01 — research
Research
I work in computational immunology with the Uhlig and Dendrou labs at the Centre for Human Genetics, University of Oxford. My focus is finding meaningful structure in large-scale biomedical data — with knowledge graphs, machine learning, and patient data — to improve understanding and classification of inborn errors of immunity and inflammatory diseases such as IBD.
In parallel, I develop nanoCITE — Nanopore sequencing pipelines and computational tools designed to bridge research and clinical practice, so data-driven insights can become actionable in patient care. Earlier work includes hidradenitis suppurativa, keloid cryosurgery, and macrophage biology.
// papers · 12 · first author 4 · citations 162 · h-index 7
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pinned
Longitudinal single-cell data informs deterministic modelling of inflammatory bowel disease
Kilian C., Ulrich H., Zouboulis V.A., Sprezyna P., Schreiber J., Landsberger T., Büttner M., Biton M., Villablanca E.J., Huber S., Adlung L.
npj Systems Biology and Applications
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Algorithmic optimization of intralesional cryosurgery for keloids: A prospective study
Vradeli G., Zouboulis V.A., Zouboulis C.C.
Journal of the European Academy of Dermatology and Venereology
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Baseline knowledge of dermatology specialists/residents on hidradenitis suppurativa and immediate learning outcome after their participation at an EADV School
Zouboulis V.A., Massa A.F., Nikolakis G., Prens E.P., Szepietowski J.C., Tzellos T., Zouboulis C.C.
Journal of the European Academy of Dermatology and Venereology
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S2k guideline for the treatment of hidradenitis suppurativa / acne inversa – Short version
Zouboulis C.C., Bechara F.G., Fritz K., Goebeler M., Hetzer F.H., Just E., Kirsten N., Kokolakis G., Kurzen H., Nikolakis G., Pinter A., Podda M., Rosinski K., Schneider-Burrus S., Taube K., Volz T., Winkler T., Kristandt A., Presser D., Zouboulis V.A.
JDDG: Journal der Deutschen Dermatologischen Gesellschaft
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S2k-Leitlinie zur Therapie der Hidradenitis suppurativa/Acne inversa (ICD-10-Code: L73.2)
Zouboulis C.C., Bechara F.G., Fritz K., Goebeler M., Hetzer F.H., Just E., Kirsten N., Kokolakis G., Kurzen H., Nikolakis G., Pinter A., Podda M., Rosinski K., Schneider-Burrus S., Taube K., Volz T., Winkler T., Kristandt A., Presser D., Zouboulis V.A.
Aktuelle Dermatologie
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The inter-rater reliability of IHS4 corroborates its aptitude as primary outcome measurement instrument for large clinical studies in hidradenitis suppurativa
Zouboulis C.C., Hrvatin Stancic B., Abaitancei A., Guimarães M.J., Lobo I.L., Massa A.F., Nikolakis G., Nogueira M.O., Özdemir A.O., Pirogova A., Prens E.P., Szepietowski J.C., Tusheva I., Tzellos T., Zouboulis V.A.
Journal of the European Academy of Dermatology and Venereology
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Different Types of Auricular Keloids and Treatment by Intralesional Cryosurgery: Best Practice for Obtaining Long-Lasting Clinical Results
Har-Shai Y., Har-Shai L., Zouboulis V.A., Zouboulis C.C.
Dermatology
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A novel experimental model for studying efficacy of cryosurgery in keloids
Zouboulis V., Zouboulis C.C.
Journal of the European Academy of Dermatology and Venereology
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Intralesional cryosurgery of keloids: required treatment hold time
Zouboulis C.C., Wild T., Zouboulis V.A., Har-Shai Y.
