Hélène Ruffieux, PhD

Senior Statistician • Statistical Machine Learning for Health & Life Sciences
Based in Lausanne, Switzerland

I am a statistician specialising in statistical machine learning for complex biomedical data, particularly high-dimensional, longitudinal and multimodal measurements. My work addresses questions around molecular regulation, patient heterogeneity and disease trajectories, with an emphasis on methods that are interpretable, robust and computationally scalable.

I am affiliated with the MRC Biostatistics Unit, University of Cambridge, where I previously served as Assistant Research Professor. At Cambridge, I established and led an independent research programme, directing a team of postdoctoral researchers and PhD students and working closely with clinical, biological and computational teams. My work spans methodological development and applied research, from statistical modelling and validation to scientific interpretation and the delivery of reproducible software and interactive tools.

I also have industry R&D experience, having worked at Nestlé Research as a statistician and, more recently, as an independent consultant. I provide statistical consulting for biomedical research and life-sciences R&D, advising on study design, analytical strategies, model validation and methodological review.
Get in touch to discuss a potential collaboration.

Read more »

Team & scientific leadership

I have the pleasure of working with talented researchers at the MRC Biostatistics Unit (MRC BSU):

  • Hanxi Chen, PhD Candidate (co-advised with Brian Tom);
  • Joseph Feest, PhD Candidate (co-advised with Paul Kirk);
  • Yiran Li, PhD Candidate (co-advised with John Whittaker and Sylvia Richardson);
  • Xinzhi Zhang, PhD Candidate (co-advised with Chris Wallace).

Former team members:

  • Camilla Lingjærde, PhD Candidate & Research Associate (Oct 2019-Apr 2024), co-advised with Sylvia Richardson, now Research Fellow at the University of Oslo;
  • Daniel Temko, Research Associate (Oct 2022-Dec 2024), now Research Associate at the Early Cancer Institute of Cambridge University;
  • Joseph Feest, Intern & Research Assistant (Jul 2023-Dec 2024);
  • Marion Kerioui, Research Associate (Jan 2024-Oct 2025), now INSERM Research Scientist in Paris;
  • Tudor Benea, Intern (Apr 2024-Aug 2024), Lecturer at the University of Sibiu;
  • Xiaoyue Xi, Research Associate (Apr 2022-March 2025), now Senior Research Associate at the Big Data Institute of Oxford University.

I regularly supervise Bachelor’s and Master’s students from the University of Cambridge and EPFL (Lausanne). The MRC BSU provides a stimulating environment to begin a career in biostatistics, with a PhD Programme offering several positions each year.

I am a founding co-organiser of the MRC BSU Internship Programme (50+ interns placed) and the AI Discussion Group. I also co-organise the MRC BSU Open Science Committee and serve on the MRC BSU Fellowship Committee.

Recent activity

See all »

Aug 2026: Co-launched the MRC BSU AI Discussion Group, a forum for peer learning and discussion around statistical and AI methods in biomedical research.

July 13, 2026: New preprint on a Partition FPCA model for time-course gene expression data – lead author Marion Kerioui, joint with Daniel Temko and Shahin Tavakoli.

July 1, 2026: I look forward to speaking at the Statistical and AI methods for multi-modal multi-scale modeling of biological systems Conference in Ascona about latent trajectory modelling for longitudinal molecular data – joint work with Salima Jaoua and Daniel Temko.

May 19, 2026: I look forward to presenting our work at the IBS-CEN2026 Conference in Warsaw, on Bayesian network inference with node-level information – joint work with Xiaoyue Xi.

Mar 21, 2026: New preprint on a Bayesian latent factor modelling framework to uncover coordinated biological dynamics from high-dimensional longitudinal data – joint with Salima Jaoua and Daniel Temko.

Research

The landscape of biomedical research is changing rapidly, driven by technological advances for quantifying clinical and molecular data at scale. This evolution not only offers a more granular view of disease mechanisms, but also parallels a growing acknowledgment that pathogenic responses are tightly coordinated at the organismal level. Consequently, there is a need for modelling approaches capable of providing a holistic understanding of complex interplays across biological systems.

My research aims to provide principled statistical methodology for tackling this challenge, guided by collaborations with clinicians and researchers in areas such as immunology, infectiology and cancer. We have a particular interest in longitudinal and multimodal biomedical data, including patient trajectories, molecular dynamics and multimodal integration across omics, clinical, wearable and patient-reported data.

Our methodological work spans Bayesian hierarchical modelling, sparse regression, latent representation models, network models and functional data analysis. We develop scalable statistical and machine learning approaches to uncover latent and shared structure across biological systems, characterise within- and between-individual heterogeneity across biological contexts, and quantify uncertainty in the resulting inferences. We are particularly interested in addressing the tension between flexible joint estimation and practical feasibility at the scale of current biomedical studies, with a focus on accuracy, robustness and computational tractability. Common threads include (i) learning and leveraging shared biological structures across modalities, scales and contexts (molecular entities, tissues, cell types or disease subtypes), and (ii) developing approximate inference procedures, such as expectation-maximisation (EM) and model-specific variational schemes, for high-dimensional parameter spaces.

Our methods are tailored to specific scientific questions, yet remain adaptable to a broader range of applications. We support their use through accompanying statistical software and implementations (see Software).

I am strongly committed to open science and reproducible research. I contribute to these efforts through the MRC BSU Open Science Committee, which promotes transparency, collaboration and the sharing of tools, data and methods, both within the Unit and across the wider scientific community.

My research has received generous support from the Lopez–Loreta Foundation.

Short bio

Awards

Software & code

*

atlasqtl

Variable selection in sparse regression with hierarchically-related responses

bayesFPCA

Bayesian functional principal component analysis suite – with Tui Nolan

bayesSYNC

Bayesian functional factor modelling framework

book chapter on Bayesian variable selection

Source code for reproducing an example in a chapter published in the Handbook of Bayesian variable selection

covid patient trajectories app

FPCA estimates of patient disease trajectories after SARS-CoV-2 infection

covid recovery prediction app

Prediction of incomplete recovery from COVID-19

echoseq

Faithful replication and simulation of molecular and clinical data

epispot

Annotation-driven approach for large-scale joint regression with multiple responses

jointGHS

Joint graphical horseshoe for multiple network inference with shared information – creator and maintainer Camilla Lingjærde

locus

Large-scale variational inference for variable selection in sparse multiple-response regression

masterclass in variational inference

Solutions and suggested code for the 1st practical session of the Bayes4Health-CoSInES Masterclass in variational inference – with Camilla Lingjærde

mQTL analysis example

Source code for reproducing a numerical example using the method “locus” on simulated data

navigm

Variable-guided network inference using Bayesian graphical spike-and-slab modelling – creator and maintainer Xiaoyue Xi

NExON

Bayesian approach to joint network estimation informed by ordinal covariates – creator and maintainer Joseph Feest

searchable pQTL database

Online database gathering hits from a QTL mapping of human protein abundance in plasma

sensitivity analysis for atlasqtl

Source code for assessing the sensitivity of the method “atlasqtl” to hyperparameter settings

software corner IBS bulletin

Source code for reproducing article on the atlasqtl R package published in the Software Corner of the IBS Bulletin