TY  - JOUR
AU  - Maróti, Zoltán
AU  - Tombácz, Dóra
AU  - Prazsák, István
AU  - Moldován, Norbert
AU  - Csabai, Zsolt
AU  - Torma, Gábor
AU  - Balázs, Zsolt
AU  - Kalmár, Tibor
AU  - Dénes, Béla
AU  - Snyder, Michael
AU  - Boldogkői, Zsolt
TI  - Time-course transcriptome analysis of host cell response to poxvirus infection using a dual long-read sequencing approach
JF  - BMC RESEARCH NOTES
J2  - BMC RES NOTES
VL  - 14
PY  - 2021
IS  - 1
PG  - 7
SN  - 1756-0500
DO  - 10.1186/s13104-021-05657-x
UR  - https://m2.mtmt.hu/api/publication/32080152
ID  - 32080152
LA  - English
DB  - MTMT
ER  - 

TY  - JOUR
AU  - Tombácz, Dóra
AU  - Prazsák, István
AU  - Torma, Gábor
AU  - Csabai, Zsolt
AU  - Balázs, Zsolt
AU  - Moldován, Norbert
AU  - Dénes, Béla
AU  - Snyder, Michael
AU  - Boldogkői, Zsolt
TI  - Time-Course Transcriptome Profiling of a Poxvirus Using Long-Read Full-Length Assay
JF  - PATHOGENS
J2  - PATHOGENS
VL  - 10
PY  - 2021
IS  - 8
PG  - 17
SN  - 2076-0817
DO  - 10.3390/pathogens10080919
UR  - https://m2.mtmt.hu/api/publication/32109464
ID  - 32109464
LA  - English
DB  - MTMT
ER  - 

TY  - JOUR
AU  - Tombácz, Dóra
AU  - Prazsák, István
AU  - Csabai, Zsolt
AU  - Moldován, Norbert
AU  - Dénes, Béla
AU  - Snyder, Michael
AU  - Boldogkői, Zsolt
TI  - Long-read assays shed new light on the transcriptome complexity of a viral pathogen.
JF  - SCIENTIFIC REPORTS
J2  - SCI REP
VL  - 10
PY  - 2020
IS  - 1
PG  - 13
SN  - 2045-2322
DO  - 10.1038/s41598-020-70794-5
UR  - https://m2.mtmt.hu/api/publication/31406099
ID  - 31406099
AB  - 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.
LA  - English
DB  - MTMT
ER  - 

TY  - JOUR
AU  - Tombácz, Dóra
AU  - Prazsák, István
AU  - Szűcs, Attila
AU  - Dénes, Béla
AU  - Snyder, Michael
AU  - Boldogkői, Zsolt
TI  - Dynamic Transcriptome Profiling Dataset of Vaccinia Virus Obtained from Long-read Sequencing Techniques
JF  - GIGASCIENCE
J2  - GIGASCIENCE
VL  - 7
PY  - 2018
IS  - 12
PG  - 17
SN  - 2047-217X
DO  - 10.1093/gigascience/giy139
UR  - https://m2.mtmt.hu/api/publication/30330053
ID  - 30330053
AB  - Poxviruses are large DNA viruses infecting humans and animals. Vaccinia virus (VACV) has been applied as a live vaccine for immunization against smallpox, which was eradicated by 1980 as a result of worldwide vaccination. VACV is the prototype of poxviruses in the investigation of the molecular pathogenesis of the virus. Short-read sequencing methods have revolutionized transcriptomics; but, they are not efficient in distinguishing between the RNA isoforms and transcript overlaps. Long-read sequencing (LRS) is much better suited to solve these problems, and also allow direct RNA sequencing. Despite the scientific relevance of VACV, no LRS data have been generated for the viral transcriptome so far.For the deep characterization of the VACV RNA profile, various LRS platforms and library preparation approaches were applied. The raw reads were mapped to the VACV reference genome and also to the host (Chlorocebus sabaeus) genome. In this study, we applied the Pacific Biosciences RSII and Sequel platforms, which altogether resulted in 937,531 mapped reads of inserts (1.42 Gb), while we obtained 2,160,348 aligned reads (1.75 Gb) from the different library preparation methods, using the MinION device from Oxford Nanopore Technologies.By applying cutting-edge technologies, we were able to generate a large dataset that can serve as a valuable resource for the investigation of the dynamic VACV transcriptome, the virus-host interactions and RNA base modifications. These data can provide useful information for novel gene annotations in the VACV genome. Our dataset can also be applied for analyzing the currently available LRS platforms, library preparation methods and bioinformatics pipelines.
LA  - English
DB  - MTMT
ER  -