This pages lists some achievements for Dylan Lawless across projects and collaborations under the STAR framework. For a curated collection of topics see the profile pages.
Scientific excellence (12)
EPFL translational cohort analyses — population-scale infection genomics
Situation: Understanding why some individuals develop severe responses to infection required integrating host genome, pathogen genome, and clinical outcome data across large population cohorts and international collaborations. Task: Design and execute statistical genetics and multi-omic analyses across four major infection programmes — RSV, tuberculosis, HBV, and chronic inflammatory disease. Action: Developed analytical workflows for GWAS, host-pathogen joint analysis, and multi-omic integration across cohorts up to 5,000 participants and biobank-scale analyses exceeding 100,000 genomes. Released R packages adopted by independent groups. Mentored 3 PhD and 22 MSc students. Contributed to Phase II trial design integrating multi-omic data with patient trajectory modelling. Result: Multiple lead-author publications in JACI, JID, Genetic Epidemiology. CHF 3M+ in collaborative funding programmes. Software adopted as independent infrastructure.
Archipelago — variant set association visualisation method
Situation: Variant set association test (VSAT) statistics lacked genomic coordinates, making visual comparison with single-variant GWAS results impossible. Task: Design a method assigning meaningful genomic positions to VSAT p-values and integrating both scales into a single navigable plot. Action: Developed the Archipelago method. Validated across three independent datasets: 1000 Genomes, Pan-UK Biobank (490,640 participants), and UK Biobank WGS. Released as an R package on CRAN with full customisation. Result: First author. Published Genetic Epidemiology (Wiley, 2026). Applied in SPSS and SwissPedHealth analyses. CRAN DOI 10.32614/CRAN.package.archipelago.
PanelAppRex — disease-gene panel aggregation and AI search
Situation: Disease-gene panel data was fragmented across sources, inconsistently annotated, and inaccessible for programmatic use in diagnostic pipelines. Task: Build a system aggregating, harmonising, and making queryable the full landscape of curated disease-gene panel evidence. Action: Aggregated 58,592 gene-disease associations from Genomics England PanelApp, ClinVar, UniProt, and Ensembl. Applied RAG on the UniProtKB human proteome to compress 6.6 million features fivefold into structured disease-aware panel summaries. Built a natural-language search interface and machine-readable export formats. Benchmarked across 15 published case studies spanning immunology, neurology, and mixed disease areas. Result: Senior/corresponding author. Published Bioinformatics Advances (OUP, 2026). 93–100% benchmark accuracy. Public dataset on Zenodo. Integrated in SwissPedHealth clinical workflows.
Leeds rare immune disease programme — 10+ disease discoveries
Situation: Approximately 500 patients with severe immune-mediated disease at St James's University Hospital lacked a genetic diagnosis, preventing targeted treatment. Task: Contribute genomic discovery and functional validation across multiple disease programmes within the NIHR BioResource rare disease cohort. Action: Led or co-led discovery of germline TET2 deficiency (Blood 2020, IUIS-classified), RAG deficiency in adults (JACI 2018), RAG1/2 variant occurrence modelling (JCI 2019), CRACR2A deficiency (eLife 2021), TNFAIP3 autoinflammation (Frontiers Immunol 2018), CFTR as a modifying cofactor in PID (JACI 2023), and pyrin pathway autoinflammation (Science Translational Medicine 2016). Applied WES/WGS, flow cytometry, B-cell differentiation, iPSC haematopoietic systems, and functional assays. Result: More than 10 peer-reviewed disease discovery and precision treatment findings. Treatments confirmed including rituximab, anakinra, and tocilizumab.
IEI prior probability database — 54,814 ClinVar classifications
Situation: Clinical variant interpretation in inborn errors of immunity lacked a quantitative prior probability baseline, forcing reliance on qualitative expert judgement without uncertainty estimates. Task: Build a systematic prior probability database covering the full IEI gene landscape from population-scale ClinVar data. Action: Processed 54,814 ClinVar variant classifications across 557 IEI genes. Derived gene-level and variant-level prior probabilities under both autosomal dominant and autosomal recessive inheritance models. Validated against NFKB1 (AD) and CFTR (AR) clinical cohorts. Result: Senior author. Under review npj Genomic Medicine. Database publicly released at iei-genetics.github.io.
