TY - GEN AU - Gulyás, Gábor AU - Kakuk, Balázs AU - Dörmő, Ákos AU - Járay, Tamás Flórián AU - Prazsák, István AU - Csabai, Zsolt AU - Miksa, Máté Henkrich AU - Boldogkői, Zsolt AU - Tombácz, Dóra TI - Cross-Comparison of Gut Metagenomic Profiling Strategies PY - 2024 UR - https://m2.mtmt.hu/api/publication/34670012 ID - 34670012 LA - English DB - MTMT ER - TY - JOUR AU - Prazsák, István AU - Tombácz, Dóra AU - Fülöp, Ádám AU - Torma, Gábor AU - Gulyás, Gábor AU - Dörmő, Ákos AU - Kakuk, Balázs AU - McKenzie, Spires Lauren AU - Toth, Zsolt AU - Boldogkői, Zsolt TI - KSHV 3.0. A State-of-the-Art Annotation of the Kaposi’s Sarcoma-Associated Herpesvirus Transcriptome Using Cross-Platform Sequencing TS - A State-of-the-Art Annotation of the Kaposi’s Sarcoma-Associated Herpesvirus Transcriptome Using Cross-Platform Sequencing JF - MSYSTEMS J2 - MSYSTEMS VL - 9 PY - 2024 IS - 2 PG - 19 SN - 2379-5077 DO - 10.1128/msystems.01007-23 UR - https://m2.mtmt.hu/api/publication/34430917 ID - 34430917 LA - English DB - MTMT ER - TY - GEN AU - Torma, Gábor AU - Tombácz, Dóra AU - Almsarrhad, Islam AU - Csabai, Zsolt AU - Nagy, Gergely Ármin AU - Kakuk, Balázs AU - Gulyás, Gábor AU - Lauren, McKenzie Spires AU - Ishaan, Gupta AU - Fülöp, Ádám AU - Dörmő, Ákos AU - Prazsák, István AU - Mizik, Máté Levente AU - Dani, Virág Éva AU - Csányi, Viktor AU - Zoltán, Zádori AU - Zsolt, Toth AU - Boldogkői, Zsolt TI - Novel Herpesvirus Transcripts with Putative Regulatory Roles in DNA Replication and Global Transcription PY - 2023 PG - 37 UR - https://m2.mtmt.hu/api/publication/34186518 ID - 34186518 LA - English DB - MTMT ER - TY - JOUR AU - Torma, Gábor AU - Tombácz, Dóra AU - Csabai, Zsolt AU - Almsarrhad, Islam AU - Nagy, Gergely Ármin AU - Kakuk, Balázs AU - Gulyás, Gábor AU - Spires, Lauren McKenzie AU - Gupta, Ishaan AU - Fülöp, Ádám AU - Dörmő, Ákos AU - Prazsák, István AU - Mizik, Máté Levente AU - Dani, Virág Éva AU - Csányi, Viktor AU - Harangozó, Ákos AU - Zádori, Zoltán AU - Toth, Zsolt AU - Boldogkői, Zsolt TI - Identification of herpesvirus transcripts from genomic regions around the replication origins JF - SCIENTIFIC REPORTS J2 - SCI REP VL - 13 PY - 2023 IS - 1 PG - 25 SN - 2045-2322 DO - 10.1038/s41598-023-43344-y UR - https://m2.mtmt.hu/api/publication/34171230 ID - 34171230 N1 - Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary MTA -SZTE Lendület GeMiNI Research Group, University of Szeged, Szeged, Hungary Department of Oral Biology, University of Florida College of Dentistry, Gainesville, FL, United States Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi, India HUN-REN Veterinary Medical Research Institute HU, Budapest, Hungary Export Date: 16 November 2023 Correspondence Address: Boldogkői, Z.; Department of Medical Biology, Hungary; email: boldogkoi.zsolt@med.u-szeged.hu AB - 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. LA - English DB - MTMT ER - TY - JOUR AU - Tombácz, Dóra AU - Torma, Gábor AU - Gulyás, Gábor AU - Fülöp, Ádám AU - Dörmő, Ákos AU - Prazsák, István AU - Csabai, Zsolt AU - Mizik, Máté Levente AU - Hornyák, Ákos AU - Zádori, Zoltán AU - Kakuk, Balázs AU - Boldogkői, Zsolt TI - Hybrid sequencing discloses unique aspects of the transcriptomic architecture in equid alphaherpesvirus 1 JF - HELIYON J2 - HELIYON VL - 