British Journal of Dermatology
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Inter-rater and intrarater agreement and reliability in clinical staging of hidradenitis suppurativa/acne inversa
Zouboulis C.C., Matusiak Ł., Jemec G.B.E., Szepietowski J.C., Álvarez-Chinchilla P., Asoskova A., Bonnekoh H., Brattoli G., Cetinarslan T., Dawicka J., Dente V., Gallyamova Y., Giovanardi G., Glasenhardt K., Ionescu A., Janushaj E., Lakhssassi M., Lőrincz K., Ludew D., Makmatov-Rys M., Malickova M., Mengesha S., Mintoff D., Otlewska A., Papakou M., Pirvan A., Provvidenziale L., Quadrana F., Savickaja N., Tamulyté G., Trifu A., Vīgante A., Włodarek K., Zouboulis V.
British Journal of Dermatology
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Small cryotherapy devices for the treatment of skin warts
Zouboulis V.A., Zouboulis C.C.
Journal of Dermatological Treatment
// citations by year
↓ posters› 159 citations across 12 papers · click a bar to filter by year
// posters
↓ projects-
Inference of metabolic properties and transcriptional programmes across altered adipocyte/immune cell ratios
Zouboulis V.A., Ullrich H., Kilian C., Homayon O., Adlung L.
German Conference on Bioinformatics (GCB) 2023, Hamburg
snRNA-seq analysis of adipocyte–LAM interactions across obesity states; proposing the LAM/Adipo ratio as a biologically meaningful sample-alignment metric. Affiliation: Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, Germany. Research thesis in the Adlung lab — linked to medical studies at UKE and the Digital Health elective track.
bioinformatics GCB single-cell adipose macrophages poster digital health thesis
// projects
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pinned
Knowledge graphs & ML for immune disease classification
Using knowledge graphs, machine learning, and patient data to uncover patterns in complex biomedical datasets and improve understanding and classification of inborn errors of immunity and inflammatory diseases such as IBD.
knowledge graphs machine learning graph machine learning databases LLM APIs IEI IBD
2025 active -
pinned · building in stealth
longIBD
Longitudinal work on inflammatory bowel disease — connecting clinical phenotypes, immune mechanisms, and computational approaches to better understand disease course and classification, with a particular focus on anti–IL-10 IBD. Includes biomarker trajectories, patient-reported outcomes, and related longitudinal measures.
IBD longitudinal immunology IL-10 autoantibodies biomarkers PROs
2025 stealth -
pinned
Virtual Cell Challenge 2026
Student research group building models for the Virtual Cell Challenge — designing virtual cells, backed by a Studentische Forschungsgruppen Grant from Exzellenzuniversität Hamburg.
2025 active -
Building databases for Uhlig Lab
Designing and building research databases for the Uhlig Lab, with a focus on anti–IL-10 IBD cohorts and related clinical–molecular data.
2025 active -
SPECS gene expression scraper
Unofficial script to pull SPECS/GTEX-based gene expression results and evaluate in which tissues a gene is most expressed.
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Keloid cryosurgery
Intralesional cryosurgery for keloids — experimental models, treatment hold time, algorithmic optimisation, and auricular best practice.
2020 completed -
planned · stealth
Single-cell meta-analysis in hidradenitis suppurativa
Integrating single-cell datasets and meta-analytic approaches in hidradenitis suppurativa — planned, in stealth.
— planned stealth - — planned stealth
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planned · stealth
GWAS
Genome-wide association work in collaboration with the AdlungLab — planned, in stealth.
— planned stealth
// interesting papers
↑ papersPapers by others that shaped how I think about the field — not my own publications.
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Interleukin-10 Autoantibodies and HLA-DRB1*01:03 in Inflammatory Bowel Disease
Gharahdaghi N., Yeh P.J., Ceron-Gutierrez L., Griffin H., Gordon H., Jayamanne C., Fracchia A., Chong A.Y., Walsh A., Brain O., Baker K., Kockelbergh H., Luo Y., Guevara Becerra M., Vadakethala K., Coy M., Kabiri L., Barnardo M., Dunachie S., Kronsteiner B., Adams A., Fowler D., Zhang Q., Fachal L., Anderson C.A., Desoki R., Vestergaard M.V., Larsen L., Wyatt N.J., Lees R.D., Mulligan R.J., Dong C., Sharip M.T., Faustini S.E., Shields A., Pakpoor J., Naz B., Richter A., Satsangi J., Lamb C.A., Parkes M., Powrie F., Mentzer A.J., Sazonovs A., Jess T., Klenerman P., Travis S., Hambleton S., Doffinger R., Uhlig H.H.
