Publications citing CLC Genomics Workbench


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Publications citing CLC Genomics Workbench

Genome research scientists want a powerful, end-to-end solution that easily integrates into their existing NGS analysis workflows. CLC Genomics Workbench is developed by scientists, for scientists, to analyze and visualize next generation sequencing (NGS) data.

We enjoy learning how it’s being used to support a wide range of NGS bioinformatics applications, from veterinary research to wastewater treatment. Read on for details from some recent publications.

Chicken Interferome: Avian Interferon-Stimulated Genes Identified by Microarray and RNA-seq of Primary Chick Embryo Fibroblasts Treated with a Chicken Type I Interferon (IFN-α)
First author: Efstathios S. Giotis

Earlier this year, Veterinary Research ran a report by a team from the Imperial College of London studying the interferon response in virus-infected chickens. The findings were significant not only because of the major threat of viral disease to both avian and human species, but also because they were robust: the team used two or more technologies to detect 128 genes from a compiled, curated list of 193 potentially anti-viral genes. CLC Workbench was among these technologies, used as a bioinformatics tools for RNA-seq data to allow gene-level visualization of the reads, mapped to the chicken genome. This enabled the team to identify potentially anti-viral genes induced just by interferon in primary chick embryo fibroblasts.

Genome-based Microbial Ecology of Anammox Granules in a Full-scale Wastewater Treatment System
First author: Daan Speth

CLC Genomics Workbench was used for several purposes in a recent Nature report from a Netherlands-based team focused on the latest wastewater treatment methods. Using metagenomics, the team built a genome-based ecological model of the microbial community that results from the partial-nitration anaerobic ammonium oxidation (PNA) treatment system. They used CLC Genomics Workbench across the scope of their work, from reducing data to de novo assembly, which ultimately helped them to create 23 near-complete draft genomes — the majority of their PNA microbial community.

Transcriptomic Analysis of Staphylococcus epidermidis Biofilm-Released Cells upon Interaction with Human Blood Circulating Immune Cells and Soluble Factors
First author: Angela França

Frontiers in Microbiology published a paper this summer, written by a team based in Boston, MA, and Braga, Portugal. The focus was a major cause of healthcare-associated infections: the colonization of indwelling medical devices (commonly intravascular catheters) by biofilm-forming bacteria. They used RNA-seq technology to shed light on the interaction between biofilm-released cells and hosts’ blood components. In the course of their work, the team used CLC Genomics Workbench for quality, ambiguity, length trimming, alignment, read normalization, and differential gene expression analysis. This aided their efforts to better understand how bacteria thrive in human blood — and to identify potential study areas that might lead to preventive or therapeutic strategies for these frequently fatal, often indolent types of infection.

Effective De Novo Assembly of Fish Genome Using Haploid Larvae
First author: Yuki Iwasaki

As NGS technology becomes more powerful, it enables whole genome sequencing on non-model eukaryote species — overcoming the challenges inherent in de novo assembly of diploid genomes, even without the benefit of an available reference genome. A Japanese team used the haploid genome of yellowtail (Seriola quinqueradiata) to compare the efficiency of assembly with that of the diploid genome from the dam. They used CLC Genomics Workbench to filter reads prior to the de novo assembly, then to test the de Brujin graph assembly algorithm. Their results, published in Gene, showed that using the genome of haploid larvae improves the de novo assembly process and potentially points toward a new strategy to construct reference genomes in non-model diploid organisms.

Draft genome sequences of Armillaria fuscipes, Ceratocystiopsis minuta, Ceratocystis adiposa, Endoconidiophora laricicola, E. polonica and Penicillium freii DAOMC 242723
First author: Brenda D. Wingfield

A joint Canadian-South African team published draft genome sequences of six fungal species from plant pathogens to help clarify taxonomies within their genera. Their report ran in IMA Fungus and includes details about assembling sequences using CLC Genomics Workbench for several of the species, including the first-ever genome for the genus Endoconidiophora. The team’s work will contribute to the understanding of how pathogens cause disease.

CLC Genomics Workbench is a powerful tool being used around the world to advance our genomic knowledge. If you’d like to share how you’re using it, please contact us — we might even feature your work on our blog!

You can find more information about CLC Genomics Workbench and request a trial here.