From Computational Biology Group
In collaboration with the group of Sophie Martin from DMF (UNIL), we developed Cellophane, an ImageJ plugin that semi-automatically quantifies fluorescent protein concentration profiles along the cell cortex. This plugin enabled the quantification of hundreds of profiles of two key regulators of the fission yeast cell cycle, Pom2 and Cdr2. The data analysis, along with other experimental evidence, showed that two important functions of Pom1, deciding when and where to divide, require distinct levels of Pom1. Lower Pom1 level are sufficient for division positioning, but higher levels are required to delay mitotic entry until the proper size is reached. The paper has been published in Cell Cycle .
Together with the group of Christian Fankhauser from the CIG at UNIL, CBG post-doc Tim Hohm showed that the sites of light perception for phototropism is located in the upper hypocotyl, where asymmetric elongation occurs. Thus, in contrast to monocots where a phototropism signal is sent from the leaves to the stem, in Arabidopsis it all happens "on site". The paper has just been published in Current Biology
Daniel joins the CBG after his postdoctoral fellowship in the group of Manolis Kellis at the Massachusetts Institute of Technology (MIT) and the Broad Institute. During his postdoc at MIT, he led a community-based challenge in gene regulatory network inference (the DREAM challenge) and developed novel methods to predict regulatory relationships more accurately. At the CBG, he now intends to leverage these networks to interpret genetic variants associated with complex diseases and traits in the human.
In collaboration with the group of Christian Fankhauser at CIG, UNIL, we developed the HypoPhen software for the high throughput quantification of seedling elongation and bending from time-lapsed images. Using this tool, hundreds of Arabidopsis seedlings were measured to show that phytochrome A in the nucleus is important for phototropism. The results have been published in Plant Cell on February 28 2012.
A genome-wide association study by the HYPERGENES Consortium unravelled a novel hypertension susceptibility locus in the promoter region of the eNOS gene and essential hypertension. The article appeared online in Hypertension on 19 December 2011.
In a recent work, we developed a general formalism allowing to model diffusive gradient formation from an arbitrary source. This formalism applies to various diffusion problems and we illustrate our theory with the explicit example of the Bicoid gradient establishment in Drosophila embryos. The article appeared online in Journal of Theoretical Biology on 10 November 2011.
On June 25 2010, during the 8th [BC]2 Computational Biology Conference in Basel, SIB Swiss Institute of Bioinformatics announced that CBG member [[Aitana Morton de Lachapelle]] is the winner of the SIB Young Bioinformatician Award 2010.
Our calcium meta-analysis paper was published in PLoS Genetics.
We published an application note about the ExpressionView bicluster visualization tool in Bioinformatics. Please see the [[ExpressionView]] page for more — documentation, downloads, screenshots — on ExpressionView.
In collaboration with Mehdi Tafti's research group we have published our recent discovery on a newly identified HLA haplotype that protects individuals from narcolepsy even if they carry the famous risk haplotype. Our article appeared online in Nature Genetics on 15 August 2010.
Via the CoLaus and Hypergenes cohorts our group contributed to the meta-analysis of the GIANT consortium that revealed hundreds of genetic variants associated with human height; 18 new loci for body mass index; and 13 new loci for waist-hip-ratio.
In collaboration with John Whittaker (GSK) we have published a new methodology to infer total explained variance of [[Genome Wide Association Studies | GWAS]] hits. Our method was applied to the most recent GIANT association summary statistics and revealed that GWAS hits explain at least 30% of human height variations. The article appeared online in Genetic Epidemiology on 6 April 2011.
In collaboration with the Basler group (University of Zurich), we developed a theoretical model allowing to understand which is the leading mechanism involved in the Dpp long range gradient formation. The article appeared online in PLoS Biology on 26 July 2011.
A collaborative study with the Kaessmann group on "The evolution of gene expression levels in mammalian organs" where we first applied the [[ISA]] to RNAseq data has been published online as article in Nature on 19 October 2011.
Sven Bergmann has successfully completed his tenure-track as Assistant Professor and is Associate Professor since August 2010.