QuantBayes — Bayesian evidence sufficiency for variant interpretation
Situation: Genomic variant evidence is expressed heterogeneously across pipelines and institutions; no quantitative standard existed for measuring evidence sufficiency with calibrated uncertainty. Task: Build a closed-form Bayesian model producing posterior evidence sufficiency estimates with credible intervals from binary evidence matrices. Action: Designed a Beta-Binomial model, implemented as a deterministic C algorithm (no simulation required), released as standalone macOS/Linux binaries and as an R package on CRAN, validated on the GIAB trio WGS dataset, and preprinted with full methodology. A user survey (DESAT ethics approved) confirmed improved clinician understanding with explicit evidence reporting. Result: Senior/corresponding author. CRAN-released December 2025. Over 3,000 combined downloads per quarter. Implementation at quantbayes.com.
Qualifying variant framework — published open standard
Situation: Variant selection criteria were embedded in pipeline code, making them invisible to reviewers, impossible to audit, and unable to be reused across studies. Task: Propose and publish a unified framework for expressing variant criteria as standalone, versioned, pipeline-independent specifications. Action: Designed the QV framework with YAML/JSON criteria, a reference model covering 16 variant states, and three validation studies (rare disease WES cohort of 940 individuals, HapMap3 GWAS, GIAB WGS trio) each achieving bitwise-identical outputs to conventional hard-coded methods. Released as a public database and peer-reviewed paper. Result: First author. Published OUP Bioinformatics (2026). CRAN-released. Adopted in the SwissPedHealth clinical pipeline serving approximately 1,000 children. NHS Genomic Test Directory panels integrated.
Germline TET2 deficiency — new disease entity in Blood
Situation: A cluster of children with immunodeficiency and lymphoma had no genetic diagnosis despite extensive workup across multiple centres. Task: Lead genomic interpretation and support functional validation to identify the mechanism in an international collaborative study. Action: Identified germline TET2 loss-of-function as the causal mechanism; supported functional validation including B-cell differentiation assays, flow cytometry, and immunofluorescence; coordinated IUIS disease classification submission. Result: Germline TET2 deficiency established as a new disease entity. Published Blood (2020, IF ~20). Added to the IUIS inborn errors of immunity classification. Treatment implications confirmed (rituximab). Joint lead author on 30-centre study.
Paediatric sepsis rare variant pathways — 66 IEI candidates
Situation: Common variants explain little sepsis heritability; rare immune pathway variants had not been systematically tested in a paediatric clinical cohort. Task: Design and execute multi-tiered rare variant analyses — single-case, single-variant, gene-level, and protein pathway — across 940 children with confirmed sepsis. Action: Built automated interpretation pipelines covering SKAT-O, burden testing, and protein pathway clustering. Applied novel pathway grouping to identify enriched immune pathway hits. Result: Identified 66 candidate inborn error of immunity cases and two immune pathway hits spanning 50 genes. Findings inform treatment decisions at the Molecular Board. First author. Under review.
Paediatric sepsis GWAS — first reproducible susceptibility locus
Situation: Sepsis is the leading infectious cause of childhood death; no reproducible genome-wide susceptibility locus had been identified in a paediatric cohort. Task: Lead the statistical genetics analysis within a national multi-centre programme (CHF 930K, three Swiss children's hospitals). Action: Designed and executed a GWAS in 650 blood-culture-confirmed paediatric sepsis cases and 1,395 controls; applied case-control and case-only designs; coordinated genotype data governance across institutions; built analysis pipelines from QC through to fine-mapping. Result: Identified the first reproducible paediatric sepsis susceptibility signal at the CTNNAL1/ELP1 locus. First author. Accepted Lancet eBioMedicine 2025. GWAS summary statistics deposited in EBI GWAS Catalogue (GCST90726424).
RSV viral genomics — birth cohort determinants of prolonged infection
Situation: The viral genetic determinants of prolonged RSV infection in infants were unknown, limiting understanding of why some children suffer more severe and extended illness. Task: Identify viral genetic factors associated with prolonged RSV infection in a healthy term birth cohort. Action: Analysed RSV genome sequences from 300+ infants in the Vanderbilt birth cohort. Applied viral genome-wide association methods and gene-level tests to identify viral loci associated with infection duration. Result: First author. Published Journal of Infectious Diseases (2022). Identified specific RSV genomic loci associated with prolonged infection, providing targets for intervention strategy.
