Niko Beerenwinkel
Full Professor
Leads the Computational Biology Group, developing probabilistic models and machine learning for tumour evolution, single-cell sequencing and viral genomics.
Niko Beerenwinkel's lab at ETH Zurich works on genomics & computational biology and probabilistic & causal inference. 59 papers since 2023, 10 at top venues, mostly Nature Communications and Bioinformatics. 88 alumni.
At a glance
- papers, 2023–2026
- 15/ year
- at T1 venues
- 17%
- PhD students
- 0
- MS students
- 0
- alumni listed
- 88
Papers by yearfrom the lab homepage, 2023–2026
- 16 papers2026 · T1 3 · collecting
- 14 papers2025 · T1 3
- 14 papers2024 · T1 1
- 15 papers2023 · T1 3
T1 venuesOtherVenues: Nature Communications, Bioinformatics, Briefings in Bioinformatics, TMLR
Research focuspaper titles that use each topic's words
- Genomics & computational biology14 papers
- Probabilistic & causal inference7 papers
- tumour1 paper
- biosystems0 papers
- biosystems science0 papers
Paper list
From the lab homepage.
202616 papers
- Journal of VirologyA recurrent adaptive mutation in the transmembrane 2B protein of an insect picorna-like virus in a nonnative host (opens in a new tab)
- Nature Communications (T1)A tumor profiling resource for ovarian cancer: insights into chemotherapy-driven heterogeneity and personalized treatment strategy (opens in a new tab)
- Cancer ResearchCanSig Benchmarks Methods for Reproducible Cancer Cell State Discovery from Single-Cell Transcriptomic Data (opens in a new tab)
- Water ResearchCorrigendum to “Characterizing Influenza A Virus Lineages and Clinically Relevant Mutations Through High-Coverage Wastewater Sequencing” [Water Research (2025) Article No. 124453] (opens in a new tab)
- BioinformaticsECCB 2026: the 25th European Conference on Computational Biology (opens in a new tab)
- GigaScienceGeneralizable machine learning models for rapid antimicrobial resistance prediction in unseen healthcare settings (opens in a new tab)
- Briefings in BioinformaticsGillespie-based simulation and inference for non-Markovian stochastic reaction networks (opens in a new tab)
- Water ResearchLearning and forecasting selection dynamics of SARS-CoV-2 variants from wastewater sequencing data using Covvfit (opens in a new tab)
- Bioinformatics Advancesmhn: a Python package for analyzing cancer progression with Mutual Hazard Networks (opens in a new tab)
- Nature Communications (T1)Ovarian cancer metastasis to the human omentum disrupts organ homeostasis and induces fundamental tissue reprogramming (opens in a new tab)
- Genome BiologyPhylogenetic tree inference from single-cell RNA sequencing data with SCITE-RNA (opens in a new tab)
- BioinformaticsQuantifying uncertainty of predictions from cancer progression models (opens in a new tab)
202514 papers
- Genome ResearchAccurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution (opens in a new tab)
- BioinformaticsBayesian inference of fitness landscapes via tree-structured branching processes (opens in a new tab)
- Water ResearchCharacterizing influenza A virus lineages and clinically relevant mutations through high-coverage wastewater sequencing (opens in a new tab)
- Genome ResearchDe novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data (opens in a new tab)
- Genome BiologyDelSIEVE: cell phylogeny modeling of single nucleotide variants and deletions from single-cell DNA sequencing data (opens in a new tab)
- BioinformaticsELLIPSIS: robust quantification of splicing in scRNA-seq (opens in a new tab)
- Nature Communications (T1)Estimated transmission dynamics of SARS-CoV-2 variants from wastewater are unbiased and robust to differential shedding (opens in a new tab)
- Conference on Causal Learning and Reasoning (CLeaR ), Lausanne, SwitzerlandFair clustering: a causal perspective
- Nature MedicineFeasibility of multiomics tumor profiling for guiding treatment of melanoma (opens in a new tab)
- Nature Communications (T1)Network-based clustering unveils interconnected landscapes of genomic and clinical features across myeloid malignancies (opens in a new tab)
- TMLR (T1)On the Properties and Estimation of Pointwise Mutual Information Profiles
- Bioinformatics AdvancesOncotreeVIS—an interactive graphical user interface for visualizing mutation tree cohorts (opens in a new tab)
202414 papers
