Expertise in genomics, transcriptomics & quantitative bioinformatics

Analytical approaches selected according to study design, data provenance, available controls and the desired level of inference.

Human genomics

Human genomics & variation

Analysis of human sequencing data to characterise germline or somatic variation, using a strategy adapted to the design, cohort and research question.

Processing & detection

Data qualification, alignment and pre-processing, detection of SNVs/indels, CNVs and structural variants, plus comparisons or cohort analyses when relevant.

Annotation & prioritisation

Functional annotation, population frequencies, phenotypic or tumour context, prioritisation using documented criteria and explicit review of call quality.

Analyses are intended for research or bioinformatics exploration and do not, on their own, constitute a medical diagnosis.

Microbial genomics

Microbial genomics, pathogens & surveillance

Characterisation and comparison of bacterial, viral or fungal genomes to study diversity, lineages, genetic determinants and relationships between isolates.

Characterisation & comparison

Quality control, de novo assembly or mapping, annotation, typing, comparative genomics, pan-genome analysis and investigation of resistance or virulence determinants according to the organism studied.

Phylogenomics & contextualisation

SNP comparisons, cgMLST or other appropriate typing approaches, lineage analysis, phylogenetic reconstruction and integration of temporal, geographic or epidemiological metadata when available.

NGS detection

NGS detection of adventitious agents

Bioinformatics analysis of NGS/HTS data to distinguish expected signal from biological and technical background and broadly screen for exogenous sequences, with controls, traceability and explicit interpretation criteria.

Signal detection & qualification

Quality control, in silico subtraction of expected host, vector or construct sequences, taxonomic classification, reference alignment and de novo assembly to confirm or refine candidate detections.

Controls, traceability & review

Assessment of read distribution and coverage, comparison with positive and negative controls, investigation of contamination or non-specific homology, versioning of reference databases and pipeline, and documentation of thresholds, results and limitations.

Transcriptomics

Transcriptomics & expression regulation

Transcriptomics analysis built around experimental design, biological contrasts and technical factors that may influence the signal.

Quantification & modelling

Quality control, quantification, normalisation and expression modelling accounting for covariates, batch effects and model diagnostics.

Functional interpretation

Differential expression, gene-set and pathway enrichment, alternative splicing, isoform quantification and differential isoform usage, small RNA/miRNA, fusions and breakpoint characterisation when supported by the technology and design.

Microbiome & metagenomics

Analysis of microbial communities accounting for the compositional nature of the data, controls, metadata, batch effects and sequencing technology.

Profiling & community structure

For 16S/ITS approaches: appropriate filtering and denoising, taxonomic assignment, community structure, diversity, ordination and differential analyses compatible with the compositional nature of the data.

Functional profiling

For shotgun data: taxonomic and functional profiling, metabolic pathways, resistome, virulence determinants and MAG reconstruction when depth, quality and study objectives allow.

Biostatistics & integration

Biostatistics & data integration

Statistical modelling defined from the hypotheses, study structure and data properties, with attention to bias, covariates and sources of variability.

Inference & bias control

Exploration, univariate or multivariate models, multiple-testing control, dimensionality reduction, sensitivity analyses and explicit handling of confounders.

Validation & integration

Cross-validation or independent validation where relevant, data integration, diagnostic visualisations and reporting of model assumptions, performance and limitations.

Tailored analysis

Specific methodological need?

The analytical scope can be extended when the question, design and data justify a specific approach or the integration of several methods.

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