RAG1/RAG2 variant occurrence — probabilistic precursor to QuantBayes
Situation: RAG1 and RAG2 deficiency spans a spectrum of rare immune disease; no quantitative basis existed for predicting which variants would be observed clinically versus in the general population. Task: Develop a probabilistic framework for predicting variant occurrence across RAG1 and RAG2 using population genetics and functional annotation. Action: Integrated gnomAD population allele frequencies, Hardy-Weinberg priors, inheritance models, and structural/functional annotation. Applied to approximately 500 severe clinical cases from the NIHR BioResource rare disease cohort. Result: First author. Published Journal of Clinical Immunology (2019). Established the quantitative variant occurrence methodology that became the conceptual precursor to the QuantBayes framework.
Digital innovation (10)
Switzerland Omics — scientific product ecosystem from IP to revenue
Situation: Probabilistic genomics methods existed in research code but lacked the product architecture, IP positioning, and brand credibility for adoption outside the originating institution. Task: Build a complete scientific product environment from intellectual property registration through to deployed products and commercial revenue. Action: Established Switzerland Omics. Registered the trademark (Swissreg, Nice classes 9 and 42, valid to 2035). Designed the product taxonomy. Built and shipped QuantBayes Studio, PanelAppRex, Genomic Vault, and Variant Impact. Structured the commercial spin-off and AWS research funding application. Result: Registered trademark valid 2035. Multiple live deployed products. Commercial revenue via QuantBayes Studio. AWS research funding secured 2026. Products in clinical and research use internationally.
Archipelago — variant set association visualisation method
Situation: Variant set association test (VSAT) statistics lacked genomic coordinates, making visual comparison with single-variant GWAS results impossible. Task: Design a method assigning meaningful genomic positions to VSAT p-values and integrating both scales into a single navigable plot. Action: Developed the Archipelago method. Validated across three independent datasets: 1000 Genomes, Pan-UK Biobank (490,640 participants), and UK Biobank WGS. Released as an R package on CRAN with full customisation. Result: First author. Published Genetic Epidemiology (Wiley, 2026). Applied in SPSS and SwissPedHealth analyses. CRAN DOI 10.32614/CRAN.package.archipelago.
Secure LLM deployment — clinical variant interpretation at BioMedIT
Situation: Clinical genetics teams required AI-assisted variant interpretation but could not expose patient data to external cloud APIs under Swiss data protection law. Task: Deploy open-weight LLMs on secure HPC infrastructure for clinical report generation with Molecular Board review. Action: Deployed Llama and DeepSeek R1 on BioMedIT HPC. Built a structured report generation pipeline integrating WGS, RNA-seq, and proteomics outputs, reviewed by geneticists, clinicians, and researchers. Implemented audit-trail logging meeting Swiss data governance requirements. Result: High-throughput clinical variant interpretation with full audit trail, operational at University Children's Hospital Zurich within SwissPedHealth.
PanelAppRex — disease-gene panel aggregation and AI search
Situation: Disease-gene panel data was fragmented across sources, inconsistently annotated, and inaccessible for programmatic use in diagnostic pipelines. Task: Build a system aggregating, harmonising, and making queryable the full landscape of curated disease-gene panel evidence. Action: Aggregated 58,592 gene-disease associations from Genomics England PanelApp, ClinVar, UniProt, and Ensembl. Applied RAG on the UniProtKB human proteome to compress 6.6 million features fivefold into structured disease-aware panel summaries. Built a natural-language search interface and machine-readable export formats. Benchmarked across 15 published case studies spanning immunology, neurology, and mixed disease areas. Result: Senior/corresponding author. Published Bioinformatics Advances (OUP, 2026). 93–100% benchmark accuracy. Public dataset on Zenodo. Integrated in SwissPedHealth clinical workflows.
IEI prior probability database — 54,814 ClinVar classifications
Situation: Clinical variant interpretation in inborn errors of immunity lacked a quantitative prior probability baseline, forcing reliance on qualitative expert judgement without uncertainty estimates. Task: Build a systematic prior probability database covering the full IEI gene landscape from population-scale ClinVar data. Action: Processed 54,814 ClinVar variant classifications across 557 IEI genes. Derived gene-level and variant-level prior probabilities under both autosomal dominant and autosomal recessive inheritance models. Validated against NFKB1 (AD) and CFTR (AR) clinical cohorts. Result: Senior author. Under review npj Genomic Medicine. Database publicly released at iei-genetics.github.io.
