In-Depth Temporal Transcriptome Profiling of an Alphaherpesvirus Using Nanopore Sequencing

Integrative profiling of Epstein–Barr virus transcriptome using a multiplatform approach

(2022) Ádám Fülöp et al.   Virology Journal

Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue

(2022) Simon A. Hardwick et al.   NATURE BIOTECHNOLOGY

Combined Short and Long-Read Sequencing Reveals a Complex Transcriptomic Architecture of African Swine Fever Virus

(2021) Gábor Torma et al.   Viruses-Basel

Dynamic Transcriptome Sequencing of Bovine Alphaherpesvirus Type 1 and Host Cells Carried Out by a Multi-Technique Approach

(2021) Dóra Tombácz et al.   Frontiers in Genetics

Combined nanopore and single-molecule real-time sequencing survey of human betaherpesvirus 5 transcriptome

(2021) Balázs Kakuk et al.   Scientific Reports

Nanopore Assay Reveals Cell-Type-Dependent Gene Expression of Vesicular Stomatitis Indiana Virus and Differential Host Cell Response

(2021) Balázs Kakuk et al.   Pathogens

Meta-analytic approach for transcriptome profiling of herpes simplex virus type 1

(2020) Dóra Tombácz et al.   Scientific Data

Long-read assays shed new light on the transcriptome complexity of a viral pathogen

(2020) Dóra Tombácz et al.   Scientific Reports

The Role of VP16 in the Life Cycle of Alphaherpesviruses

(2020) Dengjian Fan et al.   Frontiers in Microbiology

Time-course profiling of bovine alphaherpesvirus 1.1 transcriptome using multiplatform sequencing

(2020) Norbert Moldován et al.   Scientific Reports

Novel classes of replication-associated transcripts discovered in viruses

(2019) Zsolt Boldogkői et al.   RNA Biology

Analysis of Transcriptome and Epitranscriptome in Plants Using PacBio Iso-Seq and Nanopore-Based Direct RNA Sequencing

(2019) Liangzhen Zhao et al.   Frontiers in Genetics

Evidence that alternative transcriptional initiation is largely nonadaptive

(2019) Chuan Xu et al.   PLOS BIOLOGY

Direct RNA sequencing on nanopore arrays redefines the transcriptional complexity of a viral pathogen

(2019) Daniel P. Depledge et al.   Nature Communications

Interactions between the transcription and replication machineries regulate the RNA and DNA synthesis in the herpesviruses

(2019) Zsolt Boldogkői et al.   VIRUS GENES

Long-Read Sequencing – A Powerful Tool in Viral Transcriptome Research

(2019) Zsolt Boldogkői et al.   TRENDS IN MICROBIOLOGY

SignalP 5.0 improves signal peptide predictions using deep neural networks

(2019) José Juan Almagro Armenteros et al.   NATURE BIOTECHNOLOGY

Long-read direct RNA sequencing by 5’-Cap capturing reveals the impact of Piwi on the widespread exonization of transposable elements in locusts

(2019) Feng Jiang et al.   RNA Biology

Multiple Long-Read Sequencing Survey of Herpes Simplex Virus Dynamic Transcriptome

(2019) Dóra Tombácz et al.   Frontiers in Genetics

Template-switching artifacts resemble alternative polyadenylation

(2019) Zsolt Balázs et al.   BMC GENOMICS

Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules

(2019) Camille Sessegolo et al.   Scientific Reports

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

A survey of transcriptome complexity in Sus scrofa using single-molecule long-read sequencing

(2018) Yao Li et al.   DNA RESEARCH

Eukaryotic core promoters and the functional basis of transcription initiation

(2018) Vanja Haberle et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding

(2018) Bálint Mészáros et al.   NUCLEIC ACIDS RESEARCH

Third-generation Sequencing Reveals Extensive Polycistronism and Transcriptional Overlapping in a Baculovirus

(2018) Norbert Moldován et al.   Scientific Reports

Multi-Platform Sequencing Approach Reveals a Novel Transcriptome Profile in Pseudorabies Virus

(2018) Norbert Moldován et al.   Frontiers in Microbiology

High resolution annotation of zebrafish transcriptome using long-read sequencing

(2018) German Nudelman et al.   GENOME RESEARCH

Full-length RNA sequencing reveals unique transcriptome composition in bermudagrass

