@article{MTMT:34772438,
	title = {Mitochondrial Differentiation during Spermatogenesis: Lessons from Drosophila melanogaster},
	url = {https://m2.mtmt.hu/api/publication/34772438},
	author = {Vedelek, Viktor and Jankovics, Ferenc and Zádori, János and Sinka, Rita},
	doi = {10.3390/ijms25073980},
	journal-iso = {INT J MOL SCI},
	journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
	volume = {25},
	unique-id = {34772438},
	issn = {1661-6596},
	abstract = {Numerous diseases can arise as a consequence of mitochondrial malfunction. Hence, there is a significant focus on studying the role of mitochondria in cancer, ageing, neurodegenerative diseases, and the field of developmental biology. Mitochondria could exist as discrete organelles in the cell; however, they have the ability to fuse, resulting in the formation of interconnected reticular structures. The dynamic changes between these forms correlate with mitochondrial function and mitochondrial health, and consequently, there is a significant scientific interest in uncovering the specific molecular constituents that govern these transitions. Moreover, the specialized mitochondria display a wide array of variable morphologies in their cristae formations. These inner mitochondrial structures are closely associated with the specific functions performed by the mitochondria. In multiple cases, the presence of mitochondrial dysfunction has been linked to male sterility, as it has been observed to cause a range of abnormal spermatogenesis and sperm phenotypes in different species. This review aims to elucidate the dynamic alterations and functions of mitochondria in germ cell development during the spermatogenesis of Drosophila melanogaster.},
	year = {2024},
	eissn = {1422-0067},
	orcid-numbers = {Vedelek, Viktor/0000-0002-0420-8226; Sinka, Rita/0000-0003-4040-4184}
}

@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}
}

@article{MTMT:34430917,
	title = {KSHV 3.0. A State-of-the-Art Annotation of the Kaposi’s Sarcoma-Associated Herpesvirus Transcriptome Using Cross-Platform Sequencing},
	url = {https://m2.mtmt.hu/api/publication/34430917},
	author = {Prazsák, István and Tombácz, Dóra and Fülöp, Ádám and Torma, Gábor and Gulyás, Gábor and Dörmő, Ákos and Kakuk, Balázs and McKenzie, Spires Lauren and Toth, Zsolt and Boldogkői, Zsolt},
	doi = {10.1128/msystems.01007-23},
	journal-iso = {MSYSTEMS},
	journal = {MSYSTEMS},
	volume = {9},
	unique-id = {34430917},
	issn = {2379-5077},
	year = {2024},
	eissn = {2379-5077},
	orcid-numbers = {Tombácz, Dóra/0000-0001-5520-2978; Torma, Gábor/0000-0003-3241-0955; Kakuk, Balázs/0000-0002-4314-5707; Boldogkői, Zsolt/0000-0003-1184-7293}
}

@article{MTMT:34402081,
	title = {Hypoxia and HIF-1α promote lytic de novo KSHV infection},
	url = {https://m2.mtmt.hu/api/publication/34402081},
	author = {Lee, See-Chi and Naik, Nenavath Gopal and Tombácz, Dóra and Gulyás, Gábor and Kakuk, Balázs and Boldogkői, Zsolt and Hall, Kevin and Papp, Bernadett and Boulant, Steeve and Toth, Zsolt},
	doi = {10.1128/jvi.00972-23},
	journal-iso = {J VIROL},
	journal = {JOURNAL OF VIROLOGY},
	volume = {97},
	unique-id = {34402081},
	issn = {0022-538X},
	abstract = {The impact of different stress conditions on the oncogenic Kaposi's sarcoma-associated herpesvirus (KSHV) primary infection that can occur in vivo remains largely unknown. We hypothesized that KSHV can establish a latency or lytic cycle following de novo infection, depending on the conditions of the cellular environment. Previous studies showed that hypoxia is a natural stress condition that promotes lytic reactivation and contributes to KSHV pathogenesis, but its effect on de novo KSHV infection is unknown. To test the effect of hypoxia on KSHV infection, we infected cells under normoxia and hypoxia, performed a comparative analysis of viral gene expression and viral replication, and tested chromatinization of the KSHV genome during infection. We found that hypoxia induces viral lytic gene expression and viral replication following de novo infection in several biologically relevant cell types, in which the virus normally establishes latency under normoxia. We also found that hypoxia reduces the level of repressive heterochromatin and promotes the formation of a transcriptionally permissive chromatin on the incoming viral DNA during infection. We demonstrate that silencing hypoxia-inducible factor-1 alpha (HIF-1 alpha) during hypoxia abrogates lytic KSHV infection, while the overexpression of HIF-1 alpha under normoxia is sufficient to drive lytic KSHV infection. Also, we determined that the DNA-binding domain and the N-terminal but not the C-terminal transactivation domain of HIF-1 alpha are required for HIF-1 alpha-induced lytic gene expression. Altogether, our data indicate that HIF-1 alpha accumulation, which can be induced by hypoxia, prevents the establishment of latency and promotes lytic KSHV infection following primary infection.},
	year = {2023},
	eissn = {1098-5514},
	orcid-numbers = {Tombácz, Dóra/0000-0001-5520-2978; Kakuk, Balázs/0000-0002-4314-5707; Boldogkői, Zsolt/0000-0003-1184-7293}
}

