Patrick Bohn
YOU?
Author Swipe
View article: High-Fidelity and Cost-Effective Engineering of SARS-CoV-2
High-Fidelity and Cost-Effective Engineering of SARS-CoV-2 Open
Efficient reverse genetics systems are essential for understanding SARS-CoV-2 pathogenesis, host–virus interactions, and potential therapeutic interventions. Here, we developed a cost-effective PCR-based reverse genetics platform that spli…
View article: Molecular characterization of arenavirus defective viral genomes reveals sequence features associated with their formation
Molecular characterization of arenavirus defective viral genomes reveals sequence features associated with their formation Open
Defective viral genomes (DVGs) are byproducts of replication that arise during infection with diverse RNA viruses and can impact virus infection and disease outcome. To gain insight into DVG generation during arenavirus infection, we seria…
View article: Demultiplexing and barcode-specific adaptive sampling for nanopore direct RNA sequencing
Demultiplexing and barcode-specific adaptive sampling for nanopore direct RNA sequencing Open
Nanopore direct RNA sequencing (dRNA-seq) enables unique insights into RNA biology. However, applications are currently limited by the lack of accurate and cost-effective sample multiplexing. Here we introduce WarpDemuX, an ultra-fast and …
View article: The translational landscape of HIV-1 infected cells reveals key gene regulatory principles
The translational landscape of HIV-1 infected cells reveals key gene regulatory principles Open
Human immunodeficiency virus-1 (HIV-1) uses a number of strategies to modulate viral and host gene expression during its life cycle. To characterize the transcriptional and translational landscape of HIV-1 infected cells, we used a combina…
View article: Selectively expressed RNA molecules as a versatile tool for functionalized cell targeting
Selectively expressed RNA molecules as a versatile tool for functionalized cell targeting Open
View article: Acid ceramidase of macrophages traps herpes simplex virus in multivesicular bodies and protects from severe disease
Acid ceramidase of macrophages traps herpes simplex virus in multivesicular bodies and protects from severe disease Open
Macrophages have important protective functions during infection with herpes simplex virus type 1 (HSV-1). However, molecular mechanisms that restrict viral propagation and protect from severe disease are unclear. Here we show that macroph…
View article: Demultiplexing and barcode-specific adaptive sampling for nanopore direct RNA sequencing
Demultiplexing and barcode-specific adaptive sampling for nanopore direct RNA sequencing Open
Nanopore direct RNA sequencing (dRNA-seq) enables unique insights into (epi-)transcriptomics. However, applications are currently limited by the lack of accurate and cost-effective sample multiplexing. We introduce WarpDemuX, an ultra-fast…
View article: NEAT1 promotes genome stability via m <sup>6</sup> A methylation-dependent regulation of CHD4
NEAT1 promotes genome stability via m <sup>6</sup> A methylation-dependent regulation of CHD4 Open
Long noncoding (lnc)RNAs emerge as regulators of genome stability. The nuclear-enriched abundant transcript 1 (NEAT1) is overexpressed in many tumors and is responsive to genotoxic stress. However, the mechanism that links NEAT1 to DNA dam…
View article: Demultiplexing and barcode-specific adaptive sampling for nanopore direct RNA sequencing
Demultiplexing and barcode-specific adaptive sampling for nanopore direct RNA sequencing Open
Nanopore direct RNA sequencing (dRNA-seq) enables unique insights into (epi-)transcriptomics. However, applications are currently limited by the lack of accurate and cost-effective sample multiplexing. We introduce WarpDemuX, an ultra-fast…
View article: Sequencing accuracy and systematic errors of nanopore direct RNA sequencing
Sequencing accuracy and systematic errors of nanopore direct RNA sequencing Open
View article: Recruitment of multi-segment genomic RNAs by Bluetongue virus requires a preformed RNA network
Recruitment of multi-segment genomic RNAs by Bluetongue virus requires a preformed RNA network Open
How do segmented RNA viruses correctly recruit their genome has yet to be clarified. Bluetongue virus is a double-stranded RNA virus with 10 segments of different sizes, but it assembles its genome in single-stranded form through a series …
View article: Building Blocks of Understanding: Constructing a Reverse Genetics Platform for studying determinants of SARS-CoV-2 replication
Building Blocks of Understanding: Constructing a Reverse Genetics Platform for studying determinants of SARS-CoV-2 replication Open
To better understand viral pathogenesis, host-virus interactions, and potential therapeutic interventions, the development of robust reverse genetics systems for SARS-CoV-2 is crucial. Here, we present a reverse genetics platform that enab…
View article: NEAT1 promotes genome stability via m6A methylation-dependent regulation of CHD4
NEAT1 promotes genome stability via m6A methylation-dependent regulation of CHD4 Open
Long non-coding (lnc)RNA emerge as regulators of genome stability. The nuclear enriched abundant transcript 1 ( NEAT1 ) locus encodes two lncRNA isoforms that modulate gene expression, growth and proliferation in mammals. Interestingly, NE…
View article: Alternative translation contributes to the generation of a cytoplasmic subpopulation of the Junín virus nucleoprotein that inhibits caspase activation and innate immunity
Alternative translation contributes to the generation of a cytoplasmic subpopulation of the Junín virus nucleoprotein that inhibits caspase activation and innate immunity Open
