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Huber Group

Computational biology and genomics

Large-scale mapping of genetic interactions by combinatorial RNAi, automated image analysis and computational phenotpying. The double knockdown of Rho1 and Dlic (right) shows a phenotype that is different from what is expected from the single-gene knockdowns of Dlic (left) and Rho1 (middle).

Detection of differentially expressed genes in RNASeq experiments using the DESeq method.

The Huber group develops computational and statistical methods to design and analyse novel experimental approaches in genetics and cell biology.

Previous and current research

Our aim is to understand biological systems through large-scale data acquisition and quantitative models. Our main tool is statistics – the science of computing with uncertainty, drawing conclusions from incomplete and noisy data. Together with its sister discipline, machine learning, it helps humans to discover patterns in large datasets and to infer underlying mechanisms, and predictive and causal relationships.

Our projects have a mix of two objectives: method development and biological discovery – to understand genetic and phenotypic variation between individuals on a genome-wide scale. We have projects in the areas of gene expression and regulation, in the genetics of complex phenotypes and genetic interactions, in cell division and cell migration, and in cancer genomics.

The group brings together expertise from quantitative disciplines – mathematics, statistics, physics and computer science – and from different areas of biology to design and analyse genomic experiments and their biological interpretation. Computational and statistical methods are at the heart of systematic, large-scale experimental approaches. Our aim is to develop high-quality methods of general applicability that can be widely used in genomic research. We regard the publication of scientific software as an integral part of the publication of new methodical approaches and contribute to the Bioconductor Project, an open source software initiative to provide tools for the analysis and study of high-throughput genomic data.

Future projects and goals

An emphasis of the group’s work is on project-oriented collaborations with experimenters. We aim to develop the computational techniques needed to make new types of experiments feasible and to turn the data into biology. Among our current projects are:

  • Mapping of gene-gene and gene-drug interactions through high-throughput microscopy of cells, computational image analysis, machine learning and mathematical modelling.
  • RNA-Seq analysis.
  • 3D nuclear organisation by HiC-related techniques.
  • Cancer genomics and precision oncology.
  • Image analysis for systems biology: measuring the dynamics of cell cycle and of migration of individual cells under normal conditions and many different perturbations (RNAi, drugs).
  • Systematic mapping of molecular interactions and life cycles within single cells.
  • Open source software for genomics, high-throughput phenotyping and statistical bioinformatics, to support reproducible research and wide dissemination of state-of-the-art methods.