@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 Gábor, E. Tóth and Jiří, Holoubek and Daniel, Růžek and Kakuk, Balázs and Boldogkői, Zsolt},
	doi = {10.1128/msphere.00356-24},
	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}
}

@article{MTMT:33156471,
	title = {High temporal resolution Nanopore sequencing dataset of SARS-CoV-2 and host cell RNAs},
	url = {https://m2.mtmt.hu/api/publication/33156471},
	author = {Tombácz, Dóra and Dörmő, Ákos and Gulyás, Gábor and Csabai, Zsolt and Prazsák, István and Kakuk, Balázs and Harangozó, Ákos and Jankovics, István and Dénes, Béla and Boldogkői, Zsolt},
	doi = {10.1093/gigascience/giac094},
	journal-iso = {GIGASCIENCE},
	journal = {GIGASCIENCE},
	volume = {11},
	unique-id = {33156471},
	issn = {2047-217X},
	abstract = {Background: Recent studies have disclosed the genome, transcriptome, and epigenetic compositions of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the effect of viral infection on gene expression of the host cells. It has been demonstrated that, besides the major canonical transcripts, the viral genome also codes for noncanonical RNA molecules. While the structural characterizations have revealed a detailed transcriptomic architecture of the virus, the kinetic studies provided poor and often misleading results on the dynamics of both the viral and host transcripts due to the low temporal resolution of the infection event and the low virus/cell ratio (multiplicity of infection [MOI] = 0.1) applied for the infection. It has never been tested whether the alteration in the host gene expressions is caused by aging of the cells or by the viral infection.Findings: In this study, we used Oxford Nanopore's direct cDNA and direct RNA sequencing methods for the generation of a highcoverage, high temporal resolution transcriptomic dataset of SARS-CoV-2 and of the primate host cells, using a high infection titer (MOI = 5). Sixteen sampling time points ranging from 1 to 96 hours with a varying time resolution and 3 biological replicates were used in the experiment. In addition, for each infected sample, corresponding noninfected samples were employed. The raw reads were mapped to the viral and to the host reference genomes, resulting in 49,661,499 mapped reads (54,62 Gbs). The genome of the viral isolate was also sequenced and phylogenetically classified.Conclusions: This dataset can serve as a valuable resource for profiling the SARS-CoV-2 transcriptome dynamics, the virus-host interactions, and the RNA base modifications. Comparison of expression profiles of the host gene in the virally infected and in noninfected cells at different time points allows making a distinction between the effect of the aging of cells in culture and the viral infection. These data can provide useful information for potential novel gene annotations and can also be used for studying the currently available bioinformatics pipelines.},
	keywords = {CORONAVIRUS; Long-read sequencing; Oxford Nanopore Technologies; full-length transcriptome; MinION system; direct RNA sequencing; SARS-CoV-2; direct cDNA sequencing},
	year = {2022},
	eissn = {2047-217X},
	orcid-numbers = {Tombácz, Dóra/0000-0001-5520-2978; Csabai, Zsolt/0000-0003-0031-0116; Kakuk, Balázs/0000-0002-4314-5707; Dénes, Béla/0000-0002-9889-529X; Boldogkői, Zsolt/0000-0003-1184-7293}
}

@article{MTMT:32895951,
	title = {Transcriptome dataset of six human pathogen RNA viruses generated by nanopore sequencing},
	url = {https://m2.mtmt.hu/api/publication/32895951},
	author = {Prazsák, István and Csabai, Zsolt and Torma, Gábor and Papp, Henrietta and Földes, Fanni Vivien and Kemenesi, Gábor and Jakab, Ferenc and Gulyás, Gábor and Fülöp, Ádám and Megyeri, Klára and Dénes, Béla and Boldogkői, Zsolt and Tombácz, Dóra},
	doi = {10.1016/j.dib.2022.108386},
	journal-iso = {DATA BRIEF},
	journal = {DATA IN BRIEF},
	volume = {43},
	unique-id = {32895951},
	issn = {2352-3409},
	year = {2022},
	eissn = {2352-3409},
	orcid-numbers = {Csabai, Zsolt/0000-0003-0031-0116; Torma, Gábor/0000-0003-3241-0955; Papp, Henrietta/0000-0003-3887-5657; Kemenesi, Gábor/0000-0001-9775-3065; Dénes, Béla/0000-0002-9889-529X; Boldogkői, Zsolt/0000-0003-1184-7293; Tombácz, Dóra/0000-0001-5520-2978}
}