A limited coding capacity means that RNA viruses need strategies to diversify their proteome. The nucleoprotein (NP) of the highly pathogenic arenavirus Junín virus (JUNV) produces three N-terminally truncated isoforms: two (NP 47kD and NP…
View article: Unlocking the Full Potential of Nanopore Sequencing: Tips, Tricks, and Advanced Data Analysis Techniques
Unlocking the Full Potential of Nanopore Sequencing: Tips, Tricks, and Advanced Data Analysis Techniques Open
Nucleic acid sequencing is the process of identifying the sequence of DNA or RNA, with DNA used for genomes and RNA for transcriptomes. Deciphering this information has the potential to greatly advance our understanding of genomic features…
View article: The translational landscape of HIV-1 infected cells reveals novel gene regulatory principles
The translational landscape of HIV-1 infected cells reveals novel gene regulatory principles Open
Human Immunodeficiency Virus-1 (HIV-1) uses a number of strategies to modulate viral and host gene expression during its lifecycle. To characterize the transcriptional and translational landscape of HIV-1 infected cells, we used a combinat…
View article: Nano-DMS-MaP allows isoform-specific RNA structure determination
Nano-DMS-MaP allows isoform-specific RNA structure determination Open
Genome-wide measurements of RNA structure can be obtained using reagents that react with unpaired bases, leading to adducts that can be identified by mutational profiling on next-generation sequencing machines. One drawback of these experi…
View article: Sequencing accuracy and systematic errors of nanopore direct RNA sequencing
Sequencing accuracy and systematic errors of nanopore direct RNA sequencing Open
Direct RNA sequencing (dRNA-seq) on the Oxford Nanopore Technologies (ONT) platforms can produce reads covering up to full-length gene transcripts while containing decipherable information about RNA base modifications and poly-A tail lengt…
View article: Author Correction: Short- and long-range interactions in the HIV-1 5′ UTR regulate genome dimerization and packaging
Author Correction: Short- and long-range interactions in the HIV-1 5′ UTR regulate genome dimerization and packaging Open
View article: A dsRNA-binding mutant reveals only a minor role of exonuclease activity in interferon antagonism by the arenavirus nucleoprotein
A dsRNA-binding mutant reveals only a minor role of exonuclease activity in interferon antagonism by the arenavirus nucleoprotein Open
The arenavirus nucleoprotein (NP) plays an important role in the virus’ ability to block interferon (IFN) production, and its exonuclease function appears to contribute to this activity. However, efforts to analyze this contribution are co…
View article: Nano-DMS-MaP-seq allows isoform specific RNA structure determination
Nano-DMS-MaP-seq allows isoform specific RNA structure determination Open
Chemical probing experiments interrogate RNA structure by reacting with unpaired residues whose positions are typically read out by mutational profiling on short-read sequencing machines. Such experiments make rapid and genome-wide measure…
View article: Short- and long-range interactions in the HIV-1 5′ UTR regulate genome dimerization and packaging
Short- and long-range interactions in the HIV-1 5′ UTR regulate genome dimerization and packaging Open
View article: Short- and long-range interactions in the HIV-1 5’UTR regulate genome dimerization and packaging
Short- and long-range interactions in the HIV-1 5’UTR regulate genome dimerization and packaging Open
Genome dimerization is a conserved feature of retroviral replication and a critical step in the HIV-1 life cycle, but how it is regulated is incompletely understood. Here, we developed FARS-seq (Functional Analysis of RNA Structure) to com…
View article: RNA Structures and Their Role in Selective Genome Packaging
RNA Structures and Their Role in Selective Genome Packaging Open
To generate infectious viral particles, viruses must specifically select their genomic RNA from milieu that contains a complex mixture of cellular or non-genomic viral RNAs. In this review, we focus on the role of viral encoded RNA structu…
View article: Acid ceramidase of macrophages traps herpes simplex virus in multivesicular bodies and protects from severe disease
Acid ceramidase of macrophages traps herpes simplex virus in multivesicular bodies and protects from severe disease Open
Macrophages have important protective functions during infection with herpes simplex virus type 1 (HSV-1). However, molecular mechanisms that restrict viral propagation and protect from severe disease are unclear. Here we show that macroph…
View article: A novel SIV gag-specific CD4+T-cell clone suppresses SIVmac239 replication in CD4+T cells revealing the interplay between antiviral effector cells and their infected targets
A novel SIV gag-specific CD4+T-cell clone suppresses SIVmac239 replication in CD4+T cells revealing the interplay between antiviral effector cells and their infected targets Open
View article: Rapid identification of major histocompatibility complex class I haplotypes using deep sequencing in an endangered Old World monkey
Rapid identification of major histocompatibility complex class I haplotypes using deep sequencing in an endangered Old World monkey Open
View article: The TB-specific CD4+ T cell immune repertoire in both cynomolgus and rhesus macaques largely overlap with humans
The TB-specific CD4+ T cell immune repertoire in both cynomolgus and rhesus macaques largely overlap with humans Open