@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},
	issn = {2045-2322},
	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:34130955,
	title = {Regulation of the methanogenesis pathways by hydrogen at transcriptomic level in time},
	url = {https://m2.mtmt.hu/api/publication/34130955},
	author = {Szuhaj, Márk and Kakuk, Balázs and Wirth, Roland and Rákhely, Gábor and Kovács, Kornél Lajos and Bagi, Zoltán},
	doi = {10.1007/s00253-023-12700-3},
	journal-iso = {APPL MICROBIOL BIOT},
	journal = {APPLIED MICROBIOLOGY AND BIOTECHNOLOGY},
	volume = {107},
	unique-id = {34130955},
	issn = {0175-7598},
	abstract = {The biomethane formation from 4 H-2 + CO2 by pure cultures of two methanogens, Methanocaldococcus fervens and Methanobacterium thermophilum, has been studied. The goal of the study was to understand the regulation of the enzymatic steps associated with biomethane biosynthesis by H-2, using metagenomic, pan-genomic, and transcriptomic approaches. Methanogenesis in the autotrophic methanogen M. fervens could be easily "switched off" and "switched on" by H-2/CO2 within about an hour. In contrast, the heterotrophic methanogen M. thermophilum was practically insensitive to the addition of the H-2/CO2 trigger although this methanogen also converted H-2/CO2 to CH4. From practical points of view, the regulatory function of H-2/CO2 suggests that in the power-to-gas (P2G) renewable excess electricity conversion and storage systems, the composition of the biomethane-generating methanogenic community is essential for sustainable operation. In addition to managing the specific hydrogenotrophic methanogenesis biochemistry, H-2/CO2 affected several, apparently unrelated, metabolic pathways. The redox-regulated overall biochemistry and symbiotic relationships in the methanogenic communities should be explored in order to make the P2G technology more efficient.},
	keywords = {metabolism; IDENTIFICATION; HYDROGEN; REDUCTION; METHANE; ACETATE; STRAINS; ANAEROBIC-DIGESTION; methanogenesis; Dehydrogenases; Hydrogenotrophic methanogens; Power to gas; THERMOPHILICUM},
	year = {2023},
	eissn = {1432-0614},
	pages = {6315-6324},
	orcid-numbers = {Szuhaj, Márk/0000-0001-7160-3173; Kakuk, Balázs/0000-0002-4314-5707; Wirth, Roland/0000-0002-2383-2323; Rákhely, Gábor/0000-0003-2557-3641; Kovács, Kornél Lajos/0000-0002-3926-0497; Bagi, Zoltán/0000-0001-7795-2024}
}

@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:33713093,
	title = {Life style and structure differences between species of freshwater fish},
	url = {https://m2.mtmt.hu/api/publication/33713093},
	author = {Szűts, Viktória and Kelemen-Valkony, Ildikó and Ötvös, Ferenc and Repas, Zoltan and Kovács, András Sándor and Tóth, László and Kiss, András Attila and Lőrincz, Ádám and Szabó, P. Balázs and Gajdán, Krisztina and Kertai, Zoltán and Houshmand, Nazanin and Szutcs, Marcella and Obistioui, Diana and Velciov, Ariana B. and Halasy, Katalin and Deim, Zoltán and Deák, Dalma and Gál, József and Csanádi, József and Racskóné Domonkos, Ildikó},
	journal-iso = {MED INT REV},
	journal = {MEDICINA INTERNACIA REVUO},
	volume = {30},
	unique-id = {33713093},
	issn = {0465-5435},
	year = {2022},
	pages = {98-106},
	orcid-numbers = {Kiss, András Attila/0000-0003-2633-292X; Deim, Zoltán/0000-0003-3925-5564; Gál, József/0000-0002-4923-7282}
}