(2018) Bing Zhang et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Three newly identified Immediate Early Genes of Bovine herpesvirus 1 lack the characteristic Octamer binding motif- 1

(2018) Mayank Pokhriyal et al.   Scientific Reports

Long-read sequencing uncovers a complex transcriptome topology in varicella zoster virus

(2018) István Prazsák et al.   BMC GENOMICS

The bovine herpesvirus 1 regulatory proteins, bICP4 and bICP22, are expressed during the escape from latency

(2018) Junqing Guo et al.   JOURNAL OF NEUROVIROLOGY

Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells

(2018) Ishaan Gupta et al.   NATURE BIOTECHNOLOGY

Dynamic transcriptome profiling dataset of vaccinia virus obtained from long-read sequencing techniques

(2018) Dóra Tombácz et al.   GigaScience

The Landscape of Isoform Switches in Human Cancers

(2017) Kristoffer Vitting-Seerup et al.   MOLECULAR CANCER RESEARCH

Multi-platform analysis reveals a complex transcriptome architecture of a circovirus

(2017) Norbert Moldován et al.   VIRUS RESEARCH

Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells

(2017) Ashley Byrne et al.   Nature Communications

The FANTOM5 collection, a data series underpinning mammalian transcriptome atlases in diverse cell types

(2017) Hideya Kawaji et al.   Scientific Data

Characterization of the Dynamic Transcriptome of a Herpesvirus with Long-read Single Molecule Real-Time Sequencing

(2017) Dóra Tombácz et al.   Scientific Reports

A transcriptome atlas of rabbit revealed by PacBio single-molecule long-read sequencing

(2017) Shi-Yi Chen et al.   Scientific Reports

Long-Read Sequencing of Human Cytomegalovirus Transcriptome Reveals RNA Isoforms Carrying Distinct Coding Potentials

(2017) Zsolt Balázs et al.   Scientific Reports

Complete genomic sequence and comparative analysis of four genital and respiratory isolates of bovine herpesvirus subtype 1.2b (BoHV-1.2b), including the prototype virus strain K22

(2016) Jean M. d’Offay et al.   ARCHIVES OF VIROLOGY

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Global transcript structure resolution of high gene density genomes through multi-platform data integration

(2016) Tina O'Grady et al.   NUCLEIC ACIDS RESEARCH

Full-Length Isoform Sequencing Reveals Novel Transcripts and Substantial Transcriptional Overlaps in a Herpesvirus

(2016) Dóra Tombácz et al.   PLoS One

Characterization of pseudorabies virus transcriptome by Illumina sequencing

(2015) Péter Oláh et al.   BMC MICROBIOLOGY

Characterization of Novel Transcripts in Pseudorabies Virus

(2015) Dóra Tombácz et al.   Viruses-Basel

A promoter-level mammalian expression atlas

(2014)   NATURE

Pervasive transcription: illuminating the dark matter of bacterial transcriptomes

(2014) Joseph T. Wade et al.   NATURE REVIEWS MICROBIOLOGY

Dual Short Upstream Open Reading Frames Control Translation of a Herpesviral Polycistronic mRNA

(2013) Lisa M. Kronstad et al.   PLoS Pathogens

Complete genome sequence of the NVSL BoHV-1.1 Cooper reference strain

(2012) Jean M. d’Offay et al.   ARCHIVES OF VIROLOGY

High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression

(2012) P. Batut et al.   GENOME RESEARCH

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

Herpes Simplex Virus 1 ICP22 Inhibits the Transcription of Viral Gene Promoters by Binding to and Blocking the Recruitment of P-TEFb

(2012) Lei Guo et al.   PLoS One

Transcriptional interference networks coordinate the expression of functionally related genes clustered in the same genomic loci

(2012) Zsolt Boldogköi   Frontiers in Genetics

A paired-end sequencing strategy to map the complex landscape of transcription initiation

(2010) Ting Ni et al.   NATURE METHODS

Characterization of microRNAs encoded by the bovine herpesvirus 1 genome

(2009) E. A. Glazov et al.   JOURNAL OF GENERAL VIROLOGY