Andreas S. Puschnik

Systematic mapping of the prokaryotic noncoding sequence space with a genomic language model

The paper uses a genomic language model to cluster and annotate noncoding sequences in prokaryotic genomes, identifying structured RNAs and their potential functions.

Genetic accessibility, not superior fitness, determines which anti-HBs antibody escape variants are selected in patients

This study identifies that genetic accessibility, not superior fitness, determines the selection of anti-HBs antibody escape variants in patients using in vivo screening.

Orthogonal CRISPR screens and human liver chimeric mice identify hepatitis B virus host factors

The paper identifies HBV host factors using CRISPR screens and human liver chimeric mice, finding that EXOC1 is antiviral and ZCCHC14 is proviral.

Defining the host dependencies and the transcriptional landscape of RSV infection and bystander activation

This study uses CRISPR screening and single-cell RNA sequencing to analyze host factors and transcriptional changes in RSV-infected and bystander cells, revealing distinct gene expression patterns and host dependencies.

Genome-wide CRISPR knockout screening with viral replicons for identification of host factors involved in viral replication

This paper develops a CRISPR knockout screening method using viral replicons to identify host factors essential for viral replication, successfully identifying known and novel genes for dengue, chikungunya, and Ebola viruses.

CZ ID: a cloud-based, no-code platform enabling advanced long read metagenomic analysis

CZ ID introduces a long-read metagenomic analysis pipeline, benchmarked against Kraken2, for virus detection and antimicrobial resistance gene identification.

Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq

This study uses Perturb-seq to functionally interrogate SARS-CoV-2 host factors in human lung epithelial cells, identifying key factors that influence infection and host response.

Genome-scale analysis of cellular restriction factors that inhibit transgene expression from adeno-associated virus vectors

The paper identifies cellular restriction factors that inhibit AAV transgene expression using CRISPR screens and shows that inactivating these factors increases transgene levels in human cells.

Genome-wide, bidirectional CRISPR screens identify mucins as critical host factors modulating SARS-CoV-2 infection

The paper uses CRISPR screens to identify mucins as key host factors that restrict SARS-CoV-2 infection in human lung cells.

Identification of a polymorphism in the N gene of SARS-CoV-2 that adversely impacts detection by a widely-used RT-PCR assay

The paper identifies a SARS-CoV-2 N gene polymorphism that reduces RT-PCR assay sensitivity and emphasizes the need for multi-target testing.