9 PY - 2023 IS - 7 PG - 16 SN - 2405-8440 DO - 10.1016/j.heliyon.2023.e17716 UR - https://m2.mtmt.hu/api/publication/34043441 ID - 34043441 LA - English DB - MTMT ER - TY - JOUR AU - Kakuk, Balázs AU - Dörmő, Ákos AU - Csabai, Zsolt AU - Kemenesi, Gábor AU - Holoubek, Jiří AU - Růžek, Daniel AU - Prazsák, István AU - Dani, Virág Éva AU - Dénes, Béla AU - Torma, Gábor AU - Jakab, Ferenc AU - Tóth, Gábor Endre AU - Földes, Fanni Vivien AU - Zana, Brigitta AU - Lanszki, Zsófia AU - Harangozó, Ákos AU - Fülöp, Ádám AU - Gulyás, Gábor AU - Mizik, Máté Levente AU - Kiss, András Attila AU - Tombácz, Dóra AU - Boldogkői, Zsolt TI - In-depth Temporal Transcriptome Profiling of Monkeypox and Host Cells using Nanopore Sequencing JF - SCIENTIFIC DATA J2 - SCI DATA VL - 10 PY - 2023 IS - 1 PG - 12 SN - 2052-4463 DO - 10.1038/s41597-023-02149-4 UR - https://m2.mtmt.hu/api/publication/33809377 ID - 33809377 AB - 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. LA - English DB - MTMT ER - TY - JOUR AU - Tombácz, Dóra AU - Dörmő, Ákos AU - Gulyás, Gábor AU - Csabai, Zsolt AU - Prazsák, István AU - Kakuk, Balázs AU - Harangozó, Ákos AU - Jankovics, István AU - Dénes, Béla AU - Boldogkői, Zsolt TI - High temporal resolution Nanopore sequencing dataset of SARS-CoV-2 and host cell RNAs JF - GIGASCIENCE J2 - GIGASCIENCE VL - 11 PY - 2022 PG - 11 SN - 2047-217X DO - 10.1093/gigascience/giac094 UR - https://m2.mtmt.hu/api/publication/33156471 ID - 33156471 AB - 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. LA - English DB - MTMT ER - TY - JOUR AU - Prazsák, István AU - Csabai, Zsolt AU - Torma, Gábor AU - Papp, Henrietta AU - Földes, Fanni Vivien AU - Kemenesi, Gábor AU - Jakab, Ferenc AU - Gulyás, Gábor AU - Fülöp, Ádám AU - Megyeri, Klára AU - Dénes, Béla AU - Boldogkői, Zsolt AU - Tombácz, Dóra TI - Transcriptome dataset of six human pathogen RNA viruses generated by nanopore sequencing JF - DATA IN BRIEF J2 - DATA BRIEF VL - 43 PY - 2022 PG - 11 SN - 2352-3409 DO - 10.1016/j.dib.2022.108386 UR - https://m2.mtmt.hu/api/publication/32895951 ID - 32895951 LA - English DB - MTMT ER - TY - JOUR AU - Torma, Gábor AU - Tombácz, Dóra AU - Moldován, Norbert AU - Fülöp, Ádám AU - Prazsák, István AU - Csabai, Zsolt AU - Michael, Snyder AU - Boldogkői, Zsolt TI - Dual isoform sequencing reveals complex transcriptomic and epitranscriptomic landscapes of a prototype baculovirus JF - SCIENTIFIC REPORTS J2 - SCI REP VL - 12 PY - 2022 IS - 1 PG - 16 SN - 2045-2322 DO - 10.1038/s41598-022-05457-8 UR - https://m2.mtmt.hu/api/publication/32618973 ID - 32618973 N1 - Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, 6720, Hungary Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, United States Cited By :2 Export Date: 20 February 2024 Correspondence Address: Boldogkői, Z.; Department of Medical Biology, Hungary; email: boldogkoi.zsolt@med.u-szeged.hu LA - English DB - MTMT ER - TY - THES AU - Prazsák, István TI - Long Read Sequencing of the Varicella-Zoster Virus and Vaccinia Virus Transcriptome [A Varicella-Zoster Vírus és a Vaccinia Vírus Transzkriptom analízise hosszú-leolvasást adó szekvenálással] PB - Szegedi Tudományegyetem (SZTE) PY - 2021 SP - 99 DO - 10.14232/phd.10911 UR - https://m2.mtmt.hu/api/publication/32477243 ID - 32477243 LA - English DB - MTMT ER -