A5072587260- Cancer Genomics and Diagnostics
- Single-cell and spatial transcriptomics
- Plant Virus Research Studies
- RNA modifications and cancer
- Cancer-related molecular mechanisms research
- Bacteriophages and microbial interactions
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Animal Virus Infections Studies
- Health, Environment, Cognitive Aging
- SARS-CoV-2 and COVID-19 Research
- Child Nutrition and Water Access
- Molecular Biology Techniques and Applications
- RNA Research and Splicing
- SARS-CoV-2 detection and testing
- Extracellular vesicles in disease
- Fecal contamination and water quality
- Evolution and Genetic Dynamics
ETH Zurich
2020-2025
SIB Swiss Institute of Bioinformatics
2020-2025
Gene fusions are found as cancer drivers in diverse adult and pediatric cancers. Accurate detection of fusion transcripts is essential clinical diagnostics prognostics for guiding therapeutic development. Most currently available methods transcript compatible with Illumina RNA-seq involving highly accurate short-read sequences. Recent advances long-read isoform sequencing enable the at unprecedented resolution bulk single-cell samples. Here, we developed a new computational tool,...
In cancer, genetic and transcriptomic variations generate clonal heterogeneity, leading to treatment resistance. Long-read single-cell RNA sequencing (LR scRNA-seq) has the potential detect simultaneously. Here, we present LongSom, a computational workflow leveraging high-quality LR scRNA-seq data call de novo somatic single-nucleotide variants (SNVs), including in mitochondria (mtSNVs), copy number alterations (CNAs), gene fusions, reconstruct tumor heterogeneity. Before variant calling,...
Understanding the complex background of cancer requires genotype-phenotype information in single-cell resolution. Here, we perform long-read RNA sequencing (scRNA-seq) on clinical samples from three ovarian patients presenting with omental metastasis and increase PacBio depth to 12,000 reads per cell. Our approach captures 152,000 isoforms, which over 52,000 were not previously reported. Isoform-level analysis accounting for non-coding isoforms reveals 20% overestimation protein-coding gene...
Gene fusions are found as cancer drivers in diverse adult and pediatric cancers. Accurate detection of fusion transcripts is essential clinical diagnostics, prognostics, for guiding therapeutic development. Most currently available methods transcript compatible with Illumina RNA-seq involving highly accurate short read sequences. Recent advances long isoform sequencing enable the at unprecedented resolution bulk single cell samples. Here we developed a new computational tool CTAT-LR-fusion...
Abstract SARS-CoV-2, the virus responsible for current COVID-19 pandemic, is evolving into different genetic variants by accumulating mutations as it spreads globally. In addition to this diversity of consensus genomes across patients, RNA viruses can also display within individual hosts, and co-existing viral may affect disease progression success medical interventions. To systematically examine intra-patient we processed a large cohort 3939 publicly-available deeply sequenced with...
Abstract The large amount and diversity of viral genomic datasets generated by next-generation sequencing technologies poses a set challenges for computational data analysis workflows, including rigorous quality control, scaling to sample sizes, tailored steps specific applications. Here, we present V-pipe 3.0, pipeline designed analyzing short genomes. It is developed enable reproducible, scalable, adaptable, transparent inference genetic samples. By presenting 2 large-scale projects,...
Abstract Understanding the complex background of cancer requires genotype-phenotype information in single-cell resolution. Here, we perform long-read RNA sequencing (scRNA-seq) on clinical samples from three ovarian patients presenting with omental metastasis and increase PacBio depth to 12,000 reads per cell. Our approach captures 152,000 isoforms, which over 52,000 are novel. Isoform-level analysis accounting for non-coding isoforms reveals 20% overestimation protein-coding gene expression...
Wastewater-based epidemiology has proven to be an important public health asset during the COVID-19 pandemic. It can provide less biassed and more cost-effective population-level monitoring of disease burden as compared clinical testing. An essential component SARS-CoV-2 wastewater is next-generation sequencing, providing genomic data identify quantify circulating viral strains rapidly. However, specific choice sequencing method influences quality timeliness generated hence its usefulness...
Abstract The large amount and diversity of viral genomic datasets generated by next-generation sequencing technologies poses a set challenges for computational data analysis workflows, including rigorous quality control, adaptation to higher sample coverage, tailored steps specific applications. Here, we present V-pipe 3.0, pipeline designed analyzing short genomes. It is developed enable reproducible, scalable, adaptable, transparent inference genetic samples. By presenting two large-scale...
In cancer, genetic and transcriptomic variations generate clonal heterogeneity, leading to treatment resistance. Long-read single-cell RNA sequencing (LR scRNA-seq) has the potential detect simultaneously. Here, we present LongSom, a computational workflow leveraging high-quality LR scRNA-seq data call de novo somatic single-nucleotide variants (SNVs), including in mitochondria (mtSNVs), copy-number alterations (CNAs), gene fusions, reconstruct tumor heterogeneity. Before calling, LongSom...
Abstract Wastewater-based epidemiology has proven to be an important public health asset during the COVID-19 pandemic. It can provide less biassed and more cost-effective population-level monitoring of disease burden as compared clinical testing. An essential component SARS-CoV-2 wastewater is next-generation sequencing, providing genomic data identify quantify circulating viral strains rapidly. However, specific choice sequencing method influences quality timeliness generated hence its...