Bioinformatics Case Studies
Target discovery & validation
The ATT is an innovative service that has been meticulously packaged as a product with a clear mission: to validate drug or biomarker targets effectively.
Features:
•Mining valid targets in literature
•Evidence-driven target scoring:
•Disease association
•Expression analysis
•Pathway analysis
•Safety inspection
•Validation existing studies and cohorts
•Target interactive visualization and filtering
•Binding evaluation
•Smart summaries & recommendations
End-to-end OMICs pipelines
Solutions Streamlines Operations with Advanced Pipeline Solutions
Supported to optimise the design, and developed OMICs pipelines. The aim was to increase data analysis speed and operational efficiency, enabling seamless study re-runs and effective presentation of research outcomes.
Solutions:
•Optimised existing pipelines using Nextflow
•Implemented CI/CD on company infrastructure
•Benchmarked tools and processes
•Delivered end-to-end OMICs analysis from demultiplexing to reporting
•Provided custom variant analysis (SV, CNV, SP)
•Enabled genomics biomarker discovery (MSIs, TMBs)
•Supported WGS, WES, and targeted panels like Amplicon
End-to-end Single Cell Solutions
From Vision to Reality: Revolutionised Single-Cell Analysis
Our partnered company aimed to empower clinics and research institutes to use their sequencing technologies and interpret genome and transcriptome sequencing results, while expanding their user base.
Solutions:
•Designed, developed, and validated single-cell OMICs pipelines in Nextflow
•Handled single-cell (SC) pre-processing, alignment, and variant calling (SPs, CNVs, SVs)
•SC genomic biomarker discovery (MSIs, TMB) and transcriptomics (VC, Expression, Fusion detection)
•Developed cloud platform for real-time pipeline runs and interactive result interpretation
•Delivered the first production-ready solution in under a year.
R&D OMICs pipelines
Nextflow-Powered Pipelines: Boosting Research
The partnered company needed a fast, efficient way to ensure their computational solutions were reusable and easily shareable with colleagues, aiming to accelerate research and innovation processes.
Solutions:
•End-to-end OMICs pipelines written in Nextflow
•Deployment to company internal systems and/or Nextflow Tower
•SC Transcriptomics pipeline
•Early Drug Discovery pipeline
•Alignment and VC pipeline
•Optimisation of a bash GWAS analysis pipeline with Nextflow
Breast Cancer Subtyping
Biostatistical and software development support for distinguishing 5 breast cancer clinicopathological subtypes based on 4 markers: ESR1, PGR, HER2, KI67
Activities:
Exploratory analysis of multiple data transfers
Defining performance metrics and machine learning model
Design of the workflow for the best performing biomarker selection
Analysis and interpretation of BC Subtyping assay results
Development of web-based software solution for analysis, interpretation and reporting