QuantBayes — Bayesian evidence sufficiency for variant interpretation
Situation: Genomic variant evidence is expressed heterogeneously across pipelines and institutions; no quantitative standard existed for measuring evidence sufficiency with calibrated uncertainty. Task: Build a closed-form Bayesian model producing posterior evidence sufficiency estimates with credible intervals from binary evidence matrices. Action: Designed a Beta-Binomial model, implemented as a deterministic C algorithm (no simulation required), released as standalone macOS/Linux binaries and as an R package on CRAN, validated on the GIAB trio WGS dataset, and preprinted with full methodology. A user survey (DESAT ethics approved) confirmed improved clinician understanding with explicit evidence reporting. Result: Senior/corresponding author. CRAN-released December 2025. Over 3,000 combined downloads per quarter. Implementation at quantbayes.com.
Qualifying variant framework — published open standard
Situation: Variant selection criteria were embedded in pipeline code, making them invisible to reviewers, impossible to audit, and unable to be reused across studies. Task: Propose and publish a unified framework for expressing variant criteria as standalone, versioned, pipeline-independent specifications. Action: Designed the QV framework with YAML/JSON criteria, a reference model covering 16 variant states, and three validation studies (rare disease WES cohort of 940 individuals, HapMap3 GWAS, GIAB WGS trio) each achieving bitwise-identical outputs to conventional hard-coded methods. Released as a public database and peer-reviewed paper. Result: First author. Published OUP Bioinformatics (2026). CRAN-released. Adopted in the SwissPedHealth clinical pipeline serving approximately 1,000 children. NHS Genomic Test Directory panels integrated.
Genomic Vault — custodianship and governance platform
Situation: Genome data custody was handled informally, with no auditable access control, governance trail, or payment infrastructure for institutional or individual use. Task: Build a working custodianship and governance platform deployable commercially and institutionally. Action: Built fullstack application with encrypted storage, Drizzle ORM, Supabase row-level security, Stripe payment webhooks, immutable audit logs, and SPHN-compliant RDF metadata. Deployed with operational access controls. Result: Live at genomicvault.switzerlandomics.ch. Working payments, access governance, and immutable audit trail. Designed to SPHN compliance standards.
Microsoft Azure Research Award — USD 100K competitive cloud funding
Situation: Population-scale genomic data science required cloud computing capacity not available through standard academic infrastructure at Leeds. Task: Compete for and secure external research funding to enable cloud-based genomic data science and machine learning work. Action: Wrote and submitted a competitive proposal for data science and ML in predictive genomics. Award granted as USD 100,000 in Azure cloud computing credits. Result: Enabled population-scale genomic analysis and ML pipeline development that contributed to subsequent peer-reviewed publications.
Variant Impact — fullstack molecular informatics platform
Situation: Protein variant interpretation required integration of gnomAD, UniProt, ClinVar, AlphaFold, and RCSB PDB — no single platform combined all with an interactive 3D structure viewer and variant landscape visualisation. Task: Build a fullstack web application demonstrating end-to-end molecular informatics. Action: Built with Next.js, React, TypeScript, and Tailwind. Integrated Molstar 3D protein structure viewer, variant landscape heatmaps, protein feature tracks, gnomAD constraint scores, ClinVar classifications, AlphaFold confidence scores, and RCSB structure data. Deployed on Vercel. Result: Deployed at variantimpact.vercel.app. Demonstrates the complete fullstack molecular informatics stack: molecular databases, interactive 3D visualisation, and variant landscape analysis in a single application.
Stakeholder influence (4)
Swiss Genomics Association — founded neutral standards body
Situation: No institution-neutral standard existed for expressing genomic evidence matrices or reporting statistical evidence ratios across heterogeneous study designs and institutions. Task: Found an independent scientific association capable of issuing and maintaining normative standards for the Swiss and international genomics community. Action: Established the Swiss Genomics Association (2024). Issued the Qualifying Evidence Matrix (QEM, Zenodo DOI 10.5281/zenodo.17936587) and the Evidence Ratio Reporting Standard (ERRS, Zenodo DOI 10.5281/zenodo.18261075). Registered both as versioned standards with permanent DOIs. Built a member network spanning Swiss academic, clinical, and industry bioinformatics. Result: Two normative published standards cited in peer-reviewed work. 35+ members across Swiss institutions. ERRS implemented in the CRAN evidenceratio package.
