Niko Popitsch
YOU?
Author Swipe
View article: Separable roles for Microprocessor and its cofactors ERH and SAFB1/2 during microRNA cluster assistance
Separable roles for Microprocessor and its cofactors ERH and SAFB1/2 during microRNA cluster assistance Open
While most conserved microRNA (miRNA) transcripts harbor a suite of features that mediate their efficient biogenesis into small RNAs, some loci bear suboptimal attributes that enable additional layers of processing regulation. A notable ex…
View article: ERH regulates type II interferon immune signaling through post-transcriptional regulation of <i>JAK2</i> mRNA
ERH regulates type II interferon immune signaling through post-transcriptional regulation of <i>JAK2</i> mRNA Open
Type II interferon (IFNγ) signaling is essential for innate immunity and critical for effective immunological checkpoint blockade in cancer immunotherapy. Genetic screen identification of post-transcriptional regulators of this pathway has…
View article: Hierarchical assembly and functional resilience of the mammalian RNA exosome
Hierarchical assembly and functional resilience of the mammalian RNA exosome Open
Summary Most eukaryotic proteins assemble into multisubunit complexes that coordinate essential cellular functions, yet the principles governing their assembly and proteostatic control remain largely undefined. Here, we systematically diss…
View article: Rnalib: a Python library for custom transcriptomics analyses
Rnalib: a Python library for custom transcriptomics analyses Open
Motivation The efficient and reproducible analysis of high-throughput sequencing datasets necessitates the development of methodical and robust computational pipelines that integrate established and bespoke bioinformatics analysis tools, o…
View article: ERH regulates type II interferon immune signaling through post-transcriptional regulation of<i>JAK2</i>mRNA
ERH regulates type II interferon immune signaling through post-transcriptional regulation of<i>JAK2</i>mRNA Open
Type II interferon (IFNγ) signaling is essential for innate immunity and critical for effective immunological checkpoint blockade in cancer immunotherapy. Genetic screen identification of post-transcriptional regulators of this pathway has…
View article: Splice_sim: a nucleotide conversion-enabled RNA-seq simulation and evaluation framework
Splice_sim: a nucleotide conversion-enabled RNA-seq simulation and evaluation framework Open
Nucleotide conversion RNA sequencing techniques interrogate chemical RNA modifications in cellular transcripts, resulting in mismatch-containing reads. Biases in mapping the resulting reads to reference genomes remain poorly understood. We…
View article: Mime-seq 2.0: a method to sequence microRNAs from specific mouse cell types
Mime-seq 2.0: a method to sequence microRNAs from specific mouse cell types Open
View article: Structural and non-coding variants increase the diagnostic yield of clinical whole genome sequencing for rare diseases
Structural and non-coding variants increase the diagnostic yield of clinical whole genome sequencing for rare diseases Open
Background Whole genome sequencing is increasingly being used for the diagnosis of patients with rare diseases. However, the diagnostic yields of many studies, particularly those conducted in a healthcare setting, are often disappointingly…
View article: Mime-seq 2.0: a method to sequence microRNAs from specific mouse cell types
Mime-seq 2.0: a method to sequence microRNAs from specific mouse cell types Open
Many microRNAs (miRNAs) are expressed with high spatiotemporal specificity during organismal development, with some being limited to rare cell types, often embedded in complex tissues. Yet most miRNA profiling efforts remain at the tissue …
View article: Mime-seq 2.0: a method to sequence microRNAs from specific mouse cell types
Mime-seq 2.0: a method to sequence microRNAs from specific mouse cell types Open
<p>These files contain the raw sequencing data (demultiplexed, unaligned BAM files or FASTQ files) collected as part of following manuscript: "Mime-seq 2.0: a method to sequence microRNAs from specific mouse cell types.". Includ…