New England Journal of Medicine
Neutralizing anti–IL-10 autoantibodies in ~3.5% of IBD patients, strongly linked to HLA-DRB1*01:03 — extending the phenocopy story from rare infantile cases into adult IBD cohorts.
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The 2024 update of IUIS phenotypic classification of human inborn errors of immunity
Bousfiha A.A., Jeddane L., Moundir A., Poli M.C., Aksentijevich I., Cunningham-Rundles C., Hambleton S., Klein C., Morio T., Picard C., Puel A., Rezaei N., Seppänen M., Somech R., Su H.C., Sullivan K.E., Torgerson T.R., Tangye S.G., Meyts I.
Journal of Human Immunity
Bedside-facing IUIS phenotypic decision trees for 559 IEIs (67 novel monogenic defects, 2 phenocopies) — the clinical classification backbone for structuring IEI knowledge graphs and machine-assisted disease classification.
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Towards multimodal foundation models in molecular cell biology
Cui H., Tejada-Lapuerta A., Brbić M., Sáez-Rodríguez J., Cristea S., Goodarzi H., Lotfollahi M., Theis F.J., Wang B.
Nature
Perspective on multimodal foundation models for molecular cell biology — the modelling stack virtual-cell efforts sit inside.
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preprint
Virtual Cells: Predict, Explain, Discover
Noutahi E., Hartford J., Tossou P., Whitfield S., Denton A.K., Wognum C., Ulicna K., Craig M., Hsu J., Cuccarese M.F., Bengio E., Beaini D., Gibson C.C., Cohen D.C., Earnshaw B.
arXiv
Preprint framing virtual cells as models that predict, explain, and discover — a complementary lens on what a useful virtual cell should do beyond challenge leaderboards.
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Virtual Cell Challenge: Toward a Turing test for the virtual cell
Roohani Y., Hua T.J., Tung P., Bounds L.R., Yu F.B., Dobin A., Teyssier N., Adduri A., Woodrow A., Plosky B.S., Mehta R., Hsu B., Sullivan J.A., Ricci-Tam C., Li N., Kazaks J., Gilbert L.A., Konermann S., Hsu P.D., Goodarzi H., Burke D.P.
Cell
Perspective framing the Virtual Cell Challenge as a community Turing-test for models that predict cellular responses — the competition brief this student research group is building toward.
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Neutralizing Autoantibodies against Interleukin-10 in Inflammatory Bowel Disease
Griffin H., Ceron-Gutierrez L., Gharahdaghi N., Ebrahimi S., Davies S., Loo P.S., Szabo A., Williams E., Mukhopadhyay A., McLoughlin L., Irwin S., Travis S., Klenerman P., Bunn S., Cant A.J., Hambleton S., Uhlig H.H., Doffinger R.
New England Journal of Medicine
Neutralizing anti–IL-10 autoantibodies as a phenocopy of inborn errors of IL-10 signalling in infantile-onset IBD — with therapeutic implications for B-cell depletion.
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An Integrated Taxonomy for Monogenic Inflammatory Bowel Disease
Bolton C., Smillie C.S., Pandey S., Elmentaite R., Wei G., Argmann C., Aschenbrenner D., James K.R., McGovern D., Macchi M., Cho J.H., Shouval D.S., Kammermeier J., Koletzko S., Bagalopal K., Capitani M., Cavounidis A., Pires E., Weidinger C., McCullagh J., Arkwright P.D., Haller W., Siegmund B., Peters L., Jostins L., Travis S., Anderson C.A., Snapper S.B., Klein C., Schadt E.E., Uhlig H.H., et al.
Gastroenterology
Pathway- and cell-type–aware taxonomy of monogenic IBD — a structured classification resource that underpins knowledge-graph modelling of rare intestinal inflammatory disease.