EPFL translational cohort analyses — population-scale infection genomics
Situation: Understanding why some individuals develop severe responses to infection required integrating host genome, pathogen genome, and clinical outcome data across large population cohorts and international collaborations. Task: Design and execute statistical genetics and multi-omic analyses across four major infection programmes — RSV, tuberculosis, HBV, and chronic inflammatory disease. Action: Developed analytical workflows for GWAS, host-pathogen joint analysis, and multi-omic integration across cohorts up to 5,000 participants and biobank-scale analyses exceeding 100,000 genomes. Released R packages adopted by independent groups. Mentored 3 PhD and 22 MSc students. Contributed to Phase II trial design integrating multi-omic data with patient trajectory modelling. Result: Multiple lead-author publications in JACI, JID, Genetic Epidemiology. CHF 3M+ in collaborative funding programmes. Software adopted as independent infrastructure.
SwissPedHealth — CHF 5M national multi-omics infrastructure
Situation: A CHF 5M national programme required unified multi-omics analytical infrastructure across multiple children's hospitals with heterogeneous data systems, governance structures, and clinical workflows. Task: Design and deliver the computational workflows, database architecture, and reporting systems connecting WGS, RNA-seq, proteomics, metabolomics, and EHR data across UZH, ETHZ, CHUV, HUG, and EPFL. Action: Built reproducible pipelines on BioMedIT secure HPC. Structured clinical research outputs for Molecular Board review. Coordinated technical delivery across 30+ collaborators spanning wet-lab, bioinformatics, governance, ethics, and clinical teams simultaneously. Result: Approximately 1,000 children enrolled. Over 100 TB biomedical data under traceable infrastructure. Multiple peer-reviewed publications. Programme completed on schedule across seven institutions.
EPFL BIO-491 guest lecturer — personalised health master programme
Situation: BIO-491 is a flagship EPFL MSc course on personalised health requiring research-active guest lecturers with current clinical genomics expertise. Task: Deliver annual guest lectures to Life Sciences Engineering Master students over four consecutive years. Action: Designed and delivered lectures on human genomics of infection and immunity, probabilistic variant interpretation, and translational precision medicine, drawing on active research at EPFL and University Children's Hospital Zurich. Result: Four years of annual contribution (2021–2024). Spring semester, 2 hours per week format.
Delivery (10)
Quantitative Omics Epidemiology Group — founding, direction, and delivery
Situation: Clinical genomics at the children's hospital needed a computational group with a shared methodological foundation that could build trusted infrastructure rather than disposable in-house pipelines. Task: Found and lead a research group delivering validated, reusable, openly published genomics infrastructure within a CHF 5M+ national programme. Action: Founded the Quantitative Omics Epidemiology Group within SwissPedHealth. Defined the core strategy: validate every method using public biobank-scale data before clinical deployment, publish reusable open software rather than internal pipelines, and require independent peer review before clinical use. Coordinated 30+ collaborators across wet-lab, bioinformatics, molecular board, ethics, and clinical teams. Result: Five lead/senior-author publications across OUP, Wiley, Lancet journals within two years. Multiple CRAN packages with 3,000+ combined downloads per quarter. Technologies adopted in clinical diagnostic workflows.
SwissPedHealth — CHF 5M national multi-omics infrastructure
Situation: A CHF 5M national programme required unified multi-omics analytical infrastructure across multiple children's hospitals with heterogeneous data systems, governance structures, and clinical workflows. Task: Design and deliver the computational workflows, database architecture, and reporting systems connecting WGS, RNA-seq, proteomics, metabolomics, and EHR data across UZH, ETHZ, CHUV, HUG, and EPFL. Action: Built reproducible pipelines on BioMedIT secure HPC. Structured clinical research outputs for Molecular Board review. Coordinated technical delivery across 30+ collaborators spanning wet-lab, bioinformatics, governance, ethics, and clinical teams simultaneously. Result: Approximately 1,000 children enrolled. Over 100 TB biomedical data under traceable infrastructure. Multiple peer-reviewed publications. Programme completed on schedule across seven institutions.