View article: Mime-seq 2.0: a method to sequence microRNAs from specific mouse cell types
Mime-seq 2.0: a method to sequence microRNAs from specific mouse cell types Open
These files contain the raw sequencing data (demultiplexed, unaligned BAM files or FASTQ files) collected as part of following manuscript: "Mime-seq 2.0: a method to sequence microRNAs from specific mouse cell types.". Included are oxidize…
View article: mRNA stability and m6A are major determinants of subcellular mRNA localization in neurons
mRNA stability and m6A are major determinants of subcellular mRNA localization in neurons Open
For cells to perform their biological functions, they need to adopt specific shapes and form functionally distinct subcellular compartments. This is achieved in part via an asymmetric distribution of mRNAs within cells. Currently, the main…
View article: The identification of protein and RNA interactors of the splicing factor Caper in the adult Drosophila nervous system
The identification of protein and RNA interactors of the splicing factor Caper in the adult Drosophila nervous system Open
Post-transcriptional gene regulation is a fundamental mechanism that helps regulate the development and healthy aging of the nervous system. Mutations that disrupt the function of RNA-binding proteins (RBPs), which regulate post-transcript…
View article: Data from Novel Clinically Relevant Genes in Gastrointestinal Stromal Tumors Identified by Exome Sequencing
Data from Novel Clinically Relevant Genes in Gastrointestinal Stromal Tumors Identified by Exome Sequencing Open
Purpose: Chromosomal gains and losses resulting in altered gene dosage are known to be recurrent in gastrointestinal stromal tumors (GIST). The aim of our study was the identification of clinical relevant genes in these candidate re…
View article: Supplementary Tables 3 and 4 from Novel Clinically Relevant Genes in Gastrointestinal Stromal Tumors Identified by Exome Sequencing
Supplementary Tables 3 and 4 from Novel Clinically Relevant Genes in Gastrointestinal Stromal Tumors Identified by Exome Sequencing Open
PDF file, 24K, Supplemental Table 3 Variants per sample Supplemental Table 4 Variants unique per normal/cancer pair.
View article: Supplementary Tables 3 and 4 from Novel Clinically Relevant Genes in Gastrointestinal Stromal Tumors Identified by Exome Sequencing
Supplementary Tables 3 and 4 from Novel Clinically Relevant Genes in Gastrointestinal Stromal Tumors Identified by Exome Sequencing Open
PDF file, 24K, Supplemental Table 3 Variants per sample Supplemental Table 4 Variants unique per normal/cancer pair.
View article: Data from Novel Clinically Relevant Genes in Gastrointestinal Stromal Tumors Identified by Exome Sequencing
Data from Novel Clinically Relevant Genes in Gastrointestinal Stromal Tumors Identified by Exome Sequencing Open
Purpose: Chromosomal gains and losses resulting in altered gene dosage are known to be recurrent in gastrointestinal stromal tumors (GIST). The aim of our study was the identification of clinical relevant genes in these candidate re…
View article: Supplementary Tables 1 and 2 and 5 from Novel Clinically Relevant Genes in Gastrointestinal Stromal Tumors Identified by Exome Sequencing
Supplementary Tables 1 and 2 and 5 from Novel Clinically Relevant Genes in Gastrointestinal Stromal Tumors Identified by Exome Sequencing Open
PDF file, 95K, Supplemental Table 1: Comparision of copy number variation regions of interest by FISH (n=125) and microarray (n=29). Supplemental Table 2: Antibodies used for detection of genes in regions of recurrent losses or gains Suppl…
View article: Supplementary Tables 1 and 2 and 5 from Novel Clinically Relevant Genes in Gastrointestinal Stromal Tumors Identified by Exome Sequencing
Supplementary Tables 1 and 2 and 5 from Novel Clinically Relevant Genes in Gastrointestinal Stromal Tumors Identified by Exome Sequencing Open
PDF file, 95K, Supplemental Table 1: Comparision of copy number variation regions of interest by FISH (n=125) and microarray (n=29). Supplemental Table 2: Antibodies used for detection of genes in regions of recurrent losses or gains Suppl…
