazsák, István and Mizik, Máté Levente and Dani, Virág Éva and Csányi, Viktor and Zoltán, Zádori and Zsolt, Toth and Boldogkői, Zsolt},
	unique-id = {34186518},
	year = {2023},
	orcid-numbers = {Torma, Gábor/0000-0003-3241-0955; Tombácz, Dóra/0000-0001-5520-2978; Csabai, Zsolt/0000-0003-0031-0116; Kakuk, Balázs/0000-0002-4314-5707; Dani, Virág Éva/0000-0001-9715-2569; Boldogkői, Zsolt/0000-0003-1184-7293}
}

@article{MTMT:34171230,
	title = {Identification of herpesvirus transcripts from genomic regions around the replication origins},
	url = {https://m2.mtmt.hu/api/publication/34171230},
	author = {Torma, Gábor and Tombácz, Dóra and Csabai, Zsolt and Almsarrhad, Islam and Nagy, Gergely Ármin and Kakuk, Balázs and Gulyás, Gábor and Spires, Lauren McKenzie and Gupta, Ishaan and Fülöp, Ádám and Dörmő, Ákos and Prazsák, István and Mizik, Máté Levente and Dani, Virág Éva and Csányi, Viktor and Harangozó, Ákos and Zádori, Zoltán and Toth, Zsolt and Boldogkői, Zsolt},
	doi = {10.1038/s41598-023-43344-y},
	journal-iso = {SCI REP},
	journal = {SCIENTIFIC REPORTS},
	volume = {13},
	unique-id = {34171230},
	abstract = {Long-read sequencing (LRS) techniques enable the identification of full-length RNA molecules in a single run eliminating the need for additional assembly steps. LRS research has exposed unanticipated transcriptomic complexity in various organisms, including viruses. Herpesviruses are known to produce a range of transcripts, either close to or overlapping replication origins (Oris) and neighboring genes related to transcription or replication, which possess confirmed or potential regulatory roles. In our research, we employed both new and previously published LRS and short-read sequencing datasets to uncover additional Ori-proximal transcripts in nine herpesviruses from all three subfamilies (alpha, beta and gamma). We discovered novel long non-coding RNAs, as well as splice and length isoforms of mRNAs. Moreover, our analysis uncovered an intricate network of transcriptional overlaps within the examined genomic regions. We demonstrated that herpesviruses display distinct patterns of transcriptional overlaps in the vicinity of or at the Oris. Our findings suggest the existence of a ‘super regulatory center’ in the genome of alphaherpesviruses that governs the initiation of both DNA replication and global transcription through multilayered interactions among the molecular machineries.},
	year = {2023},
	eissn = {2045-2322},
	orcid-numbers = {Torma, Gábor/0000-0003-3241-0955; Tombácz, Dóra/0000-0001-5520-2978; Csabai, Zsolt/0000-0003-0031-0116; Kakuk, Balázs/0000-0002-4314-5707; Dani, Virág Éva/0000-0001-9715-2569; Boldogkői, Zsolt/0000-0003-1184-7293}
}

@article{MTMT:34043441,
	title = {Hybrid sequencing discloses unique aspects of the transcriptomic architecture in equid alphaherpesvirus 1},
	url = {https://m2.mtmt.hu/api/publication/34043441},
	author = {Tombácz, Dóra and Torma, Gábor and Gulyás, Gábor and Fülöp, Ádám and Dörmő, Ákos and Prazsák, István and Csabai, Zsolt and Mizik, Máté Levente and Hornyák, Ákos and Zádori, Zoltán and Kakuk, Balázs and Boldogkői, Zsolt},
	doi = {10.1016/j.heliyon.2023.e17716},
	journal-iso = {HELIYON},
	journal = {HELIYON},
	volume = {9},
	unique-id = {34043441},
	year = {2023},
	eissn = {2405-8440},
	orcid-numbers = {Tombácz, Dóra/0000-0001-5520-2978; Torma, Gábor/0000-0003-3241-0955; Csabai, Zsolt/0000-0003-0031-0116; Kakuk, Balázs/0000-0002-4314-5707; Boldogkői, Zsolt/0000-0003-1184-7293}
}

@article{MTMT:33809377,
	title = {In-depth Temporal Transcriptome Profiling of Monkeypox and Host Cells using Nanopore Sequencing},
	url = {https://m2.mtmt.hu/api/publication/33809377},
	author = {Kakuk, Balázs and Dörmő, Ákos and Csabai, Zsolt and Kemenesi, Gábor and Holoubek, Jiří and Růžek, Daniel and Prazsák, István and Dani, Virág Éva and Dénes, Béla and Torma, Gábor and Jakab, Ferenc and Tóth, Gábor Endre and Földes, Fanni Vivien and Zana, Brigitta and Lanszki, Zsófia and Harangozó, Ákos and Fülöp, Ádám and Gulyás, Gábor and Mizik, Máté Levente and Kiss, András Attila and Tombácz, Dóra and Boldogkői, Zsolt},
	doi = {10.1038/s41597-023-02149-4},
	journal-iso = {SCI DATA},
	journal = {SCIENTIFIC DATA},
	volume = {10},
	unique-id = {33809377},
	abstract = {The recent human Monkeypox outbreak underlined the importance of studying basic biology of orthopoxviruses. However, the transcriptome of its causative agent has not been investigated before neither with short-, nor with long-read sequencing approaches. This Oxford Nanopore long-read RNA-Sequencing dataset fills this gap. It will enable the in-depth characterization of the transcriptomic architecture of the monkeypox virus, and may even make possible to annotate novel host transcripts. Moreover, our direct cDNA and native RNA sequencing reads will allow the estimation of gene expression changes of both the virus and the host cells during the infection. Overall, our study will lead to a deeper understanding of the alterations caused by the viral infection on a transcriptome level.},
	year = {2023},
	eissn = {2052-4463},
	orcid-numbers = {Kakuk, Balázs/0000-0002-4314-5707; Csabai, Zsolt/0000-0003-0031-0116; Kemenesi, Gábor/0000-0001-9775-3065; Růžek, Daniel/0000-0003-4655-2380; Dani, Virág Éva/0000-0001-9715-2569; Dénes, Béla/0000-0002-9889-529X; Torma, Gábor/0000-0003-3241-0955; Tóth, Gábor Endre/0000-0002-7201-9646; Lanszki, Zsófia/0000-0003-3116-4633; Kiss, András Attila/0000-0003-2633-292X; Tombácz, Dóra/0000-0001-5520-2978; Boldogkői, Zsolt/0000-0003-1184-7293}
}