Secure LLM deployment — clinical variant interpretation at BioMedIT
Situation: Clinical genetics teams required AI-assisted variant interpretation but could not expose patient data to external cloud APIs under Swiss data protection law. Task: Deploy open-weight LLMs on secure HPC infrastructure for clinical report generation with Molecular Board review. Action: Deployed Llama and DeepSeek R1 on BioMedIT HPC. Built a structured report generation pipeline integrating WGS, RNA-seq, and proteomics outputs, reviewed by geneticists, clinicians, and researchers. Implemented audit-trail logging meeting Swiss data governance requirements. Result: High-throughput clinical variant interpretation with full audit trail, operational at University Children's Hospital Zurich within SwissPedHealth.
Leeds rare immune disease programme — 10+ disease discoveries
Situation: Approximately 500 patients with severe immune-mediated disease at St James's University Hospital lacked a genetic diagnosis, preventing targeted treatment. Task: Contribute genomic discovery and functional validation across multiple disease programmes within the NIHR BioResource rare disease cohort. Action: Led or co-led discovery of germline TET2 deficiency (Blood 2020, IUIS-classified), RAG deficiency in adults (JACI 2018), RAG1/2 variant occurrence modelling (JCI 2019), CRACR2A deficiency (eLife 2021), TNFAIP3 autoinflammation (Frontiers Immunol 2018), CFTR as a modifying cofactor in PID (JACI 2023), and pyrin pathway autoinflammation (Science Translational Medicine 2016). Applied WES/WGS, flow cytometry, B-cell differentiation, iPSC haematopoietic systems, and functional assays. Result: More than 10 peer-reviewed disease discovery and precision treatment findings. Treatments confirmed including rituximab, anakinra, and tocilizumab.
Paediatric sepsis rare variant pathways — 66 IEI candidates
Situation: Common variants explain little sepsis heritability; rare immune pathway variants had not been systematically tested in a paediatric clinical cohort. Task: Design and execute multi-tiered rare variant analyses — single-case, single-variant, gene-level, and protein pathway — across 940 children with confirmed sepsis. Action: Built automated interpretation pipelines covering SKAT-O, burden testing, and protein pathway clustering. Applied novel pathway grouping to identify enriched immune pathway hits. Result: Identified 66 candidate inborn error of immunity cases and two immune pathway hits spanning 50 genes. Findings inform treatment decisions at the Molecular Board. First author. Under review.
Paediatric sepsis GWAS — first reproducible susceptibility locus
Situation: Sepsis is the leading infectious cause of childhood death; no reproducible genome-wide susceptibility locus had been identified in a paediatric cohort. Task: Lead the statistical genetics analysis within a national multi-centre programme (CHF 930K, three Swiss children's hospitals). Action: Designed and executed a GWAS in 650 blood-culture-confirmed paediatric sepsis cases and 1,395 controls; applied case-control and case-only designs; coordinated genotype data governance across institutions; built analysis pipelines from QC through to fine-mapping. Result: Identified the first reproducible paediatric sepsis susceptibility signal at the CTNNAL1/ELP1 locus. First author. Accepted Lancet eBioMedicine 2025. GWAS summary statistics deposited in EBI GWAS Catalogue (GCST90726424).
Genomic Vault — custodianship and governance platform
Situation: Genome data custody was handled informally, with no auditable access control, governance trail, or payment infrastructure for institutional or individual use. Task: Build a working custodianship and governance platform deployable commercially and institutionally. Action: Built fullstack application with encrypted storage, Drizzle ORM, Supabase row-level security, Stripe payment webhooks, immutable audit logs, and SPHN-compliant RDF metadata. Deployed with operational access controls. Result: Live at genomicvault.switzerlandomics.ch. Working payments, access governance, and immutable audit trail. Designed to SPHN compliance standards.
Microsoft Azure Research Award — USD 100K competitive cloud funding
Situation: Population-scale genomic data science required cloud computing capacity not available through standard academic infrastructure at Leeds. Task: Compete for and secure external research funding to enable cloud-based genomic data science and machine learning work. Action: Wrote and submitted a competitive proposal for data science and ML in predictive genomics. Award granted as USD 100,000 in Azure cloud computing credits. Result: Enabled population-scale genomic analysis and ML pipeline development that contributed to subsequent peer-reviewed publications.
