A5027259274- Genomics and Phylogenetic Studies
- Cancer-related molecular mechanisms research
- Molecular Biology Techniques and Applications
- RNA modifications and cancer
- Nanopore and Nanochannel Transport Studies
- Neuroblastoma Research and Treatments
- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- Single-cell and spatial transcriptomics
- Gene Regulatory Network Analysis
- Cell Image Analysis Techniques
- Lung Cancer Research Studies
- Plant and Fungal Interactions Research
- Gene expression and cancer classification
- Cancer, Hypoxia, and Metabolism
Canada's Michael Smith Genome Sciences Centre
2019-2024
University of British Columbia
2019-2023
Genome British Columbia
2023
Middle East Technical University
2016-2019
BC Cancer Agency
2019
Abstract The Long-read RNA-Seq Genome Annotation Assessment Project Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. Using different protocols and sequencing platforms, consortium generated over 427 million sequences from complementary DNA direct RNA datasets, encompassing human, mouse manatee species. Developers utilized these data address challenges in transcript isoform detection, quantification de novo detection. study revealed that...
Abstract The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. consortium generated over 427 million sequences from cDNA and direct RNA datasets, encompassing human, mouse, manatee species, using different protocols sequencing platforms. These data were utilized by developers address challenges in transcript isoform detection quantification, as well de novo identification....
Long-read sequencing technologies have improved significantly since their emergence. Their read lengths, potentially spanning entire transcripts, is advantageous for reconstructing transcriptomes. Existing long-read transcriptome assembly methods are primarily reference-based and to date, there little focus on reference-free assembly. We introduce "RNA-Bloom2 [ https://github.com/bcgsc/RNA-Bloom ]", a method data. Using simulated datasets spike-in control data, we show that the quality of...
Recent studies show that RNA-binding proteins (RBPs) and microRNAs (miRNAs) function in coordination with each other to control post-transcriptional regulation (PTR). Despite this, the majority of research date has focused on regulatory effect individual RBPs or miRNAs. Here, we mapped both RBP miRNA binding sites human 3′UTRs utilized this collection better understand PTR. We transcripts lack competition for HuR are destabilized more after depletion. also confirm finding PUM1(2) by...
Compared with second-generation sequencing technologies, third-generation single-molecule RNA has unprecedented advantages; the long reads it generates facilitate isoform-level transcript characterization. In particular, Oxford Nanopore Technology platforms have become more popular in recent years owing to their relatively high affordability and portability compared other technologies. To aid development of analytical tools that leverage power this technology, simulated data provide a...
Nanopore sequencing is crucial to metagenomic studies as its kilobase-long reads can contribute resolving genomic structural differences among microbes. However, platform-specific challenges, including high base-call error rate, nonuniform read lengths, and the presence of chimeric artifacts, necessitate specifically designed analytical algorithms. The use simulated datasets with characteristics that are true platform under evaluation a cost-effective way assess performance bioinformatics...
Abstract Summary Long non-coding RNAs (lncRNAs) can act as molecular sponge or decoys for an RNA-binding protein (RBP) through their RBP-binding sites, thereby modulating the expression of all target genes corresponding RBP interest. Here, we present a web tool named RBPSponge to explore lncRNAs based on potential identifies occurrences sites and CLIP peaks lncRNAs, enables users run statistical analyses investigate regulatory network between RBPs targets RBPs. Availability implementation...
Neuroblastoma is a heterogeneous disease with diverse clinical outcomes. Current risk group models require improvement as patients within the same can still show variable prognosis. Recently collected genome-wide datasets provide opportunities to infer neuroblastoma subtypes in more unified way. Within this context, data integration critical different molecular characteristics contain complementary signals. To end, we utilized genomic available for SEQC cohort develop supervised and...
ABSTRACT Long-read sequencing technologies have improved significantly since their emergence. Their read lengths, potentially spanning entire transcripts, is advantageous for reconstructing transcriptomes. Existing long-read transcriptome assembly methods are primarily reference-based and to date, there little focus on reference-free assembly. We introduce RNA-Bloom2, a method data. Using simulated datasets spike-in control data, we show that the quality of RNA-Bloom2 competitive those...
ABSTRACT Enabled by the explosion of data and substantial increase in computational power, deep learning has transformed fields such as computer vision natural language processing (NLP) it become a successful method to be applied many transcriptomic analysis tasks. A core advantage is its inherent capability incorporate feature computation within machine models. This results comprehensive machine-readable representation sequences, facilitating downstream classification clustering Compared...
Abstract We introduce Trans-NanoSim, the first tool that simulates reads with technical and transcriptome-specific features learnt from nanopore RNA-seq data. Through benchmarking on sets of human mouse reference transcriptomes, we show robustness Trans-NanoSim in capturing characteristics cDNA direct RNA reads. As a cost-effective alternative to sequencing real would facilitate rapid development analytical tools for is freely accessible at https://github.com/bcgsc/NanoSim
Abstract Summary Long noncoding RNAs (lncRNAs) can act as molecular sponges or decoys for an RNA-binding protein (RBP) through their RBP binding sites, thereby modulating the expression of all target genes corresponding interest. Here, we present a web tool named RBPSponge to explore lncRNAs based on potential sponge identifies occurrences sites and CLIP peaks lncRNAs, enables users run statistical analyses investigate regulatory network between RBPs targets RBPs. Availability The server is...
Abstract Recent advances in single-cell RNA sequencing technologies have made detection of transcripts single cells possible. The level resolution provided by these can be used to study changes transcript usage across cell populations and help investigate new biology. Here, we introduce RNA-Scoop, an interactive cluster transcriptome visualization tool analyze categories clusters. allows users examine differential expression clusters how specific mechanisms varies groups.
ABSTRACT Nanopore sequencing is crucial to metagenomic studies as its kilobase-long reads can contribute resolving genomic structural differences among microbes. However, platform-specific challenges, including high base-call error rate, non-uniform read lengths, and the presence of chimeric artifacts, necessitate specifically designed analytical tools. Here, we present Meta-NanoSim, a fast versatile utility that characterizes simulates unique properties nanopore reads. Further, Meta-NanoSim...
Abstract Background: Nanopore sequencing is crucial to metagenomic studies as its kilobase-long reads can contribute resolving genomic structural differences among microbes. However, platform-specific challenges, including high base-call error rate, non-uniform read lengths, and the presence of chimeric artifacts, necessitate specifically designed analytical tools, such microbial abundance estimation metagenome assembly algorithms. When developing testing bioinformatics tools pipelines, use...