Use Cases

We are proud to work with top flight clients from pharma, biotech and academia.
Here’s a selection of just a few recent partnerships.

Supporting NGS-based research at Baylor College of Medicine

We deployed Genialis Platform at BCM to advance the research mission of the College. The software supports biologists and bioinformaticians to manage, analyze, visualize and disseminate their data more easily. The diversity of research at Baylor—with dozens of model organisms and various flavors of -Seq—has proven a great opportunity to stretch our legs and extend the software to meet the challenges of today’s and tomorrow’s workflows. Prominent laboratories engaged on Genialis Platform include those of Dr.s Brendan Lee, Charles Lin, Peggy Goodell and Gad Shaulsky.

A transatlantic research commons for translational neuromedicine

The Center for Translational Neuromedicine, with laboratories at the Universities of Rochester and Copenhagen, collaborates on data analysis and interpretation via Genialis Platform. Researchers can easily explore their own results and the data generated by colleagues. Further, as the lab publishes its data, it can readily share the results with the rest of the world. For example, data from a recent Cell publication exploring differential gene expression in schizophrenia models are available to browse and compare.

Robust variant calling and interactive visualization for Accel-AmpliconTM panels

The streamlined interface makes reproducible data analysis as easy as 1-2-3. Users benefit from a bioinformatics pipeline developed and validated by Swift Biosciences’ R&D team, and the most frictionless user interface imaginable. The application supports any Accel-Amplicon kit, including custom panels, germline and somatic variant calling, auto-generated reports and an in-app interactive variant browser. Users include researchers at renowned institutions such as CPMCRI and Jackson Labs.

Reproducible discovery of interactions between RNA and proteins

Professor Ule is a group leader at The Francis Crick Institute and UCL Institute of Neurology, London, UK. His group uses immunoprecipitation-based methods such as iCLIP and hiCLIP to study protein-RNA complexes, their dynamics and evolution. Together with the bioinformatics group from Ljubljana (Dr. Curk) and lately with Genialis, they developed a comprehensive set of bioinformatics tools to analyse this type of data (iCOUNT). We wrapped these tools within Genialis Platform and enabled Ule lab to build a repository of well-curated CLIP-based data that will soon be made into a public resource.

Reliable identification of exogenous DNA inserted into mammalian genomes

TLA (Target Locus Amplification) is a technology developed by Cergentis that allows researchers to sequence a target region of a genome of interest. “We created an application to analyze TLA-derived data, so that biologists and informaticians can confidently identify transgene insertions in CHO cell lines.” Powered by Genialis Platform, the software allows data management, one-click analysis, and interactive visual exploration of the results.

Automated analysis and exploratory visualizations of RNA-sequencing transcript data

We linked the Genialis Platform visualizations suite to a pipeline tailored for Diagenode’s CATS RNA-seq Kit. The result: the easiest and most interactive way to explore one’s transcriptome data. CATS—Capture and Amplification by Tailing and Switching—is an innovative, ligation-free library prep method. With this cloud application, we’ve removed the bioinformatics complexity so biologists can dive right into their analysis of genes or transcripts.

Other Use Cases

transmart

tranSMART Integration for the Exploration of Clinical Gene Expression

We have developed an elegant web-application for researchers to explore data sets with hundreds of patient gene expression profiles and related clinical parameters. The app provides a seamless integration with the tranSMART data repository, granting users the power to interrogate these data using our Real Time Interactive Visualization environment.

dicty

Hypothesis Testing and Exploratory Omics in Dictyostelium discoideum

Baylor College of Medicine, USA

dictyExpress is a data analytics web-app that facilitates exploration of RNA-, ChIP- and whole genome sequencing experiments in Dictyostelium. This configuration includes data management, automated analysis pipelines and custom real time interactive visualization modules.
www.dictyexpress.org

mouse

Real-Time Interactive Visualization Application For Mus musculus

Baylor College of Medicine, USA

We have developed an interactive, exploratory data analytics web-app that provides access to gene expression experiments in Mus musculus by Knockout Mouse Project. In progress are various custom data analysis pipelines that are required by the web-apps.
www.kompexpress.org

brain

Profiling Neurons One Cell at a Time

Baylor College of Medicine, USA

neuroExpress is an interactive data analytics web-app that facilitates exploration of single-neuron gene expression profiling. The various RTIV modules include in situ hybridization maps from Allen Brain Atlas.

gencover

Variant Reporting of Clinical WGS

Garvan Institute of Medical Research, Australia

genCover is a clinical web tool for variant visualization that produces an interactive output summarizing the coverage of genes, exons and variants from WGS of tumor/normal and other clinical samples. The nucleotide level coverage is displayed in an interactive genome browser showing multiple predictor tracks.

vaccine

Monitoring Vaccine Program Progress

Marie Skłodowska-Curie Research and Innovation Staff Exchange (RISE)

vaccineSurvey is an ongoing collaboration to develop and validate an innovative tool to monitor the progress of different vaccination programs and experimentally validate record-based coverage data.
https://www.vaccinesurveyproject.eu/