- Water ResearchAssessing different next-generation sequencing technologies for wastewater-based epidemiology (opens in a new tab)
- Journal of Computational BiologyCorrecting for Observation Bias in Cancer Progression Modeling (opens in a new tab)
- Genome BiologyGenomic reproducibility in the bioinformatics era (opens in a new tab)
- BMJ OpenHIV-1 subtype-specific drug resistance on dolutegravir-based antiretroviral therapy: protocol for a multicentre study (DTG RESIST) (opens in a new tab)
- Microbiology SpectrumHow much should we sequence? An analysis of the Swiss SARS-CoV-2 surveillance effort (opens in a new tab)
- BioinformaticsModeling metastatic progression from cross-sectional cancer genomics data (opens in a new tab)
- LeukemiaMutation order in acute myeloid leukemia identifies uncommon patterns of evolution and illuminates phenotypic heterogeneity (opens in a new tab)
- BioinformaticsOncotree2vec - a method for embedding and clustering of tumor mutation trees (opens in a new tab)
- PLOS ONEOptimal timing of a colonoscopy screening schedule depends on adenoma detection, adenoma risk, adherence to screening and the screening objective: A microsimulation study (opens in a new tab)
- Annual International Conference on Research in Computational Molecular Biology (RECOMB ), Cambridge, MA, USAOvercoming Observation Bias for Cancer Progression Modeling (opens in a new tab)
- Nature Communications (T1)Single-cell landscape of innate and acquired drug resistance in acute myeloid leukemia (opens in a new tab)
- Microbial GenomicsTracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data (opens in a new tab)
202315 papers
- Journal of Statistical SoftwareBayesian Structure Learning and Sampling of Bayesian Networks with the R Package BiDAG (opens in a new tab)
- Therapeutic Advances in GastroenterologyBecause I’m happy – positive affect and its predictive value for future disease activity in patients with inflammatory bowel diseases: a retrospective cohort study (opens in a new tab)
- Annual Conference on Neural Information Processing Systems (NeurIPS ), New Orleans, LA, USABeyond Normal: On the Evaluation of Mutual Information Estimators
- Modern PathologyBiallelic ELOC-Inactivated Renal Cell Carcinoma: Molecular Features Supporting Classification as a Distinct Entity (opens in a new tab)
- BioinformaticsCoherent pathway enrichment estimation by modeling inter-pathway dependencies using regularized regression (opens in a new tab)
- Nature Communications (T1)COMPASS: joint copy number and mutation phylogeny reconstruction from amplicon single-cell sequencing data (opens in a new tab)
- VirusesDetection and Molecular Characterization of the SARS-CoV-2 Delta Variant and the Specific Immune Response in Companion Animals in Switzerland (opens in a new tab)
- Nature Communications (T1)Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing in ovarian cancer (opens in a new tab)
- JHEP ReportsExpanding epidemic of recently acquired HCV in HIV-coinfected patients over a period of 10 years (opens in a new tab)
- Clinical EpigeneticsGenome-wide DNA methylation profiling of HPV-negative leukoplakia and gingivobuccal complex cancers (opens in a new tab)
- Nature Communications (T1)Joint inference of exclusivity patterns and recurrent trajectories from tumor mutation trees (opens in a new tab)
- Virus EvolutionParallel evolution and enhanced virulence upon in vivo passage of an RNA virus in Drosophila melanogaster (opens in a new tab)
Where alumni went88 listed
Apply to ETH ZurichRolling
Not announced yet
Computer Science Doctorate (D-INFK)
- Round
- Rolling (no deadline)
- Opens
- —
- GRE
- See program page
- English
- Proficiency in written and spoken English
- Fee
- See program page
Confirmed on the program page.
Similar labsnearest by research summary
- USUC Berkeley
Doris Tsao
- Genomics & computational biology
- USMIT
Ericmoore Jossou
- Proteins, drugs & materials
- USUW
Sara Mostafavi
- Genomics & computational biology
- USUCSD
Pengtao Xie
- Medical imaging & healthcare AI
- USMIT
Marzyeh Ghassemi
- Medical imaging & healthcare AI
- USStanford
Ron Dror
- Proteins, drugs & materials
Your notes
Save this lab to keep notes.
Data
Checked against the lab homepage.
- Collected
- Verified
- Papers
- The lab homepage
- Members
- Lab homepage
- Alumni
- Lab homepage
Tiers are venue classifications, not lab rankings.