View article: Splice_sim: a nucleotide-conversion enabled RNA-seq simulation and evaluation framework
Splice_sim: a nucleotide-conversion enabled RNA-seq simulation and evaluation framework Open
Data accompanying the splice_sim paper. GRCm38.splice_sim.nc_mapping_accuracies.20230309.tar.gz: m_big mapping accuracies (mouse) GRCh38.splice_sim.nc_mapping_accuracies.20230309.tar.gz: h_big mapping accu…
View article: Hijacking of transcriptional condensates by endogenous retroviruses
Hijacking of transcriptional condensates by endogenous retroviruses Open
View article: GREEN-DB: a framework for the annotation and prioritization of non-coding regulatory variants from whole-genome sequencing data
GREEN-DB: a framework for the annotation and prioritization of non-coding regulatory variants from whole-genome sequencing data Open
Non-coding variants have long been recognized as important contributors to common disease risks, but with the expansion of clinical whole genome sequencing, examples of rare, high-impact non-coding variants are also accumulating. Despite r…
View article: Genomic and transcriptomic correlates of Richter transformation in chronic lymphocytic leukemia
Genomic and transcriptomic correlates of Richter transformation in chronic lymphocytic leukemia Open
The transformation of chronic lymphocytic leukemia (CLL) to high-grade B-cell lymphoma is known as Richter syndrome (RS), a rare event with dismal prognosis. In this study, we conducted whole-genome sequencing (WGS) of paired circulating C…
View article: Nanopanel2 calls phased low-frequency variants in Nanopore panel sequencing data
Nanopanel2 calls phased low-frequency variants in Nanopore panel sequencing data Open
Clinical decision making is increasingly guided by accurate and recurrent determination of presence and frequency of (somatic) variants and their haplotype through panel sequencing of disease-relevant genomic regions. Haplotype calling (ph…
View article: Nanopanel2 ABL1 datasets
Nanopanel2 ABL1 datasets Open
This dataset contains all ABL1 datasets used in the evaluation of Nanopanel2, a somatic variant calling for Nanopore panel sequencing data. Please refer to out paper 'Nanopanel2 calls phased low-freque…
View article: Targeting foam cell formation in inflammatory brain diseases by the histone modifier MS‐275
Targeting foam cell formation in inflammatory brain diseases by the histone modifier MS‐275 Open
Objective To assess class I‐histone deacetylase (HDAC) inhibition on formation of lipid‐accumulating, disease‐promoting phagocytes upon myelin load in vitro, relevant for neuroinflammatory disorders like multiple sclerosis (MS) and cerebra…
View article: GREEN-DB: A framework for the annotation and prioritization of non-coding regulatory variants from whole-genome sequencing data
GREEN-DB: A framework for the annotation and prioritization of non-coding regulatory variants from whole-genome sequencing data Open
Non-coding variants have emerged as important contributors to the pathogenesis of human diseases, not only as common susceptibility alleles but also as rare high-impact variants. Despite recent advances in the study of regulatory elements …
View article: GREEN-DB: Genomic Regulatory Elements ENcyclopedia
GREEN-DB: Genomic Regulatory Elements ENcyclopedia Open
<p>GREEN-DB is a comprehensive collection of 2.4 million regulatory elements in the human genome collected from previously published databases, high-throughput screenings and functional studies. Regulatory regions are classified…
View article: GREEN-DB: Genomic Regulatory Elements ENcyclopedia
GREEN-DB: Genomic Regulatory Elements ENcyclopedia Open
GREEN-DB is a comprehensive collection of 2.4 million regulatory elements in the human genome collected from previously published databases, high-throughput screenings and functional studies. Regulatory regions are classified as enhancers,…
View article: GREEN-DB: Genomic Regulatory Elements ENcyclopedia
GREEN-DB: Genomic Regulatory Elements ENcyclopedia Open
<p>GREEN-DB is a standardized collection of 2.4 million regulatory elements in the human genome. Information on controlled gene(s), tissue(s) and associated phenotype(s) are provided for each element when possible. We also …