Variant Impact — fullstack molecular informatics platform
Situation: Protein variant interpretation required integration of gnomAD, UniProt, ClinVar, AlphaFold, and RCSB PDB — no single platform combined all with an interactive 3D structure viewer and variant landscape visualisation. Task: Build a fullstack web application demonstrating end-to-end molecular informatics. Action: Built with Next.js, React, TypeScript, and Tailwind. Integrated Molstar 3D protein structure viewer, variant landscape heatmaps, protein feature tracks, gnomAD constraint scores, ClinVar classifications, AlphaFold confidence scores, and RCSB structure data. Deployed on Vercel. Result: Deployed at variantimpact.vercel.app. Demonstrates the complete fullstack molecular informatics stack: molecular databases, interactive 3D visualisation, and variant landscape analysis in a single application.
ACM Global Laboratories — regulated bioanalytical delivery
Situation: Global clinical trial sponsors required high-quality bioanalytical assay delivery under GCP-aligned standards. Task: Deliver ELISA, flow cytometry, and metabolomics assays within regulated commercial clinical trial workflows. Action: Executed biomarker and assay workflows under GCP/GLP-adjacent quality standards. Maintained documentation, chain of custody, and reporting to sponsor requirements. Result: Reliable quality-controlled assay delivery in a regulated commercial laboratory environment. Direct experience of the documentation and quality culture required in pharmaceutical analytical operations.
Leadership (4)
Switzerland Omics — scientific product ecosystem from IP to revenue
Situation: Probabilistic genomics methods existed in research code but lacked the product architecture, IP positioning, and brand credibility for adoption outside the originating institution. Task: Build a complete scientific product environment from intellectual property registration through to deployed products and commercial revenue. Action: Established Switzerland Omics. Registered the trademark (Swissreg, Nice classes 9 and 42, valid to 2035). Designed the product taxonomy. Built and shipped QuantBayes Studio, PanelAppRex, Genomic Vault, and Variant Impact. Structured the commercial spin-off and AWS research funding application. Result: Registered trademark valid 2035. Multiple live deployed products. Commercial revenue via QuantBayes Studio. AWS research funding secured 2026. Products in clinical and research use internationally.
Quantitative Omics Epidemiology Group — founding, direction, and delivery
Situation: Clinical genomics at the children's hospital needed a computational group with a shared methodological foundation that could build trusted infrastructure rather than disposable in-house pipelines. Task: Found and lead a research group delivering validated, reusable, openly published genomics infrastructure within a CHF 5M+ national programme. Action: Founded the Quantitative Omics Epidemiology Group within SwissPedHealth. Defined the core strategy: validate every method using public biobank-scale data before clinical deployment, publish reusable open software rather than internal pipelines, and require independent peer review before clinical use. Coordinated 30+ collaborators across wet-lab, bioinformatics, molecular board, ethics, and clinical teams. Result: Five lead/senior-author publications across OUP, Wiley, Lancet journals within two years. Multiple CRAN packages with 3,000+ combined downloads per quarter. Technologies adopted in clinical diagnostic workflows.
Swiss Genomics Association — founded neutral standards body
Situation: No institution-neutral standard existed for expressing genomic evidence matrices or reporting statistical evidence ratios across heterogeneous study designs and institutions. Task: Found an independent scientific association capable of issuing and maintaining normative standards for the Swiss and international genomics community. Action: Established the Swiss Genomics Association (2024). Issued the Qualifying Evidence Matrix (QEM, Zenodo DOI 10.5281/zenodo.17936587) and the Evidence Ratio Reporting Standard (ERRS, Zenodo DOI 10.5281/zenodo.18261075). Registered both as versioned standards with permanent DOIs. Built a member network spanning Swiss academic, clinical, and industry bioinformatics. Result: Two normative published standards cited in peer-reviewed work. 35+ members across Swiss institutions. ERRS implemented in the CRAN evidenceratio package.
EPFL BIO-491 guest lecturer — personalised health master programme
Situation: BIO-491 is a flagship EPFL MSc course on personalised health requiring research-active guest lecturers with current clinical genomics expertise. Task: Deliver annual guest lectures to Life Sciences Engineering Master students over four consecutive years. Action: Designed and delivered lectures on human genomics of infection and immunity, probabilistic variant interpretation, and translational precision medicine, drawing on active research at EPFL and University Children's Hospital Zurich. Result: Four years of annual contribution (2021–2024). Spring semester, 2 hours per week format.
